The one hundred volumes of Genes & Genetic Systems: An outline of their evolution.

Recent discussions of genetic and epigenetic systems pertain to the central biological problem of heritable control over development and function of organisms. Distinguishing between genetic and epigenetic phenomena involves difficulties due to their mutual characteristics. Epigenetic systems, if controlling the action of genetic systems, nevertheless, must be genetically persistent. However, genetic systems also have an epigenetic aspect concerned with the physiology of their own reproduction, distinct from the physiology of their heterocatalytic function. Epigenetics re-emphasizes a basic distinction between genotype and phenotype, between stored information and the expression of information. Confusion results if this primary concept is violated by subsequent restricting definitions. Thus, in addition to code sequence of nucleotides, other chromosomal differentiations having hereditary persistence are likely. Demonstrated position effects imply a code of genotypic significance residing in higher level chromosomal organization. Therefore, our concept of a genetic system storing information should not be restricted to the denotation of "gene" or to limited aspects of DNA structure. It is preferable to retain the broader connotation of hereditary persistence for a genetic system. We would then recognize more than one type of genetic code and several classes of genetic change. Interactions among genetic systems, their products, and their cellular environment have epigenetic or developmental significance, but may also result in alteration of certain types of genetic code. Biochemical and biophysical refinements of description may be superposed upon this complex of interacting systems, using terminology such as has been suggested by Lederberg.

The next goals in the development of a synthetic biology that uses artificial genetic systems will require chemistry-biology combinations that allow the amplification of DNA containing any number of sequential and nonsequential nonstandard nucleotides. This amplification must ensure that the nonstandard nucleotides are not unidirectionally lost during PCR amplification (unidirectional loss would cause the artificial system to revert to an all-natural genetic system). Further, technology is needed to sequence artificial genetic DNA molecules. The work reported here meets all three of these goals for a six-letter artificially expanded genetic information system (AEGIS) that comprises four standard nucleotides (G, A, C, and T) and two additional nonstandard nucleotides (Z and P). We report polymerases and PCR conditions that amplify a wide range of GACTZP DNA sequences having multiple consecutive unnatural synthetic genetic components with low (0.2% per theoretical cycle) levels of mutation. We demonstrate that residual mutation processes both introduce and remove unnatural nucleotides, allowing the artificial genetic system to evolve as such, rather than revert to a wholly natural system. We then show that mechanisms for these residual mutation processes can be exploited in a strategy to sequence "six-letter" GACTZP DNA. These are all not yet reported for any other synthetic genetic system.

The Genetic Code, the Golden Section and Genetic Music<strong> </strong>

This work presents an infant cry automatic recognizer development, with the objective of classifying three kinds of infant cries, normal, deaf and asphyxia from recently born babies. We use extraction of acoustic features such as LPC (Linear Predictive Coefficients) and MFCC (Mel Frequency Cepstral Coefficients) for the cry's sound waves, and a genetic feature selection system combined with a feed forward input delay neural network, trained by adaptive learning rate back-propagation. We show a comparison between Principal Component Analysis and the proposed genetic feature selection system, to reduce the feature vectors. In this paper we describe the whole process; in which we include the acoustic features extraction, the hybrid system design, implementation, training and testing. We also show the results from some experiments, in which we improve the infant cry recognition up to 96.79% using our genetic system. We also show different features extractions that result on vectors that go from 145 up to 928 features, from cry segments of 1 and 3 seconds respectively.

This paper presents the results of molecular genetic test system GenoType multyresistentens MTBDRplus. It was established that the presence of mutations associated with resistance to isoniazid, only 93.1 % of cases of MBT to isoniazid during the test in a liquid medium. Work carried out under the National Programme to combat tuberculosis Materials and methods. We investigated the clinical sputum samples from patients with pulmonary tuberculosis. The applied system GenoType. Principle DNA strip technology GenoType is that the DNA-coated strip specific test that are complementary to the derived PCR amplicon. After the single-stranded amplicon denaturation associated with tests on strip (hybridize), and visualized in a sequential enzymatic reaction with streptavydynom and alkaline phosphatase. Evaluation of hybridization is performed automatically. For culturing sputum liquid culture medium used - Middlebrook broth 7N9 VASTES MGIT system. Results and discussion . The results of molecular genetic studies of samples of sputum-concentrated and concentrated by a system GenoType not differed (P>0.05). Diagnostic value of two methods (molecular and genetic – system GenoType and phenotype – VASTES MGIT 960 system) was very high (100%). Two systems have tested positive in the study 756 (95.5 %) Mycobacterium strains that were identified in the system VASTES MGIT 960, formed Cord Factor and the results were positive identification test ID MTB MGIT they attributed to Mycobacterium tuberculosis complex. 36 (4.5 %) samples from positive MGIT tubes were negative. As a result of molecular-genetic identification of nontuberculous mycobacteria complex it was found that 18 (2.3 %) strains of mycobacteria belonging to the M. avium-intracellulare, 12 (1.5 %) mycobacterial cultures were attributed to M. kansasii, 6 (0, 7 %) cultures were identified as M. fortuitum. The results of the molecular study of MS on Mycobacterium resistance profile INN + RIF coincided in 95.5 % (894 strains) the results of testing by phenotypic proportions. In the presence of mutations associated with resistance to INH, only 93.1 % of cases observed MC M. tuberculosis to INH during TMCH in a liquid medium Middlebrook 7N9. In the presence of mutations in the genes responsible for resistance to the presence of Q, in a liquid medium only 288 (90.6 %) strains of M. tuberculosis have MS to Ofx. The strains of mycobacteria DNA were detected mutations in genes associated with MS to aminoglycosides / cyclic peptides in 299 (94.0%) cases were resistant to Am and 302 (94.9 %) cases were resistant to the results Cm DST system VASTES MGIT 960. In determining the resistance to E major differences were found between the productivity of molecular genetic and phenotypic research methods – only 206 (64, 2 %) strains of M. tuberculosis were resistant to the analysis system VASTES MGIT 960. Conclusions. GenoType system allows you to quickly carry out the identification and differentiation of Mycobacterium strains of nontuberculous mycobacteria. The results of the molecular genetic studies multyrezystents system GenoType MTBDRplus match in 95,5 % of the phenotypic test results by proportions. Using DNA strip technology GenoType to determine mutations in the genes of Mycobacterium responsible for the IPU to TDC, necessarily requires a parallel DST setting in a liquid medium

This work presents an infant cry automatic recognizer development, with the objective of classifying two kinds of infant cries, normal and pathological, from recently born babies. Extraction of acoustic features is used such as MFCC (Mel Frequency Cepstral Coefficients), obtained from Infant Cry Units sound waves, and a genetic feature selection system combined with a feed forward input delay neural network, trained by adaptive learning rate back-propagation. For the experiments, recordings from Cuban and Mexican babies are used, classifying normal and pathological cry in three different experiments; Cuban babies, Mexican Babies, and Cuban & Mexican babies. It is also shown a comparison between a simple traditional feed-forward neural network and another complemented with the proposed genetic feature selection system, to reduce the feature input vectors. In this paper the whole process is described; in which the acoustic features extraction is included, the hybrid system design, implementation, training and testing. The results from some experiments are also shown, in which the infant cry recognition rate obtained is of up to 100% using our genetic system.

The article is written for the special journal issue dedicated to Alan L. Mackay on his 90th birthday. The remarkable ideas of Alan L. Mackay about generalized crystallography, its connections with encoding of information, and also the interrelationship between art and science generate many ideas and their consequences. Mackay paid a special attention to the theme of five-fold symmetry, Fibonacci numbers and the golden section, which are essential in the structures of quasicrystals and living bodies. The present article considers a continuation of this theme in relation to the genetic coding system and to ratios of musical harmony. Hidden connections between the matrix representations the genetic code system and the golden section and the Pythagoras’s theory of esthetics of proportions are described. Such connections testify the validity of the molecular-genetic foundation of many known facts about inborn feeling of harmony in our perceptions, which becomes a part of the scientific field of “biochemical esthetics” (the term first introduced by Russian biophysicist S. Shnoll, 7). Data from theory of resonances and mathematics of noise-immunity coding of information are used in the article.

We review the rapidly evolving efforts to analyze, model, simulate, and engineer genetic and biochemical information processing systems within living cells. We begin by showing that the fundamental elements of information processing in electronic and genetic systems are strikingly similar, and follow this theme through a review of efforts to create synthetic genetic circuits. In particular, we describe and review the silicon mimetic approach, where genetic circuits are engineered to mimic the functionality of semiconductor devices such as logic gates, latched circuits, and oscillators. This is followed with a review of the analysis, modeling, and simulation of natural and synthetic genetic circuits, which often proceed in a manner similar to that used for electronic systems. We conclude by presenting examples of naturally occurring genetic and biochemical systems that recently have been conceptualized in terms familiar to systems engineers. Our review of these newly forming fields of research demonstrates that the expertise and skills contained within electrical and computer engineering disciplines apply not only to design within biological systems, but also to the development of a deeper understanding of biological functionality. This review of these efforts points to the emergence of both engineering and basic science disciplines following parallel paths.

The present paper proposes the use of a basic element for the infant cry analysis: the cry unit. In order to display the real possibility of the cry unit for the detection of pathological features (based on Hypoxia) in newborns, a novel combined treatment of the cry signal was implemented using an evolutionary-neural system. For that purpose the cry signal was segmented into cry units, the MFCC were computed as acoustic features, and a genetic feature selection system combined with a feed forward input delay neural network, trained by adaptive learning rate back-propagation were properly developed. The data for the experiments were obtained from a Mexican-Cuban infant cry database. It is also shown a comparison between a simple neural network and the proposed genetic feature selection system, to reduce the feature input vectors. The results are also shown from some experiments, in which the infant cry recognition is improved to 100% using our genetic system.

Music and the Modeling Approach to Genetic Systems of Biological Resonances

There are compelling reasons for choosing to develop the human as the highest-order experimental system in genetics: an obvious social context that stirs interest, wide medical observation of the population that permits identification of an abundance of genetic defects, and our ability to perceive in the human subtle or complex variations that may not be observable in other species. Various lines of genetic inquiry that are based on research in other systems--cytogenetic analysis, biochemical studies, mapping of defective loci by linkage analysis in affected families, and in vitro techniques such as the creation of transgenic organisms--complement and enrich each other. New phenomena that would not have been predicted from investigations in other organisms have been found in humans, such as the discovery of the "giant" Duchenne muscular dystrophy gene and the identification of recessive cancer genes. Genetic research is yielding insights into human biology that are raising new possibilities for therapy and prevention of disease, as well as challenges to society in the form of ethical decisions about the appropriate application of genetic information.

Biasing the sex ratio of populations of different organisms, including plants, insects, crustacean, and fish, has been demonstrated by genetic and non-genetic approaches. However, biasing the sex ratio of mammalian populations has not been demonstrated genetically. Here, we provide a first proof of concept for such a genetic system in mammals by crossing two genetically engineered mouse lines. The maternal line encodes a functional Cas9 protein on an autosomal chromosome, whereas the paternal line encodes guide RNAs on the Y chromosome targeting vital mouse genes. After fertilization, the presence of both the Y-encoded guide RNAs from the paternal sperm and the Cas9 protein from the maternal egg targets the vital genes in males. We show that these genes are specifically targeted in males and that this breeding consequently self-destructs solely males. Our results pave the way for a genetic system that allows biased sex production of livestock.

The Genetic Systems Corp. Integra HIV-1 Pageblot system was evaluated as a supplementary assay to confirm the presence of antibodies to human immunodeficiency virus type 1 in 57 specimens from individuals at high risk of infection with the virus. Forty-one specimens identified as reactive in the Genetic Systems Integra HIV-1 Pageblot system were likewise identified as reactive in a U.S. Food and Drug Administration-licensed (Biotech/Dupont) Western blot (immunoblot). Six specimens identified as indeterminate in either or both immunoblot assays were all identified as nonreactive in a U.S. Food and Drug Administration-licensed enzyme immunoassay with recombinant antigens.

The correlated noise-based switches and stochastic resonance are investigated in a bistable single gene switching system driven by an additive noise (environmental fluctuations), a multiplicative noise (fluctuations of the degradation rate). The correlation between the two noise sources originates from on the lysis-lysogeny pathway system of the λ phage. The steady state probability distribution is obtained by solving the time-independent Fokker-Planck equation, and the effects of noises are analyzed. The effects of noises on the switching time between the two stable states (mean first passage time) is investigated by the numerical simulation. The stochastic resonance phenomenon is analyzed by the power amplification factor. The results show that the multiplicative noise can induce the switching from “on” → “off” of the protein production, while the additive noise and the correlation between the noise sources can induce the inverse switching “off” → “on”. A nonmonotonic behaviour of the average switching time versus the multiplicative noise intensity, for different cross-correlation and additive noise intensities, is observed in the genetic system. There exist optimal values of the additive noise, multiplicative noise and cross-correlation intensities for which the weak signal can be optimal amplified.

Mutagenic studies on the hair dye 2-(2′,4′-diaminophenoxy)ethanol with different genetic systems