Genetic code expansion and its application in characterization and imaging of proteins / 生物工程学报

Genetic code expansion (GCE) allows the incorporation of unnatural amino acids into proteins via using stop codons. GCE may achieve site-specific labeling of proteins in combination with the click reaction. Compared with other labeling tools such as fluorescent proteins and tagged antibodies, the compound molecules used in protein labeling by GCE technology are smaller, and therefore, may less interfere the conformational structure of proteins. In addition, through click reaction, GCE allows a 1:1 stoichiometric ratio of the target protein molecule and the fluorescent dye, and the protein can be quantified based on the fluorescence intensity. Thus, GCE technology has great advantages in the researches that require the exposition of living cells under high laser power for longer time, for example, in the context of single molecule tracing and super-resolution microscopic imaging. Meanwhile, this technology lays the foundation for improving the accuracy of positioning and molecule counting in the imaging process of living cells. This review summarized the GCE technology and its recent applications in functionally characterizing, labeling and imaging of proteins.

Epigenética y ontogenia humana, baluarte inestimable en la promoción de salud y prevención de enfermedad / Epigenetics and human ontogeny, invaluable bulkward in health promotion and disease prevention

RESUMEN La ontogenia humana está basada en fundamentos genéticos y epigenéticos. Con el objetivo de estructurar los referentes teóricos sobre el papel relevante de la epigenética en la ontogenianormal y defectuosa que contribuyan a la promoción de salud y prevención de enfermedad, se realizó la revisión de 37 referencias bibliográficas. La epigenética es el conjunto de procesos químicos dependientes del ambiente que modifican la expresión del ácido desoxirribonucleico, sin alterar su secuencia. Su acción está presente durante toda la vida, especialmente en la prenatal cuando, por modificaciones ambientales intraútero ocurre la programación epigenética que hace al humano susceptible a defectos en la ontogenia, incluso a padecer ulteriormente de enfermedades crónicas no transmisibles. Se han reportado factores ambientales inductores de marcas epigenéticas, entre ellos: alimentación, hábitos tóxicos, estrés, consumo inadecuado de ácido fólico y técnicas de reproducción asistida, todos modificables; su conocimiento constituye un baluarte inestimable en la promoción de salud y prevención de enfermedad.

ABSTRACT Human ontogeny is based in genetic and epigenetic fundaments. 37 bibliographic references were reviewed with the objective of structuring the theoretical referents on the relevant role of epigenetics in normal and defective ontogeny to contribute to health promotion and disease prevention. Epigenetics is the whole of chemical processes depending from the environment that modify the deoxyribonucleic acid expression without modifying its sequence. Its action is present during all lifetime, especially at pre-natal times; when due to intrauterine environmental modifications the epigenetic programming takes place, making humans susceptible to defects in ontogeny, even to subsequently suffer non-communicable chronic diseases. Environmental factors inducing epigenetic marks have been reported: food, toxic habits, stress, folic acid inadequate intake and assisted reproduction techniques, all modifiable. Its knowledge is an invaluable bulkward in health promotion and disease prevention.

[Hepatitis B virus x protein coding sequence variation in chronically infected patient]

Background and Objective: Chronic infection with Hepatitis B virus [HBV] is one of the main causes of cirrhosis and hepatocellular carcinoma [HCC]

The pathogenicity of the virus is determined by the multi-functional protein x [HBx]. Changing the sequence of the gene encoding this protein causes the regulation of transcription and pathogenicity factors. This study was done to analyze the genetic dynamics of the HBx coding gene in a person with chronic HBV

Methods: In this descriptive laboratory study, an infected person with chronic hepatitis B virus infection was first amplified and cloned into complete sequence of HBx encoder. Then, the reference sequences of genotypes, serotypes and different virus subtypes of the GenBank database were matched by CLC Sequence Viewer software. The comparative result was used to plot the phylogenic tree by T-rex server and population genetic analysis using DnaSP software. Natural selection at the nucleotide and protein level was performed by the Tajima's D test

Results: No known mutation at the level of the protein was found in the chronic sequence of the HBx encoder. The results of natural selection indicated neutral mutations in the HBx gene. The phylogenetic results showed that the HBx encoding sequences in the chronic infected individual had a genetic affinity with genotype D and ayw2 subtype

Conclusion: Neutrality polymorphism takes place in HBx coding region. Also, the phylogenetic results of the present study are consistent with the previous findings of Golestan province and Iran which have reported the prevalence of genotype D and subspecies ayw2

EL CONCEPTO JURÍDICO DE PERSONA Y LA FILOSOFÍA DEL "IMPERSONAL" / THE CONCEPT OF PERSON UNDER THE LAW AND THE PHILOSOPHY OF "IMPERSONAL" / O CONCEITO JURÍDICO DE PESSOA E A FILOSOFIA DO "IMPESSOAL"

El artículo se centrará en presentar tres argumentos que irán de menos a más en su postura radical frente al actual concepto jurídico de persona. El aporte del primer argumento en la discusión sobre la persona, radica principalmente en aclaraciones terminológicas. En el segundo argumento, Roberto Esposito, aunque considera reemplazar a "alguien" con "algo" y de esta manera dar como resultado la salvación de la humanidad, no sobrepasa a su maestra Simone Weil, que es mucho más importante gracias al impacto de su personalidad, sus cualidades de escritora y su radicalidad. En el tercer argumento, Simone Weil hace una demostración de poder intelectual que estremece. Sus escritos reflejan una mente consecuente, a ratos inalcanzable, pero su idea de una "filosofía del impersonal" resulta inaceptable. En cada hombre hay elementos impersonales, como por ejemplo su idioma, y elementos personales, como por ejemplo su manera de hablar y escribir. Un mundo sin estos dos elementos es simplemente inconcebible.

The article focuses on presenting three arguments that range from less to more in terms of their radical stance on the current legal definition of person. The contribution of the first argument to this discussion lies mainly with a clarification of terminology. In the second argument, Roberto Esposito, despite considering replacing "someone" with "something" and saving humanity as a result, does not surpass his teacher Simone Weil. She is far more important, thanks to the impact of her personality, her qualities as a writer and her radicalism. In the third argument, Simone Weil provides a demonstration of intellectual power that makes one shudder. Her writing reflects a consistent mind, at times out of reach, but her idea of a "philosophy of the impersonal" is unacceptable. Every human being has impersonal elements, such as language, and personal elements, including their manner of speaking and writing. A world without these two elements is simply inconceivable.

Este artigo se centra em apresentar três argumentos que vão de menos a mais em sua posição radical ante o atual conceito jurídico de pessoa. A contribuição do primeiro argumento na discussão sobre a pessoa reside principalmente em esclarecimentos terminológicos. No segundo argumento, Roberto Esposito, embora considere substituir "alguém" com "algo" e, dessa maneira, dar como resultado a salvação da humanidade, não ultrapassa sua mestra Simone Weil, que é muito mais importante graças ao impacto de sua personalidade, suas qualidades de escritora e sua radicalidade. No terceiro argumento, Simone Weil faz uma demonstração de poder intelectual impactante. Seus textos refletem uma mente consequente, às vezes inatingível, mas sua ideia de uma "filosofia do impessoal" resulta inaceitável. Em cada homem, há elementos impessoais, como seu idioma, e elementos pessoais, como sua maneira de falar e escrever. Um mundo sem esses dois elementos é simplesmente inconcebível.

Next Generation DNA Sequencing and Its Application in Clinical Medicine / 대한주산의학회잡지

Watson and Crick published a paper on the double helical structure of DNA in Nature in April 25, 1953. The human genome is contained in the 23 pairs of chromosomes and in the mitochondrial DNA of each cell. The Human Genome Project was launched in 1990 under the direction of Watson and concluded in 2003, on the 50th anniversary of Watson and Crick paper. Over 6 billion of nucleotides of genetic codes are in single cells. There are 23,000 protein coding genes and the remainder are non-coding DNA, regulatory DNA. Since the completion of Human Genome Project, these huge genomic information has been translated into clinically usable medical information. With the advent of massively parallel DNA sequencing, known as next generation DNA sequencing, the cost and turn-around time were significantly reduced so that the era of Whole Genome Sequencing entered into hospitals and medical clinics. On June 16, 2014 American Society of Human Genetics revised its mission statement as follows. "Our mission is to advance human genetics in science, health and society through research, education and advocacy". Finally medical genetics nestled its roots in the midst of genetics and genomics.

Presencia del elemento genético transportable dTdic1 en Dianthus caryophyllus con flores variegadas y no variegadas / Presence of the transposable genetic element dTdic1 in Dianthus caryophyllus with variegated and no variegated flowers

El objetivo de este trabajo era la búsqueda del EGT (Elemento Genético Transponible) dTdic1 que ha sido asociado con la variegación del color de las flores de clavel y su relación con dos genes que codifican para enzimas involucradas en la biosíntesis de antocianinas, Chalcona isomerasa (CHI) y Dihidroflavonol reductasa (DFR). Su presencia y expresión se evaluó en siete genotipos con flores variegadas (líneas híbridas) y en cuatro genotipos de flores no variegadas (una línea híbrida y tres cultivares comerciales). Un alto número (indefinido) de copias del elemento dTdic1 se detectó en todas las líneas variegadas y no variegadas. En consecuencia, la sola presencia de este EGT no pudo asociarse directamente con la variegación de los pigmentos florales de flores de clavel. Adicionalmente, dTdic1 se encontró interrumpiendo el gen CHI en cuatro genotipos variegados y uno no variegado. No se observó evidencia de inserción de dTdic1 en el gen DFR en ninguno de los genotipos.

The objective of this work was to search for the EGT (Transposable Genetic Element) dTdic1 that has been associated with color variegation of carnation flowers and its relationship with two genes that code for enzymes involved in the synthesis of anthocyanins, Chalcona isomerase (CHI) and Dihidroflavonol reductase (DFR). Its presence and expression was evaluated in seven genotypes of variegated flowers and four no variegated flower genotypes (one hybrid line and three commercial cultivars). A high number of copies (undefined) of copies of the dTdic1 element was detected in variegaated and no variegated lines. Therefore, the main presence of this EGT was not associated directly with variegation of floral pigments. Additionally, dTdic1 was found interrupting the CHI gene in four variegated and one no variegated phenotypes. No evidence was observed of insertion of dTdic1 in the DFR gene in any of the genotypes.

Molecular recognition code between pathogenic bacterial TAL-effectors and host target genes: a review / 生物工程学报

As the pathogenic bacterial virulence and avirulence factors, transcription activator like (TAL) effectors of Xanthomonas can resulted in the host diseases or resistance responses. TAL effectors can specifically bind the target DNA of host plant with a novel protein-DNA binding pattern in which two amino acids recognize one nucleotide. The complexities of TAL-DNA binding have the feasibility in use of gene therapy through homologous recombination and site-specific mutation. By using the molecular recognition code between TAL-effectors and host target genes, we can exploit both the susceptible and resistance genes; broad spectrum resistance induced by multiple TAL effectors could also be manipulated. Deeper insight in the area of protein-DNA binding mechanism will benefit the application in the biomedical engineering and agricultural engineering. This article reviews the findings and functions of TAL effectors, the binding specificity and recognition code between TAL-effectors and host target genes. The possible applications and future prospects of the molecular recognition code have been discussed.

ORF Miner: a Web-based ORF Search Tool

The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.

De genotipos e isonimias: análisis de correlación entre el apellido y el patrimonio genético heredado en el cromosoma Y en la población de tres departamentos del suroccidente colombiano / Correlation analysis of surnames and Y-chromosome genetic heritage in 3 provinces of southwestern Colombia

Introducción. Es bien sabido que, entre los caracteres transmitidos por la línea paterna, el apellido se ha configurado en diferentes culturas como un carácter semejante a un alelo genético neutral asociado al cromosoma Y. Objetivo. En este estudio se determinaron las frecuencias en la población de 17 STR del cromosoma Y en 308 individuos provenientes de las poblaciones de los departamentos del Valle del Cauca, Cauca y Nariño. Además, se propuso definir la correlación de los haplotipos obtenidos en cada individuo con su apellido paterno, para comparar estos dos códigos de identidad. Materiales y métodos. Se extrajo el ADN de cada individuo a partir de sangre periférica y se utilizó el estuche comercial AmpFLSTR® Yfiler™ (Applied Biosystems) para tipificarlo. Los resultados de los haplotipos moleculares se compararon con los apellidos reportados por cada individuo y se asociaron apellidos amerindios y europeos con haplotipos que incluyeran o no el marcador DYS19/13, característico de la población amerindia. Resultados. Se reportan las frecuencias alélicas de cada uno de los 17 marcadores del cromosoma Y analizados en esta región de Colombia, así como la diversidad génica y haplotípica hallada en los tres departamentos. Al comparar los resultados obtenidos a nivel molecular con los apellidos de origen europeo o amerindio reportados por cada uno de los individuos, se encontró cerca de 40 por ciento de inconsistencia de linaje. Conclusiones. La utilización del apellido como marcador de población debe hacerse con cautela, por cuanto las genealogías fundamentadas en éstos pueden no corresponder al origen biológico de sus portadores.

From geochemistry and biochemistry to prebiotic evolution... we necessarily enter into Gánti's fluid automata

The present study is just an overview of the opening of the geochemical stage for the appearance of life. But that opening would not have been sufficient for the intellectual discovery of the origin of life! The excellent works and many commendable efforts that advance this explanation have not shown the fundamental elements that participate in the theoretical frame of biological evolution. The latter imply the existence of evolutionary transitions and the production of new levels of organization. In this brief analysis we do not intend to introduce the audience to the philosophy of biology. But we do expect to provide a modest overview, in which the geochemical chemolithoautotrophic opening of the stage should be seen, at most, as the initial metabolism that enabled organic compounds to follow the road where a chemical fluid machinery was thus able to undertake the more [quot ]sublime[quot ] course of organic biological evolution. We think that Tibor Gánti's chemoton is the most significant contribution to theoretical biology, and the only course now available to comprehend the unit of evolution problem without the structuralist and functionalist conflict prevalent in theoretical biology. In our opinion Gánti's chemoton theory travels to the [quot ]locus[quot ] where evolutionary theory dares to extend itself to entities at many levels of structural organization, beyond the gene or the group above. Therefore, in this and subsequent papers on the prebiotic conditions for the eventual appearance of the genetic code, we explore the formation and the presence of metal sulfide minerals, from the assembly of metal sulfide clusters through the precipitation of nanocrystals and the further reactions resulting in bulk metal sulfide phases. We endeavor to characterize pristine reactions and the modern surfaces, utilizing traditional surface science techniques and computational methods. Moreover, mechanistic details of the overall...

A scenario on the stepwise evolution of the genetic code / 基因组蛋白质组与生物信息学报·英文版

It is believed that in the RNA world the operational (ribozymes) and the informational (riboscripts) RNA molecules were created with only three (adenosine, uridine, and guanosine) and two (adenosine and uridine) nucleosides, respectively, so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigorous editing (adenosine to inosine); the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially, the genetic code, encoding seven amino acids, was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 12, 15, and 20 amino acids through the relief of guanine from its roles as operational signals and through the recruitment of cytosine. Therefore, the maturation of the genetic code also coincided with (1) the departure of aminoacyl-tRNA synthetases (AARSs) from the primordial translation machinery, (2) the replacement of informational RNA by DNA, and (3) the co-evolution of AARSs and their cognate tRNAs. This model predicts gradual replacements of RNA-made molecular mechanisms, cellular processes by proteins, and informational exploitation by DNA.

Screening and characterization of human phage Fab antibody gene to prostate specific membrane antigen / 中华男科学杂志

<p><b>OBJECTIVE</b>To screen and characterize the variable region gene about prostate specific membrane antigen (PSMA) of the Chinese Fab fragment, and to establish a new approach to researches on PSMA and prostate gene therapy.</p><p><b>METHODS</b>We used purified PSMA protein as antigen, stuck it on the ELISA plate and scanned the phage Fab fragment antibody library by phage display technology. After five cycles of "absorbing-elution-amplification", we got the Fab fragment phage antibody of PSMA with high antigen binding ability and specificity, and tested it with immunodetection and sequencing.</p><p><b>RESULTS</b>The sequence of Fd fragment was 696 base pairs encoding 232 amino-acid residues, with 98% homological similarity to the human immunoglobulin gamma chain, while the light chain was constructed by 630 base pairs encoding 210 amino-acid residues, with 93% homological similarity to kappa chain.</p><p><b>CONCLUSION</b>Using phage display technology, we obtained the gene sequence of Fab antibody fragment specific to PSMA, and the antibody gene has the classic structural features of immunoglobulin light chain and heavy chain. The coding output of the antibody gene has the specificity and immunological competence to PSMA.</p>

Grupos de simetría de codones sinónimos revelados en un nuevo espacio de representación / Symmetric groups of codon usage correlations in a new space of representation

El presente trabajo presenta un nuevo espacio de configuración de codones fundado en el carácter dual que las bases poseen considerando dos propiedades fisicoquímicas esenciales: (a) especie química (Y o R) y (b) número de puentes de H (3 ó 2) involucrados en la interacción codón-anticodón. La concepción de esta nueva representación de codones se basa en la construcción de un espacio" bidimensional definido por dos ejes ortogonales cuyos "valores" quedan definidos por las ocho combinatorias posibles de las propiedades Y y R para uno de los ejes y por las ocho combinatorias posibles de las propiedades 2 y 3 para el otro eje...En este trabajo se presentan, discuten contribuciones a la teoría y utilidades prácticas

TcZFP8, a novel member of the Trypanosoma cruzi CCHC zinc finger protein family with nuclear localization

In a 17-kb genomic fragment of Trypanosoma cruzi chromosome XX, we identified three tandemly linked genes coding for CX2CX4HX4C zinc finger proteins. We also showed that similar genes are present in T. brucei and Leishmania major, sharing three monophyletic groups among these trypanosomatids. In T. cruzi, TcZFP8 corresponds to a novel gene coding for a protein containing eight zinc finger motifs. Molecular cloning of this gene and heterologous expression as a fusion with a His-tag were performed in Escherichia coli. The purified recombinant protein was used to produce antibody in rabbits. Using Western blot analysis, we observed the presence of this protein in all three forms of the parasite: amastigote, trypomastigote and epimastigote. An analysis of cytoplasmic and nuclear cell extracts showed that this protein is present in nuclear extracts, and indirect immunofluorescence microscopy confirmed the nuclear localization of TcZFP8. Homologues of TcZFP8 in T. brucei are apparently absent, while one candidate in L. major was identified.