Identification and Characterization of the ATG8, a Marker of Eimeria tenella Autophagy / Identificação e Caracterização do ATG8, um marcador de autofagia em Eimeria tenella

Abstract Autophagy plays an important role in maintaining cell homeostasis through degradation of denatured proteins and other biological macromolecules. In recent years, many researchers focus on mechanism of autophagy in apicomplexan parasites, but little was known about this process in avian coccidia. In our present study. The cloning, sequencing and characterization of autophagy-related gene (Etatg8) were investigated by quantitative real-time PCR (RT-qPCR), western blotting (WB), indirect immunofluorescence assays (IFAs) and transmission electron microscopy (TEM), respectively. The results have shown 375-bp ORF of Etatg8, encoding a protein of 124 amino acids in E. tenella, the protein structure and properties are similar to other apicomplexan parasites. RT-qPCR revealed Etatg8 gene expression during four developmental stages in E. tenella, but their transcriptional levels were significantly higher at the unsporulated oocysts stage. WB and IFA showed that EtATG8 was lipidated to bind the autophagosome membrane under starvation or rapamycin conditions, and aggregated in the cytoplasm of sporozoites and merozoites, however, the process of autophagosome membrane production can be inhibited by 3-methyladenine. In conclusion, we found that E. tenella has a conserved autophagy mechanism like other apicomplexan parasites, and EtATG8 can be used as a marker for future research on autophagy targeting avian coccidia.

Resumo A autofagia desempenha um papel importante na manutenção da homeostase celular através da degradação de proteínas desnaturadas e outras macromoléculas biológicas. Nos últimos anos, muitos pesquisadores se concentraram no mecanismo da autofagia em parasitas apicomplexos, mas pouco se sabe sobre esse processo na coccidia aviária. No presente estudo, a clonagem, sequenciamento e caracterização de gene relacionado à autofagia Etatg8 foram investigados pela PCR quantitativa em tempo real (RT-qPCR), mancha ocidental (WB), ensaios indiretos de imunofluorescência (IFAs) e microscopia eletrônica de transmissão (TEM), respectivamente. Os resultados mostraram que o gene Etatg8 de E. tenella possui uma ORF de 375 bp, codificando uma proteína de 124 aminoácidos com estrutura e propriedades semelhantes à de outros apicomplexos. RT-qPCR revelou que Etatg8 é expresso durante os quatro estágios de desenvolvimento de E. tenella. Entretanto, seus níveis transcricionais foram significativamente mais elevados na fase de oocisto não esporulados. Os ensaios de manchas ocidental (WB) e de imunofluorescência (IFA) mostraram que a proteína EtATG8 foi lipidada para ligar-se à membrana do autofagossomo sob condições de deficiência nutritiva (em presença de rapamicina) e se agregar no citoplasma de esporozoítas e merozoítas. No entanto, o processo de produção de membrana do autofagossomo pode ser inibido por um inibidor de autofagia (3-meetiladeninatiladenina, 3-MA). Em conclusão, foi demonstrado que E. tenella tem um mecanismo de autofagia conservado, semelhante ao de outros parasitas apicomplexos, e que EtATG8 pode ser usado como um marcador para futuras pesquisas sobre autofagia direcionada à coccidiose aviária.

In-Situ Gel-Free Plasmid Reassembling for Rapid Gene Subcloning and Truncation

Abstract Gene subcloning, a process in which the nucleotide sequence of interest is excised from on plasmid and inserted into another, seems to be an easy task to done. However, not all subcloning attempts are successful, even when the insert sequence and the double digested target plasmid are successfully purified form agarose gel and thought to be ready for subsequent ligation. In the current study we introduce a reliable, easy, and time consuming method for gene subcloning and also truncation. The stages are all carried out in a single microtube without any running on a gel, making it possible to accomplish a successful gene subcloning or truncation even with low concentrations of DNA molecules. Summarily, subcloning is achieved by mixing the plasmids of interest in a microtube and subjecting to restriction enzymes whose restriction sites flank the segment that is going to be subcloned. Digestion mixture is precipitated in the same microtube using isopropanol and the resultant DNA molecules are allowed to take part in a ligation reaction. The recombinant plasmids of interest are screened by colony PCR. Truncation is achieved by double- digestion of the plasmid of interest using a restriction enzyme whose restriction site flanks the segment that is going to be cut out.

Clonación y expresión en Escherichia coli de un gen L1 completo del virus del papiloma humano 18 aislado de una paciente cubana y variantes delecionadas / Cloning and expression in Escherichia coli of the full-length and deletion variants of a human papillomavirus 18 L1 gene isolated from a Cuban patients

Introduction: Human papillomavirus (HPV) vaccines are based on the L1 major capsid protein. Objectives: To clone the HPV-18 L1 gene from a Cuban female HPV-18-infected patient and to express the full-length and deletion variants of the cloned HPV-18 L1 gene in Escherichia coli. Methods: The full-length HPV-18 L1 gene was PCR-amplified from total DNA isolated from a Cuban patient, cloned and finally subcloned into the E. coli expression vector pET26b. Three deletion mutants were constructed, which encode truncated proteins lacking 30 amino acids at the C-terminus in combination with 5, 6 or none deleted residue at the N-terminus. Production of L1 proteins in E. coli BL21(DE3) and E. coli SHuffle T7 was assessed by SDS-PAGE and Western blotting. Results: The cloned HPV-18 L1 gene was 99.9 por ciento similar to the African variant EF202152 and probably shares a common origin with the B lineage of genotype 18. The three truncated variants of HPV-18 L1 were produced at higher levels than the full-length HPV-18 L1 protein, attaining higher levels in E. coli BL21(DE3) and higher solubility in E. coli SHuffle. The C-terminus-only truncated variant, L1∆C30, was produced at similar levels to the HPV-18 L1s truncated at both termini. E. coli SHuffle produced about three times more amounts of L1∆C30 when grown under autoinduction conditions with respect to conventional induction and thus, amounts were comparable to those obtained in E. coli BL21(DE3) under conventional induction. Conclusions: Truncation of thirty amino acid residues at the carboxy-terminus of the HPV-18 L1 made a major contribution to the production and solubility of this wild-type protein in E. coli. This is the first report about soluble production of HPV-18 L1 protein in an E. coli SHuffle strain. However, higher amounts of L1 are needed to scale-up its production for developing an HPV vaccine candidate(AU)

Introducción: Las vacunas contra el virus del papiloma humano (VPH) se fundamentan en la proteína principal de la cápsida L1. Objetivo: Clonar el gen L1 del VPH-18 a partir de una paciente cubana infectada con VPH-18 y expresar las variantes de longitud completa y delecionadas del gen L1 del VPH-18 en Escherichia coli. Métodos: El gen L1 del VPH-18 de longitud completa se amplificó por PCR a partir de ADN total aislado de un paciente cubana, se clonó y finalmente se subclonó en el vector de expresión de E. coli pET26b. Se construyeron tres mutantes de deleción, que codifican para proteínas truncadas que carecen de 30 aminoácidos por el extremo carboxilo, en combinación con 5, 6 o ningún residuo delecionado por el extremo amino. La producción de las proteínas L1 en E. coli BL21(DE3) y E. coli SHuffle T7 se evaluó mediante SDS-PAGE y Western blot. Resultados: El gen L1 del VPH-18 clonado fue 99.9 percent similar a la variante africana EF202152 y probablemente comparte un origen común con el linaje B del genotipo 18. Las tres variantes truncadas de la proteína L1 del VPH-18 se produjeron a mayores niveles que la proteína L1 del VPH-18 de longitud completa, alcanzando mayores niveles en E. coli BL21(DE3) y mayor solubilidad en E. coli SHuffle. La variante truncada solo por el extremo carboxilo, L1(C30, se produjo a niveles similares a las proteínas L1 del VPH-18 truncadas por ambos extremos. E. coli SHuffle produjo aproximadamente tres veces más cantidades de L1(C30 cuando creció en condiciones de autoinducción, con respecto a la inducción convencional y, por ende, las cantidades fueron comparables a las obtenidas por E. coli BL21(DE3) bajo inducción convencional. Conclusiones: La truncación de treinta residuos de aminoácidos por el extremo carboxilo de la proteína L1 del VPH-18 tuvo una importante contribución a la producción y solubilidad de la proteína L1 nativa en E. coli. Este es el primer informe sobre la producción soluble de la proteína L1 del VPH-18 en una cepa de E. coli SHuffle. Sin embargo, se necesitan mayores cantidades de la proteína L1 para escalar su producción para desarrollar un candidato vacunal contra el VPH(AU)

Development of RAPD-SCAR markers for Lonicera japonica (Caprifolicaceae) variety authentication by improved RAPD and DNA cloning / Desarrollo de marcadores RAPD-SCAR para Lonicera japonica Thunb. (Caprifolicaceae) para la autenticación de variedades mediante RAPD mejorados y clonación de ADN

Genetic diversity within a species is a common feature, which plays a vital role in its survival and adaptability, and is important for the identification and authentication of a species. Lonicera japonica is a traditionally used medicinal plant, which have been recently genetically characterized by an improved ran- dom amplified polymorphic DNA (RAPD) analysis. In this study, the molecular markers on the basis of these RAPD fragments have been developed to identify specific L. japonica variety. The DNAs were extracted from fresh young leaves of different samples of L. japonica collected from Shenzhen, Yichang, Leshan, Emei and Loudi, China. The DNA materials were amplified using improved RAPD PCR. Different RAPD bands were excised, cloned and developed for stable sequence-characterized amplified region (SCAR) markers with differ- ent species. Two SCAR markers, JYH3-3 and JYH4-3, have been successfully cloned from improved RAPD fragments. The SCAR marker JYH3-3 was found specific for all of the L. japonica samples collected from the different regions, and another marker JYH 4-3 was strictly specific to the Shenzhen sample from Guangdong province, which is geographically distant from Hubei, Sichuan and Hunan Provinces (source of other L. japonica samples). The marker JYH3-3 was found as specific molecular marker for the identification of L. japonica, while JYH4-3 was found as molecular marker strictly specific for the Shenzhen sample. The developed SCAR mark- ers might serve as more specific molecular markers for L. japonica variety authentication. The combination of improved RAPD analysis and SCAR marker development have resulted useful tools to study the genetic variety of any organism, which we have successfully applied here in L. japonica.

La diversidad genética dentro de una especie es una característica común, que juega un papel vital en su supervivencia y adaptabilidad, y es importante para la identificación y la autenticación de una especie. Lonicera japonica es una planta medicinal utilizada tradicionalmente, que han sido recientemente caracterizada genéticamente por amplificación aleatoria mejorada de ADN polimórfico (RAPD). En este estudio, los marcadores moleculares basados en estos fragmentos de RAPD se han desarrollado para identificar una variedad específica de L. japonica. Los ADN se extrajeron de las hojas jóvenes frescas de diferentes muestras de L. japonica recogidas de Shenzhen, Yichang, Leshan, Emei y Loudi, China. Los materiales de ADN fueron amplificados utilizando el RAPD PCR mejorado. Diferentes bandas RAPD fueron extraídas, clonadas y desarrolladas para las regiones amplificadas de secuencia conocida (SCAR) con marcado- res de diferentes especies. Dos marcadores SCAR, JYH3-3 y JYH4-3, se clonaron con éxito de los RAPD mejorados. El marcador SCAR JYH3-3 se encontró específico para todas las muestras de L. japonica recolectadas en las diferentes regiones, mientras que el otro marcador JYH4-3 era estrictamente específico para la muestra de Shenzhen de la provincia de Guangdong, que está geográficamente distante de Hubei, Sichuan y Provincias Hunan (fuente de otras muestras de L. japonica). Se encontró que JYH3-3 es un marcador molecular específico para la identificación de L. japonica, mientras que JYH4-3 se encontró como marcador molecular estrictamente específico para la muestra de Shenzhen. Los marcadores SCAR desarrollados podrían servir como marcadores moleculares más específicos para la autenticación de la variedad L. japonica. La combi- nación de RAPD mejorado y el desarrollo del marcador SCAR han dado como resultado herramientas útiles para el estudio de la variedad genética de cualquier organismo, que hemos aplicado con éxito en L. japonica.

Molecular cloning of a hyaluronidase from Bothrops pauloensis venom gland

Hyaluronate is one of the major components of extracellular matrix from vertebrates whose breakdown is catalyzed by the enzyme hyaluronidase. These enzymes are widely described in snake venoms, in which they facilitate the spreading of the main toxins in the victim’s body during the envenoming. Snake venoms also present some variants (hyaluronidases-like substances) that are probably originated by alternative splicing, even though their relevance in envenomation is still under investigation. Hyaluronidases-like proteins have not yet been purified from any snake venom, but the cDNA that encodes these toxins was already identified in snake venom glands by transcriptomic analysis. Herein, we report the cloning and in silico analysis of the first hyaluronidase-like proteins from a Brazilian snake venom.

Molecular cloning of a hyaluronidase from Bothrops pauloensis venom gland

Hyaluronate is one of the major components of extracellular matrix from vertebrates whose breakdown is catalyzed by the enzyme hyaluronidase. These enzymes are widely described in snake venoms, in which they facilitate the spreading of the main toxins in the victim’s body during the envenoming. Snake venoms also present some variants (hyaluronidases-like substances) that are probably originated by alternative splicing, even though their relevance in envenomation is still under investigation. Hyaluronidases-like proteins have not yet been purified from any snake venom, but the cDNA that encodes these toxins was already identified in snake venom glands by transcriptomic analysis. Herein, we report the cloning and in silico analysis of the first hyaluronidase-like proteins from a Brazilian snake venom.

Análise de quasiespécies do vírus da hepatite C (HCV) e implicação na transmissão intrauterina / Analysis of quasispecies of the hepatitis C virus (HCV) and involvement in transmitting utero

A transmissão materno-infantil (TMI) é a causa mais comum de infecção pelo vírus da hepatite C (HCV) entre as crianças. Objetivo: Esse estudo teve como objetivo avaliar fatores virais implicados na TMI do HCV. Materiais e métodos: Quatro gestantes e um par mãe-recém-nascido (RN), todos infectados pelo HCV, foram incluídos neste estudo. Sequências das regiões 5’UTR, E1, HVR1, E2 e NS5B foram obtidas através de sequenciamento direto do produto do PCR e clonagem. A diversidade quasiespécie foi analisada utilizando-se diferentes parâmetros (taxa de clonotipos, frequência de mutações, Pn e entropia de Shannon normalizada), comparando (1) grupos TMI+ e TMI-, e (2) par mãe-RN. Um framework foi usado para avaliar a associação entre a frequência dos nucleotídeos e a TMI. Resultados: Dois casos de TMI foram identificados, mas apenas a amostra de um RN estava disponível. As cargas virais de todos os sujeitos estavam acima do limite de quantificação. Ambos os casos de TMI pertenciam ao genótipo 1a apenas este subtipo foi analisado subsequentemente. O sequenciamento direto dos produtos de PCR não representou, de maneira confiável, a complexidade quasiespécie e não foi utilizado. Não houve clonotipos coincidentes entre os grupos TMI+ e TMI-, exceto pela região 5’UTR. Em nível de aminoácido, mãe e RN compartilharam apenas do clonotipo predominante. Todos os clonotipos minoritários foram exclusivos. Foi observada maior diversidade quasiespécie nas regiões E2 e NS5B. A HVR1 apresentou a menor diversidade dentro da região codificante. A diversidade quasiespécie do grupo TMI+ foi sempre maior do que aquela vista no grupo TMI-; no entanto, não houve significância estatística. Trinta e cinco mutações na região codificante foram associadas significativamente com a TMI. Dados do par mãe-RN sugerem que a transmissão intrauterina ocorreu em um momento inicial da gestação e que o vírus provavelmente atravessou o tecido placentário, levando a um gargalo de garrafa. Conclusões: A diversidade quasiespécie não foi associada à TMI, mas a presença de mutações ao longo da região codificante sugere que o genoma completo contribui para a capacidade de transmissão intrauterina. São necessários estudos adicionais para determinar se essas variantes podem ser úteis para predizer a TMI.

Cloning and characterization of a gene encoding novel zinc finger protein transcription factor induced under water deficit stress from rice (Oryza sativa) cv. N-22.

A gene OsZnI encoding Cys3/His1-type zinc finger protein was isolated from the water stress-induced cDNA library of rice (Oryza sativa) cv. N-22, an early maturing, deep-rooted, drought-tolerant genotype adapted to upland conditions. The in-silico analysis revealed an insert of 800 bp with an ORF of 663 nucleotides, encoding 221 amino acids. OsZnI had three distinct features — nuclear localization signal (NLS) present in Arg152-Arg168, Zn finger domain between 185-193 amino acids and 12 amino acids conserved domain in 71-82 amino acids homologous to LEA motif, and belonged to C-type family of Zn finger protein. OsZnI showed induced expression under water deficit stress.

Ligation independent cloning of polycistronic, genetically modified, HuMAb4D5-8 F [ab'] 2, in bacterial plasmid

In recent years, recombinant monoclonal antibodies and their derivatives have emerged as important targeted therapy agents. Monoclonal antibodies are ex-tremely difficult to produce. So, the cost of production is very high and many people cannot afford these drugs. In this regard, choosing inexpensive and easy ways to manipulate production systems such as bacterial hosts to reduce the cost of manufacturing these critical components are considered as vital step for developmental issues in recombinant expression systems. We, therefore, at-tempted to generate a polycistronic construct of anti HER-2 F[ab']2 fragment antibody for insertion in an expression bacterial plasmid. Also some modifica-tions were made in the hinge region to express antibody F[ab']2 fragment in its authentic form preventing from multiple varieties of disulfide bond formation. Finally, synthesized construct was cloned in pET-32 Ek/LIC vector without using restriction enzyme digestion or ligation reactions. The results of this study showed that modified F[ab']2 fragment was simply and successfully inserted in Escherichia coli [E.coli] using the Ligation Independent Cloning technology

Identification, cloning and expression of core protein gene of hepatitis C genotype 4A

Although Egypt has very high rates of HCV, not much is known about genotype 4a which is the most predominant genotype in Egypt. In the present study, core [C_ED43] gene of the Egyptian strain ED43 of HCV genotype 4a was first analyzed using PC/GENE program. Computer analysis of Core region of the isolate ED43 revealed that the Egyptian genotype 4a is different from those isolated from Europe and Central Africa and that it is closely related to genotype Ib. The DNA region coding for the Core was amplified from HCV_ED43/PUC19 plasmid. The PCR product was then cloned and expressed in E. coli M15 using pQE-30 vector. The expression and antigenicity of the core [Core_4a] protein in E. coli was confirmed by SDS-PAGE and western blotting, which will make it useful for developing assay systems for detecting anti-HCV antibodies and HCV antigen, respectively and which might help in the design of a vaccine against the Egyptian genotype 4a

Characterization, cloning and expression of NS3 protein gene of hepatitis c genotype 4A

Clone and express NS3 gene of the Egyptian strain ED43 of HCV genotype 4a in E. coli was studied. Gene and protein sequences of NS3 gene of the ED43 strain were first analyzed using PC/GENE program. DNA homology was 89% the homologies and that of the protein was 78.8% indicating that NS3 gene of the genotype 4a is different from those isolated from other strains. DNA of NS3 region of genotype 4a was amplified from HCV_ED43/PUC19 plasmid. The PCR product was cloned and expressed in E. coli M15 using pQE-30 vector. Fusion protein containing the peptides coded by HCV NS3 [NS3_4a] was expressed by Escherichia coli. The specific HCV antigenicity of the NS3_4a fusion protein was identified by western blotting

Isolation and characterization of a chitinase gene from entomopathogenic fungus Verticillium lecanii / Isolamento e caracterização de um gene de quitinase do fungo entomopatogênico Verticillium lecanii

Entomopathogenic fungus Verticillium lecanii is a promising whitefly and aphid control agent. Chitinases secreted by this insect pathogen have considerable importance in the biological control of some insect pests. An endochitinase gene Vlchit1 from the fungus was cloned and overexpressed in Escherichia coli. The Vlchit1 gene not only contains an open reading frame (ORF) which encodes a protein of 423 amino acids (aa), but also is interrupted by three short introns. A homology modelling of Vlchit1 protein showed that the chitinase Vlchit1 has a (α/β)8 TIM barrel structure. Overexpression test and Enzymatic activity assay indicated that the Vlchit1 is a functional enzyme that can hydrolyze the chitin substrate, so the Vlchit1 gene can service as a useful gene source for genetic manipulation leading to strain improvement of entomopathogenic fungi or constructing new transgenic plants with resistance to various fungal and insects pests.

O fungo entomopatogênico Verticillium lecanii é um agente promissor no controle da mosca-branca e do pulgão. As quitinases secretadas por esse patógeno de insetos têm uma grande importância no controle biológico de doenças causadas por insetos. Um gene de endoquitinase Vlchit1 desse fungo foi clonado e expresso em Escherichia coli. O gene Vlchit contém não apenas um ORF que codifica uma proteína de 423 aminoácidos, mas também é interrompido por três pequenos introns. A modelagem de homologia da proteína Vlchit1indicou que a quitinase Vlchit1 tem uma estrutura (α/β) 8 TIM barrel. Testes de expressão e de atividade enzimática indicaram que Vlchit1 é uma enzima funcional que hidroliza quitina, portanto o gene Vlchit pode ser um gene útil para manipulação genética para melhoramento de cepas de fungos entomopatogênicos ou para a construção de novas plantas transgênicas com resistência a várias doenças causadas por fungos e insetos.

Heterologous expression of an insecticidal gene from the armed spider (Phoneutria nigriventer)

Insect-pests are global problems that cause severe damage to crop plants, and their control is commonly based on chemical insecticides. However, negative effects of pesticides on the environment and human health emphasize the necessity to develop alternative methods for insect-pest control. In the present study, a gene coding for the insecticidal peptide TX4(6-1) of the Brazilian armed spider (Phoneutria nigriventer) was cloned in fusion with maltose binding protein (MBP) and expressed in Escherichia coli. The affinity purified protein MBP-GlyTX4 was cleaved with the Xa factor and used for a bioassay against Spodoptera frugiperda and rabbit immunization. Five micrograms GlyTX4 protein injected into the hemocoel of larvae and abdominal cavity of adults produced trembling and uncoordinated movements immediately after injection and all adult insects died after 12h. After two days, larvae became paralyzed and the epidermal color changed to dark brown. Furthermore, the development stage was prolonged for two weeks. Alternatively, slices of maize leaves were imbibed with 15 micrograms of the recombinant protein cleaved with the Xa factor and used as diet for larvae. In this experiment, all larvae died in about 30 minutes. Polyclonal antibodies anti-MBP-GlyTX4 were effective for recognizing MBP and GlyTX4 in whole cell extract from E. coli expressing the recombinant protein.