Molecular characterization and functional analysis of scavenger receptor class B from black tiger shrimp (Penaeus monodon)

BACKGROUND: Scavenger receptor class B (SRB) is a multifunctional protein in animals that participates in physiological processes, including recognition of a wide range of ligands. Astaxanthin is a major carotenoid found in shrimp. However, the molecular mechanism of astaxanthin and SRB protein binding has not been reported. RESULTS: In the present study, a member of the SRB subfamily, named PmSRB, was identified from the transcriptome of black tiger shrimp (Penaeus monodon). The open reading frame of PmSRB was 1557 bp in length and encoded 518 amino acids. The structure of PmSRB included a putative transmembrane structure at the N-terminal region and a CD36 domain. Multiple sequence alignment indicated that the CD36 domain were conserved. Phylogenetic analysis showed four separate branches (SRA, SRB, SRC, and croquemort) in the phylogenetic tree and that PmSRB was clustered with SRB of Eriocheir sinensis. Quantitative real-time polymerase chain reaction showed that the PmSRB gene was widely expressed in all tissues tested, with the highest expression level observed in the lymphoid organ and brain. Subcellular localization analysis revealed that PmSRB-GFP (green fluorescent protein) fusion proteins were predominantly localized in the cell membrane. The recombinant proteins of PmSRB showed binding activities against astaxanthin in vitro. CONCLUSIONS: PmSRB was identified and characterized in this study. It is firstly reported that PmSRB may take as an important mediator of astaxanthin uptake in shrimp.

Identification and characterization of DIR gene family in Schisandra chinensis / 中国中药杂志

Dirigent(DIR) proteins are involved in the biosynthesis of lignin, lignans, and gossypol in plants and respond to biotic and abiotic stresses. Based on the full-length transcriptome of Schisandra chinensis, bioinformatics methods were used to preliminarily identify the DIR gene family and analyze the physico-chemical properties, subcellular localization, conserved motifs, phylogeny, and expression patterns of the proteins. The results showed that a total of 34 DIR genes were screened and the encoded proteins were 156-387 aa. The physico-chemical properties of the proteins were different and the secondary structure was mainly random coil. Half of the DIR proteins were located in chloroplast, while the others in extracellular region, endoplasmic reticulum, cytoplasm, etc. Phylogenetic analysis of DIR proteins from S. chinensis and the other 8 species such as Arabidopsis thaliana, Oryza sativa, and Glycine max demonstrated that all DIR proteins were clustered into 5 subfamilies and that DIR proteins from S. chinensis were in 4 subfamilies. DIR-a subfamily has the unique structure of 8 β-sheets, as verified by multiple sequence alignment. Finally, through the analysis of the transcriptome of S. chinensis fruit at different development stages, the expression pattern of DIR was clarified. Combined with the accumulation of lignans in fruits at different stages, DIR might be related to the synthesis of lignans in S. chinensis. This study lays a theoretical basis for exploring the biological functions of DIR genes and elucidating the biosynthesis pathway of lignans in S. chinensis.

Enzyme ancestral sequence reconstruction and directed evolution / 生物工程学报

The amino acid sequence of ancestral enzymes from extinct organisms can be deduced through in silico approach termed ancestral sequence reconstruction (ASR). ASR usually has six steps, which are the collection of nucleic acid/amino acid sequences of modern enzymes, multiple sequence alignment, phylogenetic tree construction, computational deduction of ancestral enzyme sequence, gene cloning, and characterization of enzyme properties. This method is widely used to study the adaptation and evolution mechanism of molecules to the changing environmental conditions on planetary time scale. As enzymes play key roles in biocatalysis, this method has become a powerful method for studying the relationship among the sequence, structure, and function of enzymes. Notably, most of the ancestral enzymes show better temperature stability and mutation stability, making them ideal protein scaffolds for further directed evolution. This article summarizes the computer algorithms, applications, and commonly used computer software of ASR, and discusses the potential application in directed evolution of enzymes.

Molecular modification and highly efficient expression of L-asparaginase from Rhizomucor miehei / 生物工程学报

L-asparaginase hydrolyzes L-asparagine to produce L-aspartic acid and ammonia. It is widely distributed in microorganisms, plants and serum of some rodents, and has important applications in the pharmaceutical and food industries. However, the poor thermal stability, low catalytic efficiency and low yield hampered the further application of L-asparaginase. In this paper, rational design and 5' untranslated region (5'UTR) design strategies were used to increase the specific enzyme activity and protein expression of L-asparaginase derived from Rhizomucor miehei (RmAsnase). The results showed that among the six mutants constructed through homology modeling combined with sequence alignment, the specific enzyme activity of the mutant A344E was 1.5 times higher than the wild type. Subsequently, a food-safe strain Bacillus subtilis 168/pMA5-A344E was constructed, and the UTR strategy was used for the construction of recombinant strain B. subtilis 168/pMA5 UTR-A344E. The enzyme activity of B. subtilis 168/pMA5 UTR-A344E was 7.2 times higher than that of B. subtilis 168/pMA5-A344E. The recombinant strain B. subtilis 168/pMA5 UTR-A344E was scaled up in 5 L fermenter, and the final yield of L-asparaginase was 489.1 U/mL, showing great potential for industrial application.

Development and application of chloroplast molecular markers in Panax notoginseng / 中国中药杂志

The molecular markers(cpSSR, cpSNP and cpIndel) were developed based on the whole genome sequence of Panax notoginseng chloroplast genome, which provide a powerful tool for the evaluation and analysis of the future P. notoginseng germplasm resources. The 89 P. notoginseng samples from 9 groups were used for the experiment, and the data for the study were derived from NCBI and the GenBank numbers were: KJ566590, KP036468, KR021381 and KT001509. Through sequence alignment, 30 polymorphic sites(SNP and Indel) were identified, including 16 cpSNP and 14 cpIndel; cpSNP and cpIndel accounted for far more than the gene region in the intergenic region. The developed cpSSR reached 87-89, the repeat unit was mainly composed of trinucleotide, accounting for 70%-71%, and the dinucleotide was the least, accounting for 7%. Eighteen cpDNA molecular markers were developed, including 7 cpSSR primers, 6 cpIndel primers, and 5 cpSNP primers. The MatK gene and ycf1 primers were chosen as control. According to the results of DNA gel electrophoresis, cpSSR-5, pgcpir019 and pncp08 can be used to distinguish different cultivated populations of P. notoginseng. Among them, cpSSR-5 and pgcpir019 can also be used to distinguish the inter-species resources of ginseng by comprehensive sequence length, population π value and average nucleotide difference. However, pncp08 can only be used to distinguish different populations of P. notoginseng. In addition, the effect of distinguishing the groups of P. notoginseng, which the primer pncp-M(based on the MatK gene) is weaker than the cpSSR-5, pgcpir019 and pncp08.

Cloning and expression analysis of 5-phosphomevalonate kinase gene (CcPMK) in Cinnamomum camphora / 中国中药杂志

The 5-phosphomevalonate kinase(PMK) is a key enzyme in mevalonate(MVA) pathway which reversibly catalyzes the phosphorylation of mevalonate 5-phosphate(MVAP) to form mevalonate-5-diphosphate(MVAPP) in the presence of ATP and divalent metal ion such as Mg~(2+). In this research, on the basis of the transciptome database of Cinnamomum camphora, the PMK was cloned by cDNA from C. camphora, and was named CcPMK(GenBank number KU886266). The ORF of CcPMK was composed of 1 545 bp, encoding 514 amino acids. The bioinformatics analysis of CcPMK indicated that the molecular weight of the encoded protein was 56.14 kDa, with a theoretically isoelectric point of 7.64, and there was no signal peptide and transmembrane structure in putative protein. By multiple sequence alignment and phylogenetic tree analysis, we found that similarity between CcPMK and PMK amino acid sequence of other plants was as high as 75%. Among the similar sequences, 45% of them belonged to the alpha helix, while 16% belonged to the beta strand. CcPMK obtained 3 PMK protein family motifs and 1 ATP binding site Gly-Leu-Gly-Ser-Ser-Ala-Ala, and its 3 D structure contained a catalytic pocket structure, proving CcPMK as a member of PMK gene family. The result of phylogenetic tree showed that CcPMK was closely related to monocotyledon plants such as Phonenix dactylifera. The results of the Real-time PCR indicated that the expression level of CcPMK in borneol type was higher than that in linalool type, cineol type, iso-nerolidol type and camphor type. CcPMK expressed highest in roots and lowest in branches. Our results revealed that the expression level of CcPMK was different among five chemical types and different plant tissues, and the research provides foundation for further study of the terpenoids biosynthetic pathway in C. camphora.

RNA-seq analysis of the response of plant-pathogenic oomycete Phytophthora parasitica to the fungicide dimethomorph / Análisis RNA-seq de la respuesta del oomiceto fitopatógeno Phytophthora parasitica al fungicida dimetomorf

Phytophthora parasitica is an important oomycete that causes disease in a variety of plants, dimethomorph fungicides being specific for oomycetes. The aim of this study was to use RNA-seq to rapidly discover the mechanism by which dimethomorph acts in the treatment of P. parasitica. We found that the expression of 832 genes changed significantly after the dimethomorph treatment, including 365 up-regulated genes and 467 down-regulated genes. According to the Gene Ontology (GO) enrichment analysis, pathway enrichment and verification test results, the following conclusions are obtained: (i) the treatment of P. parasitica with dimethomorph causes changes in the expression levels of genes associated with the cell wall and cell wall synthesis; (ii) dimethomorph treatment results in reduced permeability of the cell membrane and changes in the expression of certain transport-related proteins; (iii) dimethomorph treatment increased reactive oxygen species and reduced the expression of genes related to the control of oxidative stress.

Phytophthora parasitica es un importante oomiceto que origina enfermedades en una variedad de plantas; el fungicida dimetomorf es específico contra oomicetos. El objetivo de este estudio fue utilizar la tecnología de RNA-seq para descubrir rápidamente el mecanismo por el que el dimetomorf actúa en el tratamiento de P. parasitica. Descubrimos que la expresión de 832 genes se modificaba significativamente tras el tratamiento con dimetomorf, incluyendo 365 genes que son sobrerregulados y 467 genes que son subrregulados. El análisis de enriquecimiento de ontología de genes (GO), análisis de enriquecimiento de las vías y pruebas de verificación permitieron extraer las conclusiones siguientes: 1) el tratamiento de P. parasitica con dimetomorf origina cambios en los niveles de expresión de los genes relacionados con la pared celular y su síntesis; 2) el tratamiento con dimetomorf origina una reducción de la permeabilidad de la membrana celular, así como cambios en la expresión de ciertas proteínas relacionadas con el transporte, y 3) el tratamiento con dimetomorf incrementó las especies reactivas del oxígeno y redujo la expresión de los genes relacionados con el control del estrés oxidativo.

DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

OBJECTIVE@#This study aimed to investigate DNA sequences that are substantially homologous to the corresponding RNA sequence sections of the hepatitis C virus (HCV). These DNA sequences are present in the whole DNA extracted from peripheral blood mononuclear cells (PBMCs) of HCV-negative subjects. We presumed that these experimentally proven 5'-noncoding region (5'-NCR) homologous DNA sequences could be contained in the extrachromosomal circular DNA (eccDNA) fraction as part of the whole cellular DNA.@*METHODS@#Home-made polymerase chain reaction (PCR) with whole cellular and isolated eccDNA, nucleotide basic local alignment search tool (BLASTn) alignments, and tests for patterns of methylation in selected sequence sections were performed.@*RESULTS@#The PCR tests revealed DNA sequences of up to 320 bp that broadly matched the corresponding sequence sections of known HCV genotypes. In contrast, BLASTn alignment searches of published HCV 5'-NCR sequences with human genome databases revealed only sequence segments of up to 36 bp of the 5'-NCR. The composition of these sequences shows missing base pairs, base pair mismatches as well as complete homology with HCV reference sequences. These short sequence sections are present in numerous copies on both the same and different chromosomes. The selected sequence region within the DNA sequences of the 5'-NCR revealed a broad diversity of individual patterns of methylation.@*CONCLUSIONS@#The experimental results confirm our assumption that parts of the HCV 5'-NCR genomic RNA sequences are present at the DNA level in the eccDNA fraction of PBMCs. The tests for methylation patterns therein revealed individual methylomes which could represent an epigenetic feature. The respective sequence section might be subject to genetic regulation.

Identification of three novel SRD5A2 mutations in Chinese patients with 5α-reductase 2 deficiency / 亚洲男科学杂志(英文版)

In this study, we investigated the genetics, clinical features, and therapeutic approach of 14 patients with 5α-reductase deficiency in China. Genotyping analysis was performed by direct sequencing of PCR products of the steroid 5α-reductase type 2 gene (SRD5A2). The 5α-reductase activities of three novel mutations were investigated by mutagenesis and an in vitro transfection assay. Most patients presented with a microphallus, variable degrees of hypospadias, and cryptorchidism. Eight of 14 patients (57.1%) were initially reared as females and changed their social gender from female to male after puberty. Nine mutations were identified in the 14 patients. p.G203S, p.Q6X, and p.R227Q were the most prevalent mutations. Three mutations (p.K35N, p.H162P, and p.Y136X) have not been reported previously. The nonsense mutation p.Y136X abolished enzymatic activity, whereas p.K35N and p.H162P retained partial enzymatic activity. Topical administration of dihydrotestosterone during infancy or early childhood combined with hypospadia repair surgery had good therapeutic results. In conclusion, we expand the mutation profile of SRD5A2 in the Chinese population. A rational clinical approach to this disorder requires early and accurate diagnosis, especially genetic diagnosis.

Especies de flebotomíneos (Diptera: Psychodidae) recolectados en reservas naturales de las regiones del Darién y del Pacífico en Colombia / Species of sand flies (Diptera: Psychodidae) collected from natural reserves in the Pacific and Darien regions of Colombia

Resumen Introducción. Los departamentos de Chocó y Antioquia en Colombia presentan condiciones climáticas y de vegetación que favorecen el establecimiento de especies de vectores del género Lutzomyia y la transmisión de Leishmania spp. a poblaciones humanas que ingresan a ambientes selváticos conservados. Objetivo. Reportar las especies de flebotomíneos presentes en tres reservas naturales de las regiones del Darién y del Pacífico en Colombia. Materiales y métodos. Los flebotomíneos se recolectaron en las reservas naturales El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) y Tulenapa (Carepa, Antioquia). La recolección se hizo con trampas de luz CDC, mediante búsqueda activa en sitios de reposo y con trampas Shannon. La determinación taxonómica de especies se basó en las claves taxonómicas. En algunas especies de interés taxonómico, se evaluó el uso de secuencias parciales de la región 5' del gen COI. Resultados. Se recolectaron 611 flebotomíneos adultos: 531 en Acandí, 45 en Carepa y 35 en Bahía Solano. Se identificaron 17 especies del género Lutzomyia, tres del género Brumptomyia y una del género Warileya. Las distancias genéticas (K2P) y los soportes de agrupación (>99 %) en el dendrograma de neighbor joining correspondieron a la mayoría de unidades taxonómicas operacionales moleculares (Molecular Operational Taxonomic Units, MOTU) establecidas para el grupo Aragaoi y confirmaron claramente la identidad de Lu. coutinhoi. Conclusión. Se identificaron especies que tienen importancia en la transmisión de la leishmaniasis en Acandí, Bahía Solano y Carepa. Se confirmó la presencia de Lu. coutinhoi en Colombia.

Abstract Introduction: The departments of Chocó and Antioquia in Colombia show climatic and vegetation conditions favoring the establishment of vector species of the genus Lutzomyia and the transmission of Leishmania spp. to human populations entering conserved forest environments. Objective: To report the species of Phlebotomine sandflies present in three natural reserves in the Darien and Pacific regions of Colombia. Materials and methods: Sand flies were collected specifically in the natural reserves El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) and Tulenapa (Carepa, Antioquia). Sand flies were collected with CDC light traps, active search in resting places and Shannon traps. The taxonomic determination of species was based on taxonomic keys. For some species of taxonomic interest, we evaluated the partial sequences of the 5' region of COI gene. Results: A total of 611 adult sand flies were collected: 531 in Acandí, 45 in Carepa and 35 in Bahía Solano. Seventeen species of the genus Lutzomyia, three of the genus Brumptomyia and one of the genus Warileya were identified. The genetic distances (K2P) and grouping supported (>99%) in the neighbor joining dendrogram were consistent for most established molecular operational taxonomic units (MOTU) of the Aragaoi group and clearly confirmed the identity of Lu. coutinhoi. Conclusion: Species that have importance in the transmission of leishmaniasis in Acandí, Bahía Solano and Carepa were identified. The presence of Lu. coutinhoi was confirmed and consolidated in Colombia.

Genome analysis of yellow fever virus of the ongoing outbreak in Brazil reveals polymorphisms

The current yellow fever outbreak in Brazil is the most severe one in the country in recent times. It has rapidly spread to areas where YF virus (YFV) activity has not been observed for more than 70 years and vaccine coverage is almost null. Here, we sequenced the whole YFV genome of two naturally infected howler-monkeys (Alouatta clamitans) obtained from the Municipality of Domingos Martins, state of Espírito Santo, Brazil. These two ongoing-outbreak genome sequences are identical. They clustered in the 1E sub-clade (South America genotype I) along with the Brazilian and Venezuelan strains recently characterised from infections in humans and non-human primates that have been described in the last 20 years. However, we detected eight unique amino acid changes in the viral proteins, including the structural capsid protein (one change), and the components of the viral replicase complex, the NS3 (two changes) and NS5 (five changes) proteins, that could impact the capacity of viral infection in vertebrate and/or invertebrate hosts and spreading of the ongoing outbreak.

Epidemiologia da leishmaniose tegumentar americana (LTA) no município de Xapuri, Estado do Acre, Brasil: estudo em população humana, cães domésticos e vetores / Epidemiology of American cutaneous leishmaniasis (ACL) in Xapuri municipality, Acre state, Brazil study in human population, domestic dogs and vectors

Introdução. A leishmaniose tegumentar americana (LTA) é uma endemia de importância em saúde pública na Amazônia Brasileira, onde possui diferentes perfis de transmissão com a participação de diversas espécies de vetores e de protozoários do gênero Leishmania. O Estado do Acre apresenta altos índices de LTA e, no ano de 2015, apresentou o mais alto coeficiente de detecção de casos (137,7/100.000 hab.) da doença no Brasil. Objetivo. Analisar aspectos epidemiológicos da LTA no município de Xapuri, Estado do Acre, Brasil, envolvendo população humana, cães domésticos, vetores e identificação de Leishmania. Materiais e Métodos. Para a avaliação epidemiológica, foram analisadas fichas de notificação dos casos humanos no período de 2008 a 2014 obtidas do sistema de vigilância epidemiológica do município. Foram analisadas as variáveis: sexo, grupo etário, escolaridade, forma clínica, diagnóstico, tratamento e evolução clínica. Os dados foram submetidos à análise descritiva e teste estatístico do qui-quadrado de Pearson utilizando o pacote estatístico STATA. Também foram obtidas amostras de material de pacientes (escarificação das lesões fixadas em lâminas) atendidos no centro médico do município, durante o período de novembro de 2014 a janeiro de 2016. As amostras foram submetidas à análise molecular para diagnóstico de Leishmania spp. O inquérito canino foi realizado em áreas urbanas e rurais; nestas, predominantemente, em seringais, onde a doença foi reportada em humanos avaliação clínica dos animais para busca de lesões e sinais característicos de leishmanioses, foram coletadas amostras de sangue venoso por punção jugular ou cefálica, e quando havia lesões sugestivas da doença, foram anestesiados e submetidos à biopsia para colheita do fragmento de lesão. Amostras destes fragmentos foram submetidas a técnicas parasitológicas, inoculação em meio de cultura Neal, Novy e Nicolle, exame direto e técnicas moleculares para detecção do parasita. A identificação de Leishmania spp. foi realizada por técnicas moleculares. Os flebotomíneos foram coletados em ambiente domiciliar e florestal de dois seringais (Floresta e Cachoeira) e na área urbana, com armadilhas luminosas tipo CDC, instaladas mensalmente, no período de agosto de 2013 a julho de 2015. Neste período, apenas no seringal Cachoeira, também foram feitas coletas utilizando armadilhas de Shannon nas cores branca e preta, e de janeiro a maio de 2016, coletas em trocos de árvores com aspiradores manuais. Uma amostra de fêmeas coletadas pelas diferentes técnicas foi dissecada viii para investigação da presença de flagelados. Para a análise do comportamento da fauna flebotomínea foram utilizados índices ecológicos como de Shannon, Pielou e Abundância das Espécies Padronizado, média geométrica de Williams e análise dos componentes principais. Para estimar a atratividade dos flebotomíneos pelas cores branca e preta foi utilizado o teste de Mann-Whitney (p<0,05). Análises morfométricas utilizando o teste de Gabriel (teste F, p <0,05) foram feitas para distinguir alguns táxons. Para as análises moleculares dos parasitas foi empregada a técnica de Nested-PCR SSU rRNA utilizando os iniciadores S4/S12 e S17/S18 e sequenciamento. Resultados. No estudo de casos humanos, constatou-se que a doença ocorre predominantemente em populações rurais e isoladas do município, em indivíduos de ambos os sexos, com as incidências mais elevadas em crianças e adolescentes. Em 33 dos 45 pacientes com clínica positiva para LTA foram detectadas a presença de DNA de Leishmania spp. Nos cães domésticos, verificou-se alta taxa de infecção (20,0 por cento ) por Leishmania (Viannia) sp. Nos estudos de flebotomíneos, foram coletados 21.197 espécimes (14.210 fêmeas e 7.107 machos) com armadilhas CDC, e 6.309 (864 machos e 5.445 fêmeas) com armadilhas de Shannon. As frequências, abundâncias e densidades mais elevadas foram dos gêneros Nyssomyia, Psychodopygus e Trichophoromyia, coletados em ambientes silvestres, peri e intradomiciliares. Em ambiente rural foram coletados 99,9 por cento dos espécimes e no urbano apenas 0,1 por cento . Nyssomyia shawi predominou no Seringal Cachoeira, e Trichophoromyia spp. (Th. auraensis/Th. ruifreitasi) no Seringal Floresta. Espécies do gênero Psychodopygus predominaram no período chuvoso, enquanto as de Nyssomyia, no período seco. Infecções por Leishmania spp. foram detectadas em Brumptomyia sp., Nyssomyia antunesi, Ny. shawi, Lutzomyia sherlocki, Psathyromyia aragaoi, Psychodopygus carrerai carrerai, Ps. davisi, Ps. hirsutus hisutus, Ps. llanosmartinsi, Ps. lainsoni, Thrichophoromyia ubiquitalis e Trichophoromyia spp. Por meio de análises morfológicas e morfométricas das fêmeas de Trichophoromyia sugeriu-se a distinção de Th. octavioi de Trichophoromyia spp. (Th. auraensis/Th. ruifreitasi) e descreveu-se, Psathyromyia elizabethdorvalae sp. n. Conclusões. A LTA em Xapuri apresenta um perfil de transmissão silvestre e outro domiciliar. As populações humanas e caninas que frequentam ambientes florestais estão expostas a uma alta diversidade de vetores e de agentes etiológicos, o que aumenta o risco de infecção de LTA. As informações aqui apresentadas podem nortear as medidas de controle, planejamento das ações e definição de prioridades dos órgãos de vigilância epidemiológica do Estado do Acre, visando o diagnóstico precoce e tratamento adequado dos casos de leishmanioses da população humana de Xapuri

Introduction. American cutaneous leishmaniasis (ACL) is an endemic disease that deserves the attention of public health in the Brazilian Amazon, where it has various transmission profiles with the participation of several species of vectors and protozoa of the genus Leishmania. The state of Acre registers high rates of ACL, having in 2015 the highest coefficient of detection of cases (137.7 / 100,000 inhab.) in Brazil. Objective. To analyze the epidemiological aspects of LTA in the municipality of Xapuri, State of Acre, Brazil, involving the human population, domestic dogs, vectors and the identification of Leishmania ssp. Materials and Methods. For the epidemiological evaluation, records of the human cases notified between 2008 and 2014 obtained from the epidemiological surveillance system of the municipality, were analyzed. The following variables were selected for analysis: sex, age group, schooling, clinical form, diagnosis, treatment and clinical evolution. The data were submitted to descriptive analysis and the Pearson chi-squared statistical test using the statistical package STATA. Samples of patient material (scarification of lesions fixed on slides) were also obtained from the medical center of the city during the period from November 2014 to January 2016. These samples were submitted to molecular analysis for the diagnosis of Leishmania spp. The canine survey was carried out in both urban and rural areas, in the latter rubber plantations where the disease had been reported in humans predominated. After a clinical evaluation to search for lesions and characteristic signs of leishmaniasis, samples of venous blood were collected by jugular or cephalic puncture, and when the animals presented lesions suggestive of cutaneous leishmaniasis, they were anesthetized and submitted to biopsy to harvest the lesion fragment. Samples of these fragments were submitted to parasitological techniques, inoculation in Neal, Novy and Nicolle culture medium, direct examination and molecular techniques to detect Leishmania spp. The samples were submitted to molecular analysis for the diagnosis of Leishmania spp. The phlebotomine survey was carried out in forest and the domiciliary environment of the city and in two rubber plantation areas (Seringal Cachoeira and Seringal Floresta), monthly using CDC light traps, from August 2013 to July 2015. In this period, only in the Seringal Cachoeira were collections also made using black and white Shannon traps. Collections in tree trunks and among tree roots with manual aspirators were also undertaken from January to May 2016. xi Samples of females collected by different techniques were dissected to investigate the presence of flagellates. For the analysis of the behavior of the phlebotomine fauna, ecological indexes such as Shannon, Pielou, and Standardized Species Abundance, Williams geometric mean and main component analysis were used. The Mann-Whitney test (p <0.05) was used to estimate the attractiveness of the black and white colors to sandflies. Morphometric analyses using the Gabriel test (test F, p <0.05) were made to distinguish between some taxa. For the molecular analyses of the parasites the Nested-PCR SSU rRNA technique was used using primers S4 / S12 and S17 / S18 and sequencing. Results. In the study of human cases, it was found that the disease occurs in rural and isolated populations and in individuals of both sexes, especially in children and adolescents. In 33 of the 45 patients with positive ACL, the presence of Leishmania spp DNA was detected. The domestic dogs have shown a high infection rate (20.0 per cent ) attributed to Leishmania (Viannia) sp. In the sandfly studies, 21,197 specimens (14,210 females and 7,107 males) were collected in CDC traps, and 6,309 (864 males and 5,445 females) were collected in Shannon traps. The highest frequencies, abundances and densities were of the genera Nyssomyia, Psychodopygus and Trichophoromyia collected in wild, peri and intradomiciliary environments. Nyssomyia shawi predominated in the Seringal Cachoeira, and the Trichophoromyia spp. (Th. auraensis/Th. ruifreitasi) in the Seringal Floresta. Species of the genus Psychodopygus predominated in the rainy season while those of Nyssomyia in the dry period. Natural infections by Leishmania spp were detected in Brumptomyia sp., Nyssomyia antunesi, Ny. shawi, Lutzomyia sherlocki, Psathyromyia aragaoi, Psychodopygus carrerai carrerai, Ps. davisi, Ps. hirsutus hirsutus, Ps. llanosmartinsi, Ps. lainsoni, Trichophoromyia ubiquitalis and Trichophoromyia sp. Morphological and morphometric analyses of Trichophoromyia females were suggested to distinguish Th. octavioi from Trichophoromyia spp (Th. auraensis/Th. ruifreitasi), Pa. elizabethdorvalae being described for the first time. Conclusions. ACL in Xapuri presents one profile of wild transmission and another of domiciliar transmission. Both populations, human and canine, because they live in forest environments are exposed to a high diversity of vectors and etiological agents, which increases the risk of ACL infection. The information presented here may guide the measures of control, planning of actions and definition of priorities taken by the organs of surveillance and epidemiology of the State of Acre, aiming at the early diagnosis and appropriate treatment of the human cases in Xapuri

The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection

Entero virus 71 (EV71) causes hand, foot, and mouth disease (HFMD) and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 (SCARB2) is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody (mAb) that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the region containing residues 77-113 of human SCARB2 contributes significantly to JL2 binding. The structure of the SCARB2-JL2 complex revealed that JL2 binds to the apical region of SCARB2 involving α-helices 2, 5, and 14. Our results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.

HPPR encodes the hydroxyphenylpyruvate reductase required for the biosynthesis of hydrophilic phenolic acids in Salvia miltiorrhiza / 中国天然药物

Salvia miltiorrhiza is a medicinal plant widely used in the treatment of cardiovascular and cerebrovascular diseases. Hydrophilic phenolic acids, including rosmarinic acid (RA) and lithospermic acid B (LAB), are its primary medicinal ingredients. However, the biosynthetic pathway of RA and LAB in S. miltiorrhiza is still poorly understood. In the present study, we accomplished the isolation and characterization of a novel S. miltiorrhiza Hydroxyphenylpyruvate reductase (HPPR) gene, SmHPPR, which plays an important role in the biosynthesis of RA. SmHPPR contained a putative catalytic domain and a NAD(P)H-binding motif. The recombinant SmHPPR enzyme exhibited high HPPR activity, converting 4-hydroxyphenylpyruvic acid (pHPP) to 4-hydroxyphenyllactic acid (pHPL), and exhibited the highest affinity for substrate 4-hydroxyphenylpyruvate. SmHPPR expression could be induced by various treatments, including SA, GA, MeJA and Ag, and the changes in SmHPPR activity were correlated well with hydrophilic phenolic acid accumulation. SmHPPR was localized in cytoplasm, most likely close to the cytosolic NADPH-dependent hydroxypyruvate reductase active in photorespiration. In addition, the transgenic S. miltiorrhiza hairy roots overexpressing SmHPPR exhibited up to 10-fold increases in the products of hydrophilic phenolic acid pathway. In conclusion, our findings provide a new insight into the synthesis of active pharmaceutical compounds at molecular level.

Isolation and expression of two polyketide synthase genes from Trichoderma harzianum 88 during mycoparasitism

Abstract Metabolites of mycoparasitic fungal species such as Trichoderma harzianum 88 have important biological roles. In this study, two new ketoacyl synthase (KS) fragments were isolated from cultured Trichoderma harzianum 88 mycelia using degenerate primers and analysed using a phylogenetic tree. The gene fragments were determined to be present as single copies in Trichoderma harzianum 88 through southern blot analysis using digoxigenin-labelled KS gene fragments as probes. The complete sequence analysis in formation of pksT-1 (5669 bp) and pksT-2 (7901 bp) suggests that pksT-1 exhibited features of a non-reducing type I fungal PKS, whereas pksT-2 exhibited features of a highly reducing type I fungal PKS. Reverse transcription polymerase chain reaction indicated that the isolated genes are differentially regulated in Trichoderma harzianum 88 during challenge with three fungal plant pathogens, which suggests that they participate in the response of Trichoderma harzianum 88 to fungal plant pathogens. Furthermore, disruption of the pksT-2 encoding ketosynthase–acyltransferase domains through Agrobacterium -mediated gene transformation indicated that pksT-2 is a key factor for conidial pigmentation in Trichoderma harzianum 88.

The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results ofsix most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

Diagnostic Cytochrome b gene profiles for the identification of paca (Cuniculus paca) bushmeat: implications for the monitoring of illegal hunting and wildlife trade / Perfis diagnósticos do gene Citocromo b para a identificação molecular de paca (Cuniculus paca): implicações para a detecção e monitoramento de caça e comércio ilegal

Abstract Paca (Cuniculus paca Linnaeus, 1766) is the second largest rodent found in Brazil. The quality of the meat and a long tradition of hunting have contributed to the decline of the natural populations of this species. Hunting of paca is strictly prohibited in Brazil, but in spite of this restriction, no forensic tools are available for the identification of the meat. We describe an efficient method, based on single nucleotide polymorphisms of the cytochrome b gene, that can be used to differentiate biological material derived from paca from those of domestic species commonly used as sources of meat. The identification of the presence of C. paca in the samples was 100% reliable.

Resumo Paca (Cuniculus paca Linnaeus, 1766) é o segundo maior roedor brasileiro. A qualidade da carne e a forte tradição da caça de subsistência são fatores que contribuem significativamente para o declínio das populações. Apesar da proibição a caça no Brasil, no momento ainda não há ferramentas disponíveis para identificar a carne e seus produtos como prova forense. Neste trabalho propomos um método eficaz de identificação, baseado em polimorfismos de único nucleotídeo no gene Citocromo b, objetivando diferenciar material biológico de paca das espécies domésticas comumente utilizadas como alimento no Brasil. A identificação das amostras de paca foram possíveis em 100% das amostras analisadas.

MiR-29b suppresses the proliferation and migration of osteosarcoma cells by targeting CDK6

Osteosarcoma is the most common primary sarcoma of bone, and it is a leading cause of cancer death among adolescents and young adults. However, the molecular mechanism underlying osteosarcoma carcinogenesis remains poorly understood. Recently, cyclin-dependent kinase 6 (CDK6) was identified as an important oncogene. We found that CDK6 protein level, rather than CDK6 mRNA level, is much higher in osteosarcoma tissues than in normal adjacent tissues, which indicates a post-transcriptional mechanism involved in CDK6 regulation in osteosarcoma. MiRNAs are small non-coding RNAs that repress gene expression at the post-transcriptional level and have widely been shown to play important roles in many human cancers. In this study, we investigated the role of miR-29b as a novel regulator of CDK6 using bioinformatics methods. We demonstrated that CDK6 can be downregulated by miR-29b via binding to the 3'-UTR region in osteosarcoma cells. Furthermore, we identified an inverse correlation between miR-29b and CDK6 protein levels in osteosarcoma tissues. Finally, we examined the function of miR-29b-driven repression of CDK6 expression in osteosarcoma cells. The results revealed that miR-29b acts as a tumor suppressor of osteosarcoma by targeting CDK6 in the proliferation and migration processes. Taken together, our results highlight an important role for miR-29b in the regulation of CDK6 in osteosarcoma and may open new avenues for future osteosarcoma therapies.

Structural studies on MRG701 chromodomain reveal a novel dimerization interface of MRG proteins in green plants

MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701). MRG701 forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants. Our findings may provide new insights into the mechanism of MRGs in regulation of gene expression in green plants.

Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system

YfiBNR is a recently identified bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiB(L43P) complexed with YfiR with 2:2 stoichiometry. Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiB(L43P) adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiB(L43P) shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiB(L43P)-induced biofilm formation. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.