Eukaryotic expression, Co-IP and MS identify BMPR-1B protein-protein interaction network

BACKGROUND: BMPR-1B is part of the transforming growth factor ß super family and plays a pivotal role in ewe litter size. Functional loss of exon-8 mutations in the BMPR-1B gene (namely the FecB gene) can increase both the ewe ovulation rate and litter size. RESULTS: This study constructed a eukaryotic expression system, prepared a monoclonal antibody, and characterized BMPR-1B/FecB protein-protein interactions (PPIs). Using Co-immunoprecipitation coupled to mass spectrometry (Co-IP/MS), 23 proteins were identified that specifically interact with FecB in ovary extracts of ewes. Bioinformatics analysis of selected PPIs demonstrated that FecB associated with several other BMPs, primarily via signal transduction in the ovary. FecB and its associated interaction proteins enriched the reproduction process via BMP2 and BMP4 pathways. Signal transduction was identified via Smads proteins and TGF-beta signaling pathway by analyzing the biological processes and pathways. Moreover, other target proteins (GDF5, GDF9, RhoD, and HSP 10) that interact with FecB and that are related to ovulation and litter size in ewes were identified. CONCLUSIONS: In summary, this research identified a novel pathway and insight to explore the PPi network of BMPR-1B.

Habitat conditions drive phylogenetic structure of dominant bacterial phyla of microbialite communities from several locations in Mexico / Las condiciones del hábitat determinan la estructura filogenética de filos (phyla) bacterianos dominantes de comunidades de microbialitos de diferentes regiones en México

Abstract:Community structure and composition are dictated by evolutionary and ecological assembly processes which are manifested in signals of, species diversity, species abundance and species relatedness. Analysis of species coexisting relatedness, has received attention as a tool to identify the processes that influence the composition of a community within a particular habitat. In this study, we tested if microbialite genetic composition is dependent on random events versus biological/abiotical factors. This study was based on a large genetic data set of two hypervariable regions (V5 and V6) from previously generated barcoded 16S rRNA amplicons from nine microbialite communities distributed in Northeastern, Central and Southeastern Mexico collected in May and June of 2009. Genetic data of the most abundant phyla (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes, and Cyanobacteria) were investigated in order to state the phylogenetic structure of the complete communities as well as each phylum. For the complete dataset, Webb NTI index showed positive and significant values in the nine communities analysed, where values ranged from 31.5 in Pozas Azules I to 57.2 in Bacalar Pirate Channel; meanwhile, NRI index were positive and significant in six of the nine communities analysed with values ranging from 18.1 in Pozas Azules I to 45.1 in Río Mesquites. On the other hand, when comparing each individual phylum, NTI index were positive and significant in all groups, except in Cyanobacteria for which positive and significant values were only found in three localities; finally, NRI index was significant in only a few of the comparisons performed. The results suggest that habitat filtering is the main process that drives phylogenetic structure in bacterial communities associated to microbialites with the exception of Cyanobacteria where different lineages can contribute to microbialite formation and growth. Rev. Biol. Trop. 64 (3): 10571065. Epub 2016 September 01.

ResumenLa estructura y composición de las comunidades son determinadas por procesos evolutivos y ecológicos que se manifiestan en señales de diversidad, abundancia y la relación de especies. El análisis de la relación de especies que coexisten ha recibido atención como una herramienta para identificar los procesos que influyen en la composición de una comunidad dentro de un hábitat particular. En este estudio, evaluamos si la composición genética de bacterias microbialíticas depende de acontecimientos al azar vs factores biológicos/ abióticos. Este estudio se basa en un conjunto de datos genéticos de dos regiones hipervariables (V5 y V6) de gen 16S rRNA generados previamente de nueve comunidades de microbialitos distribuidos en el Noreste, Centro y Sureste de México, recolectados en mayo y junio 2009. Los datos genéticos de los filos más abundantes (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes y Cyanobacteria) fueron analizados para determinar la estructura filogenética de la comunidad y de cada filo por separado. Para el análisis conjunto, el índice NTI de Webb mostró valores positivos y significativos en las nueve comunidades analizadas, en donde los valores oscilaron entre 31.5 en Pozas Azules I y 57.2 en el Canal Pirata en Bacalar; en contraste, los valores del índice NRI fueron positivos y significativos en seis de las nueve comunidades analizadas con valores oscilando desde 18.1 en Pozas Azules I hasta 45.1 en Río Mezquites. Por otro lado, en la comparación de cada filo individual, el índice NTI fue positivo y significativo en todos los grupos excepto en Cyanobacteria, en donde valores positivos y significativos fueron encontrados sólo en tres localidades; finalmente, el índice NRI fue significativo sólo en unas cuantas de las comparaciones realizadas. Los resultados sugieren que el filtrado del hábitat es el proceso principal que determina la estructura filogenética de las comunidades bacterianas asociadas a microbialitos con la excepción de las cianobacterias en donde diferentes linajes pueden contribuir a la formación y crecimiento del microbialito.

Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes

To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia), rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

Isolation and characterization of high quality DNA from marine benthic macroalgae.

The isolation of high quality DNA is essential for many molecular biology applications including polymerase chain reaction (PCR) and endonuclease restriction digestion based techniques. An easy and inexpensive protocol has been developed for extracting genomic DNA from seven species of algae viz. Lola capillaries, Enteromorpha intestinalis, Ulva lactuca and Rhizoclonium sp belonging to Chlorophyceae, Catenella nipae, Polysiphonia mollis belonging to Rhodophyceae and Dictyota ceylanica belonging to Phaeophyceae group were collected from the coastal regions of Sunderban delta in West Bengal, India dominantly growing on mud flats, bark of different mangrove trees, pneumatophores, stilt roots, concrete surfaces, wooden and bamboo poles, sides of the boats and other water vehicles inundated during high tides. The DNA was found suitable for restriction endonuclease digestion and PCR amplification with randomely amplified polymorphic DNA (RAPD) primers. The A260/A280 ratio of 1.15 0.14 to 1.94 indicated little contamination from proteins and polysaccharides. The PCR amplification with RAPD primers showed its suitability in PCR based techniques and the restriction digestion with Eco RV confirmed its suitability for hybridization based techniques. The protocol is equally good for isolating DNA from both fresh as well as preserved materials.

RNA Interference in Infectious Tropical Diseases

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.

RNA Interference in Infectious Tropical Diseases

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.

La ADN topoisomerasa tipo I de protozoos patógenos como Diana terapéutica de fármacos antitumorales / Type I DNA topoisomerase from protozoan pathogens as a potential target for anti-tumoral drugs

La utilización intensiva de fármacos antiparasitarios es la causa principal de la aparición de microorganismos parásitos multirresistentes en las regiones del planeta donde son precisamente endémicos. Los agentes etiológicos de las denominadas enfermedades tropicales -malaria, criptosporiodiosis, enfermedad del sueño, enfermedad de Chagas o los distintos tipos de leishmaniosis- son protozoos unicelulares sobre los que no se ha desarrollado en la actualidad ninguna vacuna eficaz y cuyo tratamiento se basa en medidas sanitarias preventivas y en el uso de medicamentos. La quimioterapia antiparasitaria actual es cara, no está ausente de efectos adversos y no supone beneficios a las empresas que la comercializan, por lo que la inversión en I & D es marginal comparada con la llevada a cabo para otros procesos patológicos de menor relevancia médica. La identificación de las ADN topoisomerasas como dianas farmacológicas se basa en los excelentes resultados obtenidos en los ensayos clínicos llevados a cabo con los derivados de la camptotecina en la terapia antitumoral. Las importantes diferencias estructurales entre las ADN topoisomerasas de tipo I de tripanosomas y leishmanias con respecto a sus homólogas de mamífero ha abierto un nuevo campo de investigación que combina las técnicas de biología molecular con la cristalización de proteínas para poder diseñar nuevos fármacos dirigidos específicamente a su inhibición. Revisamos aquí las características de estas nuevas dianas farmacológicas, así como los compuestos que en el momento están siendo utilizados para su inhibición en los agentes parasitarios que causan las principales enfermedades tropicales.

The intensive use of antiparasitic drugs is the main cause of the emergence of multiresistant parasite strains on those regions where these parasites are endemic. The aetiological agents of the so-called tropical diseases viz. malaria, cryptosporidiosis, sleeping sickness, Chagas disease or leishmaniasis, among others, are unicellular protozoan parasites with no immune-prophylactic treatment and where the chemotherapeutical treatment is still under controversy. At present, the chemotherapeutic approach to these diseases is expensive, has side or toxic effects and it does not provide economic profits to the Pharmaceuticals which then have no or scarce enthusiasm in R & D investments in this field. The identification of type I DNAtopoisomerases as promising drug targets is based on the excellent results obtained with camptothecin derivatives in anticancer therapy. The recent finding of significant structural differences between human type I DNAtopoisomerase and their counterparts in trypanosomatids has open a new field in drug discovery, the aim is to find structural insights to be targeted by new drugs. This review is an update of DNA-topoisomerases as potential chemotherapeutic targets against the most important protozoan agents of medical interest.

Separation and mapping of chromosomes of parasitic protozoa

Many protozoan parasites represent an important group of human pathogens. Pulsed Field Gradient Gel Electrophoresis (PFGE) analysis has been an important tool fundamental genetic studies of parasites like Trypanosoma, Leishmania Giardia or the human malaria Plasmodium falciparum. We present PFGE conditions allowing a high resolution separation of chromosomes ranging from 500 to 4000 kb within a two day electrophoresis run. In addition, we present conditions for separating large chromosomes (2000-6000 kb) within 36 hr. We demontrate that the application of two dimentional PFGE (2D-PFGE) technique to parasite karyotypes is a very useful method for the analysis of dispersed gene families and comparative studies of the intrachomosomal genome organization.

Micropropagación clonal, una alternativa biotecnológica en el cultivo de macroalgas marinas chilenas de importancia económica / Clonal micropropagation, a biotechnological alternative in the culture of chilean marine macroalgae of economical importance

Vegetative propagation of higler plants have been practiced since antiquity. He modern approach relies upon the totipotency of somatic cells to give rise to a fully differentiated plant. In this context, this paper presntes the potential of plant biotechonology on economically interesting marine algae from Chile and outlines the ongoing research on seaweeds micropropagatin. Micropropagation techniques are seen as the means of speeding up the production of desirable strains (e.g., higher growth rate, enhanced phycocolloid production, epiphyte resistance, etc.) that would be available as seed stocks for the development of chilean mariculture. We report our advances in tissue culture techniques on Gracilaria chilensis Bird, MacLachlan & Oliveira; Gelidium lingulatum Kützing; Gelidium rex Santelices & Abbbott and Lessonia nigrescens Bory. Our efforts are focused on the development of procedures for calli or totipotent cells induction and their pathways to plantlets,stages of micropropagation, its limitations, advantages and future research involving protoplasts isolation