Publications by authors named "Adrián Ochoa-Leyva"

40 Publications

Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences.

BMC Genomics 2021 May 25;22(1):385. Epub 2021 May 25.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico.

Background: Mycobacterium abscessus (MAB) is a widely disseminated pathogenic non-tuberculous mycobacterium (NTM). Like with the M. tuberculosis complex (MTBC), excreted / secreted (ES) proteins play an essential role for its virulence and survival inside the host. Here, we used a robust bioinformatics pipeline to predict the secretome of the M. abscessus ATCC 19977 reference strain and 15 clinical isolates belonging to all three MAB subspecies, M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense.

Results: We found that ~ 18% of the proteins encoded in the MAB genomes were predicted as secreted and that the three MAB subspecies shared > 85% of the predicted secretomes. MAB isolates with a rough (R) colony morphotype showed larger predicted secretomes than isolates with a smooth (S) morphotype. Additionally, proteins exclusive to the secretomes of MAB R variants had higher antigenic densities than those exclusive to S variants, independent of the subspecies. For all investigated isolates, ES proteins had a significantly higher antigenic density than non-ES proteins. We identified 337 MAB ES proteins with homologues in previously investigated M. tuberculosis secretomes. Among these, 222 have previous experimental support of secretion, and some proteins showed homology with protein drug targets reported in the DrugBank database. The predicted MAB secretomes showed a higher abundance of proteins related to quorum-sensing and Mce domains as compared to MTBC indicating the importance of these pathways for MAB pathogenicity and virulence. Comparison of the predicted secretome of M. abscessus ATCC 19977 with the list of essential genes revealed that 99 secreted proteins corresponded to essential proteins required for in vitro growth.

Conclusions: This study represents the first systematic prediction and in silico characterization of the MAB secretome. Our study demonstrates that bioinformatics strategies can help to broadly explore mycobacterial secretomes including those of clinical isolates and to tailor subsequent, complex and time-consuming experimental approaches accordingly. This approach can support systematic investigation exploring candidate proteins for new vaccines and diagnostic markers to distinguish between colonization and infection. All predicted secretomes were deposited in the Secret-AAR web-server ( http://microbiomics.ibt.unam.mx/tools/aar/index.php ).
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http://dx.doi.org/10.1186/s12864-021-07670-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8152154PMC
May 2021

PmAP2-β depletion enhanced activation of the Toll signaling pathway during yellow head virus infection in the black tiger shrimp Penaeus monodon.

Sci Rep 2021 May 18;11(1):10534. Epub 2021 May 18.

Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.

Yellow head virus (YHV) is a pathogen which causes high mortality in penaeid shrimp. Previous studies suggested that YHV enters shrimp cells via clathrin-mediated endocytosis. This research investigated the roles of clathrin adaptor protein 2 subunit β (AP-2β) from Penaeus monodon during YHV infection. PmAP2-β was continuously up-regulated more than twofold during 6-36 hpi. Suppression of PmAP2-β significantly reduced YHV copy numbers and delayed shrimp mortality. Quantitative RT-PCR revealed that knockdown of PmAP2-β significantly enhanced the expression level of PmSpätzle, a signaling ligand in the Toll pathway, by 30-fold at 6 and 12 hpi. Moreover, the expression levels of gene components in the Imd and JAK/STAT signaling pathways under the suppression of PmAP2-β during YHV infection were also investigated. Interestingly, anti-lipopolysaccharide factor isoform 3 (ALFPm3) was up-regulated by 40-fold in PmAP2-β knockdown shrimp upon YHV infection. In addition, silencing of PmAP2-β dramatically enhanced crustinPm1 expression in YHV-infected shrimp. Knockdown of ALFPm3 and crustinPm1 significantly reduced shrimp survival rate. Taken together, this work suggested that PmAP2-β-deficiency promoted the Toll pathway signalings, resulting in elevated levels of ALFPm3 and crustinPm1, the crucial antimicrobial peptides in defence against YHV.
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http://dx.doi.org/10.1038/s41598-021-89922-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131699PMC
May 2021

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters.

Genes (Basel) 2021 Apr 13;12(4). Epub 2021 Apr 13.

Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico.

The interplay between shrimp immune system, its environment, and microbiota contributes to the organism's homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method's choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.
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http://dx.doi.org/10.3390/genes12040564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070570PMC
April 2021

A novel, sequencing-free strategy for the functional characterization of Taenia solium proteomic fingerprint.

PLoS Negl Trop Dis 2021 02 18;15(2):e0009104. Epub 2021 Feb 18.

Unidad Periférica de Neuroinflamación para el estudio de patologías neurológicas del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, México, México.

The flatworm Taenia solium causes human and pig cysticercosis. When cysticerci are established in the human central nervous system, they cause neurocysticercosis, a potentially fatal disease. Neurocysticercosis is a persisting public health problem in rural regions of Mexico and other developing countries of Latin America, Asia, and Africa, where the infection is endemic. The great variability observed in the phenotypic and genotypic traits of cysticerci result in a great heterogeneity in the patterns of molecules secreted by them within their host. This work is aimed to identify and characterize cysticercal secretion proteins of T. solium cysticerci obtained from 5 naturally infected pigs from Guerrero, Mexico, using 2D-PAGE proteomic analysis. The isoelectric point (IP) and molecular weight (MW) of the spots were identified using the software ImageMaster 2D Platinum v.7.0. Since most secreted proteins are impossible to identify by mass spectrometry (MS) due to their low concentration in the sample, a novel strategy to predict their sequence was applied. In total, 108 conserved and 186 differential proteins were identified in five cysticercus cultures. Interestingly, we predicted the sequence of 14 proteins that were common in four out of five cysticercus cultures, which could be used to design vaccines or diagnostic methods for neurocysticercosis. A functional characterization of all sequences was performed using the algorithms SecretomeP, SignalP, and BlastKOALA. We found a possible link between signal transduction pathways in parasite cells and human cancer due to deregulation in signal transduction pathways. Bioinformatics analysis also demonstrated that the parasite release proteins by an exosome-like mechanism, which could be of biological interest.
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http://dx.doi.org/10.1371/journal.pntd.0009104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924735PMC
February 2021

Biochemical characterization and inhibition of thermolabile hemolysin from by phenolic compounds.

PeerJ 2021 6;9:e10506. Epub 2021 Jan 6.

Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico.

(), a typical microorganism inhabiting marine ecosystems, uses pathogenic virulence molecules such as hemolysins to cause bacterial infections of both human and marine animals. The thermolabile hemolysin TLH lyses human erythrocytes by a phospholipase B/A2 enzymatic activity in egg-yolk lecithin. However, few studies have been characterized the biochemical properties and the use of TLH as a molecular target for natural compounds as an alternative to control infection. Here, we evaluated the biochemical and inhibition parameters of the recombinant TLH using enzymatic and hemolytic assays and determined the molecular interactions by in silico docking analysis. The highest enzymatic activity was at pH 8 and 50 °C, and it was inactivated by 20 min at 60 °C with Tm = 50.9 °C. Additionally, the flavonoids quercetin, epigallocatechin gallate, and morin inhibited the TLH activity with IC50 values of 4.5 µM, 6.3 µM, and 9.9 µM, respectively; while phenolics acids were not effective inhibitors for this enzyme. Boltzmann and Arrhenius equation analysis indicate that TLH is a thermolabile enzyme. The inhibition of both enzymatic and hemolytic activities by flavonoids agrees with molecular docking, suggesting that flavonoids could interact with the active site's amino acids. Future research is necessary to evaluate the antibacterial activity of flavonoids against in vivo.
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http://dx.doi.org/10.7717/peerj.10506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7796666PMC
January 2021

Enteric parasitic infection disturbs bacterial structure in Mexican children with autoantibodies for type 1 diabetes and/or celiac disease.

Gut Pathog 2020 11;12:37. Epub 2020 Aug 11.

Dept. Nutrición, Centro de Investigación en Alimentación y Desarrollo, A.C., Astiazarán Rojas No. 46, Hermosillo, 83304 Sonora Mexico.

Background: Intestinal bacterial dysbiosis and increased gut permeability are associated with higher risk of developing type 1 diabetes (T1D) or celiac disease (CD). There is a lack of information on parasitism involved in gut disturbance of predisposed children. We evaluated the effect of enteropathogenic parasites ( spp., spp. , and spp.) on the bacterial structure of feces from children with autoantibodies for T1D or CD. Participants included 37 children under 18 years of age, from whom stools were analyzed for enteric parasites by qPCR and 22/37 for bacterial profile by sequencing the V3-V4 region of the 16s rRNA gene. Dietary, clinical, and socioeconomic data was recorded.

Results: Pathogens parasitized 28/37 participants, spp. was the most prevalent (62.2%), followed by both and spp (37.8%). There were no dietary differences (> 0.05) attributable to parasitism. Co-infected participants with and differ (p = 0.064) from non-infected participants in bacterial alpha phylogenetic diversity. The same parasites' co-infection was associated with a decreased abundance of the Ruminococaceae (p = 0.04) and Verrucomicrobioceae families, of the genus (p = 0.009). There was a lower Firmicutes/Bacteroidetes ratio (p = 0.02) in infected than in uninfected participants.

Conclusions: and affected the bacterial structure at family and genus levels, decreasing the ratio between Firmicutes and Bacteroidetes in children with auto-antibodies for T1D or CD, which could increase the risk of illness onset.
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http://dx.doi.org/10.1186/s13099-020-00376-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418185PMC
August 2020

Evidence for the Effect of Vaccination on Host-Pathogen Interactions in a Murine Model of Pulmonary Tuberculosis by .

Front Immunol 2020 19;11:930. Epub 2020 May 19.

Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.

The global control of Tuberculosis remains elusive, and Bacillus Calmette-Guérin (BCG) -the most widely used vaccine in history-has proven insufficient for reversing this epidemic. Several authors have suggested that the mass presence of vaccinated hosts might have affected the (MTB) population structure, and this could in turn be reflected in a prevalence of strains with higher ability to circumvent BCG-induced immunity, such as the recent Beijing genotype. The effect of vaccination on vaccine-escape variants has been well-documented in several bacterial pathogens; however the effect of the interaction between MTB strains and vaccinated hosts has never been previously described. In this study we show for the first time the interaction between MTB Beijing-genotype strains and BCG-vaccinated hosts. Using a well-controlled murine model of progressive pulmonary tuberculosis, we vaccinated BALB/c mice with two different sub-strains of BCG (BCG-Phipps and BCG-Vietnam). Following vaccination, the mice were infected with either one of three selected MTB strains. Strains were selected based on lineage, and included two Beijing-family clinical isolates (strains 46 and 48) and a well-characterized laboratory strain (H37Rv). Two months after infection, mice were euthanized and the bacteria extracted from their lungs. We characterized the genomic composite of the bacteria before and after exposure to vaccinated hosts, and also characterized the local response to the bacteria by sequencing the lung transcriptome in animals during the infection. Results from this study show that the interaction within the lungs of the vaccinated hosts results in the selection of higher-virulence bacteria, specifically for the Beijing genotype strains 46 and 48. After exposure to the BCG-induced immune response, strains 46 and 48 acquire genomic mutations associated with several virulence factors. As a result, the bacteria collected from these vaccinated hosts have an increased ability for immune evasion, as shown in both the host transcriptome and the histopathology studies, and replicates far more efficiently compared to bacteria collected from unvaccinated hosts or to the original-stock strain. Further research is warranted to ascertain the pathways associated with the genomic alterations. However, our results highlight novel host-pathogen interactions induced by exposure of MTB to BCG vaccinated hosts.
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http://dx.doi.org/10.3389/fimmu.2020.00930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248268PMC
March 2021

Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children.

Microb Cell Fact 2020 Mar 6;19(1):61. Epub 2020 Mar 6.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, C.P. 62210, Cuernavaca, Morelos, Mexico.

Background: In the last decade, increasing evidence has shown that changes in human gut microbiota are associated with diseases, such as obesity. The excreted/secreted proteins (secretome) of the gut microbiota affect the microbial composition, altering its colonization and persistence. Furthermore, it influences microbiota-host interactions by triggering inflammatory reactions and modulating the host's immune response. The metatranscriptome is essential to elucidate which genes are expressed under diseases. In this regard, little is known about the expressed secretome in the microbiome. Here, we use a metatranscriptomic approach to delineate the secretome of the gut microbiome of Mexican children with normal weight (NW) obesity (O) and obesity with metabolic syndrome (OMS). Additionally, we performed the 16S rRNA profiling of the gut microbiota.

Results: Out of the 115,712 metatranscriptome genes that codified for proteins, 30,024 (26%) were predicted to be secreted, constituting the Secrebiome of the gut microbiome. The 16S profiling confirmed an increased abundance in Firmicutes and decreased in Bacteroidetes in the obesity groups, and a significantly higher richness and diversity than the normal weight group. We found novel biomarkers for obesity with metabolic syndrome such as increased Coriobacteraceae, Collinsela, and Collinsella aerofaciens; Erysipelotrichaceae, Catenibacterium and Catenibacterium sp., and decreased Parabacteroides distasonis, which correlated with clinical and anthropometric parameters associated to obesity and metabolic syndrome. Related to the Secrebiome, 16 genes, homologous to F. prausniitzi, were overexpressed for the obese and 15 genes homologous to Bacteroides, were overexpressed in the obesity with metabolic syndrome. Furthermore, a significant enrichment of CAZy enzymes was found in the Secrebiome. Additionally, significant differences in the antigenic density of the Secrebiome were found between normal weight and obesity groups.

Conclusions: These findings show, for the first time, the role of the Secrebiome in the functional human-microbiota interaction. Our results highlight the importance of metatranscriptomics to provide novel information about the gut microbiome's functions that could help us understand the impact of the Secrebiome on the homeostasis of its human host. Furthermore, the metatranscriptome and 16S profiling confirmed the importance of treating obesity and obesity with metabolic syndrome as separate conditions to better understand the interplay between microbiome and disease.
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http://dx.doi.org/10.1186/s12934-020-01319-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060530PMC
March 2020

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota.

Microorganisms 2020 Jan 17;8(1). Epub 2020 Jan 17.

Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM) Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico.

The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus was significantly abundant in the intestine, as well as and in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.
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http://dx.doi.org/10.3390/microorganisms8010134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7022540PMC
January 2020

Role of Clathrin Assembly Protein-2 Beta Subunit during White Spot Syndrome Virus Infection in Black Tiger Shrimp Penaeus monodon.

Sci Rep 2019 09 17;9(1):13489. Epub 2019 Sep 17.

Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.

White spot syndrome virus (WSSV) is one of the most lethal viruses severely affecting shrimp industry. This disease can cause 100% mortality of farmed shrimp within a week. This work aims to characterize clathrin assembly proteins in Penaeus monodon and investigate their roles in WSSV entry. In general, clathrin assembly proteins form complexes with specific receptors and clathrins, leading to clathrin-mediated endocytosis. Adaptor protein 2 (AP-2), which is responsible for endocytosis at plasma membrane, consists of four subunits including α, β2, μ2 and σ2. Knockdown of clathrin coat AP17, or σ subunit of AP-2 dramatically reduced WSSV infectivity. Similar results were observed, when shrimp were pre-treated with chlorpromazine (CPZ), an inhibitor of clathrin-dependent endocytosis. The complete open reading frames of AP-2β and μ subunits of P. monodon are reported. PmAP-2 β was up-regulated about 4-fold at 6 and 36 h post-WSSV infection. Knockdown of PmAP-2β delayed shrimp mortality during WSSV infection, of which WSSV intermediate early 1 gene expression was also down-regulated. Immunogold-labelling and transmission electron microscopy revealed that PmAP-2β co-localized with WSSV particles at plasma membrane. In addition, PmAP-2β-silencing significantly affected the expression levels of PmSTAT, PmDOME, PmDorsal and ALFPm3 during WSSV infection. It is possible that PmAP-2β is associated with the JAK/STAT and the Toll pathway.
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http://dx.doi.org/10.1038/s41598-019-49852-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748913PMC
September 2019

Genome-Wide Identification of Mango ( L.) Polygalacturonases: Expression Analysis of Family Members and Total Enzyme Activity During Fruit Ripening.

Front Plant Sci 2019 30;10:969. Epub 2019 Jul 30.

Laboratorio de Genética y Biología Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Mexico.

Mango (.) is an important commercial fruit that shows a noticeable loss of firmness during ripening. Polygalacturonase (PG, E.C. 3.2.1.15) is a crucial enzyme for cell wall loosening during fruit ripening since it solubilizes pectin and its activity correlates with fruit softening. Mango PGs were mapped to a genome draft using seventeen PGs found in mango transcriptomes and 48 bonafide PGs were identified. The phylogenetic analysis suggests that they are related to , which may indicate a recent evolutive divergence and related functions with orthologs in the tree. Gene expression analysis for nine PGs showed differential expression for them during post-harvest fruit ripening, , , , , , , and were highly up-regulated. PG enzymatic activity also increased during maturation and these results correlate with the loss of firmness observed in mango during post-harvest ripening, between the ethylene production burst and the climacteric peak. The analysis of PGs promoter regions identified regulatory sequences associated to ripening such as MADS-box, ethylene regulation like ethylene insensitive 3 (EIN3) factors, APETALA2-like and ethylene response element factors. During mango fruit ripening the action of at least these nine PGs contribute to softening, and their expression is regulated at the transcriptional level. The prediction of the tridimensional structure of some PGs showed a conserved parallel beta-helical fold related to polysaccharide hydrolysis and a modular architecture, where exons correspond to structural elements. Further biotechnological approaches could target specific softening-related PGs to extend mango post-harvest shelf life.
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http://dx.doi.org/10.3389/fpls.2019.00969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6682704PMC
July 2019

Bacterial Diversity and Population Dynamics During the Fermentation of Palm Wine From Guerrero Mexico.

Front Microbiol 2019 22;10:531. Epub 2019 Mar 22.

Laboratorio de Investigación en Biotecnología, Universidad Autónoma de Guerrero, Chilpancingo, Mexico.

Palm wine is obtained by fermentation of palm tree sap. In the Pacific coast of Mexico, palm wine is called Tuba and it is consumed as a traditional fermented beverage. Tuba has empirical applications such as an auxiliary in gastrointestinal diseases and a good source of nutrients. In the present study, a next-generation sequencing of the V3-V4 regions of the 16S rRNA gene was employed to analyze bacterial diversity and population dynamics during the fermentation process of Tuba, both in laboratory controlled conditions and in commercial samples from local vendors. Taxonomic identification showed that was the main genus in all the samples, following by , , , and . Alpha diversity analysis demonstrated variability between all the samples. Beta diversity clustered the bacterial population according to the collection origin of the sample. Metabolic functional profile inference showed that the members of the bacterial communities may present the vitamin, antibiotic and antioxidant biosynthesis genes. Additionally, we further investigated the correlation between the predominant genera and some composition parameters of this beverage. This study provides the basis of the bacterial community composition and functionality of the fermented beverage.
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http://dx.doi.org/10.3389/fmicb.2019.00531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440455PMC
March 2019

Microbiome-MX 2018: microbiota and microbiome opportunities in Mexico, a megadiverse country.

Res Microbiol 2019 Jun - Aug;170(4-5):235-241. Epub 2019 Mar 25.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico. Electronic address:

A weekly conference series paired with lectures entitled "Microbiome-MX: exploring the Microbiota and Microbiome Research in Mexico" was organized to provide a multidisciplinary overview of the most recent research done in Mexico using high-throughput sequencing. Scientists and postgraduate students from several disciplines such as microbiology, bioinformatics, virology, immunology, nutrition, and medical genomics gathered to discuss state of the art in each of their respective subjects of expertise, as well as advances, applications and new opportunities on microbiota/microbiome research. In particular, high-throughput sequencing is a crucial tool to understand the challenges of a megadiverse developing country as Mexico, and moreover to know the scientific capital and capabilities available for collaboration. The conference series addressed three main topics important for Mexico: i) the complex role of microbiota in health and prevalent diseases such as obesity, diabetes, inflammatory bowel disease, tuberculosis, HIV, autoimmune diseases and gastric cancer; ii) the use of local, traditional and prehispanic products as pre/probiotics to modulate the microbiota and improve human health; and iii) the impact of the microbiota in shaping the biodiversity of economically important terrestrial and marine ecosystems. Herein, we summarize the contributions that Mexican microbiota/microbiome research is making to the global trends, describing the highlights of the conferences and lectures, rather than a review of the state-of-the-art of this research. This meeting report also presents the efforts of a multidisciplinary group of scientist to encourage collaborations and bringing this research field closer for younger generations.
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http://dx.doi.org/10.1016/j.resmic.2019.03.001DOI Listing
August 2019

The CDR1 and Other Regions of Immunoglobulin Light Chains are Hot Spots for Amyloid Aggregation.

Sci Rep 2019 02 28;9(1):3123. Epub 2019 Feb 28.

Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de México, 14610, Mexico.

Immunoglobulin light chain-derived (AL) amyloidosis is a debilitating disease without known cure. Almost nothing is known about the structural factors driving the amyloidogenesis of the light chains. This study aimed to identify the fibrillogenic hotspots of the model protein 6aJL2 and in pursuing this goal, two complementary approaches were applied. One of them was based on several web-based computational tools optimized to predict fibrillogenic/aggregation-prone sequences based on different structural and biophysical properties of the polypeptide chain. Then, the predictions were confirmed with an ad-hoc synthetic peptide library. In the second approach, 6aJL2 protein was proteolyzed with trypsin, and the products incubated in aggregation-promoting conditions. Then, the aggregation-prone fragments were identified by combining standard proteomic methods, and the results validated with a set of synthetic peptides with the sequence of the tryptic fragments. Both strategies coincided to identify a fibrillogenic hotspot located at the CDR1 and β-strand C of the protein, which was confirmed by scanning proline mutagenesis analysis. However, only the proteolysis-based strategy revealed additional fibrillogenic hotspots in two other regions of the protein. It was shown that a fibrillogenic hotspot associated to the CDR1 is also encoded by several κ and λ germline variable domain gene segments. Some parts of this study have been included in the chapter "The Structural Determinants of the Immunoglobulin Light Chain Amyloid Aggregation", published in Physical Biology of Proteins and Peptides, Springer 2015 (ISBN 978-3-319-21687-4).
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http://dx.doi.org/10.1038/s41598-019-39781-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395779PMC
February 2019

Whole-genome of Mexican-crAssphage isolated from the human gut microbiome.

BMC Res Notes 2018 Dec 17;11(1):902. Epub 2018 Dec 17.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico.

Objectives: crAssphage is a newly found phage described as the most abundant virus in the human gut microbiome. The majority of the crAssphage proteins are unknown in sequences databases, and its pathogenicity and epidemiology in humans are yet unclear. Hence, being one of the most abundant phages in the human gut microbiome more investigation at the genomic level is necessary to improve our understanding, especially in the Latin American population.

Data Description: In this article, we provide the whole genome of a crAssphage isolated from the human gut microbiome of the Mexican population, which was named Mexican-crAssphage. The genome consists of 96,283 bp, G+C content of 29.24% and 87 coding sequences. Notably, we did not find any transfer RNA genes in the genome sequence. We also sequenced viral-like enriched particles from 28 fecal samples, and we detected the presence of the Mexican-crAssphage genome in 8 samples (28.5%). To our knowledge, our data is the first whole genome report of the crAssphage isolated from the Latin American Population and provides valuable information for the experimental characterization of the most abundant human gut bacteriophage. The whole genome shotgun project of the Mexican-crAssphage is available at DDBJ/ENA/GenBank under the GenBank MK069403.
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http://dx.doi.org/10.1186/s13104-018-4010-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296078PMC
December 2018

Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic Bacteria .

Front Mol Biosci 2018 27;5:103. Epub 2018 Nov 27.

Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.

In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insight into the reasons for this gene replacement in plants, we characterized the TPI from the photosynthetic bacteria (SyTPI). SyTPI presents typical TPI enzyme kinetics profiles and assembles as a homodimer composed of two subunits that arrange in a (β-α) fold. We found that oxidizing agents diamide (DA) and HO, as well as thiol-conjugating agents such as oxidized glutathione (GSSG) and methyl methanethiosulfonate (MMTS), do not inhibit the catalytic activity of SyTPI at concentrations required to inactivate plastidic and cytosolic TPIs from the plant model (AtpdTPI and AtcTPI, respectively). The crystal structure of SyTPI revealed that each monomer contains three cysteines, C47, C127, and C176; however only the thiol group of C176 is solvent exposed. While AtcTPI and AtpdTPI are redox-regulated by chemical modifications of their accessible and reactive cysteines, we found that C176 of SyTPI is not sensitive to redox modification . Our data let us postulate that SyTPI was replaced by a eukaryotic TPI, because the latter contains redox-sensitive cysteines that may be subject to post-translational modifications required for modulating TPI's enzymatic activity.
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http://dx.doi.org/10.3389/fmolb.2018.00103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277545PMC
November 2018

Functional and taxonomic classification of a greenhouse water drain metagenome.

Stand Genomic Sci 2018 5;13:20. Epub 2018 Oct 5.

1Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos Mexico.

Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides. This study aimed to identify the bacteria and functional gene composition of a greenhouse water drain sample and also provide a genomic resource to search novel proteins from a previously unexplored niche. All the metagenome proteins and their annotations are available to the scientific community via http://microbiomics.ibt.unam.mx/tools/metagreenhouse/.
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http://dx.doi.org/10.1186/s40793-018-0326-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173933PMC
October 2018

Secret-AAR: a web server to assess the antigenic density of proteins and homology search against bacterial and parasite secretome proteins.

Genomics 2019 12 11;111(6):1514-1516. Epub 2018 Oct 11.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico. Electronic address:

The secretome refers to all the Excreted/Secreted (ES) proteins of a cell, and these are involved in critical biological processes, such as cell-cell communication, and host immune responses. Recently, we introduced the Abundance of Antigenic Aegions (AAR) value to assess the protein antigenic density and to evaluate the antigenic potential of secretomes. Here, to facilitate the AAR calculation, we implemented it as a user-friendly webserver. We extended the webserver capabilities implementing a sequence-based tool for searching homologous proteins across secretomes, including experimental and predicted secretomes of Mycobacterium tuberculosis and Taenia solium. Additionally, twelve secretomes of helminths, five of Mycobacterium and two of Gram-negative bacteria are also available. Our webserver is a useful tool for researchers working on immunoinformatics and reverse vaccinology, aiming at discovering candidate proteins for new vaccines or diagnostic tests, and it can be used to prioritize the experimental analysis of proteins for druggability assays. The Secret-AAR web server is available at http://microbiomics.ibt.unam.mx/tools/aar/.
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http://dx.doi.org/10.1016/j.ygeno.2018.10.007DOI Listing
December 2019

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota.

PeerJ 2018 10;6:e5382. Epub 2018 Aug 10.

Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico.

The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (, and ), and 36.7% were from freshwater () shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM  = 0.54,  = 0.001; PERMANOVA pseudo- = 21.8,  = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM  = 0.341,  = 0.001; PERMANOVA pseudo- = 8.50,  = 0.0001), organ (ANOSIM  = 0.279,  = 0.001; PERMANOVA pseudo- = 6.68,  = 0.001) and developmental stage (ANOSIM  = 0.240,  = 0.001; PERMANOVA pseudo- = 5.05,  = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.
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http://dx.doi.org/10.7717/peerj.5382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089209PMC
August 2018

A novel thymidylate synthase from the , , , and (VAAP) clade with altered nucleotide and folate binding sites.

PeerJ 2018 15;6:e5023. Epub 2018 Jun 15.

Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.

Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is , which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the gene in the genome of the strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains , , , and (VAAP) from the class. In this work, we studied the biochemical properties of recombinant TS from FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.
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http://dx.doi.org/10.7717/peerj.5023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005164PMC
June 2018

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

PeerJ 2017 8;5:e4133. Epub 2017 Dec 8.

Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México.

Background: In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays.

Methods: We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR).

Results: From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment.

Discussion: Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.
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http://dx.doi.org/10.7717/peerj.4133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724404PMC
December 2017

Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing.

Nat Commun 2017 10 18;8(1):1005. Epub 2017 Oct 18.

Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, 14610, Mexico.

Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago. The proportion of missense variants predicted as damaging is higher for undescribed (~ 30%) than for previously reported variants (~ 15%). Several variants previously associated with biological traits are highly frequent in the Native American genomes. These findings suggest that the demographic and adaptive processes that occurred in these groups shaped their genetic architecture and could have implications in biological processes of the Native Americans and Mestizos of today.
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http://dx.doi.org/10.1038/s41467-017-01194-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647344PMC
October 2017

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.

Sci Rep 2017 09 18;7(1):11783. Epub 2017 Sep 18.

Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico.

Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.
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http://dx.doi.org/10.1038/s41598-017-11805-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603525PMC
September 2017

Experimental and Theoretical Approaches To Investigate the Immunogenicity of Taenia solium-Derived KE7 Antigen.

Infect Immun 2017 12 17;85(12). Epub 2017 Nov 17.

Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México

cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Both peptides have proven protective capacity against cysticercosis and are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated with membrane processes and may participate in several vital cell pathways. The aim of this study was to identify the KE7 (TsKE7) full-length protein and to determine its immunogenic properties. Recombinant TsKE7 (rTsKE7) was expressed in Rosetta2 cells and used to obtain mouse polyclonal antibodies. Anti-rTsKE7 antibodies detected the expected native protein among the 350 spots developed from cyst vesicular fluid in a mass spectrometry-coupled immune proteomic analysis. These antibodies were then used to screen a phage-displayed 7-random-peptide library to map B-cell epitopes. The recognized phages displayed 9 peptides, with the consensus motif Y(F/Y)PS sequence, which includes YYYPS (named GK-1M, for being a GK-1 mimotope), exactly matching a part of GK-1. GK-1M was recognized by 58% of serum samples from cysticercotic pigs with 100% specificity but induced weak protection against murine cysticercosis. analysis revealed a universal T-cell epitope(s) in native TsKE7 potentially capable of stimulating cytotoxic T lymphocytes and helper T lymphocytes under different major histocompatibility complex class I and class II mouse haplotypes. Altogether, these results provide a rationale for the efficacy of the KETc7, rTsKE7, and GK-1 peptides as vaccines.
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http://dx.doi.org/10.1128/IAI.00395-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695116PMC
December 2017

De novo assembly and transcriptome characterization of the freshwater prawn Palaemonetes argentinus: Implications for a detoxification response.

Mar Genomics 2018 Feb 3;37:74-81. Epub 2017 Oct 3.

Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD). Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico. Electronic address:

Palaemonetes argentinus, an abundant freshwater prawn species in the northern and central region of Argentina, has been used as a bioindicator of environmental pollutants as it displays a very high sensitivity to pollutants exposure. Despite their extraordinary ecological relevance, a lack of genomic information has hindered a more thorough understanding of the molecular mechanisms potentially involved in detoxification processes of this species. Thus, transcriptomic profiling studies represent a promising approach to overcome the limitations imposed by the lack of extensive genomic resources for P. argentinus, and may improve the understanding of its physiological and molecular response triggered by pollutants. This work represents the first comprehensive transcriptome-based characterization of the non-model species P. argentinus to generate functional genomic annotations and provides valuable resources for future genetic studies. Trinity de novo assembly consisted of 24,738 transcripts with high representation of detoxification (phase I and II), anti-oxidation, osmoregulation pathways and DNA replication and bioenergetics. This crustacean transcriptome provides valuable molecular information about detoxification and biochemical processes that could be applied as biomarkers in further ecotoxicology studies.
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http://dx.doi.org/10.1016/j.margen.2017.08.009DOI Listing
February 2018

Secretome Prediction of Two Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets.

Front Microbiol 2017 7;8:128. Epub 2017 Feb 7.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico.

The Excreted/Secreted (ES) proteins play important roles during invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34-41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a druggability analysis of the secretomes, we found potential drug targets such as cytochrome P450, thiol peroxidase, the Ag85C, and Ribonucleoside Reductase in the secreted proteins that could be used as drug targets for novel treatments against Tuberculosis.
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http://dx.doi.org/10.3389/fmicb.2017.00128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5293778PMC
February 2017

Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei.

Biochim Biophys Acta 2016 12 7;1864(12):1696-1706. Epub 2016 Sep 7.

Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico. Electronic address:

Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5071168PMC
http://dx.doi.org/10.1016/j.bbapap.2016.09.002DOI Listing
December 2016

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.

Comput Struct Biotechnol J 2015 9;13:390-401. Epub 2015 Jun 9.

Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico.

The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.
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http://dx.doi.org/10.1016/j.csbj.2015.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484546PMC
July 2015

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

Sci Rep 2015 May 19;5:9683. Epub 2015 May 19.

Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica (INMEGEN), Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan México, D.F. C.P. 14610, México.

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.
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http://dx.doi.org/10.1038/srep09683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437048PMC
May 2015