ISCB-LA SoIBio BioNetMX Symposium 2020 Virtual Viewing Hall
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Computational Evolutionary Biology of Microorganisms
- Titilayo Mabel Olotu, Adeleke University, Ede, Nigeria, Nigeria
- Idowu Jesulayomi Adeosun, Adeleke University, Ede, Nigeria, Nigeria
- Mary Oluwatosin Kaka, Adeleke University, Ede, Nigeria, Nigeria
- Kolawole Elijah Oladipo, Adeleke University, Ede., Nigeria
Short Abstract: Introduction: HIV-1 has nine genes, with only the gag, pol, and env genes common to all replication-competent retroviruses and the pol genes is very unique because its encodes the enzymes for replication. The aim of this study is to describe the relatedness of these HIV-1 pol genes with each other and its antiviral drug susceptibility which will give more information on its sensitivity and resistivity to antiviral drugs. Methodology: 17 different partial genome sequences of HIV-1 Pol gene in some West African countries were retrieved from NCBI nucleotide database. Evolutionary relationship of the sequence was determined by Multiple sequence alignment using ClustaW and were further analyzed by neighbor-joining method using MEGA 6 to plot its phylogenetic tree. The sensitivity and resistance to antiviral agents were analyzed using the Stanford University HIV Drug Resistance Database. Results: Isolate SN-042062 from Kenya and DR138-13 from Uganda; isolate G_01035 from Sudan reverse and isolate NGA-INF-2016-618 from Nigeria have similar branch length of 89 and 88 respectively. The percentage susceptibility of each viral drug ranged from 82.35% (Tenofovir) to 64.70% (Rilpivirine) and the percentage resistivity ranged from 35.29% (Rilpivirine) to 23.52% (Nevirapine). Discussion: Isolates from Nigeria and Sudan has the highest the closest homology to one another because of the distance in their branch length and it is show that Tenofovir is the most effective antiviral drug to the pol gene which might be because it’s a nucleoside reverse transcriptase inhibitors. Conclusion: The phylogenetic relationship and information on its sensitivity and resistivity of the HIV-1 pol gene will lead to better treatment of HIV-1 from the researched regions.
- Angel de Jesus Estrada Gonzalez, Instituto Potosino de Investigación Científica y Tecnológica A.C., Mexico
- Nguyen Esmeralda Lopez Lozano, Instituto Potosino de Investigación Científica y Tecnológica A.C., Mexico
- Joel David Flores Rivas, Instituto Potosino de Investigación Científica y Tecnológica A.C., Mexico
Short Abstract: Arid lands are characterized by seasonal and scarce rainfall (<500 mm year), that can cause water stress in plants expressed in their physiological changes. It has been postulated that plants can modify their rhizospheric bacterial communities through radical exudates, selecting plant growth promoters that can help plants tolerate water stress, establishing mutual cooperation to survive in those conditions. In this work we identify the possible physiological mechanisms that have allowed Echinocactus platyacanthus to survive and grow during drought seasons in an arid zone and if its interaction with the rhizospheric bacterial community is influence by those mechanisms. For this, physiological variables (chlorophyll fluorescence, pigments, nocturnal acidity, osmotic potential and ROS), physicochemical soil properties, root exudates (amino acids), and rhizosphere bacterial community were evaluated. Our results indicated that E. platyacanthus did not present signals of stress in their photosynthetic system during drought season. However, the content of chlorophylls, acidity and osmotic potential decreased, and the content of ROS and carotenoids increased during drought season, indicating a physiological regulation of the plant. The profile of amino acids exudated changed between seasons. At the same time, rhizospheric bacterial community was possibly modified t, being the taxa Gemmataceae, Entotheonellaceae_ge, Dehalococcoidia, Pirellula, Nitrosococcaceae, Dehalococcoidia and Actinobacteriota more abundant during drought season. This work shows that the high tolerance to drought of E. platyacanthus is probably due to a interaction between mechanisms of adaptation intrinsic to the plant and to beneficial symbiotic relationships with its microbiota regulated by the physiology of the plant through its exudates.
- Sara Berenice Martínez Luna, Instituto de Biotecnología, Mexico
- José Luis Puente Garcia, Instituto de Biotecnología, Mexico
- Yalbi Itzel Balderas Martínez, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
Short Abstract: Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic Escherichia coli (EHEC) have acquired by horizontal transference the locus of enterocyte effacement (LEE) pathogenic island which contains the virulence genes that confer the ability to produce the Attaching and Effacing (A/E) lesion in humans causing acute diarrhea. Albeit it is of medical importance, there are few efforts to build the regulatory network of the genes related to this island. At this moment, it has not been integrated all the information due to the complexity of the global and local regulation, and because the manual extraction of the data accumulated in the literature can take a lot of time and effort. Semi-automatic biocuration systems are tools that help to obtain, in a reasonable time, the complete regulatory interactions. Once all the available information is recovered, it is possible to detect mechanisms that have not been described together, such as feedback loops, and to generate new predictions. Here, we show a semi-automatic curation workflow to obtain the LEE pathogenicity island regulatory network from scientific articles, through the extraction of regulatory interactions and their properties. This regulatory network contains the genes belonging to the LEE island and genes non-encoded in this island but that they are regulated by LEE regulators in EPEC and EHEC strains. Our network is composed of 239 regulatory interactions obtained from 250 papers, which include 43 transcription factors and 84 target genes. The interactions from this network are classified as either direct or indirect relationships and as interactions with weak or strong evidence based on the experimental methods used to obtain them. The network integration allowed us to find new feedback loops that have not been previously integrated and we conclude that our network contains 85 regulatory interactions of which the representative and dual nodes are Ler (LEE1) and GrlR-A (LEE7) the master regulators of the pathogenicity island. Our workflow can be used to reconstruct the genetic regulatory network with supporting evidence in any organism.
- Claudia Silva, Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor., Chile
- Alberto J. Martin, Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor., Chile
- Daniel Garrido, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontifical Catholic University of Chile., Chile
Short Abstract: Clostridium baratii and Clostridium ventriculi are species found in human gut microbiota that could be carried asymptomatically or produce toxins. In normal conditions, these species colonize gastrointestinal tracts where they metabolize host-indigestible oligosaccharides. Although, there is evidence that some strains of C. baratii could cause botulism and C. ventriculi have been involved in cases of gastric perforation, emphysematous gastritis, and peritonitis, our knowledge regarding the genomic features and phylogenic characteristics of both species is currently limited. We analyzed the pangenome of C. baratii and C. ventriculi to understand the composition and phylogenic and genomic characteristics of these species. Our analysis employed all existing genomes in public databases, including two genomes we isolated from two asymptomatic subjects, in addition to genomes obtained from available metagenomes. Both pangenomes were found to be open. The core genome contained 47.6%, and 62.9% of the total genes of the pangenome in C. baratii and C. ventriculi respectively. In both cases, glycoside hydrolases were identified as the highest fraction of total CAZys categories versus other carbohydrate-active enzymes, reflecting their critical role in processing plant- and host-derived carbohydrates. Clostridium species are well known to be spore-forming, observing the difference in the distribution of key sporulation genes, both C. baratii and C. ventriculi are endowed with spo0A, spoIIID, spoT, spoVAC, spoVAD, spoVG, and spoVR sporulation genes, but only C. ventriculi genomes contained spo0J and spoVC sporulation genes. Some C. baratii strains produce the botulinum toxin. We confirmed the presence of all genes of the BonT/F7 cluster in the majority strains of C. baratii. BonT/F7 is one of the seven gene subtypes of botulinum neurotoxin (types F1 to F7), which is the second-most divergent subtype of this group and has characteristic mutations in the C. botulinum and C. baratii species. Our current analysis is a starting point to advance the knowledge of commensal species present in human gut microbiota which have been little studied and how they can impact health.
- Heidy Elkhaligy, Florida International University, United States
- Christian A. Balbin, Florida International University, United States
- Jessica Gonzalez, Florida International University, United States
- Teresa Liberatore, Florida International University, United States
- Christopher Mederos, Florida International University, United States
- Patricia Milanes, Florida International University, United States
- Daniel Morales, Florida International University, United States
- Gisselle Prida, Florida International University, United States
- Kyana Rodriguez, Florida International University, United States
- Alberto Sigler, Florida International University, United States
- William Vidal, Florida International University, United States
- Jessica Siltberg-Liberles, Florida International University, United States
Short Abstract: COVID-19, caused by SARS-CoV-2, is running berserk across the globe. SARS-CoV-2 is a coronavirus that recently crossed the species barrier to infect humans and successfully transmits from human-to-human. Two other coronaviruses, SARS-CoV and MERS-CoV, have also crossed the human species barrier. The SARS-CoV outbreak in 2002-2003 resulted in about 8,000 cases with a mortality rate of 10%. The MERS-CoV outbreak started in 2012 and has currently resulted in >2,500 cases with a mortality rate of ~35%. As of September 29, 2020, SARS-CoV-2 has caused over 33 million confirmed cases and a million deaths worldwide. While some get severely ill from COVID-19 others are asymptomatic. Coronaviruses are not newcomers to the human immune system but most cause mild cold-like symptoms. Altogether, this suggests different interactions between the human host and proteins from different coronaviruses. Viruses are known to mimic functional signatures in their host’s proteins. These functional signatures consist of short linear motifs (SLiMs) that may occur by chance in viral proteins as a result of convergent evolution. We present an evolutionary and structural approach to address the evolutionary dynamics of SLiMs across the coronavirus proteome. Our preliminary results indicate high diversity of SLiMs in the SARS clade, while the total number of SLiMs is often greater in the MERS clade. Some motifs are unique to specific human coronaviruses and some are found in structurally flexible regions. These motifs may enable virus-specific transient interactions between e.g. SARS-CoV-2 and human proteins and nucleic acids.
- Janelle Nunez-Castilla, Florida International University, United States
- Jessica Siltberg-Liberles, Florida International University, United States
Short Abstract: As biology continues to shift towards a big data science, more and more principal investigators are finding that a lack of bioinformatics training among researchers entering the workforce is becoming a pressing issue. One solution for meeting bioinformatics training needs has been course-based undergraduate research experiences (CUREs), which have been linked to persistence and increased interest in science. To better facilitate bioinformatics integration into life science education, a set of bioinformatics core competencies has been previously developed. Thus, a 6-week upper division introductory computational biology CURE lab centering on coronavirus and SARS-CoV-2 research was debuted in Summer 2020, at Florida International University, a large public minority serving institution with over 4,000 biology majors. Students were asked to participate in a pre- and post-assessment designed to measure self-efficacy of bioinformatics core competencies, attitude towards bioinformatics, bioinformatics knowledge, and bioinformatics skill. Across all measured categories, we observed statistically significant improvements at the end of the course (n=32; p-values = 0.0, 0.001, 0.0, and 0.002, respectively). Notably, students reported that learning bioinformatics changed their ideas about how the natural world works. There was a slight decrease from beginning to end of the course (96.9% vs 93.8%) in the perceived relevance of bioinformatics towards a student’s major or career interests. Although this difference was not statistically significant, this suggests that bioinformatics is not for everyone. Still, students overwhelmingly felt that bioinformatics should receive more coverage at the undergraduate level with many stating that bioinformatics should be a requirement for graduation.