Posters - Schedules

Transmembrane transport proteins are essential in cell life for the passage of substrates through the cell membrane. Metabolic network reconstruction requires transport reactions that describe the specific substrate transported as well as the
metabolic reactions of enzyme catalysis. In this paper, we utilize a protein language model called ProtBERT (Protein Bidirectional Encoder Representations from Transformers) to predict 96 specific substrates. An automatically constructed dataset using the
ChEBI and GO ontologies is introduced, called UniProt-SPEC-100, with 4,455 sequences from 96 specific substrates. This dataset is extremely imbalanced with a ratio of 1:408 for samples in the smallest class to the largest. Our model TooT-SPEC, predicts 83 classes out of 96 with an F1-score of 0.92 and MCC of 0.91 on an independent testset. The results of 3-fold cross-validation experiments, specifically, the performance on small-scale classes suggest the potential suitability of the ProtBERT protein representation language model for the classification of imbalanced datasets.

Cytokinins (CKs) are hormones that promote cell division and have growth regulatory functions in plant. The process by which perception of CKs occurs is given by a multistep phosphorylation system. Three elements are involved in this process, a receptor (Histidine kinase - HK), a transmitter and two responses regulators (A & B). CKs are not only produced by plants, other organisms have also been found capable of producing cytokinins, e. g. the fungi Claviceps purpurea and Magnaporthe oryzae, pathogens of rye and rice, respectively. In these fungi, mutant strains have been generated that are unable to produce CKs and are characterized by reduced virulence and infection capacity. Likewise in other organisms, for this reason CKs have begun to be categorized as virulence factors.
The organism we are working with is Trichoderma atroviride, a cosmopolitan plant beneficial fungus found in the rhizosphere of plants. It can act antagonistically against other pathogenic fungi, enhancing plant defense against pathogens and promotes plant growth. Our group has found that T. atroviride produces CKs and identified two genes involved in their synthesis, an Isopentenyltransferase (ipt) and a LONELY GUY (log). The Δipt mutant strain does not produce CKs and it was observed that it has an accelerated radial growth and early germination, relative to the WT strain. Therefore, the objective of this work is to determine the role of CKs and identify the elements involved in their perception in T. atroviride. Consequently, we intend to perform heterologous expression of the 12 T. atroviride HKs in E. coli to evaluate if any of them is involved in the perception of CKs. We also carried out a transcriptomic analysis during germination of conidia to identify differentially expressed genes between WT strain and ΔIPT mutant strain. Finally, we will perform a mutagenesis assay coupled to a selection system to identify other possible elements involved in the putative CK signaling pathway.
The results we have obtained show that the Δipt mutant strain germinates faster than the T. atroviride WT strain. Analysis of the differentially expressed genes showed induction of genes related to the cellular biosynthetic process, cell cycle and RNA metabolism in the Δipt, which correlates with the accelerated growth and germination of the Δipt mutant strain.

The first membranes emerged from primordial and simplistic amphiphilic molecule assemblies to accelerate the chemical evolution in confined systems.
Whether the source is the primitive ocean or delivered to Earth by extraterrestrial materials, the decanoic acids were plausible and chemically compatible amphiphiles with the prebiotic conditions 4.5 billion years ago.
The macroscopic properties of decanoic acid assemblies rely on several factors, such as CMC, ionic forces lower than 200mM, and temperature. On the temperature side, the early Earth's ranged from 60-608 ºC (Knauth, 2005). Therefore, volcanic activity or hydrothermal vents appear as plausible chemical reactors to explore the origins of life and have been used to understand the long-lasting stability of a membrane in contemporary times (Holm, 1992). However, there is still much knowledge to discover, and the biophysical properties of prebiotic membranes are barely known.

In this work, we take advantage of molecular dynamics to study a minimal composition of decanoic acids. As a result, we were able to characterize the first point of the aggregation of decanoic acid into vesicles under temperatures ranging from 29.8ºC to 109.8ºC. Altogether, we explored the translocation process of a simple prebiotic-like peptide into the decanoic acids membrane to give insights into triggering "a self-sustaining chemical system capable of Darwinian evolution" (Joyce 1994).

R.V.S. acknowledges the support of Proyecto FONDECYT Postdoctorado 3200951

Creating paths for the development and application of bioinformatics in Mexico
Since 2006, the Center for Genomic Sciences-UNAM has carried out programs to improve bioinformatics skills, mainly for students, but also for researchers, technicians and the general public, through workshops, seminars and courses, among others, promoting the bioinformatics in Mexico. and Latin America.
To achieve these objectives, several efforts were made, first at the local level in 2006. Later, a more ambitious project was started, with the support of the Ibero-American Society of Bioinformatics (SoIBio), changing the perspective to an international format, including participants from Latin America. At the same time, we became the National Bioinformatics Node of Mexico based at the Center for Genomic Sciences of the UNAM (NNB-CCG). In 2010, we had the first national event called "International Bioinformatics Workshops"; and as of 2012 we carry them out internationally. All our events are focused on a Spanish-speaking public, mainly.
As of 2018, to integrate all initiatives, we support the creation of the "Mexican Bioinformatics Network" (RMB) as an organization that promotes the organized collaboration of all related groups. We currently have collaboration alliances with national and international entities; and we have the support of several organizations such as Code for Science & Society, among others. We carry out events and continuous activities for the benefit of collaborating groups and users of bioinformatics.