Sergio Emilio Mares 🌵☀️

I am a graduate student at UC Berkeley studying Computational Biology. Currently, I am in a joint rotation with the Ni-lab (Dr. Ioannidis) at UC Berkeley and the Costello Lab at UCSF.

Here is my most up-to date CV.

Ioannidis (Ni-lab) at UC Berkeley and Costello lab at UCSF

Abtrasct in progress.

Nuñez Lab | Ioannidis (Ni-lab) at UC Berkeley

We use a deep convolutional neural network (CNN) that can capture the complex relation between CpG methylation and heritability. I hypothesize that a combination of convolutional and fully connected components can elucidate genetic and epigenetic features that establish epigenetic inheritance. Specifically, I predict that our results will support a model that heritability is not predictable solely on CpG Islands, CG content or CpG methylations in human gene promoters. Our novel approach will determine the complex relationship between CpG methylation and heritability to elucidate features that establish epigenetic memory. The data from this work is from here.

Patrauchan Lab at Oklahoma State University

Here, we studied the conservation of carP sequence and its occurrence in diverse phylogenetic groups of bacteria. In silico analysis revealed that carP and its two paralogues PA2017 and PA0319 are primarily present in P. aeruginosa and belong to the core genome of the species. We identified 155 single nucleotide alterations within carP, 42 of which lead to missense mutations with only three that affected the predicted 3D structure of the protein. PCR analyses with carP-specific primers detected P. aeruginosa specifically in 70 clinical and environmental samples. Sequence comparison demonstrated that carP is overall highly conserved in P. aeruginosa isolated from diverse environments. Such evolutionary preservation of carP illustrates its importance for P. aeruginosa adaptations to diverse environments and demonstrates its potential as a biomarker.

You can access my repository with protein models, figures and other files from the study here

• Sergio E. Mares , M. King, A. Kubo, A. Khavov, E. Lutter, N. Youssef and M. Patrauchan. carP, encoding a Ca 2+–regulated putative phytase, is evolutionarily conserved in Pseudomonas aeruginosa and has potential as a biomarker. Journal of Microbiology. December 2020. https://doi.org/10.1099/mic.0.001004

Patrauchan Lab at Oklahoma State University

Calcium is well known as a second messenger in eukaryotes, where Ca2+ signaling controls life-sustaining cellular processes. Although bacteria produce the components required for Ca2+ signaling, little is known about the mechanisms of bacterial Ca2+ signaling. Previously, we have identified a putative Ca2+-binding protein EfhP (PA4107) and CalC as proteins involved in the calcum network.

• Biraj B. Kayastha, A. Kubo, J. Burch-Konda, R. L. Dohmen, J. L. McCoy, R. R. Rogers, S. E. Mares , J. Bevere, A. Huckaby, W. Witt, S. Peng, B. Chaudhary, S. Mohanty, M. Barbier, G. Cook, J. Deng & M. Patrauchan. EF-hand protein, EfhP, specifically binds Ca2+ and mediates Ca2+ regulation of virulence in a human pathogen Pseudomonas aeruginosa. Nature Scientific reports. May 2022. https://doi.org/10.1038/s41598-022-12584-9

Welch Lab at UC Berkeley

Studies has shown that the AcMNPV protein actin rearrangement inducing factor-1 (Arif-1) is necessary and sufficient to induce the formation of cortical concentrations of polymerized actin, termed ventral aggregates (VAs), in cultured insect cells. Bombyx mori nucleopolyhedrosis virus (BmNPV), plays a role in enhancing systemic infection in B. mori larvae. However, it is still unknown if BmNPV Arif-1 is sufficient to cause the formation of VAs, or what role membrane anchoring regions of Arif-1 play in this process.

• Domokos I. Lauko, Taro Ohkawa, Sergio E. Mares , Matthew D. Welch. Baculovirus actin-rearrangement-inducing factor ARIF-1 induces the formation of dynamic clusters of invadosome structures. Molecular Biology of the Cell. July 2021. https://doi.org/10.1091/mbc.E20-11-0705

Youssef Lab at Oklahoma State University

Detailed analysis of 13 distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors, outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 million years ago (Mya) in response to the rise of soil as a distinct habitat on Earth.

• Chelsea L. Murphy, R. Yang, T. Decker, C. Cavalliere, V. Andreev, N. Bircher, J.Cornell, R. Dohmen, C. J. Pratt, A. Grinnell, J. Higgs, C. Jett, E. Gillett, R. Khadka, S. E. Mares , C. Meili, J. Liu, H. Mukhtar, Mostafa S. Elshahed, Noha H. Youssef. Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation. BioXRv. July 2021. https://doi.org/10.1101/2021.07.06.451402

Ortiz-Zauzaga Lab at University of Puerto Rico, Rio Piedras

Rhizosphere communities from similar niches and variants in geologies have shown to impact the composition and plant phenotype. Methodologies conducted to process metagenomics begin by relying on pre-filtering steps of redundant, low quality sequences, and assembly of contigs. Authors have claimed that metagenomic research is computationally constrained, and novel algorithms and techniques must be developed to further the field.

If you would like to play a game of chess add me as a friend in chess.com!