Nicholas A. Kovacs' Scientific Gallery
Biological Data Scientist | Bioinformatics PhD candidate | Adviser: Dr. Loren Williams | Georgia Tech

Here are some examples of figures I have made for scientific publications that I co-authored. The experimental data was performed by my workers, but the figures were made by me, as well as much of the analysis.

The LSU rRNA of S. cerevisiae, highlighting expansion segments. A) Secondary structure and B) three dimensional structure of LSU rRNA. Common core rRNA, which is common to all cytoplasmic ribosomes, is dark gray. Expansions of S. cerevisiae rRNA from the common core are green, except for expansion segment 7 (ES7) which is pink and is enclosed in a shaded box in panel A. For panel B, the top shows the back view of the LSU, and the bottom shows the front (interfacial) view. Locations of structural hallmarks such as the peptidyl transferase center (PTC), the central protuberance, stalk and tunnel exit are indicated. Thick dashed lines in panel A represent RNA that is not observed in the three dimensional structure and is absent in panel B.

ES7 rRNA interacts with ribosomal proteins in the assembled ribosome. A) Secondary structure and B) three dimensional structure of S. cerevisiae ES7. Interactions of ribosomal proteins with ES7 are mapped on to the A) secondary and B) three dimensional structures. In panel A, nucleotides are colored by the protein with which they interact. Nucleotides not present in the three dimensional structure are shown in gray. In panel B, amino acids interacting with ES7 rRNA are colored by the proteins to which they belong. Coordinates are from PDB entry 4V88.

SHAPE reactivities in Na+ only and in Na+/Mg2+ reveal Mg2+-dependent structural changes of S. cerevisiae ES7 rRNA. SHAPE reactivities are mapped onto S. cerevisiae ES7 rRNA secondary structure. Shape reactivities were determined in presence of A) Na+ or B) Na+ and Mg2+. Orange or red nucleotides show moderate to high SHAPE reactivity. Ivory or white nucleotides show low or no SHAPE reactivity. C) Mg2+ induces changes in SHAPE reactivity. Nucleotides in red show increased reactivity in the presence of Mg2+. Nucleotides in blue show decreased reactivity. These figures were generated with RiboVision. All samples contained 200 mM NaOAc, 50 mM NaHEPES at pH 8.

MS proteomics data of cell lysate pull-down assay of ES 7 in S. cerevisiae.

Nucleotide-level Shannon entropies mapped by color onto the secondary structure of the SSU rRNA of E. coli. The lowest value (0) indicates universal conservation over the entire tree of life (dark blue). The highest value (2) indicates uniform variation and / or high gap frequency (red). The SSU domains (3’M, 3’m, 5’, and C) and helices are labeled. Nucleotides are numbered.

Eukaryotic-specific ribosomal protein contacts mapped onto the secondary structure of S. cerevisiae. Ribosomal protein contacts are shown within a cutoff distance of 3.4Å. The initial figure was prepared using RiboVision. Eukaryotic expansion segments are highlighted by black outlines. Ribosomal proteins that contact eukaryotic expansion segments are bold in the legend.