Jessica Bowman

• Georgia Institute of Technology

Many open questions about the origins of life are centred on the generation of complex chemical species. Past work has characterized specific chemical reactions that might lead to biological molecules. Here we establish an experimental model of chemical evolution to investigate general processes by which chemical systems continuously change. We use...

Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of complex and functional chemical species. The processes that generated the spectacular biopolymers that underlay biology demonstrate an untapped, by modern science, creative potential. We have es...

Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of new complex and functional chemical species. The spectacular polymers that underlay biology demonstrate an untapped, by modern science, creative potential. We hypothesized that prebiotic chemica...

Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of new complex and functional chemical species. The spectacular polymers that underlay biology demonstrate an untapped, by modern science, creative potential. We hypothesized that prebiotic chemica...

Widespread testing for the presence of the novel coronavirus SARS-CoV-2 in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse trans...

Widespread testing for the presence novel coronavirus SARS-CoV-2 in patients remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. The early testing shortfall in some parts of the US can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quanti...

Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the...

The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologue...

Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg ²⁺ as a primary mediator of ribosomal structure and function. Possible contributions of Fe ²⁺ as a ribosomal cofactor have been largely overlooked, despite t...

Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We observe that all three biopolymer...

Significance Ribosomes are found in every living organism, where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ∼4 billion years ago when ecosystems were anoxic and metal-rich...

Today, Mg ²⁺ is an essential cofactor with diverse structural and functional roles in life’s oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O 2 , high Fe ²⁺ , high Mn ²⁺ ) can revert the ribosome to a functional ancestral state. First, SHAPE (Selective 2’ H ydroxyl A cylation analyzed by P rim...

There is broad consensus that during and immediately following the origin of life, RNA was the single biopolymer or was among a small group of cooperating biopolymers. During the origin of life, the Archean Earth was anoxic; Fe²⁺ was abundant and relatively benign. We hypothesize that RNA used Fe²⁺ as a cofactor instead of, or along with, Mg²⁺ duri...

Virus Like Particles (VLPs) are devices for RNA packaging, protection and delivery, with utility in fundamental research, drug discovery, and disease treatment. Using E. coli for combined expression and packaging of non-viral RNAs into Qβ VLPs, we investigated the extent of chemical protection conferred by packaging of RNA in VLPs. We also probed r...

Life originated in an anoxic, Fe 2+-rich environment. We hypothesize that on early Earth, Fe 2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as processing of nucleic acids by protein enzymes. In this model, Mg 2+ replaced Fe 2+ as the primary cofactor for nucleic acids in parallel with known metal sub...

An RNA World that predated the modern world of polypeptide and polynucleotide is one of the most widely accepted models in origin of life research. In this model, the translation system shepherded the RNA World into the extant biology of DNA, RNA, and protein. Here, we examine the RNA World Hypothesis in the context of increasingly detailed informa...

RiboVision is a visualization and analysis tool for simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component to life responsible for synthesis of p...

Mg(2+) is essential for RNA folding and catalysis. However, for the first 1.5 billion years of life on Earth RNA inhabited an anoxic Earth with abundant and benign Fe(2+). We hypothesize that Fe(2+) was an RNA cofactor when iron was abundant, and was substantially replaced by Mg(2+) during a period known as the 'great oxidation', brought on by phot...

Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-li...

Satellite tobacco mosaic virus (STMV) is a T = 1 icosahedral virus with a single-stranded RNA genome. It is widely accepted that the RNA genome plays an important structural role during assembly of the STMV virion. While the encapsidated form of the RNA has been extensively studied, less is known about the structure of the free RNA, aside from a pu...

Quantitative correlation between peak area data in overlapping primer reads. This demonstrates that signal decay in the regions of overlapping data is similar. Pearson’s r-values are shown. (TIF)

Predicted secondary structures for STMV RNA. SHAPE MFE and Subopts #1–9 were predicted using the SHAPE experimental data as constraints. Default MFE was predicted without the SHAPE data. Each secondary structure is shown as an arc diagram, in which the sequence is arranged along a horizontal line and base pairs are shown as arcs connecting the corr...

Primers used to analyze the STMV RNA. (PDF)

In vitro transcribed STMV RNA runs as a single band on a native gel. STMV RNA is run on a 1% agarose gel. No sample was loaded in lanes 2 or 4. Lanes 1 and 3 contain STMV RNA in SHAPE probing buffer without Mg2+ (50 mM HEPES pH 8.0, 200 mM sodium acetate pH 8.0) and lane 5 contains STMV RNA in 100 mM Tris-HCl pH 8.0. All samples were heated to 90°C...

(PDF)

Signal decay correction. The regions of overlapping data from different primers are not on the same scale (top). After scaling all of the primers to one another such that the overlapping regions match up, the resulting signal decays rapidly (middle). After correcting for signal decay, the overlapping regions are in agreement (bottom). (TIF)

Combined peak area signal after decay correction. The thick black line fitted to the corrected peak area data has a slope of zero, ensuring that intense values in the beginning, middle, and end of the signal are of uniform height. (TIF)

Preparing conventional DNA templates for in vitro RNA transcription involves PCR amplification of the DNA gene coding for the RNA of interest from plasmid or genomic DNA, subsequent amplification with primers containing a 5' T7 promoter region, and confirmation of the amplified DNA sequence. Complications arise in applications where long, nonnative...

Mg²⁺ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments tha...

8% polyacryalamide – 8 M urea denaturing gels showing L1 Ribozyme Ligase reaction progress. Only species tagged with 5′-Cy3 dye (substrate and product) are visible. The L1 Ribozyme Ligase is visible when the gel is stained with cyber gold or ethidium. The reaction rate increases when [Fe2+] is increased from 100 µM (LH panel, reaction product obser...

Electronic energies, interaction energies and the corresponding counterpoise-corrected interaction energies calculated at the (U)B3LYP/6–311++G(d,p) level of theory within the framework of IEFPCM in water. (DOCX)

RNA Synthesis and Purification. (DOCX)

Electronic configurations of Mg2+ and Fe2+ in the RNA2− -Mg2+(H2O)4 and RNA2− -Fe2+(H2O)4 complexes as revealed by the NBO at the (U)B3LYP/6–31G(d,p) level of theory. (DOCX)

Highlights ► Mg2+ is a uniquely suited partner for RNA due to its ability to localize water molecules and pack RNA phosphate groups. ► Current and past work supports the ubiquity of Mg2+, both diffuse and coordinated, in RNA folding and catalysis. ► Review of recent literature reveals inaccuracy in the treatment of RNA-divalent cation interactions...

The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structura...

Magnesium plays a special role in RNA function and folding. Although water is magnesium's most common first-shell ligand, the oxyanions of RNA have significant affinity for magnesium. Here we provide a quantum mechanical description of first-shell RNA-magnesium and DNA-magnesium interactions, demonstrating the unique features that characterize the...

In RNA, A-form helices are commonly terminated by tetraloops or 3' dangling ends. Aside from helices themselves, these helix-breaking motifs appear to be among the most frequent and repetitive structural elements of large folded RNAs. We show here that within a frequent type of tetraloop, cGNRAg (G is guanine, N is any base, R is purine, A is adeni...

We discuss the molecular paleontology of the ribosomes of H. marismortui and T. thermophilus, which represent lineages that diverged at the LUCA, several billions of years ago.

EPA guidance defines an exceedance in water quality standards as an inconsistency between ambient conditions and the combined three elements of numeric water quality criteria: magnitude, duration and frequency. A single sample exceeding a numeric criterion is defined as a digression and an average exceeding a criterion an excursion. EPA guidance al...

Over the last decade substantial research has been conducted to characterize, control and cost-effectively mitigate urban area wet weather bacteria for compliance with CSO, SSO, blending and stormwater policies and regulations. Approaches to disinfecting wastewaters impacted by wet weather flows, including chemical and UV disinfection following mul...

Over the last decade, substantial research has been conducted to characterize, control and optimize cost-effective mitigation of urban area wet weather pathogens. Disinfection approaches including chlorination and UV disinfection were tested in Atlanta and Columbus, GA and Syracuse, NY under variable wet weather pollutant loadings following treatme...

Under the Middle Chattahoochee Watershed Plan, the Columbus Water Work's adaptive TMDL Implementation Planning strategy utilizes comprehensive watershed modeling and implementation of innovative non-point source BMPs to address TMDLs and protect beneficial uses of two waterways in Columbus, GA. Calibrated BASINS modeling is used to demonstrate comp...