Publications

Showing 17 results for Author: William G. Alexander

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Sep, 2026

Journal

Evading native restriction-modification systems improves electroporation efficiency of the methanotroph Methylococcus capsulatus Bath

Methylococcus capsulatus Bath is a unique methanotrophic bacterium that uses methane (CH4) as a carbon and energy source and encodes the RubisCO enzyme for inorganic carbon assimilation, positioning it as an excellent candidate for biotechnology to capture atmospheric CH4 and carbon dioxide (CO2) for chemical production. However, a limited genetic toolbox and minimal high-…
Sep, 2026

Journal

Lignin to adipic acid in a high-yield chemical and biological redox process

Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin current…
Aug, 2026

Journal

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, imp…
Jun, 2026

Journal

Empirical evaluation of all unique Cas9 protospacers in E. coli reveal widespread functionality and rules for gRNA design

The Cas9 nuclease has become central to modern methods and technologies in synthetic biology, largely due to the ease with which it can be targeted to specific DNA loci via guide RNAs (gRNAs). Reports vary widely on the actual specificity of this targeting, with some studies observing 60% of gRNAs possessing no activity against the genome, yet an assumption persists within…
Feb, 2026

Journal

Complete genome sequences of five Variovorax strains isolated from the Populus rhizosphere and endosphere

We report the complete genome sequences of five Variovorax strains isolated from the roots of Populus species in greenhouse and field settings. Genome sizes range from 7.44 to 7.71 Mbp and encode 6,077–6,879 predicted protein-coding genes. These genome assemblies expand the known genomic catalog of Variovorax in plant-associated environments.
Jan, 2026

Journal

Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli

Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for…
Dec, 2025

Journal

Building an expanded bio-based economy through synthetic biology

The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconv…
Aug, 2025

Journal

Improving the Transformation Efficiency of Synechococcus sp. PCC 7002 via Methylome-Guided Premethylation of DNA

Cyanobacteria are promising microbial platforms for a diverse set of biotechnology applications, from living materials to photosynthetic chemical production, but are less well characterized than commonly engineered microbes such as Escherichia coli. This study facilitates genetic engineering in Synechococcus sp. PCC 7002, a fast-growing, halotolerant, and naturally compete…
Jul, 2025

Journal

Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

Bacterial DNA methylation is involved in diverse cellular functions ranging from modulation of gene expression, DNA repair, and restriction-modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation.…
Apr, 2025

Journal

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify t…
Feb, 2025

Journal

Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

Lignin contains a variety of interunit linkages, leading to a range of potential decomposition products that can be used as carbon and energy sources by microbes. β-O-4 linkages are the most common in native lignin, and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from β-O-4 dimer cleavage has…
Dec, 2024

Journal

Complete genome sequence of Promicromonospora sp. strain Populi, an actinobacterium isolated from Populus trichocarpa rhizosphere

Promicromonospora sp. strain Populi is an actinobacterium isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa. We completely sequenced its 5.2-Mbp chromosome using Oxford Nanopore long reads and predicted it to encode 4,685 proteins, 3 rRNA operons, and 54 tRNAs and noncoding RNAs.

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Publications

Evading native restriction-modification systems improves electroporation efficiency of the methanotroph Methylococcus capsulatus Bath

Lignin to adipic acid in a high-yield chemical and biological redox process

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

Empirical evaluation of all unique Cas9 protospacers in E. coli reveal widespread functionality and rules for gRNA design

Complete genome sequences of five Variovorax strains isolated from the Populus rhizosphere and endosphere

Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli

Building an expanded bio-based economy through synthetic biology

Improving the Transformation Efficiency of Synechococcus sp. PCC 7002 via Methylome-Guided Premethylation of DNA

Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

Complete genome sequence of Promicromonospora sp. strain Populi, an actinobacterium isolated from Populus trichocarpa rhizosphere