DSpace Repository :: Browsing by Author "Fierst, Janna L."

Browsing by Author "Fierst, Janna L."

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Acetylenotrophy: a hidden but ubiquitous microbial metabolism?
(Oxford University Press, 2018) Akob, Denise M.; Sutton, John M.; Fierst, Janna L.; Haase, Karl B.; Baesman, Shaun; Luther, George W., III; Miller, Laurence G.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa; University of Delaware
Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.
Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection in Drosophila
(Oxford University Press, 2021) Sheffield, Lakbira; Sciambra, Noah; Evans, Alysa; Hagedorn, Eli; Goltz, Casey; Delfeld, Megan; Kuhns, Haley; Fierst, Janna L.; Chtarbanova, Stanislava; University of Alabama Tuscaloosa; University of Alabama Birmingham
Advanced age in humans is associated with greater susceptibility to and higher mortality rates from infections, including infections with some RNA viruses. The underlying innate immune mechanisms, which represent the first line of defense against pathogens, remain incompletely understood. Drosophila melanogaster is able to mount potent and evolutionarily conserved innate immune defenses against a variety of microorganisms including viruses and serves as an excellent model organism for studying host-pathogen interactions. With its relatively short lifespan, Drosophila also is an organism of choice for aging studies. Despite numerous advantages that this model offers, Drosophila has not been used to its full potential to investigate the response of the aged host to viral infection. Here, we show that, in comparison to younger flies, aged Drosophila succumb more rapidly to infection with the RNA-containing Flock House virus due to an age-dependent defect in disease tolerance. Relative to younger individuals, we find that older Drosophila mount transcriptional responses characterized by differential regulation of more genes and genes regulated to a greater extent. We show that loss of disease tolerance to Flock House virus with age associates with a stronger regulation of genes involved in apoptosis, some genes of the Drosophila immune deficiency NF-kappa B pathway, and genes whose products function in mitochondria and mitochondrial respiration. Our work shows that Drosophila can serve as a model to investigate host-virus interactions during aging and furthermore sets the stage for future analysis of the age-dependent mechanisms that govern survival and control of virus infections at older age.
Caenorhabditis elegansdauers vary recovery in response to bacteria from natural habitat
(Wiley, 2020) Bubrig, Louis T.; Sutton, John M.; Fierst, Janna L.; University of Alabama Tuscaloosa
Many species use dormant stages for habitat selection by tying recovery to informative external cues. Other species have an undiscerning strategy in which they recover randomly despite having advanced sensory systems. We investigated whether elements of a species' habitat structure and life history can bar it from developing a discerning recovery strategy. The nematodeCaenorhabditis eleganshas a dormant stage called the dauer larva that disperses between habitat patches. On one hand,C. eleganscolonization success is profoundly influenced by the bacteria found in its habitat patches, so we might expect this to select for a discerning strategy. On the other hand,C. elegans' habitat structure and life history suggest that there is no fitness benefit to varying recovery, which might select for an undiscerning strategy. We exposed dauers of three genotypes to a range of bacteria acquired from the worms' natural habitat. We found thatC. elegansdauers recover in all conditions but increase recovery on certain bacteria depending on the worm's genotype, suggesting a combination of undiscerning and discerning strategies. Additionally, the worms' responses did not match the bacteria's objective quality, suggesting that their decision is based on other characteristics.
Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil
(American Society of Microbiology, 2022) Sutton, John M.; Bushman, Timothy J.; Akob, Denise M.; Fierst, Janna L.; University of Alabama Tuscaloosa; United States Department of the Interior; United States Geological Survey
We report the genome of Rhodococcus opacus strain MoAcy1 (DSM 44186), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of similar to 8 Mbp and two closed plasmids, with a G+C content of 67.3%.
Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei
(Oxford University Press, 2021) O'Connor, Christine H.; Sikkink, Kristin L.; Nelson, Thomas C.; Fierst, Janna L.; Cresko, William A.; Phillips, Patrick C.; University of Oregon; University of Alabama Tuscaloosa; University of Minnesota Twin Cities; University of Montana
The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. The structure of the genotype-phenotype maps is critical because pleiotropic effects can generate widespread correlated responses to selection and potentially restrict the extent of evolutionary change. In this study, we use experimental evolution to dissect the genetic architecture of natural variation for acute heat stress and oxidative stress response in the nematode Caenorhabiditis remanei. Previous work in the classic model nematode Caenorhabiditis elegans has found that abiotic stress response is controlled by a handful of genes of major effect and that mutations in any one of these genes can have widespread pleiotropic effects on multiple stress response traits. Here, we find that acute heat stress response and acute oxidative response in C. remanei are polygenic, complex traits, with hundreds of genomic regions responding to selection. In contrast to expectation from mutation studies, we find that evolved acute heat stress and acute oxidative stress response for the most part display independent genetic bases. This lack of correlation is reflected at the levels of phenotype, gene expression, and in the genomic response to selection. Thus, while these findings support the general view that rapid adaptation can be generated by changes at hundreds to thousands of sites in the genome, the architecture of segregating variation is likely to be determined by the pleiotropic structure of the underlying genetic networks.
Decontaminating eukaryotic genome assemblies with machine learning
(BMC, 2017) Fierst, Janna L.; Murdock, Duncan A.; University of Alabama Tuscaloosa
Background: High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few existing methods for rigorously decontaminating eukaryotic assemblies. Those that do exist filter sequences based on nucleotide similarity to contaminants and risk eliminating sequences from the target organism. Results: We introduce a novel application of an established machine learning method, a decision tree, that can rigorously classify sequences. The major strength of the decision tree is that it can take any measured feature as input and does not require a priori identification of significant descriptors. We use the decision tree to classify de novo assembled sequences and compare the method to published protocols. Conclusions: A decision tree performs better than existing methods when classifying sequences in eukaryotic de novo assemblies. It is efficient, readily implemented, and accurately identifies target and contaminant sequences. Importantly, a decision tree can be used to classify sequences according to measured descriptors and has potentially many uses in distilling biological datasets.
Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp Strain SFB93
(American Society of Microbiology, 2017) Akob, Denise M.; Baesman, Shaun M.; Sutton, John M.; Fierst, Janna L.; Mumford, Adam C.; Shrestha, Yesha; Poret-Peterson, Amisha T.; Bennett, Stacy; Dunlap, Darren S.; Haase, Karl B.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa; United States Department of Agriculture (USDA); Boeing
Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N(2)ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N(2)ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N(2)ase. Diazotrophic growth was observed under N-2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N(2)ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days. IMPORTANCE Here we show that a single Pelobacter strain can grow via acetylene fermentation and carry out nitrogen fixation, using the only two enzymes known to transform acetylene. These findings provide new insights into acetylene transformations and adaptations for nutrient (C and N) and energy acquisition by microorganisms. Enhanced understanding of acetylene transformations (i.e., extent, occurrence, and rates) in modern environments is important for the use of acetylene as a potential biomarker for extraterrestrial life and for degradation of anthropogenic contaminants.
Exploring Genetic Diversity and Bioinformatic Strategies for Complex Data in the Genomic Revolution
(University of Alabama Libraries, 2022) Adams, Paula Elizabeth; Lozier, Jeffrey D.; Fierst, Janna L.; University of Alabama Tuscaloosa
Over the past twenty-five years, we have gone from completing the first eukaryotic genome assembly to the new goal of sequencing and completing genome assemblies representing all known taxa on Earth. Genomic data has improved research across fields of biology from evolution and genetics to medicine and conservation. As genomic technologies rapidly improve and the amount of genomic data explodes, the need for complex genomic analysis tools has given rise to the field of Bioinformatics. Strategies are needed to address sequence read quality, sequence alignment, genomic variation estimation from sequence data, de-novo genome assembly, post assembly quality assessments and quantification, and genomic comparisons across species. Here we explore complexities in genomic analyses and how using large-scale genomic data can help us better understand the genomic variation that gives rise to the diversity of life. We show that using pooled-sequencing data we can assess recovery from inbreeding depression in Caenorhabditis remanei and the genomic changes that take place during inbreeding. We find that C. remanei is unable to recover from inbreeding even after 300 generations of recovery at large population size. Despite 23 generations of inbreeding, large portions of the genome remained heterozygous, suggesting that pseudo-overdominance may be preventing the ability to purge deleterious mutations. Our results indicate that recovery from inbreeding in the presence of high genetic load is unlikely. One improvement in genomics is the ability to use long-read sequencing to address complex genomic architecture. Using long-read, third-generation sequencing (TGS) generated with Oxford Nanopore Technologies (ONT) we assembled and identified novel insertions in Caenorhabditis elegans mutants, used for studies of human disease phenotypes. While genome assembly has rapidly improved, identifying contamination post-assembly has remained challenging. We show that using supervised machine-learning ensemble decision tree methods we can quickly and accurately identify contamination in genome assemblies. As genomic resources continue to improve and databases grow, developing new tools and analysis methods that can harness this large-scale genomic data will reveal a greater understanding of organisms across the tree of life.
Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms
(Oxford University Press, 2023) Adams, Paula E.; Eggers, Victoria K.; Millwood, Joshua D.; Sutton, John M.; Pienaar, Jason; Fierst, Janna L.; University of Alabama Tuscaloosa; Auburn University; Florida International University
Genome size has been measurable since the 1940s but we still do not understand genome size variation. Caenorhabditis nematodes show strong conservation of chromosome number but vary in genome size between closely related species. Androdioecy, where populations are composed of males and self-fertile hermaphrodites, evolved from outcrossing, female-male dioecy, three times in this group. In Caenorhabditis, androdioecious genomes are 10-30% smaller than dioecious species, but in the nematode Pristionchus, androdioecy evolved six times and does not correlate with genome size. Previous hypotheses include genome size evolution through: 1) Deletions and "genome shrinkage" in androdioecious species; 2) Transposable element (TE) expansion and DNA loss through large deletions (the "accordion model"); and 3) Differing TE dynamics in androdioecious and dioecious species. We analyzed nematode genomes and found no evidence for these hypotheses. Instead, nematode genome sizes had strong phylogenetic inertia with increases in a few dioecious species, contradicting the "genome shrinkage" hypothesis. TEs did not explain genome size variation with the exception of the DNA transposon Mutator which was twice as abundant in dioecious genomes. Across short and long evolutionary distances Caenorhabditis genomes evolved through small structural mutations including gene-associated duplications and insertions. Seventy-one protein families had significant, parallel decreases across androdioecious Caenorhabditis including genes involved in the sensory system, regulatory proteins and membrane-associated immune responses. Our results suggest that within a dynamic landscape of frequent small rearrangements in Caenorhabditis, reproductive mode mediates genome evolution by altering the precise fates of individual genes, proteins, and the phenotypes they underlie.
Metabolic engineering and process development in butanol production with clostridium tyrobutyricum
(University of Alabama Libraries, 2016) Ma, Chao; Liu, X. Margaret; University of Alabama Tuscaloosa
As a sustainable and environmentally friendly biofuel, biobutanol is a potential substitute for gasoline without any engine modification. The multiple Omics studies were applied to evaluate the change of the expression of host protein and intracellular metabolism in Clostridium tyrobutyricum in response to butanol production. The key enzymes related to carbon balance (i.e. acid and solvent end products and carbohydrates in central pathway), redox balance, energy balance, and cell growth has been studied. It was found that rebalancing both carbon and redox was critical to improve butanol production. These findings were used to achieve high production of biobutanol via integrated metabolic cell-process engineering (MCPE). In a comparative genomics study, the wild type C. tyrobutyricum, the metabolically engineered mutant with down-regulated acetate kinase and evolutionarily engineered strain showing fast cell growth were used to evaluated in butyrate fermentation at pH 6.0 and 37 oC. It was found that the cell growth rate was increased by 61-100% and butyrate productivity was improved by 44-102% by the evolutionarily engineered strain. To understand the mechanism of butyric acid production and cell growth regulation in engineered C. tyrobutyricum mutant, a comparative genomics study was performed. It was concluded that the genome mutations in transcription, translation, amino acid and phosphate transportation and cofactor binding might play important role in regulating cell growth and butyric acid production. Comparative proteomics, which covered 78.1% of open reading frames and 95% of core enzymes, was performed using wild type, mutant producing 37.30 g/L of butyrate and mutant producing 16.68 g/L of butanol. Carbon regulation enzymes in the central metabolic pathway that correlated with butanol production were identified, including thiolase (thl), acetyl-CoA acetyltransferase (ato), 3-hydroxybutyryl-CoA dehydrogenase (hbd) and crotonase (crt). The apparent imbalance of energy and redox was also observed due to the downregulation of acids production and the addition of butanol synthesis pathway. The understanding of the mechanism of carbon redistribution enabled the rational design of metabolic cell and process engineering strategies were revealed to achieve high butanol production in C. tyrobutyricum. With the fundamental understanding, the C. tyrobutyricum was metabolically engineered by rebalancing carbon and redox simultaneously. The overexpression of aldehyde/alcohol dehydrogenase (adhE2) and formate dehydrogenase (fdh) improved butanol titer by 2.15 fold in serum bottle and 2.72 fold in bioreactor. In addition, the proteomics study and metabolite analysis showed that more than 90% of the amino acid in the medium was consumed before the cell entered the stationary phase and some enzymes involved in amino acid metabolism had low expression in butanol producing mutant. Extra yeast extract or casamino acids was fed to the free-cell fermentation the mid-log phase, improving the butanol titer to more than 18 g/L compared to 14 g/L without extra nitrogen supplement. The rational metabolic cell-process engineering facilitated with systems biology understanding was demonstrated a powerful approach in butanol production. Finally, the C. tyrobutyricum was further rationally engineered by integrating multiple regualtors, including 1) heterologous NAD+-fdh that provides extra reducing power, 2) the thiolase (thl) that redirects metabolic flux from C2 to C4, and 3) AdhE2. Two novel mutatns, ACKKO-adhE2-fdh and ACKKO-thl-adhE2-fdh, were constructed and produced 18.37 g/L and 19.41 g/L, respectively. This study demonstrated that systems biology-based metabolic cell-process engineering of C. tyrobutyricum enabled a high production of butanol.
De NovoGenome Assemblies for Three North American Bumble Bee Species:Bombus bifarius,Bombus vancouverensis, andBombus vosnesenskii
(Oxford University Press, 2020) Heraghty, Sam D.; Sutton, John M.; Pimsler, Meaghan L.; Fierst, Janna L.; Strange, James P.; Lozier, Jeffrey D.; University of Alabama Tuscaloosa; Ohio State University
Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America,Bombus bifarius,Bombus vancouverensis, andBombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We presentde novogenome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 - 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome,Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.
Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations
(Oxford University Press, 2022) Adams, Paula E.; Crist, Anna B.; Young, Ellen M.; Willis, John H.; Phillips, Patrick C.; Fierst, Janna L.; University of Alabama Tuscaloosa; UDICE-French Research Universities; Universite Paris Cite; Le Reseau International des Instituts Pasteur (RIIP); Institut Pasteur Paris; University of Oregon; Florida International University
The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Haploid organisms and selfing organisms like the nematode Caenorhabditis elegans are capable of rapid recovery from the fixation of novel deleterious mutation; however, the potential for recovery and genomic consequences of inbreeding in diploid, outcrossing organisms are not well understood. We sought to answer two questions: 1) Can a diploid, outcrossing population recover from inbreeding via standing genetic variation and new mutation? and 2) How does allelic diversity change during recovery? We inbred C. remanei, an outcrossing relative of C. elegans, through brother-sister mating for 30 generations followed by recovery at large population size. Inbreeding reduced fitness but, surprisingly, recovery from inbreeding at large populations sizes generated only very moderate fitness recovery after 300 generations. We found that 65% of ancestral single nucleotide polymorphisms (SNPs) were fixed in the inbred population, far fewer than the theoretical expectation of similar to 99%. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous, and reproductive systems changed reproducibly across replicates, indicating that strong selection for fitness recovery does exist. Our results indicate that recovery from inbreeding depression via standing genetic variation and mutation is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for recovery of small populations.
Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments
(Microbiology Society, 2021) Baesman, Shaun M.; Sutton, John M.; Fierst, Janna L.; Akob, Denise M.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa
A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93(T), was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93(T) was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 degrees C, pH 6.3-8.5 and in the presence of 10-45 g l(-1) NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93(T) represented a member of the genus Syntrophotalea with highest 16S rRNA gene sequence similarities to Syntrophotalea acetylenica DSM 3246(T) (96.6 %), Syntrophotalea carbinolica DSM 2380(T) (96.5 %), and Syntrophotalea venetiana DSM 2394(T) (96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93(T) had low genome-wide average nucleotide identity (81?87.5 %) and <70 % digital DNA-DNA hybridization value with other members of the genus Syntrophotalea. The phylogenetic position of SFB93(T) within the family Syntrophotaleaceae and as a novel member of the genus Syntrophotalea was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species, Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93(T) (=DSM 106009(T)=JCM 33327(T)=ATCC TSD-118(T)) as the type strain.
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools
(Frontiers, 2015) Fierst, Janna L.; University of Alabama Tuscaloosa
Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.

Browsing by Author "Fierst, Janna L."

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