Research and Publications - Department of Biological Sciences

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Aboveground competition influences density-dependent effects of cordgrass on sediment biogeochemistry
(Wiley, 2022) Walker, Janet B.; Rinehart, Shelby; Greenberg-Pines, Gabriel; White, Wendi K.; DeSantiago, Ric; Lipson, David A.; Long, Jeremy D.; San Diego State University; Southern California Coastal Water Research Project; University of Alabama Tuscaloosa; University of British Columbia; University of Massachusetts Boston; University of California Davis
Interspecific interactions between plants influence plant phenotype, distribution, abundance, and community structure. Each of these can, in turn, impact sediment biogeochemistry. Although the population and community level impacts of these interactions have been extensively studied, less is known about their effect on sediment biogeochemistry. This is surprising given that many plants are categorized as foundation species that exert strong control on community structure. In southern California salt marshes, we used clipping experiments to manipulate aboveground neighbor presence to study interactions between two dominant plants, Pacific cordgrass (Spartina foliosa) and perennial pickleweed (Sarcocornia pacifica). We also measured how changes in cordgrass stem density influenced sediment biogeochemistry. Pickleweed suppressed cordgrass stem density but had no effect on aboveground biomass. For every cordgrass stem lost per square meter, porewater ammonium increased 0.3-1.0 mu M. Thus, aboveground competition with pickleweed weakened the effects of cordgrass on sediment biogeochemistry. Predictions about plant-soil feedbacks, especially under future climate scenarios, will be improved when plant-plant interactions are considered, particularly those containing dominant and foundation species.
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.
Activation of the cnidarian oxidative stress response by ultraviolet radiation, polycyclic aromatic hydrocarbons and crude oil
(Company of Biologists, 2014) Tarrant, A. M.; Reitzel, A. M.; Kwok, C. K.; Jenny, M. J.; Woods Hole Oceanographic Institution; University of North Carolina; University of North Carolina Charlotte; Chinese University of Hong Kong; University of Alabama Tuscaloosa
Organisms are continuously exposed to reactive chemicals capable of causing oxidative stress and cellular damage. Antioxidant enzymes, such as superoxide dismutases (SODs) and catalases, are present in both prokaryotes and eukaryotes and provide an important means of neutralizing such oxidants. Studies in cnidarians have previously documented the occurrence of antioxidant enzymes (transcript expression, protein expression and/or enzymatic activity), but most of these studies have not been conducted in species with sequenced genomes or included phylogenetic analyses, making it difficult to compare results across species due to uncertainties in the relationships between genes. Through searches of the genome of the sea anemone Nematostella vectensis Stephenson, one catalase gene and six SOD family members were identified, including three copper/zinc-containing SODs (CuZnSODs), two manganese-containing SODs (MnSODs) and one copper chaperone of SOD (CCS). In 24 h acute toxicity tests, juvenile N. vectensis showed enhanced sensitivity to combinations of ultraviolet radiation (UV) and polycyclic aromatic hydrocarbons (PAHs, specifically pyrene, benzo[ a] pyrene and fluoranthene) relative to either stressor alone. Adult N. vectensis exhibited little or no mortality following UV, benzo[ a] pyrene or crude oil exposure but exhibited changes in gene expression. Antioxidant enzyme transcripts were both upregulated and downregulated following UV and/or chemical exposure. Expression patterns were most strongly affected by UV exposure but varied between experiments, suggesting that responses vary according to the intensity and duration of exposure. These experiments provide a basis for comparison with other cnidarian taxa and for further studies of the oxidative stress response in N. vectensis.
Adapterama III: Quadruple-Indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)
(PeerJ, 2019) Bayona-Vasquez, Natalia J.; Glenn, Travis C.; Kieran, Troy J.; Pierson, Todd W.; Hoffberg, Sandra L.; Scott, Peter A.; Bentley, Kerin E.; Finger, John W.; Louha, Swarnali; Troendle, Nicholas; Diaz-Jaimes, Pindaro; Mauricio, Rodney; Faircloth, Brant C.; University of Georgia; Universidad Nacional Autonoma de Mexico; University of Alabama Tuscaloosa; Louisiana State University; University of Tennessee Knoxville; Columbia University; University of California Los Angeles; Auburn University
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
Advances, applications, and prospects in aquatic botany
(Wiley, 2022) Cherry, Julia A.; Pec, Gregory J.; University of Alabama Tuscaloosa; University Nebraska Kearney
Aggression and Related Behavioral Traits: The Impact of Winning and Losing and the Role of Hormones
(Oxford University Press, 2012) Chang, Ching; Li, Cheng-Yu; Earley, Ryan L.; Hsu, Yuying; National Taiwan Normal University; University of Alabama Tuscaloosa
A suite of correlated behaviors reflecting between-individual consistency in behavior across multiple situations is termed a "behavioral syndrome." Researchers have suggested that a cause for the correlation between different behaviors might lie in the neuroendocrine system. In this study, we examined the relationships between aggressiveness (a fish's readiness to perform gill display to its mirror image) and each of boldness (the readiness to emerge from a shelter), exploratory tendency (the readiness to approach a novel shelter), and learning performance (the probability of entering the correct reservoir in a T-maze test) in a mangrove rivulus, Kryptolebias marmoratus. We explored the possibility that the relationships between them arise because these behaviors are all modulated by cortisol and testosterone. We also tested the stability of the relationships between these behaviors shortly after using a winning or losing experience to alter individuals' aggressiveness. The results were that aggressiveness correlated positively with boldness and the tendency to explore, and that these three behavioral traits were all positively correlated with pre-experience testosterone levels. Aggressiveness and boldness also positively correlated with pre-experience cortisol levels; exploratory tendency did not. The relationship between aggressiveness and boldness appeared to be stronger than that between either of them and exploratory tendency. These results suggest that testosterone and cortisol play important roles in mediating the correlations between these behavioral traits. Learning performance was not significantly correlated with the other behavioral traits or with levels of testosterone or cortisol. Recent experience in contests influenced individuals' aggressiveness, tendency to explore, and learning performance but not their boldness; individuals that received a winning experience were quicker to display to their mirror image and performed better in the learning task but were slower to approach a novel object than were individuals that lost. Contest experience did not, however, significantly influence the relationships between aggressiveness and any of boldness, exploratory tendency, or learning performance. The results show that the individual components of a suite of correlated behaviors can preserve a flexibility to respond differently to environmental stimuli.
Ancient Polyploidy and Genome Evolution in Palms
(Oxford University Press, 2019) Barrett, Craig F.; McKain, Michael R.; Sinn, Brandon T.; Ge, Xue-Jun; Zhang, Yuqu; Antonelli, Alexandre; Bacon, Christine D.; West Virginia University; University of Alabama Tuscaloosa; Chinese Academy of Sciences; South China Botanical Garden, CAS; University of Gothenburg; Royal Botanic Gardens, Kew
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
ApoE-associated modulation of neuroprotection from A beta-mediated neurodegeneration in transgenic Caenorhabditis elegans
(Company of Biologists, 2019) Griffin, Edward F.; Scopel, Samuel E.; Stephen, Cayman A.; Holzhauer, Adam C.; Vaji, Madeline A.; Tuckey, Ryan A.; Berkowitz, Laura A.; Caldwell, Kim A.; Caldwell, Guy A.; University of Alabama Tuscaloosa; University of Alabama Birmingham
Allele-specific distinctions in the human apolipoprotein E (APOE) locus represent the best-characterized genetic predictor of Alzheimer's disease (AD) risk. Expression of isoform APOE epsilon 2 is associated with reduced risk, while APOE epsilon 3 is neutral and APOE epsilon 4 carriers exhibit increased susceptibility. Using Caenorhabditis elegans, we generated a novel suite of humanized transgenic nematodes to facilitate neuronal modeling of amyloid-beta peptide (A beta) co-expression in the context of distinct human APOE alleles. We found that co-expression of human APOE epsilon 2 with A beta attenuated A beta-induced neurodegeneration, whereas expression of the APOE epsilon 4 allele had no effect on neurodegeneration, indicating a loss of neuroprotective capacity. Notably, the APOE epsilon 3 allele displayed an intermediate phenotype; it was not neuroprotective in young adults but attenuated neurodegeneration in older animals. There was no functional impact from the three APOE isoforms in the absence of A beta co-expression. Pharmacological treatment that examined neuroprotective effects of APOE alleles on calcium homeostasis showed allele-specific responses to changes in ER-associated calcium dynamics in the A beta background. Additionally, A beta suppressed survival, an effect that was rescued by APOE epsilon 2 and APOE epsilon 3, but not APOE epsilon 4. Expression of the APOE alleles in neurons, independent of A beta, exerted no impact on survival. Taken together, these results illustrate that C. elegans provides a powerful in vivo platform with which to explore how AD-associated neuronal pathways are modulated by distinct APOE gene products in the context of A beta-associated neurotoxicity. The significance of both ApoE and A beta to AD highlights the utility of this new pre-clinical model as a means to dissect their functional inter-relationship.
Arabidopsis Toxicos en Levadura 12 (ATL12): A Gene Involved in Chitin-Induced, Hormone-Related and NADPH Oxidase-Mediated Defense Responses
(MDPI, 2021) Kong, Feng; Guo, Tingwei; Ramonell, Katrina M.; University of Alabama Tuscaloosa; University of Southern California
Plants, as sessile organisms, have evolved complex systems to respond to changes in environmental conditions. Chitin is a Pathogen-Associated-Molecular Pattern (PAMP) that exists in the fungal cell walls, and can be recognized by plants and induce plant pattern-triggered immunity (PTI). Our previous studies showed that Arabidopsis Toxicos en Levadura 12 (ATL12) is highly induced in response to fungal infection and chitin treatment. We used the model organism Arabidopsis thaliana to characterize ATL12 and explore its role in fungal defense. Histochemical staining showed that pATL12-GUS was continually expressed in roots, leaves, stems, and flowers. Subcellular co-localization of the ATL12-GFP fusion protein with the plasma membrane-mcherry marker showed that ATL12 localizes to the plasma membrane. Mutants of atl12 are more susceptible to Golovinomyces cichoracearum infection, while overexpression of ATL12 increased plant resistance to the fungus. ATL12 is highly induced by chitin after two hours of treatment and ATL12 may act downstream of MAPK cascades. Additionally, 3,3 '-diaminobenzidine (DAB) staining indicated that atl12 mutants generate less reactive oxygen species compared to wild-type Col-0 plants and RT-PCR indicated that ATL12-regulated ROS production may be linked to the expression of respiratory burst oxidase homolog protein D/F (AtRBOHD/F). Furthermore, we present evidence that ATL12 expression is upregulated after treatment with both salicylic acid and jasmonic acid. Taken together, these results suggest a role for ATL12 in crosstalk between hormonal, chitin-induced, and NADPH oxidase-mediated defense responses in Arabidopsis.
Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense
(Royal Society of London, 2019) Greenspan, Sasha E.; Lyra, Mariana L.; Migliorini, Gustavo H.; Kersch-Becker, Monica F.; Bletz, Molly C.; Lisboa, Cybele Sabino; Pontes, Mariana R.; Ribeiro, Luisa P.; Neely, Wesley J.; Rezende, Felipe; Romero, Gustavo Q.; Woodhams, Douglas C.; Haddad, Celio F. B.; Toledo, Luis Felipe; Becker, C. Guilherme; University of Alabama Tuscaloosa; Universidade Estadual Paulista; University of Massachusetts Boston; Universidade Estadual de Campinas
The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness.
The asparagus genome sheds light on the origin and evolution of a young Y chromosome
(Nature Portfolio, 2017) Harkess, Alex; Zhou, Jinsong; Xu, Chunyan; Bowers, John E.; Van der Hulst, Ron; Ayyampalayam, Saravanaraj; Mercati, Francesco; Riccardi, Paolo; McKain, Michael R.; Kakrana, Atul; Tang, Haibao; Ray, Jeremy; Groenendijk, John; Arikit, Siwaret; Mathioni, Sandra M.; Nakano, Mayumi; Shan, Hongyan; Telgmann-Rauber, Alexa; Kanno, Akira; Yue, Zhen; Chen, Haixin; Li, Wenqi; Chen, Yanling; Xu, Xiangyang; Zhang, Yueping; Luo, Shaochun; Chen, Helong; Gao, Jianming; Mao, Zichao; Pires, J. Chris; Luo, Meizhong; Kudrna, Dave; Wing, Rod A.; Meyers, Blake C.; Yi, Kexian; Kong, Hongzhi; Lavrijsen, Pierre; Sunseri, Francesco; Falavigna, Agostino; Ye, Yin; Leebens-Mack, James H.; Chen, Guangyu; University of Georgia; Jiangxi Academy of Agricultural Sciences; Beijing Genomics Institute (BGI); Universita Mediterranea di Reggio Calabria; Consiglio Nazionale delle Ricerche (CNR); Istituto di Bioscienze e Biorisorse (IBBR-CNR); Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA); Donald Danforth Plant Science Center; University of Alabama Tuscaloosa; University of Delaware; Fujian Agriculture & Forestry University; Chinese Academy of Sciences; Institute of Botany, CAS; KWS Saat AG; Tohoku University; Chinese Academy of Tropical Agricultural Sciences; Yunnan Agricultural University; University of Missouri Columbia; Huazhong Agricultural University; Dalian University of Technology; University of Copenhagen; Bayer AG; Kasetsart University
Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution.
Assessing coastal wetland vulnerability to sea-level rise along the northern Gulf of Mexico coast: Gaps and opportunities for developing a coordinated regional sampling network
(PLOS, 2017) Osland, Michael J.; Griffith, Kereen T.; Larriviere, Jack C.; Feher, Laura C.; Cahoon, Donald R.; Enwright, Nicholas M.; Oster, David A.; Tirpak, John M.; Woodrey, Mark S.; Collini, Renee C.; Baustian, Joseph J.; Breithaupt, Joshua L.; Cherry, Julia A.; Conrad, Jeremy R.; Cormier, Nicole; Coronado-Molina, Carlos A.; Donoghue, Joseph F.; Graham, Sean A.; Harper, Jennifer W.; Hester, Mark W.; Howard, Rebecca J.; Krauss, Ken W.; Kroes, Daniel E.; Lane, Robert R.; McKee, Karen L.; Mendelssohn, Irving A.; Middleton, Beth A.; Moon, Jena A.; Piazza, Sarai C.; Rankin, Nicole M.; Sklar, Fred H.; Steyer, Greg D.; Swanson, Kathleen M.; Swarzenski, Christopher M.; Vervaeke, William C.; Willis, Jonathan M.; Van Wilson, K.; United States Department of the Interior; United States Geological Survey; US Fish & Wildlife Service; Nature Conservancy; University of South Florida; University of Alabama Tuscaloosa; South Florida Water Management District; University of Central Florida; Nicholls State University; University of Louisiana Lafayette; Louisiana State University
Coastal wetland responses to sea-level rise are greatly influenced by biogeomorphic processes that affect wetland surface elevation. Small changes in elevation relative to sea level can lead to comparatively large changes in ecosystem structure, function, and stability. The surface elevation table-marker horizon (SET-MH) approach is being used globally to quantify the relative contributions of processes affecting wetland elevation change. Historically, SET-MH measurements have been obtained at local scales to address site-specific research questions. However, in the face of accelerated sea-level rise, there is an increasing need for elevation change network data that can be incorporated into regional ecological models and vulnerability assessments. In particular, there is a need for long-term, high-temporal resolution data that are strategically distributed across ecologically-relevant abiotic gradients. Here, we quantify the distribution of SET-MH stations along the northern Gulf of Mexico coast (USA) across political boundaries (states), wetland habitats, and ecologically-relevant abiotic gradients (i.e., gradients in temperature, precipitation, elevation, and relative sea-level rise). Our analyses identify areas with high SET-MH station densities as well as areas with notable gaps. Salt marshes, intermediate elevations, and colder areas with high rainfall have a high number of stations, while salt flat ecosystems, certain elevation zones, the mangrove-marsh ecotone, and hypersaline coastal areas with low rainfall have fewer stations. Due to rapid rates of wetland loss and relative sea-level rise, the state of Louisiana has the most extensive SET-MH station network in the region, and we provide several recent examples where data from Louisiana's network have been used to assess and compare wetland vulnerability to sea-level rise. Our findings represent the first attempt to examine spatial gaps in SET-MH coverage across abiotic gradients. Our analyses can be used to transform a broadly disseminated and unplanned collection of SET-MH stations into a coordinated and strategic regional network. This regional network would provide data for predicting and preparing for the responses of coastal wetlands to accelerated sea-level rise and other aspects of global change.
Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics
(BMC, 2021) Varney, Rebecca M.; Brenzinger, Bastian; Malaquias, Manuel Antonio E.; Meyer, Christopher P.; Schroedl, Michael; Kocot, Kevin M.; University of Alabama Tuscaloosa; University of Bergen; Smithsonian Institution; Smithsonian National Museum of Natural History; University of Munich
BackgroundHeterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the "lower heterobranchs". Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia.ResultsTo assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of "lower heterobranchs". Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT+GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.ConclusionsAnalysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT+GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.
Associations between Self-Reported Gastrointestinal Illness and Water System Characteristics in Community Water Supplies in Rural Alabama: A Cross-Sectional Study
(PLOS, 2016) Stauber, Christine E.; Wedgworth, Jessica C.; Johnson, Pauline; Olson, Julie B.; Ayers, Tracy; Elliott, Mark; Brown, Joe; Georgia State University; University of Alabama Tuscaloosa; Georgia Institute of Technology
Background Community water supplies in underserved areas of the United States may be associated with increased microbiological contamination and risk of gastrointestinal disease. Microbial and health risks affecting such systems have not been systematically characterized outside outbreak investigations. The objective of the study was to evaluate associations between self-reported gastrointestinal illnesses (GII) and household-level water supply characteristics. Methods We conducted a cross-sectional study of water quality, water supply characteristics, and GII in 906 households served by 14 small and medium-sized community water supplies in Alabama's underserved Black Belt region. Results We identified associations between respondent-reported water supply interruption and any symptoms of GII (adjusted odds ratio (aOR): 3.01, 95% confidence interval (CI) = 1.65-5.49), as well as low water pressure and any symptoms of GII (aOR: 4.51, 95% CI = 2.5-57.97). We also identified associations between measured water quality such as lack of total chlorine and any symptoms of GII (aOR: 5.73, 95% CI = 1.09-30.1), and detection of E. coli in water samples and increased reports of vomiting (aOR: 5.01, 95% CI = 1.62-15.52) or diarrhea (aOR: 7.75, 95% CI = 2.06-29.15). Conclusions Increased self-reported GII was associated with key water system characteristics as measured at the point of sampling in a cross-sectional study of small and medium water systems in rural Alabama in 2012 suggesting that these water supplies can contribute to endemic gastro-intestinal disease risks. Future studies should focus on further characterizing and managing microbial risks in systems facing similar challenges.
An asymptotic model of particle deposition at an airway bifurcation
(Oxford University Press, 2013) Zierenberg, Jennifer R.; Halpern, David; Filoche, Marcel; Sapoval, Bernard; Grotberg, James B.; University of Michigan; University of Alabama Tuscaloosa; Institut Polytechnique de Paris
Particle transport and deposition associated with flow over a wedge is investigated as a model for particle transport and flow at the carina of an airway bifurcation during inspiration. Using matched asymptotics, a uniformly valid solution is obtained to represent the high Reynolds number flow over a wedge that considers the viscous boundary layer near the wedge and the outer inviscid region and is then used to solve the particle transport equations. Sometimes particle impaction on the wedge is prevented due to the boundary layer. We call this boundary layer shielding (BLS). This effect can be broken down into different types: rejection, trapping and deflection that are described by what happens to the particle's initial negative velocity normal to the wall either changing sign, reaching zero, or remaining negative in the boundary layer region. The deposition efficiency depends on the critical Stokes number but exhibits a weak dependence on Reynolds number. Deposition efficiency for S-c in the range 0 < S-c < 0.4 yields the following relationship at large Reynolds numbers, where beta pi is the wedge angle. For a specific deposition efficiency, S-c decreases as beta pi increases. The distribution of impacted particles was also computed and revealed that particles primarily impact within one airway diameter of the carina, consistent with computational fluid dynamics approaches. This work provides a new insight that the BLS inherent to the wedge component of the structure is the dominant reason for the particle distribution. This finding is important in linking aerosol deposition to the location of airway disease as well as target sites for therapeutic deposition.
Atmospheric Circulation Patterns Associated with Extreme United States Floods Identified via Machine Learning
(Nature Portfolio, 2019) Schlef, Katherine E.; Moradkhani, Hamid; Lall, Upmanu; University of Alabama Tuscaloosa; Columbia University
The massive socioeconomic impacts engendered by extreme floods provides a clear motivation for improved understanding of flood drivers. We use self-organizing maps, a type of artificial neural network, to perform unsupervised clustering of climate reanalysis data to identify synoptic-scale atmospheric circulation patterns associated with extreme floods across the United States. We subsequently assess the flood characteristics (e.g., frequency, spatial domain, event size, and seasonality) specific to each circulation pattern. To supplement this analysis, we have developed an interactive website with detailed information for every flood of record. We identify four primary categories of circulation patterns: tropical moisture exports, tropical cyclones, atmospheric lows or troughs, and melting snow. We find that large flood events are generally caused by tropical moisture exports (tropical cyclones) in the western and central (eastern) United States. We identify regions where extreme floods regularly occur outside the normal flood season (e.g., the Sierra Nevada Mountains due to tropical moisture exports) and regions where multiple extreme flood events can occur within a single year (e.g., the Atlantic seaboard due to tropical cyclones and atmospheric lows or troughs). These results provide the first machine-learning based near-continental scale identification of atmospheric circulation patterns associated with extreme floods with valuable insights for flood risk management.
Attenuation of Dopaminergic Neurodegeneration in a C. elegans Parkinson's Model through Regulation of Xanthine Dehydrogenase (XDH-1) Expression by the RNA Editase, ADR-2
(MDPI, 2023) Starr, Lindsey A.; McKay, Luke E.; Peter, Kylie N.; Seyfarth, Lena M.; Berkowitz, Laura A.; Caldwell, Kim A.; Caldwell, Guy A.; University of Alabama Tuscaloosa; University of Alabama Birmingham
Differential RNA editing by adenosine deaminases that act on RNA (ADARs) has been implicated in several neurological disorders, including Parkinson's disease (PD). Here, we report results of a RNAi screen of genes differentially regulated in adr-2 mutants, normally encoding the only catalytically active ADAR in Caenorhabditis elegans, ADR-2. Subsequent analysis of candidate genes that alter the misfolding of human alpha-synuclein (alpha-syn) and dopaminergic neurodegeneration, two PD pathologies, reveal that reduced expression of xdh-1, the ortholog of human xanthine dehydrogenase (XDH), is protective against alpha-synuclein-induced dopaminergic neurodegeneration. Further, RNAi experiments show that WHT-2, the worm ortholog of the human ABCG2 transporter and a predicted interactor of XDH-1, is the rate-limiting factor in the ADR-2, XDH-1, WHT-2 system for dopaminergic neuroprotection. In silico structural modeling of WHT-2 indicates that the editing of one nucleotide in the wht-2 mRNA leads to the substitution of threonine with alanine at residue 124 in the WHT-2 protein, changing hydrogen bonds in this region. Thus, we propose a model where wht-2 is edited by ADR-2, which promotes optimal export of uric acid, a known substrate of WHT-2 and a product of XDH-1 activity. In the absence of editing, uric acid export is limited, provoking a reduction in xdh-1 transcription to limit uric acid production and maintain cellular homeostasis. As a result, elevation of uric acid is protective against dopaminergic neuronal cell death. In turn, increased levels of uric acid are associated with a decrease in ROS production. Further, downregulation of xdh-1 is protective against PD pathologies because decreased levels of XDH-1 correlate to a concomitant reduction in xanthine oxidase (XO), the form of the protein whose by-product is superoxide anion. These data indicate that modifying specific targets of RNA editing may represent a promising therapeutic strategy for PD.
Back to the future through the wormhole: Caenorhabditis elegans as a preclinical model
(Company of Biologists, 2023) Caldwell, Guy A.; University of Alabama Tuscaloosa; University of Alabama Birmingham
On the 15th Anniversary of Disease Models & Mechanisms as a trailblazing venue for the dissemination of discoveries pertaining to human health involving model systems, we celebrate the journey of this journal, as mirrored through the evolution of research using the nematode roundworm, Caenorhabditis elegans. Driven by the exponential growth of genomic data, worms have advanced from a basic research tool to precise and elegant models for disease and have yielded substantive insights into numerous human disorders. A harbinger of functional genomic analysis since the inception of RNA interference screening, the directed application of C. elegans for identification of disease-modifying factors has revealed new pathways and therapeutic targets to accelerate translational outcomes. Together with advances in gene editing, worm models are now ushering in the era of precision medicine with characteristic expedience.
A bacterial metabolite induces glutathione-tractable proteostatic damage, proteasomal disturbances, and PINK1-dependent autophagy in C. elegans
(Nature Portfolio, 2015) Martinez, B. A.; Kim, H.; Ray, A.; Caldwell, G. A.; Caldwell, K. A.; University of Alabama Tuscaloosa; University of Alabama Birmingham
Gene-by-environment interactions are thought to underlie the majority of idiopathic cases of neurodegenerative disease. Recently, we reported that an environmental metabolite extracted from Streptomyces venezuelae increases ROS and damages mitochondria, leading to eventual neurodegeneration of C. elegans dopaminergic neurons. Here we link those data to idiopathic disease models that predict loss of protein handling as a component of disorder progression. We demonstrate that the bacterial metabolite leads to proteostatic disruption in multiple protein-misfolding models and has the potential to synergistically enhance the toxicity of aggregate-prone proteins. Genetically, this metabolite is epistatically regulated by loss-of-function to pink-1, the C. elegans PARK6 homolog responsible for mitochondrial maintenance and autophagy in other animal systems. In addition, the metabolite works through a genetic pathway analogous to loss-of-function in the ubiquitin proteasome system (UPS), which we find is also epistatically regulated by loss of PINK-1 homeostasis. To determine remitting counter agents, we investigated several established antioxidants and found that glutathione (GSH) can significantly protect against metabolite-induced proteostasis disruption. In addition, GSH protects against the toxicity of MG132 and can compensate for the combined loss of both pink-1 and the E3 ligase pdr-1, a Parkin homolog. In assessing the impact of this metabolite on mitochondrial maintenance, we observe that it causes fragmentation of mitochondria that is attenuated by GSH and an initial surge in PINK-1-dependent autophagy. These studies mechanistically advance our understanding of a putative environmental contributor to neurodegeneration and factors influencing in vivo neurotoxicity.
Bcl-xL Is Required by Primary Hippocampal Neurons during Development to Support Local Energy Metabolism at Neurites
(MDPI, 2021) Jansen, Joseph; Scott, Madison; Amjad, Emma; Stumpf, Allison; Lackey, Kimberly H.; Caldwell, Kim A.; Park, Han-A; University of Alabama Tuscaloosa
Simple Summary B-cell lymphoma-extra large (Bcl-xL) is an anti-apoptotic protein that regulates energy metabolism in neurons. In this study, we found that primary hippocampal neurons transduced with Bcl-xL shRNA or treated with a pharmacological inhibitor of Bxl-xL had a decrease in the population of motile mitochondria. Primary hippocampal neurons lacking Bcl-xL failed to retain ATP at their neurites, which hindered the formation of complex neurite arbors, and ultimately had enhanced vulnerability to excitotoxic challenge. B-cell lymphoma-extra large (Bcl-xL) is a mitochondrial protein known to inhibit mitochondria-dependent intrinsic apoptotic pathways. An increasing number of studies have demonstrated that Bcl-xL is critical in regulating neuronal energy metabolism and has a protective role in pathologies associated with an energy deficit. However, it is less known how Bcl-xL regulates physiological processes of the brain. In this study, we hypothesize that Bcl-xL is required for neurite branching and maturation during neuronal development by improving local energy metabolism. We found that the absence of Bcl-xL in rat primary hippocampal neurons resulted in mitochondrial dysfunction. Specifically, the ATP/ADP ratio was significantly decreased in the neurites of Bcl-xL depleted neurons. We further found that neurons transduced with Bcl-xL shRNA or neurons treated with ABT-263, a pharmacological inhibitor of Bcl-xL, showed impaired mitochondrial motility. Neurons lacking Bcl-xL had significantly decreased anterograde and retrograde movement of mitochondria and an increased stationary mitochondrial population when Bcl-xL was depleted by either means. These mitochondrial defects, including loss of ATP, impaired normal neurite development. Neurons lacking Bcl-xL showed significantly decreased neurite arborization, growth and complexity. Bcl-xL depleted neurons also showed impaired synapse formation. These neurons showed increased intracellular calcium concentration and were more susceptible to excitotoxic challenge. Bcl-xL may support positioning of mitochondria at metabolically demanding regions of neurites like branching points. Our findings suggest a role for Bcl-xL in physiological regulation of neuronal growth and development.

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