Research and Publications - Department of Biological Sciences
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Item Microbiological Assay for Estimating Salivary Concentrations of the Cariostatic Antibiotic Actinobolin(American Society for Microbiology, 1970-10-01) Hunt, D.E.; Bradley, E.L.; Bachmann, Joan W.A logarithmic-ratio microbiological assay has been developed for the estimation of concentrations of actinobolin (or inhibitory equivalents) in human saliva. The utility of this assay has been demonstrated by presenting data that show concentrations of this antibiotic (or inhibitory equivalents) detected in saliva or saline after incubation at 37 C for periods as long as 6 hr. The results of some statistical analyses of the assay data have been included.Item Survey of the Sensitivity of Microorganisms to Rubratoxin B(American Society for Microbiology, 1970-06-30) Hayes, A. Wallace; Wyatt, Elwanda P.Of the 133 microorganisms tested, Tetrahymena pyriformis and Volvox aureus were the most sensitive to rubratoxin B, being inhibited at 25 and 50 mug/ml, respectively.Item Environmental and Nutritional Factors Affecting the Production of Rubratoxin B by Penicillium rubrum Stoll(American Society for Microbiology, 1970-09-01) Hayes, A. Wallace; Wyatt, Elwanda P.; King, Patricia A.Rubratoxin B can be produced in a semisynthetic medium by Penicillium rubrum under varying environmental and nutritional conditions. Maximum production (552.0 mg/500 ml) was obtained with P. rubrum NRRL A-11785 grown in stationary cultures of Mosseray's simplified Raulin solution supplemented with 2.5% malt extract broth at ambient temperature. Zinc is required at levels of at least 0.4 mg per liter. In the absence of iron sulfate, there was a 50-fold reduction in rubratoxin B production but not in growth. No toxin was produced by this isolate in 5- or 7-liter fermentors.Item A Terminal Inversion in Drosophila Ananassae(National Academy of Sciences, 1936-10-15) Kaufmann, B.P.Item Mitotic Behavior of Induced Chromosomal Fragments Lacking Spindle Attachments in the Neuroblasts of the Grasshopper(National Academy of Sciences, 1938-11-15) Carlson, J. GordonItem Morphology of the Chromosomes of Drosophila ananassae(The Japan Mendel Society, 1937-08-31) Kaufmann, Berwind P.1) The chromosome complement of D. ananassae, studied in the neurocytes, consists of three pairs of V-shaped autosom.es and the sex chromosomes. These are a pair of V-shaped X-chromosomes in the female, an X and a J-shaped Y-chromosome in the male. The chromosomes may be distinguished by relative, sizes and characteristic constrictions. 2) The fourth chromosomes and the Y-chromosome appear totally heteropyknotic in resting and early prophase stages of mitotic cells. Short heteropyknotic regions lie adjacent to the spindle attachment regions of the X-chromosomes and the four longer autosomes. 3) In salivary gland nuclei there are but six chromosome arms with euchromatic sections. Four of these represent the paired arms of the longer autosomes, the other two the X-chromosome arms. The fourth chromosomes are represented in salivary gland nuclei by a small bipartite mass of heterochromatin which forms part of the chromocenter. 4) In mitotic prophases of female larvae the fourth chromosomes are associated with the nucleolus, which separates a small satellite-like portion from the remainder of the long arm of these chromosomes. In the male the Y-chromosome forms a third member of the group associated with the nucleolus. 5) The fourth chromosome-nucleolus-satellite relationship is. also evident, in salivary gland nuclei, the satellite appearing as a banded body associated with the nucleolus, and also connected with the fourth chromosomes by chromatic strands. 6) The chromocenter of mitotic cells and of the salivary gland cells is not amorphous, but discloses, under suitable conditions, the limits of the component chromosomes.Item A New Leptothorax From Alabama (Hymenoptera: Formicidae)(Cambridge Entomological Club, 1950-01-01) Wilson, Edward OsborneItem Suboxic Deposition of Ferric Iron by Bacteria in Opposing Gradients of Fe(II) and Oxygen at Circumneutral pH(American Society for Microbiology, 2001) Sobolev, Dmitri; Roden, Eric E.The influence of lithotrophic Fe(II)-oxidizing bacteria on patterns of ferric oxide deposition in opposing gradients of Fe(II) and O(2) was examined at submillimeter resolution by use of an O(2) microelectrode and diffusion microprobes for iron. In cultures inoculated with lithotrophic Fe(II)-oxidizing bacteria, the majority of Fe(III) deposition occurred below the depth of O(2) penetration. In contrast, Fe(III) deposition in abiotic control cultures occurred entirely within the aerobic zone. The diffusion microprobes revealed the formation of soluble or colloidal Fe(III) compounds during biological Fe(II) oxidation. The presence of mobile Fe(III) in diffusion probes from live cultures was verified by washing the probes in anoxic water, which removed ca. 70% of the Fe(III) content of probes from live cultures but did not alter the Fe(III) content of probes from abiotic controls. Measurements of the amount of Fe(III) oxide deposited in the medium versus the probes indicated that ca. 90% of the Fe(III) deposited in live cultures was formed biologically. Our findings show that bacterial Fe(II) oxidation is likely to generate reactive Fe(III) compounds that can be immediately available for use as electron acceptors for anaerobic respiration and that biological Fe(II) oxidation may thereby promote rapid microscale Fe redox cycling at aerobic-anaerobic interfaces.Item Microbially Catalyzed Nitrate-Dependent Oxidation of Biogenic Solid-Phase Fe(II) Compounds(American Chemical Society, 2001) Weber, Karrie A.; Picardal, Flynn W.; Roden, Eric E.The potential for microbially catalyzed NO3—-dependent oxidation of solid-phase Fe(II) compounds was examined using a previously described autotrophic, denitrifying, Fe(II)-oxidizing enrichment culture. The following solid-phase Fe(II)-bearing minerals were considered: microbially reduced synthetic goethite, two differ ent end products of microbially hydrous ferric oxide (HFO) reduc tion (biogenic Fe3O4 and biogenic FeCO3), chemically precipitated FeCO3, and two microbially reduced iron(III) oxide-rich subsoils. The microbially reduced goethite, subsoils, and chemically precip itated FeCO3 were subject to rapid NO3 —-dependent Fe(II) oxida tion. Significant oxidation of biogenic Fe3O4 was observed. Very little biogenic FeCO3 was oxidized. No reduction of NO3 — or ox idation of Fe(II) occurred in pasteurized cultures. The molar ratio of NO3 — reduced to Fe(II) oxidized in cultures containing chemi cally precipitated FeCO3, and one of the microbially reduced sub soils approximated the theoretical stoichiometry of 0.2:1. However, molar ratios obtained for oxidation of microbially reduced goe thite, the other subsoil, and the HFO reduction end products did not agree with this theoretical value. These discrepancies may be related to heterotrophic NO3 — reduction coupled to oxidation of dead Fe(III)-reducing bacterial biomass. Our findings demonstrate that microbally catalyzed NO3 —-dependent Fe(II) oxidation has the potential to significantly accelerate the oxidation of solid-phase Fe(II) compounds by oxidized N species. This process could have an important influence on the migration of contaminant metals and radionuclides in subsurface environments.Item Book Review of Strictly for the Chickens by Frances Hamerstrom(1981-03-01) Sandy, John H.Item Ubiquitin conjugating enzymes participate in polyglutamine protein aggregation(BMC, 2007) Howard, Rebecca A.; Sharma, Pratima; Hajjar, Connie; Caldwell, Kim A.; Caldwell, Guy A.; Du Breuil, Rusla; Moore, Rhonda; Boyd, Lynn; University of Alabama Huntsville; University of Alabama TuscaloosaBackground: Protein aggregation is a hallmark of several neurodegenerative diseases including Huntington's disease and Parkinson's disease. Proteins containing long, homopolymeric stretches of glutamine are especially prone to form aggregates. It has long been known that the small protein modifier, ubiquitin, localizes to these aggregates. In this report, nematode and cell culture models for polyglutamine aggregation are used to investigate the role of the ubiquitin pathway in protein aggregation. Results: Ubiquitin conjugating enzymes (Ubc's) were identified that affect polyglutamine aggregates in C. elegans. Specifically, RNAi knockdown of ubc-2 or ubc-22 causes a significant increase in the size of aggregates as well as a reduction in aggregate number. In contrast, RNAi of ubc-1, ubc-13, or uev-1 leads to a reduction of aggregate size and eliminates ubiquitin and proteasome localization to aggregates. In cultured human cells, shRNA knockdown of human homologs of these Ubc's (Ube2A, UbcH5b, and E2- 25K) causes similar effects indicating a conserved role for ubiquitination in polyglutamine protein aggregation. Conclusion: Results of knockdown of different Ubc enzymes indicate that at least two different and opposing ubiquitination events occur during polyglutamine aggregation. The loss of ubiquitin localization after ubc-1, ubc-13, or uev-1 knockdown suggests that these enzymes might be directly involved in ubiquitination of aggregating proteins.Item Maple syrup urine disease: new insights from a zebrafish model(Company of Biologists, 2012) Roberts, Nathan B.; University of Alabama TuscaloosaItem Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill(PLOS, 2012) Beazley, Melanie J.; Martinez, Robert J.; Rajan, Suja; Powell, Jessica; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Hazen, Terry C.; Van Nostrand, Joy D.; Zhou, Jizhong; Mortazavi, Behzad; Sobecky, Patricia A.; University of Alabama Tuscaloosa; United States Department of Energy (DOE); Lawrence Berkeley National Laboratory; University of California Berkeley; University of Tennessee Knoxville; University of Oklahoma - Norman; Dauphin Island Sea LabCoastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.Item Rediscovery of Leptoxis compacta (Anthony, 1854) (Gastropoda: Cerithioidea: Pleuroceridae)(PLOS, 2012) Whelan, Nathan V.; Johnson, Paul D.; Harris, Phil M.; University of Alabama TuscaloosaThe Mobile River Basin is a hotspot of molluscan endemism, but anthropogenic activities have caused at least 47 molluscan extinctions, 37 of which were gastropods, in the last century. Nine of these suspected extinctions were in the freshwater gastropod genus Leptoxis (Cerithioidea: Pleuroceridae). Leptoxis compacta, a Cahaba River endemic, has not been collected for > 70 years and was formally declared extinct in 2000. Such gastropod extinctions underscore the imperilment of freshwater resources and the current biodiversity crisis in the Mobile River Basin. During a May 2011 gastropod survey of the Cahaba River in central Alabama, USA, L. compacta was rediscovered. The identification of snails collected was confirmed through conchological comparisons to the L. compacta lectotype, museum records, and radulae morphology of historically collected L. compacta. Through observations of L. compacta in captivity, we document for the first time that the species lays eggs in short, single lines. Leptoxis compacta is restricted to a single location in the Cahaba River, and is highly susceptible to a single catastrophic extinction event. As such, the species deserves immediate conservation attention. Artificial propagation and reintroduction of L. compacta into its native range may be a viable recovery strategy to prevent extinction from a single perturbation event.Item Lactate-starved neurons in ALS(Company of Biologists, 2012) Martinez, Bryan A.; University of Alabama TuscaloosaItem Homeotic functions of the Teashirt transcription factor during adult Drosophila development(Company of Biologists, 2013) Wang, Wei; Tindell, Neil; Yan, Shun; Yoder, John H.; University of Alabama TuscaloosaDuring Drosophila development region-specific regulation of target genes by Hox proteins is modulated by genetic interactions with various cofactors and genetic collaborators. During embryogenesis one such modulator of Hox target specificity is the zinc-finger transcription factor Teashirt (Tsh) that is expressed in the developing trunk and cooperatively functions with trunk-specific Hox proteins to promote appropriate segment fate. This embryonic function of Tsh is characterized as homeotic since loss of embryonic Tsh activity leads to transformation of trunk segments toward head identity. In addition to this embryonic homeotic role, Tsh also performs vital Hox-independent functions through patterning numerous embryonic, larval and adult structures. Here we address whether the homeotic function of Tsh is maintained throughout development by investigating its contribution to patterning the adult abdomen. We show that Tsh is expressed throughout the developing abdomen and that this expression is dependent on the three Bithorax Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B. Conditional reduction of Tsh activity during pupation reveals broad homeotic roles for this transcription factor throughout the adult abdomen. Additionally we show that, as during embryogenesis, the tsh paralog tiptop (tio) plays a partially redundant role in this homeotic activity. (C) 2012. Published by The Company of Biologists Ltd.Item Diurnal patterns of gas-exchange and metabolic pools in tundra plants during three phases of the arctic growing season(Wiley, 2013) Patankar, Rajit; Mortazavi, Behzad; Oberbauer, Steven F.; Starr, Gregory; University of Alabama Tuscaloosa; Dauphin Island Sea Lab; Florida International UniversityArctic tundra plant communities are subject to a short growing season that is the primary period in which carbon is sequestered for growth and survival. This period is often characterized by 24-h photoperiods for several months a year. To compensate for the short growing season tundra plants may extend their carbon uptake capacity on a diurnal basis, but whether this is true remains unknown. Here, we examined in situ diurnal patterns of physiological activity and foliar metabolites during the early, mid, and late growing season in seven arctic species under light-saturated conditions. We found clear diurnal patterns in photosynthesis and respiration, with midday peaks and midnight lulls indicative of circadian regulation. Diurnal patterns in foliar metabolite concentrations were less distinct between the species and across seasons, suggesting that metabolic pools are likely governed by proximate external factors. This understanding of diurnal physiology will also enhance the parameterization of process-based models, which will aid in better predicting future carbon dynamics for the tundra. This becomes even more critical considering the rapid changes that are occurring circumpolarly that are altering plant community structure, function, and ultimately regional and global carbon budgets.Item Characterization of Amoeboaphelidium protococcarum, an Algal Parasite New to the Cryptomycota Isolated from an Outdoor Algal Pond Used for the Production of Biofuel(PLOS, 2013) Letcher, Peter M.; Lopez, Salvador; Schmieder, Robert; Lee, Philip A.; Behnke, Craig; Powell, Martha J.; McBride, Robert C.; University of Alabama Tuscaloosa; San Diego State UniversityMass culture of algae for the production of biofuels is a developing technology designed to offset the depletion of fossil fuel reserves. However, large scale culture of algae in open ponds can be challenging because of incidences of infestation with algal parasites. Without knowledge of the identity of the specific parasite and how to control these pests, algal-based biofuel production will be limited. We have characterized a eukaryotic parasite of Scenedesmus dimorphus growing in outdoor ponds used for biofuel production. We demonstrated that as the genomic DNA of parasite FD01 increases, the concentration of S. dimorphus cells decreases; consequently, this is a highly destructive pathogen. Techniques for culture of the parasite and host were developed, and the endoparasite was identified as the Aphelidea, Amoeboaphelidium protococcarum. Phylogenetic analysis of ribosomal sequences revealed that parasite FD01 placed within the recently described Cryptomycota, a poorly known phylum based on two species of Rozella and environmental samples. Transmission electron microscopy demonstrated that aplanospores of the parasite produced filose pseudopodia, which contained fine fibers the diameter of actin microfilaments. Multiple lipid globules clustered and were associated with microbodies, mitochondria and a membrane cisternae, an arrangement characteristic of the microbody-lipid globule complex of chytrid zoospores. After encystment and attachment to the host cells, the parasite injected its protoplast into the host between the host cell wall and plasma membrane. At maturity the unwalled parasite occupied the entire host cell. After cleavage of the protoplast into aplanospores, a vacuole and lipids remained in the host cell. Amoeboaphelidium protococcarum isolate FD01 is characteristic of the original description of this species and is different from strain X-5 recently characterized. Our results help put a face on the Cryptomycota, revealing that the phylum is more diverse than previously understood and include some of the Aphelidea as well as Rozella species and potentially Microsporidia.Item The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae)(PLOS, 2013) DePriest, Michael S.; Bhattacharya, Debashish; Lopez-Bautista, Juan M.; University of Alabama Tuscaloosa; Rutgers State University New BrunswickThe complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M. Lin & H.-Y. Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.Item Intraspecific phenotypic variation in a fish predator affects multitrophic lake metacommunity structure(Wiley, 2013) Howeth, Jennifer G.; Weis, Jerome J.; Brodersen, Jakob; Hatton, Elizabeth C.; Post, David M.; Yale University; University of Alabama Tuscaloosa; Swiss Federal Institutes of Technology Domain; Swiss Federal Institute of Aquatic Science & Technology (EAWAG)Contemporary insights from evolutionary ecology suggest that population divergence in ecologically important traits within predators can generate diversifying ecological selection on local community structure. Many studies acknowledging these effects of intraspecific variation assume that local populations are situated in communities that are unconnected to similar communities within a shared region. Recent work from metacommunity ecology suggests that species dispersal among communities can also influence species diversity and composition but can depend upon the relative importance of the local environment. Here, we study the relative effects of intraspecific phenotypic variation in a fish predator and spatial processes related to plankton species dispersal on multitrophic lake plankton metacommunity structure. Intraspecific diversification in foraging traits and residence time of the planktivorous fish alewife (Alosa pseudoharengus) among coastal lakes yields lake metacommunities supporting three lake types which differ in the phenotype and incidence of alewife: lakes with anadromous, landlocked, or no alewives. In coastal lakes, plankton community composition was attributed to dispersal versus local environmental predictors, including intraspecific variation in alewives. Local and beta diversity of zooplankton and phytoplankton was additionally measured in response to intraspecific variation in alewives. Zooplankton communities were structured by species sorting, with a strong influence of intraspecific variation in A. pseudoharengus. Intraspecific variation altered zooplankton species richness and beta diversity, where lake communities with landlocked alewives exhibited intermediate richness between lakes with anadromous alewives and without alewives, and greater community similarity. Phytoplankton diversity, in contrast, was highest in lakes with landlocked alewives. The results indicate that plankton dispersal in the region supplied a migrant pool that was strongly structured by intraspecific variation in alewives. This is one of the first studies to demonstrate that intraspecific phenotypic variation in a predator can maintain contrasting patterns of multitrophic diversity in metacommunities.