Browsing by Subject "bacteria"
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Item Aquatic Plants from Minnesota Part 3 - Antimicrobial Effects(Water Resources Research Center, University of Minnesota, 1972-02) Abul-Hajj, Yusuf J.; Staba, E. John; Su, K. LeeIn this study the antimicrobial activity of the following 22 Minnesotan aquatic plants was investigated: Anacharis Canadensis, Calla Polustris, Carex lacstris, Ceratophyllum demersum, Chara vulgaris, Elecharis smallii, Lemna minor, Myriophyllum exalbescens, Nuphar variegatum, Nymphaea turberosa, Potamogeton amplifolius, P. natans, P. pectinatus, P. richardsonu, P. zosteriformis, Sagittaria cuneata, S. latifolia, Sparganium eurycarpum, S. fluctuans, Typha angustifolia, Vallisneria amiercana, and Zizania aquetica, Furthermore, the chemical constituents responsible for the significant antimicrobial effect were isolated and identified. The skellysolve F. chloroform, 80% ethanol and fresh water extracts of plant species were treated for antimicrobial activity employing the qualitative filter paper disc diffusion method and reference antibiotic discs. Ethanol (80%) extracts of Myriophyllum exalbescens (activity ratio of .34 as compared to the 30 mcg chloramphenicol discs) Nymphaea tuberose (leaf: .40, stem: .45) were moderately active against S. aureus. Ethanol (80%) extracts of Carex lacustris (activity ratio of .34 as compared to the 10 mcg streptomycin discs), Nymphaea tuberose (leaf: 1.01, stem: 1.10) and Nuphar variegatum collected in Lake Minnetonka (leaf: .73, stem: .58) were active against M. smegmatis. All extracts were relatively inactive against E. coli except the water extract of Potamogeton natans where a low activity ration of .10 as compare to the 30 mcg chloramphenicol discs was indicated. Skellysolve F stem extracts of Nuphar variegatum collected in the Pine Lake and Sparganium fluctuans showed a rather distinct action against C. albicans, the activity ratio as compared to the 100 units mycostatin discs were 2.06 and 1.08, respectively. Regarding antifungal activity, ethanol (80%) extracts of Carex lacustris (activity ratio of 1.08 as compared to 5% aq. Phenol standard), Nymphaea tuberosa (stem: .72) and skellysolve F extract of Potamogeton zosteriformis (.60) were active against Alternaria sp., 80% ethanol stem extracts of Nymphaea tuberosa and Nuphar variegatum were active against F. roseum with the activity ratios of .41 and .48 respectively, as compared to the 5% aqueous phenol standard. In general, the plant pathogenic fungi are more resistant than animal pathogenic organisms toward the actions of aquatic plant extract.Item Bacterial Response to Nanoparticles at the Molecular Level(2018-05) Qiu, TianNanotechnology has been an emerging field due to the promising properties of engineered nanomaterials, materials with at least one dimension less than 100 nanometers. With increasing application of NPs, the risk of these novel materials to environment requires thorough investigation to prevent negative impacts. NPs have enormous variety due to combinations of chemical compositions, sizes, shapes, structures and surface modifications. Building predictive models that link NP properties to biological outcomes is the key to proactive safer NP design. High-throughput toxicity screening and investigating toxicity mechanisms are the common two strategies building towards predictive models of nanotoxicity. These two strategies work together: high-throughput assays facilitate preliminary screening of potentially toxic materials for further mechanistic studies to discover biomarkers and molecular pathways of interest, which will in turn be validated on multiple materials and organisms with high-throughput screening. My thesis work combines both strategies to develop high-throughput screening assays and mechanistic understanding at different molecular levels of how an environmental bacterium, Shewanella oneidensis MR-1, responds to various NP exposures. In this work, Chapter 1 reviews recent advances in analytical nanotoxicology and identifies four key areas that would further bring the field to its maturity. Chapter 2 represents a comprehensive mechanistic study on bacteria responding to TiO2 NPs with UVA illumination. Chapter 3 uses gene expression to explore molecular response among two organisms at different trophic levels to positively and negatively charged gold NPs. Chapter 4 identifies that purification method can be one neglected source of apparent NP toxicity. A high-throughput bacterial viability assay that is free of NP interference is presented in Chapter 5. Finally, in Chapter 6, DNA damage is revealed as a toxicity mechanism for nanoscale complex metal oxide nanomaterials to bacteria.Item Characterization and cellular roles of a bacterial O-GlcNAc transferase in Synechococcus elongatus PCC 7942(2015-05) Sokol, KerryThe post-translational addition of a single O-linked 2-N-acetylglucosamine (O-GlcNAc) to serine or threonine residues is an important element in an ever-increasing array of metazoan cellular and regulatory processes. The enzyme responsible for this modification, O-GlcNAc transferase (OGT), is conserved among a wide variety of organisms and is critical for viability in many eukaryotes, including humans, mice, and Drosophila. Although OGTs with domain structure similar to eukaryotic OGTs are predicted for numerous bacteria species, their cellular roles remain unknown. I have identified an OGT in the cyanobacterium Synechococcus elongatus PCC 7942 that has active site homology and similar domain structure to eukaryotic OGTs. An OGT deletion mutant was created ([delta]ogt), which is viable and has no defect in growth rate, but has several phenotypes of interest. Without agitation, [delta]ogt cells aggregate, and settle out of media. Compared to wild type cells, the [delta]ogt cells also have higher free cellular phosphate levels, wider thylakoid lumen, and differential organization of electron dense inclusion bodies. These phenotypes are rescued by re-introduction of the wild type OGT, but are not fully rescued by OGTs with single amino acid substitutions corresponding to mutations that reduce eukaryotic OGT activity. S. elongatus OGT purified from E. coli hydrolyzes the donor sugar, UDP-GlcNAc, while mutant OGTs that do not fully rescue the deletion mutant have reduced or no activity. These results suggest that the eukaryotic-like OGTs of bacteria affect multiple processes. Although the substrates for the SeOGT remain elusive, I have uncovered a relationship between the SeOGT and pili through a mutation that suppresses the [delta]ogt settling phenotype. A single amino acid substitution (alanine 107 to aspartic acid) in the protein PilA suppresses two mutant phenotypes, settling and loss of pili. PilA is a subunit of type four pili (fimbriae), which are frequently found on the surfaces of gram-negative bacteria. Fimbriae are involved in virulence, DNA uptake, twitching motility, and adhesion. Although pilus assembly is a complex process, pili are primarily homopolymers of PilA, which is added or subtracted via ATPases to either extend or retract the pilus. No pili are detectable in [delta]ogt cells, while pili are restored to [delta]ogt cells by the pilA(A107D) mutation. When present together, mutant and wild type pilA genes prevent the assembly of pili, suggesting that there is a toxic interaction between mutant and wild type proteins which results in inability to assemble pili. This occurs regardless of the presence of OGT. Glycosylation of extra-cellular appendages have been widely reported. Pili are known substrates of glycosylation and glycosylation states have been reported to be important in the function of pili. The suppression of [delta]ogt phenotypes by mutant PilA suggests that PilA is either a substrate of the OGT or that another protein involved in pilus synthesis is modified by OGT.Item Data for The colloidal nature of complex fluids enhances bacterial motility(2022) Kamdar, Shashank; Shin, Seunghwan; Leishangthem, Premkumar; Francis, Lorraine F; Xu, XinLiang; Cheng, Xiang; xcheng@umn.edu; Cheng, XiangThe archived data are the post-processed final data corresponding to figures in the manuscript as well as codes used for generating key plots.Item Effects of a novel fiber blend on human gut function(2013-09) Koecher, KatieEnteral nutrition (EN) or enteral tube feeding is an effective means of nutritional support for individuals who do not or cannot eat adequately. Patients restricted to EN frequently suffer from abnormal bowel function which affects their intestinal bacteria and impacts quality of life. Dietary fibers have a variety of physiological benefits; fibers that provide fecal bulk promote regular bowel movements while fermentable fibers are utilized by gut bacteria to produce short chain fatty acids (SCFA) and gas in the process. SCFAs positively influence gut health, gut transit time, and fecal moisture while gas may reduce the tolerance of fibers. Fortification of EN with a blend of fibers with various physicochemical properties more closely represents a normal diet, and may maximize physiological benefits. Moreover, using a blend of fibers with different rates of fermentation may minimize gas and bloating commonly associated with highly fermentable fibers. Batch in vitro systems allow fiber fermentation modeling without absorption and may help to estimate potential health benefits and gastrointestinal tolerance of fiber in vivo. Well controlled, blinded and randomized intervention human studies are the "gold standard" for human nutrition research. The primary aim of this project was to conduct a human clinical trial utilizing a fiber blend fortified EN product. The secondary aim was to relate the human study findings to the in vitro fermentation profiles of the fiber blend and its individual components. The objective of the human study was to compare the effects of a fiber blend fortified enteral formula (FB, 15 g/L), a fiber-free formula (FF) and habitual diet on bowel function, fecal bacteria and quality of life. The fiber blend consisted of a 50:50 insoluble:soluble ratio of fructo-oligosaccharides (FOS), inulin, gum acacia and outer pea hull fiber. In a randomized, double-blind, crossover design, 20 healthy subjects consumed both FF and FB for 14 days with a 4 week washout. Fecal samples were collected the last 5 days of each period and assessed for fecal output, whole gut transit time (WGTT), and major bacterial groups. Subject gastrointestinal quality of life index (GIQLI) and tolerance were also measured. On formula diets, 5-day fecal output decreased by more than 55% from habitual diet, but was 38% higher on FB than FF (p=0.0321). WGTT was approximately 1.5 times longer on formula diets than habitual diet (p<0.0004). Total bacteria declined from habitual diet on FF (p<0.004), but not on FB. Numbers of bifidobacteria and lactobacilli declined from habitual diet on both formula diets, but bifidobacteria was higher on FB compared to FF (p<0.0001). Bacteroides and clostridia numbers did not change between diets. GIQLI and incidence of gas symptoms did not differ between formulas. The objectives of the second project were to compare the in vitro fermentation profiles of FOS, inulin, gum acacia, and pea fiber alone or blended using a 24 h batch model and relate these finding to the human study results. For the in vivo measurements, stool samples were collected to measure pH and SCFA. Tolerance was also measured. The in vitro fermentation of the fiber blend resulted in a delayed pH decrease and gas and SCFA production compared to the FOS and inulin. Human samples had higher total SCFA on the fiber formula compared to the fiber free formula (p=0.029), and both formulas yielded lower SCFA than habitual diet (both p<0.0001). Mean fecal pH for both formulas was 7.5; higher than habitual diet pH 6.5 (p<0.0001). No differences in gas/bloating were found between any diet. By blending fibers, a slower fermentation was observed in vitro and was well tolerated in human subjects. Fiber addition to enteral formula increases fecal short chain fatty acids which may reflect increased fermentation.Item A Flourometric Technique for Sampling in Large-River Ecosystems(Water Resources Research Center, University of Minnesota, 1971-06) Johann, D.R.; McNabb, C.D.; Miller, E.F.Boat-mounted equipment for detecting the movement of rhodamine WT was used in Pool 6 of the upper Mississippi Rover, between navigation dams at Trempealeau, Wisconsin and Winona, Minnesota, to develop a procedure for sampling on paths of turbulent flow in large-river ecosystems. A means of relating sampling points in space and time is described. The expression Cm = (c2 . n) -c1/n-1 where c1 and c2 are concentrations of suspended or dissolved materials on upstream and downstream transects and n is a measure of dilution, can be used to obtain the mean concentration of material in suspension or solution in the water between points that are separated by at least as much as 2400 meters. This procedure in combination with conventional sampling programs in quiet backwaters may allow for more rigorous analysis of large-river ecosystems than has been achieved.Item The Impact of Length of Starvation on Sinorhizobium meliloti Dormancy Depth(2022-08) O'Connor, Madeline R; Denison, Robert FItem Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning(Wiley, 2016) Delgado‐Baquerizo, Manuel; Giaramida, Luca; Reich, Peter B; Khachane, Amit N; Hamonts, Kelly; Edwards, Christine; Lawton, Linda A; Singh, Brajesh KBiodiversity is declining world-wide with detrimental effects on ecosystems. However, we lack a quantitative understanding of the shape of the relationship between microbial biodiversity and ecosystem function (BEF). This limits our understanding of how microbial diversity depletion can impact key functions for human well-being, including pollutant detoxification. Three independent microcosm experiments were conducted to evaluate the direction (i.e. positive, negative or null) and the shape of the relationships between bacterial diversity and both broad (i.e. microbial respiration) and specialized (i.e. toxin degradation) functions in five Australian and two UK freshwater ecosystems using next-generation sequencing platforms. Reduced bacterial diversity, even after accounting for biomass, caused a decrease in broad (i.e. cumulative microbial respiration) and specialized (biodegradation of two important toxins) functions in all cases. Unlike the positive but decelerating BEF relationship observed most frequently in plants and animals, most evaluated functional measurements were related to bacterial diversity in a non-redundant fashion (e.g. exponentially and/or linearly). Synthesis. Our results suggest that there is a lack of functional redundancy in the relationship between bacterial diversity and ecosystem functioning; thus, the consequences of declining microbial diversity on ecosystem functioning and human welfare have likely been considerably underestimated.Item Special crop research grand (SCRG) - MnDRIVE potato biocontrol 2014 experiment(2017-10-05) Song, Zewei; Hanson, Lindsey; Kinkel, Linda; songzewei@outlook.com; Song, ZeweiThis is the sequencing data for characterizing the soil microbiomes (fungal and bacterial communties) following the application of bacterial inoculations as biocontrols of potato tuber disease. The archived files are raw sequencing data. The detailed processing pipeline will be included in the incoming peer reviewed paper.