PCR identification of bacteria in blood culture does not fit the daily workflow of a routine microbiology laboratory.

PubMed

Karumaa, Santra; Kärpänoja, Pauliina; Sarkkinen, Hannu

2012-03-01

We have evaluated the GenoType blood culture assay (Hain Lifescience, Nehren, Germany) for the identification of bacteria in 233 positive blood cultures and assessed its suitability in the workflow of a routine microbiology laboratory. In 68/233 (29.2%) samples, the culture result could not be confirmed by the GenoType assay due to a lack of primers in the test, multiple organisms in the sample, or inconsistency with respect to the identification by culture. Although the GenoType blood culture assay gives satisfactory results for bacteria for which primers are available, there are difficulties in applying the test in the routine microbiology laboratory.

A survey of culturable aerobic and anaerobic marine bacteria in de novo biofilm formation on natural substrates in St. Andrews Bay, Scotland.

PubMed

Finnegan, Lucy; Garcia-Melgares, Manuel; Gmerek, Tomasz; Huddleston, W Ryan; Palmer, Alexander; Robertson, Andrew; Shapiro, Sarah; Unkles, Shiela E

2011-10-01

This study reports a novel study of marine biofilm formation comprising aerobic and anaerobic bacteria. Samples of quartz and feldspar, minerals commonly found on the earth, were suspended 5 m deep in the North Sea off the east coast of St. Andrews, Scotland for 5 weeks. The assemblage of organisms attached to these stones was cultivated under aerobic and anaerobic conditions in the laboratory. Bacteria isolated on Marine Agar 2216 were all Gram-negative and identified to genus level by sequencing the gene encoding 16S rRNA. Colwellia, Maribacter, Pseudoaltermonas and Shewanella were observed in aerobically-grown cultures while Vibrio was found to be present in both aerobic and anaerobic cultures. The obligate anaerobic bacterium Psychrilyobacter atlanticus, a recently defined genus, was identified as a close relative of isolates grown anaerobically. The results provide valuable information as to the main players that attach and form de novo biofilms on common minerals in sea water.

Calcium carbonate precipitation by heterotrophic bacteria isolated from biofilms formed on deteriorated ignimbrite stones: influence of calcium on EPS production and biofilm formation by these isolates.

PubMed

López-Moreno, Angélica; Sepúlveda-Sánchez, José David; Mercedes Alonso Guzmán, Elia Mercedes; Le Borgne, Sylvie

2014-01-01

Heterotrophic CaCO3-precipitating bacteria were isolated from biofilms on deteriorated ignimbrites, siliceous acidic rocks, from Morelia Cathedral (Mexico) and identified as Enterobacter cancerogenus (22e), Bacillus sp. (32a) and Bacillus subtilis (52g). In solid medium, 22e and 32a precipitated calcite and vaterite while 52g produced calcite. Urease activity was detected in these isolates and CaCO3 precipitation increased in the presence of urea in the liquid medium. In the presence of calcium, EPS production decreased in 22e and 32a and increased in 52g. Under laboratory conditions, ignimbrite colonization by these isolates only occurred in the presence of calcium and no CaCO3 was precipitated. Calcium may therefore be important for biofilm formation on stones. The importance of the type of stone, here a siliceous stone, on biological colonization is emphasized. This calcium effect has not been reported on calcareous materials. The importance of the effect of calcium on EPS production and biofilm formation is discussed in relation to other applications of CaCO3 precipitation by bacteria.

Neutrophil extracellular traps formation by bacteria causing endometritis in the mare.

PubMed

Rebordão, M R; Carneiro, C; Alexandre-Pires, G; Brito, P; Pereira, C; Nunes, T; Galvão, A; Leitão, A; Vilela, C; Ferreira-Dias, G

2014-12-01

Besides the classical functions, neutrophils (PMNs) are able to release DNA in response to infectious stimuli, forming neutrophil extracellular traps (NETs) and killing pathogens. The pathogenesis of endometritis in the mare is not completely understood. The aim was to evaluate the in vitro capacity of equine PMNs to secrete NETs by chemical activation, or stimulated with Streptococcus equi subspecies zooepidemicus (Szoo), Escherichia coli (Ecoli) or Staphylococcus capitis (Scap) strains obtained from mares with endometritis. Ex vivo endometrial mucus from mares with bacterial endometritis were evaluated for the presence of NETs. Equine blood PMNs were used either without or with stimulation by phorbol-myristate-acetate (PMA), a strong inducer of NETs, for 1-3h. To evaluate PMN ability to produce NETs when phagocytosis was impaired, the phagocytosis inhibitor cytochalasin (Cyt) was added after PMA. After the addition of bacteria, a subsequent 1-h incubation was carried out in seven groups. NETs were visualized by 4',6-diamidino-2-phenylindole (DAPI) and anti-histone. Ex vivo samples were immunostained for myeloperoxidase and neutrophil elastase. A 3-h incubation period of PMN + PMA increased NETs (p < 0.05). Bacteria + 25 nM PMA and bacteria + PMA + Cyt increased NETs (p<0.05). Szoo induced fewer NETs than Ecoli or Scap (p < 0.05). Ex vivo NETs were present in mares with endometritis. Scanning electron microscopy showed the spread of NETs formed by smooth fibers and globules that can be aggregated in thick bundles. Formation of NETs and the subsequent entanglement of bacteria suggest that equine NETs might be a complementary mechanism in fighting some of the bacteria causing endometritis in the mare. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Salt dissolution and sinkhole formation: Results of laboratory experiments

NASA Astrophysics Data System (ADS)

Oz, Imri; Eyal, Shalev; Yoseph, Yechieli; Ittai, Gavrieli; Elad, Levanon; Haim, Gvirtzman

2016-10-01

The accepted mechanism for the formation of thousands of sinkholes along the coast of the Dead Sea suggests that their primary cause is dissolution of a salt layer by groundwater undersaturated with respect to halite. This is related to the drop in the Dead Sea level, which caused a corresponding drop of the freshwater-saltwater interface, resulting in fresher groundwater replacing the brines that were in contact with the salt layer. In this study we used physical laboratory experiments to examine the validity of this mechanism by reproducing the full dynamic natural process and to examine the impact of different hydrogeological characteristics on this process. The experimental results show surface subsidence and sinkhole formation. The stratigraphic configurations of the aquifer, together with the mechanical properties of the salt layer, determine the dynamic patterns of the sinkhole formation (instantaneous versus gradual formation). Laboratory experiments were also used to study the potential impact of future stratification in the Dead Sea, if and when the "Red Sea-Dead Sea Canal" project is carried out, and the Dead Sea level remains stable. The results show that the dissolution rates are slower by 1 order of magnitude in comparison with a nonstratified saltwater body, and therefore, the processes of salt dissolution and sinkhole formation will be relatively restrained under these conditions.

Coexistence of Fe(II)- and Mn(II)-oxidizing bacteria govern the formation of deep sea umber deposits

NASA Astrophysics Data System (ADS)

Peng, Xiaotong; Ta, Kaiwen; Chen, Shun; Zhang, Lijuan; Xu, Hengchao

2015-11-01

The genesis of umber deposits has remained controversial for several decades. Recently, microbial Fe(II) oxidation associated with low-temperature diffuse venting has been identified as a key process for the formation of umber deposits, but the exact biogeochemical mechanisms involved to the precipitation of Mn oxides in umber deposits still remain unknown. Here, we used nano secondary ion mass spectrometer, synchrotron-based X-ray absorption spectroscopy, electron microscopy, and molecular techniques to demonstrate the coexistence of two types of metal-oxidizing bacteria within deep-sea hydrothermal umber deposits at the South Mid-Atlantic Ridge, where we found unique spheroids composed of biogenic Fe oxyhydroxides and Mn oxides in the deposits. Our data show that Fe oxyhydroxides and Mn oxides are metabolic by-products of lithotrophic Fe(II)-oxidizing bacteria and heterotrophic Mn(II)-oxidizing bacteria, respectively. The hydrothermal vents fuel lithotrophic microorganisms, which constitute a trophic base that might support the activities of heterogenic Mn(II)-oxidizing bacteria. The biological origin of umber deposits shed light on the importance of geomicrobiological interaction in triggering the formation of metalliferous deposits, with important implications for the generation of submarine Mn deposits and crusts.

The pediatric hematology/oncology educational laboratory in-training examination (PHOELIX): A formative evaluation of laboratory skills for Canadian pediatric hematology/oncology trainees.

PubMed

Leung, Elaine; Dix, David; Ford, Jason; Barnard, Dorothy; McBride, Eileen

2015-11-01

Pediatric hematologists/oncologists need to be skilled clinicians, and must also be adept and knowledgeable in relevant areas of laboratory medicine. Canadian training programs in this subspecialty have a minimum requirement for 6 months of training in acquiring "relevant laboratory diagnostic skills." The Canadian pediatric hematology/oncology (PHO) national specialty society, C17, recognized the need for an assessment method in laboratory skills for fellows graduating from PHO training programs. Canadian pediatric hematologists/oncologists were surveyed regarding what were felt to be the essential laboratory-related knowledge and skills deemed necessary for graduating pediatric hematology/oncology trainees. The PHOELIX (Pediatric hematology/oncology educational laboratory in-training examination) was then developed to provide an annual formative evaluation of laboratory skills in Canadian PHO trainees. The majority of PHO respondents (89%) felt that laboratory skills are important in clinical practice. An annual formative examination including review of glass slides was implemented starting in 2010; this provides feedback regarding knowledge of laboratory medicine to both trainees and program directors (PDs). We have successfully created a formative examination that can be used to evaluate and educate trainees, as well as provide PDs with a tool to gauge the effectiveness of their laboratory training curriculum. Feedback has been positive from both trainees and PDs. © 2015 Wiley Periodicals, Inc.

[Trend survey of ocular infections with bacteria at Toyama University Hospital over the past six years--from the standpoint of laboratory examination].

PubMed

Kubota, Tomomi; Hayashi, Shirou; Niimi, Hideki; Kitajima, Isao

2012-07-01

Specimens of bacterial ocular infections are frequently received in the clinical laboratory. However, a comprehensive trend survey of ocular infections with bacteria is very rare. Our objective is to understand the current tendency of ocular infections with bacteria in patients at Toyama University Hospital from the standpoint of laboratory examination. We studied 263 cases of ocular infection with bacteria diagnosed at Toyama University Hospital from January 2006 to December 2011. 123 were male and 140 were female, with a mean age of 61.2(0-98) years. Specimens were subjected to direct microscopy and culture. Cultures were positive in 174(66.2%) patients. The most common bacterial isolate was Staphylococcus (28.1%), followed by Corynebacterium (19.3%), Streptococcus (9.3%), and Propionibacterium (8.6%). MRSA accounted for 18.8% of all S. aureus isolates, and has increased in recent years. The number of bacteria detected was larger in March, June, July, August, and October. Age distribution indicated that around 70% of bacterial isolates were detected from patients over 60 years old. The most common specimen of ocular infections with bacteria was eye discharge (detection rate; 87.8%), followed by corneal scraping(41%), aqueous humor (19%), and vitreous body (27%). Nearly 80% of bacterial isolates were detected from patients with keratitis, endophthalmitis, dacryocystitis, and conjunctivitis. As for the disease specific detection rate, endophthalmitis was very low (38.3%). The detection rate by years indicated that the way doctors pick up the specimens greatly affects the detection rate. Based on this survey, we need close cooperation with medical doctors concerning laboratory examination in ocular infection with bacteria, and we must improve the detection sensitivity of specimens from patients with endophthalmitis.

The role of Proteus mirabilis cell wall features in biofilm formation.

PubMed

Czerwonka, Grzegorz; Guzy, Anna; Kałuża, Klaudia; Grosicka, Michalina; Dańczuk, Magdalena; Lechowicz, Łukasz; Gmiter, Dawid; Kowalczyk, Paweł; Kaca, Wiesław

2016-11-01

Biofilms formed by Proteus mirabilis strains are a serious medical problem, especially in the case of urinary tract infections. Early stages of biofilm formation, such as reversible and irreversible adhesion, are essential for bacteria to form biofilm and avoid eradication by antibiotic therapy. Adhesion to solid surfaces is a complex process where numerous factors play a role, where hydrophobic and electrostatic interactions with solid surface seem to be substantial. Cell surface hydrophobicity and electrokinetic potential of bacterial cells depend on their surface composition and structure, where lipopolysaccharide, in Gram-negative bacteria, is prevailing. Our studies focused on clinical and laboratory P. mirabilis strains, where laboratory strains have determined LPS structures. Adherence and biofilm formation tests revealed significant differences between strains adhered in early stages of biofilm formation. Amounts of formed biofilm were expressed by the absorption of crystal violet. Higher biofilm amounts were formed by the strains with more negative values of zeta potential. In contrast, high cell surface hydrophobicity correlated with low biofilm amount.

Indole can act as an extracellular signal to regulate biofilm formation of Escherichia coli and other indole-producing bacteria.

PubMed

Martino, P Di; Fursy, R; Bret, L; Sundararaju, B; Phillips, R S

2003-07-01

We demonstrated previously that genetic inactivation of tryptophanase is responsible for a dramatic decrease in biofilm formation in the laboratory strain Escherichia coli S17-1. In the present study, we tested whether the biochemical inhibition of tryptophanase, with the competitive inhibitor oxindolyl-L-alanine, could affect polystyrene colonization by E. coli and other indole-producing bacteria. Oxindolyl-L-alanine inhibits, in a dose-dependent manner, indole production and biofilm formation by strain S17-1 grown in Luria-Bertani (LB) medium. Supplementation with indole at physiologically relevant concentrations restores biofilm formation by strain S17-1 in the presence of oxindolyl-L-alanine and by mutant strain E. coli 3714 (S17-1 tnaA::Tn5) in LB medium. Oxindolyl-L-alanine also inhibits the adherence of S17-1 cells to polystyrene for a 3-h incubation time, but mutant strain 3714 cells are unaffected. At 0.5 mg/mL, oxindolyl-L-alanine exhibits inhibitory activity against biofilm formation in LB medium and in synthetic urine for several clinical isolates of E. coli, Klebsiella oxytoca, Citrobacter koseri, Providencia stuartii, and Morganella morganii but has no affect on indole-negative Klebsiella pneumoniae strains. In conclusion, these data suggest that indole, produced by the action of tryptophanase, is involved in polystyrene colonization by several indole-producing bacterial species. Indole may act as a signalling molecule to regulate the expression of adhesion and biofilm-promoting factors.

Exploring Iron Silicate Precursors of Ancient Iron Formations through Rock Record, Laboratory and Field Analogue Investigations

NASA Astrophysics Data System (ADS)

Johnson, J. E.; Rasmussen, B.; Muhling, J.; Benzerara, K.; Jezequel, D.; Cosmidis, J.; Templeton, A. S.

2016-12-01

In direct contrast to today's oceans, iron-rich chemical precipitates dominate the deep marine sedimentary record > 2.3 billion years ago. The deposition of these minerals resulted in massive iron formations and indicate that the ocean was previously ferruginous and largely anoxic. To precipitate and concentrate iron in the sediments, many hypotheses have centered on the oxidation of soluble Fe(II) to solid Fe(III)-oxyhydroxides; these ideas have stimulated extensive research using iron-oxidizing bacteria to produce Fe(III)-oxides and trace metal sorption experiments on Fe(III)-oxides, leading to inferences of trace metal availability and implications for enzymatic and microbial evolution as well as pO2 levels and seawater chemistry. However, recent discoveries of disseminated iron-silicate nanoparticles in early-silicifying chert indicate that iron-silicates may have instead been the primary precipitates from these Archean ferruginous oceans (Rasmussen et al, 2015). Considering the significant paradigm shift this discovery implies for interpretations of Archean elemental cycling, redox state and potential microbial metabolisms, we investigated these iron-silicate inclusions and their implications for ancient seawater chemistry in a multi-faceted approach using spectroscopic- and diffraction-based techniques. The crystal structure, Fe oxidation state and Fe coordination environment of iron-silicate nanoparticles have been interrogated using microscale X-ray absorption spectroscopy, TEM and nanoscale scanning transmission X-ray microscopy. To further explore the chemical and potential biological controls on iron-silicate formation, we have also performed laboratory experiments to mimic Archean seawater and precipitate iron-bearing silicate minerals under abiotic conditions and in the presence of iron-oxidizing bacteria. In a complementary study, sediments from a natural Archean analogue system were sampled to determine if iron-silicate minerals form in Mexican

Antibiotic resistance and biofilm formation of some bacteria isolated from sediment, water and fish farms in Malaysia

NASA Astrophysics Data System (ADS)

Faja, Orooba Meteab; Usup, Gires; Ahmad, Asmat

2018-04-01

A total of 90 isolates of bacteria were isolated, from sediment (10) samples, water (10) samples and fish (12) samples (Sea bass, Snapper, Grouper and Tilapia). These include 22 isolates of bacteria from sediment, 28 isolates from water and 40 isolates from fish. All the isolates were tested for sensitivity to 13 antibiotics using disc diffusion method. The isolates showed high resistance to some antibiotics based on samples source. Isolates from sediment showed highest resistance toward novobiocin, kanamycin, ampicillin and streptomycin while isolates from water showed highest resistance against vancomycin, penicillin, streptomycin and tetracycline, in contrast, in fish sample showed highest resistance toward vancomycin, ampicillin, streptomycin and tetracycline. Most of the isolates showed biofilm formation ability with different degrees. Out of 22 bacteria isolates from water, two isolates were weak biofilm formers, six isolates moderate biofilm formers and fourteen isolates strong biofilm formers. While, out of 28 bacteria isolates from water one isolate was weak biofilm former, five isolates moderate biofilm formers and 22 strong biofilm formers Fish isolate showed three isolates (8%) moderate biofilm formers and 27 isolates strong biofilm formers. Biofilm formation was one of the factors that lead to antibiotic resistance of the bacterial isolates from these samples.

Concentration and detection of bacteria in virtual environmental samples based on non-immunomagnetic separation and quantum dots by using a laboratory-made system

NASA Astrophysics Data System (ADS)

Cheng, Zhi; Wu, Taihu; Chen, Feng; Du, Yaohua; Gu, Biao; Li, Chao; Yang, Zijian

2012-03-01

This study investigated a method that simultaneously detects three bacteria, Salmonella typhimurium, Escherichia coli, and Staphylococcus aureus via an approach that combines un-immunized magnetic nanoparticles for the enrichment and antibody-conjugated quantum dots (QDs) as fluorescence markers, by using a laboratory-made system. In the enrichment procedure, the un-immunized superparamagnetic polymer nanoparticles and the three bacteria formed "beadcell" complex. Magnetic nanoparticles with different size were used and some interferents were added into the bacteria suspension respectively to check the influence on concentration efficiency. In the immuno-fluorescence labeling procedure, QDs with different emission wavelenghs were immobilized with antibody. Antibody conjugated QDs capture the bacteria selectively and specifically so that "sandwich" complex were formed. The suspension of the labeled bacteria was trickled onto a microporous membrane. A 450nm semiconductor laser was used as a part of the laboratory-made system to excite the QDs. Three PMT detectors were utilized to detect the fluorescence intensity. These un-immunized magnetic nanoparticles can be applied in nonspecific separation and enrichment of bacteria from environmental samples, and this method, of which the detection procedures are completed within 2 h, can be applied to the cost-effective and rapid detecting of bacterial contamination.

Oil spill dispersants induce formation of marine snow by phytoplankton-associated bacteria.

PubMed

van Eenennaam, Justine S; Wei, Yuzhu; Grolle, Katja C F; Foekema, Edwin M; Murk, AlberTinka J

2016-03-15

Unusually large amounts of marine snow, including Extracellular Polymeric Substances (EPS), were formed during the 2010 Deepwater Horizon oil spill. The marine snow settled with oil and clay minerals as an oily sludge layer on the deep sea floor. This study tested the hypothesis that the unprecedented amount of chemical dispersants applied during high phytoplankton densities in the Gulf of Mexico induced high EPS formation. Two marine phytoplankton species (Dunaliella tertiolecta and Phaeodactylum tricornutum) produced EPS within days when exposed to the dispersant Corexit 9500. Phytoplankton-associated bacteria were shown to be responsible for the formation. The EPS consisted of proteins and to lesser extent polysaccharides. This study reveals an unexpected consequence of the presence of phytoplankton. This emphasizes the need to test the action of dispersants under realistic field conditions, which may seriously alter the fate of oil in the environment via increased marine snow formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Laboratory formation of non-cementing, methane hydrate-bearing sands

USGS Publications Warehouse

Waite, William F.; Bratton, Peter M.; Mason, David H.

2011-01-01

Naturally occurring hydrate-bearing sands often behave as though methane hydrate is acting as a load-bearing member of the sediment. Mimicking this behavior in laboratory samples with methane hydrate likely requires forming hydrate from methane dissolved in water. To hasten this formation process, we initially form hydrate in a free-gas-limited system, then form additional hydrate by circulating methane-supersaturated water through the sample. Though the dissolved-phase formation process can theoretically be enhanced by increasing the pore pressure and flow rate and lowering the sample temperature, a more fundamental concern is preventing clogs resulting from inadvertent methane bubble formation in the circulation lines. Clog prevention requires careful temperature control throughout the circulation loop.

Outcomes of Individualized Formative Assessments in a Pharmacy Skills Laboratory.

PubMed

Gums, Tyler Harris; Kleppinger, Erika L; Urick, Benjamin Y

2014-11-15

To determine the effectiveness of an individualized teaching method in a pharmacy skills laboratory. All third-year students enrolled in an Accreditation Council for Pharmacy Education (ACPE) accredited doctor of pharmacy program (n=150) received an individual formative assessment from clinical pharmacists on communication skills and clinical competency after the students counseled standardized mock glaucoma patients during a laboratory focused on alternative dosing formulations. Objective structured clinical examination (OSCE) scores for this station from the 2012 and 2013 classes were compared before and after the intervention. Ophthalmic OSCE station scores were higher after the individual formative feedback intervention. Students in 2013 had a mean score of 83.2 ± 8.3% compared to a mean of 74.3 ± 12.9% in 2012 for this OSCE station. The percentage of students receiving an "A" on the OSCE station increased from 8.1% to 31.3% after the intervention. Individualized formative teaching methods benefited students in both their communication skills and clinical assessment. Future research should focus on wider implementation and overcoming obstacles, such as increased facilitator needs.

A Star-Formation Laboratory

NASA Image and Video Library

2011-05-13

The dwarf galaxy NGC 4214 is ablaze with young stars and gas clouds. Located around 10 million light-years away in the constellation of Canes Venatici (The Hunting Dogs), the galaxy's close proximity, combined with the wide variety of evolutionary stages among the stars, make it an ideal laboratory to research the triggers of star formation and evolution. Intricate patterns of glowing hydrogen formed during the star-birthing process, cavities blown clear of gas by stellar winds, and bright stellar clusters of NGC 4214 can be seen in this optical and near-infrared image. Observations of this dwarf galaxy have also revealed clusters of much older red supergiant stars. Additional older stars can be seen dotted all across the galaxy. The variety of stars at different stages in their evolution indicates that the recent and ongoing starburst periods are not the first, and the galaxy's abundant supply of hydrogen means that star formation will continue into the future. This color image was taken using the Wide Field Camera 3 in December 2009. Credit: NASA, ESA, and the Hubble Heritage (STScI/AURA)-ESA/Hubble Collaboration Acknowledgment: R. O'Connell (University of Virginia) and the WFC3 Scientific Oversight Committee NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Isolation of Potential Bacteria as Inoculum for Biofloc Formation in Pacific Whiteleg Shrimp, Litopenaeus vannamei Culture Ponds.

PubMed

Kasan, Nor Azman; Ghazali, Nurarina Ayuni; Ikhwanuddin, Mhd; Ibrahim, Zaharah

2017-01-01

A new green technology to reduce environmental damages while optimizing production of Pacific Whiteleg shrimp, Litopenaeus vannamei was developed known as "Biofloc technology". Microbial communities in biofloc aggregates are responsible in eliminating water exchange and producing microbial proteins that can be used as supplemented feed for L. vannamei. This study aimed to isolate and identify potential bioflocculant-producing bacteria to be used as inoculum for rapid formation of biofloc. For the purpose of this study, bacterial communities during 0, 30 and 70 days of culture (DOC) of L. vannamei grow-out ponds were isolated and identified through phenotypic and 16S rDNA sequences analysis. Phylogenetic relationships between isolated bacteria were then evaluated through phylogenetic tree analysis. One-way analysis of variance (ANOVA) was used to compare the differences of microbial communities at each DOC. Out of 125 bacterial isolates, nine species of bacteria from biofloc were identified successfully. Those bacteria species were identified as Halomonas venusta, H. aquamarina, Vibrio parahaemolyticus, Bacillus infantis, B. cereus, B. safensis, Providencia vermicola, Nitratireductor aquimarinus and Pseudoalteromonas sp., respectively. Through phylogenetic analysis, these isolates belong to Proteobacteria and Firmicutes families under the genera of Halomonas sp., Vibrio sp., Bacillus sp., Providencia sp., Nitratireductor sp. and Pseudoalteromonas sp. In this study, bioflocculant-producing bacteria were successfully identified which are perfect candidates in forming biofloc to reduce water pollution towards a sustainable aquaculture industry. Presence of Halomonas sp. and Bacillus sp. in all stages of biofloc formation reinforces the need for new development regarding the ability of these species to be used as inoculum in forming biofloc rapidly.

Shewanella putrefaciens Adhesion and Biofilm Formation on Food Processing Surfaces

PubMed Central

Bagge, Dorthe; Hjelm, Mette; Johansen, Charlotte; Huber, Ingrid; Gram, Lone

2001-01-01

Laboratory model systems were developed for studying Shewanella putrefaciens adhesion and biofilm formation under batch and flow conditions. S. putrefaciens plays a major role in food spoilage and may cause microbially induced corrosion on steel surfaces. S. putrefaciens bacteria suspended in buffer adhered readily to stainless steel surfaces. Maximum numbers of adherent bacteria per square centimeter were reached in 8 h at 25°C and reflected the cell density in suspension. Numbers of adhering bacteria from a suspension containing 108 CFU/ml were much lower in a laminar flow system (modified Robbins device) (reaching 102 CFU/cm2) than in a batch system (reaching 107 CFU/cm2), and maximum numbers were reached after 24 h. When nutrients were supplied, S. putrefaciens grew in biofilms with layers of bacteria. The rate of biofilm formation and the thickness of the film were not dependent on the availability of carbohydrate (lactate or glucose) or on iron starvation. The number of S. putrefaciens bacteria on the surface was partly influenced by the presence of other bacteria (Pseudomonas fluorescens) which reduced the numbers of S. putrefaciens bacteria in the biofilm. Numbers of bacteria on the surface must be quantified to evaluate the influence of environmental factors on adhesion and biofilm formation. We used a combination of fluorescence microscopy (4′,6′-diamidino-2-phenylindole staining and in situ hybridization, for mixed-culture studies), ultrasonic removal of bacteria from surfaces, and indirect conductometry and found this combination sufficient to quantify bacteria on surfaces. PMID:11319118

External occulter laboratory demonstrator for the forthcoming formation flying coronagraphs.

PubMed

Landini, Federico; Vives, Sébastien; Venet, Mélanie; Romoli, Marco; Guillon, Christophe; Fineschi, Silvano

2011-12-20

The design and optimization of the external occulter geometry is one of the most discussed topics among solar coronagraph designers. To improve the performance of future coronagraphs and to stretch their inner fields of view toward the solar limb, the new concept of coronagraphs in formation flight has been introduced in the scientific debate. Solar coronagraphs in formation flight require several mechanical and technological constraints to be met, mainly due to the large dimension of the occulter and to the spacecraft's reciprocal alignment. The occulter edge requires special attention to minimize diffraction while being compatible with the handling and integrating of large delicate space components. Moreover, it is practically impossible to set up a full-scale model for laboratory tests. This article describes the design and laboratory tests on a demonstrator for a coronagraph to be operated in formation flight. The demonstrator is based on the principle of the linear edge, thus the presented results cannot be directly extrapolated to the case of the flying circular occulter. Nevertheless, we are able to confirm the results of other authors investigating on smaller coronagraphs and provide further information on the geometry and tolerances of the optimization system. The described work is one of the results of the ESA STARTIGER program on formation flying coronagraphs ["The STARTIGER's demonstrators: toward a new generation of formation flying solar coronagraphs," in 2010 International Conference on Space Optics (ICSO) (2010), paper 39].

[Effects of long-term application of pig manure containing residual tetracycline on the formation of drug-resistant bacteria and resistance genes].

PubMed

Zhang, Jun; Yang, Xiao-Hong; Ge, Feng; Wang, Na; Jiao, Shao-Jun; Jiao, Shao-Jun

2014-06-01

The effect of residual veterinary tetracycline on the formation of drug-resistant bacteria and corresponding resistance genes was investigated. During the research, the soil with long-term application of pig manure containing residual tetracycline was collected in autumn and summer respectively in the farmland around a certain pig farm in Shuyang City, Huang Huai area, north of Jiangsu province. At the same time, soils without application of pig manure in the farmland of this area were collected as the reference sample. Composition of drug-resistant bacteria in all soil samples was analyzed and three common tetracycline-resistance genes (tetA, tetC, tetE) were studied by PCR as well. During the research, 59 drug-resistant bacteria belonging to 13 bacterial genus respectively were separated from the soil sample collected in autumn while 35 drug- resistant bacteria belonging to 10 bacterial genus respectively were separated from the soil sample collected in summer and as for the reference sample, 3 drug-resistant bacteria belonging to 1 bacterial genus (Streptomyces) were separated with pathogenic bacteria up to 38.14% of total drug-resistant bacteria. PCR result showed that resistance genes were detected in all drug-resistant bacteria and tetC accounted for the most. At the same time, the residual tetracycline in the soil which was in a range of 41.1-61.9 microg x kg(-1) correlated with the amount of resistance genes (4.63 x 10(5)-37.42 x 10(5) copies x g(-1)). Besides, the climate was found accelerating the formation of drug-resistant bacteria and resistance genes.

Induction of trap formation in nematode-trapping fungi by bacteria-released ammonia.

PubMed

Su, H N; Xu, Y Y; Wang, X; Zhang, K Q; Li, G H

2016-04-01

A total of 11 bacterial strains were assayed for bacteria-induced trap formation in the nematode-trapping fungus Arthrobotrys oligospora YMF1·01883 with two-compartmented Petri dish. These strains were identified on the basis of their 16S rRNA gene sequences. Volatile organic compounds (VOCs) of eight isolates were extracted using solid-phase micro-extraction (SPME) and their structures were identified based on gas chromatography-mass spectrometry (GC-MS). At the same time, all isolates were used for quantitative measurement of ammonia by the indophenol blue method. The effects of pure commercial compounds on inducement of trap formation in A. oligospora were tested. Taken together, results demonstrated that the predominant bacterial volatile compound inducing trap formation was ammonia. Meanwhile, ammonia also played a role in other nematode-trapping fungi, including Arthrobotrys guizhouensis YMF1·00014, producing adhesive nets; Dactylellina phymatopaga YMF1·01474, producing adhesive knobs; Dactylellina cionopaga YMF1·01472, producing adhesive columns and Drechslerella brochopaga YMF1·01829, producing constricting rings. © 2016 The Society for Applied Microbiology.

Sugar fatty acid esters inhibit biofilm formation by food-borne pathogenic bacteria

PubMed Central

Furukawa, Soichi; Akiyoshi, Yuko; O’Toole, George A.; Ogihara, Hirokazu; Morinaga, Yasushi

2010-01-01

Effects of food additives on biofilm formation by food-borne pathogenic bacteria were investigated. Thirty-three potential food additives and 3 related compounds were added to the culture medium at concentrations from 0.001 to 0.1% (w/w), followed by inoculation and cultivation of five biofilm-forming bacterial strains for the evaluation of biofilm formation. Among the tested food additives, 21 showed inhibitory effects of biofilm formation by Staphylococcus aureus and Escherichia coli, and in particular, sugar fatty acid esters showed significant anti-biofilm activity. Sugar fatty acid esters with long chain fatty acid residues (C14-16) exerted their inhibitory effect at the concentration of 0.001%(w/w), but bacterial growth was not affected at this low concentration. Activities of the sugar fatty acid esters positively correlated with the increase of the chain length of the fatty acid residues. Sugar fatty acid esters inhibited the initial attachment of the Staphylococcus aureus cells to the abiotic surface. Sugar fatty acid esters with long chain fatty acid residues (C14-16) also inhibited biofilm formation by Streptococcus mutans and Listeria monocytogenes at 0.01%(w/w), while the inhibition of biofilm formation by Pseudomonas aeruginosa required the addition of a far higher concentration (0.1%(w/w)) of the sugar fatty acid esters. PMID:20089325

Gas hydrate formation rates from dissolved-phase methane in porous laboratory specimens

USGS Publications Warehouse

Waite, William F.; Spangenberg, E.K.

2013-01-01

Marine sands highly saturated with gas hydrates are potential energy resources, likely forming from methane dissolved in pore water. Laboratory fabrication of gas hydrate-bearing sands formed from dissolved-phase methane usually requires 1–2 months to attain the high hydrate saturations characteristic of naturally occurring energy resource targets. A series of gas hydrate formation tests, in which methane-supersaturated water circulates through 100, 240, and 200,000 cm3 vessels containing glass beads or unconsolidated sand, show that the rate-limiting step is dissolving gaseous-phase methane into the circulating water to form methane-supersaturated fluid. This implies that laboratory and natural hydrate formation rates are primarily limited by methane availability. Developing effective techniques for dissolving gaseous methane into water will increase formation rates above our observed (1 ± 0.5) × 10−7 mol of methane consumed for hydrate formation per minute per cubic centimeter of pore space, which corresponds to a hydrate saturation increase of 2 ± 1% per day, regardless of specimen size.

[Infectious risk related to the formation of multi-species biofilms (Candida - bacteria) on peripheral vascular catheters].

PubMed

Seghir, A; Boucherit-Otmani, Z; Sari-Belkharroubi, L; Boucherit, K

2017-03-01

The Candida yeasts are the fourth leading cause of death from systemic infections, the risk may increase when the infection also involves bacteria. Yeasts and bacteria can adhere to medical implants, such as peripheral vascular catheters, and form a multicellular structures called "mixed biofilms" more resistant to antimicrobials agents. However, the formation of mixed biofilms on implants leads to long-term persistent infections because they can act as reservoirs of pathogens that have poorly understood interactions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Biofilm formation by the periodontopathic bacteria Treponema denticola and Porphyromonas gingivalis.

PubMed

Kuramitsu, Howard K; Chen, Wen; Ikegami, Aki

2005-11-01

Periodontitis develops as a result of the interaction of the host with subgingival plaque bacteria. Both Porphyromonas gingivalis and Treponema denticola are frequently associated together in these oral biofilms. The molecular basis for in vitro biofilm formation was investigated for P. gingivalis 381, T. denticola 35405, and mixtures of the two organisms using microtiter plate assays. In addition, the biofilms were examined following confocal laser scanning microscopy. P. gingivalis 381, but not T. denticola strains, formed biofilms in vitro. This property was dependent, in part, on the strain 381 fimA, ppk, and usp genes. Microarray and Northern blot analyses suggested that the expression of the ppk gene was required for maximal expression of the uspA gene. P. gingivalis 381 formed synergistic biofilms when incubated with T. denticola strains. This process was dependent upon the strain 381 rgpB and fimA genes as well as the T. denticola flgE and cfpA genes. P. gingivalis 381 formed synergistic biofilms with T. denticola 35405. These results may be relevant to the previous observations that the two organisms are frequently observed together in subgingival plaque with the spirochetes localized to the exterior of the oral biofilms. It is suggested that other such synergistic effects may also occur between other plaque bacteria.

Increased survival of honeybees in the laboratory after simultaneous exposure to low doses of pesticides and bacteria.

PubMed

Dickel, Franziska; Münch, Daniel; Amdam, Gro Vang; Mappes, Johanna; Freitak, Dalial

2018-01-01

Recent studies of honeybees and bumblebees have examined combinatory effects of different stressors, as insect pollinators are naturally exposed to multiple stressors. At the same time the potential influences of simultaneously occurring agricultural agents on insect pollinator health remain largely unknown. Due to different farming methods, and the drift of applied agents and manure, pollinators are most probably exposed to insecticides but also bacteria from organic fertilizers at the same time. We orally exposed honeybee workers to sub-lethal doses of the insecticide thiacloprid and two strains of the bacterium Enterococcus faecalis, which can occur in manure from farming animals. Our results show that under laboratory conditions the bees simultaneously exposed to the a bacterium and the pesticide thiacloprid thiacloprid had significant higher survival rates 11 days post exposure than the controls, which surprisingly showed the lowest survival. Bees that were exposed to diet containing thiacloprid showed decreased food intake. General antibacterial activity is increased by the insecticide and the bacteria, resulting in a higher immune response observed in treated individuals compared to control individuals. We thus propose that caloric restriction through behavioural and physiological adaptations may have mediated an improved survival and stress resistance in our tests. However, the decreased food consumption could in long-term also result in possible negative effects at colony level. Our study does not show an additive negative impact of sub-lethal insecticide and bacteria doses, when tested under laboratory conditions. In contrast, we report seemingly beneficial effects of simultaneous exposure of bees to agricultural agents, which might demonstrate a surprising biological capacity for coping with stressors, possibly through hormetic regulation.

Bacteria and Composite Particles in the Glacier-Fed Systems of British Columbia and Alberta, Canada

NASA Astrophysics Data System (ADS)

Barrett, D. C.; Hodder, K. R.

2014-12-01

In controlled environments, bacteria and suspended sediment particles are linked via the creation of a composite structure ("bacteria-sediment associations"; BSA), with associated effects on size, density and hydrodynamics. However, the presence of these particles, and their corresponding effect on sedimentary processes is not well documented in many environments. Here, we compile field data from 20 glacier-fed systems in British Columbia and Alberta, Canada, to illustrate: 1) the presence, and (quantity) of bacteria-sediment associations; 2) the presence of in-situ composite particles and their associated settling velocities; 3) the simulated impact of bacteria-sediment associations on settling velocity via controlled manipulation in the laboratory. In general, a significant portion of the fine suspended sediment typical of these systems was associated with bacteria and/or present in a composite-form -- not as primary, individual particles. Four key findings include: 1) Along a 80 kilometre river transect, up to 40% of bacteria were associated with sediment particles; 2) Manipulation of bacteria concentration in the laboratory has revealed a positive relationship between sediment settling velocity, creation of composite particles and bacteria concentration; 3) Composite particles dominated the suspended sediment load among all 20 systems, especially for larger particles; and 4) Measurements reveal these composite particles are settling at rates significantly below that predicted by Stokes Law. The formation of composite particles is especially important in lakes where laminated sediments are used for paleoenvironmental reconstruction (varved), as bacteria can modulate the rate at which some of this sediment reaches the lake floor. These results highlight the importance of bacteria in Earth surface processes and, more specifically, the sediment dynamics within glacier-fed systems.

The Effects of Sugars on the Biofilm Formation of Escherichia coli 185p on Stainless Steel and Polyethylene Terephthalate Surfaces in a Laboratory Model.

PubMed

Khangholi, Mahdi; Jamalli, Ailar

2016-09-01

Bacteria utilize various methods in order to live in protection from adverse environmental conditions. One such method involves biofilm formation; however, this formation is dependent on many factors. The type and concentration of substances such as sugars that are present in an environment can be effective facilitators of biofilm formation. First, the physico-chemical properties of the bacteria and the target surface were studied via the MATS and contact angle measurement methods. Additionally, adhesion to different surfaces in the presence of various concentrations of sugars was compared in order to evaluate the effect of these factors on the biofilm formation of Escherichia coli , which represents a major food contaminant . Results showed that the presence of sugars has no effect on the bacterial growth rate; all three concentrations of sugars were hydrophilic and demonstrated a high affinity toward binding to the surfaces. The impact of sugars and other factors on biofilm formation can vary depending on the type of bacteria present.

Identification of pink-pigmented bacteria isolated from environmental water samples and their biofilm formation abilities.

PubMed

Furuhata, Katsunori; Kato, Yuko; Goto, Keiichi; Saitou, Keiko; Sugiyama, Jun-Ichi; Hara, Motonobu; Fukuyama, Masahumi

2008-06-01

Sixty-seven strains of pink-pigmented bacteria, which were isolated from environmental water samples collected nationwide, were identified by partial 16S rDNA sequence analysis. In addition, the biofilm formation ability of the isolates was experimentally investigated. We could identify only 2 strains at the species level: Pedobacter roseus HS-38 and Runella slithyformis HS-77. The results showed that of the strains tested, 22 strains (32.8%) were Pedobacter spp., which was most frequently identified, followed by 19 strains (28.4%) of Arcicella spp., 16 strains (23.9%) of Deinococcus spp., 5 strains (7.5%) of Roseomonas spp., 4 strains (6.0%) of Flectobacillus spp. and 1 strain (1.5%) of Runella sp. Most isolates showed low similarity values to previously known species, and they were found to be novel species. At a result, it was difficult to identify environmental water-derived pink-pigmented bacteria at the species level. On the other hand, when we measured the absorbance by the crystal violet staining to examine the quantities of biofilm formation of these strains, fifty-five (82.0%) of the 67 isolates formed biofilm. The absorbance of Deinococcus sp. HS-75 was the highest (3.56). When comparing the absorbance values among the genera, Roseomonas spp. showed the highest absorbance (mean:1.62), followed by Deinococcus spp. (mean: 1.03), and Arcicella spp. (mean: 1.01). Strains of Flectobacillus spp. (mean: 0.48) and Pedobacter spp. (mean: 0.42) showed lower absorbance values. As above, it was shown that, at the species level, the pink-pigmented bacteria in the water in the Japanese environment had various levels of ability to form biofilm.

Biofilm Formation by the Periodontopathic Bacteria Treponema denticola and Porphyromonas gingivalis.

PubMed

Kuramitsu, Howard K; Chen, Wen; Ikegami, Aki

2005-11-01

Periodontitis develops as a result of the interaction of the host with subgingival plaque bacteria. Both Porphyromonas gingivalis and Treponema denticola are frequently associated together in these oral biofilms. The molecular basis for in vitro biofilm formation was investigated for P. gingivalis 381, T. denticola 35405, and mixtures of the two organisms using microtiter plate assays. In addition, the biofilms were examined following confocal laser scanning microscopy. P. gingivalis 381, but not T. denticola strains, formed biofilms in vitro. This property was dependent, in part, on the strain 381 fimA, ppk, and usp genes. Microarray and Northern blot analyses suggested that the expression of the ppk gene was required for maximal expression of the uspA gene. P. gingivalis 381 formed synergistic biofilms when incubated with T. denticola strains. This process was dependent upon the strain 381 rgpB and fimA genes as well as the T. denticola flgE and cfpA genes. P. gingivalis 381 formed synergistic biofilms with T. denticola 35405. These results may be relevant to the previous observations that the two organisms are frequently observed together in subgingival plaque with the spirochetes localized to the exterior of the oral biofilms. It is suggested that other such synergistic effects may also occur between other plaque bacteria. © 2005 American Academy of Periodontology.

An individual-based model for biofilm formation at liquid surfaces

NASA Astrophysics Data System (ADS)

Ardré, Maxime; Henry, Hervé; Douarche, Carine; Plapp, Mathis

2015-12-01

The bacterium Bacillus subtilis frequently forms biofilms at the interface between the culture medium and the air. We present a mathematical model that couples a description of bacteria as individual discrete objects to the standard advection-diffusion equations for the environment. The model takes into account two different bacterial phenotypes. In the motile state, bacteria swim and perform a run-and-tumble motion that is biased toward regions of high oxygen concentration (aerotaxis). In the matrix-producer state they excrete extracellular polymers, which allows them to connect to other bacteria and to form a biofilm. Bacteria are also advected by the fluid, and can trigger bioconvection. Numerical simulations of the model reproduce all the stages of biofilm formation observed in laboratory experiments. Finally, we study the influence of various model parameters on the dynamics and morphology of biofilms.

Effect of Diuron on aquatic bacteria in laboratory-scale wastewater treatment ponds with special reference to Aeromonas species studied by colony hybridization.

PubMed

Sumpono; Perotti, P; Belan, A; Forestier, C; Lavedrine, B; Bohatier, J

2003-01-01

Six laboratory-scale wastewater treatment ponds were filled with sediment and water obtained from a reference pond (a wastewater treatment plant located in a rural environment at Montel-de-Gelat, Puy-de-Dôme, France). They were kept at 20 degrees C, with alternative light and dark periods (12 h-12 h), and fed with raw effluent supplied weekly. Three of them were treated with Diuron (dissolved in DMSO) at a final concentration 10 mg/l, while the other three received only DMSO. Physico-chemical parameters, total bacteria, cultivable bacteria, and Aeromonas spp. were measured periodically until 41 days after the Diuron contamination. Total bacteria were treated with 4,6-diamidino 2-phenylindole (DAPI) and counted by epifluoroscence microscopy. The cultivable bacteria were quantified on plate count agar medium and Aeromonas spp. using colony hybridization. In the contaminated pilots, biochemical oxygen demand (BOD5), chemical oxygen demand (COD), suspended solids (SS), volatile suspended solids (VSS), ammonium, phosphorus, and bacteria increased, but dissolved oxygen decreased. The abundance of total bacteria, cultivable bacteria (multiplied by 30), and Aeromonas spp. increased for two weeks after Diuron introduction, reverting to initial values three weeks later. The percentage of cultivable bacteria relative to total bacteria was 0.2% in controls and 1.2% in treated pilots, while the percentage of Aeromonas spp. relative to cultivable bacteria decreased from 6-10% to 2%. Our results suggest that Diuron, which acts on the photosystem II of phototrophs, supports the development of cultivable bacteria through new carbon sources derived from the decomposition of photosynthetic micro-organisms, but does not specifically support Aeromonas spp.

Laboratory Studies of Survival Limits of Bacteria During Shock Compression: Application to Impacts on the Early Earth

NASA Astrophysics Data System (ADS)

Willis, M. J.; Ahrens, T. J.; Bertani, L. E.; Nash, C. Z.

2004-12-01

Shock recovery experiments on suspensions of 106 mm-3 E. coli bacteria contained in water-based medium, within stainless steel containers, are used to simulate the impact environment of bacteria residing in water-filled cracks in rocks. Early Earth life is likely to have existed in such environments. Some 10-2 to 10-4 of the bacteria population survived initial (800 ns duration) shock pressures in water of 219 and 260 MPa. TEM images of shock recovered bacteria indicate cell wall indentations and rupture, possibly induced by inward invasion of medium into the cell wall. Notably cell wall rupture occurs dynamically at ˜0.1 times the static pressures E.coli have been demonstrated (Sharma et al., 2002) to survive and may be caused by Rayleigh-Taylor instabilities. We infer the invading fluid pressure may exceed the tensile strength of the cell wall. We assume the overpressures are limited to the initial shock pressure in water. Parameters for the Grady & Lipkin (1980) model of tensile failure versus time-scale (strain rate) are fit to present data, assuming that at low strain rates, overpressures exceeding cell Turgor pressure require ˜103 sec. This model, if validated by experiments at other timescales, may permit using short loading duration laboratory data to infer response of organisms to lower shock overpressures for the longer times (100 to 103 s) of planetary impacts. An Ahrens & O'Keefe (1987) shock attenuation model is then applied for Earth impactors. This model suggests that Earth impactors of radius 1.5 km induce shocks within water-filled cracks in rock to dynamic pressure such that stresses exceeding the survivability threshold of E. coli bacteria, to radii of 1.7-2.6×102 km. In contrast, a giant (1500 km radius) impactor produces a non survival zone for E. coli that encompasses the entire Earth.

Molecular mechanisms involved in Bacillus subtilis biofilm formation

PubMed Central

Mielich-Süss, Benjamin; Lopez, Daniel

2014-01-01

Summary Biofilms are the predominant lifestyle of bacteria in natural environments, and they severely impact our societies in many different fashions. Therefore, biofilm formation is a topic of growing interest in microbiology, and different bacterial models are currently studied to better understand the molecular strategies that bacteria undergo to build biofilms. Among those, biofilms of the soil-dwelling bacterium Bacillus subtilis are commonly used for this purpose. Bacillus subtilis biofilms show remarkable architectural features that are a consequence of sophisticated programs of cellular specialization and cell-cell communication within the community. Many laboratories are trying to unravel the biological role of the morphological features of biofilms, as well as exploring the molecular basis underlying cellular differentiation. In this review, we present a general perspective of the current state of knowledge of biofilm formation in B. subtilis. In particular, a special emphasis is placed on summarizing the most recent discoveries in the field and integrating them into the general view of these truly sophisticated microbial communities. PMID:24909922

Evaporation-induced patterns from droplets containing motile and nonmotile bacteria.

PubMed

Nellimoottil, Tittu Thomas; Rao, Pinjala Nagaraju; Ghosh, Siddhartha Sankar; Chattopadhyay, Arun

2007-08-14

In this letter, we report the observations of specific pattern formation from the evaporation of aqueous droplets containing motile and nonmotile bacteria. We found that when motile bacteria were present the droplet evaporated into disclike patterned deposits of bacteria. However, when the bacteria were made nonmotile by treatment with liquid nitrogen, the droplet evaporated into ringlike deposits. We also observed that bacteria with higher motility produced more uniformly deposited disclike patterns. Furthermore, we propose a model with numerical simulations to explain the mechanism of formation of these patterns. The model is based on the advective fluid flow from the center of the droplet toward the edge due to enhanced evaporation from the edge of the pinned droplet in comparison to that from the free surface. For the case of motile bacteria, we have added another velocity parameter toward the axis of the droplet and directed against the fluid flow in order to account for the disclike pattern formation. The numerical simulations match the experimental observations well. The present work, by qualitative and quantitative understanding of the evaporation of bacteria droplets, demonstrates that the inherent bacterial motility is primarily responsible for the formation of these differential patterns.

Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii

PubMed Central

Gärdes, Astrid; Iversen, Morten H; Grossart, Hans-Peter; Passow, Uta; Ullrich, Matthias S

2011-01-01

Aggregation of algae, mainly diatoms, is an important process in marine systems leading to the settling of particulate organic carbon predominantly in the form of marine snow. Exudation products of phytoplankton form transparent exopolymer particles (TEP), which acts as the glue for particle aggregation. Heterotrophic bacteria interacting with phytoplankton may influence TEP formation and phytoplankton aggregation. This bacterial impact has not been explored in detail. We hypothesized that bacteria attaching to Thalassiosira weissflogii might interact in a yet-to-be determined manner, which could impact TEP formation and aggregate abundance. The role of individual T. weissflogii-attaching and free-living new bacterial isolates for TEP production and diatom aggregation was investigated in vitro. T. weissflogii did not aggregate in axenic culture, and striking differences in aggregation dynamics and TEP abundance were observed when diatom cultures were inoculated with either diatom-attaching or free-living bacteria. The data indicated that free-living bacteria might not influence aggregation whereas bacteria attaching to diatom cells may increase aggregate formation. Interestingly, photosynthetically inactivated T. weissflogii cells did not aggregate regardless of the presence of bacteria. Comparison of aggregate formation, TEP production, aggregate sinking velocity and solid hydrated density revealed remarkable differences. Both, photosynthetically active T. weissflogii and specific diatom-attaching bacteria were required for aggregation. It was concluded that interactions between heterotrophic bacteria and diatoms increased aggregate formation and particle sinking and thus may enhance the efficiency of the biological pump. PMID:20827289

Formation of stimulated electromagnetic emission of the ionosphere: laboratory modeling

NASA Astrophysics Data System (ADS)

Starodubtsev, Mikhail; Kostrov, Alexander; Nazarov, Vladimir

Laboratory modeling of some physical processes involved in generation of the stimulated elec-tromagnetic emission (SEE) is presented. SEE is a noise component observed in the spectrum of the pump electromagnetic wave reflected from the heated ionosphere during the ionospheric heating experiments. In our laboratory experiments, main attention has been paid to the experimental investigation of generation of the most pronounced SEE components connected to the small-scale filamentation of the heated area of the ionosphere. It has been shown that the main physical mechanism of thermal magnetoplasma nonlinearity in this frequency range is due to thermal self-channeling of the Langmuir waves. This mechanism has the minimal threshold and should appear when both laboratory and ionospheric plasmas are heated by high-power radiowaves. Thermal self-channeling of Langmuir waves is connected with the fact that Langmuir waves are trapped in the area of depleted plasma density. As a result, wave amplitude significantly increases in these depleted ragion, which lead to the local plasma heating and, consequently, to the deepening of the plasma density depletion due to plasma thermo-diffusion. As the result, narrow, magnetic-field-aligned plasma density irregularities are formed in a magnetoplasma. Self-channelled Langmuir waves exhibit well-pronoused spectral satellites shifted by 1-2 MHz from the fundamental frequency (about 700 MHz in our experimental conditions). It has been found that there exist two main mechanisms of satellite formation. First mechanism (dynamic) has been observed during the formation of the small-scale irregularity, when its longitudinal size increases fastly. During this process, spectrum of the trapped wave characterizes by one low-frequency satellite. Physical mechanism, which lead to the formation of this satellite is connected to Doppler shift of the frequency of Langmuir waves trapped in the non-stationar plasma irregularity. Second mechanism

UV/TiO2 photocatalytic disinfection of carbon-bacteria complexes in activated carbon-filtered water: Laboratory and pilot-scale investigation.

PubMed

Zhao, Jin Hui; Chen, Wei; Zhao, Yaqian; Liu, Cuiyun; Liu, Ranbin

2015-01-01

The occurrence of carbon-bacteria complexes in activated carbon filtered water has posed a public health problem regarding the biological safety of drinking water. The application of combined process of ultraviolet radiation and nanostructure titanium dioxide (UV/TiO2) photocatalysis for the disinfection of carbon-bacteria complexes were assessed in this study. Results showed that a 1.07 Lg disinfection rate can be achieved using a UV dose of 20 mJ cm(-2), while the optimal UV intensity was 0.01 mW cm(-2). Particle sizes ≥8 μm decreased the disinfection efficiency, whereas variation in particle number in activated carbon-filtered water did not significantly affect the disinfection efficiency. Photoreactivation ratio was reduced from 12.07% to 1.69% when the UV dose was increased from 5 mJ cm(-2) to 20 mJ cm(-2). Laboratory and on-site pilot-scale experiments have demonstrated that UV/TiO2 photocatalytic disinfection technology is capable of controlling the risk posed by carbon-bacteria complexes and securing drinking water safety.

Released products of pathogenic bacteria stimulate biofilm formation by Escherichia coli K-12 strains.

PubMed

Vacheva, Anna; Ivanova, Radka; Paunova-Krasteva, Tsvetelina; Stoitsova, Stoyanka

2012-06-01

It has recently been shown that pathogens with a limited capacity for sessile growth (like some Escherichia coli O157 strains) can benefit from the presence of other bacteria and form mixed biofilms with companion strains. This study addresses the question whether pathogens may influence attached growth of E. coli non-pathogenic strains via secreted factors. We compared the biofilm-modulating effects of sterile stationary-phase culture media of a biofilm non-producing strain of E. coli O157:H, a laboratory biofilm-producing E. coli K-12 strain and a biofilm-forming strain of the pathogen Yersina enterocolitica O:3. Sessile growth was monitored as biomass (crystal violet assay), exopolysaccharide (ELLA) and morphology (scanning electron and confocal laser microscopy). With two of the E. coli K-12 strains stimulation of biofilm formation by all supernatants was achieved, but only the pathogens' secreted products induced biomass increase in some 'biofilm-deficient' K-12 strains. Lectin-peroxidase labeling indicated changes in colanic acid and poly-N-acetylglucosamine amounts in extracellular matrices. The contribution of indole, protein and polysaccharide to the biofilm-modulating activities of the supernatants was compared. Indole, in concentrations equal to those established in the supernatants, suppressed sessile growth in one K-12 strain. Proteinase K significantly reduced the stimulatory effects of all supernatants, indicating a prominent role of protein/peptide factor(s) in biofilm promotion. The amount of released polysaccharides (rPS) in the supernatants was quantitated then comparable quantities of isolated rPS were applied during biofilm growth. The three rPS had notable strain-specific effects with regard to both the strain-source of the rPS and the E. coli K-12 target strain.

Enumerating Spore-Forming Bacteria Airborne with Particles

NASA Technical Reports Server (NTRS)

Lin, Ying; Barengoltz, Jack

2006-01-01

A laboratory method has been conceived to enable the enumeration of (1) Cultivable bacteria and bacterial spores that are, variously, airborne by themselves or carried by, parts of, or otherwise associated with, other airborne particles; and (2) Spore-forming bacteria among all of the aforementioned cultivable microbes.

Oxygen and iron isotope studies of magnetite produced by magnetotactic bacteria

USGS Publications Warehouse

Mandernack, K.W.; Bazylinski, D.A.; Shanks, Wayne C.; Bullen, T.D.

1999-01-01

A series of carefully controlled laboratory studies was carried out to investigate oxygen and iron isotope fractionation during the intracellular production of magnetite (Fe3O4) by two different species of magnetotactic bacteria at temperatures between 4??and 35??C under microaerobic and anaerobic conditions. No detectable fractionation of iron isotopes in the bacterial magnetites was observed. However, oxygen isotope measurements indicated a temperature-dependent fractionation for Fe3O4 and water that is consistent with that observed for Fe3O4 produced extracellularly by thermophilic Fe3+-reducing bacteria. These results contrast with established fractionation curves estimated from either high-temperature experiments or theoretical calculations. With the fractionation curve established in this report, oxygen-18 isotope values of bacterial Fe3O4 may be useful in paleoenvironmental studies for determining the oxygen-18 isotope values of formation waters and for inferring paleotemperatures.

High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories.

PubMed

van Veen, S Q; Claas, E C J; Kuijper, Ed J

2010-03-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.

Laboratory Verification of Occulter Contrast Performance and Formation Flight

NASA Astrophysics Data System (ADS)

Sirbu, Dan

2014-01-01

Direct imaging of an exo-Earth is a difficult technical challenge. First, the intensity ratio between the parent star and its dim, rocky planetary companion is expected to be ten billion times. Additionally, for a planetary companion in the habitable zone the angular separation to the star is very small, such that only nearby stars are feasible targets. An external occulter is a spacecraft that is flown in formation with the observing space telescope and blocks starlight prior to the entrance pupil. Its shape must be specially designed to control for diffraction and be tolerant of errors such as misalignment, manufacturing, and deformations. In this dissertation, we present laboratory results pertaining to the optical verification of the contrast performance of a scaled occulter and implementation of an algorithm for the alignment of the telescope in the shadow of the occulter. The experimental testbed is scaled from space dimensions to the laboratory by maintaining constant Fresnel numbers while preserving an identical diffraction integral. We present monochromatic results in the image plane showing contrast better than 10 orders of magnitude, consistent with the level required for imaging an Exo-earth, and obtained using an optimized occulter shape. We compare these results to a baseline case using a circular occulter and to the theoretical predictions. Additionally, we address the principal technical challenge in the formation flight problem through demonstration of an alignment algorithm that is based on out-of-band leaked light. Such leaked light can be used a map to estimate the location of the telescope in the shadow and perform fine alignment during science observations.

From Laboratory Research to a Clinical Trial

PubMed Central

Michels, Harold T.; Keevil, C. William; Salgado, Cassandra D.; Schmidt, Michael G.

2015-01-01

Objective: This is a translational science article that discusses copper alloys as antimicrobial environmental surfaces. Bacteria die when they come in contact with copper alloys in laboratory tests. Components made of copper alloys were also found to be efficacious in a clinical trial. Background: There are indications that bacteria found on frequently touched environmental surfaces play a role in infection transmission. Methods: In laboratory testing, copper alloy samples were inoculated with bacteria. In clinical trials, the amount of live bacteria on the surfaces of hospital components made of copper alloys, as well as those made from standard materials, was measured. Finally, infection rates were tracked in the hospital rooms with the copper components and compared to those found in the rooms containing the standard components. Results: Greater than a 99.9% reduction in live bacteria was realized in laboratory tests. In the clinical trials, an 83% reduction in bacteria was seen on the copper alloy components, when compared to the surfaces made from standard materials in the control rooms. Finally, the infection rates were found to be reduced by 58% in patient rooms with components made of copper, when compared to patients' rooms with components made of standard materials. Conclusions: Bacteria die on copper alloy surfaces in both the laboratory and the hospital rooms. Infection rates were lowered in those hospital rooms containing copper components. Thus, based on the presented information, the placement of copper alloy components, in the built environment, may have the potential to reduce not only hospital-acquired infections but also patient treatment costs. PMID:26163568

Maximising resource allocation in the teaching laboratory: understanding student evaluations of teaching assistants in a team-based teaching format

NASA Astrophysics Data System (ADS)

Nikolic, Sasha; Suesse, Thomas F.; McCarthy, Timothy J.; Goldfinch, Thomas L.

2017-11-01

Minimal research papers have investigated the use of student evaluations on the laboratory, a learning medium usually run by teaching assistants with little control of the content, delivery and equipment. Finding the right mix of teaching assistants for the laboratory can be an onerous task due to the many skills required including theoretical and practical know-how, troubleshooting, safety and class management. Using larger classes with multiple teaching assistants, a team-based teaching (TBT) format may be advantageous. A rigorous three-year study across twenty-five courses over repetitive laboratory classes is analysed using a multi-level statistical model considering students, laboratory classes and courses. The study is used to investigate the effectiveness of the TBT format, and quantify the influence each demonstrator has on the laboratory experience. The study found that TBT is effective and the lead demonstrator most influential, influencing up to 55% of the laboratory experience evaluation.

Elevating Learner Achievement Using Formative Electronic Lab Assessments in the Engineering Laboratory: A Viable Alternative to Weekly Lab Reports

ERIC Educational Resources Information Center

Chen, Baiyun; DeMara, Ronald F.; Salehi, Soheil; Hartshorne, Richard

2018-01-01

A laboratory pedagogy interweaving weekly student portfolios with onsite formative electronic laboratory assessments (ELAs) is developed and assessed within the laboratory component of a required core course of the electrical and computer engineering (ECE) undergraduate curriculum. The approach acts to promote student outcomes, and neutralize…

The ecological significance of biofilm formation by plant-associated bacteria.

PubMed

Morris, Cindy E; Monier, Jean-Michel

2003-01-01

Bacteria associated with plants have been observed frequently to form assemblages referred to as aggregates, microcolonies, symplasmata, or biofilms on leaves and on root surfaces and within intercellular spaces of plant tissues. In a wide range of habitats, biofilms are purported to be microniches of conditions markedly different from those of the ambient environment and drive microbial cells to effect functions not possible alone or outside of biofilms. This review constructs a portrait of how biofilms associated with leaves, roots and within intercellular spaces influence the ecology of the bacteria they harbor and the relationship of bacteria with plants. We also consider how biofilms may enhance airborne dissemination, ubiquity and diversification of plant-associated bacteria and may influence strategies for biological control of plant disease and for assuring food safety. Trapped by a nexus, coordinates uncertain Ever expanding or contracting Cannibalistic and scavenging sorties Excavations through signs of past alliances Consensus signals sound revelry Then time warped by viscosity Genomes showing codependence A virtual microbial beach party With no curfew and no time-out A few estranged cells seeking exit options, Looking for another menagerie. David Sands, Montana State University, Bozeman, February 2003

Potential coupling effects of ammonia-oxidizing and anaerobic ammonium-oxidizing bacteria on completely autotrophic nitrogen removal over nitrite biofilm formation induced by the second messenger cyclic diguanylate.

PubMed

Wang, Chao; Liu, Sitong; Xu, Xiaochen; Zhao, Chuanqi; Yang, Fenglin; Wang, Dong

2017-05-01

The objective of this study was to investigate the influence of extracellular polymeric substance (EPS) on the coupling effects between ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria for the completely autotrophic nitrogen removal over nitrite (CANON) biofilm formation in a moving bed biofilm reactor (MBBR). Analysis of the quantity of EPS and cyclic diguanylate (c-di-GMP) confirmed that the contents of polysaccharides and c-di-GMP were correlated in the AOB sludge, anammox sludge, and CANON biofilm. The anammox sludge secreted more EPS (especially polysaccharides) than AOB with a markedly higher c-di-GMP content, which could be used by the bacteria to regulate the synthesis of exopolysaccharides that are ultimately used as a fixation matrix, for the adhesion of biomass. Indeed, increased intracellular c-di-GMP concentrations in the anammox sludge enhanced the regulation of polysaccharides to promote the adhesion of AOB and formation of the CANON biofilm. Overall, the results of this study provide new comprehensive information regarding the coupling effects of AOB and anammox bacteria for the nitrogen removal process.

The influence of the chemical composition of drinking water on cuprosolvency by biofilm bacteria.

PubMed

Critchley, M M; Cromar, N J; McClure, N C; Fallowfield, H J

2003-01-01

This study investigated the influence of water chemistry on copper solvation (cuprosolvency) by pure culture biofilms of heterotrophic bacteria isolated from copper plumbing. Heterotrophic bacteria isolated from copper plumbing biofilms including Acidovorax delafieldii, Flavobacterium sp., Corynebacterium sp., Pseudomonas sp. and Stenotrophomonas maltophilia were used in laboratory coupon experiments to assess their potential for cuprosolvency. Sterile copper coupons were exposed to pure cultures of bacteria to allow biofilm formation and suspended in drinking waters with different chemical compositions. Sterile coupons not exposed to bacteria were used as controls. After 5 days of incubation, copper release and biofilm accumulation was quantified. The results demonstrated that cuprosolvency in the control experiments was influenced by water pH, total organic carbon (TOC) and conductivity. Cuprosolvency in the presence of biofilms correlated with the chemical composition of the water supplies particularly pH, Langeliers Index, chloride, alkalinity, TOC and soluble phosphate concentrations. The results suggest water quality may influence cuprosolvency by biofilms present within copper plumbing pipes. The potential for water chemistry to influence cuprosolvency by biofilms may contribute to the sporadic nature of copper corrosion problems in distribution systems.

High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories ▿

PubMed Central

van Veen, S. Q.; Claas, E. C. J.; Kuijper, Ed J.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory. PMID:20053859

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture-dependent and PCR-DGGE methods.

PubMed

Lin, Xiao-Li; Pan, Qin-Jian; Tian, Hong-Gang; Douglas, Angela E; Liu, Tong-Xian

2015-03-01

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Propensity for biofilm formation by aerobic mesophilic and thermophilic spore forming bacteria isolated from Chinese milk powders.

PubMed

Sadiq, Faizan A; Flint, Steve; Yuan, Lei; Li, Yun; Liu, TongJie; He, GuoQing

2017-12-04

Biofilms on the surface of dairy manufacturing plants are potential reservoirs of microbial contamination. These microbial aggregates may harbour pathogenic and spoilage organisms which contaminate dairy products. The biofilm forming capacity of many spore forming isolates of dairy origin has not been given much attention. The present study explored the biofilm forming potential of 148 isolates, comprising mesophilic and thermophilic bacteria, with particular emphasis on Bacillus licheniformis on polystyrene and stainless steel (SS) surfaces. We concluded that only four species are of significance for biofilm development on the surface of SS in the presence of skimmed milk, namely, B. licheniformis, Geobacillus stearothermophilus, Geobacillus thermoleovorans group and Anoxybacillus flavithermus. The maximum number of cells recovered from the biofilms developed on SS coupons in the presence of skimmed milk for these four species was as follows: 4.8, 5.2, 4.5 and 5.3logCFU/cm 2 , respectively. Number of cells recovered from biofilms on 1cm 2 SS coupons increased in the presence of tryptic soy broth (TSB) for all mesophiles including B. licheniformis, while decreased for G. stearothermophilus, G. thermoleovorans group and A. flavithermus. The crystal violet staining assay on polystyrene proved to be inadequate to predict cell counts on SS for the bacteria tested in our trial in the presence of either TSB or skimmed milk. The results support the idea that biofilm formation is an important part of bacterial survival strategy as only the most prevalent isolates from milk powders formed good biofilms on SS in the presence of skimmed milk. Biofilm formation also proved to be a strain-dependent characteristic and interestingly significant variation in biofilm formation was observed within the same RAPD groups of B. licheniformis which supports the previously reported genetic and phenotypic heterogeneity within the same RAPD based groups. The work reported in this manuscript

Pathogenesis of pigment gallstones in Western societies: the central role of bacteria.

PubMed

Stewart, Lygia; Oesterle, Adair L; Erdan, Ihsan; Griffiss, J MacLeod; Way, Lawrence W

2002-01-01

Bacteria are traditionally accorded a greater role in pigment gallstone formation in Eastern populations. Stone color is thought to predict the presence of bacteria; that is, black stones (Western predominant) are supposedly sterile and brown stones (Eastern predominant) contain bacteria. We previously reported that, regardless of appearance, most pigment gallstones contain bacteria. This study examined, in a large Western population (370 patients), the incidence, appearance, and chemical composition of pigment stones, and the characteristics of gallstone bacteria. One hundred eighty-six pigment stones were obtained aseptically. Bacteria were detected by means of scanning electron microscopy and gallstone culture. Chemical composition was determined by infrared spectroscopy. Bacteria were tested for slime and beta-glucuronidase production. Seventy-three percent of pigment stones contained bacteria. Choledocholithiasis was associated with gallstone bacteria. Ca-bilirubinate was present in all pigment stones. Ca-palmitate was characteristic of infected stones, and more than 75% Ca-carbonate was characteristic of sterile stones. Neither chemical composition nor stone appearance predicted the presence of bacteria. Ninety-five percent and 67% of infected pigment stones contained bacteria that produced slime and beta-glucuronidase, respectively. Most pigment stones contained bacteria that produced beta-glucuronidase, slime, and phospholipase, factors that facilitate stone formation. Thus bacteria have a major role in Western pigment gallstone formation. Furthermore, gallstone color did not predict composition or bacterial presence.

Martian Cryogenic Carbonate Formation: Stable Isotope Variations Observed in Laboratory Studies

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Niles, Paul B.; Sun, Tao; Fu, Qi; Romanek, Christopher S.; Gibson, Everett K. Jr.

2014-01-01

The history of water on Mars is tied to the formation of carbonates through atmospheric CO2 and its control of the climate history of the planet. Carbonate mineral formation under modern martian atmospheric conditions could be a critical factor in controlling the martian climate in a means similar to the rock weathering cycle on Earth. The combination of evidence for liquid water on the martian surface and cold surface conditions suggest fluid freezing could be very common on the surface of Mars. Cryogenic calcite forms easily from freezing solutions when carbon dioxide degasses quickly from Ca-bicarbonate-rich water, a process that has been observed in some terrestrial settings such as arctic permafrost cave deposits, lake beds of the Dry Valleys of Antarctica, and in aufeis (river icings) from rivers of N.E. Alaska. A series of laboratory experiments were conducted that simulated cryogenic carbonate formation on Mars in order to understand their isotopic systematics. The results indicate that carbonates grown under martian conditions show variable enrichments from starting bicarbonate fluids in both carbon and oxygen isotopes beyond equilibrium values.

Growth characterization of individual rye sourdough bacteria by isothermal microcalorimetry.

PubMed

Mihhalevski, A; Sarand, I; Viiard, E; Salumets, A; Paalme, T

2011-02-01

The present work tests the feasibility of the isothermal microcalorimetry method to study the performance of individual lactic acid bacteria during solid-state fermentation in rye sourdough. Another aim was to elucidate the key factors leading to the formation of different microbial consortia in laboratory and industrial sourdough during continuous backslopping propagation. Strains of the individual LAB isolated from industrial and laboratory sourdough cycle were grown in 10 kGy irradiated rye dough in vials of an isothermal calorimeter and the power-time curves were obtained. Sugars, organic acids and free amino acids in the sourdough were measured. The OD-time curves of the LAB strains during growth in flour extract or MRS (De Man, Rogosa and Sharpe) broth were also determined. The maximum specific growth rates of Lactobacillus sakei, Lactobacillus brevis, Lactobacillus curvatus and Leuconostoc citreum strains that dominated in backslopped laboratory sourdough were higher than those of Lactobacillus helveticus, Lactobacillus panis, Lactobacillus vaginalis, Lactobacillus casei and Lactobacillus pontis strains originating from industrial sourdough. Industrial strains had higher specific growth rates below pH 4·8. It was supposed that during long-run industrial backslopping processes, the oxygen sensitive species start to dominate because of the O(2) protective effect of rye sourdough. Measurements of the power-time curves revealed that the LAB strains dominating in the industrial sourdough cycle had better acid tolerance but lower maximum growth rate and oxygen tolerance than species isolated from a laboratory sourdough cycle. Isothermal microcalorimetry combined with chemical analysis is a powerful method for characterization of sourdough fermentation process and determination of growth characteristics of individual bacteria in sourdough. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

Sedimentary phosphate and associated fossil bacteria in a Paleoproterozoic tidal flat in the 1.85 Ga Michigamme Formation, Michigan, USA

NASA Astrophysics Data System (ADS)

Hiatt, Eric E.; Pufahl, Peir K.; Edwards, Cole T.

2015-04-01

Phosphorus is a nutrient fundamental to life and when it precipitates in modern environments bacteria are intimately involved in its release, concentration, and mineralization. Preserved fossil bacteria in phosphate crusts and grains from the ca. 1850 million-year-old Bijiki Iron Formation Member of the Michigamme Formation, Michigan provide insight into the longevity and nature of this relationship. The Michigamme Formation accumulated near the end of the Earth's initial phosphogenic episode (ca. 2.2 and 1.8 Ga) to produce one of the first granular phosphorites. Phosphatic lithofacies consist of fine- to medium-sand-sized francolite peloids concentrated on bedding surfaces in peritidal facies. Granular beds are up to 2 cm thick and peloids are often partially to completely replaced by dolomite and chert. The grains contain organic matter and pyrite framboids that suggest bacterial breakdown of organic matter and bacterial sulfate reduction. The peritidal nature of phosphorite in the Michigamme Formation is in sharp contrast to Phanerozoic phosphogenic environments in deeper coastal upwelling settings. Peritidal settings were well suited for phosphogenesis under the very low oxygen and low dissolved sulfate levels of the Paleoproterozoic as cyanobacteria produced oxygen in shallow water and evaporation led to increased sulfate concentrations. Such concomitant processes helped establish focused redox interfaces in the sediment that chemosynthetic bacterial communities (sulfur oxidizers, reducers, forms that concentrate P, and possibly iron oxidizers) could exploit. Phosphate released from organic matter by heterotrophic bacteria and Fe-redox pumping was further concentrated by these chemotrophs; a process that forms late Neoproterozoic to Phanerozoic phosphorites but on a much larger scale. This early example of a granular phosphorite demonstrates that, like their Phanerozoic counterparts, Paleoproterozoic phosphorites are the concentrated indirectly biomineralized

Survival of soil bacteria during prolonged desiccation.

NASA Technical Reports Server (NTRS)

Chen, M.; Alexander, M.

1973-01-01

A determination was made of the kinds and numbers of bacteria surviving when two soils were maintained in the laboratory under dry conditions for more than half a year. Certain non-spore-forming bacteria were found to survive in the dry condition for long periods. A higher percentage of drought-tolerant than drought-sensitive bacteria was able to grow at low water activities. When they were grown in media with high salt concentrations, bacteria generally became more tolerant of prolonged drought and they persisted longer. The percent of cells in a bacterial population that remained viable when exposed to drought stress varied with the stage of growth.

Proteinaceous determinants of surface colonization in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective

PubMed Central

Chagnot, Caroline; Zorgani, Mohamed A.; Astruc, Thierry; Desvaux, Mickaël

2013-01-01

Bacterial colonization of biotic or abiotic surfaces results from two quite distinct physiological processes, namely bacterial adhesion and biofilm formation. Broadly speaking, a biofilm is defined as the sessile development of microbial cells. Biofilm formation arises following bacterial adhesion but not all single bacterial cells adhering reversibly or irreversibly engage inexorably into a sessile mode of growth. Among molecular determinants promoting bacterial colonization, surface proteins are the most functionally diverse active components. To be present on the bacterial cell surface, though, a protein must be secreted in the first place. Considering the close association of secreted proteins with their cognate secretion systems, the secretome (which refers both to the secretion systems and their protein substrates) is a key concept to apprehend the protein secretion and related physiological functions. The protein secretion systems are here considered in light of the differences in the cell-envelope architecture between diderm-LPS (archetypal Gram-negative), monoderm (archetypal Gram-positive) and diderm-mycolate (archetypal acid-fast) bacteria. Besides, their cognate secreted proteins engaged in the bacterial colonization process are regarded from single protein to supramolecular protein structure as well as the non-classical protein secretion. This state-of-the-art on the complement of the secretome (the secretion systems and their cognate effectors) involved in the surface colonization process in diderm-LPS and monoderm bacteria paves the way for future research directions in the field. PMID:24133488

The structural bases of long-term anabiosis in non-spore-forming bacteria

NASA Astrophysics Data System (ADS)

Suzina, Natalia E.; Mulyukin, Andrey L.; Dmitriev, Vladimir V.; Nikolaev, Yury A.; Shorokhova, Anna P.; Bobkova, Yulia S.; Barinova, Ekaterina S.; Plakunov, Vladimir K.; El-Registan, Galina I.; Duda, Vitalii I.

2006-01-01

Peculiarities of the structural organization in non-spore-forming bacteria associated with long-term anabiosis were revealed both in laboratory cultures and in natural populations isolated from 1 3-Myr-old Eastern Siberian permafrost and tundra soil. Different advanced methods were used, including (a) high-resolution electron microscopy; (b) simulation of in situ conditions in the laboratory by varying the composition of growth medium and cultivation conditions; (c) low-temperature fractionation to isolate and concentrate microbial cells from natural soils; (d) comparative morphological analysis of microbial cells in model cultures and natural soils (in situ). Under laboratory conditions, the intense formation of resting cells by representatives of various taxa of eubacteria and halophilic archaea occurred in 2 9-month-old cultures grown in carbon-, nitrogen-, or phosphorus-limited media, in starved cell suspensions in the presence of sodium silicate, or on soil agar. Among resting cells, we revealed cystlike forms having a complicated structure and common features. These included a thick capsule; a thickened and multiprofile cell wall; the presence of large intramembrane particles on PF- and EF-fracture surfaces; fine-grained or lumpy cytoplasm; and a condensed nucleoid. The general morphological properties, ultrastructural organization, physiological features of cystlike cells, and their ability to germinate under the appropriate conditions suggest the existence of constitutive dormancy in non-spore-forming bacteria. It was found that the majority of microorganisms in permafrost and tundra soil are cystlike cells, very similar to those in laboratory cultures. Anabiotic (resting) cystlike cells are responsible for the survival of non-spore-formers in extreme Earth habitats and may be regarded as possible analogs of extraterrestrial forms of microbial life.

Magnetotactic bacteria on Earth and on Mars.

PubMed

McKay, Christopher P; Friedmann, E Imre; Frankel, Richard B; Bazylinski, Dennis A

2003-01-01

Continued interest in the possibility of evidence for life in the ALH84001 Martian meteorite has focused on the magnetite crystals. This review is structured around three related questions: is the magnetite in ALH84001 of biological or non-biological origin, or a mixture of both? does magnetite on Earth provide insight to the plausibility of biogenic magnetite on Mars? could magnetotaxis have developed on Mars? There are credible arguments for both the biological and non-biological origin of the magnetite in ALH84001, and we suggest that more studies of ALH84001, extensive laboratory simulations of non-biological magnetite formation, as well as further studies of magnetotactic bacteria on Earth will be required to further address this question. Magnetite grains produced by bacteria could provide one of the few inorganic traces of past bacterial life on Mars that could be recovered from surface soils and sediments. If there was biogenic magnetite on Mars in sufficient abundance to leave fossil remains in the volcanic rocks of ALH84001, then it is likely that better-preserved magnetite will be found in sedimentary deposits on Mars. Deposits in ancient lakebeds could contain well-preserved chains of magnetite clearly indicating a biogenic origin.

Magnetotactic bacteria on Earth and on Mars

NASA Technical Reports Server (NTRS)

McKay, Christopher P.; Friedmann, E. Imre; Frankel, Richard B.; Bazylinski, Dennis A.

2003-01-01

Continued interest in the possibility of evidence for life in the ALH84001 Martian meteorite has focused on the magnetite crystals. This review is structured around three related questions: is the magnetite in ALH84001 of biological or non-biological origin, or a mixture of both? does magnetite on Earth provide insight to the plausibility of biogenic magnetite on Mars? could magnetotaxis have developed on Mars? There are credible arguments for both the biological and non-biological origin of the magnetite in ALH84001, and we suggest that more studies of ALH84001, extensive laboratory simulations of non-biological magnetite formation, as well as further studies of magnetotactic bacteria on Earth will be required to further address this question. Magnetite grains produced by bacteria could provide one of the few inorganic traces of past bacterial life on Mars that could be recovered from surface soils and sediments. If there was biogenic magnetite on Mars in sufficient abundance to leave fossil remains in the volcanic rocks of ALH84001, then it is likely that better-preserved magnetite will be found in sedimentary deposits on Mars. Deposits in ancient lakebeds could contain well-preserved chains of magnetite clearly indicating a biogenic origin.

The emerging role for bacteria in lignin degradation and bio-product formation.

PubMed

Bugg, Timothy D H; Ahmad, Mark; Hardiman, Elizabeth M; Singh, Rahul

2011-06-01

The microbial degradation of lignin has been well studied in white-rot and brown-rot fungi, but is much less well studied in bacteria. Recent published work suggests that a range of soil bacteria, often aromatic-degrading bacteria, are able to break down lignin. The enzymology of bacterial lignin breakdown is currently not well understood, but extracellular peroxidase and laccase enzymes appear to be involved. There are also reports of aromatic-degrading bacteria isolated from termite guts, though there are conflicting reports on the ability of termite gut micro-organisms to break down lignin. If biocatalytic routes for lignin breakdown could be developed, then lignin represents a potentially rich source of renewable aromatic chemicals. Copyright © 2010 Elsevier Ltd. All rights reserved.

Bacteria, biofilm and honey: a study of the effects of honey on 'planktonic' and biofilm-embedded chronic wound bacteria.

PubMed

Merckoll, Patricia; Jonassen, Tom Øystein; Vad, Marie Elisabeth; Jeansson, Stig L; Melby, Kjetil K

2009-01-01

Chronically infected wounds are a costly source of suffering. An important factor in the failure of a sore to heal is the presence of multiple species of bacteria, living cooperatively in highly organized biofilms. The biofilm protects the bacteria from antibiotic therapy and the patient's immune response. Honey has been used as a wound treatment for millennia. The components responsible for its antibacterial properties are now being elucidated. The study aimed to determine the effects of different concentrations of 'Medihoney' therapeutic honey and Norwegian Forest Honey 1) on the real-time growth of typical chronic wound bacteria; 2) on biofilm formation; and 3) on the same bacteria already embedded in biofilm. Reference strains of MRSE, MRSA, ESBL Klebsiella pneumoniae and Pseudomonas aeruginosa were incubated with dilution series of the honeys in microtitre plates for 20 h. Growth of the bacteria was assessed by measuring optical density every 10 min. Growth curves, biofilm formation and minimum bactericidal concentrations are presented. Both honeys were bactericidal against all the strains of bacteria. Biofilm was penetrated by biocidal substances in honey. Reintroduction of honey as a conventional wound treatment may help improve individual wound care, prevent invasive infections, eliminate colonization, interrupt outbreaks and thereby preserve current antibiotic stocks.

Isolation of Lightning-Competent Soil Bacteria

PubMed Central

Cérémonie, Hélène; Buret, François; Simonet, Pascal; Vogel, Timothy M.

2004-01-01

Artificial transformation is typically performed in the laboratory by using either a chemical (CaCl2) or an electrical (electroporation) method. However, laboratory-scale lightning has been shown recently to electrotransform Escherichia coli strain DH10B in soil. In this paper, we report on the isolation of two “lightning-competent” soil bacteria after direct electroporation of the Nycodenz bacterial ring extracted from prairie soil in the presence of the pBHCRec plasmid (Tcr, Spr, Smr). The electrotransformability of the isolated bacteria was measured both in vitro (by electroporation cuvette) and in situ (by lightning in soil microcosm) and then compared to those of E. coli DH10B and Pseudomonas fluorescens C7R12. The electrotransformation frequencies measured reached 10−3 to 10−4 by electroporation and 10−4 to 10−5 by simulated lightning, while no transformation was observed in the absence of electrical current. Two of the isolated lightning-competent soil bacteria were identified as Pseudomonas sp. strains. PMID:15466589

Effect of citric acid and rhizosphere bacteria on metal plaque formation and metal accumulation in reeds in synthetic acid mine drainage solution.

PubMed

Guo, Lin; Cutright, Teresa J

2014-06-01

Many of regions in the world have been affected by acid mine drainage (AMD). The study assessed the effect of rhizosphere bacteria and citric acid (CA) on the metal plaque formation and heavy metal uptake in Phragmites australis cultured in synthetic AMD solution. Mn and Al plaque were not formed, but Fe plaque which was mediated by rhizosphere iron oxidizing bacteria (Fe(II)OB) was observed on the root system of reeds. Fe plaque did not significantly influence the uptake of Fe, Al and Mn into tissues of reeds. CA significantly (p<0.01) inhibited the growth of Fe(II)OB and decreased the formation of Fe plaque. CA also significantly improved (p<0.05) the accumulation of Fe, Mn and Al in all the tissues of reeds. Roots and rhizomes were the main organs to store metals. The roots contained 0.08±0.01mg/g Mn, 2.39±0.26mg/g Fe and 0.19±0.02mg/g Al, while the shoots accumulated 0.04±0.00mg/g Mn, 0.20±0.01mg/g Fe, 0.11±0.00mg/g Al in reeds cultured in solution amended with 2.101g/l CA and without inoculation of rhizosphere bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of Punica granatum L. Flower Water Extract on Five Common Oral Bacteria and Bacterial Biofilm Formation on Orthodontic Wire

PubMed Central

VAHID DASTJERDI, Elahe; ABDOLAZIMI, Zahra; GHAZANFARIAN, Marzieh; AMDJADI, Parisa; KAMALINEJAD, Mohammad; MAHBOUBI, Arash

2014-01-01

Background: Use of herbal extracts and essences as natural antibacterial compounds has become increasingly popular for the control of oral infectious diseases. Therefore, finding natural antimicrobial products with the lowest side effects seems necessary. The present study sought to assess the effect of Punica granatum L. water extract on five oral bacteria and bacterial biofilm formation on orthodontic wire. Methods: Antibacterial property of P. granatum L. water extract was primarily evaluated in brain heart infusion agar medium using well-plate method. The minimum inhibitory concentration and minimum bactericidal concentration were determined by macro-dilution method. The inhibitory effect on orthodontic wire bacterial biofilm formation was evaluated using viable cell count in biofilm medium. At the final phase, samples were fixed and analyzed by Scanning Electron Microscopy. Results: The growth inhibition zone diameter was proportional to the extract concentration. The water extract demonstrated the maximum antibacterial effect on Streptococcus sanguinis ATCC 10556 with a minimum inhibitory concentration of 6.25 mg/ml and maximum bactericidal effect on S. sanguinis ATCC 10556 and S. sobrinus ATCC 27607 with minimum bactericidal concentration of 25 mg/ml. The water extract decreased bacterial biofilm formation by S. sanguinis, S. sobrinus, S. salivarius, S. mutans ATCC 35608 and E. faecalis CIP 55142 by 93.7–100%, 40.6–99.9%, 85.2–86.5%, 66.4–84.4% and 35.5–56.3% respectively. Conclusion: Punica granatum L. water extract had significant antibacterial properties against 5 oral bacteria and prevented orthodontic wire bacterial biofilm formation. However, further investigations are required to generalize these results to the clinical setting. PMID:26171362

Bacteria-surface interactions.

PubMed

Tuson, Hannah H; Weibel, Douglas B

2013-05-14

The interaction of bacteria with surfaces has important implications in a range of areas, including bioenergy, biofouling, biofilm formation, and the infection of plants and animals. Many of the interactions of bacteria with surfaces produce changes in the expression of genes that influence cell morphology and behavior, including genes essential for motility and surface attachment. Despite the attention that these phenotypes have garnered, the bacterial systems used for sensing and responding to surfaces are still not well understood. An understanding of these mechanisms will guide the development of new classes of materials that inhibit and promote cell growth, and complement studies of the physiology of bacteria in contact with surfaces. Recent studies from a range of fields in science and engineering are poised to guide future investigations in this area. This review summarizes recent studies on bacteria-surface interactions, discusses mechanisms of surface sensing and consequences of cell attachment, provides an overview of surfaces that have been used in bacterial studies, and highlights unanswered questions in this field.

Air sampling to assess potential generation of aerosolized viable bacteria during flow cytometric analysis of unfixed bacterial suspensions

PubMed Central

Carson, Christine F; Inglis, Timothy JJ

2018-01-01

This study investigated aerosolized viable bacteria in a university research laboratory during operation of an acoustic-assisted flow cytometer for antimicrobial susceptibility testing by sampling room air before, during and after flow cytometer use. The aim was to assess the risk associated with use of an acoustic-assisted flow cytometer analyzing unfixed bacterial suspensions. Air sampling in a nearby clinical laboratory was conducted during the same period to provide context for the existing background of microorganisms that would be detected in the air. The three species of bacteria undergoing analysis by flow cytometer in the research laboratory were Klebsiella pneumoniae, Burkholderia thailandensis and Streptococcus pneumoniae. None of these was detected from multiple 1000 L air samples acquired in the research laboratory environment. The main cultured bacteria in both locations were skin commensal and environmental bacteria, presumed to have been disturbed or dispersed in laboratory air by personnel movements during routine laboratory activities. The concentrations of bacteria detected in research laboratory air samples were reduced after interventional cleaning measures were introduced and were lower than those in the diagnostic clinical microbiology laboratory. We conclude that our flow cytometric analyses of unfixed suspensions of K. pneumoniae, B. thailandensis and S. pneumoniae do not pose a risk to cytometer operators or other personnel in the laboratory but caution against extrapolation of our results to other bacteria and/or different flow cytometric experimental procedures. PMID:29608197

Design and process aspects of laboratory scale SCF particle formation systems.

PubMed

Vemavarapu, Chandra; Mollan, Matthew J; Lodaya, Mayur; Needham, Thomas E

2005-03-23

Consistent production of solid drug materials of desired particle and crystallographic morphologies under cGMP conditions is a frequent challenge to pharmaceutical researchers. Supercritical fluid (SCF) technology gained significant attention in pharmaceutical research by not only showing a promise in this regard but also accommodating the principles of green chemistry. Given that this technology attained commercialization in coffee decaffeination and in the extraction of hops and other essential oils, a majority of the off-the-shelf SCF instrumentation is designed for extraction purposes. Only a selective few vendors appear to be in the early stages of manufacturing equipment designed for particle formation. The scarcity of information on the design and process engineering of laboratory scale equipment is recognized as a significant shortcoming to the technological progress. The purpose of this article is therefore to provide the information and resources necessary for startup research involving particle formation using supercritical fluids. The various stages of particle formation by supercritical fluid processing can be broadly classified into delivery, reaction, pre-expansion, expansion and collection. The importance of each of these processes in tailoring the particle morphology is discussed in this article along with presenting various alternatives to perform these operations.

Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas.

NASA Astrophysics Data System (ADS)

Hippler, Rainer; Majumdar, Abhijit; Thejaswini, H. C.

Plasma chemical reaction studies with relevance to, e.g., Titan's atmosphere have been per-formed in various laboratory plasmas [1,2]. Chemical reactions in a dielectric barrier discharge at medium pressure of 250-300 mbar have been studied in CH4 /N2 and CH4 /Ar gas mixtures by means of mass spectrometry. The main reaction scheme is production of H2 by fragmenta-tion of CH4 , but also production of larger hydrocarbons like Cn Hm with n up to 10 including formation of different functional CN groups is observed. [1] A. Majumdar and R. Hippler, Development of dielectric barrier discharge plasma processing apparatus for mass spectrometry and thin film deposition, Rev. Sci. Instrum. 78, 075103 (2007) [2] H.T. Do, G. Thieme, M. Frühlich, H. Kersten, and R. Hippler, Ion Molecule and Dust Particle Formation in Ar/CH4 , Ar/C2 H2 and Ar/C3 H6 Radio-frequency Plasmas, Contrib. Plasma Phys. 45, No. 5-6, 378-384 (2005)

Establishment of the first international repository for transfusion-relevant bacteria reference strains: ISBT working party transfusion-transmitted infectious diseases (WP-TTID), subgroup on bacteria.

PubMed

Störmer, M; Arroyo, A; Brachert, J; Carrero, H; Devine, D; Epstein, J S; Gabriel, C; Gelber, C; Goodrich, R; Hanschmann, K-M; Heath, D G; Jacobs, M R; Keil, S; de Korte, D; Lambrecht, B; Lee, C-K; Marcelis, J; Marschner, S; McDonald, C; McGuane, S; McKee, M; Müller, T H; Muthivhi, T; Pettersson, A; Radziwon, P; Ramirez-Arcos, S; Reesink, H W; Rojo, J; Rood, I; Schmidt, M; Schneider, C K; Seifried, E; Sicker, U; Wendel, S; Wood, E M; Yomtovian, R A; Montag, T

2012-01-01

Bacterial contamination of platelet concentrates (PCs) still remains a significant problem in transfusion with potential important clinical consequences, including death. The International Society of Blood Transfusion Working Party on Transfusion-Transmitted Infectious Diseases, Subgroup on Bacteria, organised an international study on Transfusion-Relevant Bacteria References to be used as a tool for development, validation and comparison of both bacterial screening and pathogen reduction methods. Four Bacteria References (Staphylococcus epidermidis PEI-B-06, Streptococcus pyogenes PEI-B-20, Klebsiella pneumoniae PEI-B-08 and Escherichia coli PEI-B-19) were selected regarding their ability to proliferate to high counts in PCs and distributed anonymised to 14 laboratories in 10 countries for identification, enumeration and bacterial proliferation in PCs after low spiking (0·3 and 0·03 CFU/ml), to simulate contamination occurring during blood donation. Bacteria References were correctly identified in 98% of all 52 identifications. S. pyogenes and E. coli grew in PCs in 11 out of 12 laboratories, and K. pneumoniae and S. epidermidis replicated in all participating laboratories. The results of bacterial counts were very consistent between laboratories: the 95% confidence intervals were for S. epidermidis: 1·19-1·32 × 10(7) CFU/ml, S. pyogenes: 0·58-0·69 × 10(7) CFU/ml, K. pneumoniae: 18·71-20·26 × 10(7) CFU/ml and E. coli: 1·78-2·10 × 10(7) CFU/ml. The study was undertaken as a proof of principle with the aim to demonstrate (i) the quality, stability and suitability of the bacterial strains for low-titre spiking of blood components, (ii) the property of donor-independent proliferation in PCs, and (iii) their suitability for worldwide shipping of deep frozen, blinded pathogenic bacteria. These aims were successfully fulfilled. The WHO Expert Committee Biological Standardisation has approved the adoption of these four bacteria strains as the first

Maintenance of Laboratory Strains of Obligately Anaerobic Rumen Bacteria †

PubMed Central

Teather, Ronald M.

1982-01-01

Cultures of rumen bacteria can be stored at −20°C for at least 2 years in a liquid medium containing 20% glycerol. Thawing, sampling, and refreezing do not significantly affect viability. PMID:7125660

Effects of porous media preparation on bacteria transport through laboratory columns.

PubMed

Brown, Derick G; Stencel, Joseph R; Jaffé, Peter R

2002-01-01

Bacterial and colloid transport experiments related to environmental systems are typically performed in the laboratory, with sand often used as the porous media. In order to prepare the sand, mechanical sieving is frequently used to tighten the sand grain size distribution. However, mechanical sieving has been reported to provide insufficient repeatability between identical colloidal transport experiments. This work examined the deficiencies of mechanical sieving with respect to bacterial transport through sand columns. It was found that sieving with standard brass sieves (1) contaminates the sand with copper and zinc as a linear function of sieving time and (2) inefficiently sizes sand grains below 300 microm (the largest size examined in this study) due to rapid clogging of the sieves. A procedure was developed that allows utilization of brass sieves for sizing the sand grains and removes the metal contamination introduced from the sieves. Bacterial transport experiments utilizing this column preparation procedure gave repeatable breakthrough curves. Further examination of the effects of these treatments on bacterial transport showed interesting results. First, it was found that the metal contamination did not affect the clean-bed bacterial transport. Second. it was found that variations of the column flushing procedure did not alter the clean-bed breakthrough of the bacteria, but did alter the inter-particle blocking. Finally, it was found that the shape of the sand grains (oblong vs. rounded) significantly alters the bacterial transport. with the transport being dominated by the smallest dimension of the oblong grains.

Laboratory formation of a scaled protostellar jet by coaligned poloidal magnetic field.

PubMed

Albertazzi, B; Ciardi, A; Nakatsutsumi, M; Vinci, T; Béard, J; Bonito, R; Billette, J; Borghesi, M; Burkley, Z; Chen, S N; Cowan, T E; Herrmannsdörfer, T; Higginson, D P; Kroll, F; Pikuz, S A; Naughton, K; Romagnani, L; Riconda, C; Revet, G; Riquier, R; Schlenvoigt, H-P; Skobelev, I Yu; Faenov, A Ya; Soloviev, A; Huarte-Espinosa, M; Frank, A; Portugall, O; Pépin, H; Fuchs, J

2014-10-17

Although bipolar jets are seen emerging from a wide variety of astrophysical systems, the issue of their formation and morphology beyond their launching is still under study. Our scaled laboratory experiments, representative of young stellar object outflows, reveal that stable and narrow collimation of the entire flow can result from the presence of a poloidal magnetic field whose strength is consistent with observations. The laboratory plasma becomes focused with an interior cavity. This gives rise to a standing conical shock from which the jet emerges. Following simulations of the process at the full astrophysical scale, we conclude that it can also explain recently discovered x-ray emission features observed in low-density regions at the base of protostellar jets, such as the well-studied jet HH 154. Copyright © 2014, American Association for the Advancement of Science.

Biofilm formation, communication and interactions of leaching bacteria during colonization of pyrite and sulfur surfaces.

PubMed

Bellenberg, Sören; Díaz, Mauricio; Noël, Nanni; Sand, Wolfgang; Poetsch, Ansgar; Guiliani, Nicolas; Vera, Mario

2014-11-01

Bioleaching of metal sulfides is an interfacial process where biofilm formation is considered to be important in the initial steps of this process. Among the factors regulating biofilm formation, molecular cell-to-cell communication such as quorum sensing is involved. A functional LuxIR-type I quorum sensing system is present in Acidithiobacillus ferrooxidans. However, cell-to-cell communication among different species of acidophilic mineral-oxidizing bacteria has not been studied in detail. These aspects were the scope of this study with emphasis on the effects exerted by the external addition of mixtures of synthetic N-acyl-homoserine-lactones on pure and binary cultures. Results revealed that some mixtures had inhibitory effects on pyrite leaching. Some of them correlated with changes in biofilm formation patterns on pyrite coupons. We also provide evidence that A. thiooxidans and Acidiferrobacter spp. produce N-acyl-homoserine-lactones. In addition, the observation that A. thiooxidans cells attached more readily to pyrite pre-colonized by living iron-oxidizing acidophiles than to heat-inactivated or biofilm-free pyrite grains suggests that other interactions also occur. Our experiments show that pre-cultivation conditions influence A. ferrooxidans attachment to pre-colonized pyrite surfaces. The understanding of cell-to-cell communication may consequently be used to develop attempts to influence biomining/bioremediation processes. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Laboratory Formation of Fullerenes from PAHs: Top-down Interstellar Chemistry

NASA Astrophysics Data System (ADS)

Zhen, Junfeng; Castellanos, Pablo; Paardekooper, Daniel M.; Linnartz, Harold; Tielens, Alexander G. G. M.

2014-12-01

Interstellar molecules are thought to build up in the shielded environment of molecular clouds or in the envelope of evolved stars. This follows many sequential reaction steps of atoms and simple molecules in the gas phase and/or on (icy) grain surfaces. However, these chemical routes are highly inefficient for larger species in the tenuous environment of space as many steps are involved and, indeed, models fail to explain the observed high abundances. This is definitely the case for the C60 fullerene, recently identified as one of the most complex molecules in the interstellar medium. Observations have shown that, in some photodissociation regions, its abundance increases close to strong UV-sources. In this Letter we report laboratory findings in which C60 formation can be explained by characterizing the photochemical evolution of large polycyclic aromatic hydrocarbons (PAHs). Sequential H losses lead to fully dehydrogenated PAHs and subsequent losses of C2 units convert graphene into cages. Our results present for the first time experimental evidence that PAHs in excess of 60 C-atoms efficiently photo-isomerize to buckminsterfullerene, C60. These laboratory studies also attest to the importance of top-down synthesis routes for chemical complexity in space.

Laboratory investigations on the role of sediment surface and ground water chemistry in transport of bacteria through a contaminated Sandy Aquifer

USGS Publications Warehouse

Scholl, M.A.; Harvey, R.W.

1992-01-01

The effects of pH and sediment surface characteristics on sorption of indigenous groundwater bacteria were determined using contaminated and uncontaminated aquifer material from Cape Cod, MA. Over the pH range of the aquifer (5-7), the extent of bacterial sorption onto sediment in uncontaminated groundwater was strongly pH-dependent, but relatively pH-insensitive in contaminated groundwater from the site. Bacterial sorption was also affected by the presence of oxyhydroxide coatings (iron, aluminum, and manganese). Surface coating effects were most pronounced in uncontaminated groundwater (pH 6.4 at 10??C). Desorption of attached bacteria (up to 14% of the total number of labeled cells added) occurred in both field and laboratory experiments upon adjustment of groundwater to pH 8. The dependence of bacterial sorption upon environmental conditions suggests that bacterial immobilization could change substantially over relatively short distances in contaminated, sandy aquifers and that effects caused by changes in groundwater geochemistry can be significant.

Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Haiyan; Lin, Hui; Zheng, Wang

2013-08-04

Methylmercury is a neurotoxin that poses significant health risks to humans. Some anaerobic sulphate- and iron-reducing bacteria can methylate oxidized forms of mercury, generating methylmercury1-4. One strain of sulphate-reducing bacteria (Desulfovibrio desulfuricans ND132) can also methylate elemental mercury5. The prevalence of this trait among different bacterial strains and species remains unclear, however. Here, we compare the ability of two strains of the sulphate-reducing bacterium Desulfovibrio and one strain of the iron-reducing bacterium Geobacter to oxidise and methylate elemental mercury in a series of laboratory incubations. Experiments were carried out under dark, anaerobic conditions, in the presence of environmentally-relevant concentrations ofmore » elemental mercury. We report differences in the ability of these organisms to oxidise and methylate elemental mercury. In line with recent findings5, we show that Desulfovibrio desulfuricans ND132 can both oxidise and methylate elemental mercury. However, the rate of methylation of elemental mercury is only about one third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidise, but not methylate, elemental mercury. Geobacter sulfurreducens PCA is able to oxidise and methylate elemental mercury in the presence of cysteine. We suggest that the activity of methylating and non-methylating bacteria may together enhance the formation of methylmercury in anaerobic environments.« less

Dynamics of mono- and dual-species biofilm formation and interactions between Staphylococcus aureus and Gram-negative bacteria.

PubMed

Makovcova, Jitka; Babak, Vladimir; Kulich, Pavel; Masek, Josef; Slany, Michal; Cincarova, Lenka

2017-07-01

Microorganisms are not commonly found in the planktonic state but predominantly form dual- and multispecies biofilms in almost all natural environments. Bacteria in multispecies biofilms cooperate, compete or have neutral interactions according to the involved species. Here, the development of mono- and dual-species biofilms formed by Staphylococcus aureus and other foodborne pathogens such as Salmonella enterica subsp. enterica serovar Enteritidis, potentially pathogenic Raoultella planticola and non-pathogenic Escherichia coli over the course of 24, 48 and 72 h was studied. Biofilm formation was evaluated by the crystal violet assay (CV), enumeration of colony-forming units (CFU cm -2 ) and visualization using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). In general, Gram-negative bacterial species and S. aureus interacted in a competitive manner. The tested Gram-negative bacteria grew better in mixed dual-species biofilms than in their mono-species biofilms as determined using the CV assay, CFU ml -2 enumeration, and CLSM and SEM visualization. In contrast, the growth of S. aureus biofilms was reduced when cultured in dual-species biofilms. CLSM images revealed grape-like clusters of S. aureus and monolayers of Gram-negative bacteria in both mono- and dual-species biofilms. S. aureus clusters in dual-species biofilms were significantly smaller than clusters in S. aureus mono-species biofilms. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Bacteria can mobilize nematode-trapping fungi to kill nematodes

PubMed Central

Wang, Xin; Li, Guo-Hong; Zou, Cheng-Gang; Ji, Xing-Lai; Liu, Tong; Zhao, Pei-Ji; Liang, Lian-Ming; Xu, Jian-Ping; An, Zhi-Qiang; Zheng, Xi; Qin, Yue-Ke; Tian, Meng-Qing; Xu, You-Yao; Ma, Yi-Cheng; Yu, Ze-Fen; Huang, Xiao-Wei; Liu, Shu-Qun; Niu, Xue-Mei; Yang, Jin-Kui; Huang, Ying; Zhang, Ke-Qin

2014-01-01

In their natural habitat, bacteria are consumed by bacterivorous nematodes; however, they are not simply passive preys. Here we report a defensive mechanism used by certain bacteria to mobilize nematode-trapping fungi to kill nematodes. These bacteria release urea, which triggers a lifestyle switch in the fungus Arthrobotrys oligospora from saprophytic to nematode–predatory form; this predacious form is characterized by formation of specialized cellular structures or ‘traps’. The bacteria significantly promote the elimination of nematodes by A. oligospora. Disruption of genes involved in urea transport and metabolism in A. oligospora abolishes the urea-induced trap formation. Furthermore, the urea metabolite ammonia functions as a signal molecule in the fungus to initiate the lifestyle switch to form trap structures. Our findings highlight the importance of multiple predator–prey interactions in prey defense mechanisms. PMID:25514608

BACTERIOPHAGE FORMATION WITHOUT BACTERIAL GROWTH

PubMed Central

Price, Winston H.

1947-01-01

1. Iodoacetate, fluoride, and azide have been found to prevent the formation of phage and to inhibit the synthesis of ATP by Staphylococcus muscae. It is suggested that energy-rich phosphate is needed for the synthesis of phage. 2. Gramicidin prevented the formation of phage. 3. No differences were found between normal bacteria and phage-infected bacteria in the inorganic phosphate, adenosinetriphosphate, ribonucleic acid, and desoxyribonucleic acid content of the cells. 4. The mechanism of phage formation is discussed. PMID:18896936

Seed-vectored endophytic bacteria modulate development of rice seedlings.

PubMed

Verma, S K; Kingsley, K; Irizarry, I; Bergen, M; Kharwar, R N; White, J F

2017-06-01

The aim of the present study was to evaluate the effects of the removal of indigenous bacteria from rice seeds on seedling growth and development. Here we report the presence of three indigenous endophytic bacteria in rice seeds that play important roles in modulating seedling development (shoot and root lengths, and formation of root hairs and secondary roots) and defence against pathogens. Seed-associated bacteria were removed using surface sterilization with NaOCl (bleach) followed by antibiotic treatment. When bacteria were absent, growth of seedlings in terms of root hair development and overall seedling size was less than that of seedlings that contained bacteria. Reactive oxygen staining of seedlings showed that endophytic bacteria became intracellular in root parenchyma cells and root hairs. Roots containing endophytic bacteria were seen to stain densely for reactive oxygen, while roots free of bacteria stained lightly for reactive oxygen. Bacteria were isolated and identified as Enterobacter asburiae (VWB1), Pantoea dispersa (VWB2) and Pseudomonas putida (VWB3) by 16S rDNA sequencing. Bacteria were found to produce indole acetic acid (auxins), inhibited the pathogen Fusarium oxysporum and solubilized phosphate. Reinoculation of bacteria onto seedlings derived from surface-disinfected rice and Bermuda grass seeds significantly restored seedling growth and development. Rice seeds harbour indigenous bacterial endophytes that greatly influence seedling growth and development, including root and shoot lengths, root hair formation and disease susceptibility of rice seedlings. This study shows that seeds of rice naturally harbour bacterial endophytes that play key roles in modulation of seedling development. © 2017 The Society for Applied Microbiology.

Human cathelicidin peptide LL37 inhibits both attachment capability and biofilm formation of Staphylococcus epidermidis.

PubMed

Hell, E; Giske, C G; Nelson, A; Römling, U; Marchini, G

2010-02-01

The aim of this work was to investigate the possible effect of human cathelicidin antimicrobial peptide LL37 on biofilm formation of Staphylococcus epidermidis, a major causative agent of indwelling device-related infections. We performed initial attachment assay and biofilm formation solid surface assay in microtitre plates, as well as growth experiment in liquid medium using laboratory strain Staph. epidermidis ATCC35984. We found that already a low concentration of the peptide LL37 (1 mg l(-1)) significantly decreased both the attachment of bacteria to the surface and also the biofilm mass. No growth inhibition was observed even at 16 mg l(-1) concentration of LL37, indicating a direct effect of the peptide on biofilm production. As biofilm protects bacteria during infections in humans and allows their survival in a hostile environment, inhibition of biofilm formation by LL37 may have a key role to prevent bacterial colonization on indwelling devices. Our findings suggest that this host defence factor can be a potential candidate in prevention and treatment strategies of Staph. epidermidis infections in humans.

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories.

PubMed

Woo, P C Y; Lau, S K P; Teng, J L L; Tse, H; Yuen, K-Y

2008-10-01

In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a pivotal role in the accurate identification of bacterial isolates and the discovery of novel bacteria in clinical microbiology laboratories. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. Not only has it provided insights into aetiologies of infectious disease, but it also helps clinicians in choosing antibiotics and in determining the duration of treatment and infection control procedures. With the use of 16S rDNA sequencing, 215 novel bacterial species, 29 of which belong to novel genera, have been discovered from human specimens in the past 7 years of the 21st century (2001-2007). One hundred of the 215 novel species, 15 belonging to novel genera, have been found in four or more subjects. The largest number of novel species discovered were of the genera Mycobacterium (n = 12) and Nocardia (n = 6). The oral cavity/dental-related specimens (n = 19) and the gastrointestinal tract (n = 26) were the most important sites for discovery and/or reservoirs of novel species. Among the 100 novel species, Streptococcus sinensis, Laribacter hongkongensis, Clostridium hathewayi and Borrelia spielmanii have been most thoroughly characterized, with the reservoirs and routes of transmission documented, and S. sinensis, L. hongkongensis and C. hathewayi have been found globally. One of the greatest hurdles in putting 16S rDNA sequencing into routine use in clinical microbiology laboratories is automation of the technology. The only step that can be automated at the moment is input of the 16S rDNA sequence of the bacterial isolate for identification into one of the software packages that will generate the result of the identity of the isolate on the basis of its sequence database. However

Mycorrhiza helper bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deveau, Aurelie; Labbe, Jessy

This chapter focuses on the Mycorrhiza Helper Bacteria (MHB), a generic name given to bacteria which stimulate the formation of mycorrhizal symbiosis. By extension, some bacterial strains that positively impact the functioning of mycorrhizal symbiosis are also called MHB. These bacteria have applicative interests, as they indirectly improve the health and growth of tree seedlings. MHB are not restricted to a specific type of ecosystem, but are rather generalist in the way that they associate with both herbaceous and woody mycorrhizal plants from boreal, temperate, arid and tropical ecosystems. However, understanding the molecular mechanisms and their specificities will help usmore » to know more about the ecology of the MHB. The process of acquisition varies between fungal species; while ectomycorrhizal fungi most probably recurrently acquire them from the environment, the association between bacterial endosymbionts and Glomeromycota probably dates back to very ancient times, and has since been vertically transmitted.« less

Formation of Guaiacol by Spoilage Bacteria from Vanillic Acid, a Product of Rice Koji Cultivation, in Japanese Sake Brewing.

PubMed

Ito, Toshihiko; Konno, Mahito; Shimura, Yoichiro; Watanabe, Seiei; Takahashi, Hitoshi; Hashizume, Katsumi

2016-06-08

The formation of guaiacol, a potent phenolic off-odor compound in the Japanese sake brewing process, was investigated. Eight rice koji samples were analyzed, and one contained guaiacol and 4-vinylguaiacol (4-VG) at extraordinarily high levels: 374 and 2433 μg/kg dry mass koji, respectively. All samples contained ferulic and vanillic acids at concentrations of mg/kg dry mass koji. Guaiacol forming microorganisms were isolated from four rice koji samples. They were identified as Bacillus subtilis, B. amyloliquefaciens/subtilis, and Staphylococcus gallinarum using 16S rRNA gene sequence. These spoilage bacteria convert vanillic acid to guaiacol and ferulic acid to 4-VG. However, they convert very little ferulic acid or 4-VG to guaiacol. Nine strains of koji fungi tested produced vanillic acid at the mg/kg dry mass koji level after cultivation. These results indicated that spoilage bacteria form guaiacol from vanillic acid, which is a product of koji cultivation in the sake brewing process.

Laboratory Simulations on Haze Formation in Cool Exoplanet Atmospheres

NASA Astrophysics Data System (ADS)

He, Chao; Horst, Sarah; Lewis, Nikole; Yu, Xinting; McGuiggan, Patricia; Moses, Julianne I.

2017-10-01

The Kepler mission has shown that the most abundant types of planets are super-Earths and mini-Neptunes among ~3500 confirmed exoplanets, and these types of exoplanets are expected to exhibit a wide variety of atmospheric compositions. Recent transit spectra have demonstrated that clouds and/or hazes could play a significant role in these planetary atmospheres (Deming et al. 2013, Knutson et al. 2014, Kreidberg et al. 2014, Pont, et al. 2013). However, very little laboratory work has been done to understand the formation of haze over a broad range of atmospheric compositions. Here we conducted a series of laboratory simulations to investigate haze formation in a range of planetary atmospheres using our newly built Planetary HAZE Research (PHAZER) chamber (He et al. 2017). We ran experimental simulations for nine different atmospheres: three temperatures (300 K, 400 K, and 600 K) and three metallicities (100, 1000, and 10000 times solar metallicity) using AC glow discharge as an energy source to irradiate gas mixtures. We found that haze particles are formed in all nine experiments, but the haze production rates are dramatically different for different cases. We investigated the particle sizes of the haze particles deposited on quartz discs using atomic force microscopy (AFM). The AFM images show that the particle size varies from 30 nm to 200 nm. The haze particles are more uniform for 100x solar metallicity experiments (30 nm to 40 nm) while the particles sizes for 1000x and 10000x solar metallicity experiments have wider distributions (30 nm to 200 nm). The particle size affects the scattering of light, and thus the temperature structure of planetary atmospheres. The haze production rates and particle size distributions obtained here can serve as critical inputs to atmospheric physical and chemical tools to understand the exoplanetary atmospheres and help guide future TESS and JWST observations of super-Earths and mini-Neptunes.Ref:Deming, D., et al. 2013, Ap

Hyperbiofilm Formation by Bordetella pertussis Strains Correlates with Enhanced Virulence Traits

PubMed Central

Cattelan, Natalia; Jennings-Gee, Jamie; Dubey, Purnima

2017-01-01

ABSTRACT Pertussis, or whooping cough, caused by the obligate human pathogen Bordetella pertussis is undergoing a worldwide resurgence. The majority of studies of this pathogen are conducted with laboratory-adapted strains which may not be representative of the species as a whole. Biofilm formation by B. pertussis plays an important role in pathogenesis. We conducted a side-by-side comparison of the biofilm-forming abilities of the prototype laboratory strains and the currently circulating isolates from two countries with different vaccination programs. Compared to the reference strain, all strains examined herein formed biofilms at high levels. Biofilm structural analyses revealed country-specific differences, with strains from the United States forming more structured biofilms. Bacterial hyperaggregation and reciprocal expression of biofilm-promoting and -inhibitory factors were observed in clinical isolates. An association of increased biofilm formation with augmented epithelial cell adhesion and higher levels of bacterial colonization in the mouse nose and trachea was detected. To our knowledge, this work links for the first time increased biofilm formation in bacteria with a colonization advantage in an animal model. We propose that the enhanced biofilm-forming capacity of currently circulating strains contributes to their persistence, transmission, and continued circulation. PMID:28893915

Establishing a laboratory model of dental unit waterlines bacterial biofilms using a CDC biofilm reactor.

PubMed

Yoon, Hye Young; Lee, Si Young

2017-11-01

In this study, a laboratory model to reproduce dental unit waterline (DUWL) biofilms was developed using a CDC biofilm reactor (CBR). Bacteria obtained from DUWLs were filtered and cultured in Reasoner's 2A (R2A) for 10 days, and were subsequently stored at -70°C. This stock was cultivated on R2A in batch mode. After culturing for five days, the bacteria were inoculated into the CBR. Biofilms were grown on polyurethane tubing for four days. Biofilm accumulation and thickness was 1.3 × 10 5  CFU cm -2 and 10-14 μm respectively, after four days. Bacteria in the biofilms included cocci and rods of short and medium lengths. In addition, 38 bacterial genera were detected in biofilms. In this study, the suitability and reproducibility of the CBR model for DUWL biofilm formation were demonstrated. The model provides a foundation for the development of bacterial control methods for DUWLs.

Manipulating Genetic Material in Bacteria

NASA Technical Reports Server (NTRS)

1998-01-01

Lisa Crawford, a graduate research assistant from the University of Toledo, works with Laurel Karr of Marshall Space Flight Center (MSFC) in the molecular biology laboratory. They are donducting genetic manipulation of bacteria and yeast for the production of large amount of desired protein. Photo credit: NASA/Marshall Space Flight Center (MSFC)

Assessment of drinking water quality using indicator bacteria and bacteriophages.

PubMed

Méndez, Javier; Audicana, Ana; Cancer, Mercedes; Isern, Anna; Llaneza, Julian; Moreno, Belén; Navarro, Mercedes; Tarancón, M Lluisa; Valero, Fernando; Ribas, Ferran; Jofre, Juan; Lucena, Francisco

2004-09-01

Bacterial indicators and bacteriophages suggested as potential indicators of water quality were determined by public laboratories in water from springs, household water wells, and rural and metropolitan water supplies in north-eastern Spain. Indicator bacteria were detected more frequently than bacteriophages in springs, household water wells and rural water supplies. In contrast, positive bacteriophage detections were more numerous than those of bacteria in metropolitan water supplies. Most of the metropolitan water supply samples containing indicators had concentrations of chlorine below 0.1 mg l(-1), their indicator loads resembling more closely those of rural water supplies than any other samples taken from metropolitan water supplies. The number of samples from metropolitan water supplies containing more than 0.1 mg l(-1) of chlorine that contained phages clearly outnumbered those containing indicator bacteria. Some association was observed between rainfall and the presence of indicators. Sediments from service reservoirs and water from dead ends in the distribution network of one of the metropolitan water supplies were also tested. Bacterial indicators and phages were detected in a higher percentage than in samples of tap water from the same network. Additionally, indicator bacteria were detected more frequently than bacteriophages in sediments of service reservoirs and water from dead end samples. We conclude that naturally occurring indicator bacteria and bacteriophages respond differently to chlorination and behave differently in drinking water distribution networks. Moreover, this study has shown that testing for the three groups of phages in routine laboratories is easy to implement and feasible without the requirement for additional material resources for the laboratories.

Stimulation of Indigenous Carbonate Precipitating Bacteria for Ground Improvement

NASA Astrophysics Data System (ADS)

Rajasekar, Adharsh; Moy, Charles K. S.; Wilkinson, Stephen

2017-05-01

Calcite minerals are precipitated in soil through biomineralisation which can be either organic or inorganic in nature. Biomineralisation can be employed to improve ground conditions in its natural state. Usually, studies of applied biomineralisation are highly interdisciplinary involving expertise from engineers, chemists and microbiologists. In this paper, we study the potential of biomineralisation from indigenous bacteria present in soil. The soil samples were collected from a high permeable zone and the bacteria that inhabit the soil were stimulated at a temperature of 15°C. A cementation solution consisting of 500mM calcium chloride, urea and nutrient broth at a pH of 7.5 was added to the soil samples. Inorganic precipitation was found to be dominant and was more efficient when compared to organic precipitation. Carbonate precipitation data indicated that inorganic precipitation were 1.37 times better at carbonate formation in comparison to organic precipitation. Scanning Electron Microscopy analysis identified cementation bonds formed between soil particles. It was deducted that organic precipitation is dependent on temperature, and may take an extended time at such low temperature. The preliminary data presented in this paper suggests that the implementation of biomineralisation with in-situ microbes is promising but requires further laboratory and field investigation before being considered for engineering application.

A Comparison of Heat versus Methanol Fixation for Gram Staining Bacteria

ERIC Educational Resources Information Center

Minnerath, Jeanne M.; Roland, Jenna M.; Rossi, Lucas C.; Weishalla, Steven R.; Wolf, Melissa M.

2009-01-01

Gram staining bacteria is a fundamental technique introduced in general biology and microbiology laboratory courses. Two common problems students encounter when Gram staining bacteria are (1) having a difficult time locating bacterial cells on the microscope slide and (2) over-decolorizing bacterial cells during the staining procedure such that…

Lactic acid bacteria of meat and meat products.

PubMed

Egan, A F

1983-09-01

When the growth of aerobic spoilage bacteria is inhibited, lactic acid bacteria may become the dominant component of the microbial flora of meats. This occurs with cured meats and with meats packaged in films of low gas permeability. The presence of a flora of psychrotrophic lactic acid bacteria on vacuum-packaged fresh chilled meats usually ensures that shelf-life is maximal. When these organisms spoil meats it is generally by causing souring, however other specific types of spoilage do occur. Some strains cause slime formation and greening of cured meats, and others may produce hydrogen sulphide during growth on vacuum-packaged beef. The safety and stability of fermented sausages depends upon fermentation caused by lactic acid bacteria. Overall the presence on meats of lactic acid bacteria is more desirable than that of the types of bacteria they have replaced.

Biliary bacterial factors determine the path of gallstone formation.

PubMed

Stewart, Lygia; Grifiss, J McLeod; Jarvis, Gary A; Way, Lawrence W

2006-11-01

Bacteria cause pigment gallstones and can act as a nidus for cholesterol gallstone formation. Bacterial factors that facilitate gallstone formation include beta-glucuronidase (bG), phospholipase (PhL), and slime. The current study sought to determine whether bacterial factors influence the path of gallstone formation. A total of 382 gallstones were cultured and/or examined using scanning electron microscopy (SEM). Bacteria were tested for bG and slime production. Gallstone composition was determined using infrared spectrography. Ca-palmitate presence documented bacterial PhL production. Groups were identified based upon bacterial factors present: slime and bGPhL (slime/bGPhL), bGPhL only, and slime only. Influence of bacterial stone-forming factors on gallstone composition and morphology was analyzed. Bacteria were present in 75% of pigment, 76% of mixed, and 20% of cholesterol stones. Gallstones with bGPhL producing bacteria contained more pigment (71% vs. 26%, P < .0001). The slime/bGPhL group was associated (79%) with pigment stones, bGPhL was associated (56%) with mixed stones, while slime (or none) only was associated (67%) with cholesterol stones (P < .031, all comparisons). Bacterial properties determined the path of gallstone formation. Bacteria that produced all stone-forming factors promoted pigment stone formation, while those that produced only bGPhL promoted mixed stone formation. Bacteria that only produced slime lacked the ability to generate pigment solids, and consequently were more common in the centers of cholesterol stones. This shows how bacterial characteristics may govern the process of gallstone formation.

Activity and adaptation of nitrilotriacetate (NTA)-degrading bacteria: field and laboratory studies

NASA Technical Reports Server (NTRS)

McFeters, G. A.; Egli, T.; Wilberg, E.; Alder, A.; Schneider, R.; Suozzi, M.; Giger, W.

1990-01-01

Adaptation of bacterial activity for the degradation of nitrilotriacetate (NTA) was studied using natural sediment samples and an NTA-degrading bacterium (strain ATCC 29600). Sediment samples from a river with persistent levels of NTA had much higher NTA-degradative activity than comparable samples from a less contaminated control site. When sediment from the control site was exposed to high levels of NTA a 5 day lag preceded an abrupt increase in NTA degradation while strain 29600 colonized on sand and grown in the absence of NTA became induced within eight hours. The induction of strain 29600 was compared between bacteria in suspension and cells attached to sand. The sand-associated bacteria became induced 4 to 5 h before the planktonic suspension and displayed over threefold greater specific activity. Suspensions of strain 29600 became adapted within 8 h when placed in membrane diffusion chambers that were immersed within a municipal wastewater reactor containing NTA. These findings support the concept that induction is a part of the process of bacterial adaptation to degrade NTA and sand-associated bacteria can adapt more quickly to and have a greater degradative activity for NTA than planktonic cells.

Acetic acid bacteria: A group of bacteria with versatile biotechnological applications.

PubMed

Saichana, Natsaran; Matsushita, Kazunobu; Adachi, Osao; Frébort, Ivo; Frebortova, Jitka

2015-11-01

Acetic acid bacteria are gram-negative obligate aerobic bacteria assigned to the family Acetobacteraceae of Alphaproteobacteria. They are members of the genera Acetobacter, Gluconobacter, Gluconacetobacter, Acidomonas, Asaia, Kozakia, Swaminathania, Saccharibacter, Neoasaia, Granulibacter, Tanticharoenia, Ameyamaea, Neokomagataea, and Komagataeibacter. Many strains of Acetobacter and Komagataeibacter have been known to possess high acetic acid fermentation ability as well as the acetic acid and ethanol resistance, which are considered to be useful features for industrial production of acetic acid and vinegar, the commercial product. On the other hand, Gluconobacter strains have the ability to perform oxidative fermentation of various sugars, sugar alcohols, and sugar acids leading to the formation of several valuable products. Thermotolerant strains of acetic acid bacteria were isolated in order to serve as the new strains of choice for industrial fermentations, in which the cooling costs for maintaining optimum growth and production temperature in the fermentation vessels could be significantly reduced. Genetic modifications by adaptation and genetic engineering were also applied to improve their properties, such as productivity and heat resistance. Copyright © 2014 Elsevier Inc. All rights reserved.

Isolation of iron bacteria from terrestrial and aquatic environments

NASA Astrophysics Data System (ADS)

Schmidt, Bertram; Szewzyk, Ulrich

2010-05-01

Bacteria, which are capable of iron oxidation or at least iron deposition are widely distributed in environments where zones of dissolved ferrous iron and oxygen gradients are overlapping [1]. They take part in the biological cycling of iron and influence other cycles of elements for example carbon [2]. Manganese can be used for similar metabolic purposes as iron, because it can be biologically oxidized by chemolithotrophs or can be reduced by respirating bacteria as well [3, 4]. Bacterial activity is responsible for the accumulation of ferric iron compounds in their surroundings. The formation of bog ore is a well known example for a soil horizon, with an extreme enrichment of biogenic ferric iron [5]. We focused on the isolation of neutrophilic iron bacteria and bacteria capable of manganese oxidation. We used samples from Tierra del Fuego (Argentina) the National Park "Unteres Odertal" (Germany) and Berlin ground water wells. Microscopic examination of the samples revealed a considerable diversity of iron encrusted structures of bacterial origin. Most of these morphologic types are already well known. The taxonomic classification of many of these organisms is based on morphologic features and is not reliable compared to recent methods of molecular biology. That is mainly due to the fact, that most of these bacteria are hardly culturable or do not show their characteristic morphologic features under culture conditions. We established a collection of more than 300 iron depositing strains. Phylogenetic analyses showed that we have many yet uncultured strains in pure culture. We obtained many isolates which form distinct branches within long known iron bacteria groups like the Sphaerotilus-Leptothrix cluster. But some of the strains belong to groups, which have not yet been associated with iron oxidation activity. The strains deposit high amounts of oxidized iron and manganese compounds under laboratory conditions. However it is unclear if these precipitations are

Laboratory activity to effectively teach introductory geomicrobiology concepts to non-geology majors.

PubMed

Marvasi, Massimiliano; Davila-Vazquez, Yarely C; Martinez, Lilliam Casillas

2013-01-01

We have designed a three-week experiment that can complement any microbiology course, to teach main geomicrobiology concepts for non-geology majors. One of the most difficult concepts for non-geology majors to comprehend is how bacteria serve as a platform for different mineralization reactions. In our three-week laboratory practice, students learn the main principles and conditions required for an induced bacterial mineralization. Upon completion of the laboratory experience, students will: 1) learn how microbial-induced mineralization (such as calcium carbonate formation) is affected by differential media and growth conditions; 2) understand how bacterial physiology affects any induced in situ or in vitro mineralization; 3) comprehend how growing conditions and bacterial physiologies interrelate, resulting in differential crystal formation. The teaching-learning process was assessed using a pre-/posttest with an increase from 26% to 76% in the number of positive answers from the students. We also measured the students' proficiency while conducting specific technical tasks, revealing no major difficulties while conducting the experiments. A final questionnaire was provided with satisfactory evaluations from the students regarding the organization and content of the practices. 84-86% of the students agreed that the exercises improved their knowledge in geomicrobiology and would like to attend similar laboratories in the future. Such response is the best indicator that the laboratory practice can be implemented in any undergraduate/graduate microbiology course to effectively teach basic geomicrobiology concepts to non-geology majors.

Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet.

PubMed

Zeng, Huawei; Ishaq, Suzanne L; Liu, Zhenhua; Bukowski, Michael R

2018-04-01

The increasing worldwide incidence of colon cancer has been linked to obesity and consumption of a high-fat Western diet. To test the hypothesis that a high-fat diet (HFD) promotes colonic aberrant crypt (AC) formation in a manner associated with gut bacterial dysbiosis, we examined the susceptibility to azoxymethane (AOM)-induced colonic AC and microbiome composition in C57/BL6 mice fed a modified AIN93G diet (AIN, 16% fat, energy) or an HFD (45% fat, energy) for 14 weeks. Mice receiving the HFD exhibited increased plasma leptin, body weight, body fat composition and inflammatory cell infiltration in the ileum compared with those in the AIN group. Consistent with the gut inflammatory phenotype, we observed an increase in colonic AC, plasma interleukin-6, tumor necrosis factor-α, monocyte chemoattractant protein-1 and inducible nitric oxide synthase in the ileum of the HFD-AOM group compared with the AIN-AOM group. Although the HFD and AIN groups did not differ in bacterial species number, the HFD and AIN diets resulted in different bacterial community structures in the colon. The abundance of certain short-chain fatty acid (SCFA) producing bacteria (e.g., Barnesiella) and fecal SCFA (e.g., acetic acid) content were lower in the HFD-AOM group compared with the AIN and AIN-AOM groups. Furthermore, we identified a high abundance of Anaeroplasma bacteria, an opportunistic pathogen in the HFD-AOM group. Collectively, we demonstrate that an HFD promotes AC formation concurrent with an increase of opportunistic pathogenic bacteria in the colon of C57BL/6 mice. Published by Elsevier Inc.

Cable Bacteria in Freshwater Sediments

PubMed Central

Kristiansen, Michael; Frederiksen, Rasmus B.; Dittmer, Anders Lindequist; Bjerg, Jesper Tataru; Trojan, Daniela; Schreiber, Lars; Damgaard, Lars Riis; Schramm, Andreas; Nielsen, Lars Peter

2015-01-01

In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage. PMID:26116678

Petroleum residues degradation in laboratory-scale by rhizosphere bacteria isolated from the mangrove ecosystem

NASA Astrophysics Data System (ADS)

Rinanti, A.; Nainggolan, I. J.

2018-01-01

This research is about petroleum bioremediation experiment to obtain bacterial isolate from mangrove ecosystem which potentially degrade petroleum. It was conducted in an Erlenmeyer batch system filled with growth medium of Stone Mineral Salt Solution (SMSS) plus petroleum residue, placed in an incubator shaker with a rotation speed of 120 rpm, temperature 3000C, for 14 research days. Indigenous bacteria that have been isolated and identified from the roots of mangrove plants are Ochrobactrum anthropi and Bacillus sp., Ralstonia pickettii and Bacillus circulans. Those bacteriain both monoculture and consortium form (mixed culture) are incorporated into erlenmeyer as remediator agents. All bacteria can utilize hydrocarbon compounds, but Ralstonia pickettii and Bacillus circulans reached exponential phase faster with more cell count than other bacteria. Compared to single cultures, petroleum degradation by a bacterial consortium provides a higher TPH reduction efficiency, i.e. at 5%, 10%, and 15% of initial TPH of 94.4%, 72%, and 80.3%, respectively. This study proved that all bacteria could optimize hydrocarbon compounds up to 15% TPH load.

The role of adhesins in bacteria motility modification

NASA Astrophysics Data System (ADS)

Conrad, Jacinta; Gibiansky, Maxsim; Jin, Fan; Gordon, Vernita; Motto, Dominick; Shrout, Joshua; Parsek, Matthew; Wong, Gerard

2010-03-01

Bacterial biofilms are multicellular communities responsible for a broad range of infections. To investigate the early-stage formation of biofilms, we have developed high-throughput techniques to quantify the motility of surface-associated bacteria. We translate microscopy movies of bacteria into a searchable database of trajectories using tracking algorithms adapted from colloidal physics. By analyzing the motion of both wild-type (WT) and isogenic knockout mutants, we have previously characterized fundamental motility mechanisms in P. aeruginosa. Here, we develop biometric routines to recognize signatures of adhesion and trapping. We find that newly attached bacteria move faster than previously adherent bacteria, and are more likely to be oriented out-of-plane. Motility appendages influence the bacterium's ability to become trapped: WT bacteria exhibit two types of trapped trajectories, whereas flagella-deficient bacteria rarely become trapped. These results suggest that flagella play a key role in adhesion.

Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids.

PubMed

Hackmann, Timothy J; Ngugi, David Kamanda; Firkins, Jeffrey L; Tao, Junyi

2017-11-01

Bacteria have been thought to follow only a few well-recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well-recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden-Meyerhof-Parnas pathway. This study shows that reconstruction of metabolic pathways - a common goal of omics studies - could be incorrect if well-recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Chemotaxis by natural populations of coral reef bacteria.

PubMed

Tout, Jessica; Jeffries, Thomas C; Petrou, Katherina; Tyson, Gene W; Webster, Nicole S; Garren, Melissa; Stocker, Roman; Ralph, Peter J; Seymour, Justin R

2015-08-01

Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.

The Formation of Indicators on Engineering Laboratory Management

ERIC Educational Resources Information Center

Yasin, Ruhizan M.; Mohamad, Zunuwanas; Rahman, Mohd Nizam Ab.; Hashim, Mohamad Hisyam Mohd

2012-01-01

This research is a developmental study of Engineering Laboratory Management indicators. It is formed to assess the level of quality management of the polytechnic level laboratory. The purpose of indicators is to help provide input into the management process of an engineering laboratory. Effectiveness of teaching and learning at technical…

Water Mediated Wittig Reactions of Aldehydes in the Teaching Laboratory: Using Sodium Bicarbonate for the in Situ Formation of Stabilized Ylides

ERIC Educational Resources Information Center

Kelly, Michael J. B.; Fallot, Lucas B.; Gustafson, Jeffrey L.; Bergdahl, B. Mikael

2016-01-01

The synthesis of alkenes using the Wittig reaction is a traditional part of many undergraduate organic chemistry teaching laboratory curricula. The aqueous medium version of the Wittig reaction presented is a reliable adaptation of this alkene formation reaction as a very safe alternative in the introductory organic chemistry laboratory. The…

Bacteria turn a tiny gear

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aronson, Igor

2009-01-01

Thousands of tiny Bacillus subtillis bacteria turn a single gear, just 380 microns across. (A human hair is about 100 microns across.) The method could be used to create micro-machines. Argonne National Laboratory scientist Igor Aronson pioneered this technique. Read more at the New York Times: http://ow.ly/ODfI or at Argonne: http://ow.ly/ODfa Video courtesy Igor Aronson.

The structural bases of long-term anabiosis in non-spore-forming bacteria

NASA Astrophysics Data System (ADS)

Suzina, N. E.; Mulyukin, A. L.; Dmitriev, V. V.; Nikolaev, Yu. A.; Plakunov, V. K.; El-Registan, G. I.; Duda, V. I.

Peculiarities of the structural and functional organization related to extended and long-term anabiosis were revealed for non-spore-forming bacteria both in stored laboratory cultures and natural substrates: (1) 1-3-Myr-old Eastern Siberian permafrost, (2) tundra soils, and (3) oil slurry. Different advanced or specially designed methods were used such as (a) high-resolution electron microscopy; (b) simulation of in situ conditions in laboratory by varying of growth composition media and cultivation conditions; (c) low-temperature fractionation to isolate and concentrate microbial cells from natural substrates; (d) specimen selection and preparation; (e) comparative ultrastructural and morphometric analysis of microbial cells in model cultures and natural substrates (in situ). Under laboratory conditions, the intense formation of anabiotic (resting) cells by representatives of various taxa of eubacteria and halophilic archaea were observed in 2-9-month-old cultures grown in carbon-, nitrogen-, or phosphorus-deficient media, in starved cell suspensions in the presence of sodium silicate at environmentally occurring concentrations, or on soil agar. Among resting cells were revealed cyst-like forms possessing the complicated structure. The most common peculiarities of cyst-like resting cells were thick and distinguishable capsule; thickened and multilamellar cell wall with 1 to 3 de novo synthesized murein layers; large intramembrane particles on PF- and EF-fractures; finely granulated or coarse textured cytoplasm; condensed nucleoid. The data of morphological and ultrastructural analyses of cyst-like cells, as well as their experimentally proved resistance to prolonged desiccation, heat shock, etc. and the ability to germinate under the effect of lysozyme, gives an evidence for constitutive dormancy in the studied non-spore-forming bacteria at least. Noteworthy, it was found that the majority of microorganisms in permafrost, tundra soils, and oil slurry was presented

A mathematical model for expected time to extinction of pathogenic bacteria through antibiotic

NASA Astrophysics Data System (ADS)

Ghosh, M. K.; Nandi, S.; Roy, P. K.

2016-04-01

Application of antibiotics in human system to prevent bacterial diseases like Gastritis, Ulcers, Meningitis, Pneumonia and Gonorrhea are indispensable. Antibiotics saved innumerable lives and continue to be a strong support for therapeutic application against pathogenic bacteria. In human system, bacterial diseases occur when pathogenic bacteria gets into the body and begin to reproduce and crowd out healthy bacteria. In this process, immature bacteria releases enzyme which is essential for bacterial cell-wall biosynthesis. After complete formation of cell wall, immature bacteria are converted to mature or virulent bacteria which are harmful to us during bacterial infections. Use of antibiotics as drug inhibits the bacterial cell wall formation. After application of antibiotics within body, the released bacterial enzyme binds with antibiotic molecule instead of its functional site during the cell wall synthesis in a competitive inhibition approach. As a consequence, the bacterial cell-wall formation as well as maturation process of pathogenic bacteria is halted and the disease is cured with lysis of bacterial cells. With this idea, a mathematical model has been developed in the present research investigation to review the inhibition of biosynthesis of bacterial cell wall by the application of antibiotics as drug in the light of enzyme kinetics. This approach helps to estimate the expected time to extinction of the pathogenic bacteria. Our mathematical approach based on the enzyme kinetic model for finding out expected time to extinction contributes favorable results for understanding of disease dynamics. Analytical and numerical results based on simulated findings validate our mathematical model.

Laboratory Activity to Effectively Teach Introductory Geomicrobiology Concepts to Non-Geology Majors †

PubMed Central

Marvasi, Massimiliano; Davila-Vazquez, Yarely C.; Martinez, Lilliam Casillas

2013-01-01

We have designed a three-week experiment that can complement any microbiology course, to teach main geomicrobiology concepts for non-geology majors. One of the most difficult concepts for non-geology majors to comprehend is how bacteria serve as a platform for different mineralization reactions. In our three-week laboratory practice, students learn the main principles and conditions required for an induced bacterial mineralization. Upon completion of the laboratory experience, students will: 1) learn how microbial-induced mineralization (such as calcium carbonate formation) is affected by differential media and growth conditions; 2) understand how bacterial physiology affects any induced in situ or in vitro mineralization; 3) comprehend how growing conditions and bacterial physiologies interrelate, resulting in differential crystal formation. The teaching-learning process was assessed using a pre-/posttest with an increase from 26% to 76% in the number of positive answers from the students. We also measured the students’ proficiency while conducting specific technical tasks, revealing no major difficulties while conducting the experiments. A final questionnaire was provided with satisfactory evaluations from the students regarding the organization and content of the practices. 84–86% of the students agreed that the exercises improved their knowledge in geomicrobiology and would like to attend similar laboratories in the future. Such response is the best indicator that the laboratory practice can be implemented in any undergraduate/graduate microbiology course to effectively teach basic geomicrobiology concepts to non-geology majors. PMID:24358384

Newly-synthesized chalcones-inhibition of adherence and biofilm formation of methicillin-resistant Staphylococcus aureus

PubMed Central

Bozic, Dragana D.; Milenkovic, Marina; Ivkovic, Branka; Cirkovic, Ivana

2014-01-01

Biofilm formation and adherence of bacteria to host tissue are one of the most important virulence factors of methicillin-resistant strains of Staphylococcus aureus (MRSA). The number of resistant strains is seriously increasing during the past years and bacteria have become resistant, not only to methicillin, but also to other commonly used antistaphylococcal antibiotics. There is a great need for discovering a novel antimicrobial agent for the treatment of staphylococcal infections. One of the most promising groups of compounds appears to be chalcones. In present study we evaluated the in vitro effect of three newly synthesized chalcones: 1,3- Bis-(2-hydroxy-phenyl)-propenone, 3-(3-Hydroxy-phenyl)-1-(2-hydroxy-phenyl)-propenone and 3-(4-Hydroxy-phenyl)-1-(2-hydroxy-phenyl)-propenone on glycocalyx production, biofilm formation and adherence to human fibronectin of clinical isolates and laboratory control strain of MRSA (ATCC 43300). Subinhibitory concentrations of the tested compounds reduced the production of glycocalyx, biofilm formation and adherence to human fibronectin of all MRSA strains. Inhibition of biofilm formation was dose dependent and the most effective was 1,3- Bis-(2-hydroxy-phenyl)-propenone. In our study we demonstrated that three newly-synthesized chalcones exhibited significant effect on adherence and biofilm formation of MRSA strains. Chalcones may be considered as promising new antimicrobial agents that can be used for prevention of staphylococcal infections or as adjunct to antibiotics in conventional therapy. PMID:24948943

[Infection control team (ICT) in cooperation with microbiology laboratories].

PubMed

Okazaki, Mitsuhiro

2012-10-01

Infection control as a medical safety measure is an important issue in all medical facilities. In order to tackle this measure, cooperation between the infection control team (ICT) and microbiological laboratory is indispensable. Multiple drug-resistant bacteria have shifted from Gram-positive bacteria to Gram-negative bacilli within the last ten years. There are also a variety of bacilli, complicating the examination method and test results further. Therefore, cooperation between the ICT and microbiological laboratory has become important to understand examination results and to use them. In order to maintain functional cooperation, explanatory and communicative ability between the microbiological laboratory and ICT is required every day. Such positive information exchange will develop into efficient and functional ICT activity.

Culturing marine bacteria – an essential prerequisite for biodiscovery

PubMed Central

Joint, Ian; Mühling, Martin; Querellou, Joël

2010-01-01

Summary The potential for using marine microbes for biodiscovery is severely limited by the lack of laboratory cultures. It is a long‐standing observation that standard microbiological techniques only isolate a very small proportion of the wide diversity of microbes that are known in natural environments from DNA sequences. A number of explanations are reviewed. The process of establishing laboratory cultures may destroy any cell‐to‐cell communication that occurs between organisms in the natural environment and that are vital for growth. Bacteria probably grow as consortia in the sea and reliance on other bacteria for essential nutrients and substrates is not possible with standard microbiological approaches. Such interactions should be considered when designing programmes for the isolation of marine microbes. The benefits of novel technologies for manipulating cells are reviewed, including single cell encapsulation in gel micro‐droplets. Although novel technologies offer benefits for bringing previously uncultured microbes into laboratory culture, many useful bacteria can still be isolated using variations of plating techniques. Results are summarized for a study to culture bacteria from a long‐term observatory station in the English Channel. Bacterial biodiversity in this assemblage has recently been characterized using high‐throughput sequencing techniques. Although Alphaproteobacteria dominated the natural bacterial assemblage throughout the year, Gammaproteobacteria were the most frequent group isolated by plating techniques. The use of different gelling agents and the addition of ammonium to seawater‐based agar did lead to the isolation of a higher proportion of Alphaproteobacteria. Variation in medium composition was also able to increase the recovery of other groups of particular interest for biodiscovery, such as Actinobacteria. PMID:21255353

Pigment gallstone pathogenesis: slime production by biliary bacteria is more important than beta-glucuronidase production.

PubMed

Stewart, L; Ponce, R; Oesterle, A L; Griffiss, J M; Way, L W

2000-01-01

Pigment stones are thought to form as a result of deconjugation of bilirubin by bacterial beta-glucuronidase, which results in precipitation of calcium bilirubinate. Calcium bilirubinate is then aggregated into stones by an anionic glycoprotein. Slime (glycocalyx), an anionic glycoprotein produced by bacteria causing foreign body infections, has been implicated in the formation of the precipitate that blocks biliary stents. We previously showed that bacteria are present within the pigment portions of gallstones and postulated a bacterial role in pigment stone formation through beta-glucuronidase or slime production. Ninety-one biliary bacterial isolates from 61 patients and 12 control stool organisms were tested for their production of beta-glucuronidase and slime. The average slime production was 42 for biliary bacteria and 2.5 for stool bacteria (P <0.001). Overall, 73% of biliary bacteria and 8% of stool bacteria produced slime (optical density >3). In contrast, only 38% of biliary bacteria produced beta-glucuronidase. Eighty-two percent of all patients, 90% of patients with common bile duct (CBD) stones, 100% of patients with primary CBD stones, and 93% of patients with biliary tubes had one or more bacterial species in their stones that produced slime. By comparison, only 47% of all patients, 60% of patients with CBD stones, 62% of patients with primary CBD stones, and 50% of patients with biliary tubes had one or more bacteria that produced beta-glucuronidase. Most biliary bacteria produced slime, and slime production correlated better than beta-glucuronidase production did with stone formation and the presence of biliary tubes or stents. Patients with primary CBD stones and biliary tubes had the highest incidence of slime production. These findings suggest that bacterial slime is important in gallstone formation and the blockage of biliary tubes.

Isolation of carbohydrate-metabolizing, extremely halophilic bacteria.

NASA Technical Reports Server (NTRS)

Tomlinson, G. A.; Hochstein, L. I.

1972-01-01

Four previously unrecognized strains of extremely halophilic bacteria that utilize carbohydrates have been isolated. Gas production proved an unreliable index of carbohydrate metabolism; therefore, carbohydrate utilization was measured by determining acid formation and sugar disappearance during growth. By these procedures, carbohydrate utilization was readily detected. The results suggest that carbohydrate dissimilation by extremely halophilic bacteria may be more common than previously thought and that the apparent rarity of carbohydrate-metabolizing halophiles may be an artifact of the isolation procedures used.

Influence of surfaces on sulphidogenic bacteria.

PubMed

Bass, C J; Webb, J S; Sanders, P F; Lappin-Scott, H M

1996-01-01

Sulphidogenic bacteria in oil reservoirs are of great economic importance in terms of souring, fouling and corrosion. Mixed cultures containing these bacteria were isolated from chalk formations in North Sea oil reservoirs. These were thermophilic cultures, growing optimally at 60°C. Oil formations are porous matrices, providing a very large surface area and ideal conditions for bacterial attachment, survival and growth. This study included assessments of sulphide production rates of thermophilic (t-)sulphidogen consortia with and without additional surfaces. The availability of a surface contributed significantly to the rate and extent of sulphide generation. Surfaces were offered in varying amounts to growing planktonic cultures: significantly more sulphide was produced from cultures in contact with a surface than from identical cultures in the absence of a surface. In another series of experiments, t-sulphidogens were added to chalk rock chips in the presence of nutrients and incubated for several months. This resulted in rapid sulphide generation, the final concentration being related to the initial nutrient concentration. Subsequent nutrient addition resulted in renewed sulphide generation. It is suggested that bacteria in reservoirs can withstand long periods of nutrient deprivation while attached within the porous rock matrix and opportunistically utilise nutrients when they become available.

New insight on the response of bacteria to fluoride.

PubMed

Breaker, R R

2012-01-01

Fluoride has been used for decades to prevent caries and it is well established that this anion can inhibit the growth of bacteria. However, the precise effects that fluoride has on bacteria and the mechanisms that bacteria use to overcome fluoride toxicity have largely remained unexplored. Recently, my laboratory reported the discovery of biological systems that bacteria use to sense fluoride and reduce fluoride toxicity. These sensors and their associated genes are very widespread in biology, which has implications for a number of issues that are central to the use of fluoride for dental care. Below I provide a summary of our findings, comment on some of the key prospects for expanding our understanding of fluoride's effects on biology, and propose some future uses of this knowledge. Copyright © 2012 S. Karger AG, Basel.

New Insight on the Response of Bacteria to Fluoride

PubMed Central

Breaker, R.R.

2012-01-01

Fluoride has been used for decades to prevent caries and it is well established that this anion can inhibit the growth of bacteria. However, the precise effects that fluoride has on bacteria and the mechanisms that bacteria use to overcome fluoride toxicity have largely remained unexplored. Recently, my laboratory reported the discovery of biological systems that bacteria use to sense fluoride and reduce fluoride toxicity. These sensors and their associated genes are very widespread in biology, which has implications for a number of issues that are central to the use of fluoride for dental care. Below I provide a summary of our findings, comment on some of the key prospects for expanding our understanding of fluoride's effects on biology, and propose some future uses of this knowledge. PMID:22327376

Situ microbial plugging process for subterranean formations

DOEpatents

McInerney, Michael J.; Jenneman, Gary E.; Knapp, Roy M.; Menzie, Donald E.

1985-12-17

Subterranean paths of water flow are impeded or changed by the facilitation of microbial growth therein. Either indigenous bacterial growth may be stimulated with nutrients or the formation may be first seeded with bacteria or their spores which inhibit fluid flow after proliferation. These methods and bacteria are usable to alter the flow of water in a waterflooded oil formation and to impede the outflow of contaminated water.

Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation

NASA Astrophysics Data System (ADS)

Brocks, Jochen J.; Schaeffer, Philippe

2008-03-01

Carbonates of the 1640 million years (Ma) old Barney Creek Formation (BCF), McArthur Basin, Australia, contain more than 22 different C 40 carotenoid derivatives including lycopane, γ-carotane, β-carotane, chlorobactane, isorenieratane, β-isorenieratane, renieratane, β-renierapurpurane, renierapurpurane and the monoaromatic carotenoid okenane. These biomarkers extend the geological record of carotenoid derivatives by more than 1000 million years. Okenane is potentially derived from the red-colored aromatic carotenoid okenone. Based on a detailed review of the ecology and physiology of all extant species that are known to contain okenone, we interpret fossil okenane as a biomarker for planktonic purple sulfur bacteria of the family Chromatiaceae. Okenane is strictly a biomarker for anoxic and sulfidic conditions in the presence of light (photic zone euxinia) and indicates an anoxic/oxic transition (temporarily) located at less than 25 m depth and, with a high probability, less than 12 m depth. For the BCF, we also interpret renierapurpurane, renieratane and β-renierapurpurane as biomarkers for Chromatiaceae with a possible contribution of cyanobacterial synechoxanthin to the renierapurpurane pool. Although isorenieratane may, in principle, be derived from actinobacteria, in the BCF these biomarkers almost certainly derive from sulfide-oxidizing phototrophic green sulfur bacteria (Chlorobiaceae). Biological precursors of γ-carotane, β-carotane and lycopane are found among numerous autotrophic and almost all phototrophic organisms in the three domains of life. In the BCF, a paucity of diagnostic eukaryotic steroids suggests that algae were rare and, therefore, that cyanobacterial carotenoids such as β-carotene, echinenone, canthaxanthin and zeaxanthin are the most likely source of observed β-carotane. γ-Carotane may be derived from cyanobacteria, Chlorobiaceae and green non-sulfur bacteria (Chloroflexi), while the most likely biological sources for lycopane

Tyramine and phenylethylamine biosynthesis by food bacteria.

PubMed

Marcobal, Angela; De las Rivas, Blanca; Landete, José María; Tabera, Laura; Muñoz, Rosario

2012-01-01

Tyramine poisoning is caused by the ingestion of food containing high levels of tyramine, a biogenic amine. Any foods containing free tyrosine are subject to tyramine formation if poor sanitation and low quality foods are used or if the food is subject to temperature abuse or extended storage time. Tyramine is generated by decarboxylation of the tyrosine through tyrosine decarboxylase (TDC) enzymes derived from the bacteria present in the food. Bacterial TDC have been only unequivocally identified and characterized in Gram-positive bacteria, especially in lactic acid bacteria. Pyridoxal phosphate (PLP)-dependent TDC encoding genes (tyrDC) appeared flanked by a similar genetic organization in several species of lactic acid bacteria, suggesting a common origin by a single mobile genetic element. Bacterial TDC are also able to decarboxylate phenylalanine to produce phenylethylamine (PEA), another biogenic amine. The molecular knowledge of the genes involved in tyramine production has led to the development of molecular methods for the detection of bacteria able to produce tyramine and PEA. These rapid and simple methods could be used for the analysis of the ability to form tyramine by bacteria in order to evaluate the potential risk of tyramine biosynthesis in food products.

The Trophic Significance of Bacteria in a Detritus-Based Stream Food Web

Treesearch

Robert O. Hall; Judy L. Meyer

1998-01-01

We compared relative use of streamwater dissolved organic carbon (DOC) by bacteria and the trophic significance of bacteria to invertebrates in two headwater streams at Coweeta Hydrologic Laboratory in North Carolina: a stream with all leaf litter inputs excluded for 1 yr, and a reference stream. Leaf litter standing crop in the treatment stream was

EFFECT OF AEROSOLIZATION ON CULTURABILITY AND VIABILITY OF GRAM-NEGATIVE BACTERIA

EPA Science Inventory

Estimations of the bacterial content of air can be more easily made now than a decade ago, with colony formation the method of choice for enumeration of airborne bacteria.However, plate counts are subject to error because bacteria exposed to the air may remain viable yet lose the...

Active invasion of bacteria into living fungal cells

PubMed Central

Moebius, Nadine; Üzüm, Zerrin; Dijksterhuis, Jan; Lackner, Gerald; Hertweck, Christian

2014-01-01

The rice seedling blight fungus Rhizopus microsporus and its endosymbiont Burkholderia rhizoxinica form an unusual, highly specific alliance to produce the highly potent antimitotic phytotoxin rhizoxin. Yet, it has remained a riddle how bacteria invade the fungal cells. Genome mining for potential symbiosis factors and functional analyses revealed that a type 2 secretion system (T2SS) of the bacterial endosymbiont is required for the formation of the endosymbiosis. Comparative proteome analyses show that the T2SS releases chitinolytic enzymes (chitinase, chitosanase) and chitin-binding proteins. The genes responsible for chitinolytic proteins and T2SS components are highly expressed during infection. Through targeted gene knock-outs, sporulation assays and microscopic investigations we found that chitinase is essential for bacteria to enter hyphae. Unprecedented snapshots of the traceless bacterial intrusion were obtained using cryo-electron microscopy. Beyond unveiling the pivotal role of chitinolytic enzymes in the active invasion of a fungus by bacteria, these findings grant unprecedented insight into the fungal cell wall penetration and symbiosis formation. DOI: http://dx.doi.org/10.7554/eLife.03007.001 PMID:25182414

Small Talk: Cell-to-Cell Communication in Bacteria

ScienceCinema

Bassler, Bonnie [Princeton University, Princeton, New Jersey, United States

2017-12-09

Cell-cell communication in bacteria involves the production, release, and subsequent detection of chemical signaling molecules called autoinducers. This process, called quorum sensing, allows bacteria to regulate gene expression on a population-wide scale. Processes controlled by quorum sensing are usually ones that are unproductive when undertaken by an individual bacterium but become effective when undertaken by the group. For example, quorum sensing controls bioluminescence, secretion of virulence factors, biofilm formation, sporulation, and the exchange of DNA. Thus, quorum sensing is a mechanism that allows bacteria to function as multi-cellular organisms. Bacteria make, detect, and integrate information from multiple autoinducers, some of which are used exclusively for intra-species communication while others enable communication between species. Research is now focused on the development of therapies that interfere with quorum sensing to control bacterial virulence.

Laboratory assessment of bioleaching of shallow eutrophic sediment by immobilized photosynthetic bacteria.

PubMed

Sun, Shiyong; Fan, Shenglan; Shen, Kexuan; Lin, Shen; Nie, Xiaoqin; Liu, Mingxue; Dong, Faqin; Li, Jian

2017-10-01

Eutrophic sediment is a serious problem in ecosystem restoration, especially in shallow lake ecosystems. We present a novel bioleaching approach to treat shallow eutrophic sediment with the objective of preventing the release of nitrate, phosphate, and organic compounds from the sediment to the water column, using porous mineral-immobilized photosynthetic bacteria (PSB). Bioactivity of bacteria was maintained during the immobilization process. Immobilized PSB beads were directly deposited on the sediment surface. The deposited PSB utilized pollutants diffused from the sediment as a nutritive matrix for growth. We evaluated the effects of light condition, temperature, initial pH, amount of PSB beads, and frequency of addition of PSB beads for contaminant removal efficiency during bioleaching operations. The presented study indicated that immobilized PSB beads using porous minerals as substrates have considerable application potential in bioremediation of shallow eutrophic lakes.

Location-Related Differences in Weathering Behaviors and Populations of Culturable Rock-Weathering Bacteria Along a Hillside of a Rock Mountain.

PubMed

Wang, Qi; Wang, Rongrong; He, Linyan; Sheng, Xiafang

2017-05-01

Bacteria play important roles in rock weathering, elemental cycling, and soil formation. However, little is known about the weathering potential and population of bacteria inhabiting surfaces of rocks. In this study, we isolated bacteria from the top, middle, and bottom rock samples along a hillside of a rock (trachyte) mountain as well as adjacent soils and characterized rock-weathering behaviors and populations of the bacteria. Per gram of rock or surface soil, 10 6 -10 7 colony forming units were obtained and total 192 bacteria were isolated. Laboratory rock dissolution experiments indicated that the proportions of the highly effective Fe (ranging from 67 to 92 %), Al (ranging from 40 to 48 %), and Cu (ranging from 54 to 81 %) solubilizers were significantly higher in the top rock and soil samples, while the proportion of the highly effective Si (56 %) solubilizers was significantly higher in the middle rock samples. Furthermore, 78, 96, and 6 % of bacteria from the top rocks, soils, and middle rocks, respectively, significantly acidified the culture medium (pH < 4.0) in the rock dissolution process. Most rock-weathering bacteria (79 %) from the rocks were different to those from the soils and most of them (species level) have not been previously reported. Furthermore, location-specific rock-weathering bacterial populations were found and Bacillus species were the most (66 %) frequently isolated rock-weathering bacteria in the rocks based on cultivation methods. Notably, the top rocks and soils had the highest and lowest diversity of rock-weathering bacterial populations, respectively. The results suggested location-related differences in element (Si, Al, Fe, and Cu) releasing effectiveness and communities of rock-weathering bacteria along the hillside of the rock mountain.

Bacteria-based concrete: from concept to market

NASA Astrophysics Data System (ADS)

Wiktor, V.; Jonkers, H. M.

2016-08-01

The concept of self-healing concrete—a concrete which can autonomously repair itself after crack formation, with no or limited human intervention—has received a lot of attention over the past 10 years as it could help structures to last longer and at a lower maintenance cost. This paper gives an overview on the key aspects and recent advances in the development of the bacteria-based self-healing concrete developed at the University of Technology of Delft (The Netherlands). Research started with the screening and selection of concrete compatible bacteria and nutrients. Several types of encapsulated bacteria and nutrients have been developed and tested. The functionality of these healing agents was demonstrated by showing metabolic activity of activated bacterial spores by oxygen consumption measurements and by regain of material functionality in form of regain of water tightness. Besides development of bacteria-based self-healing concrete, a bacteria-based repair mortar and liquid system were developed for the treatment of aged concrete structures. Field trials have been carried out with either type of bacteria-based systems and the promising results have led to a spinoff company Basilisk Self-Healing Concrete with the aim to further develop these systems and bring them to the market.

Molecular pathways underlying inhibitory effect of antimicrobial peptide Nal-P-113 on bacteria biofilms formation of Porphyromonas gingivalis W83 by DNA microarray.

PubMed

Wang, Hong-Yan; Lin, Li; Tan, Li-Si; Yu, Hui-Yuan; Cheng, Jya-Wei; Pan, Ya-Ping

2017-02-17

Wound-related infection remains a major challenge for health professionals. One disadvantage in conventional antibiotics is their inability to penetrate biofilms, the main protective strategy for bacteria to evade irradiation. Previously, we have shown that synthetic antimicrobial peptides could inhibit bacterial biofilms formation. In this study, we first delineated how Nal-P-113, a novel antimicrobial peptide, exerted its inhibitory effects on Porphyromonas gingivalis W83 biofilms formation at a low concentration. Secondly, we performed gene expression profiling and validated that Nal-P-113 at a low dose significantly down-regulated genes related to mobile and extrachromosomal element functions, transport and binding proteins in Porphyromonas gingivalis W83. These findings suggest that Nal-P-113 at low dose is sufficient to inhibit the formation of biofilms although Porphyromonas gingivalis W83 may maintain its survival in the oral cavity. The newly discovered molecular pathways may add the knowledge of developing a new strategy to target bacterial infections in combination with current first-line treatment in periodontitis.

Effect of estradiol on planktonic growth, coaggregation, and biofilm formation of the Prevotella intermedia group bacteria.

PubMed

Fteita, Dareen; Könönen, Eija; Söderling, Eva; Gürsoy, Ulvi Kahraman

2014-06-01

Alterations in the quantity and quality of biofilms at gingival margin are considered to play a role in the initiation and development of pregnancy-related gingivitis. Prevotella intermedia sensu lato is able to consume estradiol, the major sex hormone secreted during pregnancy, in the absence of vitamin K. The aim of the study was to examine the effect of estradiol on the planktonic growth, coaggregation, polysaccharide production, and biofilm formation of the P. intermedia group bacteria, namely P. intermedia, Prevotella nigrescens, and Prevotella pallens. In all experiments, the type strain (ATCC) and a clinical strain (AHN) of P. intermedia, P. nigrescens, and P. pallens were incubated with the concentrations of 0, 30, 90, and 120 nmol/L of estradiol. Planktonic growth was assessed by means of the colony forming unit method, while coaggregation and biofilm formation were assessed by spectrophotometric methods. In the determination of protein and polysaccharide levels, the Bradford and phenol-sulfuric acid methods were used, respectively. P. pallens AHN 9283 and P. nigrescens ATCC 33563 increased their numbers at planktonic stage with increasing estradiol concentrations. In 48-h biofilm tests, elevated protein levels were found for both strains of P. intermedia, and the strains P. nigrescens ATCC 33563 and P. pallens AHN 9283 in the presence of estradiol. The P. intermedia strains also increased the levels of polysaccharide formation in the biofilm. Coaggregation of the P. intermedia group organisms with Fusobacterium nucleatum was enhanced only in P. intermedia AHN 8290. In conclusion, our in vitro experiments indicate that estradiol regulates planktonic growth, coaggregation, polysaccharide production, and biofilm formation characteristics of P. intermedia, P. nigrescens, and P. pallens differently. These results may, at least partly, explain the differences seen in their contribution to the pathogenesis of pregnancy-related gingivitis

Pleomorphic Structures in Human Blood Are Red Blood Cell-Derived Microparticles, Not Bacteria.

PubMed

Mitchell, Adam J; Gray, Warren D; Schroeder, Max; Yi, Hong; Taylor, Jeannette V; Dillard, Rebecca S; Ke, Zunlong; Wright, Elizabeth R; Stephens, David; Roback, John D; Searles, Charles D

2016-01-01

Red blood cell (RBC) transfusions are a common, life-saving therapy for many patients, but they have also been associated with poor clinical outcomes. We identified unusual, pleomorphic structures in human RBC transfusion units by negative-stain electron microscopy that appeared identical to those previously reported to be bacteria in healthy human blood samples. The presence of viable, replicating bacteria in stored blood could explain poor outcomes in transfusion recipients and have major implications for transfusion medicine. Here, we investigated the possibility that these structures were bacteria. Flow cytometry, miRNA analysis, protein analysis, and additional electron microscopy studies strongly indicated that the pleomorphic structures in the supernatant of stored RBCs were RBC-derived microparticles (RMPs). Bacterial 16S rDNA PCR amplified from these samples were sequenced and was found to be highly similar to species that are known to commonly contaminate laboratory reagents. These studies suggest that pleomorphic structures identified in human blood are RMPs and not bacteria, and they provide an example in which laboratory contaminants may can mislead investigators.

Antibacterial Activity of Ethanolic Extract of Cinnamon Bark, Honey, and Their Combination Effects against Acne-Causing Bacteria

PubMed Central

Julianti, Elin; Rajah, Kasturi K.; Fidrianny, Irda

2017-01-01

Propionibacterium acnes and Staphylococcus epidermidis are the major skin bacteria that cause the formation of acne. The present study was conducted to investigate antibacterial activity of ethanolic extract of cinnamon bark, honey, and their combination against acne bacteria. The antibacterial activity of extract of cinnamon bark and honey were investigated against P. acnes and S. epidermidis using disc diffusion. Minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) were attained using Clinical and Laboratory Standard Institute (CLSI) methods. The interaction between cinnamon bark extract and honey was determined using a checkerboards method. The results showed that the MICs of cinnamon bark extract and honey against P. acne were 256 µg/mL and 50% v/v, respectively, while those against S. epidermidis were 1024 µg/mL and 50% v/v, respectively. The MBC of cinnamon bark extract against P. acnes and S. epidermidis were more than 2048 µg/mL, whereas the MBC for honey against P. acnes and S. epidermidis were 100%. The combination of cinnamon bark extract and honey against P. acnes and S. epidermidis showed additive activity with a fractional inhibitory concentration index (FICI) value of 0.625. Therefore, the combination of cinnamon bark extract and honey has potential activity against acne-causing bacteria. PMID:28398231

Bacteria interface pickering emulsions stabilized by self-assembled bacteria-chitosan network.

PubMed

Wongkongkatep, Pravit; Manopwisedjaroen, Khajohnpong; Tiposoth, Perapon; Archakunakorn, Somwit; Pongtharangkul, Thunyarat; Suphantharika, Manop; Honda, Kohsuke; Hamachi, Itaru; Wongkongkatep, Jirarut

2012-04-03

An oil-in-water Pickering emulsion stabilized by biobased material based on a bacteria-chitosan network (BCN) was developed for the first time in this study. The formation of self-assembled BCN was possible due to the electrostatic interaction between negatively charged bacterial cells and polycationic chitosan. The BCN was proven to stabilize the tetradecane/water interface, promoting formation of highly stable oil-in-water emulsion (o/w emulsion). We characterized and visualized the BCN stabilized o/w emulsions by scanning electron microscopy (SEM) and laser scanning confocal microscopy (LSCM). Due to the sustainability and low environmental impact of chitosan, the BCN-based emulsions open up opportunities for the development of an environmental friendly new interface material as well as the novel type of microreactor utilizing bacterial cells network.

Probing minority population of antibiotic-resistant bacteria.

PubMed

Huang, Tianxun; Zheng, Yan; Yan, Ya; Yang, Lingling; Yao, Yihui; Zheng, Jiaxin; Wu, Lina; Wang, Xu; Chen, Yuqing; Xing, Jinchun; Yan, Xiaomei

2016-06-15

The evolution and spread of antibiotic-resistant pathogens has become a major threat to public health. Advanced tools are urgently needed to quickly diagnose antibiotic-resistant infections to initiate appropriate treatment. Here we report the development of a highly sensitive flow cytometric method to probe minority population of antibiotic-resistant bacteria via single cell detection. Monoclonal antibody against TEM-1 β-lactamase and Alexa Fluor 488-conjugated secondary antibody were used to selectively label resistant bacteria green, and nucleic acid dye SYTO 62 was used to stain all the bacteria red. A laboratory-built high sensitivity flow cytometer (HSFCM) was applied to simultaneously detect the side scatter and dual-color fluorescence signals of single bacteria. By using E. coli JM109/pUC19 and E. coli JM109 as the model systems for antibiotic-resistant and antibiotic-susceptible bacteria, respectively, as low as 0.1% of antibiotic-resistant bacteria were accurately quantified. By monitoring the dynamic population change of a bacterial culture with the administration of antibiotics, we confirmed that under the antimicrobial pressure, the original low population of antibiotic-resistant bacteria outcompeted susceptible strains and became the dominant population after 5hours of growth. Detection of antibiotic-resistant infection in clinical urine samples was achieved without cultivation, and the bacterial load of susceptible and resistant strains can be faithfully quantified. Overall, the HSFCM-based quantitative method provides a powerful tool for the fundamental studies of antibiotic resistance and holds the potential to provide rapid and precise guidance in clinical therapies. Copyright © 2016 Elsevier B.V. All rights reserved.

Rock weathering by indigenous heterotrophic bacteria of Bacillus spp. at different temperature: a laboratory experiment

NASA Astrophysics Data System (ADS)

Štyriaková, I.; Štyriak, I.; Oberhänsli, H.

2012-07-01

The bio-weathering of basalt, granite and gneiss was experimentally investigated in this study. These rock-forming minerals weathered more rapidly via the ubiquitous psychrotrophic heterotrophic bacteria . With indigenous bacteria of Bacillus spp. from sediments of Lake Baikal, we traced the degradation process of silicate minerals to understand the weathering processes occurring at the change temperature in the subsurface environment with organic input. The bacteria mediated dissolution of minerals was monitored with solution and solid chemistry, X-ray analyses as well as microscopic techniques. We determined the impact of the bacteria on the mineral surface and leaching of K, Ca, Mg, Si, Fe, and Al from silicate minerals. In the samples the release of major structural elements of silicates was used as an overall indicator of silicate mineral degradation at 4°C and 18°C from five medium exchanges over 255 days of rock bioleaching. The increase of temperature importantly affected the efficiency of Fe extraction from granite and basalt as well as Si extraction from granite and gneiss. In comparison with elemental extraction order at 4°C, Ca was substituted first by Fe or Si. It is evident that temperature influences rock microbial weathering and results in a change of elements extraction.

Bytes and Bugs: Integrating Computer Programming with Bacteria Identification.

ERIC Educational Resources Information Center

Danciger, Michael

1986-01-01

By using a computer program to identify bacteria, students sharpen their analytical skills and gain familiarity with procedures used in laboratories outside the university. Although it is ideal for identifying a bacterium, the program can be adapted to many other disciplines. (Author)

The impact of permafrost-associated microorganisms on hydrate formation kinetics

NASA Astrophysics Data System (ADS)

Luzi-Helbing, Manja; Liebner, Susanne; Spangenberg, Erik; Wagner, Dirk; Schicks, Judith M.

2016-04-01

The relationship between gas hydrates, microorganisms and the surrounding sediment is extremely complex: On the one hand, microorganisms producing methane provide the prerequisite for gas hydrate formation. As it is known most of the gas incorporated into natural gas hydrates originates from biogenic sources. On the other hand, as a result of microbial activity gas hydrates are surrounded by a great variety of organic compounds which are not incorporated into the hydrate structure but may influence the formation or degradation process. For gas hydrate samples from marine environments such as the Gulf of Mexico a direct association between microbes and gas hydrates was shown by Lanoil et al. 2001. It is further assumed that microorganisms living within the gas hydrate stability zone produce biosurfactants which were found to enhance the hydrate formation process significantly and act as nucleation centres (Roger et al. 2007). Another source of organic compounds is sediment organic matter (SOM) originating from plant material or animal remains which may also enhance hydrate growth. So far, the studies regarding this relationship were focused on a marine environment. The scope of this work is to extend the investigations to microbes originating from permafrost areas. To understand the influence of microbial activity in a permafrost environment on the methane hydrate formation process and the stability conditions of the resulting hydrate phase we will perform laboratory studies. Thereby, we mimic gas hydrate formation in the presence and absence of methanogenic archaea (e.g. Methanosarcina soligelidi) and other psychrophilic bacteria isolated from permafrost environments of the Arctic and Antarctic to investigate their impact on hydrate induction time and formation rates. Our results may contribute to understand and predict the occurrences and behaviour of potential gas hydrates within or adjacent to the permafrost. Lanoil BD, Sassen R, La Duc MT, Sweet ST, Nealson KH

Population of Nitrifying Bacteria and Nitrification in Ammonium Saturated Clinoptilolite

NASA Technical Reports Server (NTRS)

McGilloway, R. L.; Weaver, R. W.; Ming, Douglas W.; Gruener, J.

1999-01-01

As humans begin to spend longer periods of time in space, plants will be incorporated into life support systems. Ammonium saturated clinoptilolite is one plant growth substrate but a balance between ammonium and nitrate is needed. A laboratory study was conducted to determine effects of nitrifying bacteria on ammonium concentrations and kinetics of nitrification. Columns containing clinoptilolite substrate amended with nitrifying bacteria obtained from soil enrichment were analyzed weekly for a 90 day period. The enrichment culture initially contained 1 x 10(exp 5) ammonium oxidizing bacteria and 1 x 10(exp 2) nitrite oxidizing bacteria per gram of substrate. Populations of ammonium oxidizing bacteria increased to 1 x 10(exp 6) and nitrite oxidizing bacteria increased to 1 x 10(exp 3) per gram of substrate. The nitrification rate was approximately 0.25mg NO3(-)-N/kg.hr. Experiments were also conducted to enumerate nitrifying bacteria in a clinoptilolite substrate used to grow wheat (Triticum aestivum L.). Seventy days following the initial inoculation with an unknown number of commercial nitrifying bacteria, 1 x 10(exp 5) ammonium oxidizing bacteria per gram of substrate were present. The number of nitrite oxidizing bacteria was between 1 x 10(exp 3) to 10(exp 4) per gram of substrate as measured by the most probable number method. Nitrification rates were approximately 0.20mg NO3(-)-N/kg.hr. Clinoptilolite readily exchanged sufficient concentrations of ammonium to support nitrifying bacteria and they survived well in this medium.

Coryneform bacteria in infectious diseases: clinical and laboratory aspects.

PubMed Central

Coyle, M B; Lipsky, B A

1990-01-01

Coryneform isolates from clinical specimens frequently cannot be identified by either reference laboratories or research laboratories. Many of these organisms are skin flora that belong to a large number of taxonomic groups, only 40% of which are in the genus Corynebacterium. This review provides an update on clinical presentations, microbiological features, and pathogenic mechanisms of infections with nondiphtheria Corynebacterium species and other pleomorphic gram-positive rods. The early literature is also reviewed for a few coryneforms, especially those whose roles as pathogens are controversial. Recognition of newly emerging opportunistic coryneforms is dependent on sound identification schemes which cannot be developed until cell wall analyses and nucleic acid studies have defined the taxonomic groups and all of the reference strains within each taxon have been shown by molecular methods to be authentic members. Only then can reliable batteries of biochemical tests be selected for distinguishing each taxon. PMID:2116939

Antimicrobial resistance patterns of bacteria isolated from canine urinary samples submitted to a New Zealand veterinary diagnostic laboratory between 2005-2012.

PubMed

McMeekin, C H; Hill, K E; Gibson, I R; Bridges, J P; Benschop, J

2017-03-01

To identify and describe culture and antimicrobial resistance (AMR) patterns in bacteria isolated from canine urinary samples submitted to a New Zealand veterinary diagnostic laboratory. Records from a veterinary diagnostic laboratory were examined for bacterial isolates cultured from canine urine samples between January 2005 and December 2012. Culture and susceptibility results were compiled with information on the age, sex and breed of dog. Repeat submissions were removed. Susceptibility was assessed using results of the Kirby-Bauer disk diffusion method, for a standard panel including amoxicillin-clavulanic acid (AMC), cefovecin (from 2010-2012), cephalothin, clindamycin, enrofloxacin and trimethoprim-sulphonamide (TMS). A total of 5,786 urine samples were submitted for analysis, and 3,135 bacterial isolates were cultured from 2,184 samples. Of these 3,135 isolates, 1,104 (35.2%) were Escherichia coli, 442 (14.1%) were Staphylococcus spp., 357 (11.4%) Proteus mirabilis and 276 (8.8%) were Enterococcus spp. The frequency of culture-positive samples increased with increasing age in both female and male dogs (p<0.001). The percentage of E. coli isolates resistant to AMC and cephalothin increased between 2005 and 2012 (p<0.001), as did resistance to enrofloxacin (p=0.022), but there was no change in resistance to TMS (p=0.696). Enrofloxacin was the antimicrobial with the least resistance shown by the four most common bacteria isolated during the course of the study. The results of this study provide important regional information regarding the prevalence of bacterial uropathogens and their susceptibility patterns. There was an increase in resistance to some commonly used antimicrobials in the treatment of urinary tract infections. Having access to regional antimicrobial susceptibility results is crucial when forming guidelines for the use of antimicrobials for the treatment of urinary tract infections. Given changes in practising habits and antimicrobial usage over

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria

PubMed Central

Chui, Huixia; Domish, Larissa; Hernandez, Drexler; Wang, Gehua

2016-01-01

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS‐based diagnosis methods for bacteria identification and typing have been created, not only on well‐accepted MALDI‐TOF‐MS‐based fingerprint matches, but also on solving the insufficiencies of MALDI‐TOF‐MS‐based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS‐based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria. PMID:26751976

Does the presence of bacteria effect basaltic glass dissolution rates? 1: Dead Pseudomonas reactants

NASA Astrophysics Data System (ADS)

Stockmann, Gabrielle J.; Shirokova, Liudmila S.; Pokrovsky, Oleg S.; Oelkers, Eric H.; Benezeth, Pascale

2010-05-01

Basaltic glass and crystalline basalt formations in Iceland have been suggested for industrial CO2 storage due to their porous and permeable properties and high reactivity. Acid CO2-saturated waters in contact with basaltic glass will lead to rapid dissolution of the glass and release of divalent cations, (Ca2+, Mg2+, Fe2+) that can react to form stable carbonates and thereby trap the CO2. However, the basalt formations in Iceland not only contains glass and mineral assemblages, but also host microbiological communities that either by their presence or by active involvement in chemical reactions could affect the amount of basaltic glass being dissolved and CO2 being trapped. Samples of natural bacteria communities from the CO2 storage grounds in Iceland were collected, separated, and purified using agar plate technique and cultured under laboratory conditions in nutrient broth-rich media. Heterotrophic aerobic Gram-negative strain of Pseudomonas reactants was selected for a series of flow-through experiments aimed at evaluation of basaltic glass dissolution rate in the presense of increasing amounts of dead bacteria and their lysis products. The experiments were carried out using mixed-flow reactors at pH 4, 6, 8 and 10 at 25 °C. Each of the four reactors contained 1 gram of basaltic glass of the size fraction 45-125 μm. This glass was dissolved in ~ 0.01 M buffer solutions (acetate, MES, bicarbonate and carbonate+bicarbonate mixture) of the desired pH. All experiments ran 2 months, keeping the flowrate and temperature stable and only changing the concentration of dead bacteria in the inlet solutions (from 0 to 430 mg/L). Experiments were performed in sterile conditions, and bacterial growth was prevented by adding NaN3 to the inlet solutions. Routine culturing of bacteria on the agar plates confirmed the sterility of experiments. Samples of outlet solutions were analyzed for major cations and trace elements by ICP-MS. Results demonstrate a slight decrease in the

Validating Laboratory Results in Electronic Health Records

PubMed Central

Perrotta, Peter L.; Karcher, Donald S.

2017-01-01

Context Laboratories must ensure that the test results and pathology reports they transmit to a patient’s electronic health record (EHR) are accurate, complete, and presented in a useable format. Objective To determine the accuracy, completeness, and formatting of laboratory test results and pathology reports transmitted from the laboratory to the EHR. Design Participants from 45 institutions retrospectively reviewed results from 16 different laboratory tests, including clinical and anatomic pathology results, within the EHR used by their providers to view laboratory results. Results were evaluated for accuracy, presence of required elements, and usability. Both normal and abnormal results were reviewed for tests, some of which were performed in-house and others at a reference laboratory. Results Overall accuracy for test results transmitted to the EHR was greater than 99.3% (1052 of 1059). There was lower compliance for completeness of test results, with 69.6% (732 of 1051) of the test results containing all essential reporting elements. Institutions that had fewer than half of their orders entered electronically had lower test result completeness rates. The rate of appropriate formatting of results was 90.9% (98 of 1010). Conclusions The great majority of test results are accurately transmitted from the laboratory to the EHR; however, lower percentages are transmitted completely and in a useable format. Laboratories should verify the accuracy, completeness, and format of test results at the time of test implementation, after test changes, and periodically. PMID:27575266

Characterization of airborne ice-nucleation-active bacteria and bacterial fragments

NASA Astrophysics Data System (ADS)

Šantl-Temkiv, Tina; Sahyoun, Maher; Finster, Kai; Hartmann, Susan; Augustin-Bauditz, Stefanie; Stratmann, Frank; Wex, Heike; Clauss, Tina; Nielsen, Niels Woetmann; Sørensen, Jens Havskov; Korsholm, Ulrik Smith; Wick, Lukas Y.; Karlson, Ulrich Gosewinkel

2015-05-01

Some bacteria have the unique capacity of synthesising ice-nucleation-active (INA) proteins and exposing them at their outer membrane surface. As INA bacteria enter the atmosphere, they may impact the formation of clouds and precipitation. We studied members of airborne bacterial communities for their capacity to catalyse ice formation and we report on the excretion of INA proteins by airborne Pseudomonas sp. We also observed for the first time that INA biological fragments <220 nm were present in precipitation samples (199 and 482 INA fragments per L of precipitation), which confirms the presence of submicron INA biological fragments in the atmosphere. During 14 precipitation events, strains affiliated with the genus Pseudomonas, which are known to carry ina genes, were dominant. A screening for INA properties revealed that ∼12% of the cultivable bacteria caused ice formation at ≤-7 °C. They had likely been emitted to the atmosphere from terrestrial surfaces, e.g. by convective transport. We tested the ability of isolated INA strains to produce outer membrane vesicles and found that two isolates could do so. However, only very few INA vesicles were released per INA cell. Thus, the source of the submicron INA proteinaceous particles that we detected in the atmosphere remains to be elucidated.

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms.

PubMed

Ho, Van Thi Thuy; Fleet, Graham H; Zhao, Jian

2018-08-20

Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of the bean pulp by microorganisms is essential for developing the precursors of chocolate flavour. Currently, the cocoa fermentation is still conducted by an uncontrolled traditional process via a consortium of indigenous species of yeasts, lactic acid bacteria and acetic acid bacteria. Although the essential contribution of yeasts to the production of good quality beans and, typical chocolate character is generally agreed, the roles of lactic acid bacteria and acetic acid bacteria are less certain. The objective of this study was to investigate the contribution of LAB and AAB in cocoa bean fermentation by conducting small scale laboratory fermentations under aseptic conditions, inoculated with different groups of microorganisms previously isolated from spontaneous cocoa fermentations. The inoculation protocols were: (1) four yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae; (2) four yeasts plus the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum; (3) four yeasts plus the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateuri and (4) four yeasts plus two lactic acid bacteria and two acetic acid bacteria. Only the inoculated species were detected in the microbiota of their respective fermentations. Beans from the inoculated fermentations showed no significant differences in colour, shell weights and concentrations of residual sugars, alcohols and esters (p>0.05), but they were slightly different in contents of lactic acid and acetic acid (p<0.05). All beans were fully brown and free of mould. Residual sugar levels were less than 2.6 mg/g while the shell contents and ethanol were in the range of 11-13.4% and 4.8-7 mg/g, respectively. Beans fermented in the presence of LAB contained higher levels of lactic acid (0.6-1.2 mg/g) whereas higher concentrations of acetic acid

Corrosion of carbon steel by bacteria from North Sea offshore seawater injection systems: laboratory investigation.

PubMed

Stipanicev, Marko; Turcu, Florin; Esnault, Loïc; Rosas, Omar; Basseguy, Régine; Sztyler, Magdalena; Beech, Iwona B

2014-06-01

Influence of sulfidogenic bacteria, from a North Sea seawater injection system, on the corrosion of S235JR carbon steel was studied in a flow bioreactor; operating anaerobically for 100days with either inoculated or filtrated seawater. Deposits formed on steel placed in reactors contained magnesium and calcium minerals plus iron sulfide. The dominant biofilm-forming organism was an anaerobic bacterium, genus Caminicella, known to produce hydrogen sulfide and carbon dioxide. Open Circuit Potentials (OCP) of steel in the reactors was, for nearly the entire test duration, in the range -80045), suggested pitting on steel samples within the inoculated environment. However, the actual degree of corrosion could neither be directly correlated with the electrochemical data and nor with the steel corrosion in the filtrated seawater environment. Further laboratory tests are thought to clarify the noticed apparent discrepancies. © 2013.

Manuka honey inhibits adhesion and invasion of medically important wound bacteria in vitro.

PubMed

Maddocks, Sarah Elizabeth; Jenkins, Rowena Eleri; Rowlands, Richard Samuel; Purdy, Kevin John; Cooper, Rose Agnes

2013-12-01

To characterize the effect of manuka honey on medically important wound bacteria in vitro, focusing on its antiadhesive properties. Crystal violet biofilm assays, fluorescent microscopy, protein adhesion assay and gentamicin protection assay were used to determine the impact of manuka honey on biofilm formation, human protein binding and adherence to/invasion into human keratinocytes. Manuka honey effectively disrupted and caused extensive cell death in biofilms of Staphylococcus aureus, Pseudomonas aeruginosa and Streptococcus pyogenes. Sublethal doses of manuka honey inhibited bacterial adhesion to the fibronectin, fibrinogen and collagen. Manuka honey impaired adhesion of laboratory and clinical isolates of S. aureus, P. aeruginosa and S. pyogenes to human keratinocytes in vitro, and inhibited invasion by S. pyogenes and homogeneous vancomycin intermediate S. aureus. Manuka honey can directly affect bacterial cells embedded in a biofilm and exhibits antiadhesive properties against three common wound pathogens.

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

NASA Technical Reports Server (NTRS)

Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

1985-01-01

Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

Expulsion of swimming bacteria by a circular flow

NASA Astrophysics Data System (ADS)

Sokolov, Andrey; Aronson, Igor

Macroscopic shear flow alters swimming trajectories in a highly nontrivial way and results in dramatic reduction of viscosity and heterogeneous bacterial distributions. We report on experimental and theoretical studies of rapid expulsion of microswimmers, such as motile bacteria, by a circular flow created by a rotating microparticle. We observed a formation of a macroscopic depletion area in a high-shear region, in the vicinity of a microparticle. The rapid migration of bacteria from the shear-rich area is caused by a circular structure of the flow rather than intrinsic random fluctuations of bacteria orientations, in stark contrast to planar shear flow. Our mathematical model revealed that expulsion is a combined effect of motility and alignment by a vortical flow. Our findings offer a novel approach for manipulation of motile microorganisms and shed new light on bacteria-flow interactions. Was supported by the US DOE, Office of Basic Energy Sciences, Division of Materials Science And Engineering, under Contract No. DE AC02-06CH11357.

Metabolic activity of permafrost bacteria below the freezing point

NASA Technical Reports Server (NTRS)

Rivkina, E. M.; Friedmann, E. I.; McKay, C. P.; Gilichinsky, D. A.

2000-01-01

Metabolic activity was measured in the laboratory at temperatures between 5 and -20 degrees C on the basis of incorporation of (14)C-labeled acetate into lipids by samples of a natural population of bacteria from Siberian permafrost (permanently frozen soil). Incorporation followed a sigmoidal pattern similar to growth curves. At all temperatures, the log phase was followed, within 200 to 350 days, by a stationary phase, which was monitored until the 550th day of activity. The minimum doubling times ranged from 1 day (5 degrees C) to 20 days (-10 degrees C) to ca. 160 days (-20 degrees C). The curves reached the stationary phase at different levels, depending on the incubation temperature. We suggest that the stationary phase, which is generally considered to be reached when the availability of nutrients becomes limiting, was brought on under our conditions by the formation of diffusion barriers in the thin layers of unfrozen water known to be present in permafrost soils, the thickness of which depends on temperature.

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories.

PubMed

Wurtz, N; Papa, A; Hukic, M; Di Caro, A; Leparc-Goffart, I; Leroy, E; Landini, M P; Sekeyova, Z; Dumler, J S; Bădescu, D; Busquets, N; Calistri, A; Parolin, C; Palù, G; Christova, I; Maurin, M; La Scola, B; Raoult, D

2016-08-01

Laboratory-acquired infections due to a variety of bacteria, viruses, parasites, and fungi have been described over the last century, and laboratory workers are at risk of exposure to these infectious agents. However, reporting laboratory-associated infections has been largely voluntary, and there is no way to determine the real number of people involved or to know the precise risks for workers. In this study, an international survey based on volunteering was conducted in biosafety level 3 and 4 laboratories to determine the number of laboratory-acquired infections and the possible underlying causes of these contaminations. The analysis of the survey reveals that laboratory-acquired infections have been infrequent and even rare in recent years, and human errors represent a very high percentage of the cases. Today, most risks from biological hazards can be reduced through the use of appropriate procedures and techniques, containment devices and facilities, and the training of personnel.

Anaerobic bacteria grow within Candida albicans biofilms and induce biofilm formation in suspension cultures.

PubMed

Fox, Emily P; Cowley, Elise S; Nobile, Clarissa J; Hartooni, Nairi; Newman, Dianne K; Johnson, Alexander D

2014-10-20

The human microbiome contains diverse microorganisms, which share and compete for the same environmental niches. A major microbial growth form in the human body is the biofilm state, where tightly packed bacterial, archaeal, and fungal cells must cooperate and/or compete for resources in order to survive. We examined mixed biofilms composed of the major fungal species of the gut microbiome, Candida albicans, and each of five prevalent bacterial gastrointestinal inhabitants: Bacteroides fragilis, Clostridium perfringens, Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis. We observed that biofilms formed by C. albicans provide a hypoxic microenvironment that supports the growth of two anaerobic bacteria, even when cultured in ambient oxic conditions that are normally toxic to the bacteria. We also found that coculture with bacteria in biofilms induces massive gene expression changes in C. albicans, including upregulation of WOR1, which encodes a transcription regulator that controls a phenotypic switch in C. albicans, from the "white" cell type to the "opaque" cell type. Finally, we observed that in suspension cultures, C. perfringens induces aggregation of C. albicans into "mini-biofilms," which allow C. perfringens cells to survive in a normally toxic environment. This work indicates that bacteria and C. albicans interactions modulate the local chemistry of their environment in multiple ways to create niches favorable to their growth and survival. Copyright © 2014 Elsevier Ltd. All rights reserved.

Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere

PubMed Central

Stiefel, Philipp; Zambelli, Tomaso

2013-01-01

In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources. PMID:23770907

Formation of complex bacterial colonies via self-generated vortices

NASA Astrophysics Data System (ADS)

Czirók, András; Ben-Jacob, Eshel; Cohen, Inon; Vicsek, Tamás

1996-08-01

Depending on the environmental conditions bacterial colonies growing on agar surfaces can exhibit complex colony formation and various types of collective motion. Experimental results are presented concerning the hydrodynamics (vortices, migration of bacteria in clusters) and colony formation of a morphotype of Bacillus subtilis. Some of these features are not specific to this morphotype but also have been observed in several other bacterial strains, suggesting the presence of universal effects. A simple model of self-propelled particles is proposed, which is capable of describing the hydrodynamics on the intermediate level, including the experimentally observed rotating disks of bacteria. The colony formation is captured by a complex generic model taking into account nutrient diffusion, reproduction, and sporulation of bacteria, extracellular slime deposition, chemoregulation, and inhomogeneous population. Our model also sheds light on some possible biological benefits of this ``multicellular behavior.''

Enrichments for phototrophic bacteria and characterization by morphology and pigment analysis

NASA Technical Reports Server (NTRS)

Brune, D.

1985-01-01

The purpose of this investigation was to examine several sulfide containing environments for the presence of phototrophic bacteria and to obtain enriched cultures of some of the bacteria present. The field sites were Alum Rock State Park, the Palo Alto salt marsh, the bay area salt ponds, and Big Soda Lake (near Fallon, Nevada). Bacteria from these sites were characterized by microscopic examination, measurement of in vitro absorption spectra, and analysis of carotenoid pigments. Field observations at one of the bay area salt ponds, in which the salt concentration was saturating (about 30 percent NaCl) and the sediments along the shore of the pond covered with a gypsum crust, revealed a layer of purple photosynthetic bacteria under a green layer in the gypsum crust. Samples of this gypsum crust were taken to the laboratory to measure light transmission through the crust and to try to identify the purple photosynthetic bacteria present in this extremely saline environment.

[The future of clinical laboratory database management system].

PubMed

Kambe, M; Imidy, D; Matsubara, A; Sugimoto, Y

1999-09-01

To assess the present status of the clinical laboratory database management system, the difference between the Clinical Laboratory Information System and Clinical Laboratory System was explained in this study. Although three kinds of database management systems (DBMS) were shown including the relational model, tree model and network model, the relational model was found to be the best DBMS for the clinical laboratory database based on our experience and developments of some clinical laboratory expert systems. As a future clinical laboratory database management system, the IC card system connected to an automatic chemical analyzer was proposed for personal health data management and a microscope/video system was proposed for dynamic data management of leukocytes or bacteria.

Remediation of Acid Mine Drainage with Sulfate Reducing Bacteria

ERIC Educational Resources Information Center

Hauri, James F.; Schaider, Laurel A.

2009-01-01

Sulfate reducing bacteria have been shown to be effective at treating acid mine drainage through sulfide production and subsequent precipitation of metal sulfides. In this laboratory experiment for undergraduate environmental chemistry courses, students design and implement a set of bioreactors to remediate acid mine drainage and explain observed…

Functional genomics of lactic acid bacteria: from food to health

PubMed Central

2014-01-01

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health. PMID:25186768

Functional genomics of lactic acid bacteria: from food to health.

PubMed

Douillard, François P; de Vos, Willem M

2014-08-29

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

The aerobic activity of metronidazole against anaerobic bacteria.

PubMed

Dione, Niokhor; Khelaifia, Saber; Lagier, Jean-Christophe; Raoult, Didier

2015-05-01

Recently, the aerobic growth of strictly anaerobic bacteria was demonstrated using antioxidants. Metronidazole is frequently used to treat infections caused by anaerobic bacteria; however, to date its antibacterial activity was only tested in anaerobic conditions. Here we aerobically tested using antioxidants the in vitro activities of metronidazole, gentamicin, doxycycline and imipenem against 10 common anaerobic and aerobic bacteria. In vitro susceptibility testing was performed by the disk diffusion method, and minimum inhibitory concentrations (MICs) were determined by Etest. Aerobic culture of the bacteria was performed at 37°C using Schaedler agar medium supplemented with 1mg/mL ascorbic acid and 0.1mg/mL glutathione; the pH was adjusted to 7.2 by 10M KOH. Growth of anaerobic bacteria cultured aerobically using antioxidants was inhibited by metronidazole after 72h of incubation at 37°C, with a mean inhibition diameter of 37.76mm and an MIC of 1μg/mL; however, strains remained non-sensitive to gentamicin. No growth inhibition of aerobic bacteria was observed after 24h of incubation at 37°C with metronidazole; however, inhibition was observed with doxycycline and imipenem used as controls. These results indicate that bacterial sensitivity to metronidazole is not related to the oxygen tension but is a result of the sensitivity of the micro-organism. In future, both culture and antibiotic susceptibility testing of strictly anaerobic bacteria will be performed in an aerobic atmosphere using antioxidants in clinical microbiology laboratories. Copyright © 2015 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Preferential Promotion of Lycopersicon esculentum (Tomato) Growth by Plant Growth Promoting Bacteria Associated with Tomato.

PubMed

Vaikuntapu, Papa Rao; Dutta, Swarnalee; Samudrala, Ram Babu; Rao, Vukanti R V N; Kalam, Sadaf; Podile, Appa Rao

2014-12-01

A total of 74 morphologically distinct bacterial colonies were selected during isolation of bacteria from different parts of tomato plant (rhizoplane, phylloplane and rhizosphere) as well as nearby bulk soil. The isolates were screened for plant growth promoting (PGP) traits such as production of indole acetic acid, siderophore, chitinase and hydrogen cyanide as well as phosphate solubilization. Seven isolates viz., NR4, NR6, RP3, PP1, RS4, RP6 and NR1 that exhibited multiple PGP traits were identified, based on morphological, biochemical and 16S rRNA gene sequence analysis, as species that belonged to four genera Aeromonas, Pseudomonas, Bacillus and Enterobacter. All the seven isolates were positive for 1-aminocyclopropane-1-carboxylate deaminase. Isolate NR6 was antagonistic to Fusarium solani and Fusarium moniliforme, and both PP1 and RP6 isolates were antagonistic to F. moniliforme. Except RP6, all isolates adhered significantly to glass surface suggestive of biofilm formation. Seed bacterization of tomato, groundnut, sorghum and chickpea with the seven bacterial isolates resulted in varied growth response in laboratory assay on half strength Murashige and Skoog medium. Most of the tomato isolates positively influenced tomato growth. The growth response was either neutral or negative with groundnut, sorghum and chickpea. Overall, the results suggested that bacteria with PGP traits do not positively influence the growth of all plants, and certain PGP bacteria may exhibit host-specificity. Among the isolates that positively influenced growth of tomato (NR1, RP3, PP1, RS4 and RP6) only RS4 was isolated from tomato rhizosphere. Therefore, the best PGP bacteria can also be isolated from zones other than rhizosphere or rhizoplane of a plant.

Effects of Grazing on Bacteria-Mediated Corrosion of Metals in Seawater

DTIC Science & Technology

1986-05-01

NUMBEER2. GOVT ACCESSION NO. 3. RECIPIENT’S CATA’.00 NJUMIIER 4. TITLE (mESubtitle) S*TYPE OF REPORT a ’!;.iOO COVERED IL’ Effects of Grazing on... Effects of Grazing on Bacteria-Mediated Corrosion of Metals in Seawater ONR Contract No. : N00014-83-0652 Project Period: August 1983-August, 1985 Principal...the laboratory to address the next two objectives. II. Effect of Protozoa on Total Numbers of Bacteria on Metals This objective included testing a

Endosymbiotic calcifying bacteria across sponge species and oceans

NASA Astrophysics Data System (ADS)

Garate, Leire; Sureda, Jan; Agell, Gemma; Uriz, Maria J.

2017-03-01

From an evolutionary point of view, sponges are ideal targets to study marine symbioses as they are the most ancient living metazoans and harbour highly diverse microbial communities. A recently discovered association between the sponge Hemimycale columella and an intracellular bacterium that generates large amounts of calcite spherules has prompted speculation on the possible role of intracellular bacteria in the evolution of the skeleton in early animals. To gain insight into this purportedly ancestral symbiosis, we investigated the presence of symbiotic bacteria in Mediterranean and Caribbean sponges. We found four new calcibacteria OTUs belonging to the SAR116 in two orders (Poecilosclerida and Clionaida) and three families of Demospongiae, two additional OTUs in cnidarians and one more in seawater (at 98.5% similarity). Using a calcibacteria targeted probe and CARD-FISH, we also found calcibacteria in Spirophorida and Suberitida and proved that the calcifying bacteria accumulated at the sponge periphery, forming a skeletal cortex, analogous to that of siliceous microscleres in other demosponges. Bacteria-mediated skeletonization is spread in a range of phylogenetically distant species and thus the purported implication of bacteria in skeleton formation and evolution of early animals gains relevance.

Airborne bacteria in the atmosphere: Presence, purpose, and potential

NASA Astrophysics Data System (ADS)

Smets, Wenke; Moretti, Serena; Denys, Siegfried; Lebeer, Sarah

2016-08-01

Numerous recent studies have highlighted that the types of bacteria present in the atmosphere often show predictable patterns across space and time. These patterns can be driven by differences in bacterial sources of the atmosphere and a wide range of environmental factors, including UV intensity, precipitation events, and humidity. The abundance of certain bacterial taxa is of interest, not only for their ability to mediate a range of chemical and physical processes in the atmosphere, such as cloud formation and ice nucleation, but also for their implications -both beneficial and detrimental-for human health. Consequently, the widespread importance of airborne bacteria has stimulated the search for their applicability. Improving air quality, modelling the dispersal of airborne bacteria (e.g. pathogens) and biotechnological purposes are already being explored. Nevertheless, many technological challenges still need to be overcome to fully understand the roles of airborne bacteria in our health and global ecosystems.

The effect of lactic acid bacteria on cocoa bean fermentation.

PubMed

Ho, Van Thi Thuy; Zhao, Jian; Fleet, Graham

2015-07-16

Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of cocoa pulp by microorganisms is crucial for developing chocolate flavor precursors. Yeasts conduct an alcoholic fermentation within the bean pulp that is essential for the production of good quality beans, giving typical chocolate characters. However, the roles of bacteria such as lactic acid bacteria and acetic acid bacteria in contributing to the quality of cocoa bean and chocolate are not fully understood. Using controlled laboratory fermentations, this study investigated the contribution of lactic acid bacteria to cocoa bean fermentation. Cocoa beans were fermented under conditions where the growth of lactic acid bacteria was restricted by the use of nisin and lysozyme. The resultant microbial ecology, chemistry and chocolate quality of beans from these fermentations were compared with those of indigenous (control) fermentations. The yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae, the lactic acid bacteria Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus fermentum and the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateurii were the major species found in control fermentations. In fermentations with the presence of nisin and lysozyme, the same species of yeasts and acetic acid bacteria grew but the growth of lactic acid bacteria was prevented or restricted. These beans underwent characteristic alcoholic fermentation where the utilization of sugars and the production of ethanol, organic acids and volatile compounds in the bean pulp and nibs were similar for beans fermented in the presence of lactic acid bacteria. Lactic acid was produced during both fermentations but more so when lactic acid bacteria grew. Beans fermented in the presence or absence of lactic acid bacteria were fully fermented, had similar shell weights and gave acceptable chocolates with no differences

Modeling the Endogenous Sunlight Inactivation Rates of Laboratory Strain and Wastewater E. coli and Enterococci Using Biological Weighting Functions.

PubMed

Silverman, Andrea I; Nelson, Kara L

2016-11-15

Models that predict sunlight inactivation rates of bacteria are valuable tools for predicting the fate of pathogens in recreational waters and designing natural wastewater treatment systems to meet disinfection goals. We developed biological weighting function (BWF)-based numerical models to estimate the endogenous sunlight inactivation rates of E. coli and enterococci. BWF-based models allow the prediction of inactivation rates under a range of environmental conditions that shift the magnitude or spectral distribution of sunlight irradiance (e.g., different times, latitudes, water absorbances, depth). Separate models were developed for laboratory strain bacteria cultured in the laboratory and indigenous organisms concentrated directly from wastewater. Wastewater bacteria were found to be 5-7 times less susceptible to full-spectrum simulated sunlight than the laboratory bacteria, highlighting the importance of conducting experiments with bacteria sourced directly from wastewater. The inactivation rate models fit experimental data well and were successful in predicting the inactivation rates of wastewater E. coli and enterococci measured in clear marine water by researchers from a different laboratory. Additional research is recommended to develop strategies to account for the effects of elevated water pH on predicted inactivation rates.

Endocarditis Due to Rare and Fastidious Bacteria

PubMed Central

Brouqui, P.; Raoult, D.

2001-01-01

The etiologic diagnosis of infective endocarditis is easily made in the presence of continuous bacteremia with gram-positive cocci. However, the blood culture may contain a bacterium rarely associated with endocarditis, such as Lactobacillus spp., Klebsiella spp., or nontoxigenic Corynebacterium, Salmonella, Gemella, Campylobacter, Aeromonas, Yersinia, Nocardia, Pasteurella, Listeria, or Erysipelothrix spp., that requires further investigation to establish the relationship with endocarditis, or the blood culture may be uninformative despite a supportive clinical evaluation. In the latter case, the etiologic agents are either fastidious extracellular or intracellular bacteria. Fastidious extracellular bacteria such as Abiotrophia, HACEK group bacteria, Clostridium, Brucella, Legionella, Mycobacterium, and Bartonella spp. need supplemented media, prolonged incubation time, and special culture conditions. Intracellular bacteria such as Coxiella burnetii cannot be isolated routinely. The two most prevalent etiologic agents of culture-negative endocarditis are C. burnetti and Bartonella spp. Their diagnosis is usually carried out serologically. A systemic pathologic examination of excised heart valves including periodic acid-Schiff (PAS) staining and molecular methods has allowed the identification of Whipple's bacillus endocarditis. Pathologic examination of the valve using special staining, such as Warthin-Starry, Gimenez, and PAS, and broad-spectrum PCR should be performed systematically when no etiologic diagnosis is evident through routine laboratory evaluation. PMID:11148009

A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria.

PubMed

Winans, Nathan J; Walter, Alec; Chouaia, Bessem; Chaston, John M; Douglas, Angela E; Newell, Peter D

2017-09-01

Various bacterial taxa have been identified both in association with animals and in the external environment, but the extent to which related bacteria from the two habitat types are ecologically and evolutionarily distinct is largely unknown. This study investigated the scale and pattern of genetic differentiation between bacteria of the family Acetobacteraceae isolated from the guts of Drosophila fruit flies, plant material and industrial fermentations. Genome-scale analysis of the phylogenetic relationships and predicted functions was conducted on 44 Acetobacteraceae isolates, including newly sequenced genomes from 18 isolates from wild and laboratory Drosophila. Isolates from the external environment and Drosophila could not be assigned to distinct phylogenetic groups, nor are their genomes enriched for any different sets of genes or category of predicted gene functions. In contrast, analysis of bacteria from laboratory Drosophila showed they were genetically distinct in their universal capacity to degrade uric acid (a major nitrogenous waste product of Drosophila) and absence of flagellar motility, while these traits vary among wild Drosophila isolates. Analysis of the competitive fitness of Acetobacter discordant for these traits revealed a significant fitness deficit for bacteria that cannot degrade uric acid in culture with Drosophila. We propose that, for wild populations, frequent cycling of Acetobacter between Drosophila and the external environment prevents genetic differentiation by maintaining selection for traits adaptive in both the gut and external habitats. However, laboratory isolates bear the signs of adaptation to persistent association with the Drosophila host under tightly defined environmental conditions. © 2017 John Wiley & Sons Ltd.

Exobiology Robotics Laboratory to Search for Life on Martian Subsurface Water and Permafrost

NASA Astrophysics Data System (ADS)

Gan, D. C.; Kuznetz, L.; Chu, D.; Chang, V.; Yamada, M.; Lee, C.; Lee, R.

2000-07-01

A conceptual design of a robotics laboratory was constructed to search for life forms in Martian subsurface water and permafrost by cultivation of bacteria by using a variety of media to grow bacteria of the Archea group and Eubacteria. Other growth, morphology, motility and mode of reproduction of bacteria and organisms of the Protista will be observed with microscopy. The entire operations is controlled by a computer.

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria.

PubMed

Cheng, Keding; Chui, Huixia; Domish, Larissa; Hernandez, Drexler; Wang, Gehua

2016-04-01

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS-based diagnosis methods for bacteria identification and typing have been created, not only on well-accepted MALDI-TOF-MS-based fingerprint matches, but also on solving the insufficiencies of MALDI-TOF-MS-based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS-based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria. © 2016 The Authors. PROTEOMICS - Clinical Applications Published by WILEY-VCH Verlag GmbH & Co. KGaA.

Formation of Polyhydroxyalkanoate in Aerobic Anoxygenic Phototrophic Bacteria and Its Relationship to Carbon Source and Light Availability▿

PubMed Central

Xiao, Na; Jiao, Nianzhi

2011-01-01

Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (Dinoroseobacter sp. JL1447, Roseobacter denitrificans OCh 114, Roseobacter litoralis OCh 149, Dinoroseobacter shibae DFL 12T, Labrenzia alexandrii DFL 11T, and Erythrobacter longus DSMZ 6997) were examined, and all of them demonstrated the ability to form the carbon polymer polyhydroxyalkanoate (PHA) in the cell. The PHA in Dinoroseobacter sp. JL1447 was identified as poly-beta-hydroxybutyrate (PHB) according to evidence from Fourier transform infrared spectroscopy, differential scanning calorimetry, and 1H nuclear magnetic resonance spectroscopy examinations. Carbon sources turned out to be critical for PHA production in AAPB. Among the eight media tested with Dinoroseobacter sp. JL1447, sodium acetate, giving a PHA production rate of 72%, was the most productive carbon source, followed by glucose, with a 68% PHA production rate. Such PHA production rates are among the highest recorded for all bacteria. The C/N ratio of substrates was verified by the experiments as another key factor in PHA production. In the case of R. denitrificans OCh 114, PHA was not detected when the organism was cultured at C/N ratios of <2 but became apparent at C/N ratios of >3. Light is also important for the formation of PHA in AAPB. In the case of Dinoroseobacter sp. JL1447, up to a one-quarter increase in PHB production was observed when the culture underwent growth in a light-dark cycle compared to growth completely in the dark. PMID:21908634

The influence of marine microbial activities on aerosol production: A laboratory mesocosm study

NASA Astrophysics Data System (ADS)

Alpert, Peter A.; Kilthau, Wendy P.; Bothe, Dylan W.; Radway, JoAnn C.; Aller, Josephine Y.; Knopf, Daniel A.

2015-09-01

The oceans cover most of the Earth's surface, contain nearly half the total global primary biomass productivity, and are a major source of atmospheric aerosol particles. Here we experimentally investigate links between biological activity in seawater and sea spray aerosol (SSA) flux, a relationship of potential significance for organic aerosol loading and cloud formation over the oceans and thus for climate globally. Bubbles were generated in laboratory mesocosm experiments either by recirculating impinging water jets or glass frits. Experiments were conducted with Atlantic Ocean seawater collected off the eastern end of Long Island, NY, and with artificial seawater containing cultures of bacteria and phytoplankton Thalassiosira pseudonana, Emiliania huxleyi, and Nannochloris atomus. Changes in SSA size distributions occurred during all phases of bacterial and phytoplankton growth, as characterized by cell concentrations, dissolved organic carbon, total particulate carbon, and transparent exopolymer particles (gel-forming polysaccharides representing a major component of biogenic exudate material). Over a 2 week growth period, SSA particle concentrations increased by a factor of less than 2 when only bacteria were present and by a factor of about 3 when bacteria and phytoplankton were present. Production of jet-generated SSA particles of diameter less than 200 nm increased with time, while production of all particle diameters increased with time when frits were used. The implications of a marine biological activity dependent SSA flux are discussed.

Antibacterial potential of phytochemicals alone or in combination with antimicrobials against fish pathogenic bacteria.

PubMed

Bandeira Junior, G; Sutili, F J; Gressler, L T; Ely, V L; Silveira, B P; Tasca, C; Reghelin, M; Matter, L B; Vargas, A P C; Baldisserotto, B

2018-05-09

This study investigated the antibacterial activity of five phytochemicals (carvacrol, citral, eugenol, linalool, and thymol) alone or in combination with florfenicol or oxytetracycline against bacteria isolated from silver catfish (Rhamdia quelen). We also analyzed the potential of these compounds to inhibit biofilm formation and hemolysis caused by the bacteria. Bacteria were tested with antimicrobials to calculate the multiple antibiotic resistance (MAR). The checkerboard assay was used to evaluate a putative synergy between five phytochemicals and antimicrobials against the strains isolated. The biofilm formation inhibition assay was performed with phytochemicals and antimicrobials, and the hemolysis inhibition assay was performed with the phytochemicals. Carvacrol, eugenol and thymol were the most effective phytochemicals. Three combinations (linalool with florfenicol or oxytetracycline against Aeromonas hydrophila and citral with oxytetracycline against Citrobacter freundii) demonstrated synergy in the checkerboard assay. All phytochemicals inhibited biofilm formation and hemolysis activity. The tested phytochemicals showed satisfactory activity against fish pathogenic bacteria. The phytochemicals did not present antagonistic interactions with the antimicrobials, allowing their combined use, which may contribute to a decrease in the use of conventional drugs and their residues in aquatic environment. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Do wheelchairs spread pathogenic bacteria within hospital walls?

PubMed

Peretz, Avi; Koiefman, Anna; Dinisman, Eleonora; Brodsky, Diana; Labay, Kozitta

2014-02-01

Transmission of nosocomial pathogens has been linked to transient colonization of health care workers, medical devices and other constituents of patients' environment. In this paper we present our findings concerning the presence of pathogenic bacteria on wheelchairs, and the possibility that wheelchairs constitute a reservoir of these bacteria and a means of spreading them. In this work we examined four wheelchairs, each from a different location: the internal medicine ward, the emergency department, the general surgery ward and wheelchair stockpile of the transportation unit of the hospital. The samples were collected and cultured on different media. Bacterial identification and antimicrobial sensitivity testing were carried out using accepted practices in the microbiology laboratory. We found that wheelchairs are contaminated with several pathogenic bacteria, among them antibiotic-resistant strains such as MRSA, Pseudomonas aeruginosa, Acinetobacter baumanni etc. Since there is no specific guideline protocol that deals with disinfection and cleaning frequency of wheelchairs in hospitals, we suggest each hospital to write one.

Investigation of N-acyl homoserine lactone (AHL) molecule production in Gram-negative bacteria isolated from cooling tower water and biofilm samples.

PubMed

Haslan, Ezgi; Kimiran-Erdem, Ayten

2013-09-01

In this study, 99 Gram-negative rod bacteria were isolated from cooling tower water, and biofilm samples were examined for cell-to-cell signaling systems, N-acyl homoserine lactone (AHL) signal molecule types, and biofilm formation capacity. Four of 39 (10 %) strains isolated from water samples and 14 of 60 (23 %) strains isolated from biofilm samples were found to be producing a variety of AHL signal molecules. It was determined that the AHL signal molecule production ability and the biofilm formation capacity of sessile bacteria is higher than planktonic bacteria, and there was a statistically significant difference between the AHL signal molecule production of these two groups (p < 0.05). In addition, it was found that bacteria belonging to the same species isolated from cooling tower water and biofilm samples produced different types of AHL signal molecules and that there were different types of AHL signal molecules in an AHL extract of bacteria. In the present study, it was observed that different isolates of the same strains did not produce the same AHLs or did not produce AHL molecules, and bacteria known as AHL producers did not produce AHL. These findings suggest that detection of signal molecules in bacteria isolated from cooling towers may contribute to prevention of biofilm formation, elimination of communication among bacteria in water systems, and blockage of quorum-sensing controlled virulence of these bacteria.

Flagella-Mediated Adhesion and Extracellular DNA Release Contribute to Biofilm Formation and Stress Tolerance of Campylobacter jejuni

PubMed Central

Svensson, Sarah L.; Pryjma, Mark; Gaynor, Erin C.

2014-01-01

Campylobacter jejuni is a leading cause of foodbourne gastroenteritis, despite fragile behaviour under standard laboratory conditions. In the environment, C. jejuni may survive within biofilms, which can impart resident bacteria with enhanced stress tolerance compared to their planktonic counterparts. While C. jejuni forms biofilms in vitro and in the wild, it had not been confirmed that this lifestyle confers stress tolerance. Moreover, little is understood about molecular mechanisms of biofilm formation in this pathogen. We previously found that a ΔcprS mutant, which carries a deletion in the sensor kinase of the CprRS two-component system, forms enhanced biofilms. Biofilms were also enhanced by the bile salt deoxycholate and contained extracellular DNA. Through more in-depth analysis of ΔcprS and WT under conditions that promote or inhibit biofilms, we sought to further define this lifestyle for C. jejuni. Epistasis experiments with ΔcprS and flagellar mutations (ΔflhA, ΔpflA) suggested that initiation is mediated by flagellum-mediated adherence, a process which was kinetically enhanced by motility. Lysis was also observed, especially under biofilm-enhancing conditions. Microscopy suggested adherence was followed by release of eDNA, which was required for biofilm maturation. Importantly, inhibiting biofilm formation by removal of eDNA with DNase decreased stress tolerance. This work suggests the biofilm lifestyle provides C. jejuni with resilience that has not been apparent from observation of planktonic bacteria during routine laboratory culture, and provides a framework for subsequent molecular studies of C. jejuni biofilms. PMID:25166748

Bacterial aggregation and biofilm formation in a vortical flow

PubMed Central

Yazdi, Shahrzad; Ardekani, Arezoo M.

2012-01-01

Bacterial aggregation and patchiness play an important role in a variety of ecological processes such as competition, adaptation, epidemics, and succession. Here, we demonstrate that hydrodynamics of their environment can lead to their aggregation. This is specially important since microbial habitats are rarely at rest (e.g., ocean, blood stream, flow in porous media, and flow through membrane filtration processes). In order to study the dynamics of bacterial collection in a vortical flow, we utilize a microfluidic system to mimic some of the important microbial conditions at ecologically relevant spatiotemporal scales. We experimentally demonstrate the formation of “ring”-shaped bacterial collection patterns and subsequently the formation of biofilm streamers in a microfluidic system. Acoustic streaming of a microbubble is used to generate a vortical flow in a microchannel. Due to bacteria's finite-size, the microorganisms are directed to closed streamlines and trapped in the vortical flow. The collection of bacteria in the vortices occurs in a matter of seconds, and unexpectedly, triggers the formation of biofilm streamers within minutes. Swimming bacteria have a competitive advantage to respond to their environmental conditions. In order to investigate the role of bacterial motility on the rate of collection, two strains of Escherichia coli bacteria with different motilities are used. We show that the bacterial collection in a vortical flow is strongly pronounced for high motile bacteria. PMID:24339847

Environmental bacteria produce abundant and diverse antibiofilm compounds.

PubMed

Farmer, J T; Shimkevitch, A V; Reilly, P S; Mlynek, K D; Jensen, K S; Callahan, M T; Bushaw-Newton, K L; Kaplan, J B

2014-12-01

The aim of this study was to isolate novel antibiofilm compounds produced by environmental bacteria. Cell-free extracts were prepared from lawns of bacteria cultured on agar. A total of 126 bacteria isolated from soil, cave and river habitats were employed. Extracts were tested for their ability to inhibit Staphylococcus aureus biofilm in a 96-well microtitre plate assay. A total of 55/126 extracts (44%) significantly inhibited Staph. aureus biofilm. Seven extracts were selected for further analysis. The antibiofilm activities in all seven extracts exhibited unique patterns of molecular mass, chemical polarity, heat stability and spectrum of activity against Staph. aureus, Staphylococcus epidermidis and Pseudomonas fluorescens, suggesting that these seven antibiofilm activities were mediated by unique chemical compounds with different mechanisms of action. Environmental bacteria produce abundant and diverse antibiofilm compounds. Screening cell-free extracts is a useful method for identifying secreted compounds that regulate biofilm formation. Such compounds may represent a novel source of antibiofilm agents for technological development. © 2014 The Society for Applied Microbiology.

Secondary mineral formation associated with respiration of nontronite, NAu-1 by iron reducing bacteria

PubMed Central

O'Reilly, S Erin; Watkins, Janet; Furukawa, Yoko

2005-01-01

Experimental batch and miscible-flow cultures were studied in order to determine the mechanistic pathways of microbial Fe(III) respiration in ferruginous smectite clay, NAu-1. The primary purpose was to resolve if alteration of smectite and release of Fe precedes microbial respiration. Alteration of NAu-1, represented by the morphological and mineralogical changes, occurred regardless of the extent of microbial Fe(III) reduction in all of our experimental systems, including those that contained heat-killed bacteria and those in which O2, rather than Fe(III), was the primary terminal electron acceptor. The solid alteration products observed under transmission electron microscopy included poorly crystalline smectite with diffuse electron diffraction signals, discrete grains of Fe-free amorphous aluminosilicate with increased Al/Si ratio, Fe-rich grains, and amorphous Si globules in the immediate vicinity of bacterial cells and extracellular polymeric substances. In reducing systems, Fe was also found as siderite. The small amount of Fe partitioned to the aqueous phase was primarily in the form of dissolved Fe(III) species even in the systems in which Fe(III) was the primary terminal electron acceptor for microbial respiration. From these observations, we conclude that microbial respiration of Fe(III) in our laboratory systems proceeded through the following: (1) alteration of NAu-1 and concurrent release of Fe(III) from the octahedral sheets of NAu-1; and (2) subsequent microbial respiration of Fe(III).

Adaptations of indigenous bacteria to fuel contamination in karst aquifers in south-central Kentucky

USGS Publications Warehouse

Byl, Thomas D.; Metge, David W.; Agymang, Daniel T.; Bradley, Michael W.; Hileman, Gregg; Harvey, Ronald W.

2014-01-01

The karst aquifer systems in southern Kentucky can be dynamic and quick to change. Microorganisms that live in these unpredictable aquifers are constantly faced with environmental changes. Their survival depends upon adaptations to changes in water chemistry, taking advantage of positive stimuli and avoiding negative environmental conditions. The U.S. Geological Survey conducted a study in 2001 to determine the capability of bacteria to adapt in two distinct regions of water quality in a karst aquifer, an area of clean, oxygenated groundwater and an area where the groundwater was oxygen depleted and contaminated by jet fuel. Water samples containing bacteria were collected from one clean well and two jet fuel contaminated wells in a conduit-dominated karst aquifer. Bacterial concentrations, enumerated through direct count, ranged from 500,000 to 2.7 million bacteria per mL in the clean portion of the aquifer, and 200,000 to 3.2 million bacteria per mL in the contaminated portion of the aquifer over a twelve month period. Bacteria from the clean well ranged in size from 0.2 to 2.5 mm, whereas bacteria from one fuel-contaminated well were generally larger, ranging in size from 0.2 to 3.9 mm. Also, bacteria collected from the clean well had a higher density and, consequently, were more inclined to sink than bacteria collected from contaminated wells. Bacteria collected from the clean portion of the karst aquifer were predominantly (,95%) Gram-negative and more likely to have flagella present than bacteria collected from the contaminated wells, which included a substantial fraction (,30%) of Gram-positive varieties. The ability of the bacteria from the clean portion of the karst aquifer to biodegrade benzene and toluene was studied under aerobic and anaerobic conditions in laboratory microcosms. The rate of fuel biodegradation in laboratory studies was approximately 50 times faster under aerobic conditions as compared to anaerobic, sulfur-reducing conditions. The

A novel antimicrobial peptide against dental-caries-associated bacteria.

PubMed

Chen, Long; Jia, Lili; Zhang, Qiang; Zhou, Xirui; Liu, Zhuqing; Li, Bingjie; Zhu, Zhentai; Wang, Fenwei; Yu, Changyuan; Zhang, Qian; Chen, Feng; Luo, Shi-Zhong

2017-10-01

Dental caries, a highly prevalent oral disease, is primarily caused by pathogenic bacteria infection, and most of them are anaerobic. Herein, we investigated the activity of a designed antimicrobial peptide ZXR-2, and found it showed broad-spectrum activity against a variety of Gram-positive and Gram-negative oral bacteria, particularly the caries-related taxa Streptococcus mutans. Time-course killing assays indicated that ZXR-2 killed most bacterial cells within 5 min at 4 × MIC. The mechanism of ZXR-2 involved disruption of cell membranes, as observed by scanning electron microscopy. Moreover, ZXR-2 inhibited the formation of S. mutans biofilm, but showed limited hemolytic effect. Based on its potent antimicrobial activity, rapid killing, and inhibition of S. mutans biofilm formation, ZXR-2 represents a potential therapeutic for the prevention and treatment of dental caries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Topological Defects in a Living Nematic Ensnare Swimming Bacteria

NASA Astrophysics Data System (ADS)

Genkin, Mikhail M.; Sokolov, Andrey; Lavrentovich, Oleg D.; Aranson, Igor S.

2017-01-01

Active matter exemplified by suspensions of motile bacteria or synthetic self-propelled particles exhibits a remarkable propensity to self-organization and collective motion. The local input of energy and simple particle interactions often lead to complex emergent behavior manifested by the formation of macroscopic vortices and coherent structures with long-range order. A realization of an active system has been conceived by combining swimming bacteria and a lyotropic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics, we develop a computational model describing intricate properties of such a living nematic. In faithful agreement with the experiment, the model reproduces the onset of periodic undulation of the director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields a testable prediction on the accumulation of bacteria in the cores of +1 /2 topological defects and depletion of bacteria in the cores of -1 /2 defects. Our dedicated experiment on motile bacteria suspended in a freestanding liquid crystalline film fully confirms this prediction. Our findings suggest novel approaches for trapping and transport of bacteria and synthetic swimmers in anisotropic liquids and extend a scope of tools to control and manipulate microscopic objects in active matter.

On the usage of classical nucleation theory in predicting the impact of bacteria on weather and climate

NASA Astrophysics Data System (ADS)

Sahyoun, Maher; Woetmann Nielsen, Niels; Havskov Sørensen, Jens; Finster, Kai; Bay Gosewinkel Karlson, Ulrich; Šantl-Temkiv, Tina; Smith Korsholm, Ulrik

2014-05-01

Bacteria, e.g. Pseudomonas syringae, have previously been found efficient in nucleating ice heterogeneously at temperatures close to -2°C in laboratory tests. Therefore, ice nucleation active (INA) bacteria may be involved in the formation of precipitation in mixed phase clouds, and could potentially influence weather and climate. Investigations into the impact of INA bacteria on climate have shown that emissions were too low to significantly impact the climate (Hoose et al., 2010). The goal of this study is to clarify the reason for finding the marginal impact on climate when INA bacteria were considered, by investigating the usability of ice nucleation rate parameterization based on classical nucleation theory (CNT). For this purpose, two parameterizations of heterogeneous ice nucleation were compared. Both parameterizations were implemented and tested in a 1-d version of the operational weather model (HIRLAM) (Lynch et al., 2000; Unden et al., 2002) in two different meteorological cases. The first parameterization is based on CNT and denoted CH08 (Chen et al., 2008). This parameterization is a function of temperature and the size of the IN. The second parameterization, denoted HAR13, was derived from nucleation measurements of SnomaxTM (Hartmann et al., 2013). It is a function of temperature and the number of protein complexes on the outer membranes of the cell. The fraction of cloud droplets containing each type of IN as percentage in the cloud droplets population were used and the sensitivity of cloud ice production in each parameterization was compared. In this study, HAR13 produces more cloud ice and precipitation than CH08 when the bacteria fraction increases. In CH08, the increase of the bacteria fraction leads to decreasing the cloud ice mixing ratio. The ice production using HAR13 was found to be more sensitive to the change of the bacterial fraction than CH08 which did not show a similar sensitivity. As a result, this may explain the marginal impact of

Virulence properties of cariogenic bacteria

PubMed Central

Kuramitsu, Howard K; Wang, Bing-Yan

2006-01-01

The importance of Streptococcus mutans in the etiology of dental caries has been well documented. However, there is growing recognition that the cariogenic potential of dental plaque may be determined by the composite interactions of the total plaque bacteria rather than solely the virulence properties of a single organism. This study will examine how the interactions of S. mutans with other biofilm constituents may influence the cariogenicity of plaque samples. In order to begin to investigate the effects of nonmutans streptococci on the cariogenic potential of S. mutans, we have examined the effects of Streptococcus gordonii on the virulence properties of the former organisms. These studies have indicated that S.gordonii can attenuate several potential virulence properties of S. mutans including bacteriocin production, genetic transformation, and biofilm formation. Therefore, modulation of the interactions between plaque bacteria might be a novel approach for attenuating dental caries initiation. PMID:16934112

Effect of bacteria and dissolved organics on mineral dissolution kinetics:

NASA Astrophysics Data System (ADS)

Pokrovsky, Oleg; Shirokova, Liudmila; Benezeth, Pascale; Zabelina, Svetlana

2010-05-01

Quantification of the effect of microorganisms and associated organic ligands on mineral dissolution rate is one among the last remaining challenges in modeling of water-rock interactions under earth surface and subsurface environments. This is especially true for deep underground settings within the context of CO2 capture, sequestration and storage. First, elevated CO2 pressures create numerous experimental difficulties for performing robust flow-through experiments at a given saturation state. Second, reactivity of main rock-forming minerals in abiotic systems at pCO2 >> 1 atm and circumneutral pH is still poorly constrained. And third, most of microbial habitats of the subsurface biosphere are not suitable for routine culturing in the laboratory, many of them are anaerobic and even strictly anaerobic, and many bacteria and archae cultures can live only in the consortium of microorganisms which is very hard to maintain at a controlled and stable biomass concentration. For experimental modeling of bio-mineral interactions in the laboratory, two other main conceptual challenges exist. Typical concentration of dissolved organic carbon that serves as a main nutrient for heterotrophic bacteria in underground waters rarely exceeds 3-5 mg/L. Typical concentration of DOC in nutrient media used for bacteria culturing is between 100 and 10,000 mg/L. Therefore, performing mineral-bacteria interactions in the laboratory under environmentally-sound conditions requires significant dilution of the nutrient media or the use of flow-through reactors. Concerning the effect of organic ligands and bacterial excudates on rock-forming mineral dissolution, at the present time, mostly empirical (phenomenological) approach can be used. Indeed, the pioneering studies of Stumm and co-workers have established a firm basis for modeling the catalyzing and inhibiting effects of ligands on metal oxide dissolution rate. This approach, very efficient for studying the interaction of organic and

Sorption of lead onto two gram-negative marine bacteria in seawater

USGS Publications Warehouse

Harvey, Ronald W.; Leckie, James O.

1985-01-01

Laboratory adsorption experiments performed at environmentally significant lead (Pb) and cell concentrations indicate that the marine bacteria examined have significant binding capacities for Pb. However, the behavior governing Pb sorption onto gram-negative bacteria in seawater may be quite complex. The sorption kinetics appear to involve two distinct phases, i.e., a rapid removal of Pb from solution within the first few minutes, followed by a slow but nearly constant removal over many hours. Also, the average binding coefficient, calculated for Pb sorption onto bacteria and a measure of binding intensity, increases with decreasing sorption density (amounts of bacteria-associated Pb per unit bacterial surface) at low cell concentrations (105 cells ml−1), but decreases with decreasing sorption density at higher cell concentrations (107 cells ml−1). The latter effect is apparently due to the production of significant amounts of extra-cellular organics at high cell concentrations that compete directly with bacterial surfaces for available lead. Lead toxicity and active uptake by marine bacteria did not appear significant at the Pb concentrations used.

Laboratory Course on "Streptomyces" Genetics and Secondary Metabolism

ERIC Educational Resources Information Center

Siitonen, Vilja; Räty, Kaj; Metsä-Ketelä, Mikko

2016-01-01

The "'Streptomyces' genetics and secondary metabolism" laboratory course gives an introduction to the versatile soil dwelling Gram-positive bacteria "Streptomyces" and their secondary metabolism. The course combines genetic modification of "Streptomyces"; growing of the strain and protoplast preparation, plasmid…

A novel, optical, on-line bacteria sensor for monitoring drinking water quality

PubMed Central

Højris, Bo; Christensen, Sarah Christine Boesgaard; Albrechtsen, Hans-Jørgen; Smith, Christian; Dahlqvist, Mathis

2016-01-01

Today, microbial drinking water quality is monitored through either time-consuming laboratory methods or indirect on-line measurements. Results are thus either delayed or insufficient to support proactive action. A novel, optical, on-line bacteria sensor with a 10-minute time resolution has been developed. The sensor is based on 3D image recognition, and the obtained pictures are analyzed with algorithms considering 59 quantified image parameters. The sensor counts individual suspended particles and classifies them as either bacteria or abiotic particles. The technology is capable of distinguishing and quantifying bacteria and particles in pure and mixed suspensions, and the quantification correlates with total bacterial counts. Several field applications have demonstrated that the technology can monitor changes in the concentration of bacteria, and is thus well suited for rapid detection of critical conditions such as pollution events in drinking water. PMID:27040142

A novel, optical, on-line bacteria sensor for monitoring drinking water quality.

PubMed

Højris, Bo; Christensen, Sarah Christine Boesgaard; Albrechtsen, Hans-Jørgen; Smith, Christian; Dahlqvist, Mathis

2016-04-04

Today, microbial drinking water quality is monitored through either time-consuming laboratory methods or indirect on-line measurements. Results are thus either delayed or insufficient to support proactive action. A novel, optical, on-line bacteria sensor with a 10-minute time resolution has been developed. The sensor is based on 3D image recognition, and the obtained pictures are analyzed with algorithms considering 59 quantified image parameters. The sensor counts individual suspended particles and classifies them as either bacteria or abiotic particles. The technology is capable of distinguishing and quantifying bacteria and particles in pure and mixed suspensions, and the quantification correlates with total bacterial counts. Several field applications have demonstrated that the technology can monitor changes in the concentration of bacteria, and is thus well suited for rapid detection of critical conditions such as pollution events in drinking water.

Anaerobic bacteria

MedlinePlus

Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these bacteria ... Brook I. Diseases caused by non-spore-forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman-Cecil ...

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory

PubMed Central

Kozyreva, Varvara K.; Truong, Chau-Linda; Greninger, Alexander L.; Crandall, John; Mukhopadhyay, Rituparna

2017-01-01

ABSTRACT Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits. PMID:28592550

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.

PubMed

Kozyreva, Varvara K; Truong, Chau-Linda; Greninger, Alexander L; Crandall, John; Mukhopadhyay, Rituparna; Chaturvedi, Vishnu

2017-08-01

Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits. Copyright © 2017 Kozyreva et al.

Application of MALDI-TOF MS for the Identification of Food Borne Bacteria

PubMed Central

Pavlovic, Melanie; Huber, Ingrid; Konrad, Regina; Busch, Ulrich

2013-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful tool for the routine identification of clinical isolates. MALDI-TOF MS based identification of bacteria has been shown to be more rapid, accurate and cost-efficient than conventional phenotypic techniques or molecular methods. Rapid and reliable identification of food-associated bacteria is also of crucial importance for food processing and product quality. This review is concerned with the applicability of MALDI-TOF MS for routine identification of foodborne bacteria taking the specific requirements of food microbiological laboratories and the food industry into account. The current state of knowledge including recent findings and new approaches are discussed. PMID:24358065

Improved oil recovery using bacteria isolated from North Sea petroleum reservoirs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davey, R.A.; Lappin-Scott, H.

1995-12-31

During secondary oil recovery, water is injected into the formation to sweep out the residual oil. The injected water, however, follows the path of least resistance through the high-permeability zones, leaving oil in the low-permeability zones. Selective plugging of these their zones would divert the waterflood to the residual oil and thus increase the life of the well. Bacteria have been suggested as an alternative plugging agent to the current method of polymer injection. Starved bacteria can penetrate deeply into rock formations where they attach to the rock surfaces, and given the right nutrients can grow and produce exo-polymer, reducingmore » the permeability of these zones. The application of microbial enhanced oil recovery has only been applied to shallow, cool, onshore fields to date. This study has focused on the ability of bacteria to enhance oil recovery offshore in the North Sea, where the environment can be considered extreme. A screen of produced water from oil reservoirs (and other extreme subterranean environments) was undertaken, and two bacteria were chosen for further work. These two isolates were able to grow and survive in the presence of saline formation waters at a range of temperatures above 50{degrees}C as facultative anaerobes. When a solution of isolates was passed through sandpacks and nutrients were added, significant reductions in permeabilities were achieved. This was confirmed in Clashach sandstone at 255 bar, when a reduction of 88% in permeability was obtained. Both isolates can survive nutrient starvation, which may improve penetration through the reservoir. Thus, the isolates show potential for field trials in the North Sea as plugging agents.« less

Molecular mechanisms of magnetosome formation.

PubMed

Komeili, Arash

2007-01-01

Magnetotactic bacteria are a diverse group of microorganisms with the ability to use geomagnetic fields for direction sensing. This unique feat is accomplished with the help of magnetosomes, nanometer-sized magnetic crystals surrounded by a lipid bilayer membrane and organized into chains via a dedicated cytoskeleton within the cell. Because of the special properties of these magnetic crystals, magnetotactic bacteria have been exploited for a variety of applications in diverse disciplines from geobiology to biotechnology. In addition, magnetosomes have served as a powerful model system for the study of biomineralization and cell biology in bacteria. This review focuses on recent advances in understanding the molecular mechanisms of magnetosome formation and magnetite biomineralization.

Outcome of a one-week intensive training workshop for veterinary diagnostic laboratory workers in Liberia.

PubMed

Williamson, Julie A; Tornquist, Susan J

2014-01-01

There is a huge unmet need for veterinary diagnostic laboratory services in developing nations such as Liberia. One way of bridging the service gap is for visiting experts to provide veterinary laboratory training to technicians in a central location in a short-course format. An intensive 1-week training workshop was organized for 18 student and faculty participants from the College of Agriculture and Integrated Development Studies (CAIDS) at Cuttington University in rural central Liberia. The training was designed and delivered by the non-governmental organization Veterinarians Without Borders US and funded through a Farmer-to-Farmer grant provided by the United States Agency for International Development. Although at the start of training none of the students had any veterinary laboratory experience, by the end of the course over 80% of the students were able to discuss appropriate care and use of a microscope and name at least three important components of laboratory record keeping; over 60% were able to describe how to make and stain a blood smear and how to perform a passive fecal flotation; and over 30% were able to describe what a packed cell volume is and how it is measured and name at least three criteria for classifying bacteria. The intensive training workshop greatly improved the knowledge of trainees about veterinary diagnostic laboratory techniques. The training provided initial skills to students and faculty who are awaiting the arrival of additional grant-funded laboratory equipment to continue their training.

Constraints on Grain Formation Around Carbon Stars from Laboratory Studies of Presolar Graphite

NASA Technical Reports Server (NTRS)

Bernatowicz, T. J.; Akande, O. W.; Croat, T. K.; Cowsik, R.

2005-01-01

We report the results of an investigation into the physical conditions in the mass outflows of asymptotic giant branch (AGB) carbon stars that are required for the formation of micron-sized presolar graphite grains, either with or without internal crystals of titanium carbide (TiC). In addition to providing detailed information about stellar nucleosynthesis, the structure and composition of presolar grains give unique information about the conditions of grain formation. In the present work we use laboratory observations of presolar graphite to gain insight into the physical conditions in circumstellar outflows from carbon AGB stars. The periodic pulsation of AGB stars enhances the gas density through shocks in the stellar atmosphere above the photosphere, promoting the condensation of dust grains. Copious mass outflow occurs largely because grains are coupled to the radiation field of the star, which accelerates them by radiation pressure; momentum is in turn transferred to gas molecules by collisions with grains. The dust/gas mixture is effectively a two-component fluid whose motion depends on atmospheric structure and which, in turn, influences that structure. In particular, the radiation pressure on the grains determines the velocity field of the outflow and thus the density distribution, while the density distribution itself determines the conditions of radiative transfer within the outflow and thus the effective radiation pressure.

Application of micro-PIV to the study of staphylococci bacteria bio-film dynamics

NASA Astrophysics Data System (ADS)

Sherman, Erica; Bayles, Kenneth; Moormeier, Derek; Wei, Timothy

2012-11-01

Staphylococci bacteria are recognized as the most frequent cause of biofilm-associated infections. Although humans are regularly exposed to staphylococcus bacteria without consequence, a localized staph infection has the potential to enter the bloodstream and lead to serious infections such as endocarditis, pneumonia, or toxic shock syndrome. The mechanics of staphylococci biofilm formation and dispersion through the bloodstream are not well known. It has recently been observed that under certain flow conditions, bacteria grow in stable bio-films. Under other conditions, they organize in tower-like structures which break and are transported downstream by the flow. The fundamental questions addressed in this study are i) whether or not fluid mechanics plays a role in differentiating between film or tower formation and ii) whether or not the faulty towers are a bio-film propagation mechanism. This talk focuses on the application of micro-PIV to study this problem. Bacteria were cultured in a glass microchannel and subjected to a range of steady shear rates. Micro-PIV measurements were made to map the flow over and around different types of bio-film structures. Measurements and control volume analysis will be presented quantifying forces acting on these structures.

LESSONS LEARNED REGARDING THE USE OF AN IMPINGER FOR COLLECTING AIRBORNE BACTERIA DURING A BIOSOLIDS APPLICATION FIELD STUDY

EPA Science Inventory

The National Risk Management Research Laboratory (NRMRL) of the USEPA has performed laboratory wind tunnel studies as well as large field studies to evaluate specific bioaerosol components (bacteria, fungi, endotoxin, β-d glucan) that may be associated with various practices for ...

The Biodiversity of Lactic Acid Bacteria in Greek Traditional Wheat Sourdoughs Is Reflected in Both Composition and Metabolite Formation

PubMed Central

De Vuyst, Luc; Schrijvers, Vincent; Paramithiotis, Spiros; Hoste, Bart; Vancanneyt, Marc; Swings, Jean; Kalantzopoulos, George; Tsakalidou, Effie; Messens, Winy

2002-01-01

Lactic acid bacteria (LAB) were isolated from Greek traditional wheat sourdoughs manufactured without the addition of baker's yeast. Application of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total cell protein, randomly amplified polymorphic DNA-PCR, DNA-DNA hybridization, and 16S ribosomal DNA sequence analysis, in combination with physiological traits such as fructose fermentation and mannitol production, allowed us to classify the isolated bacteria into the species Lactobacillus sanfranciscensis, Lactobacillus brevis, Lactobacillus paralimentarius, and Weissella cibaria. This consortium seems to be unique for the Greek traditional wheat sourdoughs studied. Strains of the species W. cibaria have not been isolated from sourdoughs previously. No Lactobacillus pontis or Lactobacillus panis strains were found. An L. brevis-like isolate (ACA-DC 3411 t1) could not be identified properly and might be a new sourdough LAB species. In addition, fermentation capabilities associated with the LAB detected have been studied. During laboratory fermentations, all heterofermentative sourdough LAB strains produced lactic acid, acetic acid, and ethanol. Mannitol was produced from fructose that served as an additional electron acceptor. In addition to glucose, almost all of the LAB isolates fermented maltose, while fructose as the sole carbohydrate source was fermented by all sourdough LAB tested except L. sanfranciscensis. Two of the L. paralimentarius isolates tested did not ferment maltose; all strains were homofermentative. In the presence of both maltose and fructose in the medium, induction of hexokinase activity occurred in all sourdough LAB species mentioned above, explaining why no glucose accumulation was found extracellularly. No maltose phosphorylase activity was found either. These data produced a variable fermentation coefficient and a unique sourdough metabolite composition. PMID:12450829

The biodiversity of lactic acid bacteria in Greek traditional wheat sourdoughs is reflected in both composition and metabolite formation.

PubMed

De Vuyst, Luc; Schrijvers, Vincent; Paramithiotis, Spiros; Hoste, Bart; Vancanneyt, Marc; Swings, Jean; Kalantzopoulos, George; Tsakalidou, Effie; Messens, Winy

2002-12-01

Lactic acid bacteria (LAB) were isolated from Greek traditional wheat sourdoughs manufactured without the addition of baker's yeast. Application of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total cell protein, randomly amplified polymorphic DNA-PCR, DNA-DNA hybridization, and 16S ribosomal DNA sequence analysis, in combination with physiological traits such as fructose fermentation and mannitol production, allowed us to classify the isolated bacteria into the species Lactobacillus sanfranciscensis, Lactobacillus brevis, Lactobacillus paralimentarius, and Weissella cibaria. This consortium seems to be unique for the Greek traditional wheat sourdoughs studied. Strains of the species W. cibaria have not been isolated from sourdoughs previously. No Lactobacillus pontis or Lactobacillus panis strains were found. An L. brevis-like isolate (ACA-DC 3411 t1) could not be identified properly and might be a new sourdough LAB species. In addition, fermentation capabilities associated with the LAB detected have been studied. During laboratory fermentations, all heterofermentative sourdough LAB strains produced lactic acid, acetic acid, and ethanol. Mannitol was produced from fructose that served as an additional electron acceptor. In addition to glucose, almost all of the LAB isolates fermented maltose, while fructose as the sole carbohydrate source was fermented by all sourdough LAB tested except L. sanfranciscensis. Two of the L. paralimentarius isolates tested did not ferment maltose; all strains were homofermentative. In the presence of both maltose and fructose in the medium, induction of hexokinase activity occurred in all sourdough LAB species mentioned above, explaining why no glucose accumulation was found extracellularly. No maltose phosphorylase activity was found either. These data produced a variable fermentation coefficient and a unique sourdough metabolite composition.

Effects of temperature on bacterial transport and destruction in bioretention media: field and laboratory evaluations.

PubMed

Zhang, Lan; Seagren, Eric A; Davis, Allen P; Karns, Jeffrey S

2012-06-01

Microbial activities are significantly influenced by temperature. This study investigated the effects of temperature on the capture and destruction of bacteria from urban stormwater runoff in bioretention media using 2-year field evaluations coupled with controlled laboratory column studies. Field data from two bioretention cells show that the concentration of indicator bacteria (fecal coliforms and Escherichia coli) was reduced during most storm events, and that the probability of meeting specific water quality criteria in the discharge was increased. Indicator bacteria concentration in the input flow typically increased with higher daily temperature. Although bacterial removal efficiency was independent of temperature in the field and laboratory, column tests showed that bacterial decay coefficients in conventional bioretention media (CBM) increase exponentially with elevated temperature. Increases in levels of protozoa and heterotrophic bacteria associated with increasing temperature appear to contribute to faster die-off of trapped E. coli in CBM via predation and competition.

Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Rhopaloeides odorabile†

PubMed Central

Webster, Nicole S.; Wilson, Kate J.; Blackall, Linda L.; Hill, Russell T.

2001-01-01

Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the Actinobacteria, low-G+C gram-positive bacteria, the β- and γ-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in R. odorabile. High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge. PMID:11133476

Transfer of DNA from Bacteria to Eukaryotes

PubMed Central

2016-01-01

ABSTRACT Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen), Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium), or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs), the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer. PMID:27406565

Increased production of outer membrane vesicles by cultured freshwater bacteria in response to ultraviolet radiation.

PubMed

Gamalier, Juliana P; Silva, Thiago P; Zarantonello, Victor; Dias, Felipe F; Melo, Rossana C N

2017-01-01

Secretion of membrane vesicles is an important biological process of both eukaryotic and prokaryotic cells. This process has been characterized in pathogenic bacteria, but is less clear in non-pathogenic bacteria from aquatic ecosystems. Here, we investigated, for the first time, the process of formation of outer membranes vesicles (OMVs), nanoscale vesicles extruded from the outer membrane (OM) of gram-negative bacteria, in cultures of freshwater bacteria after exposure or not to ultraviolet radiation (UVR) as an environmental stressor. Non-axenic cultures of freshwater bacteria isolated from a Brazilian aquatic ecosystem (Funil reservoir) were exposed or not to UVR (UVA+UVB) over a 3h period, during which cell density, viability and ultrastructure were analyzed. First, we showed that UVR induce bacterial death. UVR triggered significant negative effect on cell density after 3h of UVR treatment. This decrease was directly associated with cell death as revealed by a cell viability fluorescent probe that enables the distinction of live/dead bacteria. Transmission electron microscopy (TEM) revealed changes indicative of cell death after 3h of UVR exposure, with significant increase of damaged cells compared to the control group. Second, we demonstrated that gram-negative bacteria release OMVs during normal growth and after UVR exposure. OMVs were clearly identified as round, membrane-bound vesicles budding off from the bacterial OM as isolated or clustered vesicles or free in the extracellular medium. Remarkably, quantitative TEM analyses showed that bacteria respond to UVR with increased formation of OMVs. Moreover, while OMVs numbers per intact or damaged cell did not differ in the untreated group, UVR led to a higher vesiculation by bacteria in process of death. This means that degenerating bacteria release OMVs before lysis and that this secretion might be an adaptive/protective response to rapid changes in environmental conditions such as UV radiation. Copyright

Blended learning within an undergraduate exercise physiology laboratory.

PubMed

Elmer, Steven J; Carter, Kathryn R; Armga, Austin J; Carter, Jason R

2016-03-01

In physiological education, blended course formats (integration of face-to-face and online instruction) can facilitate increased student learning, performance, and satisfaction in classroom settings. There is limited evidence on the effectiveness of using blending course formats in laboratory settings. We evaluated the impact of blended learning on student performance and perceptions in an undergraduate exercise physiology laboratory. Using a randomized, crossover design, four laboratory topics were delivered in either a blended or traditional format. For blended laboratories, content was offloaded to self-paced video demonstrations (∼15 min). Laboratory section 1 (n = 16) completed blended laboratories for 1) neuromuscular power and 2) blood lactate, whereas section 2 (n = 17) completed blended laboratories for 1) maximal O2 consumption and 2) muscle electromyography. Both sections completed the same assignments (scored in a blinded manner using a standardized rubric) and practicum exams (evaluated by two independent investigators). Pre- and postcourse surveys were used to assess student perceptions. Most students (∼79%) watched videos for both blended laboratories. Assignment scores did not differ between blended and traditional laboratories (P = 0.62) or between sections (P = 0.91). Practicum scores did not differ between sections (both P > 0.05). At the end of the course, students' perceived value of the blended format increased (P < 0.01) and a greater percentage of students agreed that learning key foundational content through video demonstrations before class greatly enhanced their learning of course material compared with a preassigned reading (94% vs. 78%, P < 0.01). Blended exercise physiology laboratories provided an alternative method for delivering content that was favorably perceived by students and did not compromise student performance. Copyright © 2016 The American Physiological Society.

Survival of bacteria of laboratory animal origin on cage bedding and inactivation by hydrogen peroxide vapour.

PubMed

Benga, Laurentiu; Benten, W Peter M; Engelhardt, Eva; Gougoula, Christina; Schulze-Röbbecke, Roland; Sager, Martin

2017-08-01

This study aims to determine the ability of laboratory animal bacteria to resist desiccation and inactivation by hydrogen peroxide vapour (HPV) on paper bedding pieces. Bedding pieces were saturated with bacterial suspensions in water or 2% (w/v) bovine serum albumin (BSA) in water, and held in a mouse facility. Viable counts showed variable survival rates over time for the bacterial species used ([ Pasteurella] pneumotropica, Muribacter muris, Pseudomonas aeruginosa, Acinetobacter redioresistens, Escherichia coli, Klebsiella oxytoca, Bordetella bronchiseptica, Bordetella hinzii, Enterococcus faecalis, β-haemolytic Streptococcus spp., Staphylococcus aureus and Staphylococcus xylosus). Overall, BSA increased bacterial survival in the bedding pieces. The survival rates of Bacillus safensis were not influenced by BSA but depended on sporulation. When bedding pieces and Petri dishes inoculated with E. coli, P. aeruginosa and S. aureus were subjected to HPV disinfection, all bacterial species on the bedding pieces inoculated with bacterial suspensions in water were readily inactivated. By contrast, S. aureus and P. aeruginosa, but not E. coli cells survived HPV treatment in high numbers when inoculated on bedding pieces as a BSA suspension. Notably, all three bacterial species were readily inactivated by HPV even in the presence of BSA when smeared on smooth surfaces. In conclusion, the suspension medium and the carrier can influence the environmental survival and susceptibility of bacterial species to HPV. Our results may help to develop standard protocols that can be used to ensure the microbiological quality of experimental rodent housing.

An Environmentally Focused General Chemistry Laboratory

ERIC Educational Resources Information Center

Mihok, Morgan; Keiser, Joseph T.; Bortiatynski, Jacqueline M.; Mallouk, Thomas E.

2006-01-01

The environmentally focused general chemistry laboratory provides a format for teaching the concepts of the mainstream laboratory within an environmental context. The capstone integrated exercise emerged as the overwhelming favorite part of this laboratory and the experiment gave students an opportunity to do a self-directed project, using the…

[Resting forms of gram negative chemolithoautotrophic bacteria Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum].

PubMed

Loĭko, N G; Soina, V S; Sorokin, D Iu; Mitiushina, L L; El'-Registan, G I

2003-01-01

The haloalkaliphilic chemoautotrophic gram-negative bacteria Thioalkalivibrio versutus, strain AL2, and Thioalkalimicrobium aerophilum, strain AL3, were shown to possess the capacity to produce resting forms, namely cyst-like refractile cells (CRC), whose production was controlled by the level of the d1 extracellular factors, exhibiting the function of anabiosis autoinducers. The conditions were elucidated that promoted the formation of CRC in the developmental cycles of the cultures studied, in condensed cell suspensions undergoing autolysis, and under the action of exogenously introduced chemical analogues of anabiosis autoinducers (alkylhydroxybenzenes). The peculiarities of the fine structure of the resting cells obtained were studied. Distinctions were revealed (with respect to viability and thermotolerance) between the CRC formed under different conditions. The relationship between the growth strategy and survival strategy of extremophilic bacteria is discussed with taking into account the effect of the d1 autoregulatory factors. A new model of CRC formation is proposed: CRC production in the life cycle of bacteria developing under conditions of increased concentration of anabiosis autoinducers.

Vectors and Fomites: An Investigative Laboratory for Undergraduates.

ERIC Educational Resources Information Center

Adamo, Joseph A.; Gealt, Michael A.

1996-01-01

Presents a laboratory model system for introductory microbiology students that involves hands-on studies of bacteria vectored in soil nematodes. Describes a series of experiments designed to demonstrate vector-fomite transmission, bacterial survival, and disinfectant activity. Introduces the concept of genetically engineered microorganisms and the…

Laboratory Comparison of the Anti-Bacterial Effects of Spearmint Extract and Hypochlorite Sodium on Enterococcus Faecalis Bacteria.

PubMed

S, Hajimaghsoodi; H, Zandi; M, Bahrami; R, Hakimian

2016-12-01

It is necessary to use irrigation solutions during cleaning and shaping of root canals to efficiently reduce the number of micro organisms. Sodium hypochlorite is used as an effective antibacterial endodontic irrigants. However, the extract of pennyroyal plant has also shown anti-bacterial characteristics comparable with antibacterial drugs. To compare the anti-bacterial effect of spearmint extract on Enterococcus faecalis bacteria with that of sodium hypochlorite 5.25%. In this experimental study, Muller Hinton medium, including 5% sheep blood was prepared. The two solutions used including sodium hypochlorite 5.25% and spearmint extracts were put adjacent to Enterococcus faecalis bacteria after preparing. Two groups, each containing 10 samples, with the total of 20 samples were used. The disks, including each solution were placed 2 cm apart on a plate containing Muller Hinton medium and the bacteria. The plate was subsequently incubated at 37°C for 48 hours. After incubation, the mean diameter of the halo around each disk, which represents the lack of bacterial growth, was measured and compared using a ruler. Penicillin disk was used for positive control and a sterile blank disk containing physiologic serum was utilized as the negative control. This process was repeated 10 times for each solution. Data were analyzed in SPSS 17 statistical software using t -test. The results showed that the mean diameter of halo in the spearmint extract group was zero and in the sodium hypochlorite group it was 23.7 ± 1.49 mm. There was a significant difference between the mean diameter of the lack of growth halo of the spearmint extract and that of hypochlorite sodium 5.25% on Enterococcus faecalis bacteria ( p ≤ 0.001). Considering the limitations of an experimental study, it seems that spearmint extract does not have any anti-bacterial effect against Enterococcus faecalis bacteria, in contrast to hypochlorite sodium 5.25%.

MALDI-TOF mass spectrometry and high-consequence bacteria: safety and stability of biothreat bacterial sample testing in clinical diagnostic laboratories.

PubMed

Tracz, Dobryan M; Tober, Ashley D; Antonation, Kym S; Corbett, Cindi R

2018-03-01

We considered the application of MALDI-TOF mass spectrometry for BSL-3 bacterial diagnostics, with a focus on the biosafety of live-culture direct-colony testing and the stability of stored extracts. Biosafety level 2 (BSL-2) bacterial species were used as surrogates for BSL-3 high-consequence pathogens in all live-culture MALDI-TOF experiments. Viable BSL-2 bacteria were isolated from MALDI-TOF mass spectrometry target plates after 'direct-colony' and 'on-plate' extraction testing, suggesting that the matrix chemicals alone cannot be considered sufficient to inactivate bacterial culture and spores in all samples. Sampling of the instrument interior after direct-colony analysis did not recover viable organisms, suggesting that any potential risks to the laboratory technician are associated with preparation of the MALDI-TOF target plate before or after testing. Secondly, a long-term stability study (3 years) of stored MALDI-TOF extracts showed that match scores can decrease below the threshold for reliable species identification (<1.7), which has implications for proficiency test panel item storage and distribution.

Diverse metal reduction and nano- mineral formation by metal-reducing bacteria enriched from inter-tidal flat sediments

NASA Astrophysics Data System (ADS)

Kim, Y.; Park, B.; Seo, H.; Roh, Y.

2009-12-01

Dissimilatory metal-reducing bacteria utilize diverse metal oxides as electron acceptors and couple this microbial metal reduciton to growth. However, the microbe-metal interactions playing important roles in the metal geochemistry and organic matter degradation in the tidal flat sediments have not been uncovered enough to employ in various environmental and industrial applications. The objective of this study was to examine biomineralization and bioremediation by the facultative metal-reducing bacteria isolated from the inter-tidal flat sediments in southwestern of Korea. 16S-rRNA analysis showed bacterial consortium mainly consists of genus of Clostridium sp. The enriched bacteria were capable of reducing diverse metals such as iron oxide, maganese oxide, Cr(VI) and Se(VI) during glucose fermentation process at room temperature. The bacteria reduced highly toxic and reactive elements such as Cr(VI) and Se(VI) to Cr(III) and Se(0). The results showed that microbial processes induced transformation from toxic states of heavy metals to less toxic and mobile states in natural environments. Andthe bacteria also reduced iron oxyhydroxide such as ferrihydrite and akaganeite (β-FeOOH) and formed nanometer-sized magnetite (Fe3O4). This study indicates microbial processes not only can be used for bioremediation of inorganic contaminants existing in the marine environments, but also form the magnetite nanoparticles which are exhibit superparamagnetic properties that can be useful for relevant medical and industrial applications.

Automated Microbial Metabolism Laboratory

NASA Technical Reports Server (NTRS)

1973-01-01

Development of the automated microbial metabolism laboratory (AMML) concept is reported. The focus of effort of AMML was on the advanced labeled release experiment. Labeled substrates, inhibitors, and temperatures were investigated to establish a comparative biochemical profile. Profiles at three time intervals on soil and pure cultures of bacteria isolated from soil were prepared to establish a complete library. The development of a strategy for the return of a soil sample from Mars is also reported.

Identification of gram-negative and gram-positive bacteria by fluorescence studies

NASA Astrophysics Data System (ADS)

Demchak, Jonathan; Calabrese, Joseph; Tzolov, Marian

2011-03-01

Several type strains of bacteria including Vibrio fischeri, Azotobacter vinelandii, Enterobacter cloacae, and Corynebacterium xerosis, were cultured in the laboratory following standard diagnostic protocol based on their individual metabolic strategies. The bacterial cultures were not further treated and they were studied in their pristine state (pure culture - axenic). The fluorescent studies were applied using a continuous wave and a pulsed excitation light sources. Emission and excitation spectra were recorded for the continuous wave excitation and they all show similar spectral features with the exception of the gram positive bacteria showing vibronic structures. The vibrational modes involved in these vibronic bands have energy typical for carbon-carbon vibrations. The fluorescence is quenched in addition of water, even a very thin layer, which confirms that the observed spectral features originate from the outer parts of the bacteria. These results allow to conclude that the fluorescence spectroscopy can be used as a method for studying the membranes of the bacteria and eventually to discriminate between gram positive and gram negative bacteria. The pulsed experiments show that the fluorescence lifetime is in the sub-microsecond range. The results indicate that the observed spectra are superposition of the emission with different lifetimes.

Reproducing stone monument photosynthetic-based colonization under laboratory conditions.

PubMed

Miller, Ana Zélia; Laiz, Leonila; Gonzalez, Juan Miguel; Dionísio, Amélia; Macedo, Maria Filomena; Saiz-Jimenez, Cesareo

2008-11-01

In order to understand the biodeterioration process occurring on stone monuments, we analyzed the microbial communities involved in these processes and studied their ability to colonize stones under controlled laboratory experiments. In this study, a natural green biofilm from a limestone monument was cultivated, inoculated on stone probes of the same lithotype and incubated in a laboratory chamber. This incubation system, which exposes stone samples to intermittently sprinkling water, allowed the development of photosynthetic biofilms similar to those occurring on stone monuments. Denaturing gradient gel electrophoresis (DGGE) analysis was used to evaluate the major microbial components of the laboratory biofilms. Cyanobacteria, green microalgae, bacteria and fungi were identified by DNA-based molecular analysis targeting the 16S and 18S ribosomal RNA genes. The natural green biofilm was mainly composed by the Chlorophyta Chlorella, Stichococcus, and Trebouxia, and by Cyanobacteria belonging to the genera Leptolyngbya and Pleurocapsa. A number of bacteria belonging to Alphaproteobacteria, Bacteroidetes and Verrucomicrobia were identified, as well as fungi from the Ascomycota. The laboratory colonization experiment on stone probes showed a colonization pattern similar to that occurring on stone monuments. The methodology described in this paper allowed to reproduce a colonization equivalent to the natural biodeteriorating process.

Quorum quenching bacteria can be used to inhibit the biofouling of reverse osmosis membranes.

PubMed

Oh, Hyun-Suk; Tan, Chuan Hao; Low, Jiun Hui; Rzechowicz, Miles; Siddiqui, Muhammad Faisal; Winters, Harvey; Kjelleberg, Staffan; Fane, Anthony G; Rice, Scott A

2017-04-01

Over the last few decades, significant efforts have concentrated on mitigating biofouling in reverse osmosis (RO) systems, with a focus on non-toxic and sustainable strategies. Here, we explored the potential of applying quorum quenching (QQ) bacteria to control biofouling in a laboratory-scale RO system. For these experiments, Pantoea stewartii was used as a model biofilm forming organism because it was previously shown to be a relevant wastewater isolate that also forms biofilms in a quorum sensing (QS) dependent fashion. A recombinant Escherichia coli strain, which can produce a QQ enzyme, was first tested in batch biofilm assays and significantly reduced biofilm formation by P. stewartii. Subsequently, RO membranes were fouled with P. stewartii and the QQ bacterium was introduced into the RO system using two different strategies, direct injection and immobilization within a cartridge microfilter. When the QQ bacterial cells were directly injected into the system, N-acylhomoserine lactone signals were degraded, resulting in the reduction of biofouling. Similarly, the QQ bacteria controlled biofouling when immobilized within a microfilter placed downstream of the RO module to remove QS signals circulating in the system. These results demonstrate the proof-of-principle that QQ can be applied to control biofouling of RO membranes and may be applicable for use in full-scale plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pyrosequencing reveals benthic bacteria changes responsing to heavy deposition of Microcystis scum in lab — searching bacteria for bloom control

NASA Astrophysics Data System (ADS)

Tang, Yali; Cheng, Dongmei; Guan, Baohua; Zhang, Xiufeng; Liu, Zhengwen; Liu, Zejun

2017-05-01

Bacteria capable of degrading cyanobacteria Microcystis are crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. Scum derived from Microcystis blooms tends to accumulate in bays of large lakes and then sink to the sediments where it is finally consumed by benthic bacteria. Understanding the response of benthic bacterial communities to massive Microcystis deposition events may help identify the bacteria best suited to Microcystis hydrolyzation and even bloom control. For that purpose, an experimental system was set up in which intact sediment cores were incubated in the laboratory with normal and heavy deposits of Microcystis detritus. Pyrosequencing was performed in order to describe a phylogenetic inventory of bacterial communities in samples taken at 0-1, 1-2 and 2-3 cm depths in incubated sediments and in original untreated sediment. A hierarchical cluster tree was constructed expose differences between sediments. Similarity percentage calculations were also performed to identify the bacterial species contributing to variation. The results of this study suggest that: (1) deposition of Microcystis scums exerts a strong effect on the bacterial community composition in the surface (0-1 cm) and sub-surface (1-2 cm) sediment layers; (2) bacterial community responses to Microcystis detritus deposition vary across vertical gradients. A list of bacteria with potential roles in Microcystis degradation was compiled. These findings may inform the development of future measures for Microcystis bloom control in lakes.

The Effects of Allium sativum Extracts on Biofilm Formation and Activities of Six Pathogenic Bacteria.

PubMed

Mohsenipour, Zeinab; Hassanshahian, Mehdi

2015-08-01

Garlic is considered a rich source of many compounds, which shows antimicrobial effects. The ability of microorganisms to adhere to both biotic and abiotic surfaces and to form biofilm is responsible for a number of diseases of chronic nature, demonstrating extremely high resistance to antibiotics. Bacterial biofilms are complex communities of sessile microorganisms, embedded in an extracellular matrix and irreversibly attached to various surfaces. The present study evaluated the antimicrobial activity of Allium sativum extract against the biofilms of six pathogenic bacteria and their free-living forms. The clinical isolates in this study had not been studied in any other studies, especially in regard to biofilm disruption and inhibition of biofilm cell metabolic activity. Antimicrobial activities of A. sativum L. extracts (methanol and ethanol extracts) against planktonic forms of bacteria were determined using the disc diffusion method. The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) values were evaluated by a macrobroth dilution technique. The anti-biofilm effects were assessed by microtiter plate method. The results showed that the A. sativum L. extract discs did not have any zone of inhibition for the tested bacteria. However, The MIC values of A. sativum L. extracts (0.078 - 2.5 mg/mL) confirmed the high ability of these extracts for inhibition of planktonic bacteria. A. sativum L. extracts were efficient to inhibit biofilm structures and the concentration of each extract had a direct relation with the inhibitory effect. Finally, it can be suggested that the extracts of this plant be applied as antimicrobial agents against these pathogens, particularly in biofilm forms.

Isolating "Unknown" Bacteria in the Introductory Microbiology Laboratory: A New Selective Medium for Gram-Positives.

ERIC Educational Resources Information Center

McKillip, John L.; Drake, MaryAnne

1999-01-01

Describes the development, preparation, and use of a medium that can select against a wide variety of Gram-negative bacteria while still allowing growth and differentiation of a wide range of Gram-positives. (WRM)

The Formation of Sulfate and Elemental Sulfur Aerosols Under Varying Laboratory Conditions: Implications for Early Earth

NASA Technical Reports Server (NTRS)

DeWitt, H. Langley; Hasenkopf, Christa A.; Trainer, Melissa G.; Farmer, Delphine K.; Jimenez, Jose L.; McKay, Christopher P.; Toon, Owen B.; Tolbert, Margaret A.

2010-01-01

The presence of sulfur mass-independent fractionation (S-MIF) in sediments more than 2.45 x 10(exp 9) years old is thought to be evidence for an early anoxic atmosphere. Photolysis of sulfur dioxide (SO2) by UV light with lambda < 220 nm has been shown in models and some initial laboratory studies to create a S-MIF; however, sulfur must leave the atmosphere in at least two chemically different forms to preserve any S-MIF signature. Two commonly cited examples of chemically different sulfur species that could have exited the atmosphere are elemental sulfur (S8) and sulfuric acid (H2S04) aerosols. Here, we use real-time aerosol mass spectrometry to directly detect the sulfur-containing aerosols formed when SO2 either photolyzes at wavelengths from 115 to 400 nm, to simulate the UV solar spectrum, or interacts with high-energy electrons, to simulate lightning. We found that sulfur-containing aerosols form under all laboratory conditions. Further, the addition of a reducing gas, in our experiments hydrogen (H2) or methane (CH4), increased the formation of S8. With UV photolysis, formation of S8 aerosols is highly dependent on the initial SO2 pressure; and S8 is only formed at a 2% SO2 mixing ratio and greater in the absence of a reductant, and at a 0.2% SO2 mixing ratio and greater in the presence of 1000 ppmv CH4. We also found that organosulfur compounds are formed from the photolysis of CH4 and moderate amounts of SO2, The implications for sulfur aerosols on early Earth are discussed.

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria.

PubMed

Hubert, Jan; Erban, Tomas; Kopecky, Jan; Sopko, Bruno; Nesvorna, Marta; Lichovnikova, Martina; Schicht, Sabine; Strube, Christina; Sparagano, Olivier

2017-11-01

Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria. The samples of engorged adult/nymph stages had 100-fold more copies of 16S rRNA gene copies than the samples of eggs and larvae. The microbiome composition showed differences among the four poultry houses and among observed developmental stadia. In the adults' microbiome 10 OTUs comprised 90 to 99% of all sequences. Bartonella-like bacteria covered between 30 and 70% of sequences in RPM microbiome and 25% bacterial sequences in transcriptome. The phylogenetic analyses of 16S rRNA gene sequences revealed two distinct groups of Bartonella-like bacteria forming sister groups: (i) symbionts of ants; (ii) Bartonella genus. Cardinium, Wolbachia, and Rickettsiella sp. were found in the microbiomes of all tested stadia, while Spiroplasma eriocheiris and Wolbachia were identified in the laboratory RPM transcriptome. The microbiomes from eggs, larvae, and engorged adults/nymphs differed. Bartonella-like symbionts were found in all stadia and sampling sites. Bartonella-like bacteria was the most diversified group within the RPM microbiome. The presence of identified putative pathogenic bacteria is relevant with respect to human and animal health issues while the identification of symbiontic bacteria can lead to new control methods targeting them to destabilize the arthropod host.

A Stopped-Flow Kinetics Experiment for Advanced Undergraduate Laboratories: Formation of Iron(III) Thiocyannate

NASA Astrophysics Data System (ADS)

Clark, Charles R.

1997-10-01

A series of 15 stopped-flow kinetic experiments relating to the formation of iron(III)- thiocyanate at 25.0 °C and I = 1.0 M (NaClO4) is described. A methodology is given whereby solution preparation and data collection are able to be carried out within the time scale of a single laboratory period (3-4 h). Kinetic data are obtained using constant [SCN-], and at three H+ concentrations (0.10, 0.20, 0.30 M) for varying concentrations of Fe3+ (ca. 0.0025 - 0.020 M). Rate data (450 nm) are consistent with rate laws for the forward and reverse reactions: kf = (k1 + k2Ka1/[H+])[Fe3+] and kr = k-1 + k-2Ka2/[H+] respectively, with k1,k-1 corresponding to the rate constants for formation and decay of FeSCN2+, k2, k-2 to the rate constants for formation and decay of the FeSCN(OH)+ ion and Ka1,Ka2 to the acid dissociation constants (coordinated OH2 ionization) of Fe3+ and FeSCN2+. Using literature values for the latter two quantities ( Ka1 = 2.04 x 10-3 M, Ka2 = 6.5 x 10-5 M) allows values for the four rate constants to be obtained. A typical data set is analyzed to give k1 = 109(10) M-1s-1, k-1 = 0.79(0.10) s-1, k2= 8020(800) M-1s-1, k-2 = 2630(230) s-1. Absorbance change data for reaction (DeltaA) follow the expression: DeltaA = Alim.Kf.[Fe3+]/(1 + Kf.[Fe3+]), with Alim corresponding to the absorbance of fully formed FeSCN2+ (i.e. free SCN- absent) and Kf to the formation constant of this complex (value in the example 112(5) M-1, c.f. 138(29) M-1 from the kinetic data).

Recirculation System for Geothermal Energy Recovery in Sedimentary Formations: Laboratory Experiments and Numerical Simulations

NASA Astrophysics Data System (ADS)

Elkhoury, J. E.; Detwiler, R. L.; Serajian, V.; Bruno, M. S.

2012-12-01

Geothermal energy resources are more widespread than previously thought and have the potential for providing a significant amount of sustainable clean energy worldwide. In particular, hot permeable sedimentary formations provide many advantages over traditional geothermal recovery and enhanced geothermal systems in low permeability crystalline formations. These include: (1) eliminating the need for hydraulic fracturing, (2) significant reduction in risk for induced seismicity, (3) reducing the need for surface wastewater disposal, (4) contributing to decreases in greenhouse gases, and (5) potential use for CO2 sequestration. Advances in horizontal drilling, completion, and production technology from the oil and gas industry can now be applied to unlock these geothermal resources. Here, we present experimental results from a laboratory scale circulation system and numerical simulations aimed at quantifying the heat transfer capacity of sedimentary rocks. Our experiments consist of fluid flow through a saturated and pressurized sedimentary disc of 23-cm diameter and 3.8-cm thickness heated along its circumference at a constant temperature. Injection and production ports are 7.6-cm apart in the center of the disc. We used DI de-aired water and mineral oil as working fluids and explored temperatures from 20 to 150 oC and flow rates from 2 to 30 ml/min. We performed experiments on sandstone samples (Castlegate and Kirby) with different porosity, permeability and thermal conductivity to evaluate the effect of hydraulic and thermal properties on the heat transfer capacity of sediments. The producing fluid temperature followed an exponential form with time scale transients between 15 and 45 min. Steady state outflow temperatures varied between 60% and 95% of the set boundary temperature, higher percentages were observed for lower temperatures and flow rates. We used the flow and heat transport simulator TOUGH2 to develop a numerical model of our laboratory setting. Given

Biofilm formation in an ice cream plant.

PubMed

Gunduz, Gulten Tiryaki; Tuncel, Gunnur

2006-01-01

The sites of biofilm formation in an ice cream plant were investigated by sampling both the production line and the environment. Experiments were carried out twice within a 20-day period. First, stainless steel coupons were fixed to surfaces adjacent to food contact surfaces, the floor drains and the doormat. They were taken for the analysis of biofilm at three different production stages. Then, biofilm forming bacteria were enumerated and also presence of Listeria monocytogenes was monitored. Biofilm forming isolates were selected on the basis of colony morphology and Gram's reaction; Gram negative cocci and rod, Gram positive cocci and spore forming isolates were identified. Most of the biofilm formations were seen on the conveyor belt of a packaging machine 8 h after the beginning of the production, 6.5 x 10(3) cfu cm(-2). Most of the Gram negative bacteria identified belong to Enterobacteriaceae family such as Proteus, Enterobacter, Citrobacter, Shigella, Escherichia, Edwardsiella. The other Gram negative microflora included Aeromonas, Plesiomonas, Moraxella, Pseudomonas or Alcaligenes spp. were also isolated. Gram positive microflora of the ice cream plant included Staphyloccus, Bacillus, Listeria and lactic acid bacteria such as Streptococcus, Leuconostoc or Pediococcus spp. The results from this study highlighted the problems of spread of pathogens like Listeria and Shigella and spoilage bacteria. In the development of cleaning and disinfection procedures in ice cream plants, an awareness of these biofilm-forming bacteria is essential for the ice cream plants.

The Effects of Allium sativum Extracts on Biofilm Formation and Activities of Six Pathogenic Bacteria

PubMed Central

Mohsenipour, Zeinab; Hassanshahian, Mehdi

2015-01-01

Background: Garlic is considered a rich source of many compounds, which shows antimicrobial effects. The ability of microorganisms to adhere to both biotic and abiotic surfaces and to form biofilm is responsible for a number of diseases of chronic nature, demonstrating extremely high resistance to antibiotics. Bacterial biofilms are complex communities of sessile microorganisms, embedded in an extracellular matrix and irreversibly attached to various surfaces. Objectives: The present study evaluated the antimicrobial activity of Allium sativum extract against the biofilms of six pathogenic bacteria and their free-living forms. The clinical isolates in this study had not been studied in any other studies, especially in regard to biofilm disruption and inhibition of biofilm cell metabolic activity. Materials and Methods: Antimicrobial activities of A. sativum L. extracts (methanol and ethanol extracts) against planktonic forms of bacteria were determined using the disc diffusion method. The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) values were evaluated by a macrobroth dilution technique. The anti-biofilm effects were assessed by microtiter plate method. Results: The results showed that the A. sativum L. extract discs did not have any zone of inhibition for the tested bacteria. However, The MIC values of A. sativum L. extracts (0.078 - 2.5 mg/mL) confirmed the high ability of these extracts for inhibition of planktonic bacteria. A. sativum L. extracts were efficient to inhibit biofilm structures and the concentration of each extract had a direct relation with the inhibitory effect. Conclusions: Finally, it can be suggested that the extracts of this plant be applied as antimicrobial agents against these pathogens, particularly in biofilm forms. PMID:26464762

Model analysis of secondary organic aerosol formation by glyoxal in laboratory studies: the case for photoenhanced chemistry.

PubMed

Sumner, Andrew J; Woo, Joseph L; McNeill, V Faye

2014-10-21

The reactive uptake of glyoxal by atmospheric aerosols is believed to be a significant source of secondary organic aerosol (SOA). Several recent laboratory studies have been performed with the goal of characterizing this process, but questions remain regarding the effects of photochemistry on SOA growth. We applied GAMMA (McNeill et al. Environ. Sci. Technol. 2012, 46, 8075-8081), a photochemical box model with coupled gas-phase and detailed aqueous aerosol-phase chemistry, to simulate aerosol chamber studies of SOA formation by the uptake of glyoxal by wet aerosol under dark and irradiated conditions (Kroll et al. J. Geophys. Res. 2005, 110 (D23), 1-10; Volkamer et al. Atmos. Chem. Phys. 2009, 9, 1907-1928; Galloway et al. Atmos. Chem. Phys. 2009, 9, 3331- 306 3345 and Geophys. Res. Lett. 2011, 38, L17811). We find close agreement between simulated SOA growth and the results of experiments conducted under dark conditions using values of the effective Henry's Law constant of 1.3-5.5 × 10(7) M atm(-1). While irradiated conditions led to the production of some organic acids, organosulfates, and other oxidation products via well-established photochemical mechanisms, these additional product species contribute negligible aerosol mass compared to the dark uptake of glyoxal. Simulated results for irradiated experiments therefore fell short of the reported SOA mass yield by up to 92%. This suggests a significant light-dependent SOA formation mechanism that is not currently accounted for by known bulk photochemistry, consistent with recent laboratory observations of SOA production via photosensitizer chemistry.

Platelets and Infections – Complex Interactions with Bacteria

PubMed Central

Hamzeh-Cognasse, Hind; Damien, Pauline; Chabert, Adrien; Pozzetto, Bruno; Cognasse, Fabrice; Garraud, Olivier

2015-01-01

Platelets can be considered sentinels of vascular system due to their high number in the circulation and to the range of functional immunoreceptors they express. Platelets express a wide range of potential bacterial receptors, including complement receptors, FcγRII, Toll-like receptors but also integrins conventionally described in the hemostatic response, such as GPIIb–IIIa or GPIb. Bacteria bind these receptors either directly, or indirectly via fibrinogen, fibronectin, the first complement C1q, the von Willebrand Factor, etc. The fate of platelet-bound bacteria is questioned. Several studies reported the ability of activated platelets to internalize bacteria such as Staphylococcus aureus or Porphyromonas gingivalis, though there is no clue on what happens thereafter. Are they sheltered from the immune system in the cytoplasm of platelets or are they lysed? Indeed, while the presence of phagolysosome has not been demonstrated in platelets, they contain antimicrobial peptides that were shown to be efficient on S. aureus. Besides, the fact that bacteria can bind to platelets via receptors involved in hemostasis suggests that they may induce aggregation; this has indeed been described for Streptococcus sanguinis, S. epidermidis, or C. pneumoniae. On the other hand, platelets are able to display an inflammatory response to an infectious triggering. We, and others, have shown that platelet release soluble immunomodulatory factors upon stimulation by bacterial components. Moreover, interactions between bacteria and platelets are not limited to only these two partners. Indeed, platelets are also essential for the formation of neutrophil extracellular traps by neutrophils, resulting in bacterial clearance by trapping bacteria and concentrating antibacterial factors but in enhancing thrombosis. In conclusion, the platelet–bacteria interplay is a complex game; its fine analysis is complicated by the fact that the inflammatory component adds to the aggregation response

Antimicrobial Photodynamic Therapy to Kill Gram-negative Bacteria

PubMed Central

Sperandio, Felipe F; Huang, Ying-Ying; Hamblin, Michael R

2013-01-01

Antimicrobial photodynamic therapy (PDT) or photodynamic inactivation (PDI) is a new promising strategy to eradicate pathogenic microorganisms such as Gram-positive and Gram-negative bacteria, yeasts and fungi. The search for new approaches that can kill bacteria but do not induce the appearance of undesired drug-resistant strains suggests that PDT may have advantages over traditional antibiotic therapy. PDT is a non-thermal photochemical reaction that involves the simultaneous presence of visible light, oxygen and a dye or photosensitizer (PS). Several PS have been studied for their ability to bind to bacteria and efficiently generate reactive oxygen species (ROS) upon photostimulation. ROS are formed through type I or II mechanisms and may inactivate several classes of microbial cells including Gram-negative bacteria such as Pseudomonas aeruginosa, which are typically characterized by an impermeable outer cell membrane that contains endotoxins and blocks antibiotics, dyes, and detergents, protecting the sensitive inner membrane and cell wall. This review covers significant peer-reviewed articles together with US and World patents that were filed within the past few years and that relate to the eradication of Gram-negative bacteria via PDI or PDT. It is organized mainly according to the nature of the PS involved and includes natural or synthetic food dyes; cationic dyes such as methylene blue and toluidine blue; tetrapyrrole derivatives such as phthalocyanines, chlorins, porphyrins, chlorophyll and bacteriochlorophyll derivatives; functionalized fullerenes; nanoparticles combined with different PS; other formulations designed to target PS to bacteria; photoactive materials and surfaces; conjugates between PS and polycationic polymers or antibodies; and permeabilizing agents such as EDTA, PMNP and CaCl2. The present review also covers the different laboratory animal models normally used to treat Gram-negative bacterial infections with antimicrobial PDT. PMID

Characterization of specimens obtained by different sampling methods for evaluation of periodontal bacteria.

PubMed

Okada, Ayako; Sogabe, Kaoru; Takeuchi, Hiroaki; Okamoto, Masaaki; Nomura, Yoshiaki; Hanada, Nobuhiro

2017-12-27

Quantitative analysis of periodontal bacteria is considered useful for clinical diagnosis, evaluation and assessment of the risk of periodontal disease. The purpose of this study was to compare the effectiveness of sampling of saliva, supragingival and subgingival plaque for evaluation of periodontal bacteria. From each of 12 subjects, i) subgingival plaque was collected from the deepest pocket using a sterile paper point, ii) stimulated whole saliva was collected after chewing gum, and iii) supragingival plaque was collected using a tooth brush. These samples were sent to the medical examination laboratory for quantitative analysis of the counts of three periodontal bacterial species: Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. The proportions of these bacteria in subgingival plaque were higher than those in saliva or supragingival plaque, but lower in subgingival plaque than in saliva or supragingival plaque. In several cases, periodontal bacteria were below the levels of detection in subgingival plaque. We concluded that samples taken from subgingival plaque may be more useful for evaluating the proportion of periodontal bacteria in deep pockets than is the case for other samples. Therefore, for evaluation of periodontal bacteria, clinicians should consider the characteristics of the specimens obtained using different sampling methods.

Antimicrobial Peptides Targeting Gram-Positive Bacteria

PubMed Central

Malanovic, Nermina; Lohner, Karl

2016-01-01

Antimicrobial peptides (AMPs) have remarkably different structures as well as biological activity profiles, whereupon most of these peptides are supposed to kill bacteria via membrane damage. In order to understand their molecular mechanism and target cell specificity for Gram-positive bacteria, it is essential to consider the architecture of their cell envelopes. Before AMPs can interact with the cytoplasmic membrane of Gram-positive bacteria, they have to traverse the cell wall composed of wall- and lipoteichoic acids and peptidoglycan. While interaction of AMPs with peptidoglycan might rather facilitate penetration, interaction with anionic teichoic acids may act as either a trap for AMPs or a ladder for a route to the cytoplasmic membrane. Interaction with the cytoplasmic membrane frequently leads to lipid segregation affecting membrane domain organization, which affects membrane permeability, inhibits cell division processes or leads to delocalization of essential peripheral membrane proteins. Further, precursors of cell wall components, especially the highly conserved lipid II, are directly targeted by AMPs. Thereby, the peptides do not inhibit peptidoglycan synthesis via binding to proteins like common antibiotics, but form a complex with the precursor molecule, which in addition can promote pore formation and membrane disruption. Thus, the multifaceted mode of actions will make AMPs superior to antibiotics that act only on one specific target. PMID:27657092

Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls?

PubMed

Guennoc, Cora Miquel; Rose, Christophe; Labbé, Jessy; Deveau, Aurélie

2018-05-17

Ectomycorrhizal (ECM) fungi establish symbiosis with roots of most trees of boreal and temperate ecosystems and are major drivers of nutrient fluxes between trees and the soil. ECM fungi constantly interact with bacteria all along their life cycle and the extended networks of hyphae provide a habitat for complex bacterial communities. Despite the important effects these bacteria can have on the growth and activities of ECM fungi, little is known about the mechanisms by which these microorganisms interact. Here we investigated the ability of bacteria to form biofilm on the hyphae of the ECM fungus Laccaria bicolor. We showed that the ability to form biofilms on the hyphae of the ECM fungus is widely shared among soil bacteria. Conversely, some fungi, belonging to the Ascomycete class, did not allow for the formation of bacterial biofilms on their surfaces. The formation of biofilms was also modulated by the presence of tree roots and ectomycorrhizae, suggesting that biofilm formation does not occur randomly in soil but that it is regulated by several biotic factors. In addition, our study demonstrated that the formation of bacterial biofilm on fungal hyphae relies on the production of networks of filaments made of extracellular DNA.

Silver enhances antibiotic activity against gram-negative bacteria.

PubMed

Morones-Ramirez, J Ruben; Winkler, Jonathan A; Spina, Catherine S; Collins, James J

2013-06-19

A declining pipeline of clinically useful antibiotics has made it imperative to develop more effective antimicrobial therapies, particularly against difficult-to-treat Gram-negative pathogens. Silver has been used as an antimicrobial since antiquity, yet its mechanism of action remains unclear. We show that silver disrupts multiple bacterial cellular processes, including disulfide bond formation, metabolism, and iron homeostasis. These changes lead to increased production of reactive oxygen species and increased membrane permeability of Gram-negative bacteria that can potentiate the activity of a broad range of antibiotics against Gram-negative bacteria in different metabolic states, as well as restore antibiotic susceptibility to a resistant bacterial strain. We show both in vitro and in a mouse model of urinary tract infection that the ability of silver to induce oxidative stress can be harnessed to potentiate antibiotic activity. Additionally, we demonstrate in vitro and in two different mouse models of peritonitis that silver sensitizes Gram-negative bacteria to the Gram-positive-specific antibiotic vancomycin, thereby expanding the antibacterial spectrum of this drug. Finally, we used silver and antibiotic combinations in vitro to eradicate bacterial persister cells, and show both in vitro and in a mouse biofilm infection model that silver can enhance antibacterial action against bacteria that produce biofilms. This work shows that silver can be used to enhance the action of existing antibiotics against Gram-negative bacteria, thus strengthening the antibiotic arsenal for fighting bacterial infections.

Using micro-patterned surfaces to inhibit settlement and biofilm formation by Bacillus subtilis.

PubMed

Chang, Siyuan; Chen, Xiaodong; Jiang, Shuo; Chen, Jinchun; Shi, Lin

2017-07-01

Biofilm is a biological complex caused by bacteria attachment to the substrates and their subsequent reproduction and secretion. This phenomenon reduces heat transfer efficiency and causes significant losses in treated sewage heat-recovering systems. This paper describes a physical approach to inhibit bacteria settlement and biofilm formation by Bacillus subtilis, which is the dominant species in treated sewage. Here, micro-patterned surfaces with different characteristics (stripe and cube) and dimensions (1-100 μm) were fabricated as surfaces of interest. Model sewage was prepared and a rotating coupon device was used to form the biofilms. Precision balance, scanning electron microscopy, and confocal laser scanning microscopy (CLSM) were employed to investigate the inhibitory effects and the mechanisms of the biofilm-surface interactions. The results have shown that surfaces with small pattern sizes (1 and 2 μm) all reduced biofilm formation significantly. Interestingly, the CLSM images showed that the surfaces do not play a role in "killing" the bacteria. These findings are useful for future development of new process surfaces on which bacteria settlement and biofilm formation can be inhibited or minimized.

Macroalgal Morphogenesis Induced by Waterborne Compounds and Bacteria in Coastal Seawater

PubMed Central

Grueneberg, Jan; Engelen, Aschwin H.; Costa, Rodrigo; Wichard, Thomas

2016-01-01

Axenic gametes of the marine green macroalga Ulva mutabilis Føyn (Ria Formosa, locus typicus) exhibit abnormal development into slow-growing callus-like colonies with aberrant cell walls. Under laboratory conditions, it was previously demonstrated that all defects in growth and thallus development can be completely abolished when axenic gametes are inoculated with a combination of two specific bacterial strains originally identified as Roseobacter sp. strain MS2 and Cytophaga sp. strain MS6. These bacteria release diffusible morphogenetic compounds (= morphogens), which act similar to cytokinin and auxin. To investigate the ecological relevance of the waterborne bacterial morphogens, seawater samples were collected in the Ria Formosa lagoon (Algarve, Southern Portugal) at 20 sampling sites and tidal pools to assess their morphogenetic effects on the axenic gametes of U. mutabilis. Specifically the survey revealed that sterile-filtered seawater samples can completely recover growth and morphogenesis of U. mutabilis under axenic conditions. Morphogenetic activities of free-living and epiphytic bacteria isolated from the locally very abundant Ulva species (i.e., U. rigida) were screened using a multiwell-based testing system. The most represented genera isolated from U. rigida were Alteromonas, Pseudoalteromonas and Sulfitobacter followed by Psychrobacter and Polaribacter. Several naturally occurring bacterial species could emulate MS2 activity (= induction of cell divisions) regardless of taxonomic affiliation, whereas the MS6 activity (= induction of cell differentiation and cell wall formation) was species-specific and is probably a feature of difficult-to-culture bacteria. Interestingly, isolated bacteroidetes such as Algoriphagus sp. and Polaribacter sp. could individually trigger complete Ulva morphogenesis and thus provide a novel mode of action for bacterial-induced algal development. This study also highlights that the accumulation of algal growth factors in

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, R.L.

1995-05-30

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, Richard L.

1995-01-01

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Small but Mighty: Cell Size and Bacteria.

PubMed

Levin, Petra Anne; Angert, Esther R

2015-06-08

Our view of bacteria is overwhelmingly shaped by their diminutive nature. The most ancient of organisms, their very presence was not appreciated until the 17th century with the invention of the microscope. Initially, viewed as "bags of enzymes," recent advances in imaging, molecular phylogeny, and, most recently, genomics have revealed incredible diversity within this previously invisible realm of life. Here, we review the impact of size on bacterial evolution, physiology, and morphogenesis. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Bioavailability of mineral-bound iron to a snow algae-bacteria co-culture and implications for albedo-altering snow algae blooms.

PubMed

Harrold, Z R; Hausrath, E M; Garcia, A H; Murray, A E; Tschauner, O; Raymond, J; Huang, S

2018-01-26

Snow algae can form large-scale blooms across the snowpack surface and near-surface environments. These pigmented blooms can decrease snow albedo, increase local melt rates, and may impact the global heat budget and water cycle. Yet, underlying causes for the geospatial occurrence of these blooms remain unconstrained. One possible factor contributing to snow algae blooms is the presence of mineral dust as a micronutrient source. We investigated the bioavailability of iron (Fe) -bearing minerals, including forsterite (Fo 90 , Mg 1.8 Fe 0.2 SiO 4 ), goethite, smectite and pyrite as Fe sources for a Chloromonas brevispina - bacteria co-culture through laboratory-based experimentation. Fo 90 was capable of stimulating snow algal growth and increased the algal growth rate in otherwise Fe-depleted co-cultures. Fo 90 -bearing systems also exhibited a decrease in bacteria:algae ratios compared to Fe-depleted conditions, suggesting a shift in microbial community structure. The C. brevispina co-culture also increased the rate of Fo 90 dissolution relative to an abiotic control. Analysis of 16S rRNA genes in the co-culture identified Gammaproteobacteria , Betaprotoeobacteria and Sphingobacteria , all of which are commonly found in snow and ice environments. Archaea were not detected. Collimonas and Pseudomonas , which are known to enhance mineral weathering rates, comprised two of the top eight (> 1 %) OTUs. These data provide unequivocal evidence that mineral dust can support elevated snow algae growth under otherwise Fe-depleted growth conditions, and that snow algae can enhance mineral dissolution under these conditions. IMPORTANCE Fe, a key micronutrient for photosynthetic growth, is necessary to support the formation of high-density snow algae blooms. The laboratory experiments described herein allow for a systematic investigation of snow algae-bacteria-mineral interactions and their ability to mobilize and uptake mineral-bound Fe. Results provide unequivocal and

A qualitative characterization of an introductory college nonmajors biology laboratory

NASA Astrophysics Data System (ADS)

Lee, Cherin Ann

The nature of an undergraduate, nonmajors biology laboratory was investigated in this study. Student participants were enrolled in a general education biology laboratory course at the University of Northern Iowa. The researcher's purpose was to gain a characterization of the instructional format and laboratory activities experienced by students. Interpretation of student and instructor responses enabled an insider's view of the biology laboratory. The laboratory period was consistently described by both students and instructors as having three parts, Beginning, Middle, and End, with the End being of special importance for conceptual development. The instructional format of the three instructors differed within the three portions of the laboratory period, ranging from an inquiry-oriented, partial learning cycle to a fairly expository model labeled inform/verify/practice. There was striking similarity in intrasectional student and teacher descriptions of instructional format. Additionally, students experiencing the alternate instructor provided the same characterizations of instructional format as those provided by the instructor's usual students. There were no discernible patterns of instructional format based on sex or reasoning level. In addition to the central role of instructional format, three areas of importance emerged: the social aspects of learning, the collaborative and cooperative nature of laboratory work and learning, and the role of self-efficacy. Theory developed from and grounded in the data showed six factors important in the introductory college biology laboratory: collaborative and cooperative learning, student-student and teacher-student interactions, attitude and self-efficacy, learning process and learning style, effective instructional format, and science content. These factors were found to be similar to factors identified in the literature as important in K-12 science education. These factors were set in the context of schooling and learning

Transport of Chemotactic Bacteria in Porous Media with Structured Heterogeneity

NASA Astrophysics Data System (ADS)

Ford, R. M.; Wang, M.; Liu, J.; Long, T.

2008-12-01

Chemical contaminants that become trapped in low permeability zones (e.g. clay lenses) are difficult to remediate using conventional pump-and-treat approaches. Chemotactic bacteria that are transported by groundwater through more permeable regions may migrate toward these less permeable zones in response to chemical gradients created by contaminant diffusion from the low permeability source, thereby enhancing the remediation process by directing bacteria to the contaminants they degrade. What effect does the heterogeneity associated with coarse- and fine-grained layers that are characteristic of natural groundwater environments have on the transport of microorganisms and their chemotactic response? To address this question experiments were conducted over a range of scales from a single capillary tube to a laboratory- scale column in both static and flowing systems with and without chemoattractant gradients. In static capillary assays, motile bacteria accumulated at the interface between an aqueous solution and a suspension of agarose particulates. In microfluidic devices with an array of staggered cylinders, chemotactic bacteria migrated transverse to flow in response to a chemoattractant gradient. In sand columns packed with a coarse-grained core and surrounded by a fine-grained annulus, chemotactic bacteria migrated preferentially toward a chemoattractant source along the centerline. Mathematical models and computer simulations were developed to analyze the experimental observations in terms of transport parameters from the advection- disperson-sorption equation.

Role of copper oxides in contact killing of bacteria.

PubMed

Hans, Michael; Erbe, Andreas; Mathews, Salima; Chen, Ying; Solioz, Marc; Mücklich, Frank

2013-12-31

The potential of metallic copper as an intrinsically antibacterial material is gaining increasing attention in the face of growing antibiotics resistance of bacteria. However, the mechanism of the so-called "contact killing" of bacteria by copper surfaces is poorly understood and requires further investigation. In particular, the influences of bacteria-metal interaction, media composition, and copper surface chemistry on contact killing are not fully understood. In this study, copper oxide formation on copper during standard antimicrobial testing was measured in situ by spectroscopic ellipsometry. In parallel, contact killing under these conditions was assessed with bacteria in phosphate buffered saline (PBS) or Tris-Cl. For comparison, defined Cu2O and CuO layers were thermally generated and characterized by grazing incidence X-ray diffraction. The antibacterial properties of these copper oxides were tested under the conditions used above. Finally, copper ion release was recorded for both buffer systems by inductively coupled plasma atomic absorption spectroscopy, and exposed copper samples were analyzed for topographical surface alterations. It was found that there was a fairly even growth of CuO under wet plating conditions, reaching 4-10 nm in 300 min, but no measurable Cu2O was formed during this time. CuO was found to significantly inhibit contact killing, compared to pure copper. In contrast, thermally generated Cu2O was essentially as effective in contact killing as pure copper. Copper ion release from the different surfaces roughly correlated with their antibacterial efficacy and was highest for pure copper, followed by Cu2O and CuO. Tris-Cl induced a 10-50-fold faster copper ion release compared to PBS. Since the Cu2O that primarily forms on copper under ambient conditions is as active in contact killing as pure copper, antimicrobial objects will retain their antimicrobial properties even after oxide formation.

An insect-bacteria bioindicator for assessing detrimental nutrient enrichment in wetlands.

Treesearch

A. Dennis Lemly; Ryan S. King

2000-01-01

Field and laboratory studies were conducted to evaluate the use of bacterial growth on aquatic insects as a metric for determining the existence of nutrient impacts in wetlands. Results from field investigations indicated that elevated concentrations of nitrate and phosphate were associated with growth of filamentous bacteria on insect body surfaces and that there were...

The formation of sulfate and elemental sulfur aerosols under varying laboratory conditions: implications for early earth.

PubMed

DeWitt, H Langley; Hasenkopf, Christa A; Trainer, Melissa G; Farmer, Delphine K; Jimenez, Jose L; McKay, Christopher P; Toon, Owen B; Tolbert, Margaret A

2010-10-01

The presence of sulfur mass-independent fractionation (S-MIF) in sediments more than 2.45 × 10(9) years old is thought to be evidence for an early anoxic atmosphere. Photolysis of sulfur dioxide (SO(2)) by UV light with λ < 220 nm has been shown in models and some initial laboratory studies to create a S-MIF; however, sulfur must leave the atmosphere in at least two chemically different forms to preserve any S-MIF signature. Two commonly cited examples of chemically different sulfur species that could have exited the atmosphere are elemental sulfur (S(8)) and sulfuric acid (H(2)SO(4)) aerosols. Here, we use real-time aerosol mass spectrometry to directly detect the sulfur-containing aerosols formed when SO(2) either photolyzes at wavelengths from 115 to 400 nm, to simulate the UV solar spectrum, or interacts with high-energy electrons, to simulate lightning. We found that sulfur-containing aerosols form under all laboratory conditions. Further, the addition of a reducing gas, in our experiments hydrogen (H(2)) or methane (CH(4)), increased the formation of S(8). With UV photolysis, formation of S(8) aerosols is highly dependent on the initial SO(2) pressure; and S(8) is only formed at a 2% SO(2) mixing ratio and greater in the absence of a reductant, and at a 0.2% SO(2) mixing ratio and greater in the presence of 1000 ppmv CH(4). We also found that organosulfur compounds are formed from the photolysis of CH(4) and moderate amounts of SO(2). The implications for sulfur aerosols on early Earth are discussed. Key Words: S-MIF-Archean atmosphere-Early Earth-Sulfur aerosols.

Restructuring a General Microbiology Laboratory into an Investigative Experience.

ERIC Educational Resources Information Center

Deutch, Charles E.

1994-01-01

Describes an investigative laboratory sequence based upon the isolation and characterization of soil bacteria to aid microbiology teachers in providing students with activities that expose them to basic techniques of microbiology as well as demonstrates the scientific process and the experimental analysis of microorganisms. (ZWH)

Hydrogen or formate: Alternative key players in methanogenic degradation.

PubMed

Schink, Bernhard; Montag, Dominik; Keller, Anja; Müller, Nicolai

2017-06-01

Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Have sex or not? Lessons from bacteria.

PubMed

Lodé, T

2012-01-01

Sex is one of the greatest puzzles in evolutionary biology. A true meiotic process occurs only in eukaryotes, while in bacteria, gene transcription is fragmentary, so asexual reproduction in this case really means clonal reproduction. Sex could stem from a signal that leads to increased reproductive output of all interacting individuals and could be understood as a secondary consequence of primitive metabolic reactions. Meiotic sex evolved in proto-eukaryotes to solve a problem that bacteria did not have, namely a large amount of DNA material, occurring in an archaic step of proto-cell formation and genetic exchanges. Rather than providing selective advantages through reproduction, sex could be thought of as a series of separate events which combines step-by-step some very weak benefits of recombination, meiosis, gametogenesis and syngamy. Copyright © 2012 S. Karger AG, Basel.

Bacteria versus selenium: A view from the inside out

USGS Publications Warehouse

Staicu, Lucian; Oremland, Ronald S.; Tobe, Ryuta; Mihara, Hisaaki

2017-01-01

Bacteria and selenium (Se) are closely interlinked as the element serves both essential nutrient requirements and energy generation functions. However, Se can also behave as a powerful toxicant for bacterial homeostasis. Conversely, bacteria play a tremendous role in the cycling of Se between different environmental compartments, and bacterial metabolism has been shown to participate to all valence state transformations undergone by Se in nature. Bacteria possess an extensive molecular repertoire for Se metabolism. At the end of the 1980s, a novel mode of anaerobic respiration based on Se oxyanions was experimentally documented for the first time. Following this discovery, specific enzymes capable of reducing Se oxyanions and harvesting energy were found in a number of anaerobic bacteria. The genes involved in the expression of these enzymes have later been identified and cloned. This iterative approach undertaken outside-in led to the understanding of the molecular mechanisms of Se transformations in bacteria. Based on the extensive knowledge accumulated over the years, we now have a full(er) view from the inside out, from DNA-encoding genes to enzymes and thermodynamics. Bacterial transformations of Se for assimilatory purposes have been the object of numerous studies predating the investigation of Se respiration. Remarkable contributions related to the understating of the molecular picture underlying seleno-amino acid biosynthesis are reviewed herein. Under certain circumstances, Se is a toxicant for bacterial metabolism and bacteria have evolved strategies to counteract this toxicity, most notably by the formation of elemental Se (nano)particles. Several biotechnological applications, such as the production of functional materials and the biofortification of crop species using Se-utilizing bacteria, are presented in this chapter.

Rapid Evolution of Culture-Impaired Bacteria During Adaptation to Biofilm Growth

PubMed Central

Penterman, Jon; Nguyen, Dao; Anderson, Erin; Staudinger, Benjamin J.; Greenberg, Everett P.; Lam, Joseph S.; Singh, Pradeep K.

2014-01-01

Summary Biofilm growth increases the fitness of bacteria in harsh conditions. However, bacteria from clinical and environmental biofilms can exhibit impaired growth in culture, even when the species involved are readily cultureable, and permissive conditions are used. Here we show that culture-impaired variants of Pseudomonas aeruginosa rapidly and abundantly evolve in laboratory biofilms. The culture-impaired phenotype is caused by mutations that alter the outer-membrane lipopolysaccharide structure. Within biofilms, the lipopolysaccharide mutations markedly increase bacterial fitness. However, outside the protected biofilm environment, the mutations sensitize the variants to killing by a self-produced antimicrobial agent. Thus, a biofilm-mediated adaptation produces a stark fitness trade off that compromises bacterial survival in culture. Trade offs like this could limit the ability of bacteria to transition between biofilm growth and the free-living state, and produce bacterial populations that escape detection by culture-based sampling. PMID:24412364

Ketene Formation in Interstellar Ices: A Laboratory Study

NASA Technical Reports Server (NTRS)

Hudson, Reggie L.; Loeffler, Mark Josiah

2013-01-01

The formation of ketene (H2CCO, ethenone) in polar and apolar ices was studied with in situ 0.8 MeV proton irradiation, far-UVphotolysis, and infrared spectroscopic analyses at 10-20 K. Using isotopically enriched reagents, unequivocal evidencewas obtained for ketene synthesis in H2O-rich and CO2-rich ices, and several reaction products were identified. Results from scavenging experiments suggested that ketene was formed by free-radical pathways, as opposed to acid-base processes or redox reactions. Finally, we use our results to draw conclusions about the formation and stability of ketene in the interstellar medium.

Role of physical heterogeneity in the interpretation of small-scale laboratory and field observations of bacteria, microbial-sized microsphere, and bromide transport through aquifer sediments

USGS Publications Warehouse

Harvey, Ronald W.; Kinner, Nancy E.; MacDonald, Dan; Metge, David W.; Bunn, Amoret

1993-01-01

The effect of physical variability upon the relative transport behavior of microbial-sized microspheres, indigenous bacteria, and bromide was examined in field and flow-through column studies for a layered, but relatively well sorted, sandy glaciofluvial aquifer. These investigations involved repacked, sieved, and undisturbed aquifer sediments. In the field, peak abundance of labeled bacteria traveling laterally with groundwater flow 6 m downgradient from point of injection was coincident with the retarded peak of carboxylated microspheres (retardation factor, RF = 1.7) at the 8.8 m depth, but preceded the bromide peak and the retarded microsphere peak (RF = 1.5) at the 9.0 m depth. At the 9.5 m depth, the bacterial peak was coincident with both the bromide and the microsphere peaks. Although sorption appeared to be a predominant mechanism responsible for immobilization of microbial-sized microspheres in the aquifer, straining appeared to be primarily responsible for their removal in 0.6-m-long columns of repacked, unsieved aquifer sediments. The manner in which the columns were packed also affected optimal size for microsphere transport, which in one experiment was near the size of the small (∼2 μm) groundwater protozoa (flagellates). These data suggest that variability in aquifer sediment structure can be important in interpretation of both small-scale field and laboratory experiments examining microbial transport behavior.

Hydrodynamic Trapping of Swimming Bacteria by Convex Walls

NASA Astrophysics Data System (ADS)

Sipos, O.; Nagy, K.; Di Leonardo, R.; Galajda, P.

2015-06-01

Swimming bacteria display a remarkable tendency to move along flat surfaces for prolonged times. This behavior may have a biological importance but can also be exploited by using microfabricated structures to manipulate bacteria. The main physical mechanism behind the surface entrapment of swimming bacteria is, however, still an open question. By studying the swimming motion of Escherichia coli cells near microfabricated pillars of variable size, we show that cell entrapment is also present for convex walls of sufficiently low curvature. Entrapment is, however, markedly reduced below a characteristic radius. Using a simple hydrodynamic model, we predict that trapped cells swim at a finite angle with the wall and a precise relation exists between the swimming angle at a flat wall and the critical radius of curvature for entrapment. Both predictions are quantitatively verified by experimental data. Our results demonstrate that the main mechanism for wall entrapment is hydrodynamic in nature and show the possibility of inhibiting cell adhesion, and thus biofilm formation, using convex features of appropriate curvature.

Sulfate-reducing bacteria: Microbiology and physiology

NASA Technical Reports Server (NTRS)

Peck, H. D.

1985-01-01

The sulfate reducing bacteria, the first nonphotosynthetic anaerobic bacteria demonstrated to contain c type cytochromes, perform electron transfer coupled to phosphorylation. A new bioenergetic scheme for the formation of a proton gradient for growth of Desulfovibrio on organic substrates and sulfate involving vectors electron transfer and consistent with the cellular localization of enzymes and electron transfer components was proposed. Hydrogen is produced in the cytoplasm from organic substrates and, as a permease molecule diffuses rapidly across the cytoplasmic membrane, it is oxidized to protons and electrons by the periplasmic hydrogenase. The electrons only are transferred across the cytoplasmic membrane to the cytoplasm where they are used to reduce sulfate to sulfide. The protons are used for transport or to drive a reversible ATPOSE. The net effect is the transfer of protons across the cytoplasmic membrane with the intervention of a proton pump. This type of H2 cycling is relevant to the bioenergetics of other types of anaerobic microorganisms.

Inter-laboratory Comparison of Real-time PCR Methods for Quantification of General Fecal Indicator Bacteria

EPA Science Inventory

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized prot...

Hexagonal platelet-like magnetite as a biosignature of thermophilic iron-reducing bacteria and its applications to the exploration of the modern deep, hot biosphere and the emergence of iron-reducing bacteria in early precambrian oceans.

PubMed

Li, Yi-Liang

2012-12-01

Dissimilatory iron-reducing bacteria are able to enzymatically reduce ferric iron and couple to the oxidation of organic carbon. This mechanism induces the mineralization of fine magnetite crystals characterized by a wide distribution in size and irregular morphologies that are indistinguishable from authigenic magnetite. Thermoanaerobacter are thermophilic iron-reducing bacteria that predominantly inhabit terrestrial hot springs or deep crusts and have the capacity to transform amorphous ferric iron into magnetite with a size up to 120 nm. In this study, I first characterize the formation of hexagonal platelet-like magnetite of a few hundred nanometers in cultures of Thermoanaerobacter spp. strain TOR39. Biogenic magnetite with such large crystal sizes and unique morphology has never been observed in abiotic or biotic processes and thus can be considered as a potential biosignature for thermophilic iron-reducing bacteria. The unique crystallographic features and strong ferrimagnetic properties of these crystals allow easy and rapid screening for the previous presence of iron-reducing bacteria in deep terrestrial crustal samples that are unsuitable for biological detection methods and, also, the search for biogenic magnetite in banded iron formations that deposited only in the first 2 billion years of Earth with evidence of life.

Biotechnological and in situ food production of polyols by lactic acid bacteria.

PubMed

Ortiz, Maria Eugenia; Bleckwedel, Juliana; Raya, Raúl R; Mozzi, Fernanda

2013-06-01

Polyols such as mannitol, erythritol, sorbitol, and xylitol are naturally found in fruits and vegetables and are produced by certain bacteria, fungi, yeasts, and algae. These sugar alcohols are widely used in food and pharmaceutical industries and in medicine because of their interesting physicochemical properties. In the food industry, polyols are employed as natural sweeteners applicable in light and diabetic food products. In the last decade, biotechnological production of polyols by lactic acid bacteria (LAB) has been investigated as an alternative to their current industrial production. While heterofermentative LAB may naturally produce mannitol and erythritol under certain culture conditions, sorbitol and xylitol have been only synthesized through metabolic engineering processes. This review deals with the spontaneous formation of mannitol and erythritol in fermented foods and their biotechnological production by heterofermentative LAB and briefly presented the metabolic engineering processes applied for polyol formation.

An analysis of wilderness water in Kings Canyon, Sequoia, and Yosemite national parks for coliform and pathologic bacteria.

PubMed

Derlet, Robert W; Carlson, James R

2004-01-01

To determine the prevalence of coliform and potentially pathogenic bacteria in remote backcountry alpine lakes and streams of national parks in the Sierra Nevada mountains. Water was sampled at 55 predetermined lakes and streams that would stratify the risk, based on sites used by backpackers, sites used by pack animals, and uncontaminated wild areas. Sites were distributed among Kings Canyon (15), Sequoia (17), and Yosemite (23). Water was collected using Millipore bacterial samplers, which provided specific counts of coliform and other bacteria in each water sample and also served as a transport media from the wilderness to the laboratory. On return to the laboratory, bacteria were harvested from the samplers and subjected to specific identification and qualitative analysis using standard microbiology techniques for the analysis of water. Coliform bacteria were detected in 22 of the 55 sites. All of these sites were below areas used by backpackers or pack animals. Thirty-three sites were free of coliforms. These sites included both those used lightly by backpackers and those with no human or domestic animal use. All samples contained expected amounts of normal aquatic bacteria including Pseudomonas, Rahnella aquatilis, Serratia spp, and nonpathogenic species of Yersinia. Most sampling sites in these national parks are free of coliform or pathogenic organisms. Low levels of coliform bacteria are found in some bodies of water where the watershed has been affected by human or pack animal travel.

Fabrication of nonfouling, bactericidal, and bacteria corpse release multifunctional surface through surface-initiated RAFT polymerization.

PubMed

Wang, Bailiang; Ye, Zi; Tang, Yihong; Han, Yuemei; Lin, Quankui; Liu, Huihua; Chen, Hao; Nan, Kaihui

Infections after surgery or endophthalmitis are potentially blinding complications caused by bacterial adhesion and subsequent biofilm formation on the intraocular lens. Neither single-function anti-adhesion surface nor contacting killing surface can exhibit ideal antibacterial function. In this work, a novel (2-(dimethylamino)-ethyl methacrylate- co -2-methacryloyloxyethyl phosphorylcholine) (p (DMAEMA- co -MPC)) brush was synthesized by "grafting from" method through reversible-addition fragmentation chain transfer polymerization. 1-Bromoheptane was used to quaternize the p (DMAEMA- co -MPC) brush coating and to endow the surface with bactericidal function. The success of the surface functionalization was confirmed by atomic force microscopy, water contact angle, and spectroscopic ellipsometry. The quaternary ammonium salt units were employed as efficient disinfection that can eliminate bacteria through contact killing, whereas the 2-methacryloyloxyethyl phosphorylcholine units were introduced to suppress unwanted nonspecific adsorption. The functionalized poly(dimethyl siloxane) surfaces showed efficiency in reducing bovine serum albumin adsorption and in inhibiting bacteria adhesion and biofilm formation. The copolymer brushes also demonstrated excellent bactericidal function against gram-positive ( Staphylococcus aureus ) bacteria measured by bacteria live/dead staining and shake-flask culture methods. The surface biocompatibility was evaluated by morphology and activity measurement with human lens epithelial cells in vitro. The achievement of the p (DMAEMA + - co -MPC) copolymer brush coating with nonfouling, bactericidal, and bacteria corpse release properties can be used to modify intraocular lenses.

Fabrication of nonfouling, bactericidal, and bacteria corpse release multifunctional surface through surface-initiated RAFT polymerization

PubMed Central

Wang, Bailiang; Ye, Zi; Tang, Yihong; Han, Yuemei; Lin, Quankui; Liu, Huihua; Chen, Hao; Nan, Kaihui

2017-01-01

Infections after surgery or endophthalmitis are potentially blinding complications caused by bacterial adhesion and subsequent biofilm formation on the intraocular lens. Neither single-function anti-adhesion surface nor contacting killing surface can exhibit ideal antibacterial function. In this work, a novel (2-(dimethylamino)-ethyl methacrylate-co-2-methacryloyloxyethyl phosphorylcholine) (p (DMAEMA-co-MPC)) brush was synthesized by “grafting from” method through reversible–addition fragmentation chain transfer polymerization. 1-Bromoheptane was used to quaternize the p (DMAEMA-co-MPC) brush coating and to endow the surface with bactericidal function. The success of the surface functionalization was confirmed by atomic force microscopy, water contact angle, and spectroscopic ellipsometry. The quaternary ammonium salt units were employed as efficient disinfection that can eliminate bacteria through contact killing, whereas the 2-methacryloyloxyethyl phosphorylcholine units were introduced to suppress unwanted nonspecific adsorption. The functionalized poly(dimethyl siloxane) surfaces showed efficiency in reducing bovine serum albumin adsorption and in inhibiting bacteria adhesion and biofilm formation. The copolymer brushes also demonstrated excellent bactericidal function against gram-positive (Staphylococcus aureus) bacteria measured by bacteria live/dead staining and shake-flask culture methods. The surface biocompatibility was evaluated by morphology and activity measurement with human lens epithelial cells in vitro. The achievement of the p (DMAEMA+-co-MPC) copolymer brush coating with nonfouling, bactericidal, and bacteria corpse release properties can be used to modify intraocular lenses. PMID:28053527

Conceptualization, Development and Validation of an Instrument for Investigating Elements of Undergraduate Physics Laboratory Learning Environments: The UPLLES (Undergraduate Physics Laboratory Learning Environment Survey)

ERIC Educational Resources Information Center

Thomas, Gregory P; Meldrum, Al; Beamish, John

2013-01-01

First-year undergraduate physics laboratories are important physics learning environments. However, there is a lack of empirically informed literature regarding how students perceive their overall laboratory learning experiences. Recipe formats persist as the dominant form of instructional design in these sites, and these formats do not adequately…

Influence of Artisan Bakery- or Laboratory-Propagated Sourdoughs on the Diversity of Lactic Acid Bacterium and Yeast Microbiotas

PubMed Central

Minervini, Fabio; Lattanzi, Anna; De Angelis, Maria; Gobbetti, Marco

2012-01-01

Seven mature type I sourdoughs were comparatively back-slopped (80 days) at artisan bakery and laboratory levels under constant technology parameters. The cell density of presumptive lactic acid bacteria and related biochemical features were not affected by the environment of propagation. On the contrary, the number of yeasts markedly decreased from artisan bakery to laboratory propagation. During late laboratory propagation, denaturing gradient gel electrophoresis (DGGE) showed that the DNA band corresponding to Saccharomyces cerevisiae was no longer detectable in several sourdoughs. Twelve species of lactic acid bacteria were variously identified through a culture-dependent approach. All sourdoughs harbored a certain number of species and strains, which were dominant throughout time and, in several cases, varied depending on the environment of propagation. As shown by statistical permutation analysis, the lactic acid bacterium populations differed among sourdoughs propagated at artisan bakery and laboratory levels. Lactobacillus plantarum, Lactobacillus sakei, and Weissella cibaria dominated in only some sourdoughs back-slopped at artisan bakeries, and Leuconostoc citreum seemed to be more persistent under laboratory conditions. Strains of Lactobacillus sanfranciscensis were indifferently found in some sourdoughs. Together with the other stable species and strains, other lactic acid bacteria temporarily contaminated the sourdoughs and largely differed between artisan bakery and laboratory levels. The environment of propagation has an undoubted influence on the composition of sourdough yeast and lactic acid bacterium microbiotas. PMID:22635989

Impact of feathers and feather follicles on broiler carcass bacteria.

PubMed

Cason, J A; Hinton, A; Buhr, R J

2004-08-01

Genetically featherless and feathered broiler siblings were used to test the contribution of feathers and feather follicles to the numbers of aerobic bacteria, Escherichia coli, and Campylobacter in whole-carcass rinse samples taken immediately after carcasses were defeathered for 30 or 60 s. Numbers of spoilage bacteria were counted after the same fully processed carcasses were stored for 1 wk at 2 degrees C. In each of 3 replications, twenty-eight 11-wk-old, mixed-sex, genetically featherless or feathered broilers were processed in a laboratory processing facility. Immediately after individual defeathering in a mechanical picker, carcasses were sampled using a carcass rinse technique. Carcasses were eviscerated, immersion chilled at 2 degrees C for 30 min, individually bagged, and stored for 1 wk at 2 degrees C, after which all carcasses were rinsed again, and spoilage bacteria in the rinsate were enumerated. There were no significant differences (P < or = 0.05) between the featherless and feathered broilers in numbers of aerobic bacteria, E. coli, and Campylobacter in rinse samples taken immediately after defeathering and no differences between carcasses picked for 30 or 60 s. There were no differences in numbers of spoilage bacteria after 1 wk of refrigeration for any of the feather presence-picking length combinations. Although the defeathering step in poultry processing has been identified as an opportunity for bacterial contamination from the intestinal tract and cross-contamination between carcasses, the presence of feathers and feather follicles does not make a significant difference in carcass bacterial contamination immediately after defeathering or in spoilage bacteria after 1 wk of refrigeration.

Isolation and Molecular Detection of Gram Negative Bacteria Causing Urinary Tract Infection in Patients Referred to Shahrekord Hospitals, Iran.

PubMed

Tajbakhsh, Elahe; Tajbakhsh, Sara; Khamesipour, Faham

2015-05-01

Urinary Tract Infections (UTI), and their complications, cause serious health problems, which affect millions of people every year. Infections of the urinary tract are the second most common type of infection in the body and approximately 20% of women are especially prone to UTIs for reasons not yet well understood. Urinary Tract Infections in men are not as common as in women yet can be very serious when they do occur. Accurate identification of bacterial isolates is an essential task of the clinical microbiology laboratory. The purpose of this study was to determine the incidence and variety of the causative microbial agents of UTIs in patients who had referred to a medical laboratory of Kashani and Hajar hospital in Shahrekord, Iran. In this cross-sectional study 147 urine samples of patients (urine test results were positive for UTIs) were examined during April to September 2013. A total of 147 urine samples of patients with clinical symptoms of UTI who had been referred to a medical laboratory of Kashani and Hajar hospital in Shahrekord (Iran), were collected and processed immediately for laboratory analysis. Escherichia coli was identified as the most common causative agent of UTIs (51.70% of total isolates in both sexes), followed by Klebsiella pneumoniae (K. Pneumoniae) (16.32%). Frequency of Proteus spp., Acinetobacter spp., Entrobacter spp., Citrobacter spp., Pseudomonas aeruginosa (P. aeruginosa) and Providencia spp. was 10.88%, 6.12%, 5.44%, 4.08%, 3.40% and 2.04%, respectively. Statistical analysis by Fisher exact test showed that there was no significant relationship between the type of bacteria and gender (P > 0.05). Chi square test showed that there was no significant relationship between the type of bacteria and the use of catheter and age group (P > 0.05). However, there was a significant relationship between the type of bacteria and the history of hospitalization (P > 0.05). Our findings implied that a wide range of bacteria could be involved in

GC/IR computer-aided identification of anaerobic bacteria

NASA Astrophysics Data System (ADS)

Ye, Hunian; Zhang, Feng S.; Yang, Hua; Li, Zhu; Ye, Song

1993-09-01

A new method was developed to identify anaerobic bacteria by using pattern recognition. The method is depended on GC / JR data. The system is intended for use as a precise rapid and reproduceable aid in the identification of unknown isolates. Key Words: Anaerobic bacteria Pattern recognition Computeraided identification GC / JR 1 . TNTRODUCTTON A major problem in the field of anaerobic bacteriology is the difficulty in accurately precisely and rapidly identifying unknown isolates. Tn the proceedings of the Third International Symposium on Rapid Methods and Automation in Microbiology C. M. Moss said: " Chromatographic analysis is a new future for clinical microbiology" . 12 years past and so far it seems that this is an idea whose time has not get come but it close. Now two major advances that have brought the technology forword in terms ofmaking it appropriate for use in the clinical laboratory can aldo be cited. One is the development and implementation of fused silica capillary columns. In contrast to packed columns and those of'' greater width these columns allow reproducible recovery of hydroxey fatty acids with the same carbon chain length. The second advance is the efficient data processing afforded by modern microcomputer systems. On the other hand the practical steps for sample preparation also are an advance in the clinical laboratory. Chromatographic Analysis means mainly of analysis of fatty acids. The most common

KETENE FORMATION IN INTERSTELLAR ICES: A LABORATORY STUDY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hudson, Reggie L.; Loeffler, Mark J., E-mail: Reggie.Hudson@NASA.gov

2013-08-20

The formation of ketene (H{sub 2}CCO, ethenone) in polar and apolar ices was studied with in situ 0.8 MeV proton irradiation, far-UV photolysis, and infrared spectroscopic analyses at 10-20 K. Using isotopically enriched reagents, unequivocal evidence was obtained for ketene synthesis in H{sub 2}O-rich and CO{sub 2}-rich ices, and several reaction products were identified. Results from scavenging experiments suggested that ketene was formed by free-radical pathways, as opposed to acid-base processes or redox reactions. Finally, we use our results to draw conclusions about the formation and stability of ketene in the interstellar medium.

Spatial Control of Bacteria Using Screen Printing

PubMed Central

Moon, Soonhee; Fritz, Ian L.; Singer, Zakary S.

2016-01-01

Abstract Synthetic biology has led to advances in both our understanding and engineering of genetic circuits that affect spatial and temporal behaviors in living cells. A growing array of native and synthetic circuits such as oscillators, pattern generators, and cell–cell communication systems has been studied, which exhibit spatiotemporal properties. To better understand the design principles of these genetic circuits, there is a need for versatile and precise methods for patterning cell populations in various configurations. In this study, we develop a screen printing methodology to pattern bacteria on agar, glass, and paper surfaces. Initially, we tested three biocompatible resuspension media with appropriate rheological properties for screen printing. Using microscopy, we characterized the resolution and bleed of bacteria screen prints on agar and glass surfaces, obtaining resolutions as low as 188 μm. Next, we engineered bacterial strains producing visible chromoproteins analogous to the cyan, magenta, and yellow subtractive color system for the creation of multicolored bacteria images. Using this system, we printed distinct populations in overlapping or interlocking designs on both paper and agar substrates. These proof-of-principle experiments demonstrated how the screen printing method could be used to study microbial community interactions and pattern formation of biofilms at submillimeter length scales. Overall, our approach allows for rapid and precise prototyping of patterned bacteria species that will be useful in the understanding and engineering of spatiotemporal behaviors in microbial communities. PMID:29577061

Radionuclides, inorganic constitutents, organic compounds, and bacteria in water from selected wells and springs from the southern boundary of the Idaho National Engineering Laboratory to the Hagerman Area, Idaho, 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartholomay, R.C.; Edwards, D.D.; Campbell, L.J.

1994-11-01

The U.S. Geological Survey and the Idaho Department of Water Resources, in response to a request from the U.S. Department of Energy, sampled 18 sites as part of a long-term project to monitor water quality of the Snake River Plain aquifer from the southern boundary of the Idaho National Engineering Laboratory to the Hagerman area. Water samples were collected and analyzed for selected radionuclides, inorganic constituents, organic compounds, and bacteria. The samples were collected from 13 irrigation wells, 1 domestic well, 1 spring, 2 stock wells, and 1 public supply well. Quality assurance samples also were collected and analyzed. Nonemore » of the samples analyzed for radionuclides, inorganic constituents, or organic compounds exceeded the established maximum contaminant levels for drinking water. Most of the radionuclide and inorganic constituent concentrations exceeded their respective reporting levels. Most of the samples analyzed for surfactants and dissolved organic carbon had concentrations that exceeded their reporting levels. None of the samples contained reportable concentrations of purgeable organic compounds or pesticides. Total coliform bacteria was present in nine samples.« less

Vanadium removal from LD converter slag using bacteria and fungi.

PubMed

Mirazimi, S M J; Abbasalipour, Z; Rashchi, F

2015-04-15

Removal of vanadium from Linz-Donawits (LD) converter slag was investigated by means of three different species of microbial systems: Acidithiobacillus thiooxidans (autotrophic bacteria), Pseudomonas putida (heterotrophic bacteria) and Aspergillus niger (fungi). The bioleaching process was carried out in both one-step and two-step process and the leaching efficiencies in both cases were compared. Formation of inorganic and organic acids during the leaching process caused mobilization of vanadium. In order to reduce toxic effects of the metal species on the above mentioned microorganisms, a prolonged adaptation process was performed. Both bacteria, A. thiooxidans and P. putida were able to remove more than 90% of vanadium at slag concentrations of 1-5 g L(-1) after 15 days. Also, the maximum achievable vanadium removal in the fungal system was approximately 92% at a slag concentration of 1 g L(-1) after 22 days. Copyright © 2015 Elsevier Ltd. All rights reserved.

Swimming motion of rod-shaped magnetotactic bacteria: the effects of shape and growing magnetic moment

PubMed Central

Kong, Dali; Lin, Wei; Pan, Yongxin; Zhang, Keke

2014-01-01

We investigate the swimming motion of rod-shaped magnetotactic bacteria affiliated with the Nitrospirae phylum in a viscous liquid under the influence of an externally imposed, time-dependent magnetic field. By assuming that fluid motion driven by the translation and rotation of a swimming bacterium is of the Stokes type and that inertial effects of the motion are negligible, we derive a new system of the twelve coupled equations that govern both the motion and orientation of a swimming rod-shaped magnetotactic bacterium with a growing magnetic moment in the laboratory frame of reference. It is revealed that the initial pattern of swimming motion can be strongly affected by the rate of the growing magnetic moment. It is also revealed, through comparing mathematical solutions of the twelve coupled equations to the swimming motion observed in our laboratory experiments with rod-shaped magnetotactic bacteria, that the laboratory trajectories of the swimming motion can be approximately reproduced using an appropriate set of the parameters in our theoretical model. PMID:24523716

Enrichment of acetogenic bacteria in high rate anaerobic reactors under mesophilic and thermophilic conditions.

PubMed

Ryan, P; Forbes, C; McHugh, S; O'Reilly, C; Fleming, G T A; Colleran, E

2010-07-01

The objective of the current study was to expand the knowledge of the role of acetogenic Bacteria in high rate anaerobic digesters. To this end, acetogens were enriched by supplying a variety of acetogenic growth supportive substrates to two laboratory scale high rate upflow anaerobic sludge bed (UASB) reactors operated at 37 degrees C (R1) and 55 degrees C (R2). The reactors were initially fed a glucose/acetate influent. Having achieved high operational performance and granular sludge development and activity, both reactors were changed to homoacetogenic bacterial substrates on day 373 of the trial. The reactors were initially fed with sodium vanillate as a sole substrate. Although % COD removal indicated that the 55 degrees C reactor out performed the 37 degrees C reactor, effluent acetate levels from R2 were generally higher than from R1, reaching values as high as 5023 mg l(-1). Homoacetogenic activity in both reactors was confirmed on day 419 by specific acetogenic activity (SAA) measurement, with higher values obtained for R2 than R1. Sodium formate was introduced as sole substrate to both reactors on day 464. It was found that formate supported acetogenic activity at both temperatures. By the end of the trial, no specific methanogenic activity (SMA) was observed against acetate and propionate indicating that the methane produced was solely by hydrogenotrophic Archaea. Higher SMA and SAA values against H(2)/CO(2) suggested development of a formate utilising acetogenic population growing in syntrophy with hydrogenotrophic methanogens. Throughout the formate trial, the mesophilic reactor performed better overall than the thermophilic reactor. Copyright 2010 Elsevier Ltd. All rights reserved.

A Simple Method for Assessment of MDR Bacteria for Over-Expressed Efflux Pumps

PubMed Central

Martins, Marta; McCusker, Matthew P; Viveiros, Miguel; Couto, Isabel; Fanning, Séamus; Pagès, Jean-Marie; Amaral, Leonard

2013-01-01

It is known that bacteria showing a multi-drug resistance phenotype use several mechanisms to overcome the action of antibiotics. As a result, this phenotype can be a result of several mechanisms or a combination of thereof. The main mechanisms of antibiotic resistance are: mutations in target genes (such as DNA gyrase and topoisomerase IV); over-expression of efflux pumps; changes in the cell envelope; down regulation of membrane porins, and modified lipopolysaccharide component of the outer cell membrane (in the case of Gram-negative bacteria). In addition, adaptation to the environment, such as quorum sensing and biofilm formation can also contribute to bacterial persistence. Due to the rapid emergence and spread of bacterial isolates showing resistance to several classes of antibiotics, methods that can rapidly and efficiently identify isolates whose resistance is due to active efflux have been developed. However, there is still a need for faster and more accurate methodologies. Conventional methods that evaluate bacterial efflux pump activity in liquid systems are available. However, these methods usually use common efflux pump substrates, such as ethidium bromide or radioactive antibiotics and therefore, require specialized instrumentation, which is not available in all laboratories. In this review, we will report the results obtained with the Ethidium Bromide-agar Cartwheel method. This is an easy, instrument-free, agar based method that has been modified to afford the simultaneous evaluation of as many as twelve bacterial strains. Due to its simplicity it can be applied to large collections of bacteria to rapidly screen for multi-drug resistant isolates that show an over-expression of their efflux systems. The principle of the method is simple and relies on the ability of the bacteria to expel a fluorescent molecule that is substrate for most efflux pumps, ethidium bromide. In this approach, the higher the concentration of ethidium bromide required to

Ethyl Carbamate Formation Regulated by Lactic Acid Bacteria and Nonconventional Yeasts in Solid-State Fermentation of Chinese Moutai-Flavor Liquor.

PubMed

Du, Hai; Song, Zhewei; Xu, Yan

2018-01-10

This study aimed to identify specific microorganisms related to the formation of precursors of EC (ethyl carbamate) in the solid-state fermentation of Chinese Moutai-flavor liquor. The EC content was significantly correlated with the urea content during the fermentation process (R 2 = 0.772, P < 0.01). Differences in urea production and degradation were found at both species and functional gene levels by metatranscriptomic sequencing and culture-dependent analysis. Lactobacillus spp. could competitively degrade arginine through the arginine deiminase pathway with yeasts, and most Lactobacillus species were capable of degrading urea. Some dominant nonconventional yeasts, such as Pichia, Schizosaccharomyces, and Zygosaccharomyces species, were shown to produce low amounts of urea relative to Saccharomyces cerevisiae. Moreover, unusual urea degradation pathways (urea carboxylase, allophanate hydrolase, and ATP-independent urease) were identified. Our results indicate that EC precursor levels in the solid-state fermentation can be controlled using lactic acid bacteria and nonconventional yeasts.

Functional amyloid formation by Streptococcus mutans

PubMed Central

Oli, M. W.; Otoo, H. N.; Crowley, P. J.; Heim, K. P.; Nascimento, M. M.; Ramsook, C. B.; Lipke, P. N.

2012-01-01

Dental caries is a common infectious disease associated with acidogenic and aciduric bacteria, including Streptococcus mutans. Organisms that cause cavities form recalcitrant biofilms, generate acids from dietary sugars and tolerate acid end products. It has recently been recognized that micro-organisms can produce functional amyloids that are integral to biofilm development. We now show that the S. mutans cell-surface-localized adhesin P1 (antigen I/II, PAc) is an amyloid-forming protein. This conclusion is based on the defining properties of amyloids, including binding by the amyloidophilic dyes Congo red (CR) and Thioflavin T (ThT), visualization of amyloid fibres by transmission electron microscopy and the green birefringent properties of CR-stained protein aggregates when viewed under cross-polarized light. We provide evidence that amyloid is present in human dental plaque and is produced by both laboratory strains and clinical isolates of S. mutans. We provide further evidence that amyloid formation is not limited to P1, since bacterial colonies without this adhesin demonstrate residual green birefringence. However, S. mutans lacking sortase, the transpeptidase enzyme that mediates the covalent linkage of its substrates to the cell-wall peptidoglycan, including P1 and five other proteins, is not birefringent when stained with CR and does not form biofilms. Biofilm formation is inhibited when S. mutans is cultured in the presence of known inhibitors of amyloid fibrillization, including CR, Thioflavin S and epigallocatechin-3-gallate, which also inhibited ThT uptake by S. mutans extracellular proteins. Taken together, these results indicate that S. mutans is an amyloid-forming organism and suggest that amyloidogenesis contributes to biofilm formation by this oral microbe. PMID:23082034

Laboratory and Cloud Chamber Studies of Formation Processes and Properties of Atmospheric Ice Particles

NASA Astrophysics Data System (ADS)

Leisner, T.; Abdelmonem, A.; Benz, S.; Brinkmann, M.; Möhler, O.; Rzesanke, D.; Saathoff, H.; Schnaiter, M.; Wagner, R.

2009-04-01

The formation of ice in tropospheric clouds controls the evolution of precipitation and thereby influences climate and weather via a complex network of dynamical and microphysical processes. At higher altitudes, ice particles in cirrus clouds or contrails modify the radiative energy budget by direct interaction with the shortwave and longwave radiation. In order to improve the parameterisation of the complex microphysical and dynamical processes leading to and controlling the evolution of tropospheric ice, laboratory experiments are performed at the IMK Karlsruhe both on a single particle level and in the aerosol and cloud chamber AIDA. Single particle experiments in electrodynamic levitation lend themselves to the study of the interaction between cloud droplets and aerosol particles under extremely well characterized and static conditions in order to obtain microphysical parameters as freezing nucleation rates for homogeneous and heterogeneous ice formation. They also allow the observation of the freezing dynamics and of secondary ice formation and multiplication processes under controlled conditions and with very high spatial and temporal resolution. The inherent droplet charge in these experiments can be varied over a wide range in order to assess the influence of the electrical state of the cloud on its microphysics. In the AIDA chamber on the other hand, these processes are observable under the realistic dynamic conditions of an expanding and cooling cloud- parcel with interacting particles and are probed simultaneously by a comprehensive set of analytical instruments. By this means, microphysical processes can be studied in their complex interplay with dynamical processes as for example coagulation or particle evaporation and growth via the Bergeron - Findeisen process. Shortwave scattering and longwave absorption properties of the nucleating and growing ice crystals are probed by in situ polarised laser light scattering measurements and infrared extinction

Frequency of resistance and susceptible bacteria isolated from houseflies.

PubMed

Davari, B; Kalantar, E; Zahirnia, A; Moosa-Kazemi, Sh

2010-01-01

In this study, we determine the vector competence of Musca domestica with reference to the transmission of susceptible and resistance bacterial strains in hospitals and slaughter house in Sanandaj City, west Iran. Totally 908 houseflies were collected to isolate bacteria from their external body based on standard procedures.Antibiotic susceptibility testing was performed by Kirby-Bauer disc diffusion method on Mueller Hinton agar based on recommendations of CLSI (formerly the National Committee for Clinical Laboratory Standards). From collected houseflies, 366 bacteria species were isolated. The most common isolated bacterium at hospitals was Klebsiella pneumoniae 43.3% (n= 90) followed by Pseudomonas aeruginosa 37% (n= 77), while that of slaughterhouse was Proteus mirabilis. 29.1% (n= 46) followed by Citrobacter freundii 28.4% (n= 45). Among all the isolates from hospitals, cephalexin, chloramphenicol, ampicillin, and tetracycline, resistance rates were above 32.5% and gentamicin expressed the highest susceptibility among all the isolates from hospitals. It is worth to note that K. pneumoniae showed 61% and 44.5% resistance to cephalexin and chloramphenicol respectively. Similarly, all isolates from slaughterhouse were more than 28% and 30% resistant to cephalexin and chloramphenicol respectively. Surprisingly, among all the isolates, Citrobacter freundii were highly resistant to gentamicin. Houseflies collected from hospitals and slaughterhouse may be involved in the spread of drug resistant bacteria and may increase the potential of human exposure to drug resistant bacteria.

The use of colorimetric sensor arrays to discriminate between pathogenic bacteria.

PubMed

Lonsdale, Claire L; Taba, Brian; Queralto, Nuria; Lukaszewski, Roman A; Martino, Raymond A; Rhodes, Paul A; Lim, Sung H

2013-01-01

A colorimetric sensor array is a high-dimensional chemical sensor that is cheap, compact, disposable, robust, and easy to operate, making it a good candidate technology to detect pathogenic bacteria, especially potential bioterrorism agents like Yersinia pestis and Bacillus anthracis which feature on the Center for Disease Control and Prevention's list of potential biothreats. Here, a colorimetric sensor array was used to continuously monitor the volatile metabolites released by bacteria in solid media culture in an Advisory Committee on Dangerous Pathogen Containment Level 3 laboratory. At inoculum concentrations as low as 8 colony-forming units per plate, 4 different bacterial species were identified with 100% accuracy using logistic regression to classify the kinetic profile of sensor responses to culture headspace gas. The sensor array was able to further discriminate between different strains of the same species, including 5 strains of Yersinia pestis and Bacillus anthracis. These preliminary results suggest that disposable colorimetric sensor arrays can be an effective, low-cost tool to identify pathogenic bacteria.

Spectrophotometric Determination of 6-Propyl-2-Thiouracil in Pharmaceutical Formulations Based on Prussian Blue Complex Formation: An Undergraduate Instrumental Analysis Laboratory Experiment

ERIC Educational Resources Information Center

Zakrzewski, Robert; Skowron, Monika; Ciesielski, Witold; Rembisz, Zaneta

2016-01-01

The laboratory experiment challenges students to determine 6-propyl-2-thiouracil (PTU) based on Prussian blue complex formation. Prussian blue is formed by ferricyanide and Fe(II) ions which are generated in situ from Fe(III) ions reduced by PTU. The absorbance of this product was measured at a wavelength of 840 nm, after a reaction time of 30…

Kinetic analysis of strains of lactic acid bacteria and acetic acid bacteria in cocoa pulp simulation media toward development of a starter culture for cocoa bean fermentation.

PubMed

Lefeber, Timothy; Janssens, Maarten; Camu, Nicholas; De Vuyst, Luc

2010-12-01

The composition of cocoa pulp simulation media (PSM) was optimized with species-specific strains of lactic acid bacteria (PSM-LAB) and acetic acid bacteria (PSM-AAB). Also, laboratory fermentations were carried out in PSM to investigate growth and metabolite production of strains of Lactobacillus plantarum and Lactobacillus fermentum and of Acetobacter pasteurianus isolated from Ghanaian cocoa bean heap fermentations, in view of the development of a defined starter culture. In a first step, a selection of strains was made out of a pool of strains of these LAB and AAB species, obtained from previous studies, based on their fermentation kinetics in PSM. Also, various concentrations of citric acid in the presence of glucose and/or fructose (PSM-LAB) and of lactic acid in the presence of ethanol (PSM-AAB) were tested. These data could explain the competitiveness of particular cocoa-specific strains, namely, L. plantarum 80 (homolactic and acid tolerant), L. fermentum 222 (heterolactic, citric acid fermenting, mannitol producing, and less acid tolerant), and A. pasteurianus 386B (ethanol and lactic acid oxidizing, acetic acid overoxidizing, acid tolerant, and moderately heat tolerant), during the natural cocoa bean fermentation process. For instance, it turned out that the capacity to use citric acid, which was exhibited by L. fermentum 222, is of the utmost importance. Also, the formation of mannitol was dependent not only on the LAB strain but also on environmental conditions. A mixture of L. plantarum 80, L. fermentum 222, and A. pasteurianus 386B can now be considered a mixed-strain starter culture for better controlled and more reliable cocoa bean fermentation processes.

Laboratory and Numerical Modeling of Smoke Characteristics for Superfog Formation

NASA Astrophysics Data System (ADS)

Bartolome, C.; Lu, V.; Tsui, K.; Princevac, M.; Venkatram, A.; Mahalingam, S.; Achtemeier, G.; Weise, D.

2011-12-01

Land management techniques in wildland areas include prescribed fires to promote biodiversity and reduce risk of severe wildfires across the United States. Several fatal car pileups have been associated with smoke-related visibility reduction from prescribed burns. Such events have occurred in year 2000 on the interstate highways I-10 and I-95, 2001 on the I-4, 2006 on the I-95, and 2008 on the I-4 causing numerous fatalities, injuries, and damage to property. In some of the cases visibility reduction caused by smoke and fog combinations traveling over roadways have been reported to be less than 3 meters, defined as superfog. Our research focuses on delineating the conditions that lead to formation of the rare phenomena of superfog and creating a tool to enable land managers to effectively plan prescribed burns and prevent tragic events. It is hypothesized that the water vapor from combustion, live fuels, soil moisture, and ambient air condense onto the cloud condensation nuclei (CCN) particles emitted from low intensity smoldering fires. Physical and numerical modeling has been used to investigate these interactions. A physical model in the laboratory has been developed to characterize the properties of smoke resulting from smoldering pine needle litters at the PSW Forest Service in Riverside, CA. Temporal measurements of temperature, relative humidity, sensible heat flux, radiation heat flux, convective heat flux, particulate matter concentrations and visibilities have been measured for specific cases. The size distribution and number concentrations of the fog droplets formed inside the chamber by mixing cool dry and moist warm air masses to produce near superfog visibilities were measured by a Phase Doppler Particle Analyzer. Thermodynamic modeling of smoke and ambient air was conducted to estimate liquid water contents (LWC) available to condense into droplets and form significant reductions in visibility. The results show that LWC of less than 2 g m-3 can be

High prevalence of fastidious bacteria in 1520 cases of uveitis of unknown etiology.

PubMed

Drancourt, Michel; Berger, Pierre; Terrada, Céline; Bodaghi, Bahram; Conrath, John; Raoult, Didier; LeHoang, Phuc

2008-05-01

The etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. We conducted a prospective study to evaluate systematic screening for pathogens of uveitis. All patients with uveitis referred to the participating tertiary ophthalmology departments from January 2001 to September 2007 underwent intraocular and serum specimen collection. The standardized protocol for laboratory investigations included universal polymerase chain reaction (PCR)-based detection of any bacteria and mycoses, specific PCR-based detection of fastidious (difficult-to-grow) bacteria and herpes viruses, and culture of vitreous fluid. Sera were tested for fastidious bacteria. Among the 1321 included patients (1520 specimens), infection was diagnosed in 147 (11.1%) patients: 78 (53%) were caused by fastidious bacteria that included spirochetes, Bartonella species, intracellular bacteria (Chlamydia species, Rickettsia species, Coxiella burnetii), and Tropheryma whipplei; 18 by herpes viruses; and 9 by fungi. Bartonella quintana, Coxiella burnetii, Paracoccus yeei, Aspergillus oryzae, and Cryptococcus albidus were found to be associated with uveitis for the first time, to our knowledge. We recommend applying a 1-step diagnostic procedure that incorporates intraocular, specific microbial PCR with serum analyses in tertiary centers to determine the etiology of uveitis.

Aseptic laboratory techniques: plating methods.

PubMed

Sanders, Erin R

2012-05-11

Microorganisms are present on all inanimate surfaces creating ubiquitous sources of possible contamination in the laboratory. Experimental success relies on the ability of a scientist to sterilize work surfaces and equipment as well as prevent contact of sterile instruments and solutions with non-sterile surfaces. Here we present the steps for several plating methods routinely used in the laboratory to isolate, propagate, or enumerate microorganisms such as bacteria and phage. All five methods incorporate aseptic technique, or procedures that maintain the sterility of experimental materials. Procedures described include (1) streak-plating bacterial cultures to isolate single colonies, (2) pour-plating and (3) spread-plating to enumerate viable bacterial colonies, (4) soft agar overlays to isolate phage and enumerate plaques, and (5) replica-plating to transfer cells from one plate to another in an identical spatial pattern. These procedures can be performed at the laboratory bench, provided they involve non-pathogenic strains of microorganisms (Biosafety Level 1, BSL-1). If working with BSL-2 organisms, then these manipulations must take place in a biosafety cabinet. Consult the most current edition of the Biosafety in Microbiological and Biomedical Laboratories (BMBL) as well as Material Safety Data Sheets (MSDS) for Infectious Substances to determine the biohazard classification as well as the safety precautions and containment facilities required for the microorganism in question. Bacterial strains and phage stocks can be obtained from research investigators, companies, and collections maintained by particular organizations such as the American Type Culture Collection (ATCC). It is recommended that non-pathogenic strains be used when learning the various plating methods. By following the procedures described in this protocol, students should be able to: Perform plating procedures without contaminating media. Isolate single bacterial colonies by the streak

Aseptic Laboratory Techniques: Plating Methods

PubMed Central

Sanders, Erin R.

2012-01-01

Microorganisms are present on all inanimate surfaces creating ubiquitous sources of possible contamination in the laboratory. Experimental success relies on the ability of a scientist to sterilize work surfaces and equipment as well as prevent contact of sterile instruments and solutions with non-sterile surfaces. Here we present the steps for several plating methods routinely used in the laboratory to isolate, propagate, or enumerate microorganisms such as bacteria and phage. All five methods incorporate aseptic technique, or procedures that maintain the sterility of experimental materials. Procedures described include (1) streak-plating bacterial cultures to isolate single colonies, (2) pour-plating and (3) spread-plating to enumerate viable bacterial colonies, (4) soft agar overlays to isolate phage and enumerate plaques, and (5) replica-plating to transfer cells from one plate to another in an identical spatial pattern. These procedures can be performed at the laboratory bench, provided they involve non-pathogenic strains of microorganisms (Biosafety Level 1, BSL-1). If working with BSL-2 organisms, then these manipulations must take place in a biosafety cabinet. Consult the most current edition of the Biosafety in Microbiological and Biomedical Laboratories (BMBL) as well as Material Safety Data Sheets (MSDS) for Infectious Substances to determine the biohazard classification as well as the safety precautions and containment facilities required for the microorganism in question. Bacterial strains and phage stocks can be obtained from research investigators, companies, and collections maintained by particular organizations such as the American Type Culture Collection (ATCC). It is recommended that non-pathogenic strains be used when learning the various plating methods. By following the procedures described in this protocol, students should be able to: ● Perform plating procedures without contaminating media. ● Isolate single bacterial colonies by the

Biofilm inhibition of spoilage bacteria by Argentinean fruit juices with antihypertensive activity.

PubMed

Vallejo, Claudia V; Aredes-Fernández, Pedro A; Farías, Marta E; Rodríguez-Vaquero, María J

2013-01-01

Argentinean juices have been studied for their antihypertensive activity, the inhibition of bacteria biofilm formation and the effect on the viability of wine yeast. The influence of phenolic compounds on these activities was evaluated. These studies are the first step for the development of a new type of wine that includes grape must supplement with fruit juices with antihypertensive effect. All juices posses a high antihypertensive activity, higher than 50%. Strawberry juices and eureka lemon showed the highest activity, whereas clarified juices posses the lowest activity. All studied juices produce a high inhibition of bacteria biofilm formation, and the strawberry, orange and mandarin varieties not affect the growth or viability of yeast. Our results permit to conclude that it could be possible the use of these juices in a new type of wine or as a source of new antihypertensive agents for pharmaceutical industry.

Teaching Cardiovascular Integrations with Computer Laboratories.

ERIC Educational Resources Information Center

Peterson, Nils S.; Campbell, Kenneth B.

1985-01-01

Describes a computer-based instructional unit in cardiovascular physiology. The program (which employs simulated laboratory experimental techniques with a problem-solving format is designed to supplement an animal laboratory and to offer students an integrative approach to physiology through use of microcomputers. Also presents an overview of the…

The role of heterotrophic bacteria in iron-limited ocean ecosystems

NASA Astrophysics Data System (ADS)

Tortell, Philippe D.; Maldonado, Maria T.; Price, Nell M.

1996-09-01

IRON availability limits phytoplankton growth in large areas of the world's oceans1-3 and may influence the strength of the biological carbon pump4,5. Very little is known of the iron requirements of oceanic heterotrophic bacteria, which constitute up to 50% of the total particulate organic carbon in open ocean waters6,7 and are important in carbon cycling as remineralizers of dissolved organic matter and hence producers of CO2 (ref. 8). Here we report that oceanic bacteria contain more iron per biomass than phytoplankton. In the subarctic Pacific, they constitute a large fraction of biogenic iron and account for 20-45% of biological iron uptake. Bacterial iron quotas in the field are similar to those of iron-deficient laboratory cultures, which exhibit reduced elec-tron transport, slow growth, and low carbon growth efficiency. Heterotrophic bacteria therefore play a major role in the biogeo-chemical cycling of iron. In situ iron limitation of heterotrophic metabolism may have profound effects on carbon flux in the ocean.

Evaluation of portable air samplers for monitoring airborne culturable bacteria

NASA Technical Reports Server (NTRS)

Mehta, S. K.; Bell-Robinson, D. M.; Groves, T. O.; Stetzenbach, L. D.; Pierson, D. L.

2000-01-01

Airborne culturable bacteria were monitored at five locations (three in an office/laboratory building and two in a private residence) in a series of experiments designed to compare the efficiency of four air samplers: the Andersen two-stage, Burkard portable, RCS Plus, and SAS Super 90 samplers. A total of 280 samples was collected. The four samplers were operated simultaneously, each sampling 100 L of air with collection on trypticase soy agar. The data were corrected by applying positive hole conversion factors for the Burkard portable, Andersen two-stage, and SAS Super 90 air samplers, and were expressed as log10 values prior to statistical analysis by analysis of variance. The Burkard portable air sampler retrieved the highest number of airborne culturable bacteria at four of the five sampling sites, followed by the SAS Super 90 and the Andersen two-stage impactor. The number of bacteria retrieved by the RCS Plus was significantly less than those retrieved by the other samplers. Among the predominant bacterial genera retrieved by all samplers were Staphylococcus, Bacillus, Corynebacterium, Micrococcus, and Streptococcus.

Emergent pattern formation in an interstitial biofilm

NASA Astrophysics Data System (ADS)

Zachreson, Cameron; Wolff, Christian; Whitchurch, Cynthia B.; Toth, Milos

2017-01-01

Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the assumptions that rod-shaped bacteria furrow through a viscous environment and excrete extracellular polymeric substances which bias their rate of motion. Because the bacteria furrow through their environment, the substratum stiffness is a key control parameter behind the formation of distinct morphological patterns. By systematically varying this property (which we quantify with a stiffness coefficient γ ), we show that subtle changes in the substratum stiffness can give rise to a stable state characterized by a high degree of local order and long-range pattern formation. The ordered state exhibits characteristics typically associated with bacterial fitness advantages, even though it is induced by changes in environmental conditions rather than changes in biological parameters. Our findings are applicable to a broad range of biofilms and provide insights into the relationship between bacterial movement and their environment, and basic mechanisms behind self-organization of biophysical systems.

Theory and laboratory astrophysics

NASA Technical Reports Server (NTRS)

Schramm, David N.; Mckee, Christopher F.; Alcock, Charles; Allamandola, Lou; Chevalier, Roger A.; Cline, David B.; Dalgarno, Alexander; Elmegreen, Bruce G.; Fall, S. Michael; Ferland, Gary J.

1991-01-01

Science opportunities in the 1990's are discussed. Topics covered include the large scale structure of the universe, galaxies, stars, star formation and the interstellar medium, high energy astrophysics, and the solar system. Laboratory astrophysics in the 1990's is briefly surveyed, covering such topics as molecular, atomic, optical, nuclear and optical physics. Funding recommendations are given for the National Science Foundation, NASA, and the Department of Energy. Recommendations for laboratory astrophysics research are given.

Biofilm Formation Derived from Ambient Air and the Characteristics of Apparatus

NASA Astrophysics Data System (ADS)

Kanematsu, H.; Kougo, H.; Kuroda, D.; Itho, H.; Ogino, Y.; Yamamoto, Y.

2013-04-01

Biofilm is a kind of thin film on solidified matters, being derived from bacteria. Generally, planktonic bacteria float in aqueous environments, soil or air, most of which can be regarded as oligotrophic environments. Since they have to survive by instinct, they seek for nutrients that would exist on materials surfaces as organic matters. Therefore, bacteria attach materials surfaces reversibly. The attachment and detachment repeat for a while and finally, they attach on them irreversibly and the number of bacteria on them increases. At a threshold number, bacteria produce polymeric matters at the same time by quorum sensing mechanism and the biofilm produces on material surfaces. The biofilm produced in that way generally contains water (more than 80%), EPS (Exopolymeric Substance) and bacteria themselves. And they might bring about many industrial problems, fouling, corrosion etc. Therefore, it is very important for us to control and prevent the biofilm formation properly. However, it is generally very hard to produce biofilm experimentally and constantly in ambient atmosphere on labo scale. The authors invented an apparatus where biofilm could form on specimen's surfaces from house germs in the ambient air. In this experiment, we investigated the basic characteristics of the apparatus, reproducibility, the change of biofilm with experimental time, the quality change of water for biofilm formation and their significance for biofilm research.

A nitrous acid biosynthetic pathway for diazo group formation in bacteria.

PubMed

Sugai, Yoshinori; Katsuyama, Yohei; Ohnishi, Yasuo

2016-02-01

Although some diazo compounds have bioactivities of medicinal interest, little is known about diazo group formation in nature. Here we describe an unprecedented nitrous acid biosynthetic pathway responsible for the formation of a diazo group in the biosynthesis of the ortho-diazoquinone secondary metabolite cremeomycin in Streptomyces cremeus. This finding provides important insights into the biosynthetic pathways not only for diazo compounds but also for other naturally occurring compounds containing nitrogen-nitrogen bonds.

Force generation by groups of migrating bacteria

PubMed Central

Koch, Matthias D.; Liu, Guannan; Stone, Howard A.; Shaevitz, Joshua W.

2017-01-01

From colony formation in bacteria to wound healing and embryonic development in multicellular organisms, groups of living cells must often move collectively. Although considerable study has probed the biophysical mechanisms of how eukaryotic cells generate forces during migration, little such study has been devoted to bacteria, in particular with regard to the question of how bacteria generate and coordinate forces during collective motion. This question is addressed here using traction force microscopy. We study two distinct motility mechanisms of Myxococcus xanthus, namely, twitching and gliding. For twitching, powered by type-IV pilus retraction, we find that individual cells exert local traction in small hotspots with forces on the order of 50 pN. Twitching bacterial groups also produce traction hotspots, but with forces around 100 pN that fluctuate rapidly on timescales of <1.5 min. Gliding, the second motility mechanism, is driven by lateral transport of substrate adhesions. When cells are isolated, gliding produces low average traction on the order of 1 Pa. However, traction is amplified approximately fivefold in groups. Advancing protrusions of gliding cells push, on average, in the direction of motion. Together, these results show that the forces generated during twitching and gliding have complementary characters, and both forces have higher values when cells are in groups. PMID:28655845

Force generation by groups of migrating bacteria.

PubMed

Sabass, Benedikt; Koch, Matthias D; Liu, Guannan; Stone, Howard A; Shaevitz, Joshua W

2017-07-11

From colony formation in bacteria to wound healing and embryonic development in multicellular organisms, groups of living cells must often move collectively. Although considerable study has probed the biophysical mechanisms of how eukaryotic cells generate forces during migration, little such study has been devoted to bacteria, in particular with regard to the question of how bacteria generate and coordinate forces during collective motion. This question is addressed here using traction force microscopy. We study two distinct motility mechanisms of Myxococcus xanthus , namely, twitching and gliding. For twitching, powered by type-IV pilus retraction, we find that individual cells exert local traction in small hotspots with forces on the order of 50 pN. Twitching bacterial groups also produce traction hotspots, but with forces around 100 pN that fluctuate rapidly on timescales of <1.5 min. Gliding, the second motility mechanism, is driven by lateral transport of substrate adhesions. When cells are isolated, gliding produces low average traction on the order of 1 Pa. However, traction is amplified approximately fivefold in groups. Advancing protrusions of gliding cells push, on average, in the direction of motion. Together, these results show that the forces generated during twitching and gliding have complementary characters, and both forces have higher values when cells are in groups.

X-ray photoelectron spectroscopic evidence for bacteria-enhanced dissolution of hornblende

NASA Astrophysics Data System (ADS)

Kalinowski, B. E.; Liermann, L. J.; Brantley, S. L.; Barnes, A.; Pantano, C. G.

2000-04-01

An Arthrobacter species capable of extracting Fe from hornblende was isolated from a soil from the Adirondacks, NY (USA). This bacteria isolate, used in batch experiments with hornblende, accelerated the release of Fe from hornblende without measurably affecting Al release. The isolate produces both low molecular weight organic acids (LMWOA) and a catecholate siderophore. Polished hornblende (glass and crystal) discs were analyzed with X-ray photoelectron spectroscopy (XPS) before and after incubation with growing Arthrobacter sp. to investigate whether the bacteria caused a distinguishable chemical signature on the upper 100 Å of mineral surface. After removal of the arthrobacter grown on hornblende crystal or glass substrates using lysozyme, XPS revealed surface depletion of Fe for samples grown for several days in buffered (crystal) and unbuffered (crystal and glass) media. Fe/Si ratios of hornblende surfaces dissolved under biotic conditions are significantly lower than Fe/Si ratios on surfaces dissolved under abiotic conditions for similar amounts of time. Enhanced Fe release and the formation of Fe-depleted surfaces is inferred to be caused by catechol complexation at the mineral surface. Because natural siderophore was not isolated in sufficient quantities to run bacteria-free leaching experiments, parallel investigations were run with a commercially available siderophore (desferrioxamine B). Desferrioxamine B was observed to enhance release of Fe, Si, and Al from hornblende both with and without added bacteria. Formation of desferrioxamine-Fe surface complexes were probed by studying the multiple splitting and shift in intensities of the N 1s line analyzed by XPS on siderophore ± Fe on gold surfaces and siderophore + hornblende crystal surfaces. Based upon the observed formation of an hydroxamate (desferrioxamine) surface complex on hornblende, we infer that catecholate siderophores, such as those produced by the arthrobacter, also complex on the

Laboratory Studies on the Formation of Carbon-Bearing Molecules in Extraterrestrial Environments: From the Gas Phase to the Solid State

NASA Technical Reports Server (NTRS)

Jamieson, C. S.; Guo, Y.; Gu, X.; Zhang, F.; Bennett, C. J.; Kaiser, R. I.

2006-01-01

A detailed knowledge of the formation of carbon-bearing molecules in interstellar ices and in the gas phase of the interstellar medium is of paramount interest to understand the astrochemical evolution of extraterrestrial environments (1). This research also holds strong implications to comprehend the chemical processing of Solar System environments such as icy planets and their moons together with the atmospheres of planets and their satellites (2). Since the present composition of each interstellar and Solar System environment reflects the matter from which it was formed and the processes which have changed the chemical nature since the origin (solar wind, planetary magnetospheres, cosmic ray exposure, photolysis, chemical reactions), a detailed investigation of the physicochemical mechanisms altering the pristine environment is of paramount importance to grasp the contemporary composition. Once these underlying processes have been unraveled, we can identify those molecules, which belonged to the nascent setting, distinguish molecular species synthesized in a later stage, and predict the imminent chemical evolution of, for instance, molecular clouds. Laboratory experiments under controlled physicochemical conditions (temperature, pressure, chemical composition, high energy components) present ideal tools for simulating the chemical evolution of interstellar and Solar System environments. Here, laboratory experiments can predict where and how (reaction mechanisms; chemicals necessary) in extraterrestrial environments and in the interstellar medium complex, carbon bearing molecules can be formed on interstellar grains and in the gas phase. This paper overviews the experimental setups utilized in our laboratory to mimic the chemical processing of gas phase and solid state (ices) environments. These are a crossed molecular beams machine (3) and a surface scattering setup (4). We also present typical results of each setup (formation of amino acids, aldehydes, epoxides

Noncontact Cohesive Swimming of Bacteria in Two-Dimensional Liquid Films.

PubMed

Li, Ye; Zhai, He; Sanchez, Sandra; Kearns, Daniel B; Wu, Yilin

2017-07-07

Bacterial swimming in confined two-dimensional environments is ubiquitous in nature and in clinical settings. Characterizing individual interactions between swimming bacteria in 2D confinement will help to understand diverse microbial processes, such as bacterial swarming and biofilm formation. Here we report a novel motion pattern displayed by flagellated bacteria in 2D confinement: When two nearby cells align their moving directions, they tend to engage in cohesive swimming without direct cell body contact, as a result of hydrodynamic interaction but not flagellar intertwining. We further found that cells in cohesive swimming move with higher directional persistence, which can increase the effective diffusivity of cells by ∼3 times as predicted by computational modeling. As a conserved behavior for peritrichously flagellated bacteria, cohesive swimming in 2D confinement may be key to collective motion and self-organization in bacterial swarms; it may also promote bacterial dispersal in unsaturated soils and in interstitial space during infections.

Unexpected photoreactivation of Vibrio harveyi bacteria living in ionization environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alifano, P.; Tala, A.; Tredici, S. M.

2011-05-15

Bacteria undergoing environmental effects is extremely interesting for structural, mechanistic, and evolutionary implications. Luminescent bacteria that have evolved in a specific ambient have developed particular responses and their behavior can give us new suggestions on the task and production of luciferina proteins. To analyze the UV interaction under controlled laboratory conditions, we used photoluminescent bacterial strains belonging to a new species evolutionarily close to Vibrio harveyi sampled from a coastal cave with a high radon content that generates ionizing radiation. The survival of the bacterial strains was analyzed, in the light and in the dark, following a variety of genotoxicmore » treatments including UV radiation exposure. The strains were irradiated by a germicide lamp. The results demonstrated that most of the strains exhibited a low rate of survival after the UV exposure. After irradiation by visible light following the UV exposure, all strains showed a high capability of photoreactivation when grown. This capability was quite unexpected because these bacteria were sampled from a dark ambient without UV radiation. This leads us to hypothesize that the photoreactivation in these bacteria might have been evolved to repair DNA lesions also induced by different radiation sources other than UV (e.g., x-ray) and that the luminescent bacteria might use their own light emission to carry out the photoreactivation. The high capability of photoreactivation of these bacteria was also justified by the results of deconvolution. The deconvolution was applied to the emission spectra and it was able to show evidence of different light peaks. The presence of the visible peak could control the photolysis enzyme.« less

Small Molecule Inhibitors of AI-2 Signaling in Bacteria: State-of-the-Art and Future Perspectives for Anti-Quorum Sensing Agents

PubMed Central

Guo, Min; Gamby, Sonja; Zheng, Yue; Sintim, Herman O.

2013-01-01

Bacteria respond to different small molecules that are produced by other neighboring bacteria. These molecules, called autoinducers, are classified as intraspecies (i.e., molecules produced and perceived by the same bacterial species) or interspecies (molecules that are produced and sensed between different bacterial species). AI-2 has been proposed as an interspecies autoinducer and has been shown to regulate different bacterial physiology as well as affect virulence factor production and biofilm formation in some bacteria, including bacteria of clinical relevance. Several groups have embarked on the development of small molecules that could be used to perturb AI-2 signaling in bacteria, with the ultimate goal that these molecules could be used to inhibit bacterial virulence and biofilm formation. Additionally, these molecules have the potential to be used in synthetic biology applications whereby these small molecules are used as inputs to switch on and off AI-2 receptors. In this review, we highlight the state-of-the-art in the development of small molecules that perturb AI-2 signaling in bacteria and offer our perspective on the future development and applications of these classes of molecules. PMID:23994835

Effect of Food Residues in Biofilm Formation on Stainless Steel and Polystyrene Surfaces by Salmonella enterica Strains Isolated from Poultry Houses.

PubMed

Paz-Méndez, Alba María; Lamas, Alexandre; Vázquez, Beatriz; Miranda, José Manuel; Cepeda, Alberto; Franco, Carlos Manuel

2017-11-29

Salmonella spp. is a major food-borne pathogen around the world. The ability of Salmonella to produce biofilm is one of the main obstacles in reducing the prevalence of these bacteria in the food chain. Most of Salmonella biofilm studies found in the literature used laboratory growth media. However, in the food chain, food residues are the principal source of nutrients of Salmonella . In this study, the biofilm formation, morphotype, and motility of 13 Salmonella strains belonging to three different subspecies and isolated from poultry houses was evaluated. To simulate food chain conditions, four different growth media (Tryptic Soy Broth at 1/20 dilution, milk at 1/20 dilution, tomato juice, and chicken meat juice), two different surfaces (stainless steel and polystyrene) and two temperatures (6 °C and 22 °C) were used to evaluate the biofilm formation. The morphotype, motility, and biofilm formation of Salmonella was temperature-dependent. Biofilm formation was significantly higher with 1/20 Tryptic Soy Broth in all the surfaces and temperatures tested, in comparison with the other growth media. The laboratory growth medium 1/20 Tryptic Soy Broth enhanced biofilm formation in Salmonella . This could explain the great differences in biofilm formation found between this growth medium and food residues. However, Salmonella strains were able to produce biofilm on the presence of food residues in all the conditions tested. Therefore, the Salmonella strain can use food residues to produce biofilm on common surfaces of the food chain. More studies combining more strains and food residues are necessary to fully understand the mechanism used by Salmonella to produce biofilm on the presence of these sources of nutrients.

Effect of Food Residues in Biofilm Formation on Stainless Steel and Polystyrene Surfaces by Salmonella enterica Strains Isolated from Poultry Houses

PubMed Central

Paz-Méndez, Alba María; Vázquez, Beatriz; Cepeda, Alberto; Franco, Carlos Manuel

2017-01-01

Salmonella spp. is a major food-borne pathogen around the world. The ability of Salmonella to produce biofilm is one of the main obstacles in reducing the prevalence of these bacteria in the food chain. Most of Salmonella biofilm studies found in the literature used laboratory growth media. However, in the food chain, food residues are the principal source of nutrients of Salmonella. In this study, the biofilm formation, morphotype, and motility of 13 Salmonella strains belonging to three different subspecies and isolated from poultry houses was evaluated. To simulate food chain conditions, four different growth media (Tryptic Soy Broth at 1/20 dilution, milk at 1/20 dilution, tomato juice, and chicken meat juice), two different surfaces (stainless steel and polystyrene) and two temperatures (6 °C and 22 °C) were used to evaluate the biofilm formation. The morphotype, motility, and biofilm formation of Salmonella was temperature-dependent. Biofilm formation was significantly higher with 1/20 Tryptic Soy Broth in all the surfaces and temperatures tested, in comparison with the other growth media. The laboratory growth medium 1/20 Tryptic Soy Broth enhanced biofilm formation in Salmonella. This could explain the great differences in biofilm formation found between this growth medium and food residues. However, Salmonella strains were able to produce biofilm on the presence of food residues in all the conditions tested. Therefore, the Salmonella strain can use food residues to produce biofilm on common surfaces of the food chain. More studies combining more strains and food residues are necessary to fully understand the mechanism used by Salmonella to produce biofilm on the presence of these sources of nutrients. PMID:29186017

The inhibitory effect of Thymus vulgaris extracts on the planktonic form and biofilm structures of six human pathogenic bacteria

PubMed Central

Mohsenipour, Zeinab; Hassanshahian, Mehdi

2015-01-01

Objective: Microorganisms are responsible for many problems in industry and medicine because of biofilm formation. Therefore, this study was aimed to examine the effect of Thymus vulgaris (T. vulgaris) extracts on the planktonic form and biofilm structures of six pathogenic bacteria. Materials and methods: Antimicrobial activities of the plant extracts against the planktonic form of the bacteria were determined using the disc diffusion method. MIC and MBC values were evaluated using macrobroth dilution technique. Anti-biofilm effects were assessed by microtiter plate method. Results: According to disc diffusion test (MIC and MBC), the ability of Thymus vulgaris (T. vulgaris ) extracts for inhibition of bacteria in planktonic form was confirmed. In dealing with biofilm structures, the inhibitory effect of the extracts was directly correlated to their concentration. Except for the inhibition of biofilm formation, efficacy of each extract was independent from type of solvent. Conclusion: According to the potential of Thymus vulgaris (T. vulgaris) extracts to inhibit the test bacteria in planktonic and biofilm form, it can be suggested that Thymus vulgaris (T. vulgaris) extracts can be applied as antimicrobial agents against the pathogenic bacteria particularly in biofilm forms. PMID:26442753

A 96-well-plate-based optical method for the quantitative and qualitative evaluation of Pseudomonas aeruginosa biofilm formation and its application to susceptibility testing.

PubMed

Müsken, Mathias; Di Fiore, Stefano; Römling, Ute; Häussler, Susanne

2010-08-01

A major reason for bacterial persistence during chronic infections is the survival of bacteria within biofilm structures, which protect cells from environmental stresses, host immune responses and antimicrobial therapy. Thus, there is concern that laboratory methods developed to measure the antibiotic susceptibility of planktonic bacteria may not be relevant to chronic biofilm infections, and it has been suggested that alternative methods should test antibiotic susceptibility within a biofilm. In this paper, we describe a fast and reliable protocol for using 96-well microtiter plates for the formation of Pseudomonas aeruginosa biofilms; the method is easily adaptable for antimicrobial susceptibility testing. This method is based on bacterial viability staining in combination with automated confocal laser scanning microscopy. The procedure simplifies qualitative and quantitative evaluation of biofilms and has proven to be effective for standardized determination of antibiotic efficiency on P. aeruginosa biofilms. The protocol can be performed within approximately 60 h.

Bioretention column study of bacteria community response to salt-enriched artificial stormwater.

PubMed

Endreny, Theodore; Burke, David J; Burchhardt, Kathleen M; Fabian, Mark W; Kretzer, Annette M

2012-01-01

Cold climate cities with green infrastructure depend on soil bacteria to remove nutrients from road salt-enriched stormwater. Our research examined how bacterial communities in laboratory columns containing bioretention media responded to varying concentrations of salt exposure from artificial stormwater and the effect of bacteria and salt on column effluent concentrations. We used a factorial design with two bacteria treatments (sterile, nonsterile) and three salt concentrations (935, 315, and 80 ppm), including a deionized water control. Columns were repeatedly saturated with stormwater or deionized and then drained throughout 5 wk, with the last week of effluent analyzed for water chemistry. To examine bacterial communities, we extracted DNA from column bioretention media at time 0 and at week 5 and used molecular profiling techniques to examine bacterial community changes. We found that bacterial community taxa changed between time 0 and week 5 and that there was significant separation between taxa among salt treatments. Bacteria evenness was significantly affected by stormwater treatment, but there were no differences in bacterial richness or diversity. Soil bacteria and salt treatments had a significant effect on the effluent concentration of NO, PO, Cu, Pb, and Zn based on ANOVA tests. The presence of bacteria reduced effluent NO and Zn concentrations by as much as 150 and 25%, respectively, while having a mixed effect on effluent PO concentrations. Our results demonstrate how stormwater can affect bacterial communities and how the presence of soil bacteria improves pollutant removal by green infrastructure. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Kinetic Analysis of Strains of Lactic Acid Bacteria and Acetic Acid Bacteria in Cocoa Pulp Simulation Media toward Development of a Starter Culture for Cocoa Bean Fermentation ▿

PubMed Central

Lefeber, Timothy; Janssens, Maarten; Camu, Nicholas; De Vuyst, Luc

2010-01-01

The composition of cocoa pulp simulation media (PSM) was optimized with species-specific strains of lactic acid bacteria (PSM-LAB) and acetic acid bacteria (PSM-AAB). Also, laboratory fermentations were carried out in PSM to investigate growth and metabolite production of strains of Lactobacillus plantarum and Lactobacillus fermentum and of Acetobacter pasteurianus isolated from Ghanaian cocoa bean heap fermentations, in view of the development of a defined starter culture. In a first step, a selection of strains was made out of a pool of strains of these LAB and AAB species, obtained from previous studies, based on their fermentation kinetics in PSM. Also, various concentrations of citric acid in the presence of glucose and/or fructose (PSM-LAB) and of lactic acid in the presence of ethanol (PSM-AAB) were tested. These data could explain the competitiveness of particular cocoa-specific strains, namely, L. plantarum 80 (homolactic and acid tolerant), L. fermentum 222 (heterolactic, citric acid fermenting, mannitol producing, and less acid tolerant), and A. pasteurianus 386B (ethanol and lactic acid oxidizing, acetic acid overoxidizing, acid tolerant, and moderately heat tolerant), during the natural cocoa bean fermentation process. For instance, it turned out that the capacity to use citric acid, which was exhibited by L. fermentum 222, is of the utmost importance. Also, the formation of mannitol was dependent not only on the LAB strain but also on environmental conditions. A mixture of L. plantarum 80, L. fermentum 222, and A. pasteurianus 386B can now be considered a mixed-strain starter culture for better controlled and more reliable cocoa bean fermentation processes. PMID:20889778

Production of pyroglutamic acid by thermophilic lactic acid bacteria in hard-cooked mini-cheeses.

PubMed

Mucchetti, G; Locci, F; Massara, P; Vitale, R; Neviani, E

2002-10-01

Pyroglutamic acid is present in high amounts (0.5g/ 100g) in many cheese varieties-and particularly in extensively ripened Italian cheeses such as Grana Padano and Parmigiano Reggiano. An in vivo model system for cooked mini-cheese production and ripening acceleration was set up to demonstrate the ability of thermophilic lactic acid bacteria, used as a starter, to produce pyroglutamic acid (pGlu). In mini-cheeses stored at 38 and 30 degrees C for up to 45 d, all starters tested produced different amounts of pGlu. In descending order of pGlu production, the bacteria analyzed were: Lactobacillus helveticus, Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactobacillus delbrueckii subsp. lactis. Evidence for the presence of glutamine to pGlu cyclase activity in lactic acid bacteria was provided. Cell lysates obtained from cultures of L. helveticus, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, and S. thermophilus showed the ability to cyclize glutamine to pGlu, resulting in processing yields from 1.4 to 30.3%, depending on the subspecies. Formation of pGlu from free glutamine appeared to be similar to that observed using a glutamine-glutamine dipeptide substrate. Under the experimental conditions applied, pGlu aminopeptidase activity was only detected in L. helveticus. Thus, pGlu formation in long-ripened cooked cheese may depend on the activity of thermophilic lactic acid bacteria.

Measurement of fluid dynamic loading on staphylococci bacteria bio-film structures using μPIV

NASA Astrophysics Data System (ADS)

Sherman, Erica; Moormeier, Derek; Bayles, Kenneth; Davidson, John; Ryu, Sangjin; Wei, Timothy

2013-11-01

Staphylococci bacteria are recognized as the most frequent cause of biofilm-associated infections. Although humans are regularly exposed to these bacteria without consequence, a localized infection can enter the bloodstream and lead to serious infections such as endocarditis, pneumonia, or toxic shock syndrome. The mechanics of staphylococci biofilm formation and dispersion through the bloodstream are not well known. It has recently been observed that under certain flow conditions, bacteria organize in tower-like structures which break and are transported downstream by the flow. The fundamental questions of interest are i) whether or not fluid mechanics plays a role in differentiating between film or tower formation and ii) whether or not the faulty towers are a bio-film propagation mechanism. This talk focuses on the application of μPIV to study this problem. Staphylococcus aureus bacteria were cultured in the Bioflux Fluxion square microchannel of a 65 by 65 um cross section, and subjected to a steady shear rate of 0.5 dynes. μPIV measurements were made to map the flow over and around a biofilm tower structure which occluded approximately 66% of the channel width. Data were recorded around the structure at a series of two dimensional planes, which when stacked vertically show a two dimensional flow field as a function of tower height. Measurements and control volume analysis will be presented quantifying forces acting on these structures.

Isolation, identification and characterization of lignin-degrading bacteria from Qinling, China.

PubMed

Yang, C-X; Wang, T; Gao, L-N; Yin, H-J; Lü, X

2017-12-01

Lignin is an aromatic heteropolymer forming a physical barrier and it is a big challenge in biomass utilization. This paper first investigated lignin-degradation bacteria from rotten wood in Qinling Mountain. Nineteen potential strains were selected and ligninolytic enzyme activities were determined over 84 h. Strains that had higher enzyme activities were selected. Further, the biodegradation of wheat straw lignin and alkali lignin was evaluated indicating that Burkholderia sp. H1 had the highest capability. It was confirmed by gel permeation chromatography and field emission scanning electron microscope that alkali lignin was depolymerized into small fragments. The degraded products were analysed using gas chromatography-mass spectrometry. The total ion chromatograph of products treated for 7 days showed the formation of aromatic compounds, an important intermediate from lignin degradation. Interestingly, they disappeared in 15 days while the aldehyde and ester compounds increased. The results suggest that the lignin-degrading bacteria are abundant in rotten wood and strain H1 has high potential to break down lignin. The diversity of lignin-degrading bacteria in Qinling Mountain is revealed. The study of Burkholderia sp. H1 expands the range of bacteria for lignin degradation and provides novel bacteria for application to lignocellulosic biomass. © 2017 The Society for Applied Microbiology.

Investigation of diverse bacteria in cloud water at Mt. Tai, China.

PubMed

Xu, Caihong; Wei, Min; Chen, Jianmin; Sui, Xiao; Zhu, Chao; Li, Jiarong; Zheng, Lulu; Sui, Guodong; Li, Weijun; Wang, Wenxing; Zhang, Qingzhu; Mellouki, Abdelwahid

2017-02-15

Bacteria are abundant in atmospheric water phase with the potential to influence atmospheric processes and human health, yet relatively little information is known about the bacterial characteristics at high altitudes. Here we investigated the bacterial community by high throughput sequencing in 24 cloud water samples collected from September 26 to October 31, at the summit of Mt. Tai (36°15' N, 117°06' E, 1534m a.s.l) in China. Diverse bacterial population were identified and the gram-negative bacteria contributed the majority of total bacteria including Proteobacteria (81.6%) and Bacteroidetes (3.9%), followed by gram-positive bacteria Firmicutes (7.1%) and Actinobacteria (2.3%). These gram-negative taxa mainly inhabited in leaf-surface and cold environments. Meanwhile bacteria involved in the cloud condensation nuclei and ice nuclei formation were observed such as Sphingomonas (6.7%), Pseudomonas (4.1%), and Bacillus (1.1%). In addition, Sphingmonas was more active than that in daytime and participated in the cloud chemistry process. Meanwhile O 3 and SO 2 critically contributed to the variation of bacterial community. It is the first report on the bacterial community structure of cloud water over Asian area. Our results can serve as an important reference for environmental scientists, and biologists. Copyright © 2016. Published by Elsevier B.V.

Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems.

PubMed

Marcus, Daniel N; Pinto, Ameet; Anantharaman, Karthik; Ruberg, Steven A; Kramer, Eva L; Raskin, Lutgarde; Dick, Gregory J

2017-04-01

Manganese (Mn) oxides are highly reactive minerals that influence the speciation, mobility, bioavailability and toxicity of a wide variety of organic and inorganic compounds. Although Mn(II)-oxidizing bacteria are known to catalyze the formation of Mn oxides, little is known about the organisms responsible for Mn oxidation in situ, especially in engineered environments. Mn(II)-oxidizing bacteria are important in drinking water systems, including in biofiltration and water distribution systems. Here, we used cultivation dependent and independent approaches to investigate Mn(II)-oxidizing bacteria in drinking water sources, a treatment plant and associated distribution system. We isolated 29 strains of Mn(II)-oxidizing bacteria and found that highly similar 16S rRNA gene sequences were present in all culture-independent datasets and dominant in the studied drinking water treatment plant. These results highlight a potentially important role for Mn(II)-oxidizing bacteria in drinking water systems, where biogenic Mn oxides may affect water quality in terms of aesthetic appearance, speciation of metals and oxidation of organic and inorganic compounds. Deciphering the ecology of these organisms and the factors that regulate their Mn(II)-oxidizing activity could yield important insights into how microbial communities influence the quality of drinking water. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples.

PubMed

Meir-Gruber, Lital; Manor, Yossi; Gefen-Halevi, Shiraz; Hindiyeh, Musa Y; Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples

PubMed Central

Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage. PMID:27780222

Impact of Flood Spates on Denitrifying Bacteria in Low Order Streams

NASA Astrophysics Data System (ADS)

Herrman, K.; Stokdyk, J.

2011-12-01

The impact of flood events on channel design, macroinvertebrates, and periphyton in stream ecosystems has been well studied. Little is known, however, about how flood spates affect microorganisms found in stream sediments. Denitrifying bacteria are beneficial organisms because they convert nitrates to nitrogen gas. Providing data that describes the impact of flood events on denitrifiers and the time required after the disturbance for the bacteria to recover are crucial in understanding nitrogen dynamics in stream ecosystems. Three low order streams in central Wisconsin, USA are being monitored during several flood spates during July and August of 2011. Discharge is being continuously monitored in all three streams and sediments are being collected before and after several flood events for laboratory assays. Specifically, sediments are being processed for denitrification rates using the acetylene inhibition technique, microbial biomass carbon using chloroform fumigation, and the quantification of denitrifying bacteria (i.e., nirS, nirK, and nosZ genes) using real-time quantitative PCR. Preliminary data show that within 36 hours after a 90 mm rain event, microbial biomass carbon in all three streams (580 μg C g sediment-1) significantly increased (F1,23 = 650 ± 140; p < 0.001) compared to microbial biomass during baseflow (200 ± 27 μg C g sediment-1). These initial results suggest that contrary to our expectations flood events enhance bacteria in stream sediments. Denitrification rates and quantification of denitrifying bacteria still need to be analyzed to determine if these specific bacteria follow a similar pattern or if the bacterial recolonization of stream sediments follows a unique pattern.

Antimicrobial effects of a new therapeutic liquid dentifrice formulation on oral bacteria including odorigenic species.

PubMed

Sreenivasan, P K; Furgang, D; Zhang, Y; DeVizio, W; Fine, D H

2005-03-01

The control of oral malodor is well-recognized in efforts to improve oral health. Antimicrobial formulations can mitigate oral malodor, however, procedures to assess effects on oral bacteria including those implicated in halitosis are unavailable. This investigation examined the antimicrobial effects of a new liquid triclosan/copolymer dentifrice (test) formulation that demonstrated significant inhibition of oral malodor in previous organoleptic clinical studies. Procedures compared antimicrobial effects of the test and control formulations on a range of oral micro-organisms including members implicated in halitosis, substantive antimicrobial effects of formulations with hydroxyapatite as a surrogate for human teeth and ex vivo effects on oral bacteria from human volunteers. With Actinomyces viscosus, as a model system, the test formulation demonstrated a dose-dependent effect. At these concentrations the test formulation provided significant antimicrobial effects on 13 strains of oral bacteria including those implicated in bad breath at selected posttreatment time points. Treatment of hydroxyapatite by the test dentifrice resulted in a significant and substantive antimicrobial effect vs. controls. Oral bacteria from subjects treated ex vivo with the test dentifrice resulted in significant reductions in cultivable oral bacteria and odorigenic bacteria producing hydrogen sulfide. In summary, microbiological methods adapted to study odorigenic bacteria demonstrate the significant antimicrobial effects of the test (triclosan/copolymer) dentifrice with laboratory and clinical strains of oral bacteria implicated in bad breath.

New Approach To Produce Water Free of Bacteria, Viruses, and Halogens in a Recyclable System▿

PubMed Central

Ahmed, Abd El-Shafey I.; Cavalli, Gabriel; Bushell, Michael E.; Wardell, John N.; Pedley, Steve; Charles, Katarina; Hay, John N.

2011-01-01

The antimicrobial activity of a new cross-linked N-halamine polymer against bacteria and viruses was evaluated. The polymer achieved a 9-log10 reduction of bacteria (both Escherichia coli and Staphylococcus aureus) in 1.5 h and a 5-log10 reduction of bacteriophage PRD1 in 3 h. At the same time, the ability of the nonhalogenated polymer to trap halide ions was examined. The polymer was incorporated into a multifiltration system to study the ability to produce water free of bacteria, viruses, and halide ions. The antimicrobial activity, useful lifetime, halide ion level, and recycling possibilities of the system were quantified on a laboratory scale. A design for a large-scale multifiltration system based on this polymer is proposed. PMID:21115711

Laboratory procedures manual for the firefly luciferase assay for adenosine triphosphate (ATP)

NASA Technical Reports Server (NTRS)

Chappelle, E. W.; Picciolo, G. L.; Curtis, C. A.; Knust, E. A.; Nibley, D. A.; Vance, R. B.

1975-01-01

A manual on the procedures and instruments developed for the adenosine triphosphate (ATP) luciferase assay is presented. Data cover, laboratory maintenance, maintenance of bacterial cultures, bacteria measurement, reagents, luciferase procedures, and determination of microbal susceptibility to antibiotics.

Computational modeling of drug-resistant bacteria. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDougall, Preston

2015-03-12

Initial proposal summary: The evolution of antibiotic-resistant mutants among bacteria (superbugs) is a persistent and growing threat to public health. In many ways, we are engaged in a war with these microorganisms, where the corresponding arms race involves chemical weapons and biological targets. Just as advances in microelectronics, imaging technology and feature recognition software have turned conventional munitions into smart bombs, the long-term objectives of this proposal are to develop highly effective antibiotics using next-generation biomolecular modeling capabilities in tandem with novel subatomic feature detection software. Using model compounds and targets, our design methodology will be validated with correspondingly ultra-highmore » resolution structure-determination methods at premier DOE facilities (single-crystal X-ray diffraction at Argonne National Laboratory, and neutron diffraction at Oak Ridge National Laboratory). The objectives and accomplishments are summarized.« less

Aerosol Formation In The Presence of Iodine and Ozone, Atmospheric Implications Based On Laboratory and Modelling Results

NASA Astrophysics Data System (ADS)

McFiggans, G.; Plane, J.; Joseph, M.; Casey, J.; Coe, H.; Williams, P.

The magnitude of the radiative forcing by aerosol depends on the number reaching optically active size (the direct effect) and the number that will activate into cloud droplets (the indirect effect). Aerosol number will depend on coagulation and depo- sitional loss processes in addition to the generation of nucleation mode particles to repopulate the ambient aerosol distribution. Great uncertainties surround the formation mechanisms of such atmospheric ultrafine particles, the dominant mechanisms changing with location and prevailing conditions (see e.g. Coe et al., 2000 &refs therein). It has been suggested that coastal ultrafine particle bursts measured under a wide variety of conditions (e.g. O Dowd et al., 1999) are related to iodocarbon compounds (Hoffmann et al., 2001) released by macroalgae in intertidal beds exposed during low tide (Carpenter et al., 1999). Since the particle bursts are only observed during daytime, it has been postulated that they are formed as a result of iodine photochemistry, probably involving higher iodine oxides. It has been known for some time that thick smokes are formed in laboratory kinetics exper- iments where iodine has been studied in the presence of ozone (Cox &Coker, 1983). The purpose of this study is to investigate whether the mechanism responsible for the laboratory phenomenon is a candidate for the formation of particles in the atmosphere. This study presents data from flow reactor experiments in which diiodomethane was photolysed in the presence of ozone under a variety of conditions. The formation of ultrafine particles and the subsequent evolution of the distribution was measured by a SMPS system. Such distributions were collected as a function of reactant concentra- tion, light intensity, relative humidity and a variety of other conditions and the results were found to be consistent and highly repeatable. A photochemical model has been developed to investigate the laboratory system. An existing gas phase model (Mc

Materials Science Laboratory - Columnar-to-Equiaxed Transition in Solidification Processing and Microstructure Formation in Casting of Technical Alloys under Diffusive and Magnetically Controlled Convective Conditions

NASA Technical Reports Server (NTRS)

Gandin, Charles-Andre; Ratke, Lorenz

2008-01-01

The Materials Science Laboratory - Columnar-to-Equiaxed Transition in Solidification Processing and Microstructure Formation in Casting of Technical Alloys under Diffusive and Magnetically Controlled Convective Conditions (MSL-CETSOL and MICAST) are two investigations which supports research into metallurgical solidification, semiconductor crystal growth (Bridgman and zone melting), and measurement of thermo-physical properties of materials. This is a cooperative investigation with the European Space Agency (ESA) and National Aeronautics and Space Administration (NASA) for accommodation and operation aboard the International Space Station (ISS). Research Summary: Materials Science Laboratory - Columnar-to-Equiaxed Transition in Solidification Processing (CETSOL) and Microstructure Formation in Casting of Technical Alloys under Diffusive and Magnetically Controlled Convective Conditions (MICAST) are two complementary investigations which will examine different growth patterns and evolution of microstructures during crystallization of metallic alloys in microgravity. The aim of these experiments is to deepen the quantitative understanding of the physical principles that govern solidification processes in cast alloys by directional solidification.

Identification of Mucosa-Invading and Intravascular Bacteria in Feline Small Intestinal Lymphoma.

PubMed

Hoehne, S N; McDonough, S P; Rishniw, M; Simpson, K W

2017-03-01

Persistent bacterial infections of the gastrointestinal mucosa are causally linked to gastric carcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma in people and laboratory animals. We examined the relationship of mucosa-associated bacteria to alimentary lymphoma in cats. Intestinal biopsies from 50 cats with alimentary lymphoma (small cell, n = 33; large cell, n = 17) and 38 controls without lymphoma (normal to minimal change on histopathology, n = 18; lymphocytic-plasmacytic enteritis, n = 20) were evaluated. The number and spatial distribution of bacteria (ie, in luminal cellular debris, villus-associated mucus, adherent to epithelium, mucosal invasion, intravascular, or serosal) were determined by fluorescence in situ hybridization with the eubacterial probe EUB-338. Mucosa-invasive bacteria were more frequently observed in cats with large cell lymphoma (82%, P ≤ .001) than in cats with small cell lymphoma (18%), normal to minimal change on histopathology, and lymphocytic-plasmacytic enteritis (3%). Intravascular bacteria were observed solely in large cell lymphoma (29%), and serosal colonization was more common in cats with large cell lymphoma (57%) than with small cell lymphoma (11%, P ≤ .01), normal to minimal change (8%, P ≤ .01), and lymphocytic-plasmacytic enteritis (6%, P ≤ .001). The high frequency of invasive bacteria within blood vessels and serosa of cats with large cell lymphoma may account for the sepsis-related complications associated with large cell lymphoma and inform clinical management. Further studies are required to determine the role of intramucosal bacteria in the etiopathogenesis of feline alimentary lymphoma.

THE FORMATION OF METHEMOGLOBIN BY STREPTOCOCCUS VIRIDANS

PubMed Central

Blake, Francis G.

1916-01-01

Cultures of Streptococcus viridans when brought into contact with red blood corpuscles have the power of transforming oxyhemoglobin into methemoglobin. The reaction occurs only in the presence of living streptococci when they are able to carry on their metabolic activities. The intensity of the reaction runs roughly parallel with the period of growth and multiplication of the bacteria and gradually diminishes and disappears as growth ceases. There is no apparent relation between the activity of a given strain of Streptococcus viridans in producing methemoglobin and its source or virulence. If the streptococci are suspended in salt solution they are unable to change oxyhemoglobin into methemoglobin unless some nutrient substance is present. Of the various nutrient substances tested dextrose is the most efficient in enabling the organisms to bring about the reaction. The reaction does not occur in the absence of oxygen, and is retarded by an excess of oxygen. Substances which tend to reduce the metabolic activities of the bacteria to a minimum exert an inhibitory action on methemoglobin formation. While not definitely proving it to be so, the results obtained in the above experiments strongly support the supposition that the reaction is not due to injurious substances produced by the bacteria or to products arising from the decomposition of the nutrient material present, but rather to the metabolic activities of the bacteria themselves when they are surrounded by environmental conditions which render growth and multiplication possible. The exact chemical nature of the change of oxyhemoglobin to methemoglobin is not known, but it is probably an oxidation process or a combination of reduction and oxidation processes, as pointed out by Heubner. As Cole has shown, the action of aminophenol is of great interest in this connection, in that it acts like a catalytic agent in being able to transform much more hemoglobin into methemoglobin than would be possible if the

The formation of Staphylococcus aureus enterotoxin in food environments and advances in risk assessment

PubMed Central

Wallin-Carlquist, Nina; Thorup Cohn, Marianne; Lindqvist, Roland; Barker, Gary C; Rådström, Peter

2011-01-01

The recent finding that the formation of staphylococcal enterotoxins in food is very different from that in cultures of pure Staphylococcus aureus sheds new light on, and brings into question, traditional microbial risk assessment methods based on planktonic liquid cultures. In fact, most bacteria in food appear to be associated with surfaces or tissues in various ways, and interaction with other bacteria through molecular signaling is prevalent. Nowadays it is well established that there are significant differences in the behavior of bacteria in the planktonic state and immobilized bacteria found in multicellular communities. Thus, in order to improve the production of high-quality, microbiologically safe food for human consumption, in situ data on enterotoxin formation in food environments are required to complement existing knowledge on the growth and survivability of S. aureus. This review focuses on enterotoxigenic S. aureus and describes recent findings related to enterotoxin formation in food environments, and ways in which risk assessment can take into account virulence behavior. An improved understanding of how environmental factors affect the expression of enterotoxins in foods will enable us to formulate new strategies for improved food safety. PMID:22030860

The formation of Staphylococcus aureus enterotoxin in food environments and advances in risk assessment.

PubMed

Schelin, Jenny; Wallin-Carlquist, Nina; Cohn, Marianne Thorup; Lindqvist, Roland; Barker, Gary C; Rådström, Peter

2011-01-01

The recent finding that the formation of staphylococcal enterotoxins in food is very different from that in cultures of pure Staphylococcus aureus sheds new light on, and brings into question, traditional microbial risk assessment methods based on planktonic liquid cultures. In fact, most bacteria in food appear to be associated with surfaces or tissues in various ways, and interaction with other bacteria through molecular signaling is prevalent. Nowadays it is well established that there are significant differences in the behavior of bacteria in the planktonic state and immobilized bacteria found in multicellular communities. Thus, in order to improve the production of high-quality, microbiologically safe food for human consumption, in situ data on enterotoxin formation in food environments are required to complement existing knowledge on the growth and survivability of S. aureus. This review focuses on enterotoxigenic S. aureus and describes recent findings related to enterotoxin formation in food environments, and ways in which risk assessment can take into account virulence behavior. An improved understanding of how environmental factors affect the expression of enterotoxins in foods will enable us to formulate new strategies for improved food safety.

Frequency of Resistance and Susceptible Bacteria Isolated from Houseflies

PubMed Central

Davari, B; Kalantar, E; Zahirnia, A; Moosa-Kazemi, SH

2010-01-01

Background: In this study, we determine the vector competence of Musca domestica with reference to the transmission of susceptible and resistance bacterial strains in hospitals and slaughter house in Sanandaj City, west Iran. Methods: Totally 908 houseflies were collected to isolate bacteria from their external body based on standard procedures.Antibiotic susceptibility testing was performed by Kirby-Bauer disc diffusion method on Mueller Hinton agar based on recommendations of CLSI (formerly the National Committee for Clinical Laboratory Standards). Results: From collected houseflies, 366 bacteria species were isolated. The most common isolated bacterium at hospitals was Klebsiella pneumoniae 43.3% (n= 90) followed by Pseudomonas aeruginosa 37% (n= 77), while that of slaughterhouse was Proteus mirabilis. 29.1% (n= 46) followed by Citrobacter freundii 28.4% (n= 45). Among all the isolates from hospitals, cephalexin, chloramphenicol, ampicillin, and tetracycline, resistance rates were above 32.5% and gentamicin expressed the highest susceptibility among all the isolates from hospitals. It is worth to note that K. pneumoniae showed 61% and 44.5% resistance to cephalexin and chloramphenicol respectively. Similarly, all isolates from slaughterhouse were more than 28% and 30% resistant to cephalexin and chloramphenicol respectively. Surprisingly, among all the isolates, Citrobacter freundii were highly resistant to gentamicin. Conclusion: Houseflies collected from hospitals and slaughterhouse may be involved in the spread of drug resistant bacteria and may increase the potential of human exposure to drug resistant bacteria. PMID:22808400

Intermediate Scale Laboratory Testing to Understand Mechanisms of Capillary and Dissolution Trapping during Injection and Post-Injection of CO 2 in Heterogeneous Geological Formations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Illangasekare, Tissa; Trevisan, Luca; Agartan, Elif

2015-03-31

Carbon Capture and Storage (CCS) represents a technology aimed to reduce atmospheric loading of CO 2 from power plants and heavy industries by injecting it into deep geological formations, such as saline aquifers. A number of trapping mechanisms contribute to effective and secure storage of the injected CO 2 in supercritical fluid phase (scCO 2) in the formation over the long term. The primary trapping mechanisms are structural, residual, dissolution and mineralization. Knowledge gaps exist on how the heterogeneity of the formation manifested at all scales from the pore to the site scales affects trapping and parameterization of contributing mechanismsmore » in models. An experimental and modeling study was conducted to fill these knowledge gaps. Experimental investigation of fundamental processes and mechanisms in field settings is not possible as it is not feasible to fully characterize the geologic heterogeneity at all relevant scales and gathering data on migration, trapping and dissolution of scCO 2. Laboratory experiments using scCO 2 under ambient conditions are also not feasible as it is technically challenging and cost prohibitive to develop large, two- or three-dimensional test systems with controlled high pressures to keep the scCO 2 as a liquid. Hence, an innovative approach that used surrogate fluids in place of scCO 2 and formation brine in multi-scale, synthetic aquifers test systems ranging in scales from centimeter to meter scale developed used. New modeling algorithms were developed to capture the processes controlled by the formation heterogeneity, and they were tested using the data from the laboratory test systems. The results and findings are expected to contribute toward better conceptual models, future improvements to DOE numerical codes, more accurate assessment of storage capacities, and optimized placement strategies. This report presents the experimental and modeling methods and research results.« less

The Bacterium Frischella perrara Causes Scab Formation in the Gut of its Honeybee Host

PubMed Central

Bartlett, Kelsey D.; Moran, Nancy A.

2015-01-01

ABSTRACT Honeybees harbor well-defined bacterial communities in their guts. The major members of these communities appear to benefit the host, but little is known about how they interact with the host and specifically how they interface with the host immune system. In the pylorus, a short region between the midgut and hindgut, honeybees frequently exhibit scab-like structures on the epithelial gut surface. These structures are reminiscent of a melanization response of the insect immune system. Despite the wide distribution of this phenotype in honeybee populations, its cause has remained elusive. Here, we show that the presence of a common member of the bee gut microbiota, the gammaproteobacterium Frischella perrara, correlates with the appearance of the scab phenotype. Bacterial colonization precedes scab formation, and F. perrara specifically localizes to the melanized regions of the host epithelium. Under controlled laboratory conditions, we demonstrate that exposure of microbiota-free bees to F. perrara but not to other bacteria results in scab formation. This shows that F. perrara can become established in a spatially restricted niche in the gut and triggers a morphological change of the epithelial surface, potentially due to a host immune response. As an intermittent colonizer, this bacterium holds promise for addressing questions of community invasion in a simple yet relevant model system. Moreover, our results show that gut symbionts of bees engage in differential host interactions that are likely to affect gut homeostasis. Future studies should focus on how these different gut bacteria impact honeybee health. PMID:25991680

Using a Microbial Physiologic and Genetic Approach to Investigate How Bacteria Sense Physical Stimuli

ERIC Educational Resources Information Center

Mussi, María Alejandra; Actis, Luis A.; de Mendoza, Diego; Cybulski, Larisa E.

2014-01-01

A laboratory exercise was designed to illustrate how physical stimuli such as temperature and light are sensed and processed by bacteria to elaborate adaptive responses. In particular, we use the well-characterized Des pathway of "Bacillus subtilis" to show that temperature modulates gene expression, resulting ultimately in modification…

Radionuclides, inorganic constituents, organic compounds, and bacteria in water from selected wells and springs from the southern boundary of the Idaho National Engineering Laboratory to the Hagerman Area, Idaho, 1990

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartholomay, R.C.; Edwards, D.D.; Campbell, L.J.

1992-03-01

The US Geological Survey and the Idaho Department of Water Resources, in response to a request from the US Department of Energy, sampled 19 sites as part of a long-term project to monitor water quality of the Snake River Plain aquifer from the southern boundary of the Idaho National Engineering Laboratory to the Hagerman area. Water samples were collected and analyzed for manmade pollutants and naturally occurring constituents. The samples were collected from seven irrigation wells, five domestic wells, two springs, one stock well, two dairy wells, one observation well, and one commercial well. Two quality assurance samples also weremore » collected and analyzed. The water samples were analyzed for selected radionuclides, inorganic constituents, organic compounds, and bacteria. None of the radionuclides, inorganic constituents, or organic compounds exceeded the established maximum contaminant levels for drinking water. Most of the radionuclide and inorganic constituent concentrations exceeded their respective reporting levels. All samples analyzed for surfactants and dissolved organic carbon had concentrations that exceeded their reporting level. Toluene concentrations exceeded the reporting level in one water sample. Two samples contained fecal coliform bacteria counts that exceeded established maximum contaminant levels for drinking water.« less

Terminal steps of bacteriochlorophyll a phytol formation in purple photosynthetic bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shioi, Y.; Sasa, T.

1984-04-01

Four chemically different bacteriochlorophylls (Bchls) a esterified with geranylgeraniol, dihydrogeranyl-geraniol, tetrahydrogeraniol, and phytol have been detected by high-pressure liquid chromatography in cell extracts from Rhodopseudomonas sphaeroides and Chromatium vinosum. Bchl a containing phytol is the principal component, and the other three Bchls a comprise about 4% of the total Bchls a in stationary-phase cells of R. sphaeroides and C. vinosum. The high levels of the minor pigments occur in the beginning of Bchl a phytol formation, indicating that they are not degradation products, but intermediates of Bchl a phytol formation.

Streptomyces lunalinharesii strain 235 shows the potential to inhibit bacteria involved in biocorrosion processes.

PubMed

Pacheco da Rosa, Juliana; Korenblum, Elisa; Franco-Cirigliano, Marcella Novaes; Abreu, Fernanda; Lins, Ulysses; Soares, Rosângela M A; Macrae, Andrew; Seldin, Lucy; Coelho, Rosalie R R

2013-01-01

Four actinomycete strains previously isolated from Brazilian soils were tested for their antimicrobial activity against Bacillus pumilus LF-4 and Desulfovibrio alaskensis NCIMB 13491, bacteria that are well known to be involved in biofilm formation and biocorrosion. Strain 235, belonging to the species Streptomyces lunalinharesii, inhibited the growth of both bacteria. The antimicrobial activity was seen over a wide range of pH, and after treatment with several chemicals and heat but not with proteinase K and trypsin. The antimicrobial substances present in the concentrated supernatant from growth media were partially characterized by SDS-PAGE and extracellular polypeptides were seen. Bands in the size range of 12 to 14.4 kDa caused antimicrobial activity. Transmission electron microscopy of D. alaskensis cells treated with the concentrated supernatant containing the antimicrobial substances revealed the formation of prominent bubbles, the spherical double-layered structures on the cell membrane, and the periplasmic space completely filled with electron-dense material. This is the first report on the production of antimicrobial substances by actinomycetes against bacteria involved in biocorrosion processes, and these findings may be of great relevance as an alternative source of biocides to those currently employed in the petroleum industry.

Application of alkaliphilic biofilm-forming bacteria to improve compressive strength of cement-sand mortar.

PubMed

Park, Sung-Jin; Chun, Woo-Young; Kim, Wha-Jung; Ghim, Sa-Youl

2012-03-01

The application of microorganisms in the field of construction material is rapidly increasing worldwide; however, almost all studies that were investigated were bacterial sources with mineral-producing activity and not with organic substances. The difference in the efficiency of using bacteria as an organic agent is that it could improve the durability of cement material. This study aimed to assess the use of biofilm-forming microorganisms as binding agents to increase the compressive strength of cement-sand material. We isolated 13 alkaliphilic biofilmforming bacteria (ABB) from a cement tetrapod block in the West Sea, Korea. Using 16S RNA sequence analysis, the ABB were partially identified as Bacillus algicola KNUC501 and Exiguobacterium marinum KNUC513. KNUC513 was selected for further study following analysis of pH and biofilm formation. Cement-sand mortar cubes containing KNUC513 exhibited greater compressive strength than mineral-forming bacteria (Sporosarcina pasteurii and Arthrobacter crystallopoietes KNUC403). To determine the biofilm effect, Dnase I was used to suppress the biofilm formation of KNUC513. Field emission scanning electron microscopy image revealed the direct involvement of organic-inorganic substance in cement-sand mortar.

Laboratory development and field testing of sentinel toys to assess environmental faecal exposure of young children in rural India.

PubMed

Torondel, Belen; Gyekye-Aboagye, Yaw; Routray, Parimita; Boisson, Sophie; Schimdt, Wolf; Clasen, Thomas

2015-06-01

Sentinel toys are increasingly used as a method of assessing young children's exposure to faecal pathogens in households in low-income settings. However, there is no consensus on the suitability of different approaches. We evaluated three types of toy balls with different surfaces (plastic, rubber, urethane) in the laboratory to compare the uptake of faecal indicator bacteria (Escherichia coli) on their surface. We performed bacteria survival analysis under different environmental conditions and tested laboratory methods for bacteria removal and recovery. In a field study we distributed sterile urethane balls to children <5 from 360 households in rural India. After 24 hours, we collected and rinsed the toys in sterile water, assayed for thermotolerant coliforms (TTC) and explored associations between the level of contamination and household characteristics. In the laboratory, urethane foam balls took up more indicator bacteria than the other balls. Bacteria recovery did not differ based on mechanic vs no agitation. Higher temperatures and moisture levels increased bacterial yield. In the field, the only factor associated with a decreased recovery of TTC from the balls was having a soil (unpaved) floor. Sentinel toys may be an effective tool for assessing young children's exposure to faecal pathogens. However, even using methods designed to increase bacterial recovery, limited sensitivity may require larger sample sizes. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria

PubMed Central

Ferrari, Belinda C.; Binnerup, Svend J.; Gillings, Michael

2005-01-01

Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used. PMID:16332866

Predictable communities of soil bacteria in relation to nutrient concentration and successional stage in a laboratory culture experiment.

PubMed

Song, Woojin; Kim, Mincheol; Tripathi, Binu M; Kim, Hyoki; Adams, Jonathan M

2016-06-01

It is difficult to understand the processes that structure immensely complex bacterial communities in the soil environment, necessitating a simplifying experimental approach. Here, we set up a microcosm culturing experiment with soil bacteria, at a range of nutrient concentrations, and compared these over time to understand the relationship between soil bacterial community structure and time/nutrient concentration. DNA from each replicate was analysed using HiSeq2000 Illumina sequencing of the 16S rRNA gene. We found that each nutrient treatment, and each time point during the experiment, produces characteristic bacterial communities that occur predictably between replicates. It is clear that within the context of this experiment, many soil bacteria have distinct niches from one another, in terms of both nutrient concentration, and successional time point since a resource first became available. This fine niche differentiation may in part help to explain the coexistence of a diversity of bacteria in soils. In this experiment, we show that the unimodal relationship between nutrient concentration/time and species diversity often reported in communities of larger organisms is also evident in microbial communities. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Formation of palladium(0) nanoparticles at microbial surfaces.

PubMed

Bunge, Michael; Søbjerg, Lina S; Rotaru, Amelia-Elena; Gauthier, Delphine; Lindhardt, Anders T; Hause, Gerd; Finster, Kai; Kingshott, Peter; Skrydstrup, Troels; Meyer, Rikke L

2010-10-01

The increasing demand and limited natural resources for industrially important platinum-group metal (PGM) catalysts render the recovery from secondary sources such as industrial waste economically interesting. In the process of palladium (Pd) recovery, microorganisms have revealed a strong potential. Hitherto, bacteria with the property of dissimilatory metal reduction have been in focus, although the biochemical reactions linking enzymatic Pd(II) reduction and Pd(0) deposition have not yet been identified. In this study we investigated Pd(II) reduction with formate as the electron donor in the presence of Gram-negative bacteria with no documented capacity for reducing metals for energy production: Cupriavidus necator, Pseudomonas putida, and Paracoccus denitrificans. Only large and close-packed Pd(0) aggregates were formed in cell-free buffer solutions. Pd(II) reduction in the presence of bacteria resulted in smaller, well-suspended Pd(0) particles that were associated with the cells (called "bioPd(0)" in the following). Nanosize Pd(0) particles (3-30 nm) were only observed in the presence of bacteria, and particles in this size range were located in the periplasmic space. Pd(0) nanoparticles were still deposited on autoclaved cells of C. necator that had no hydrogenase activity, suggesting a hydrogenase-independent formation mechanism. The catalytic properties of Pd(0) and bioPd(0) were determined by the amount of hydrogen released in a reaction with hypophosphite. Generally, bioPd(0) demonstrated a lower level of activity than the Pd(0) control, possibly due to the inaccessibility of the Pd(0) fraction embedded in the cell envelope. Our results demonstrate the suitability of bacterial cells for the recovery of Pd(0), and formation and immobilization of Pd(0) nanoparticles inside the cell envelope. However, procedures to make periplasmic Pd(0) catalytically accessible need to be developed for future nanobiotechnological applications.

IDENTITY OF THE PINK-PIGMENTED METHANOL-OXIDIZING BACTERIA AS VIBRIO EXTORQUENS

PubMed Central

Stocks, Peter K.; McCleskey, C. S.

1964-01-01

Stocks, Peter K. (Louisiana State University, Baton Rouge), and C. S. McCleskey. Identity of the pink-pigmented methanol-oxidizing bacteria as Vibrio extorquens. J. Bacteriol. 88:1065–1070. 1964.—Pink-pigmented bacteria isolated from enrichment cultures of methane oxidizers were found to possess similar morphological, cultural, and physiological characteristics. All the strains utilized methanol, formate, oxalate, succinate, glycerol, and benzene as sole carbon sources; methanol, formate, and glycerol afforded best growth. Most strains utilized fructose and ribose; other carbohydrates tested were not available as carbon and energy sources. There was strain variation in the use of hexane, heptane, n-propanol, n-butanol, acetate, and propionate. Methane, ethane, n-propane, and n-butane were not utilized. Our isolates, and Pseudomonas methanica of Harrington and Kallio (not the methane-dependent P. methanica of Dworkin and Foster), Pseudomonas AM1 of Peele and Quayle, Pseudomonas PRL-W4 of Kaneda and Roxburgh, and Protaminobacter ruber den Dooren de Jong are nearly identical with Vibrio extorquens (Bassalik) Bhat and Barker, and should be considered the same species. Images PMID:14219020

IDENTITY OF THE PINK-PIGMENTED METHANOL-OXIDIZING BACTERIA AS VIBRIO EXTORQUENS.

PubMed

STOCKS, P K; MCCLESKEY, C S

1964-10-01

Stocks, Peter K. (Louisiana State University, Baton Rouge), and C. S. McCleskey. Identity of the pink-pigmented methanol-oxidizing bacteria as Vibrio extorquens. J. Bacteriol. 88:1065-1070. 1964.-Pink-pigmented bacteria isolated from enrichment cultures of methane oxidizers were found to possess similar morphological, cultural, and physiological characteristics. All the strains utilized methanol, formate, oxalate, succinate, glycerol, and benzene as sole carbon sources; methanol, formate, and glycerol afforded best growth. Most strains utilized fructose and ribose; other carbohydrates tested were not available as carbon and energy sources. There was strain variation in the use of hexane, heptane, n-propanol, n-butanol, acetate, and propionate. Methane, ethane, n-propane, and n-butane were not utilized. Our isolates, and Pseudomonas methanica of Harrington and Kallio (not the methane-dependent P. methanica of Dworkin and Foster), Pseudomonas AM1 of Peele and Quayle, Pseudomonas PRL-W4 of Kaneda and Roxburgh, and Protaminobacter ruber den Dooren de Jong are nearly identical with Vibrio extorquens (Bassalik) Bhat and Barker, and should be considered the same species.

Plants as sources of airborne bacteria, including ice nucleation-active bacteria.

PubMed

Lindemann, J; Constantinidou, H A; Barchet, W R; Upper, C D

1982-11-01

Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m over young corn and wet soil to 663 colony-forming units per m over dry soil and 6,500 colony-forming units per m over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach

PubMed Central

2012-01-01

Background Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. Methods We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. Results We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. Conclusions We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data. PMID:22759462

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach.

PubMed

Ratkovic, Zorana; Golik, Wiktoria; Warnier, Pierre

2012-06-26

Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-05-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

The Use of Colorimetric Sensor Arrays to Discriminate between Pathogenic Bacteria

PubMed Central

Lonsdale, Claire L.; Taba, Brian; Queralto, Nuria; Lukaszewski, Roman A.; Martino, Raymond A.; Rhodes, Paul A.; Lim, Sung H.

2013-01-01

A colorimetric sensor array is a high-dimensional chemical sensor that is cheap, compact, disposable, robust, and easy to operate, making it a good candidate technology to detect pathogenic bacteria, especially potential bioterrorism agents like Yersinia pestis and Bacillus anthracis which feature on the Center for Disease Control and Prevention’s list of potential biothreats. Here, a colorimetric sensor array was used to continuously monitor the volatile metabolites released by bacteria in solid media culture in an Advisory Committee on Dangerous Pathogen Containment Level 3 laboratory. At inoculum concentrations as low as 8 colony-forming units per plate, 4 different bacterial species were identified with 100% accuracy using logistic regression to classify the kinetic profile of sensor responses to culture headspace gas. The sensor array was able to further discriminate between different strains of the same species, including 5 strains of Yersinia pestis and Bacillus anthracis. These preliminary results suggest that disposable colorimetric sensor arrays can be an effective, low-cost tool to identify pathogenic bacteria. PMID:23671629

Laboratory experiments on liquid fragmentation during Earth's core formation

NASA Astrophysics Data System (ADS)

Landeau, M.; Deguen, R.; Olson, P.

2013-12-01

Buoyancy-driven fragmentation of one liquid in another immiscible liquid likely occurred on a massive scale during the formation of the Earth, when dense liquid metal blobs were released within deep molten silicate magma oceans. Another example of this phenomenon is the sudden release of petroleum into the ocean during the Deepwater Horizon disaster (Gulf of Mexico, 2010). We present experiments on the instability and fragmentation of blobs of a heavy liquid released into a lighter immiscible liquid. During the fragmentation process, we observe deformation of the released fluid, formation of filamentary structures, capillary instability, and eventually drop formation. We find that, at low and intermediate Weber numbers (which measures the importance of inertia versus surface tension), the fragmentation regime mainly results from the competition between a Rayleigh-Taylor instability and the roll-up of a vortex ring. At sufficiently high Weber numbers (the relevant regime for core formation), the fragmentation process becomes turbulent. The large-scale flow then behaves as a turbulent vortex ring or a turbulent thermal: it forms a coherent structure whose shape remains self-similar during the fall and which grows by turbulent entrainment of ambient fluid. An integral model based on the entrainment assumption, and adapted to buoyant vortex rings with initial momentum, is consistent with our experimental data. This indicates that the concept of turbulent entrainment is valid for non-dispersed immiscible fluids at large Weber and Reynolds numbers. Series of photographs, turbulent fragmentation regime, time intervals of about 0.2 s. Portions (red boxes) have been magnified (on the right).

Modeling Studying the Role of Bacteria on ice Nucleation Processes

NASA Astrophysics Data System (ADS)

Sun, J.

2006-12-01

Certain air-borne bacteria have been recognized as active ice nuclei at the temperatures warm than - 10°C. Ice nucleating bacteria commonly found in plants and ocean surface. These ice nucleating bacteria are readily disseminated into the atmosphere and have been observed in clouds and hailstones, and their importance in cloud formation process and precipitation, as well as causing diseases in plants and animal kingdom, have been considered for over two decades, but their significance in atmospheric processes are yet to be understood. A 1.5-D non-hydrostatic cumulus cloud model with bin-resolved microphysics is developed and is to used to examine the relative importance of sulphate aerosol concentrations on the evolution of cumulus cloud droplet spectra and ice multiplication process, as well as ice initiation process by ice nucleating bacteria in the growing stage of cumulus clouds and the key role of this process on the ice multiplication in the subsequent dissipating stage of cumulus clouds. In this paper, we will present some sensitivity test results of the evolution of cumulus cloud spectra, ice concentrations at various concentrations of sulfate aerosols, and at different ideal sounding profiles. We will discuss the implication of our results in understanding of ice nucleation processes.

Anti-Biofilm Activity of Polyazolidinammonium Modified with Iodine Hydrate Ions against Microbial Biofilms of Uropathogenic Coliform Bacteria.

PubMed

Nechaeva, O V; Tikhomirova, E I; Zayarsky, D A; Bespalova, N V; Glinskaya, E V; Shurshalova, N F; Al Bayati, B M; Babailova, A I

2017-04-01

The dynamics of microbial biofilm formation by standard strain and by clinical strains of uropathogenic coliform bacteria was investigated in vitro and the effect of sublethal concentrations of the polymer compound polyazolidinammonium modified with iodine hydrate ions on the initial stages of biofilm formation was assessed. Treatment of immunological plate wells with the polymeric compound prevented film formation, especially in case of clinical E. coli strain carrying FimH virulence gene.

Swimming Motility Mediates the Formation of Neutrophil Extracellular Traps Induced by Flagellated Pseudomonas aeruginosa

PubMed Central

Sil, Payel; Chassaing, Benoit; Yoo, Dae-goon; Gewirtz, Andrew T.; Goldberg, Joanna B.; McCarter, Linda L.; Rada, Balázs

2016-01-01

Pseudomonas aeruginosa is an opportunistic pathogen causing severe infections often characterized by robust neutrophilic infiltration. Neutrophils provide the first line of defense against P. aeruginosa. Aside from their defense conferred by phagocytic activity, neutrophils also release neutrophil extracellular traps (NETs) to immobilize bacteria. Although NET formation is an important antimicrobial process, the details of its mechanism are largely unknown. The identity of the main components of P. aeruginosa responsible for triggering NET formation is unclear. In this study, our focus was to identify the main bacterial factors mediating NET formation and to gain insight into the underlying mechanism. We found that P. aeruginosa in its exponential growth phase promoted strong NET formation in human neutrophils while its NET-inducing ability dramatically decreased at later stages of bacterial growth. We identified the flagellum as the primary component of P. aeruginosa responsible for inducing NET extrusion as flagellum-deficient bacteria remained seriously impaired in triggering NET formation. Purified P. aeruginosa flagellin, the monomeric component of the flagellum, does not stimulate NET formation in human neutrophils. P. aeruginosa-induced NET formation is independent of the flagellum-sensing receptors TLR5 and NLRC4 in both human and mouse neutrophils. Interestingly, we found that flagellar motility, not flagellum binding to neutrophils per se, mediates NET release induced by flagellated bacteria. Immotile, flagellar motor-deficient bacterial strains producing paralyzed flagella did not induce NET formation. Forced contact between immotile P. aeruginosa and neutrophils restored their NET-inducing ability. Both the motAB and motCD genetic loci encoding flagellar motor genes contribute to maximal NET release; however the motCD genes play a more important role. Phagocytosis of P. aeruginosa and superoxide production by neutrophils were also largely dependent upon

Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia

PubMed Central

Gérard, Emmanuelle; Moreira, David; Philippot, Pascal; Van Kranendonk, Martin J.; López-García, Purificación

2009-01-01

Background Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible. Methodology/Principal Findings In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper “fresh” samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth. Conclusions/Significance The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life

Rapid magnetosome formation shown by real-time x-ray magnetic circular dichroism.

PubMed

Staniland, Sarah; Ward, Bruce; Harrison, Andrew; van der Laan, Gerrit; Telling, Neil

2007-12-04

Magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. Although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process, and no real-time studies of such processes have yet been performed. Thus, suggested formation mechanisms still need substantiating with data. Here we report the examination of the magnetosome material throughout the formation process in a real-time in vivo study of Magnetospirillum gryphiswaldense, strain MSR-1. Transmission EM and x-ray absorption spectroscopy studies reveal that full-sized magnetosomes are seen 15 min after formation is initiated. These immature magnetosomes contain a surface layer of the nonmagnetic iron oxide-phase hematite. Mature magnetite is found after another 15 min, concurrent with a dramatic increase in magnetization. This rapid formation result is contrary to previously reported studies and discounts the previously proposed slow, multistep formation mechanisms. Thus, we conclude that the biomineralization of magnetite occurs rapidly in magnetotactic bacteria on a similar time scale to high-temperature chemical precipitation reactions, and we suggest that this finding is caused by a biological catalysis of the process.

Prevention of artificial dental plaque formation in vitro by plant extracts.

PubMed

Smullen, J; Finney, M; Storey, D M; Foster, H A

2012-10-01

A number of previous studies have shown that plant extracts can inhibit formation of dental plaque. The ability of extracts of Rosmarinus officianalis L., Salvia officianalis L., unfermented cocoa, red grape seed and green tea to inhibit plaque bacteria, glucosyltransferase activity, glucan and plaque formation in an in vitro model using bovine teeth was examined. The antimicrobial activity of the plant extracts against oral bacteria was determined using a standard susceptibility agar dilution technique. Inhibition of growth and acid production from glucose and sucrose by Streptococcus mutans in liquid culture was investigated. Prevention of plaque formation on bovine teeth initiated by Strep. mutans was studied using an artificial mouth. The plant extracts inhibited the growth of oral bacteria and prevented acid production by Strep. mutans. Extracts inhibited glucosyltransferase activity and glucan production and inhibited adhesion to glass. Extracts of R. officianalis L. and S. officianalis L. at 0·25 mg ml(-1) reduced plaque growth by >80%. Green tea extract completely inhibited plaque formation but resulted in a greenish discolouration of the teeth which could not be removed by scrubbing. The plant extracts, particularly those from R. officianalis L. and S. officianalis L., inhibited glucosyltranferase activity, glucan production and plaque formation in vitro. The results suggest that the extracts of R. officianalis L. and S. officianalis L. may be useful as antiplaque agents in foods and dental preparations. Bovine teeth can be used as an alternative to hydroxyapatite for studies of plaque formation, but they need to be carefully sterilized before use. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

In-vitro activity of sodium-hypochlorite gel on bacteria associated with periodontitis.

PubMed

Jurczyk, Karolina; Nietzsche, Sandor; Ender, Claudia; Sculean, Anton; Eick, Sigrun

2016-11-01

The aim of the present study was to assess the antimicrobial activity of a sodium hypochlorite formulation including its components against bacteria associated with periodontal disease. Sodium hypochlorite formulation (NaOCl gel), its components sodium hypochlorite (NaOCl), and the activating vehicle were compared with 0.1 % chlorhexidine digluconate (CHX) solution. The antimicrobial activity was proven by determination of minimal inhibitory concentrations (MIC), minimal bactericidal concentrations, and killing assays. Furthermore, the influence on formation as well as on a 4-day-old 6-species biofilm was tested. Except for one strain (Parvimonas micra ATCC 33270 in case of NaOCl gel), the MICs both of the CHX solution and NaOCl gel did not exceed 10 % of the formulations' concentration. In general, MICs of the NaOCl gel were equal as of the CHX solution against Gram-negatives but higher against Gram-positive bacteria. CHX but not NaOCl gel clearly inhibited biofilm formation; however, the activity of NaOCl gel was more remarkable on a 4-day-old biofilm. NaOCl killed bacteria in the biofilm and interfered with the matrix. The NaOCl gel acts antimicrobial in particular against Gram-negative species associated with periodontitis. Moreover, its component NaOCl hypochlorite is able to alter biofilm matrices. The NaOCl gel may represent a potential alternative for adjunctive topical antimicrobial treatment in periodontitis.

Laboratory Experiments and Modeling for Interpreting Field Studies of Secondary Organic Aerosol Formation Using an Oxidation Flow Reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jimenez, Jose-Luis

2016-02-01

This grant was originally funded for deployment of a suite of aerosol instrumentation by our group in collaboration with other research groups and DOE/ARM to the Ganges Valley in India (GVAX) to study aerosols sources and processing. Much of the first year of this grant was focused on preparations for GVAX. That campaign was cancelled due to political reasons and with the consultation with our program manager, the research of this grant was refocused to study the applications of oxidation flow reactors (OFRs) for investigating secondary organic aerosol (SOA) formation and organic aerosol (OA) processing in the field and laboratorymore » through a series of laboratory and modeling studies. We developed a gas-phase photochemical model of an OFR which was used to 1) explore the sensitivities of key output variables (e.g., OH exposure, O 3, HO 2/OH) to controlling factors (e.g., water vapor, external reactivity, UV irradiation), 2) develop simplified OH exposure estimation equations, 3) investigate under what conditions non-OH chemistry may be important, and 4) help guide design of future experiments to avoid conditions with undesired chemistry for a wide range of conditions applicable to the ambient, laboratory, and source studies. Uncertainties in the model were quantified and modeled OH exposure was compared to tracer decay measurements of OH exposure in the lab and field. Laboratory studies using OFRs were conducted to explore aerosol yields and composition from anthropogenic and biogenic VOC as well as crude oil evaporates. Various aspects of the modeling and laboratory results and tools were applied to interpretation of ambient and source measurements using OFR. Additionally, novel measurement methods were used to study gas/particle partitioning. The research conducted was highly successful and details of the key results are summarized in this report through narrative text, figures, and a complete list of publications acknowledging this grant.« less

[Development of molecular detection of food-borne pathogenic bacteria using miniaturized microfluidic devices].

PubMed

Iván, Kristóf; Maráz, Anna

2015-12-20

Detection and identification of food-borne pathogenic bacteria are key points for the assurance of microbiological food safety. Traditional culture-based methods are more and more replaced by or supplemented with nucleic acid based molecular techniques, targeting specific (preferably virulence) genes in the genomes. Internationally validated DNA amplification - most frequently real-time polymerase chain reaction - methods are applied by the food microbiological testing laboratories for routine analysis, which will result not only in shortening the time for results but they also improve the performance characteristics (e.g. sensitivity, specificity) of the methods. Beside numerous advantages of the polymerase chain reaction based techniques for routine microbiological analysis certain drawbacks have to be mentioned, such as the high cost of the equipment and reagents, as well as the risk of contamination of the laboratory environment by the polymerase chain reaction amplicons, which require construction of an isolated laboratory system. Lab-on-a-chip systems can integrate most of these laboratory processes within a miniaturized device that delivers the same specificity and reliability as the standard protocols. The benefits of miniaturized devices are: simple - often automated - use, small overall size, portability, sterility due to single use possibility. These miniaturized rapid diagnostic tests are being researched and developed at the best research centers around the globe implementing various sample preparation and molecular DNA amplification methods on-chip. In parallel, the aim of the authors' research is to develop microfluidic Lab-on-a-chip devices for the detection and identification of food-borne pathogenic bacteria.

Effectiveness of hand washing and disinfection methods in removing transient bacteria after patient nursing.

PubMed Central

Ojajärvi, J.

1980-01-01

The effectiveness of various hand washing and disinfection methods in removing transient skin bacteria was studied in hospital after dry or moist contamination of the hands when nursing burn patients. The results were compared with those of laboratory tests with volunteers. A fairly good correlation of the bacterial reductions existed between hospital and laboratory tests. All other methods removed Staph. aureus from the hands more effectively than liquid soap. Gram-negative bacilli were more easily removed than staphylococci, even with soap wash alone. In hospital, none of the washing and disinfection methods always removed all patient-borne bacteria from the hands. After dry or moist contamination and subsequent washing with soap only, colonies of Staph. aureus were often detected in finger-print samples. Staphylococci were more often completely removed by a 4% chlorhexidine detergent scrub and alcoholic solutions (either with or without previous soap wash) than by liquid soap, hexachlorophene or iodophor preparations. Gram-negative bacilli were more easily removed by all the washing and disinfection methods. After moist contamination, Gram-negative bacilli were more often completely removed from the hands by ethanol than by other treatments. The results of the present study emphasize the importance of always using gloves when nursing a profuse spreader of bacteria or one who must be protected from infection. PMID:6778914

Safety in laboratories: Indian scenario.

PubMed

Mustafa, Ajaz; Farooq, A Jan; Qadri, Gj; S A, Tabish

2008-07-01

Health and safety in clinical laboratories is becoming an increasingly important subject as a result of emergence of highly infectious diseases such as Hepatitis and HIV. A cross sectional study was carried out to study the safety measures being adopted in clinical laboratories of India. Heads of laboratories of teaching hospitals of India were subjected to a standardized, pretested questionnaire. Response rate was 44.8%. only 60% of laboratories had person in-charge of safety in laboratory. Seventy three percent of laboratories had safety education program regarding hazards. In 91% of laboratories staff is using protective clothing while working in laboratories. Hazardous material regulations are followed in 78% of laboratories. Regular health check ups are carried among laboratory staff in 43.4% of laboratories.Safety manual is available in 56.5% of laboratories. 73.9% of laboratories are equipped with fire extinguishers. Fume cupboards are provided in 34.7% of laboratories and they are regularly checked in 87.5% of these laboratories. In 78.26% of laboratories suitable measures are taken to minimize formation of aerosols.In 95.6% of laboratories waste is disposed off as per bio-medical waste management handling rules. Laboratory of one private medical college was accredited with NABL and safety parameters were better in that laboratory. Installing safety engineered devices apparently contributes to significant decrease in injuries in laboratories; laboratory safety has to be a part of overall quality assurance programme in hospitals. Accreditation has to be made necessary for all laboratories.

Nematode-trapping fungi and fungus-associated bacteria interactions: the role of bacterial diketopiperazines and biofilms on Arthrobotrys oligospora surface in hyphal morphogenesis.

PubMed

Li, Lei; Yang, Min; Luo, Jun; Qu, Qing; Chen, Ying; Liang, Lianming; Zhang, Keqin

2016-11-01

In soil, nematode-trapping fungi and bacteria often share microhabitats and interact with each other, but effects of fungus-associated bacteria on its trap formation are underestimated. We have ascertained the presence of Stenotrophomonas and Rhizobium genera associated with A. oligospora GJ-1. After A. oligospora GJ-1 without associated bacteria (cured Arthrobotrys) was co-cultivated with Stenotrophomonas and its supernatant extract, microscopic study of hyphae from co-cultivation indicated that bacterial biofilm formation on hyphae was related to trap formation in fungi and Stenotrophomonas supernatant extract. Four diketopiperazines (DKPs) were purified from Stenotrophomonas supernatant extract that could not induce traps in the cured Arthrobotrys. When cured Arthrobotrys was cultured with Stenotrophomonas and one of DKPs, polar attachment, bacterial biofilms on hyphae and trap formation in fungi were observed. After cured Arthrobotrys with bacterial biofilms was consecutively transferred several times on nutrient poor medium, trap formation disappeared with the disappearance of bacterial biofilms on hyphae. DKPs could facilitate chemotaxis of Stenotrophomonas towards fungal extract which was suggested to contribute to bacterial biofilms on hyphae. Furthermore, when cured Arthrobotrys was cultured with Stenotrophomonas and DKPs in soil, trap formation in fungi and bacterial biofilms on hyphae were also observed, and the fungal activity against nematode was enhanced. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing

NASA Technical Reports Server (NTRS)

Shi, T.; Reeves, R. H.; Gilichinsky, D. A.; Friedmann, E. I.

1997-01-01

Viable bacteria were found in permafrost core samples from the Kolyma-Indigirka lowland of northeast Siberia. The samples were obtained at different depths; the deepest was about 3 million years old. The average temperature of the permafrost is -10 degrees C. Twenty-nine bacterial isolates were characterized by 16S rDNA sequencing and phylogenetic analysis, cell morphology, Gram staining, endospore formation, and growth at 30 degrees C. The majority of the bacterial isolates were rod shaped and grew well at 30 degrees C; but two of them did not grow at or above 28 degrees C, and had optimum growth temperatures around 20 degrees C. Thirty percent of the isolates could form endospores. Phylogenetic analysis revealed that the isolates fell into four categories: high-GC Gram-positive bacteria, beta-proteobacteria, gamma-proteobacteria, and low-GC Gram-positive bacteria. Most high-GC Gram-positive bacteria and beta-proteobacteria, and all gamma-proteobacteria, came from samples with an estimated age of 1.8-3.0 million years (Olyor suite). Most low-GC Gram-positive bacteria came from samples with an estimated age of 5,000-8,000 years (Alas suite).

Biofilm formation in geometries with different surface curvature and oxygen availability

NASA Astrophysics Data System (ADS)

Chang, Ya-Wen; Fragkopoulos, Alexandros A.; Marquez, Samantha M.; Kim, Harold D.; Angelini, Thomas E.; Fernández-Nieves, Alberto

2015-03-01

Bacteria in the natural environment exist as interface-associated colonies known as biofilms . Complex mechanisms are often involved in biofilm formation and development. Despite the understanding of the molecular mechanisms involved in biofilm formation, it remains unclear how physical effects in standing cultures influence biofilm development. The topology of the solid interface has been suggested as one of the physical cues influencing bacteria-surface interactions and biofilm development. Using the model organism Bacillus subtilis, we study the transformation of swimming bacteria in liquid culture into robust biofilms in a range of confinement geometries (planar, spherical and toroidal) and interfaces (air/water, silicone/water, and silicone elastomer/water). We find that B. subtilis form submerged biofilms at both solid and liquid interfaces in addition to air-water pellicles. When confined, bacteria grow on curved surfaces of both positive and negative Gaussian curvature. However, the confinement geometry does affect the resulting biofilm roughness and relative coverage. We also find that the biofilm location is governed by oxygen availability as well as by gravitational effects; these compete with each other in some situations. Overall, our results demonstrate that confinement geometry is an effective way to control oxygen availability and subsequently biofilm growth.

Enhance wastewater biological treatment through the bacteria induced graphene oxide hydrogel.

PubMed

Shen, Liang; Jin, Ziheng; Wang, Dian; Wang, Yuanpeng; Lu, Yinghua

2018-01-01

The interaction between bacteria and graphene-family materials like pristine graphene, graphene oxide (GO) and reduced graphene oxide (rGO) is such an elusive issue that its implication in environmental biotechnology is unclear. Herein, two kinds of self-assembled bio-rGO-hydrogels (BGHs) were prepared by cultivating specific Shewanella sp. strains with GO solution for the first time. The microscopic examination by SEM, TEM and CLSM indicated a porous 3D structure of BGHs, in which live bacteria firmly anchored and extracellular polymeric substances (EPS) abundantly distributed. Spectra of XRD, FTIR, XPS and Raman further proved that GO was reduced to rGO by bacteria along with the gelation process, which suggests a potential green technique to produce graphene. Based on the characterization results, four mechanisms for the BGH formation were proposed, i.e., stacking, bridging, rolling and cross-linking of rGO sheets, through the synergistic effect of activities and EPS from special bacteria. More importantly, the BGHs obtained in this study were found able to achieve unique cleanup performance that the counterpart free bacteria could not fulfill, as exemplified in Congo red decolorization and Cr(VI) bioreduction. These findings therefore enlighten a prospective application of graphene materials for the biological treatment of wastewaters in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inhibition of biofilm formation by T7 bacteriophages producing quorum-quenching enzymes.

PubMed

Pei, Ruoting; Lamas-Samanamud, Gisella R

2014-09-01

Bacterial growth in biofilms is the major cause of recalcitrant biofouling in industrial processes and of persistent infections in clinical settings. The use of bacteriophage treatment to lyse bacteria in biofilms has attracted growing interest. In particular, many natural or engineered phages produce depolymerases to degrade polysaccharides in the biofilm matrix and allow access to host bacteria. However, the phage-produced depolymerases are highly specific for only the host-derived polysaccharides and may have limited effects on natural multispecies biofilms. In this study, an engineered T7 bacteriophage was constructed to encode a lactonase enzyme with broad-range activity for quenching of quorum sensing, a form of bacterial cell-cell communication via small chemical molecules (acyl homoserine lactones [AHLs]) that is necessary for biofilm formation. Our results demonstrated that the engineered T7 phage expressed the AiiA lactonase to effectively degrade AHLs from many bacteria. Addition of the engineered T7 phage to mixed-species biofilms containing Pseudomonas aeruginosa and Escherichia coli resulted in inhibition of biofilm formation. Such quorum-quenching phages that can lyse host bacteria and express quorum-quenching enzymes to affect diverse bacteria in biofilm communities may become novel antifouling and antibiofilm agents in industrial and clinical settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Inhibition of Biofilm Formation by T7 Bacteriophages Producing Quorum-Quenching Enzymes

PubMed Central

Lamas-Samanamud, Gisella R.

2014-01-01

Bacterial growth in biofilms is the major cause of recalcitrant biofouling in industrial processes and of persistent infections in clinical settings. The use of bacteriophage treatment to lyse bacteria in biofilms has attracted growing interest. In particular, many natural or engineered phages produce depolymerases to degrade polysaccharides in the biofilm matrix and allow access to host bacteria. However, the phage-produced depolymerases are highly specific for only the host-derived polysaccharides and may have limited effects on natural multispecies biofilms. In this study, an engineered T7 bacteriophage was constructed to encode a lactonase enzyme with broad-range activity for quenching of quorum sensing, a form of bacterial cell-cell communication via small chemical molecules (acyl homoserine lactones [AHLs]) that is necessary for biofilm formation. Our results demonstrated that the engineered T7 phage expressed the AiiA lactonase to effectively degrade AHLs from many bacteria. Addition of the engineered T7 phage to mixed-species biofilms containing Pseudomonas aeruginosa and Escherichia coli resulted in inhibition of biofilm formation. Such quorum-quenching phages that can lyse host bacteria and express quorum-quenching enzymes to affect diverse bacteria in biofilm communities may become novel antifouling and antibiofilm agents in industrial and clinical settings. PMID:24951790

A Laboratory Course for Teaching Laboratory Techniques, Experimental Design, Statistical Analysis, and Peer Review Process to Undergraduate Science Students

ERIC Educational Resources Information Center

Gliddon, C. M.; Rosengren, R. J.

2012-01-01

This article describes a 13-week laboratory course called Human Toxicology taught at the University of Otago, New Zealand. This course used a guided inquiry based laboratory coupled with formative assessment and collaborative learning to develop in undergraduate students the skills of problem solving/critical thinking, data interpretation and…

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Clara S; Fakra, Sirine C; Emerson, David

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 {micro}m h(-1)). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS)more » spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger ({approx}100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.« less

The effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.

PubMed

Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

2011-08-01

The elucidation of the mechanisms by which diverse species survive and interact in drinking water (DW) biofilm communities may allow the identification of new biofilm control strategies. The purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from DW on biofilm formation. Six opportunistic bacteria, viz. Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp. isolated from a drinking water distribution systems (DWDS) were used to form single and multispecies biofilms in the presence and absence of crude cell-free supernatants produced by the partner bacteria. Biofilms were characterized in terms of mass and metabolic activity. Additionally, several physiological aspects regulating interspecies interactions (sessile growth rates, antimicrobial activity of cell-free supernatants, and production of iron chelators) were studied to identify bacterial species with biocontrol potential in DWDS. Biofilms of Methylobacterium sp. had the highest growth rate and M. mucogenicum biofilms the lowest. Only B. cepacia was able to produce extracellular iron-chelating molecules. A. calcoaceticus, B. cepacia, Methylobacterium sp. and M. mucogenicum biofilms were strongly inhibited by crude cell-free supernatants from the other bacteria. The crude cell-free supernatants of M. mucogenicum and S. capsulata demonstrated a high potential for inhibiting the growth of counterpart biofilms. Multispecies biofilm formation was strongly inhibited in the absence of A. calcoaceticus. Only crude cell-free supernatants produced by B. cepacia and A. calcoaceticus had no inhibitory effects on multispecies biofilm formation, while metabolite molecules of M. mucogenicum showed the most significant biocontrol potential.

A formative evaluation of problem-based learning as an instructional strategy in a medical laboratory technician course

NASA Astrophysics Data System (ADS)

Nelson, Diane Patricia

2002-09-01

This study is a formative evaluation of problem-based learning as an effective course delivery strategy in a second year introductory Medical Laboratory Technician discipline-specific hematology course. This strategy can serve two purposes in this type of course: discipline specific content knowledge and process skills learning. A needs study identified that students required additional workplace skills as they entered the clinical internship. Students tested well on the national registry examinations, discipline-specific content knowledge, but group process skills needed improvement in the areas of collaboration, communication, and critical reasoning. Problem-based learning was identified as an change intervention to help provide these skills. A search of the literature revealed that the Baker College cultural and physical environment would support this intervention. Twelve cases were written, situated in a clinical laboratory environment, addressing learning issues identified in a modified Delphi survey of laboratory personnel e.g. fiscal responsibility, turn-around time, invasiveness of laboratory techniques, and holistic view of healthcare environment. A hematology class of 13 students received the intervention. The cases were structured to proceed from instructor-centered (guided) learning issues to learner-centered learning issues. Observations of the in-group collaboration processes were documented, as well as oral presentations and critical reasoning, with students given periodic feedback on these skills. Student surveys provided data about satisfaction, attitude to PBL process, and self-efficacy. Multiple choice discipline-specific content examinations were given and compared with classes from the previous four years. The study found that students receiving the PBL treatment scored as well as or better than students from previous years on traditional multiple choice exams. Recall questions showed positive significance and application/analysis questions

Bacteria of leg atheromatous arteries responsible for inflammation.

PubMed

Olszewski, Waldemar Lech; Rutkowska, Joanna; Moscicka-Wesolowska, Maria; Swoboda-Kopec, Ewa; Stelmach, Ewa; Zaleska, Marzanna; Zagozda, Malgorzata

2016-09-01

Ischaemia of the lower limbs is frequently followed by inflammation and, in advanced cases, necrosis of peripheral tissues. Whether this is caused by arterial hypoperfusion only or by the presence of bacteria in the arterial walI as well remains unclear. The aim of the study was to prove the presence and source of bacteria in arterial specimens and evaluate their chemotactic properties resulting in the formation of periarterial cellular infiltrates. Bacterial culture and testing for 16sRNA were performed in fragments of popliteal artery harvested from amputated limbs. Carotid artery plaques served as controls. Fragments of arteries were transplanted into scid mice to evaluate their chemotactic activity for macrophages. a) higher prevalence of isolates and 16sRNA in atherosclerotic popliteal than carotid arteries, b) high density of plaque and periarterial infiltrates and mRNA level for pro-inflammatory cytokines in popliteal arteries, c) prevalent microbes were Staphylococcus aureus, S. epidermidis and Enterococci, d) foot skin and arterial bacterial phenotypes and DNA revealed evident similarities, and e) more intensive mouse macrophage accumulation in popliteal than carotid implants into scid mice. The presence of bacteria in the lower limb arterial wall was documented. They may predispose to inflammation secondary to ischaemic changes.

Theory of periodic swarming of bacteria: Application to Proteus mirabilis

NASA Astrophysics Data System (ADS)

Czirók, A.; Matsushita, M.; Vicsek, T.

2001-03-01

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth), a series of concentric rings are developed as the bacteria multiply and swarm following a scenario that periodically repeats itself. We have developed a theoretical description for this process in order to obtain a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. Our approach is based on simple assumptions directly related to the latest experimental observations on colony formation under various conditions. The corresponding one-dimensional model consists of two coupled differential equations investigated here both by numerical integrations and by analyzing the various expressions obtained from these equations using a few natural assumptions about the parameters of the model. We determine the phase diagram corresponding to systems exhibiting periodic swarming, and discuss in detail how the various stages of the colony development can be interpreted in our framework. We point out that all of our theoretical results are in excellent agreement with the complete set of available observations. Thus the present study represents one of the few examples where self-organized biological pattern formation is understood within a relatively simple theoretical approach, leading to results and predictions fully compatible with experiments.

Enhancement of neutrophil autophagy by an IVIG preparation against multidrug-resistant bacteria as well as drug-sensitive strains.

PubMed

Itoh, Hiroshi; Matsuo, Hidemasa; Kitamura, Naoko; Yamamoto, Sho; Higuchi, Takeshi; Takematsu, Hiromu; Kamikubo, Yasuhiko; Kondo, Tadakazu; Yamashita, Kouhei; Sasada, Masataka; Takaori-Kondo, Akifumi; Adachi, Souichi

2015-07-01

Autophagy occurs in human neutrophils after the phagocytosis of multidrug-resistant bacteria and drug-sensitive strains, including Escherichia coli and Pseudomonas aeruginosa. The present study detected autophagy by immunoblot analysis of LC3B conversion, by confocal scanning microscopic examination of LC3B aggregate formation and by transmission electron microscopic examination of bacteria-containing autophagosomes. Patients with severe bacterial infections are often treated with IVIG alongside antimicrobial agents. Here, we showed that IVIG induced neutrophil-mediated phagocytosis of multidrug-resistant strains. Compared with untreated neutrophils, neutrophils exposed to IVIG showed increased levels of bacterial cell killing, phagocytosis, O(2)(-) release, MPO release, and NET formation. IVIG also increased autophagy in these cells. Inhibiting the late phase of autophagy (fusion of lysosomes with autophagosomes) with bafilomycin A1-reduced, neutrophil-mediated bactericidal activity. These findings indicate that autophagy plays a critical role in the bactericidal activity mediated by human neutrophils. Furthermore, the autophagosomes within the neutrophils contained bacteria only and their organelles only, or both bacteria and their organelles, a previously undocumented observation. Taken together, these results suggest that the contents of neutrophil autophagosomes may be derived from specific autophagic systems, which provide the neutrophil with an advantage. Thus, IVIG promotes the neutrophil-mediated killing of multidrug-resistant bacteria as well as drug-sensitive strains. © Society for Leukocyte Biology.

Enhancement of neutrophil autophagy by an IVIG preparation against multidrug-resistant bacteria as well as drug-sensitive strains

PubMed Central

Itoh, Hiroshi; Matsuo, Hidemasa; Kitamura, Naoko; Yamamoto, Sho; Higuchi, Takeshi; Takematsu, Hiromu; Kamikubo, Yasuhiko; Kondo, Tadakazu; Yamashita, Kouhei; Sasada, Masataka; Takaori-Kondo, Akifumi; Adachi, Souichi

2015-01-01

Autophagy occurs in human neutrophils after the phagocytosis of multidrug-resistant bacteria and drug-sensitive strains, including Escherichia coli and Pseudomonas aeruginosa. The present study detected autophagy by immunoblot analysis of LC3B conversion, by confocal scanning microscopic examination of LC3B aggregate formation and by transmission electron microscopic examination of bacteria-containing autophagosomes. Patients with severe bacterial infections are often treated with IVIG alongside antimicrobial agents. Here, we showed that IVIG induced neutrophil-mediated phagocytosis of multidrug-resistant strains. Compared with untreated neutrophils, neutrophils exposed to IVIG showed increased levels of bacterial cell killing, phagocytosis, O2− release, MPO release, and NET formation. IVIG also increased autophagy in these cells. Inhibiting the late phase of autophagy (fusion of lysosomes with autophagosomes) with bafilomycin A1-reduced, neutrophil-mediated bactericidal activity. These findings indicate that autophagy plays a critical role in the bactericidal activity mediated by human neutrophils. Furthermore, the autophagosomes within the neutrophils contained bacteria only and their organelles only, or both bacteria and their organelles, a previously undocumented observation. Taken together, these results suggest that the contents of neutrophil autophagosomes may be derived from specific autophagic systems, which provide the neutrophil with an advantage. Thus, IVIG promotes the neutrophil-mediated killing of multidrug-resistant bacteria as well as drug-sensitive strains. PMID:25908735

[Secretion analysis of pathogenic bacteria culture in 115 rural chronic nasal-sinusitis patients].

PubMed

Zhang, Xiaoyuan; Sun, Jingwu; Chu, Shu

2014-05-01

To investigate the bacteria distribution, drug bacterial sensitivity characteristics of the rural chronic rhinosinusitis (CRS). And to explore the effect of antibiotic on pathogenic bacteria culture. Choose nasal sinus secretions from 115 CRS patients living in rural areas. Aerobic bacteria culture, anaerobic bacteria culture and drug sensitive test were procedured for each sample. At the same time the use of antibiotics nearly 2 months and nearly 2 weeks were collected. Among one hundred and fifteen specimens, 17 kinds of germs were detected in 37 cases, the positive rate of aerobic bacteria was 32.17%. Staphylococcus aureus and epidermis staphylococcus aureus the most common type of aerobe in CRS patients at rural areas. There was negative result in the anaerobic bacteria culture of 17 maxillary sinus specimen. The cases of using antibiotics nearly 2 months was up to 90, accounting for 78.26%. Nearly 2 weeks, 73 cases, accounting for 63.48%. The chi-square analysis showed high bacterial culture rate, in chronic rhinosinusitis with nasal polyps (CRSwNP group), which revealed correlation between bacterial infection factors and nasal polyps formation. For CRS patients with positive result of bacterial culture, they were sensitive to ofloxacin, cefotaxime, organism, ciprofloxacin, magnitude cephalosporin, and were drug fast to penicillin G, ampicillin, erythromycin. No specific differences was found in the bacteria distribution of rural CRS. antibiotics abusage in rural CRS patients and the anaerobic bacteria culture techniques is the main factor resulting in low culture rate. Rational use of antimicrobial agents should be established on the basis of the bacterial culture and drug sensitive test.

Methanotrophic bacteria.

PubMed Central

Hanson, R S; Hanson, T E

1996-01-01

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

Towards a rational antimicrobial testing policy in the laboratory.

PubMed

Banaji, N; Oommen, S

2011-01-01

Antimicrobial policy for prophylactic and therapeutic use of antimicrobials in a tertiary care setting has gained importance. A hospital's antimicrobial policy as laid down by its hospital infection control team needs to include inputs from the microbiology laboratory, besides the pharmacy and therapeutic committee. Therefore, it is of utmost importance that clinical microbiologists across India follow international guidelines and also take into account local settings, especially detection and presence of resistance enzymes. This article draws a framework for rational antimicrobial testing in our laboratories in tertiary care centers, from the Clinical and Laboratory Standards Institute guidelines. It does not address testing methodologies but suggests ways and means by which antimicrobial susceptibility reporting can be rendered meaningful not only to the treating physician but also to the resistance monitoring epidemiologist. It hopes to initiate some standardization in rational choice of antimicrobial testing in laboratories in the country pertaining to nonfastidious bacteria.

Dormant state in bacteria: Conceptions and implications for terrestrial biogeoscience and astrobiology

NASA Astrophysics Data System (ADS)

Mulyukin, A.

2003-04-01

Gaining insight into strategies and mechanisms that ensure long term-preservation of microorganisms in various environments, including cold habitats, is a very important issue for terrestrial biogeoscience and astrobiology. This communication has a focus on the analysis of the published and our experimental data regarding the dormant state of different microorganisms, with an emphasis on non-spore-forming bacteria, which are widely spread in numerous ecological niches (e.g. permafrost sediments). Albeit it is recognized that one of the strategies to endure environmental stresses is entering of non-spore-forming bacteria into the viable-but-non-culturable state, a question of whether these microorganisms have the resting stage remains unclear. However, our previous studies showed that non-spore-forming bacteria and yeast could form cyst-like cells that possess many attributes of constitutively resting cells. As applied to the survival strategy of non-spore-forming bacteria in permafrost sediments, recognizing a very important role of the viable-but-nonculturable state in asporogenous bacteria, we however believe that their long-term maintenance in such habitats is due to the formation of cyst-like cells. Interestingly, bacterial isolates from permafrost sediments showed a greater productivity of autoregulatory factors, favoring the transition of cells into the resting state, and a more elevated resistance to some stresses than closely related collection strains. This suggests a greater potentiality of the permafrost isolates to enter the resting stage and thereby to survive for millennia years in natural habitats. However, it is known that only a little part of microorganisms that are present in environmental samples can be enumerated by standard plating on agar media, and a discrepancy between the total number of cells and those capable of forming colonies is a rather common case. Such a discrepancy can be due to either the actual non-culturability of microbial

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

PubMed Central

Young, Jonathan W; Locke, James C W; Altinok, Alphan; Rosenfeld, Nitzan; Bacarian, Tigran; Swain, Peter S; Mjolsness, Eric; Elowitz, Michael B

2014-01-01

Quantitative single-cell time-lapse microscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior. We describe the application of this method to imaging bacteria by using an automated microscopy system. This protocol has been used to analyze sporulation and competence differentiation in Bacillus subtilis, and to quantify gene regulation and its fluctuations in individual Escherichia coli cells. The protocol involves seeding and growing bacteria on small agarose pads and imaging the resulting microcolonies. Images are then reviewed and analyzed using our laboratory's custom MATLAB analysis code, which segments and tracks cells in a frame-to-frame method. This process yields quantitative expression data on cell lineages, which can illustrate dynamic expression profiles and facilitate mathematical models of gene circuits. With fast-growing bacteria, such as E. coli or B. subtilis, image acquisition can be completed in 1 d, with an additional 1–2 d for progressing through the analysis procedure. PMID:22179594

The Design of Simple Bacterial Microarrays: Development towards Immobilizing Single Living Bacteria on Predefined Micro-Sized Spots on Patterned Surfaces.

PubMed

Arnfinnsdottir, Nina Bjørk; Ottesen, Vegar; Lale, Rahmi; Sletmoen, Marit

2015-01-01

In this paper we demonstrate a procedure for preparing bacterial arrays that is fast, easy, and applicable in a standard molecular biology laboratory. Microcontact printing is used to deposit chemicals promoting bacterial adherence in predefined positions on glass surfaces coated with polymers known for their resistance to bacterial adhesion. Highly ordered arrays of immobilized bacteria were obtained using microcontact printed islands of polydopamine (PD) on glass surfaces coated with the antiadhesive polymer polyethylene glycol (PEG). On such PEG-coated glass surfaces, bacteria were attached to 97 to 100% of the PD islands, 21 to 62% of which were occupied by a single bacterium. A viability test revealed that 99% of the bacteria were alive following immobilization onto patterned surfaces. Time series imaging of bacteria on such arrays revealed that the attached bacteria both divided and expressed green fluorescent protein, both of which indicates that this method of patterning of bacteria is a suitable method for single-cell analysis.

Microbial Transformation of Dicarboxylic Acids by Airborne Bacteria

NASA Astrophysics Data System (ADS)

Cote, V.; Ariya, P.

2004-05-01

Organic aerosols are assumed to be key players in driving climatic changes and can cause health problems for human. Dicarboxylic acids (DCA) include a large fraction of identified important class of organic aerosols. In addition to direct sources, DCA are partly formed as the result of ozonolysis of terpenes and cyclic alkenes. Previous works in our laboratory show that airborne fungi collected from urban and suburban air play an important role in the transformation of severals organic aerosols such as DCA. Our present study focuses on understanding the potential chemical transformation induced by airborne bacteria and on identification of the transformation products. Airborne bacteria have been collected using a biosampler and cultivated on a solid media. Each bacterial colony is being tested by HPLC for their ability to transform DCA in liquid cultures. Also, GC-MS, SPME and NMR are being used to identify the metabolites generated from the transformation. We will present our preliminary results and we will discuss the application of bacterial activities on the chemical transformation of organics in atmosphere.

Effect of flow on bacterial transport and biofilm formation in saturated porous media

NASA Astrophysics Data System (ADS)

Rusconi, R.

2016-12-01

Understanding the transport of bacteria in saturated porous media is crucial for many applications ranging from the management of pumping wells subject to bio-clogging to the design of new bioremediation schemes for subsurface contamination. However, little is known about the spatial distribution of bacteria at the pore scale, particularly when small-scale heterogeneities - always present even in seemingly homogeneous aquifers - lead to preferential pathways for groundwater flow. In particular, the coupling of flow and motility has recently been shown to strongly affect bacterial transport1, and this leads us to predict that subsurface flow may strongly affect the dispersal of bacteria and the formation of biofilms in saturated aquifers. I present here microfluidic experiments combined with numerical simulations to show how the topological features of the flow correlate with bacterial concentration and promote the attachment of bacteria to specific regions of the pore network, which will ultimately influence the formations of biofilms. These results highlight the intimate link between small-scale biological processes and transport in porous media.

The reaction of monochloramine and hydroxylamine: implications for ammonia–oxidizing bacteria in chloraminated drinking water

EPA Science Inventory

Drinking water chloramine use may promote ammonia–oxidizing bacteria (AOB) growth because of naturally occurring ammonia, residual ammonia remaining from chloramine formation, and ammonia released from chloramine decay and demand. A rapid chloramine residual loss is often associa...

Survival of pathogenic bacteria in compost with special reference to Escherichia coli.

PubMed

Gong, Chun-ming; Koichi, Inoue; Shunji, Inanaga; Takashi, Someya

2005-01-01

Application of compost in agricultural practice could potentially cause contamination of foodstuffs with pathogenic bacteria such as Escherichia coli O157:H7 (E. Coli O157). We investigated pathogenic bacteria in compost collected from the compost facilities, and evaluated the survival of E. coli K12 and O157 in laboratory experiments. Out of 19 compost product samples, coliform bacteria and salmonella were detected in 7 and 3 samples respectively. The number of coliform bacteria was 1.8 x 10(2) to 2.5 x 10(6) CFU/g dw and that of salmonella was 4.2 x 10(1) to 6.0 x 10(3) CFU/g dw. Moreover, coliform bacteria, fecal coliform, E. coli and salmonella were detected during composting at 54 degrees C to 67 degrees C. The results indicated that moisture content was a very important factor to the heat sensitivity of pathogenic bacteria in compost, E. coil in compost of high moisture content was more sensitive than that in compost of low moisture content, cells harvested in logarithmic phase was more sensitive than these in stationary phase, and E. coli K12 was more sensitive than E. coli O157. Based on the D values, the lethal time of E. coli K12 and O157 from l0(8) to 10(0) CFU/g dw were 16.3 and 28.8 min, respectively, at 60 degrees C in compost with 40% moisture content. However, some E. coil cells survived in composting process at 54 degrees C to 67 degrees C. Water potential (low moisture content) and physiological aspects of bacteria (stationary phase) could explain only in part of the prolonged survival of E. coil in compost, and there should be some other factors that are conducive to bacterial survival in compost.

Health significance and occurrence of injured bacteria in drinking water

NASA Technical Reports Server (NTRS)

McFeters, G. A.; LeChevallier, M. W.; Singh, A.; Kippin, J. S.

1986-01-01

Enteropathogenic and indicator bacteria become injured in drinking water with exposure to sublethal levels of various biological, chemical and physical factors. One manifestation of this injury is the inability to grow and form colonies on selective media containing surfactants. The resulting underestimation of indicator bacteria can lead to a false estimation of water potability. m-T7 medium was developed specifically for the recovery of injured coliforms (both "total" and fecal) in drinking water. The m-T7 method was used to survey operating drinking water treatment and distribution systems for the presence of injured coliforms that were undetected with currently used media. The mean recovery with m-Endo LES medium was less than 1/100 ml while it ranged between 6 and 68/100ml with m-T7 agar. The majority of samples giving positive results with m-T7 medium yielded no detectable coliforms with m-Endo LES agar. Over 95% of the coliform bacteria in these samples were injured. Laboratory experiments were also done to ascribe the virulence of injured waterborne pathogens. Enteropathogens including Salmonella typhimurium, Yersinia enterocolitica and Shigella spp. required up to 20 times the chlorine levels to produce the same injury in enterotoxigenic Escherichia coli (ETEC) and nonpathogenic coliforms. Similar results were seen with Y. enterocolitica exposed to copper. The recovery of ETEC was followed by delayed enterotoxin production, both in vitro and in the gut of experimental animals. This indicates that injured waterborne enteropathogenic bacteria can be virulent.

The Efficient Clade: Lactic Acid Bacteria for Industrial Chemical Production.

PubMed

Sauer, Michael; Russmayer, Hannes; Grabherr, Reingard; Peterbauer, Clemens K; Marx, Hans

2017-08-01

Lactic acid bacteria are well known to be beneficial for food production and, as probiotics, they are relevant for many aspects of health. However, their potential as cell factories for the chemical industry is only emerging. Many physiological traits of these microorganisms, evolved for optimal growth in their niche, are also valuable in an industrial context. Here, we illuminate these features and describe why the distinctive adaptation of lactic acid bacteria is particularly useful when developing a microbial process for chemical production from renewable resources. High carbon uptake rates with low biomass formation combined with strictly regulated simple metabolic pathways, leading to a limited number of metabolites, are among the key factors defining their success in both nature and industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

How-To-Do-It: Recombinant DNA Technology in the High School Biology Laboratory.

ERIC Educational Resources Information Center

Myers, Richard

1988-01-01

Describes a basic biotechnology investigation that includes restriction and ligation of plasmid DNA, transformation of bacteria and cloning of these bacterial cells. Discusses laboratory procedures and another activity in the identification of unknown plasmids by studying agarose gel electrophoresis photographs. (CW)

Power output of microbial fuel cell emphasizing interaction of anodic binder with bacteria

NASA Astrophysics Data System (ADS)

Li, Hongying; Liao, Bo; Xiong, Juan; Zhou, Xingwang; Zhi, Huozhen; Liu, Xiang; Li, Xiaoping; Li, Weishan

2018-03-01

Electrochemically active biofilm is necessary for the electron transfer between bacteria and anodic electrode in microbial fuel cells and selecting the type of anodic electrode material that favours formation of electrochemically active biofilm is crucial for the microbial fuel cell operation. We report a new finding that the interaction of anodic binder with bacteria plays more important role than its hydrophilicity for forming an electrochemically active biofilm, which is emphasized by applying poly(bisphenol A-co-epichorohydrin) as an anodic binder of the microbial fuel cell based on carbon nanotubes as anodic electrode and Escherichia coli as bacterium. The physical characterizations and electrochemical measurements demonstrate that poly(bisphenol A-co-epichorohydrin) exhibits a strong interaction with bacteria and thus provides the microbial fuel cell with excellent power density output. The MFC using poly(bisphenol A-co-epichorohydrin) reaches a maximum power density output of 3.8 W m-2. This value is larger than that of the MFCs using polytetrafluoroethylene that has poorer hydrophilicity, or polyvinyl alcohol that has better hydrophilicity but exhibits weaker interaction with bacteria than poly(bisphenol A-co-epichorohydrin).

Formation of Glycidyl Fatty Acid Esters Both in Real Edible Oils during Laboratory-Scale Refining and in Chemical Model during High Temperature Exposure.

PubMed

Cheng, Weiwei; Liu, Guoqin; Liu, Xinqi

2016-07-27

In the present study, the formation mechanisms of glycidyl fatty acid esters (GEs) were investigated both in real edible oils (soybean oil, camellia oil, and palm oil) during laboratory-scale preparation and refining and in chemical model (1,2-dipalmitin (DPG) and 1-monopalmitin (MPG)) during high temperature exposure (160-260 °C under nitrogen). The formation process of GEs in the chemical model was monitored using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. The results showed that the roasting and pressing process could produce certain amounts of GEs that were much lower than that produced in the deodorization process. GE contents in edible oils increased continuously and significantly with increasing deodorization time below 200 °C. However, when the temperature exceeded 200 °C, GE contents sharply increased in 1-2 h followed by a gradual decrease, which could verify a simultaneous formation and degradation of GEs at high temperature. In addition, it was also found that the presence of acylglycerol (DAGs and MAGs) could significantly increase the formation yield of GEs both in real edible oils and in chemical model. Compared with DAGs, moreover, MAGs displayed a higher formation capacity but substantially lower contribution to GE formation due to their low contents in edible oils. In situ ATR-FTIR spectroscopic evidence showed that cyclic acyloxonium ion intermediate was formed during GE formation derived from DPG and MPG in chemical model heated at 200 °C.

Streptomyces lunalinharesii Strain 235 Shows the Potential to Inhibit Bacteria Involved in Biocorrosion Processes

PubMed Central

Pacheco da Rosa, Juliana; Korenblum, Elisa; Franco-Cirigliano, Marcella Novaes; Abreu, Fernanda; Lins, Ulysses; Soares, Rosângela M. A.; Macrae, Andrew; Seldin, Lucy; Coelho, Rosalie R. R.

2013-01-01

Four actinomycete strains previously isolated from Brazilian soils were tested for their antimicrobial activity against Bacillus pumilus LF-4 and Desulfovibrio alaskensis NCIMB 13491, bacteria that are well known to be involved in biofilm formation and biocorrosion. Strain 235, belonging to the species Streptomyces lunalinharesii, inhibited the growth of both bacteria. The antimicrobial activity was seen over a wide range of pH, and after treatment with several chemicals and heat but not with proteinase K and trypsin. The antimicrobial substances present in the concentrated supernatant from growth media were partially characterized by SDS-PAGE and extracellular polypeptides were seen. Bands in the size range of 12 to 14.4 kDa caused antimicrobial activity. Transmission electron microscopy of D. alaskensis cells treated with the concentrated supernatant containing the antimicrobial substances revealed the formation of prominent bubbles, the spherical double-layered structures on the cell membrane, and the periplasmic space completely filled with electron-dense material. This is the first report on the production of antimicrobial substances by actinomycetes against bacteria involved in biocorrosion processes, and these findings may be of great relevance as an alternative source of biocides to those currently employed in the petroleum industry. PMID:23484107

Metallic corrosion processes reactivation sustained by iron-reducing bacteria: Implication on long-term stability of protective layers

NASA Astrophysics Data System (ADS)

Esnault, L.; Jullien, M.; Mustin, C.; Bildstein, O.; Libert, M.

In deep geological environments foreseen for the disposal of radioactive waste, metallic containers will undergo anaerobic corrosion. In this context, the formation of corrosion products such as magnetite may reduce the rate of corrosion processes through the formation of a protective layer. This study aims at determining the direct impact of iron-reducing bacteria (IRB) activity on the stability of corrosion protective layers. Batch experiments investigating iron corrosion processes including the formation of secondary magnetite and its subsequent alteration in the presence of IRB show the bacteria ability to use structural Fe(III) for respiration which leads to the sustainment of a high corrosion rate. With the bio-reduction of corrosion products such as magnetite, and H 2 as electron donor, IRB promote the reactivation of corrosion processes in corrosive environments by altering the protective layer. This phenomenon could have a major impact on the long-term stability of metallic compounds involved in multi-barrier system for high-level radioactive waste containment.

Gut immunity in a protochordate involves a secreted immunoglobulin-type mediator binding host chitin and bacteria.

PubMed

Dishaw, Larry J; Leigh, Brittany; Cannon, John P; Liberti, Assunta; Mueller, M Gail; Skapura, Diana P; Karrer, Charlotte R; Pinto, Maria R; De Santis, Rosaria; Litman, Gary W

2016-02-15

Protochordate variable region-containing chitin-binding proteins (VCBPs) consist of immunoglobulin-type V domains and a chitin-binding domain (CBD). VCBP V domains facilitate phagocytosis of bacteria by granulocytic amoebocytes; the function of the CBD is not understood. Here we show that the gut mucosa of Ciona intestinalis contains an extensive matrix of chitin fibrils to which VCBPs bind early in gut development, before feeding. Later in development, VCBPs and bacteria colocalize to chitin-rich mucus along the intestinal wall. VCBP-C influences biofilm formation in vitro and, collectively, the findings of this study suggest that VCBP-C may influence the overall settlement and colonization of bacteria in the Ciona gut. Basic relationships between soluble immunoglobulin-type molecules, endogenous chitin and bacteria arose early in chordate evolution and are integral to the overall function of the gut barrier.

Role of Organic Acids in Bioformation of Kaolinite: Results of Laboratory Experiments

NASA Astrophysics Data System (ADS)

Bontognali, T. R. R.; Vasconcelos, C.; McKenzie, J. A.

2012-04-01

Clay minerals and other solid silica phases have a broad distribution in the geological record and greatly affect fundamental physicochemical properties of sedimentary rocks, including porosity. An increasing number of studies suggests that microbial activity and microbially produced organic acids might play an important role in authigenic clay mineral formation, at low temperatures and under neutral pH conditions. In particular, early laboratory experiments (Linares and Huertas, 1971) reported the precipitation of kaolinite in solutions of SiO2 and Al2O3 with different molar ratios SiO2/Al2O3, together with fulvic acid (a non-characterized mixture of many different acids containing carboxyl and phenolate groups) that was extracted from peat soil. Despite many attempts, these experiments could not be reproduced until recently. Fiore et al. (2011) hypothesized that the non-sterile fulvic acid might have contained microbes that participated in the formation of kaolinite. Using solutions saturated with Si and Al and containing oxalate and/or mixed microbial culture extracted from peat-moss soil, they performed incubation experiments, which produced kaolinite exclusively in solutions containing oxalate and microbes. We proposed to test the role of specific organic acids for kaolinite formation, conducting laboratory experiments at 25˚C, with solutions of sodium silicate, aluminum chloride and various organic compounds (i.e. EDTA, citric acid, succinic acid and oxalic acid). Specific organic acids may stabilize aluminum in octahedral coordination positions, which is crucial for the initial nucleation step. In our experiments, a poorly crystalline mineral that is possibly a kaolinite precursor formed exclusively in the presence of succinic acid. In experiments with other organic compounds, no incorporation of Al was observed, and amorphous silica was the only precipitated phase. In natural environments, succinic acid is produced by a large variety of microbes as an

Radionuclides, inorganic constituents, organic compounds, and bacteria in water from selected wells and springs from the southern boundary of the Idaho National Engineering Laboratory to the Hagerman Area, Idaho, 1991

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartholomay, R.C.; Edwards, D.D.; Campbell, L.J.

1993-11-01

The US Geological Survey and the Idaho Department of Water Resources, in response to a request from the US Department of Energy, sampled 18 sites as part of a long-term project to monitor water quality of the Snake River Plain aquifer from the southern boundary of the Idaho National Engineering Laboratory to the Hagerman area. Water samples were collected and analyzed for manmade pollutants and naturally occurring constituents. The samples were collected from six irrigation wells, seven domestic wells, two springs, one stock well, one dairy well, and one observation well. Quality assurance samples also were collected and analyzed. Themore » water samples were analyzed for selected radionuclides, inorganic constituents, organic compounds, and bacteria. None of the samples analyzed for radionuclides, inorganic constituents, or organic compounds exceeded the established maximum contaminant levels for drinking water. Most of the radionuclide and inorganic constituent concentrations exceeded their respective reporting levels. All the samples analyzed for dissolved organic carbon had concentrations that exceeded their reporting level. Concentrations of 1,1,1 -trichloroethane exceeded the reporting level in two water samples. Two samples and a quality assurance replicate contained reportable concentrations of 2, 4-D. One sample contained fecal coliform bacteria counts that exceeded established maximum contaminant levels for drinking water.« less

Caenorhabditis elegans star formation and negative chemotaxis induced by infection with corynebacteria.

PubMed

Antunes, Camila Azevedo; Clark, Laura; Wanuske, Marie-Therès; Hacker, Elena; Ott, Lisa; Simpson-Louredo, Liliane; de Luna, Maria das Gracas; Hirata, Raphael; Mattos-Guaraldi, Ana Luíza; Hodgkin, Jonathan; Burkovski, Andreas

2016-01-01

Caenorhabditis elegans is one of the major model systems in biology based on advantageous properties such as short life span, transparency, genetic tractability and ease of culture using an Escherichia coli diet. In its natural habitat, compost and rotting plant material, this nematode lives on bacteria. However, C. elegans is a predator of bacteria, but can also be infected by nematopathogenic coryneform bacteria such Microbacterium and Leucobacter species, which display intriguing and diverse modes of pathogenicity. Depending on the nematode pathogen, aggregates of worms, termed worm-stars, can be formed, or severe rectal swelling, so-called Dar formation, can be induced. Using the human and animal pathogens Corynebacterium diphtheriae and Corynebacterium ulcerans as well as the non-pathogenic species Corynebacterium glutamicum, we show that these coryneform bacteria can also induce star formation slowly in worms, as well as a severe tail-swelling phenotype. While C. glutamicum had a significant, but minor influence on survival of C. elegans, nematodes were killed after infection with C. diphtheriae and C. ulcerans. The two pathogenic species were avoided by the nematodes and induced aversive learning in C. elegans.

Laboratory Investigation of Ice Formation and Elimination in the Induction System of a Large Twin-engine Cargo Aircraft

NASA Technical Reports Server (NTRS)

Colis, William D

1947-01-01

The icing characteristics, the de-icing rate with hot air, and the effect of impact ice on fuel metering and mixture distribution have been determined in a laboratory investigation of that part of the engine induction system consisting of a three-barrel injection-type carburetor and a supercharger housing with spinner-type fuel injection from an 18-cylinder radial engine used on a large twin-engine cargo airplane. The induction system remained ice-free at carburetor-air temperatures above 36 F regardless of the moisture content of the air. Between carburetor-air temperatures of 32 F and 36 F with humidity ratios in excess of saturation, serious throttling ice formed in the carburetor because of expansion cooling of the air; at carburetor-air temperatures below 32 F with humidity ratios in excess of saturation, serious impact-ice formations occurred, Spinner-type fuel injection at the entrance to the supercharger and heating of the supercharger-inlet elbow and the guide vanes by the warn oil in the rear engine housing are design features that proved effective in eliminating fuel-evaporation icing and minimized the formation of throttling ice below the carburetor. Air-flow recovery time with fixed throttle was rapidly reduced as the inlet -air wet -bulb temperature was increased to 55 F; further temperature increase produced negligible improvement in recovery time. Larger ice formations and lower icing temperatures increased the time required to restore proper air flow at a given wet-bulb temperature. Impact-ice formations on the entrance screen and the top of the carburetor reduced the over-all fuel-air ratio and increased the spread between the over-all ratio and the fuel-air ratio of the individual cylinders. The normal spread of fuel-air ratio was increased from 0.020 to 0.028 when the left quarter of the entrance screen was blocked in a manner simulating the blocking resulting from ice formations released from upstream duct walls during hot-air de-icing.

Inhibition of Streptococcus mutans biofilm formation, extracellular polysaccharide production, and virulence by an oxazole derivative.

PubMed

Chen, Lulu; Ren, Zhi; Zhou, Xuedong; Zeng, Jumei; Zou, Jing; Li, Yuqing

2016-01-01

Dental caries, a biofilm-related oral disease, is a result of disruption of the microbial ecological balance in the oral environment. Streptococcus mutans, which is one of the primary cariogenic bacteria, produces glucosyltransferases (Gtfs) that synthesize extracellular polysaccharides (EPSs). The EPSs, especially water-insoluble glucans, contribute to the formation of dental plaque, biofilm stability, and structural integrity, by allowing bacteria to adhere to tooth surfaces and supplying the bacteria with protection against noxious stimuli and other environmental attacks. The identification of novel alternatives that selectively inhibit cariogenic organisms without suppressing oral microbial residents is required. The goal of the current study is to investigate the influence of an oxazole derivative on S. mutans biofilm formation and the development of dental caries in rats, given that oxazole and its derivatives often exhibit extensive and pharmacologically important biological activities. Our data shows that one particular oxazole derivative, named 5H6, inhibited the formation of S. mutans biofilms and prevented synthesis of extracellular polysaccharides by antagonizing Gtfs in vitro, without affecting the growth of the bacteria. In addition, topical applications with the inhibitor resulted in diminished incidence and severity of both smooth and sulcal surface caries in vivo with a lower percentage of S. mutans in the animals' dental plaque compared to the control group (P < 0.05). Our results showed that this oxazole derivative has the capacity to inhibit biofilm formation and cariogenicity of S. mutans.

Painting with light-powered bacteria.

PubMed

Arlt, Jochen; Martinez, Vincent A; Dawson, Angela; Pilizota, Teuta; Poon, Wilson C K

2018-02-22

Self-assembly is a promising route for micro- and nano-fabrication with potential to revolutionise many areas of technology, including personalised medicine. Here we demonstrate that external control of the swimming speed of microswimmers can be used to self assemble reconfigurable designer structures in situ. We implement such 'smart templated active self assembly' in a fluid environment by using spatially patterned light fields to control photon-powered strains of motile Escherichia coli bacteria. The physics and biology governing the sharpness and formation speed of patterns is investigated using a bespoke strain designed to respond quickly to changes in light intensity. Our protocol provides a distinct paradigm for self-assembly of structures on the 10 μm to mm scale.

Large-Scale Femtoliter Droplet Array for Single Cell Efflux Assay of Bacteria.

PubMed

Iino, Ryota; Sakakihara, Shouichi; Matsumoto, Yoshimi; Nishino, Kunihiko

2018-01-01

Large-scale femtoliter droplet array as a platform for single cell efflux assay of bacteria is described. Device microfabrication, femtoliter droplet array formation and concomitant enclosure of single bacterial cells, fluorescence-based detection of efflux activity at the single cell level, and collection of single cells from droplet and subsequent gene analysis are described in detail.

Preventive effects of an original combination of grape seed polyphenols with amine fluoride on dental biofilm formation and oxidative damage by oral bacteria.

PubMed

Furiga, A; Roques, C; Badet, C

2014-04-01

To investigate the preventive effects of an original combination of a grape seed extract (GSE) with an amine fluoride (Fluorinol(®) ) on dental plaque formation and oxidative damage caused by oral bacteria. The antibacterial activity of the compounds was assessed using the broth macrodilution method, and their antiplaque activity was evaluated on a multispecies biofilm grown on saliva-coated hydroxyapatite discs. The effect on glucosyltransferases activity was analysed through reductions in the overall reaction and the quantity of insoluble glucan synthesized. The combination of 2000 μg ml(-1) of GSE with 10·2 mg ml(-1) of Fluorinol(®) significantly decreased the biofilm formation (up to 4·76 log10 of reduction) and inhibited by 97·4% the insoluble glucan synthesis by glucosyltransferases. The antioxidant activity of this combination, alone or incorporated into a formulated mouthwash (Eludril daily(®) ), was determined using the Trolox equivalent antioxidant capacity assay (TEAC), and both showed significantly greater antioxidant capacity than vitamin C. The GSE/Fluorinol(®) combination showed both a significant antiplaque activity and an important antioxidant capacity in vitro, without any bactericidal effects. This is, to our knowledge, the first report on the properties of an original combination of a polyphenolic extract with amine fluoride that could be used for the prevention of oral diseases and oxidative damage associated. © 2013 The Society for Applied Microbiology.

Nurses’ uniforms: How many bacteria do they carry after one shift?

PubMed Central

Sanon, Marie-Anne; Watkins, Sally

2013-01-01

This pilot study investigated the pathogens that nurses are potentially bringing into the public and their home when they wear work uniforms outside of the work environment. To achieve this, sterilized uniforms were distributed to 10 nurses at a local hospital in Washington State at the beginning of their shift. Worn uniforms were collected at the end of the shifts and sent to a laboratory for analysis. Four tests were conducted: 1) a heterotrophic growth plate count, 2) methicillin-resistant Staphylococcus aureus (MRSA) growth, 3) vancomycin-resistant Enterococci (VRE), and 4) identification of the heterotrophic plate counts. Each participant completed a questionnaire and a survey. The results showed that the average bacteria colony growth per square inch was 1,246 and 5,795 for day and night shift, respectively. After 48 h, MRSA positives were present on 4 of the day shift and 3 of the night shift uniforms. Additional bacteria identified include: Bacillus sp., Micrococcus luteus, Staphylococcus aureus, Staphylococcus epidermidis, and Micrococcus roseus. The significant presence of bacteria on the uniforms 48 h after the shift ended necessitates further study, discussions and policy consideration regarding wearing health care uniforms outside of the work environment. PMID:25285235

Nurses' uniforms: How many bacteria do they carry after one shift?

PubMed

Sanon, Marie-Anne; Watkins, Sally

2012-12-01

This pilot study investigated the pathogens that nurses are potentially bringing into the public and their home when they wear work uniforms outside of the work environment. To achieve this, sterilized uniforms were distributed to 10 nurses at a local hospital in Washington State at the beginning of their shift. Worn uniforms were collected at the end of the shifts and sent to a laboratory for analysis. Four tests were conducted: 1) a heterotrophic growth plate count, 2) methicillin-resistant Staphylococcus aureus (MRSA) growth, 3) vancomycin-resistant Enterococci (VRE), and 4) identification of the heterotrophic plate counts. Each participant completed a questionnaire and a survey. The results showed that the average bacteria colony growth per square inch was 1,246 and 5,795 for day and night shift, respectively. After 48 h, MRSA positives were present on 4 of the day shift and 3 of the night shift uniforms. Additional bacteria identified include: Bacillus sp., Micrococcus luteus, Staphylococcus aureus, Staphylococcus epidermidis, and Micrococcus roseus. The significant presence of bacteria on the uniforms 48 h after the shift ended necessitates further study, discussions and policy consideration regarding wearing health care uniforms outside of the work environment.

Adaptation of six shallots varieties to phosphate solubilizing bacteria on the flower formation, seeds fromation, and yields on the lowland

NASA Astrophysics Data System (ADS)

Triharyanto, E.; Sudadi; Rawandari, S.

2018-03-01

Using seeds as planting materials is a solution to improve the quality and quantity of shallot. This study aims to determine the interaction between shallot varieties and Phosphate- Solubilizing Bacteria (PSB) on the flowering and shallot yield on the lowlands. The research was conducted in Mijil Village, Jaten, Karanganyar, 98 m altitude with Vertisol-type soil order in June to December 2016, using Randomized Complete Block Design (RCBD) with two factors. Shallot varieties used as factors are Bima, Manjung, Ilokos, Bima (bulb seeds), Mentes and Rubaru. PSB factors are control and with PSB inoculation. Observed variables included plant height, number of leaves, flowering percentage, seed formation and shallot bulb yield. Results showed that there was no interaction between varieties and PSB inoculation on all observed variables. However, PSB inoculation were able to increase the number of flowering plants and seed weight per plot. Bima variety have the highest average yield compared to other varieties in terms of number of leaves, number of bulbs per plant and bulb weight per plot (fresh harvest weight 317.74 g equivalent to 17.65 ton per hectare and dry weight 288.16 g consumption equivalent to 16 ton per hectare).

Synergistic interaction and mode of action of Citrus hystrix essential oil against bacteria causing periodontal diseases.

PubMed

Wongsariya, Karn; Phanthong, Phanida; Bunyapraphatsara, Nuntavan; Srisukh, Vimol; Chomnawang, Mullika Traidej

2014-03-01

Citrus hystrix de Candolle (Rutaceae), an edible plant regularly used as a food ingredient, possesses antibacterial activity, but there is no current data on the activity against bacteria causing periodontal diseases. C. hystrix essential oil from leaves and peel were investigated for antibiofilm formation and mode of action against bacteria causing periodontal diseases. In vitro antibacterial and antibiofilm formation activities were determined by broth microdilution and time kill assay. Mode of action of essential oil was observed by SEM and the active component was identified by bioautography and GC/MS. C. hystrix leaves oil exhibited antibacterial activity at the MICs of 1.06 mg/mL for P. gingivalis and S. mutans and 2.12 mg/mL for S. sanguinis. Leaf oil at 4.25 mg/mL showed antibiofilm formation activity with 99% inhibition. The lethal effects on P. gingivalis were observed within 2 and 4 h after treated with 4 × MIC and 2 × MIC, respectively. S. sanguinis and S. mutans were completely killed within 4 and 8 h after exposed to 4 × MIC and 2 × MIC of oil. MICs of tested strains showed 4 times reduction suggesting synergistic interaction of oil and chlorhexidine. Bacterial outer membrane was disrupted after treatment with leaves oil. Additionally, citronellal was identified as the major active compound of C. hystrix oil. C. hystrix leaf oil could be used as a natural active compound or in combination with chlorhexidine in mouthwash preparations to prevent the growth of bacteria associated with periodontal diseases and biofilm formation.

The laboratory efficiencies initiative: partnership for building a sustainable national public health laboratory system.

PubMed

Ridderhof, John C; Moulton, Anthony D; Ned, Renée M; Nicholson, Janet K A; Chu, May C; Becker, Scott J; Blank, Eric C; Breckenridge, Karen J; Waddell, Victor; Brokopp, Charles

2013-01-01

Beginning in early 2011, the Centers for Disease Control and Prevention and the Association of Public Health Laboratories launched the Laboratory Efficiencies Initiative (LEI) to help public health laboratories (PHLs) and the nation's entire PHL system achieve and maintain sustainability to continue to conduct vital services in the face of unprecedented financial and other pressures. The LEI focuses on stimulating substantial gains in laboratories' operating efficiency and cost efficiency through the adoption of proven and promising management practices. In its first year, the LEI generated a strategic plan and a number of resources that PHL directors can use toward achieving LEI goals. Additionally, the first year saw the formation of a dynamic community of practitioners committed to implementing the LEI strategic plan in coordination with state and local public health executives, program officials, foundations, and other key partners.

The Laboratory Efficiencies Initiative: Partnership for Building a Sustainable National Public Health Laboratory System

PubMed Central

Moulton, Anthony D.; Ned, Renée M.; Nicholson, Janet K.A.; Chu, May C.; Becker, Scott J.; Blank, Eric C.; Breckenridge, Karen J.; Waddell, Victor; Brokopp, Charles

2013-01-01

Beginning in early 2011, the Centers for Disease Control and Prevention and the Association of Public Health Laboratories launched the Laboratory Efficiencies Initiative (LEI) to help public health laboratories (PHLs) and the nation's entire PHL system achieve and maintain sustainability to continue to conduct vital services in the face of unprecedented financial and other pressures. The LEI focuses on stimulating substantial gains in laboratories' operating efficiency and cost efficiency through the adoption of proven and promising management practices. In its first year, the LEI generated a strategic plan and a number of resources that PHL directors can use toward achieving LEI goals. Additionally, the first year saw the formation of a dynamic community of practitioners committed to implementing the LEI strategic plan in coordination with state and local public health executives, program officials, foundations, and other key partners. PMID:23997300

Back To Bacteria.

ERIC Educational Resources Information Center

Flannery, Maura C.

1997-01-01

Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

Volatiles emitted from eight wound-isolated bacteria differentially attract and stimulate gravid screwworm flies (Diptera: Calliphoridae) to oviposit

USDA-ARS?s Scientific Manuscript database

Bovine blood inoculated with bacteria isolated from screwworm-infested animal wounds was tested against gravid screwworm flies, Cochliomyia hominivorax (Coquerel) in the laboratory in a cage bioassay as an attractant for oviposition. Eight species of gram-negative coliform (Enterobacteriaceae) bacte...

Mechanism of cell alignment in groups of Myxococcus xanthus bacteria

NASA Astrophysics Data System (ADS)

Balgam, Rajesh; Igoshin, Oleg

2015-03-01

Myxococcus xanthus is a model for studying self-organization in bacteria. These flexible cylindrical bacteria move along. In groups, M. xanthus cells align themselves into dynamic cell clusters but the mechanism underlying their formation is unknown. It has been shown that steric interactions can cause alignment in self-propelled hard rods but it is not clear how flexibility and reversals affect the alignment and cluster formation. We have investigated cell alignment process using our biophysical model of M. xanthus cell in an agent-based simulation framework under realistic cell flexibility values. We observed that flexible model cells can form aligned cell clusters when reversals are suppressed but these clusters disappeared when reversals frequency becomes similar to the observed value. However, M. xanthus cells follow slime (polysaccharide gel like material) trails left by other cells and we show that implementing this into our model rescues cell clustering for reversing cells. Our results show that slime following along with periodic cell reversals act as positive feedback to reinforce existing slime trails and recruit more cells. Furthermore, we have observed that mechanical cell alignment combined with slime following is sufficient to explain the distinct clustering patterns of reversing and non-reversing cells as observed in recent experiments. This work is supported by NSF MCB 0845919 and 1411780.

Effects of combustion temperature on PCDD/Fs formation in laboratory-scale fluidized-bed incineration.

PubMed

Hatanaka, T; Imagawa, T; Kitajima, A; Takeuchi, M

2001-12-15

Combustion experiments in a laboratory-scale fluidized-bed reactor were performed to elucidate the effects of combustion temperature on PCDD/Fs formation during incineration of model wastes with poly(vinyl chloride) or sodium chloride as a chlorine source and copper chloride as a catalyst. Each temperature of primary and secondary combustion zones in the reactor was set independently to 700, 800, and 900 degrees C using external electric heaters. The PCDD/Fs concentration is reduced as the temperature of the secondary combustion zone increases. It is effective to keep the temperature of the secondary combustion zone high enough to reduce their release during the waste incineration. On the other hand, as the temperature of the primary combustion zone rises, the PCDD/Fs concentration also increases. Lower temperature of the primary combustion zone results in less PCDD/Fs concentration in these experimental conditions. This result is probably related to the devolatilization rate of the solid waste in the primary combustion zone. The temperature decrease slows the devolatilization rate and promotes mixing of oxygen and volatile matters from the solid waste. This contributes to completing combustion reactions, resulting in reducing the PCDD/Fs concentration.

Bile Salt-induced Biofilm Formation in Enteric Pathogens: Techniques for Identification and Quantification.

PubMed

Nickerson, Kourtney P; Faherty, Christina S

2018-05-06

Biofilm formation is a dynamic, multistage process that occurs in bacteria under harsh environmental conditions or times of stress. For enteric pathogens, a significant stress response is induced during gastrointestinal transit and upon bile exposure, a normal component of human digestion. To overcome the bactericidal effects of bile, many enteric pathogens form a biofilm hypothesized to permit survival when transiting through the small intestine. Here we present methodologies to define biofilm formation through solid-phase adherence assays as well as extracellular polymeric substance (EPS) matrix detection and visualization. Furthermore, biofilm dispersion assessment is presented to mimic the analysis of events triggering release of bacteria during the infection process. Crystal violet staining is used to detect adherent bacteria in a high-throughput 96-well plate adherence assay. EPS production assessment is determined by two assays, namely microscopy staining of the EPS matrix and semi-quantitative analysis with a fluorescently-conjugated polysaccharide binding lectin. Finally, biofilm dispersion is measured through colony counts and plating. Positive data from multiple assays support the characterization of biofilms and can be utilized to identify bile salt-induced biofilm formation in other bacterial strains.

Stoichiometry and kinetics of mercury uptake by photosynthetic bacteria.

PubMed

Kis, Mariann; Sipka, Gábor; Maróti, Péter

2017-05-01

Mercury adsorption on the cell surface and intracellular uptake by bacteria represent the key first step in the production and accumulation of highly toxic mercury in living organisms. In this work, the biophysical characteristics of mercury bioaccumulation are studied in intact cells of photosynthetic bacteria by use of analytical (dithizone) assay and physiological photosynthetic markers (pigment content, fluorescence induction, and membrane potential) to determine the amount of mercury ions bound to the cell surface and taken up by the cell. It is shown that the Hg(II) uptake mechanism (1) has two kinetically distinguishable components, (2) includes co-opted influx through heavy metal transporters since the slow component is inhibited by Ca 2+ channel blockers, (3) shows complex pH dependence demonstrating the competition of ligand binding of Hg(II) ions with H + ions (low pH) and high tendency of complex formation of Hg(II) with hydroxyl ions (high pH), and (4) is not a passive but an energy-dependent process as evidenced by light activation and inhibition by protonophore. Photosynthetic bacteria can accumulate Hg(II) in amounts much (about 10 5 ) greater than their own masses by well-defined strong and weak binding sites with equilibrium binding constants in the range of 1 (μM) -1 and 1 (mM) -1 , respectively. The strong binding sites are attributed to sulfhydryl groups as the uptake is blocked by use of sulfhydryl modifying agents and their number is much (two orders of magnitude) smaller than the number of weak binding sites. Biofilms developed by some bacteria (e.g., Rvx. gelatinosus) increase the mercury binding capacity further by a factor of about five. Photosynthetic bacteria in the light act as a sponge of Hg(II) and can be potentially used for biomonitoring and bioremediation of mercury-contaminated aqueous cultures.

String Formatting Considered Harmful for Novice Programmers

ERIC Educational Resources Information Center

Hughes, Michael C.; Jadud, Matthew C.; Rodrigo, Ma. Mercedes T.

2010-01-01

In Java, "System.out.printf" and "String.format" consume a specialised kind of string commonly known as a format string. In our study of first-year students at the Ateneo de Manila University, we discovered that format strings present a substantial challenge for novice programmers. Focusing on their first laboratory we found…

Blended Learning within an Undergraduate Exercise Physiology Laboratory

ERIC Educational Resources Information Center

Elmer, Steven J.; Carter, Kathryn R.; Armga, Austin J.; Carter, Jason R.

2016-01-01

In physiological education, blended course formats (integration of face-to-face and online instruction) can facilitate increased student learning, performance, and satisfaction in classroom settings. There is limited evidence on the effectiveness of using blending course formats in laboratory settings. We evaluated the impact of blended learning…

Freeing Water from Viruses and Bacteria

NASA Technical Reports Server (NTRS)

2004-01-01

Four years ago, Argonide Corporation, a company focused on the research, production, and marketing of specialty nano materials, was seeking to develop applications for its NanoCeram[R] fibers. Only 2 nanometers in diameter, these nano aluminum oxide fibers possessed unusual bio-adhesive properties. When formulated into a filter material, the electropositive fibers attracted and retained electro-negative particles such as bacteria and viruses in water-based solutions. This technology caught the interest of NASA as a possible solution for improved water filtration in space cabins. NASA's Johnson Space Center awarded Sanford, Florida-based Argonide a Phase I Small Business Innovation Research (SBIR) contract to determine the feasibility of using the company's filter for purifying recycled space cabin water. Since viruses and bacteria can be carried aboard space cabins by space crews, the ability to detect and remove these harmful substances is a concern for NASA. The Space Agency also desired an improved filter to polish the effluent from condensed and waste water, producing potable drinking water. During its Phase I partnership with NASA, Argonide developed a laboratory-size filter capable of removing greater than 99.9999 percent of bacteria and viruses from water at flow rates more than 200 times faster than virus-rated membranes that remove particles by sieving. Since the new filter s pore size is rather large compared to other membranes, it is also less susceptible to clogging by small particles. In September 2002, Argonide began a Phase II SBIR project with Johnson to develop a full-size cartridge capable of serving a full space crew. This effort, which is still ongoing, enabled the company to demonstrate that its filter media is an efficient absorbent for DNA and RNA.

Contribution of Cell Elongation to the Biofilm Formation of Pseudomonas aeruginosa during Anaerobic Respiration

PubMed Central

Park, Yongjin; Yoon, Sang Sun

2011-01-01

Pseudomonas aeruginosa, a gram-negative bacterium of clinical importance, forms more robust biofilm during anaerobic respiration, a mode of growth presumed to occur in abnormally thickened mucus layer lining the cystic fibrosis (CF) patient airway. However, molecular basis behind this anaerobiosis-triggered robust biofilm formation is not clearly defined yet. Here, we identified a morphological change naturally accompanied by anaerobic respiration in P. aeruginosa and investigated its effect on the biofilm formation in vitro. A standard laboratory strain, PAO1 was highly elongated during anaerobic respiration compared with bacteria grown aerobically. Microscopic analysis demonstrated that cell elongation likely occurred as a consequence of defective cell division. Cell elongation was dependent on the presence of nitrite reductase (NIR) that reduces nitrite (NO2 −) to nitric oxide (NO) and was repressed in PAO1 in the presence of carboxy-PTIO, a NO antagonist, demonstrating that cell elongation involves a process to respond to NO, a spontaneous byproduct of the anaerobic respiration. Importantly, the non-elongated NIR-deficient mutant failed to form biofilm, while a mutant of nitrate reductase (NAR) and wild type PAO1, both of which were highly elongated, formed robust biofilm. Taken together, our data reveal a role of previously undescribed cell biological event in P. aeruginosa biofilm formation and suggest NIR as a key player involved in such process. PMID:21267455

[A Case of Hyperammonemia Caused by Urinary Tract Infection Due to Urease-Producing Bacteria].

PubMed

Emura, Masahiro; Tsuchihashi, Kazunari; Shimizu, Yosuke; Kanamaru, Sojun; Matoba, Shun; Ito, Noriyuki

2016-08-01

We present here a rare case of hyperammonemia without liver dysfunction or portal-systemic shunting. The patient was an 80-year-old woman with a history of neurogenic bladder. She was admitted to a nearby hospital for vomiting, diarrhea and consciousness disturbance. Two days after admission, she was transferred to our hospital because of persistant consciousness disturbance. Laboratory data revealed hyperammonemia, but there was no indication of liver dysfunction. Moreover abdominal computed tomography did not reveal any clear finding of liver disease or portal-systemic shunting, but we noted multiple large bladder diverticula. Antibiotic therapy, tracheal intubation, ventilator management and bladder catheterization were performed. The patient's level of consciousness improved rapidly. Urinary culture revealed Bacteroides ureolyticus (urease-producing bacteria). The patient was diagnosed with hyperammonemia and a urinary tract infection due to urease-producing bacteria. Thus, physicians should be aware that obstructive urinary tract infections due to urease-producing bacteria can also be the cause of hyperammonemia.

Inactivation of biofilm bacteria.

PubMed Central

LeChevallier, M W; Cawthon, C D; Lee, R G

1988-01-01

The current project was developed to examine inactivation of biofilm bacteria and to characterize the interaction of biocides with pipe surfaces. Unattached bacteria were quite susceptible to the variety of disinfectants tested. Viable bacterial counts were reduced 99% by exposure to 0.08 mg of hypochlorous acid (pH 7.0) per liter (1 to 2 degrees C) for 1 min. For monochloramine, 94 mg/liter was required to kill 99% of the bacteria within 1 min. These results were consistent with those found by other investigators. Biofilm bacteria grown on the surfaces of granular activated carbon particles, metal coupons, or glass microscope slides were 150 to more than 3,000 times more resistant to hypochlorous acid (free chlorine, pH 7.0) than were unattached cells. In contrast, resistance of biofilm bacteria to monochloramine disinfection ranged from 2- to 100-fold more than that of unattached cells. The results suggested that, relative to inactivation of unattached bacteria, monochloramine was better able to penetrate and kill biofilm bacteria than free chlorine. For free chlorine, the data indicated that transport of the disinfectant into the biofilm was a major rate-limiting factor. Because of this phenomenon, increasing the level of free chlorine did not increase disinfection efficiency. Experiments where equal weights of disinfectants were used suggested that the greater penetrating power of monochloramine compensated for its limited disinfection activity. These studies showed that monochloramine was as effective as free chlorine for inactivation of biofilm bacteria. The research provides important insights into strategies for control of biofilm bacteria. Images PMID:2849380

Direct identification of bacteria from positive BacT/ALERT blood culture bottles using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry.

PubMed

Mestas, Javier; Felsenstein, Susanna; Bard, Jennifer Dien

2014-11-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is a fast and robust method for the identification of bacteria. In this study, we evaluate the performance of a laboratory-developed lysis method (LDT) for the rapid identification of bacteria from positive BacT/ALERT blood culture bottles. Of the 168 positive bottles tested, 159 were monomicrobial, the majority of which were Gram-positive organisms (61.0% versus 39.0%). Using a cut-off score of ≥1.7, 80.4% of the organisms were correctly identified to the species level, and the identification rate of Gram-negative organisms (90.3%) was found to be significantly greater than that of Gram-positive organisms (78.4%). The simplicity and cost-effectiveness of the LDT enable it to be fully integrated into the routine workflow of the clinical microbiology laboratory, allowing for rapid identification of Gram-positive and Gram-negative bacteria within an hour of blood culture positivity. Copyright © 2014 Elsevier Inc. All rights reserved.

Evaluation of Various Metallic Coatings on Steel to Mitigate Biofilm Formation

PubMed Central

Kanematsu, Hideyuki; Ikigai, Hajime; Yoshitake, Michiko

2009-01-01

In marine environments and water systems, it is easy for many structures to form biofilms on their surfaces and to be deteriorated due to the corrosion caused by biofilm formation by bacteria. The authors have investigated the antibacterial effects of metallic elements in practical steels so far to solve food-related problems, using Escherichia coli and Staphylococcus aureus. However, from the viewpoint of material deterioration caused by bacteria and their antifouling measures, we should consider the biofilm behavior as aggregate rather than individual bacterium. Therefore, we picked up Pseudomonas aeruginosa and Pseudoalteromonas carageenovara in this study, since they easily form biofilms in estuarine and marine environments. We investigated what kind of metallic elements could inhibit the biofilm formation at first and then discussed how the thin films of those inhibitory elements on steels could affect biofilm formation. The information would lead to the establishment of effective antifouling measures against corrosion in estuarine and marine environments. PMID:19333421

Evaluation of various metallic coatings on steel to mitigate biofilm formation.

PubMed

Kanematsu, Hideyuki; Ikigai, Hajime; Yoshitake, Michiko

2009-02-01

In marine environments and water systems, it is easy for many structures to form biofilms on their surfaces and to be deteriorated due to the corrosion caused by biofilm formation by bacteria. The authors have investigated the antibacterial effects of metallic elements in practical steels so far to solve food-related problems, using Escherichia coli and Staphylococcus aureus. However, from the viewpoint of material deterioration caused by bacteria and their antifouling measures, we should consider the biofilm behavior as aggregate rather than individual bacterium. Therefore, we picked up Pseudomonas aeruginosa and Pseudoalteromonas carageenovara in this study, since they easily form biofilms in estuarine and marine environments. We investigated what kind of metallic elements could inhibit the biofilm formation at first and then discussed how the thin films of those inhibitory elements on steels could affect biofilm formation. The information would lead to the establishment of effective antifouling measures against corrosion in estuarine and marine environments.

Laboratory Astrophysics White Paper

NASA Technical Reports Server (NTRS)

Brickhouse, Nancy; Federman, Steve; Kwong, Victor; Salama, Farid; Savin, Daniel; Stancil, Phillip; Weingartner, Joe; Ziurys, Lucy

2006-01-01

Laboratory astrophysics and complementary theoretical calculations are the foundations of astronomical and planetary research and will remain so for many generations to come. From the level of scientific conception to that of the scientific return, it is our understanding of the underlying processes that allows us to address fundamental questions regarding the origins and evolution of galaxies, stars, planetary systems, and life in the cosmos. In this regard, laboratory astrophysics is much like detector and instrument development at NASA and NSF; these efforts are necessary for the astronomical research being funded by the agencies. The NASA Laboratory Astrophysics Workshop met at the University of Nevada, Las Vegas (UNLV) from 14-16 February, 2006 to identify the current laboratory data needed to support existing and future NASA missions and programs in the Astrophysics Division of the Science Mission Directorate (SMD). Here we refer to both laboratory and theoretical work as laboratory astrophysics unless a distinction is necessary. The format for the Workshop involved invited talks by users of laboratory data, shorter contributed talks and poster presentations by both users and providers that highlighted exciting developments in laboratory astrophysics, and breakout sessions where users and providers discussed each others' needs and limitations. We also note that the members of the Scientific Organizing Committee are users as well as providers of laboratory data. As in previous workshops, the focus was on atomic, molecular, and solid state physics.

The δ15N and δ18O values of N2O produced during the co-oxidation of ammonia by methanotrophic bacteria

USGS Publications Warehouse

Mandernack, Kevin W.; Mills, Christopher T.; Johnson, Craig A.; Rahn, Thomas; Kinney, Chad

2009-01-01

In order to determine if the δ15N and δ18O values of N2O produced during co-oxidation of NH4+ by methanotrophic (methane oxidizing) bacteria can be isotopically distinguished from N2O produced either by autotrophic nitrifying or denitrifying bacteria, we conducted laboratory incubation experiments with pure cultures of methanotrophic bacteria that were provided NH4Cl as an oxidation substrate. The N2O produced during NH4+ oxidation by methanotrophic bacteria showed nitrogen isotope fractionation between NH4+ and N2O (εN2O–NH4+) of − 48 and − 55‰ for Methylomonas methanica and Methylosinus trichosporium, OB3b respectively. These large fractionations are similar to those previously measured for autotrophic nitrifying bacteria and consistent with N2O formation by multiple rate limiting steps that include NH4+oxidation by the methane monooxygenase enzyme and reduction of NO2− to N2O. Consequently, N2O formed by NH4+ oxidation via methanotrophic or autotrophic nitrifying bacteria might generally be characterized by lower δ15NN2O values than that formed by denitrificaiton, although this also depends on the variability of δ15N of available nitrogen sources (e.g., NH4+, NO3−, NO2−). Additional incubations with M. trichosporium OB3b at high and low CH4 conditions in waters of different δ18O values revealed that 19–27% of the oxygen in N2O was derived from O2 with the remainder from water. The biochemical mechanisms that could explain this amount of O2 incorporation are discussed. The δ18O of N2O formed under high CH4 conditions was ~ + 15‰ more positive than that formed under lower CH4 conditions. This enrichment resulted in part from the incorporation of O2 into N2O that was enriched in 18O due to an isotope fractionation effect of − 16.1 ± 2.0‰ and − 17.5 ± 5.4‰ associated with O2 consumption during the high and low methane concentration incubations, respectively. Therefore, N2O formed by NH4+�

An in situ inventory of fungi and their associated migrating bacteria in forest soils using fungal highway columns.

PubMed

Simon, Anaele; Hervé, Vincent; Al-Dourobi, Andrej; Verrecchia, Eric; Junier, Pilar

2017-01-01

Soils are complex ecosystems in which fungi and bacteria co-exist and interact. Fungal highways are a kind of interaction by which bacteria use fungal hyphae to disperse in soils. Despite the fact that fungal highways have been studied in laboratory models, the diversity of fungi and bacteria interacting in this way in soils is still unknown. Fungal highway columns containing two different culture media were used as a selective method to study the identity of fungi and bacteria able to migrate along the hyphae in three forest soils. Regardless of the soil type, fungi of the genus Mortierella (phylum Zygomycota) were selected inside the columns. In contrast, a diverse community of bacteria dominated by Firmicutes and Proteobacteria was observed. The results confirm the importance of bacteria affiliated to Burkholderia as potentially associated migrating bacteria in soils and indicate that other groups such as Bacillus and Clostridium are also highly enriched in the co-colonization of a new habitat (columns) associated to Mortierella. The diversity of potentially associated migrating bacteria brings a novel perspective on the indirect metabolic capabilities that could be favored by r-strategist fungi and supports the fact that these fungi should be considered as crucial actors in soil functioning. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Electromechanical and Elastic Probing of Bacteria in Cell Culture Medium

PubMed Central

Thompson, G.L.; Reukov, V.V.; Nikiforov, M.P.; Jesse, S.; Kalinin, S.V.; Vertegel, A.A.

2012-01-01

Rapid phenotype characterization and identification of cultured cells, which is needed for progress in tissue engineering and drug testing, requires an experimental technique that measures physical properties of cells with sub-micron resolution. Recently, band excitation piezoresponse force microscopy (BEPFM) has been proven useful for recognition and imaging of different types of bacteria in pure water. Here, the BEPFM method is performed for the first time in physiologically-relevant electrolyte media, such as Dulbecco’s phosphate-buffered saline (DPBS) and Dulbecco’s modified Eagle’s medium (DMEM). Distinct electromechanical responses for Micrococcus lysodeikticus (Gram-positive) and Pseudomonas fluorescens (Gram-negative) bacteria are demonstrated in DPBS. The results suggest that mechanical properties of the outer surface coating each bacterium, as well as the electrical double layer around them, are responsible for the BEPFM image formation mechanism in electrolyte media. PMID:22641388

Microalgae-bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage.

PubMed

Abinandan, Sudharsanam; Subashchandrabose, Suresh R; Venkateswarlu, Kadiyala; Megharaj, Mallavarapu

2018-02-01

Microalgae and bacteria offer a huge potential in delving interest to study and explore various mechanisms under extreme environments. Acid mine drainage (AMD) is one such environment which is extremely acidic containing copious amounts of heavy metals and poses a major threat to the ecosystem. Despite its extreme conditions, AMD is the habitat for several microbes and their activities. The use of various chemicals in prevention of AMD formation and conventional treatment in a larger scale is not feasible under different geological conditions. It implies that microbe-mediated approach is a viable and sustainable alternative technology for AMD remediation. Microalgae in biofilms play a pivotal role in such bioremediation as they maintain mutualism with heterotrophic bacteria. Synergistic approach of using microalgae-bacteria biofilms provides supportive metabolites from algal biomass for growth of bacteria and mediates remediation of AMD. However, by virtue of their physiology and capabilities of metal removal, non-acidophilic microalgae can be acclimated for use in AMD remediation. A combination of selective acidophilic and non-acidophilic microalgae together with bacteria, all in the form of biofilms, may be very effective for bioremediation of metal-contaminated waters. The present review critically examines the nature of mutualistic interactions established between microalgae and bacteria in biofilms and their role in removal of metals from AMDs, and consequent biomass production for the yield of biofuel. Integration of microalgal-bacterial consortia in fuel cells would be an attractive emerging approach of microbial biotechnology for AMD remediation.

Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus.

PubMed

Labbé, Jessy L; Weston, David J; Dunkirk, Nora; Pelletier, Dale A; Tuskan, Gerald A

2014-01-01

Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite interactions are poorly understood. Through an effort to study Populus microbiome, we isolated 21 Pseudomonas strains from native Populus deltoides roots. These bacterial isolates were characterized and screened for MHB effectiveness on the Populus-Laccaria system. Two additional Pseudomonas strains (i.e., Pf-5 and BBc6R8) from existing collections were included for comparative purposes. We analyzed the effect of co-cultivation of these 23 individual Pseudomonas strains on Laccaria bicolor "S238N" growth rate, mycelial architecture and transcriptional changes. Nineteen of the 23 Pseudomonas strains tested had positive effects on L. bicolor S238N growth, as well as on mycelial architecture, with strains GM41 and GM18 having the most significant effect. Four of seven L. bicolor reporter genes, Tra1, Tectonin2, Gcn5, and Cipc1, thought to be regulated during the interaction with MHB strain BBc6R8, were induced or repressed, while interacting with Pseudomonas strains GM17, GM33, GM41, GM48, Pf-5, and BBc6R8. Strain GM41 promoted the highest roots colonization across three Populus species but most notably in P. deltoides, which is otherwise poorly colonized by L. bicolor. Here we report novel MHB strains isolated from native Populus that improve L. bicolor root colonization on Populus. This tripartite relationship could be exploited for Populus species/genotypes nursery production as a means of improving establishment and survival in marginal lands.

Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

PubMed Central

Labbé, Jessy L.; Weston, David J.; Dunkirk, Nora; Pelletier, Dale A.; Tuskan, Gerald A.

2014-01-01

Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite interactions are poorly understood. Through an effort to study Populus microbiome, we isolated 21 Pseudomonas strains from native Populus deltoides roots. These bacterial isolates were characterized and screened for MHB effectiveness on the Populus-Laccaria system. Two additional Pseudomonas strains (i.e., Pf-5 and BBc6R8) from existing collections were included for comparative purposes. We analyzed the effect of co-cultivation of these 23 individual Pseudomonas strains on Laccaria bicolor “S238N” growth rate, mycelial architecture and transcriptional changes. Nineteen of the 23 Pseudomonas strains tested had positive effects on L. bicolor S238N growth, as well as on mycelial architecture, with strains GM41 and GM18 having the most significant effect. Four of seven L. bicolor reporter genes, Tra1, Tectonin2, Gcn5, and Cipc1, thought to be regulated during the interaction with MHB strain BBc6R8, were induced or repressed, while interacting with Pseudomonas strains GM17, GM33, GM41, GM48, Pf-5, and BBc6R8. Strain GM41 promoted the highest roots colonization across three Populus species but most notably in P. deltoides, which is otherwise poorly colonized by L. bicolor. Here we report novel MHB strains isolated from native Populus that improve L. bicolor root colonization on Populus. This tripartite relationship could be exploited for Populus species/genotypes nursery production as a means of improving establishment and survival in marginal lands. PMID:25386184

[Immobilization of introduced bacteria and degradation of pyrene and benzo(alpha) pyrene in soil by immobilized bacteria].

PubMed

Wang, Xin; Li, Peijun; Song, Shouzhi; Zhong, Yong; Zhang, Hui; Verkhozina, E V

2006-11-01

In this study, introduced bacteria were applied in the bioremediation of pyrene and benzo (alpha) pyrene in organic pollutants-contaminated soils, aimed to test whether it was feasible to introduce bacteria to environmental engineering. Three introduced bacteria were immobilized separately or together to degrade the pyrene and benzo (alpha) pyrene in soil, taking dissociated bacteria as the control, and comparing with three indigenous bacteria. The results showed that immobilized introduced bacteria, either single or mixed, had higher degradation efficiency than dissociated bacteria. Compared with indigenous bacteria, some introduced bacteria had predominance to some degree. The introduced bacteria-mixture had better degradation efficiency after being immobilized. The degradation rate of pyrene and benzo(alpha) pyrene after treated with immobilized bacteria-( B61-B67)-mixture for 96 hours was 43.49% and 38.55%, respectively.

An inquiry-based biochemistry laboratory structure emphasizing competency in the scientific process: a guided approach with an electronic notebook format.

PubMed