bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and Photophysical Characterization of Porphyrin, Chlorin and Bacteriochlorin Molecules Bearing Tethers for Surface Attachment
Authors: Muthiah Chinnasamy , Taniguchi Masahiko , Kim Han‐Je , Schmidt Izabela , Kee Hooi Ling , Holten Dewey , Bocian David F. , Lindsey Jonathan S. 
Published: September 2007

AbstractThe ability to tailor synthetic porphyrin, chlorin and bacteriochlorin molecules holds promise for diverse studies in artificial photosynthesis. Toward this goal, the synthesis and photophysical characterization of five tetrapyrrole compounds is described. Each compound bears a surface attachment group. One set contains three meso‐substituted porphyrins that differ only in the nature of a surface‐binding tether—isophthalic acid, ethynylisophthalic acid or cyanoacrylic acid. The other set includes a porphyrin, chlorin and bacteriochlorin each of which bears an ethynylisophthalic acid tether. The ester derivative of each compound was prepared for solution photophysical characterization studies. The photophysical studies include determination (in toluene or acetonitrile) of the electronic absorption and fluorescence spectra, fluorescence yield and lifetime of the lowest excited singlet state. The excited‐state lifetimes range from 1 to 5.6 ns for the five compounds. The radiative rate constant for the excited‐state decay was estimated from the photophysical data (fluorescence yield and excited‐state lifetime) and from Strickler–Berg analysis of the absorption and fluorescence spectra. The synthesis and characterization of the tetrapyrrole compounds underpin their use as sensitizers in molecular‐based solar cells.
Flavin‐based Blue‐light Photosensors: A Photobiophysics Update
Authors: Losi Aba 
Published: September 2007

AbstractThis review deals with the biophysical aspects of flavin‐based photosensors, comprising cryptochromes, LOV (Light, Oxygen and Voltage) and BLUF (Blue Light sensing Using FAD) proteins. Special emphasis is given to structural issues, photocycle quantum yields and energetics, mechanism of the light‐triggered reactions, early stages in signal transduction and oligomeric states of the light sensing protein modules. For BLUF and LOV domains important parallels are emerging, despite their different α/β fold arrangement, whereas there is increasing evidence for a mechanicistic and functional splitting of the cryptochrome family.
Host‐parasite population dynamics under combined frequency‐ and density‐dependent transmission
Authors: Ryder Jonathan J. , Miller Martin R. , White Andy , Knell Robert J. , Boots Michael 
Published: September 2007

Many host‐parasite models assume that transmission increases linearly with host population density (‘density‐dependent transmission’), but various alternative transmission functions have been proposed in an effort to capture the complexity of real biological systems. The most common alternative (usually applied to sexually transmitted parasites) assumes instead that the rate at which hosts contact one another is independent of population density, leading to ‘frequency‐dependent’ transmission. This straight‐forward distinction generates fundamentally different dynamics (e.g. deterministic, parasite‐driven extinction with frequency‐ but not density‐dependence). Here, we consider the situation where transmission occurs through two different types of contact, one of which is density‐dependent (e.g. social contacts), the other density‐independent (e.g. sexual contacts). Drawing on a range of biological examples, we propose that this type of contact structure may be widespread in natural populations. When our model is characterized mainly by density‐dependent transmission, we find that allowing even small amounts of transmission to occur through density‐independent contacts leads to the possibility of deterministic, parasite‐driven extinction (and lowers the threshold for parasite persistence). Contrastingly, allowing some density‐dependent transmission to occur in a model characterized mainly by density‐independent contacts (i.e. by frequency‐dependent transmission) does not affect the extinction threshold, but does increase the likelihood of parasite persistence.The idea that directly transmitted parasites exploit different types of host contact is not new, but here we show that the impact on dynamics can be fundamental even in the simplest cases. For example, in systems where density‐dependent transmission is normally assumed de facto, we show that parasite‐driven extinction can occur if a small amount of transmission occurs through density‐independent contacts. Many empirical studies are still guided by the traditional density/frequency dichotomy, but our combined transmission function may provide a better model for systems in which both types of transmission occur.
Climate and On-Farm Risk Factors Associated with
Giardia duodenalis
Cysts in Storm Runoff from California Coastal Dairies
Authors: Miller Woutrina A. , Lewis David J. , Lennox Michael , Pereira Maria G. C. , Tate Kenneth W. , Conrad Patricia A. , Atwill Edward R. 
Published: September 2007

ABSTRACT

Climatic factors and on-farm management practices were evaluated for their association with the concentrations (cyst/liter) and instantaneous loads (cysts/second) of
Giardia duodenalis
in storm-based runoff from dairy lots and other high-cattle-use areas on five coastal California farms over two storm seasons. Direct fluorescent antibody analysis was used to quantitate cysts in 350 storm runoff samples.
G. duodenalis
was detected on all five dairy farms, with fluxes of 1 to 14,000 cysts/liter observed in 16% of samples. Cysts were detected in 41% of runoff samples collected near cattle less than 2 months old, compared to 10% of runoff samples collected near cattle over 6 months old. Furthermore, the concentrations and instantaneous loads of cysts were ≥65 and ≥79 times greater, respectively, in runoff from sites housing young calves than in sites housing other age classes of animals. Factors associated with environmental loading of
G. duodenalis
included cattle age, cattle stocking number, and precipitation but not lot area, land slope, or cattle density. Vegetated buffer strips were found to significantly reduce waterborne cysts in storm runoff: each additional meter of vegetated buffer placed below high-cattle-use areas was associated with reductions in the concentration and instantaneous load of cysts by factors of 0.86 and 0.79 (−0.07 and −0.10 log
10
/m), respectively. Straw mulch, seed application, scraping of manure, and cattle exclusion did not significantly affect the concentration or load of
G. duodenalis
cysts. The study findings suggest that vegetated buffer strips, especially when placed near dairy calf areas, should help reduce the environmental loading of these fecal protozoa discharging from dairy farms.
Influence of Native Microbiota on Survival of
Ralstonia solanacearum
Phylotype II in River Water Microcosms
Authors: Álvarez Belén , López María M. , Biosca Elena G. 
Published: September 2007

ABSTRACT

Ralstonia solanacearum
phylotype II biovar 2 causes bacterial wilt in solanaceous hosts, producing severe economic losses worldwide. Waterways can be major dissemination routes of this pathogen, which is able to survive for long periods in sterilized water. However, little is known about its survival in natural water when other microorganisms, such as bacteriophages, other bacteria, and protozoa, are present. This study looks into the fate of a Spanish strain of
R. solanacearum
inoculated in water microcosms from a Spanish river, containing different microbiota fractions, at 24°C and 14°C, for a month. At both temperatures,
R. solanacearum
densities remained constant at the initial levels in control microcosms of sterile river water while, by contrast, declines in the populations of the introduced strain were observed in the nonsterile microcosms. These decreases were less marked at 14°C. Lytic bacteriophages present in this river water were involved in the declines of the pathogen populations, but indigenous protozoa and bacteria also contributed to the reduced persistence in water.
R. solanacearum
variants displaying resistance to phage infection were observed, but only in microcosms without protozoa and native bacteria. In water microcosms, the temperature of 14°C was more favorable for the survival of this pathogen than 24°C, since biotic interactions were slower at the lower temperature. Similar trends were observed in microcosms inoculated with a Dutch strain. This is the first study demonstrating the influence of different fractions of water microorganisms on the survival of
R. solanacearum
phylotype II released into river water microcosms.
Heterologous Production of Dihomo-γ-Linolenic Acid in
Saccharomyces cerevisiae
Authors: Yazawa Hisashi , Iwahashi Hitoshi , Kamisaka Yasushi , Kimura Kazuyoshi , Aki Tsunehiro , Ono Kazuhisa , Uemura Hiroshi 
Published: September 2007

ABSTRACT

To make dihomo-γ-linolenic acid (DGLA) (20:3n-6) in
Saccharomyces cerevisiae
, we introduced
Kluyveromyces lactis
Δ12 fatty acid desaturase, rat Δ6 fatty acid desaturase, and rat elongase genes. Because Fad2p is able to convert the endogenous oleic acid to linoleic acid, this allowed DGLA biosynthesis without the need to supply exogenous fatty acids on the media. Medium composition, cultivation temperature, and incubation time were examined to improve the yield of DGLA. Fatty acid content was increased by changing the medium from a standard synthetic dropout medium to a nitrogen-limited minimal medium (NSD). Production of DGLA was higher in the cells grown at 15°C than in those grown at 20°C, and no DGLA production was observed in the cells grown at 30°C. In NSD at 15°C, fatty acid content increased up until day 7 and decreased after day 10. When the cells were grown in NSD for 7 days at 15°C, the yield of DGLA reached 2.19 μg/mg of cells (dry weight) and the composition of DGLA to total fatty acids was 2.74%. To our knowledge, this is the first report describing the production of polyunsaturated fatty acids in
S. cerevisiae
without supplying the exogenous fatty acids.
Sensitive and Specific Molecular Detection of
Burkholderia pseudomallei
, the Causative Agent of Melioidosis, in the Soil of Tropical Northern Australia
Authors: Kaestli Mirjam , Mayo Mark , Harrington Glenda , Watt Felicity , Hill Jason , Gal Daniel , Currie Bart J. 
Published: September 2007

ABSTRACT

Burkholderia pseudomallei
, the cause of the severe disease melioidosis in humans and animals, is a gram-negative saprophyte living in soil and water of areas of endemicity such as tropical northern Australia and Southeast Asia. Infection occurs mainly by contact with wet contaminated soil. The environmental distribution of
B. pseudomallei
in northern Australia is still unclear. We developed and evaluated a direct soil
B. pseudomallei
DNA detection method based on the recently published real-time PCR targeting the
B. pseudomallei
type III secretion system. The method was evaluated by inoculating different soil types with
B. pseudomallei
dilution series and by comparing
B. pseudomallei
detection rate with culture-based detection rate for 104 randomly collected soil samples from the Darwin rural area in northern Australia. We found that direct soil
B. pseudomallei
DNA detection not only was substantially faster than culture but also proved to be more sensitive with no evident false-positive results. This assay provides a new tool to detect
B. pseudomallei
in soil samples in a fast and highly sensitive and specific manner and is applicable for large-scale
B. pseudomallei
environmental screening studies or in outbreak situations. Furthermore, analysis of the 104 collected soil samples revealed a significant association between
B. pseudomallei
-positive sites and the presence of animals at these locations and also with moist, reddish brown-to-reddish gray soils.
Metabolic Engineering ofLactobacillus plantarumfor Production ofl-Ribulose
Authors: Helanto M. , Kiviharju K. , Leisola M. , Nyyssölä A. 
Published: September 2007

ABSTRACTl-Ribulose is a rare and expensive sugar that can be used as a precursor for the production of other rare sugars of high market value such asl-ribose. In this work we describe a production process forl-ribulose usingl-arabinose, a common component of polymers of lignocellulosic materials, as the starting material. A ribulokinase-deficient mutant of the heterofermentative lactic acid bacteriumLactobacillus plantarumNCIMB8826 was constructed. Expression ofaraA, which encodes the critical enzymel-arabinose isomerase, was repressed by high glucose concentrations in batch cultivations. A fed-batch cultivation strategy was therefore used to maximizel-arabinose isomerase production during growth. Resting cells of the ribulokinase-deficient mutant were used for the production ofl-ribulose. The isomerization ofl-arabinose tol-ribulose was very unfavorable forl-ribulose formation. However, highl-ribulose yields were obtained by complexing the producedl-ribulose with borate. The process forl-ribulose production in borate buffer by resting cells was optimized using central composite designs. The experiment design suggested that the process has an optimal operation point around anl-arabinose concentration of 100 g liter−1, a borate concentration of 500 mM, and a temperature of 48°C, where the statistical software predicted an initiall-ribulose production rate of 29.1 g liter−1h−1, a best-achievable process productivity of 14.8 g liter−1h−1, and a conversion ofl-arabinose tol-ribulose of 0.70 mol mol−1.
Impact of Zooplankton Grazing on the Excystation, Viability, and Infectivity of the Protozoan Pathogens
Cryptosporidium parvum
and
Giardia lamblia
Authors: Connelly S. J. , Wolyniak E. A. , Dieter K. L. , Williamson C. E. , Jellison K. L. 
Published: September 2007

ABSTRACT

Very little is known about the ability of the zooplankton grazer
Daphnia pulicaria
to reduce populations of
Giardia lamblia
cysts and
Cryptosporidium parvum
oocysts in surface waters. The potential for
D. pulicaria
to act as a biological filter of
C. parvum
and
G. lamblia
was tested under three grazing pressures (one, two, or four
D. pulicaria
grazers per 66 ml). (Oo)cysts (1 × 10
4
per 66 ml) were added to each grazing bottle along with the algal food
Selenastrum capricornutum
(6.6 × 10
4
cells per 66 ml) to stimulate normal grazing. Bottles were rotated (2 rpm) to prevent settling of (oo)cysts and algae for 24 h (a light:dark cycle of 16 h:8 h) at 20°C. The impact of
D. pulicaria
grazing on (oo)cysts was assessed by (i) (oo)cyst clearance rates, (ii) (oo)cyst viability, (iii) (oo)cyst excystation, and (iv) oocyst infectivity in cell culture. Two
D. pulicaria
grazers significantly decreased the total number of
C. parvum
oocysts by 52% and
G. lamblia
cysts by 44%. Furthermore, two
D. pulicaria
grazers significantly decreased
C. parvum
excystation and infectivity by 5% and 87%, respectively. Two
D. pulicaria
grazers significantly decreased the viability of
G. lamblia
cysts by 52%, but analysis of
G. lamblia
excystation was confounded by observed mechanical disruption of the cysts after grazing. No mechanical disruption of the
C. parvum
oocysts was observed, presumably due to their smaller size. The data provide strong evidence that zooplankton grazers have the potential to substantially decrease the population of infectious
C. parvum
and
G. lamblia
in freshwater ecosystems.
Acanthamoeba
-
Campylobacter
Coculture as a Novel Method for Enrichment of
Campylobacter
Species
Authors: Axelsson-Olsson Diana , Ellström Patrik , Waldenström Jonas , Haemig Paul D. , Brudin Lars , Olsen Björn 
Published: September 2007

ABSTRACT

In this study, we present a novel method to isolate and enrich low concentrations of
Campylobacter
pathogens. This method,
Acanthamoeba
-
Campylobacter
coculture (ACC), is based on the intracellular survival and multiplication of
Campylobacter
species in the free-living protozoan
Acanthamoeba polyphaga
. Four of the
Campylobacter
species relevant to humans and livestock,
Campylobacter jejuni
,
C. coli
,
C. lari
, and
C. hyointestinalis
, were effectively enriched by the coculture method, with growth rates comparable to those observed in other
Campylobacter
enrichment media. Studying six strains of
C. jejuni
isolated from different sources, we found that all of the strains could be enriched from an inoculum of fewer than 10 bacteria. The sensitivity of the ACC method was not negatively affected by the use of
Campylobacter
-selective antibiotics in the culture medium, but these were effective in suppressing the growth of seven different bacterial species added at a concentration of 10
4
CFU/ml of each species as deliberate contamination. The ACC method has advantages over other enrichment methods as it is not dependent on a microaerobic milieu and does not require the use of blood or other oxygen-quenching agents. Our study found the ACC method to be a promising tool for the enrichment of
Campylobacter
species, particularly from water samples with low bacterial concentrations.
Biodegradation of Bis(2-Chloroethyl) Ether by
Xanthobacter
sp. Strain ENV481
Authors: McClay Kevin , Schaefer Charles E. , Vainberg Simon , Steffan Robert J. 
Published: September 2007

ABSTRACT

Degradation of bis(2-chloroethyl) ether (BCEE) was observed to occur in two bacterial strains. Strain ENV481, a
Xanthobacter
sp. strain, was isolated by enrichment culturing of samples from a Superfund site located in the northeastern United States. The strain was able to grow on BCEE or 2-chloroethylethyl ether as the sole source of carbon and energy. BCEE degradation in strain ENV481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol and diethylene glycol (DEG), respectively. 2-Hydroxyethoxyacetic acid was detected as a product of DEG catabolism by the strain. Degradation of BCEE by strain ENV481 was independent of oxygen, and the strain was not able to grow on a mixture of benzene, ethylbenzene, toluene, and xylenes, other prevalent contaminants at the site. Another bacterial isolate,
Pseudonocardia
sp. strain ENV478 (S. Vainberg et al., Appl. Environ. Microbiol. 72:5218-5224, 2006), degraded BCEE after growth on tetrahydrofuran or propane but was not able to grow on BCEE as a sole carbon source. BCEE degradation by strain ENV478 appeared to be facilitated by a monooxygenase-mediated O-dealkylation mechanism, and it resulted in the accumulation of 2-chloroacetic acid that was not readily degraded by the strain.
Evaluation of Staphylococcal Cell Surface Display and Flow Cytometry for Postselectional Characterization of Affinity Proteins in Combinatorial Protein Engineering Applications
Authors: Löfblom John , Sandberg Julia , Wernérus Henrik , Ståhl Stefan 
Published: September 2007

ABSTRACT

For efficient generation of high-affinity protein-based binding molecules, fast and reliable downstream characterization platforms are needed. In this work, we have explored the use of staphylococcal cell surface display together with flow cytometry for affinity characterization of candidate affibody molecules directly on the cell surface. A model system comprising three closely related affibody molecules with different affinities for immunoglobulin G and an albumin binding domain with affinity for human serum albumin was used to investigate advantages and differences compared to biosensor technology in a side-by-side manner. Equilibrium dissociation constant (

K
D

) determinations as well as dissociation rate analysis were performed using both methods, and the results show that the on-cell determinations give both

K
D

and dissociation rate values in a very fast and reproducible manner and that the relative affinities are very similar to the biosensor results. Interestingly, the results also show that there are differences between the absolute affinities determined with the two different technologies, and possible explanations for this are discussed. This work demonstrates the advantages of cell surface display for directed evolution of affinity proteins in terms of fast postselectional, on-cell characterization of candidate clones without the need for subcloning and subsequent protein expression and purification but also demonstrates that it is important to be aware that absolute affinities determined using different methods often vary substantially and that such comparisons therefore could be difficult.
Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity
Authors: Zul Delita , Denzel Sabine , Kotz Andrea , Overmann Jörg 
Published: September 2007

ABSTRACT

Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of
Alphaproteobacteria
,
Betaproteobacteria
,
Bacteroidetes
,
Chloroflexi
,
Planctomycetes
, and
Verrucomicrobia
populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of
Acidobacteria
,
Actinobacteria
,
Archaea
, and
Firmicutes
populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the
Betaproteobacteria
species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.