bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and Evaluation of the Ag+‐Loaded Soy Protein Isolate‐Based Bactericidal Film‐Forming Dispersion and Films
Authors: Sun Qingshen , Li Xiaodi , Wang Pu , Du Yiyang , Han Dequan , Wang Fengjiao , Liu Xumei , Li Pengfei , Fu Honggang 
Published: June 2011

Abstract: This study aims to prepare bactericidal films developed from soy protein isolate (SPI) based film‐forming dispersions (FFDs) for use in the food and medical fields. The FFD and films were prepared after the incorporation of different concentrations of AgNO3as a bactericidal agent. The transparency, tensile strength, and antimicrobial features were evaluated. Structural characterizations were also performed by Fourier transform infrared spectroscopy, scanning electron microscope, and atomic force microscopy analysis. Results showed that the opacity of these FFD was greatly decreased after the incorporation of AgNO3. The SPI‐5 film has the largest tensile strength (P < 0.05) compared with that of the other ones. Micro structural imaging analysis showed an increase in the surface irregularities with the addition of AgNO3. The minimum inhibitory concentration of AgNO3was 336 μg/mL FFD for both Escherichia coli ATCC 25923 and Staphylococcus aureus ATCC 25922. The SPI‐AgNO3films developed from the FFD with the minimal AgNO3concentration at 336 μg/mL FFD also showed bactericidal effects for both the strains. These results may prove promising for the use of SPI‐AgNO3films in the food or medical industries.Practical Application: The films prepared in this study are biodegradable and will be used in medical and food fields.
Molecular Detection of Campylobacter spp. in California Gull (Larus californicus) Excreta
Authors: Lu Jingrang , Ryu Hodon , Santo Domingo Jorge W. , Griffith John F. , Ashbolt Nicholas 
Published: May 2011

ABSTRACT

We examined the prevalence, quantity, and diversity of
Campylobacter
species in the excreta of 159 California gull (
Larus californicus
) samples using culture-, PCR-, and quantitative PCR (qPCR)-based detection assays.
Campylobacter
prevalence and abundance were relatively high in the gull excreta examined; however,
C. jejuni
and
C. lari
were detected in fewer than 2% of the isolates and DNA extracts from the fecal samples that tested positive. Moreover, molecular and sequencing data indicated that most
L. californicus
campylobacters were novel (<97% 16S rRNA gene sequence identity to known
Campylobacter
species) and not closely related to species commonly associated with human illness.
Campylobacter
estimates were positively related with those of fecal indicators, including a gull fecal marker based on the
Catellicoccus marimammalium
16S rRNA gene.
Restructuring of Endophytic Bacterial Communities in Grapevine Yellows-Diseased and Recovered Vitis vinifera L. Plants
Authors: Bulgari Daniela , Casati Paola , Crepaldi Paola , Daffonchio Daniele , Quaglino Fabio , Brusetti Lorenzo , Bianco Piero Attilio 
Published: May 2011

ABSTRACT
Length heterogeneity-PCR assays, combined with statistical analyses, highlighted that the endophytic bacterial community associated with healthy grapevines was characterized by a greater diversity than that present in diseased and recovered plants. The findings suggest that phytoplasmas can restructure the bacterial community by selecting endophytic strains that could elicit a plant defense response.
Cell Surface Display of Poliovirus Receptor on Escherichia coli, a Novel Method for Concentrating Viral Particles in Water
Authors: Abbaszadegan Morteza , Alum Absar , Abbaszadegan Hamed , Stout Valerie 
Published: May 2011

ABSTRACT

The lack of efficient methods for concentrating viruses in water samples leads to underreporting of viral contamination in source water. A novel strategy for viral concentration was developed using the expression of target virus receptors on bacterial cells. Poliovirus type 1, the most studied enterovirus, was used as a surrogate for enteric viruses. The human poliovirus receptor (
hPVR
) gene was expressed on the surface of
Escherichia coli
cells by using the ice nucleation protein (
INP
) gene. The
hPVR
gene was ligated to the 3′ end of the
INP
gene after the removal of the stop codon. The resulting open reading frame (ORF) was used for the projection of hPVR onto the outer membrane of
E. coli
. Gene expression was tested by SDS-PAGE, Western blot, and dot blot analyses, and virion capture ability was confirmed by transmission electron microscopy. The application of engineered
E. coli
cells for capturing viruses in 1-liter samples of source and drinking water resulted in 75 to 99% procedural recovery efficiency. Cell surface display of viral receptors on bacterial cells opens a new prospect for an efficient and inexpensive alternative tool for capturing and concentrating waterborne viruses in water samples.
Comparison of Genotypic and Phylogenetic Relationships of Environmental Enterococcus Isolates by BOX-PCR Typing and 16S rRNA Gene Sequencing
Authors: Nayak Bina S. , Badgley Brian , Harwood Valerie J. 
Published: May 2011

ABSTRACT

Environmental
Enterococcus
spp. were compared by BOX-PCR genotyping and 16S rRNA gene sequencing to clarify the predictive relationship of BOX-PCR fingerprints to species designation. BOX-PCR and 16S rRNA gene relationships agreed for 77% of strains. BOX-PCR provided superior intraspecies discrimination but incorrectly identified some strains to the species level and divided some species into multiple groups.
Local Adaptation to Soil Hypoxia Determines the Structure of an Arbuscular Mycorrhizal Fungal Community in Roots from Natural CO2Springs
Authors: Maček Irena , Dumbrell Alex J. , Nelson Michaela , Fitter Alastair H. , Vodnik Dominik , Helgason Thorunn 
Published: May 2011

ABSTRACTThe processes responsible for producing and maintaining the diversity of natural arbuscular mycorrhizal (AM) fungal communities remain largely unknown. We used natural CO2springs (mofettes), which create hypoxic soil environments, to determine whether a long-term, directional, abiotic selection pressure could change AM fungal community structure and drive the selection of particular AM fungal phylotypes. We explored whether those phylotypes that appear exclusively in hypoxic soils are local specialists or widespread generalists able to tolerate a range of soil conditions. AM fungal community composition was characterized by cloning, restriction fragment length polymorphism typing, and the sequencing of small subunit rRNA genes from roots of four plant species growing at high (hypoxic) and low (control) geological CO2exposure. We found significant levels of AM fungal community turnover (β diversity) between soil types and the numerical dominance of two AM fungal phylotypes in hypoxic soils. Our results strongly suggest that direct environmental selection acting on AM fungi is a major factor regulating AM fungal communities and their phylogeographic patterns. Consequently, some AM fungi are more strongly associated with local variations in the soil environment than with their host plant's distribution.
Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants
Authors: Kolton Max , Meller Harel Yael , Pasternak Zohar , Graber Ellen R. , Elad Yigal , Cytryn Eddie 
Published: May 2011

ABSTRACT

Adding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (
Capsicum annuum
L.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with the
Proteobacteria
,
Bacteroidetes
,
Actinobacteria
, and
Firmicutes
phyla. The relative abundance of members of the
Bacteroidetes
phylum increased from 12 to 30% as a result of biochar amendment, while that of the
Proteobacteria
decreased from 71 to 47%. The
Bacteroidetes-
affiliated
Flavobacterium
was the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (
Chitinophaga
and
Cellvibrio
, respectively) and aromatic compound degraders (
Hydrogenophaga
and
Dechloromonas
). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.
Enhanced Removal of a Human Norovirus Surrogate from Fresh Vegetables and Fruits by a Combination of Surfactants and Sanitizers
Authors: Predmore Ashley , Li Jianrong 
Published: May 2011

ABSTRACT
Fruits and vegetables are major vehicles for transmission of food-borne enteric viruses since they are easily contaminated at pre- and postharvest stages and they undergo little or no processing. However, commonly used sanitizers are relatively ineffective for removing human norovirus surrogates from fresh produce. In this study, we systematically evaluated the effectiveness of surfactants on removal of a human norovirus surrogate, murine norovirus 1 (MNV-1), from fresh produce. We showed that a panel of surfactants, including sodium dodecyl sulfate (SDS), Nonidet P-40 (NP-40), Triton X-100, and polysorbates, significantly enhanced the removal of viruses from fresh fruits and vegetables. While tap water alone and chlorine solution (200 ppm) gave only <1.2-log reductions in virus titer in all fresh produce, a solution containing 50 ppm of surfactant was able to achieve a 3-log reduction in virus titer in strawberries and an approximately 2-log reduction in virus titer in lettuce, cabbage, and raspberries. Moreover, a reduction of approximately 3 logs was observed in all the tested fresh produce after sanitization with a solution containing a combination of 50 ppm of each surfactant and 200 ppm of chlorine. Taken together, our results demonstrate that the combination of a surfactant with a commonly used sanitizer enhanced the efficiency in removing viruses from fresh produce by approximately 100 times. Since SDS is an FDA-approved food additive and polysorbates are recognized by the FDA as GRAS (generally recognized as safe) products, implementation of this novel sanitization strategy would be a feasible approach for efficient reduction of the virus load in fresh produce.
Generalized Relationship between Numbers of Bacteria and Their Viability in Biofilms
Authors: Sjollema Jelmer , Rustema-Abbing Minie , van der Mei Henny C. , Busscher Henk J. 
Published: May 2011

ABSTRACT
Bacterial biofilms are confined communities that are encapsulated in protective layers of extracellular polymeric substances. Microscopic evaluation of biofilms of diverse bacterial strains on various substrata reveals that, in general, the percentage of viable bacteria decreases with the total number of bacteria in a biofilm.
SidL, an Aspergillus fumigatus Transacetylase Involved in Biosynthesis of the Siderophores Ferricrocin and Hydroxyferricrocin
Authors: Blatzer Michael , Schrettl Markus , Sarg Bettina , Lindner Herbert H. , Pfaller Kristian , Haas Hubertus 
Published: May 2011

ABSTRACT

The opportunistic fungal pathogen
Aspergillus fumigatus
produces four types of siderophores, low-molecular-mass iron chelators: it excretes fusarinine C (FsC) and triacetylfusarinine C (TAFC) for iron uptake and accumulates ferricrocin (FC) for hyphal and hydroxyferricrocin (HFC) for conidial iron distribution and storage. Siderophore biosynthesis has recently been shown to be crucial for fungal virulence. Here we identified a new component of the fungal siderophore biosynthetic machinery: AFUA_1G04450, termed SidL. SidL is conserved only in siderophore-producing ascomycetes and shows similarity to transacylases involved in bacterial siderophore biosynthesis and the
N
5
-hydroxyornithine:anhydromevalonyl coenzyme A-
N
5
-transacylase SidF, which is essential for TAFC biosynthesis. Inactivation of SidL in
A. fumigatus
decreased FC biosynthesis during iron starvation and completely blocked FC biosynthesis during iron-replete growth. In agreement with these findings, SidL deficiency blocked conidial accumulation of FC-derived HFC under iron-replete conditions, which delayed germination and decreased the size of conidia and their resistance to oxidative stress. Remarkably, the
sidL
gene is not clustered with other siderophore-biosynthetic genes, and its expression is not affected by iron availability. Tagging of SidL with enhanced green fluorescent protein suggested a cytosolic localization of the FC-biosynthetic machinery. Taken together, these data suggest that SidL is a constitutively active
N
5
-hydroxyornithine-acetylase required for FC biosynthesis, in particular under iron-replete conditions. Moreover, this study revealed the unexpected complexity of siderophore biosynthesis, indicating the existence of an additional, iron-repressed
N
5
-hydroxyornithine-acetylase.
Rapid Fluorescence-Based Screening for Wolbachia Endosymbionts in Drosophila Germ Line and Somatic Tissues
Authors: Casper-Lindley Catharina , Kimura Scott , Saxton Daniel S. , Essaw Yonathan , Simpson Isaac , Tan Vinson , Sullivan William 
Published: May 2011

ABSTRACT

Wolbachia
is a globally distributed bacterial endosymbiont present in arthropods and nematodes. The advent of sensitive PCR-based approaches has greatly facilitated the identification of
Wolbachia
-infected individuals and analysis of population infection levels. Here, a complementary visual fluorescence-based
Wolbachia
screening approach is described. Through the use of the fluorescent dye Syto-11,
Wolbachia
can be efficiently detected in various
Drosophila
tissues, including ovaries. Syto-11 also stains
Wolbachia
in other insects. Because
Wolbachia
is inherited through the maternal germ line, bacteria reside in the ovaries of flies in infected populations. An advantage of this staining approach is that it informs about
Wolbachia
titer as well as its tissue and cellular distribution. Using this method, the infection status of insect populations in two central California locations was determined, and variants with unusually low or high
Wolbachia
titers were isolated. In addition, a variant with ovarioles containing both infected and uninfected egg chambers was identified. Syto-11 staining of
Cardinium
- and
Spiroplasma
-infected insects was also analyzed.
Different IS
629
Transposition Frequencies Exhibited by Escherichia coli O157:H7 Strains in the Stepwise Evolutionary Model
Authors: Rump Lydia V. , Fischer Markus , González-Escalona Narjol 
Published: May 2011

ABSTRACT

The insertion sequence IS
629
, which is highly prevalent in
Escherichia coli
O157:H7 genomes, was found to be absent in O157:H− strains, which are on a divergent pathway in the emergence of O157:H7. Although O157:H− is deficient in IS
629
, it permits IS
629
transposition, with an excision frequency higher than that of ancestral O55:H7 strains but significantly lower than that of pathogenic O157:H7 strains.
Cultivation-Independent Detection of Autotrophic Hydrogen-Oxidizing Bacteria by DNA Stable-Isotope Probing
Authors: Pumphrey Graham M. , Ranchou-Peyruse Anthony , Spain Jim C. 
Published: May 2011

ABSTRACTKnallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of13CO2was H2dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. AhydBhomolog encoding a putative high-affinity NiFe hydrogenase was amplified from13C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H2concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.
Methylotrophy in a Lake: from Metagenomics to Single-Organism Physiology
Authors: Chistoserdova Ludmila 
Published: May 2011

ABSTRACT

This review provides a brief summary of ongoing studies in Lake Washington (Seattle, WA) directed at an understanding of the content and activities of microbial communities involved in methylotrophy. One of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence of
Methylotenera
species in the site and their inferred activity in C
1
metabolism, highlighting the local environmental importance of this group. Comparative analyses of individual genomes of
Methylophilaceae
from Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility.
Diversity, Abundance, and Potential Activity of Nitrifying and Nitrate-Reducing Microbial Assemblages in a Subglacial Ecosystem
Authors: Boyd Eric S. , Lange Rachel K. , Mitchell Andrew C. , Havig Jeff R. , Hamilton Trinity L. , Lafrenière Melissa J. , Shock Everett L. , Peters John W. , Skidmore Mark 
Published: May 2011

ABSTRACT

Subglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by
amoA
,
narG
, and
nifH
gene biomarker diversity. Although archaeal
amoA
genes were detected, they were less abundant and less diverse than bacterial
amoA
, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occur
in situ
. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ∼210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection of
nifH
, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales.
Impact of Internal RNA on Aggregation and Electrokinetics of Viruses: Comparison between MS2 Phage and Corresponding Virus-Like Particles
Authors: Dika C. , Duval J. F. L. , Ly-Chatain H. M. , Merlin C. , Gantzer C. 
Published: May 2011

ABSTRACT

We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO
3
electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggregation profiles for MS2 and MS2 VLPs. Under the given pH and concentration conditions, MS2 VLPs exhibit electrophoretic mobility larger in magnitude than that of MS2, and both have similar isoelectric point (IEP) values (∼4). The electrokinetic results reflect a greater permeability of MS2 VLPs to electroosmotic flow, developed within/around these soft particles during their migration under the action of the applied electrical field. Results also support the presence of some remaining negatively charged component within the VLPs. In addition, MS2 phage systematically forms aggregates at pH values below the IEP, regardless of the magnitude of the solution ionic strength, whereas MS2 VLPs aggregate under the strict condition where the pH is relatively equal to the IEP at sufficiently low salt concentrations (<10 mM). It is argued that the stability of VLPs against aggregation and the differences between electrokinetics of MS2 and corresponding VLPs conform to recently developed formalisms for the stability and electrohydrodynamics of soft multilayered particles. The differences between the surface properties of these two kinds of particles reported here suggest that VLPs may not be appropriate for predicting the behavior of pathogenic viruses in aqueous media.
Persistence of Avian Influenza Viruses in Lake Sediment, Duck Feces, and Duck Meat
Authors: Nazir Jawad , Haumacher Renate , Ike Anthony C. , Marschang Rachel E. 
Published: May 2011

ABSTRACT

The persistence of 3 low-pathogenicity avian influenza viruses (LPAIV) (H4N6, H5N1, and H6N8) and one human influenza virus (H1N1) as well as Newcastle disease virus (NDV) and enteric cytopathogenic bovine orphan (ECBO) virus was investigated in lake sediment, duck feces, and duck meat at 30, 20, 10, and 0°C using a germ carrier technique. Virus-loaded germ carriers were incubated in each substrate, and residual infectivity of the eluted virus was quantified on cell culture after regular intervals for a maximum of 24 weeks. Data were analyzed by a linear regression model to calculate
T
90
values (time required for 90% loss of virus infectivity) and estimated persistence of the viruses. In general, the persistence of all of the viruses was highest in lake sediment, followed by feces, and was the lowest in duck meat at all temperatures. For the avian influenza virus subtypes,
T
90
values in sediment ranged from 5 to 11, 13 to 18, 43 to 54, and 66 to 394 days at 30, 20, 10, and 0°C, respectively, which were 2 to 5 times higher than the
T
90
values of the viruses in the feces and meat. Although the individual viruses vary in tenacity, the survival time of influenza viruses was shorter than that of NDV and ECBO virus in all substrates. The results of this study suggest that lake sediment may act as a long-term source of influenza viruses in the aquatic habitat, while the viruses may remain infectious for extended periods of time in duck feces and meat at low temperatures, allowing persistence of the viruses in the environment over winter.