bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher-Level Production of Volatile Fatty Acids
In Vitro
by Chicken Gut Microbiotas than by Human Gut Microbiotas as Determined by Functional Analyses
Authors: Lei Fang , Yin Yeshi , Wang Yuezhu , Deng Bo , Yu Hongwei David , Li Lanjuan , Xiang Charlie , Wang Shengyue , Zhu Baoli , Wang Xin 
Published: June 2012

ABSTRACT

The aim of this study was to determine the relationship between the composition and function of gut microbiota. Here, we compared the bacterial compositions and fermentation metabolites of human and chicken gut microbiotas. Results generated by quantitative PCR (qPCR) and 454 pyrosequencing of the 16S rRNA gene V3 region showed the compositions of human and chicken microbiotas to be markedly different, with chicken cecal microbiotas displaying more diversity than human fecal microbiotas. The nutrient requirements of each microbiota growing under batch and chemostat conditions were analyzed. The results showed that chicken cecal microbiotas required simple sugars and peptides to maintain balanced growth
in vitro
but that human fecal microbiotas preferred polysaccharides and proteins. Chicken microbiotas also produced higher concentrations of volatile fatty acids than did human microbiotas. Our data suggest that the availability of different fermentable substrates in the chicken cecum, which exist due to the unique anatomical structure of the cecum, may provide an environment favorable to the nourishment of microbiotas suited to the production of the higher-energy metabolites required by the bird. Therefore, gut structure, nutrition, immunity, and life-style all contribute to the selection of an exclusive bacterial community that produces types of metabolites beneficial to the host.
Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater
Authors: French Elizabeth , Kozlowski Jessica A. , Mukherjee Maitreyee , Bullerjahn George , Bollmann Annette 
Published: June 2012

ABSTRACT

Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with “
Candidatus
Nitrosoarchaeum koreensis” and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the
Nitrosomonas oligotropha
group (
Nitrosomonas
cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.
Association of Cry1Ac Toxin Resistance in Helicoverpa zea (Boddie) with Increased Alkaline Phosphatase Levels in the Midgut Lumen
Authors: Caccia Silvia , Moar William J. , Chandrashekhar Jayadevi , Oppert Cris , Anilkumar Konasale J. , Jurat-Fuentes Juan Luis , Ferré Juan 
Published: June 2012

ABSTRACT

Resistance to
Bacillus thuringiensis
Cry1Ac toxin was characterized in a population of
Helicoverpa zea
larvae previously shown not to have an alteration in toxin binding as the primary resistance mechanism to this toxin. Cry1Ac-selected larvae (AR1) were resistant to protoxins and toxins of Cry1Ab, Cry1Ac, and the corresponding modified proteins lacking helix α-1 (Cry1AbMod and Cry1AcMod). When comparing brush border membrane vesicles (BBMVs) prepared from susceptible (LC) and AR1 larval midguts, there were only negligible differences in overall Cry1Ac toxin binding, though AR1 had 18% reversible binding, in contrast to LC, in which all binding was irreversible. However, no differences were detected in Cry1Ac-induced pore formation activity in BBMVs from both strains. Enzymatic activities of two putative Cry1Ac receptors (aminopeptidase N [APN] and alkaline phosphatase [ALP]) were significantly reduced (2-fold and 3-fold, respectively) in BBMVs from AR1 compared to LC larvae. These reductions corresponded to reduced protein levels in midgut luminal contents only in the case of ALP, with an almost 10-fold increase in specific ALP activity in midgut fluids from AR1 compared to LC larvae. Partially purified
H. zea
ALP bound Cry1Ac toxin in ligand blots and competed with Cry1Ac toxin for BBMV binding. Based on these results, we suggest the existence of at least one mechanism of resistance to Cry1A toxins in
H. zea
involving binding of Cry1Ac toxin to an ALP receptor in the larval midgut lumen of resistant larvae.
Cloning, Production, and Functional Expression of the Bacteriocin Enterocin A, Produced by Enterococcus faecium T136, by the Yeasts Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Arxula adeninivorans
Authors: Borrero Juan , Kunze Gotthard , Jiménez Juan J. , Böer Erik , Gútiez Loreto , Herranz Carmen , Cintas Luis M. , Hernández Pablo E. 
Published: June 2012

ABSTRACT

The bacteriocin enterocin A (EntA) produced by
Enterococcus faecium
T136 has been successfully cloned and produced by the yeasts
Pichia pastoris
X-33EA,
Kluyveromyces lactis
GG799EA,
Hansenula polymorpha
KL8-1EA, and
Arxula adeninivorans
G1212EA. Moreover,
P. pastoris
X-33EA and
K. lactis
GG799EA produced EntA in larger amounts and with higher antimicrobial and specific antimicrobial activities than the EntA produced by
E. faecium
T136.
Differences in Substrate Specificities of Five Bacterial Wax Ester Synthases
Authors: Barney Brett M. , Wahlen Bradley D. , Garner EmmaLee , Wei Jiashi , Seefeldt Lance C. 
Published: June 2012

ABSTRACT

Wax esters are produced in certain bacteria as a potential carbon and energy storage compound. The final enzyme in the biosynthetic pathway responsible for wax ester production is the bifunctional wax ester synthase/acyl-coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT), which utilizes a range of fatty alcohols and fatty acyl-CoAs to synthesize the corresponding wax ester. We report here the isolation and substrate range characterization for five WS/DGAT enzymes from four different bacteria:
Marinobacter aquaeolei
VT8,
Acinetobacter baylyi
,
Rhodococcus jostii
RHA1, and
Psychrobacter cryohalolentis
K5. The results from kinetic studies of isolated enzymes reveal a differential activity based on the order of substrate addition and reveal subtle differences between the substrate selectivity of the different enzymes. These
in vitro
results are compared to the wax ester and triacylglyceride product profiles obtained from each organism grown under neutral lipid accumulating conditions, providing potential insights into the role that the WS/DGAT enzyme plays in determining the final wax ester products that are produced under conditions of nutrient stress in each of these bacteria. Further, the analysis revealed that one enzyme in particular from
M. aquaeolei
VT8 showed the greatest potential for future study based on rapid purification and significantly higher activity than was found for the other isolated WS/DGAT enzymes. The results provide a framework to test prospective differences between these enzymes for potential biotechnological applications such as high-value petrochemicals and biofuel production.
Longitudinal Study of the Contamination of Air and of Soil Surfaces in the Vicinity of Pig Barns by Livestock-Associated Methicillin-Resistant Staphylococcus aureus
Authors: Schulz Jochen , Friese Anika , Klees Sylvia , Tenhagen Bernd A. , Fetsch Alexandra , Rösler Uwe , Hartung Jörg 
Published: June 2012

ABSTRACT

During 1 year, samples were taken on 4 days, one sample in each season, from pigs, the floor, and the air inside pig barns and from the ambient air and soil at different distances outside six commercial livestock-associated methicillin-resistant
Staphylococcus aureus
(LA-MRSA)-positive pig barns in the north and east of Germany. LA-MRSA was isolated from animals, floor, and air samples in the barn, showing a range of airborne LA-MRSA between 6 and 3,619 CFU/m
3
(median, 151 CFU/m
3
). Downwind of the barns, LA-MRSA was detected in low concentrations (11 to 14 CFU/m
3
) at distances of 50 and 150 m; all upwind air samples were negative. In contrast, LA-MRSA was found on soil surfaces at distances of 50, 150, and 300 m downwind from all barns, but no statistical differences could be observed between the proportions of positive soil surface samples at the three different distances. Upwind of the barns, positive soil surface samples were found only sporadically. Significantly more positive LA-MRSA samples were found in summer than in the other seasons both in air and soil samples upwind and downwind of the pig barns.
spa
typing was used to confirm the identity of LA-MRSA types found inside and outside the barns. The results show that there is regular airborne LA-MRSA transmission and deposition, which are strongly influenced by wind direction and season, of up to at least 300 m around positive pig barns. The described boot sampling method seems suitable to characterize the contamination of the vicinity of LA-MRSA-positive pig barns by the airborne route.
Diurnal Infection Patterns and Impact of Microcystis Cyanophages in a Japanese Pond
Authors: Kimura Shigeko , Yoshida Takashi , Hosoda Naohiko , Honda Takashi , Kuno Sotaro , Kamiji Rikae , Hashimoto Ryoya , Sako Yoshihiko 
Published: June 2012

ABSTRACT

Viruses play important roles in regulating the abundance, clonal diversity, and composition of their host populations. To assess their impact on the host populations, it is essential to understand the dynamics of virus infections in the natural environment. Cyanophages often carry host-like genes, including photosynthesis genes, which maintain host photosynthesis. This implies a diurnal pattern of cyanophage infection depending on photosynthesis. Here we investigated the infection pattern of
Microcystis
cyanophage by following the abundances of the Ma-LMM01-type phage tail sheath gene
g91
and its transcript in a natural population. The relative
g91
mRNA abundance within host cells showed a peak during the daylight hours and was lowest around midnight. The phage
g91
DNA copy numbers in host cell fractions, which are predicted to indicate phage replication, increased in the afternoon, followed by an increase in the free-phage fractions. In all fractions, at least 1 of 71
g91
genotypes was observed (in tested host cell, free-phage, and RNA fractions), indicating that the replication cycle of the cyanophage (i.e., injection, transcription, replication, and release of progeny phages) was occurring. Thus,
Microcystis
cyanophage infection occurs in a diel cycle, which may depend on the light cycle. Additionally, our data show that the abundance of mature cyanophage produced within host cells was 1 to 2 orders of magnitude greater than that of released phages, suggesting that phage production may be higher than previously reported.
Enhancement of the Structural Stability of Full-Length Clostridial Collagenase by Calcium Ions
Authors: Ohbayashi Naomi , Yamagata Noriko , Goto Masafumi , Watanabe Kimiko , Yamagata Youhei , Murayama Kazutaka 
Published: June 2012

ABSTRACT

The clostridial collagenases G and H are multidomain proteins. For collagen digestion, the domain arrangement is likely to play an important role in collagen binding and hydrolysis. In this study, the full-length collagenase H protein from
Clostridium histolyticum
was expressed in
Escherichia coli
and purified. The N-terminal amino acid of the purified protein was Ala31. The expressed protein showed enzymatic activity against azocoll as a substrate. To investigate the role of Ca
2+
in providing structural stability to the full-length collagenase H, biophysical measurements were conducted using the recombinant protein. Size exclusion chromatography revealed that the Ca
2+
chelation by EGTA induced interdomain conformational changes. Dynamic light scattering measurements showed an increase in the percent polydispersity as the Ca
2+
was chelated, suggesting an increase in protein flexibility. In addition to these conformational changes, differential scanning fluorimetry measurements revealed that the thermostability was decreased by Ca
2+
chelation, in comparison with the thermal melting point (

T
m

). The melting point changed from 54 to 49°C by the Ca
2+
chelation, and it was restored to 54°C by the addition of excess Ca
2+
. These results indicated that the interdomain flexibility and the domain arrangement of full-length collagenase H are reversibly regulated by Ca
2+
.
Outer Membrane Protein AlkL Boosts Biocatalytic Oxyfunctionalization of Hydrophobic Substrates in Escherichia coli
Authors: Julsing Mattijs K. , Schrewe Manfred , Cornelissen Sjef , Hermann Inna , Schmid Andreas , Bühler Bruno 
Published: June 2012

ABSTRACTThe outer membrane of microbial cells forms an effective barrier for hydrophobic compounds, potentially causing an uptake limitation for hydrophobic substrates. Low bioconversion activities (1.9 U gcdw−1) have been observed for the ω-oxyfunctionalization of dodecanoic acid methyl ester by recombinantEscherichia colicontaining the alkane monooxygenase AlkBGT ofPseudomonas putidaGPo1. Using fatty acid methyl ester oxygenation as the model reaction, this study investigated strategies to improve bacterial uptake of hydrophobic substrates. Admixture of surfactants and cosolvents to improve substrate solubilization did not result in increased oxygenation rates. Addition of EDTA increased the initial dodecanoic acid methyl ester oxygenation activity 2.8-fold. The use of recombinantPseudomonas fluorescensCHA0 instead ofE. coliresulted in a similar activity increase. However, substrate mass transfer into cells was still found to be limiting. Remarkably, the coexpression of thealkLgene ofP. putidaGPo1 encoding an outer membrane protein with so-far-unknown function increased the dodecanoic acid methyl ester oxygenation activity of recombinantE. coli28-fold. In a two-liquid-phase bioreactor setup, a 62-fold increase to a maximal activity of 87 U gcdw−1was achieved, enabling the accumulation of high titers of terminally oxyfunctionalized products. Coexpression ofalkLalso increased oxygenation activities toward the natural AlkBGT substrates octane and nonane, showing for the first time clear evidence for a prominent role of AlkL in alkane degradation. This study demonstrates that AlkL is an efficient tool to boost productivities of whole-cell biotransformations involving hydrophobic aliphatic substrates and thus has potential for broad applicability.
Stability and Infectivity of Cytolethal Distending Toxin Type V Gene-Carrying Bacteriophages in a Water Mesocosm and under Different Inactivation Conditions
Authors: Allué-Guardia Anna , Jofre Juan , Muniesa Maite 
Published: June 2012

ABSTRACT

Two cytolethal distending toxin (Cdt) type V-encoding bacteriophages (Φ62 and Φ125) were induced spontaneously from their wild-type
Escherichia coli
strains and from the lysogens generated in
Shigella sonnei
. The stability of Cdt phages was determined at various temperatures and pH values after 1 month of storage by means of infectivity tests using a plaque blot assay and analysis of phage genomes using real-time quantitative PCR (qPCR): both were highly stable. We assessed the inactivation of Cdt phages by thermal treatment, chlorination, UV radiation, and in a mesocosm in both summer and winter. The results for the two Cdt phages showed similar trends and were also similar to the phage SOM23 used for reference, but they showed a much higher persistence than Cdt-producing
E. coli
. Cdt phages showed maximal inactivation after 1 h at 70°C, 30 min of UV radiation, and 30 min of contact with a 10-ppm chlorine treatment. Inactivation in a mesocosm was higher in summer than in winter, probably because of solar radiation. The treatments reduced the number of infectious phages but did not have a significant effect on the Cdt phage particles detected by qPCR. Cdt phages were quantified by qPCR in 73% of river samples, and these results suggest that Cdt phages are a genetic vehicle and the natural reservoir for
cdt
in the environment.
Synthesis, Release, and Recapture of Compatible Solute Proline by Osmotically Stressed Bacillus subtilis Cells
Authors: Hoffmann Tamara , von Blohn Carsten , Stanek Agnieszka , Moses Susanne , Barzantny Helena , Bremer Erhard 
Published: June 2012

ABSTRACT

Bacillus subtilis
synthesizes large amounts of the compatible solute proline as a cellular defense against high osmolarity to ensure a physiologically appropriate level of hydration of the cytoplasm and turgor. It also imports proline for this purpose via the osmotically inducible OpuE transport system. Unexpectedly, an
opuE
mutant was at a strong growth disadvantage in high-salinity minimal media lacking proline. Appreciable amounts of proline were detected in the culture supernatant of the
opuE
mutant strain, and they rose concomitantly with increases in the external salinity. We found that the intracellular proline pool of severely salinity-stressed cells of the
opuE
mutant was considerably lower than that of its
opuE
+
parent strain. This loss of proline into the medium and the resulting decrease in the intracellular proline content provide a rational explanation for the observed salt-sensitive growth phenotype of cells lacking OpuE. None of the known MscL- and MscS-type mechanosensitive channels of
B. subtilis
participated in the release of proline under permanently imposed high-salinity growth conditions. The data reported here show that the OpuE transporter not only possesses the previously reported role for the scavenging of exogenously provided proline as an osmoprotectant but also functions as a physiologically highly important recapturing device for proline that is synthesized
de novo
and subsequently released by salt-stressed
B. subtilis
cells. The wider implications of our findings for the retention of compatible solutes by osmotically challenged microorganisms and the roles of uptake systems for compatible solutes are considered.
Two-Year Systematic Study To Assess Norovirus Contamination in Oysters from Commercial Harvesting Areas in the United Kingdom
Authors: Lowther James A. , Gustar Nicole E. , Powell Andrew L. , Hartnell Rachel E. , Lees David N. 
Published: June 2012

ABSTRACT

The contamination of bivalve shellfish with norovirus from human fecal sources is recognized as an important human health risk. Standardized quantitative methods for the detection of norovirus in molluscan shellfish are now available, and viral standards are being considered in the European Union and internationally. This 2-year systematic study aimed to investigate the impact of the application of these methods to the monitoring of norovirus contamination in oyster production areas in the United Kingdom. Twenty-four monthly samples of oysters from 39 United Kingdom production areas, chosen to represent a range of potential contamination risk, were tested for norovirus genogroups I and II by using a quantitative real-time reverse transcription (RT)-PCR method. Norovirus was detected in 76.2% (643/844) of samples, with all sites returning at least one positive result. Both prevalences (presence or absence) and norovirus levels varied markedly between sites. However, overall, a marked winter seasonality of contamination by both prevalence and quantity was observed. Correlations were found between norovirus contamination and potential risk indicators, including harvesting area classifications,
Escherichia coli
scores, and environmental temperatures. A predictive risk score for norovirus contamination was developed by using a combination of these factors. In summary, this study, the largest of its type undertaken to date, provides a systematic analysis of norovirus contamination in commercial oyster production areas in the United Kingdom. The data should assist risk managers to develop control strategies to reduce the risk of human illness resulting from norovirus contamination of bivalve molluscs.
Association of a New Wolbachia Strain with, and Its Effects on, Leptopilina victoriae, a Virulent Wasp Parasitic to Drosophila spp
Authors: Gueguen Gwenaelle , Onemola Bodunde , Govind Shubha 
Published: June 2012

ABSTRACT

Wolbachia
bacteria are ubiquitous intracellular bacteria of arthropods. Often considered reproductive parasites, they can benefit certain host species. We describe a new
Wolbachia
strain from
Leptopilina victoriae
, a
Drosophila
wasp. The strain is closely related to
Wolbachia
from
Culex
sp. Located to the posterior poles of oocytes, it manipulates its host's reproduction by inducing a male development type of cytoplasmic incompatibility. We also report its diverse effects on the wasp's life history traits.
Development and Application of an Arabinose-Inducible Expression System by Facilitating Inducer Uptake in Corynebacterium glutamicum
Authors: Zhang Yun , Shang Xiuling , Lai Shujuan , Zhang Guoqiang , Liang Yong , Wen Tingyi 
Published: June 2012

ABSTRACT

Corynebacterium glutamicum
is currently used for the industrial production of a variety of biological materials. Many available inducible expression systems in this species use
lac
-derived promoters from
Escherichia coli
that exhibit much lower levels of inducible expression and leaky basal expression. We developed an arabinose-inducible expression system that contains the
l
-arabinose regulator AraC, the

P
BAD

promoter from the
araBAD
operon, and the
l
-arabinose transporter AraE, all of which are derived from
E. coli
. The level of inducible

P
BAD

-based expression could be modulated over a wide concentration range from 0.001 to 0.4%
l
-arabinose. This system tightly controlled the expression of the uracil phosphoribosyltransferase without leaky expression. When the gene encoding green fluorescent protein (GFP) was under the control of

P
BAD

promoter, flow cytometry analysis showed that GFP was expressed in a highly homogeneous profile throughout the cell population. In contrast to the case in
E. coli
,

P
BAD

induction was not significantly affected in the presence of different carbon sources in
C. glutamicum
, which makes it useful in fermentation applications. We used this system to regulate the expression of the
odhI
gene from
C. glutamicum
, which encodes an inhibitor of α-oxoglutarate dehydrogenase, resulting in high levels of glutamate production (up to 13.7 mM) under biotin nonlimiting conditions. This system provides an efficient tool available for molecular biology and metabolic engineering of
C. glutamicum
.
Two SusD-Like Proteins Encoded within a Polysaccharide Utilization Locus of an Uncultured Ruminant Bacteroidetes Phylotype Bind Strongly to Cellulose
Authors: Mackenzie A. K. , Pope P. B. , Pedersen H. L. , Gupta R. , Morrison M. , Willats W. G. T. , Eijsink V. G. H. 
Published: June 2012

ABSTRACT

We demonstrate that two characteristic Sus-like proteins encoded within a polysaccharide utilization locus (PUL) bind strongly to cellulosic substrates and interact with plant primary cell walls. This shows associations between uncultured
Bacteroidetes
-affiliated lineages and cellulose in the rumen and thus presents new PUL-derived targets to pursue regarding plant biomass degradation.