bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Partial Characterization of Antagonistic Peptides Produced by
Paenibacillus
sp. Strain B2 Isolated from the Sorghum Mycorrhizosphere
Authors: Selim S. , Negrel J. , Govaerts C. , Gianinazzi S. , van Tuinen D. 
Published: November 2005

ABSTRACT

Paenibacillus
sp. strain B2, isolated from the mycorrhizosphere of sorghum colonized by
Glomus mosseae
, produces an antagonistic factor. This factor has a broad spectrum of activity against gram-positive and gram-negative bacteria and also against fungi. The antagonistic factor was isolated from the bacterial culture medium and purified by cation-exchange, reverse-phase, and size exclusion chromatography. The purified factor could be separated into three active compounds following characterization by amino acid analysis and by combined reverse-phase chromatography and mass spectrometry (liquid chromatography-mass spectrometry and mass spectrometry-mass spectrometry). The first compound had the same retention time as polymyxin B
1
, whereas the two other compounds were more hydrophobic. The molecular masses of the latter compounds are 1,184.7 and 1,202.7 Da, respectively, and their structure is similar to that of polymyxin B
1
, with a cyclic heptapeptide moiety attached to a tripeptide side chain and a fatty acyl residue. They both contain threonine, phenylalanine, leucine, and 2,4-diaminobutyric acid residues. The peptide with a molecular mass of 1,184.7 contains a 2,3-didehydrobutyrine residue with a molecular mass of 101 Da replacing a threonine at the A2 position of the polymyxin side chain. This modification could explain the broader range of antagonistic activity of this peptide compared to that of polymyxin B.
A Bile Salt-Resistant Derivative of
Bifidobacterium animalis
Has an Altered Fermentation Pattern When Grown on Glucose and Maltose
Authors: Ruas-Madiedo Patricia , Hernández-Barranco Ana , Margolles Abelardo , de los Reyes-Gavilán Clara G. 
Published: November 2005

ABSTRACT

The growth of
Bifidobacterium animalis
subsp.
lactis
IPLA 4549 and its derivative with acquired resistance to bile,
B. animalis
subsp.
lactis
4549dOx, was evaluated in batch cultures with glucose or the glucose disaccharide maltose as the main carbon source. The acquisition of bile salt resistance caused a change in growth pattern for both sugars, which mainly resulted in a preferential use of maltose compared to glucose, whereas the mother strain used both carbohydrates in a similar way. High-performance liquid chromatography and gas chromatography-mass spectrometry analyses were performed to determine the amounts of glucose consumption and organic acid and ethanol formation from glucose by buffered resting cells taken at different points during growth. Resting cells of the bile-adapted strain generally consumed less glucose than those of the nonadapted one but showed an enhanced production of ethanol and higher acetic acid-to-lactic acid as well as formic acid-to-lactic acid ratios. These findings suggest a shift in the catabolism of carbohydrates promoted by the acquisition of bile resistance that may cause changes in the redox potential and improvements in the cellular ATP yield.
The Halophilic Fungus
Hortaea werneckii
and the Halotolerant Fungus
Aureobasidium pullulans
Maintain Low Intracellular Cation Concentrations in Hypersaline Environments
Authors: Kogej Tina , Ramos José , Plemenitaš Ana , Gunde-Cimerman Nina 
Published: November 2005

ABSTRACT

Hortaea werneckii
and
Aureobasidium pullulans
, black yeast-like fungi isolated from hypersaline waters of salterns as their natural ecological niche, have been previously defined as halophilic and halotolerant microorganisms, respectively. In the present study we assessed their growth and determined the intracellular cation concentrations of salt-adapted and non-salt-adapted cells of both species at a wide range of salinities (0 to 25% NaCl and 0 to 20% NaCl, respectively). Although 5% NaCl improved the growth of
H. werneckii
, even the minimal addition of NaCl to the growth medium slowed down the growth rate of
A. pullulans
, confirming their halophilic and halotolerant nature. Salt-adapted cells of
H. werneckii
and
A. pullulans
kept very low amounts of internal Na
+
even when grown at high NaCl concentrations and can be thus considered Na
+
excluders, suggesting the existence of efficient mechanisms for the regulation of ion fluxes. Based on our results, we can conclude that these organisms do not use K
+
or Na
+
for osmoregulation. Comparison of cation fluctuations after a hyperosmotic shock, to which nonadapted cells of both species were exposed, demonstrated better ionic homeostasis regulation of
H. werneckii
compared to
A. pullulans
. We observed small fluctuations of cation concentrations after a hyperosmotic shock in nonadapted
A. pullulans
similar to those in salt-adapted
H.werneckii
, which additionally confirmed better regulation of ionic homeostasis in the latter. These features can be expected from organisms adapted to survival within a wide range of salinities and to occasional exposure to extremely high NaCl concentrations, both characteristic for their natural environment.
Suitability of RecombinantEscherichia coliandPseudomonas putidaStrains for Selective Biotransformation ofm-Nitrotoluene by Xylene Monooxygenase
Authors: Meyer Daniel , Witholt Bernard , Schmid Andreas 
Published: November 2005

ABSTRACTEscherichia coliJM101(pSPZ3), containing xylene monooxygenase (XMO) fromPseudomonas putidamt-2, catalyzes specific oxidations and reductions ofm-nitrotoluene and derivatives thereof. In addition to reactions catalyzed by XMO, we focused on biotransformations by native enzymes of theE. colihost and their effect on overall biocatalyst performance. Whilem-nitrotoluene was consecutively oxygenated tom-nitrobenzyl alcohol,m-nitrobenzaldehyde, andm-nitrobenzoic acid by XMO, the oxidation was counteracted by an alcohol dehydrogenase(s) from theE. colihost, which reducedm-nitrobenzaldehyde tom-nitrobenzyl alcohol. Furthermore, the enzymatic background of the host reduced the nitro groups of the reactants resulting in the formation of aromatic amines, which were shown to effectively inhibit XMO in a reversible fashion. Host-intrinsic oxidoreductases and their reaction products had a major effect on the activity of XMO during biocatalysis ofm-nitrotoluene.P. putidaDOT-T1E andP. putidaPpS81 were compared toE. coliJM101 as alternative hosts for XMO. These promising strains contained an additional dehydrogenase that oxidizedm-nitrobenzaldehyde to the corresponding acid but catalyzed the formation of XMO-inhibiting aromatic amines at a significantly lower level thanE. coliJM101.
Detection, Characterization, and In Vitro and In Vivo Expression of Genes Encoding S-Proteins in
Lactobacillus gallinarum
Strains Isolated from Chicken Crops
Authors: Hagen Karen E. , Guan Le Luo , Tannock Gerald W. , Korver Doug R. , Allison Gwen E. 
Published: November 2005

ABSTRACT

Thirty-eight isolates of
Lactobacillus gallinarum
cultured from the crops of broiler chickens were screened for the presence of genes encoding S-layer proteins. All of the isolates had two S-protein genes, which were designated
Lactobacillus gallinarum
S-protein (
lgs
) genes. One gene in each isolate was either
lgsA
or
lgsB
. The
Lactobacillus
isolates were further characterized by pulsed-field gel electrophoresis of DNA digests, which grouped the isolates into 17 genotypes (strains). The second gene in each of eight representative strains was sequenced and shown to differ among strains (
lgsC
,
lgsD
,
lgsE
,
lgsF
,
lgsG
,
lgsH
, and
lgsI
). The genome of each strain thus encoded a common S-protein (encoded by either
lgsA
or
lgsB
) and a strain-specific S-protein. The extraction of cell surface proteins from cultures of the eight strains showed that each strain produced a single S-protein that was always encoded by the strain-specific
lgs
gene. Two of the strains were used to inoculate chickens maintained in a protected environment which were
Lactobacillus
-free prior to inoculation. DNAs and RNAs extracted from the digesta of the chickens were used for PCR and reverse transcription-PCR, respectively, to demonstrate the presence and transcription of
lgs
genes in vivo. In both cases, only the strain-specific gene was transcribed. Both of the strains adhered to the crop epithelium, consistent with published data predicting that S-proteins of lactobacilli are adhesins. The results of this study provide a basis for the investigation of gene duplication and sequence variation as mechanisms by which bacterial strains of the same species can share the same habitat.
Viral Production, Decay Rates, and Life Strategies along a Trophic Gradient in the North Adriatic Sea
Authors: Bongiorni Lucia , Magagnini Mirko , Armeni Monica , Noble Rachel , Danovaro Roberto 
Published: November 2005

ABSTRACT

Although the relationships between trophic conditions and viral dynamics have been widely explored in different pelagic environments, there have been few attempts at independent estimates of both viral production and decay. In this study, we investigated factors controlling the balance between viral production and decay along a trophic gradient in the north Adriatic basin, providing independent estimates of these variables and determining the relative importance of nanoflagellate grazing and viral life strategies. Increasing trophic conditions induced an increase of bacterioplankton growth rates and of the burst sizes. As a result, eutrophic waters displayed highest rates of viral production, which considerably exceeded observed rates of viral decay (up to 2.9 × 10
9
VLP liter
−1
h
−1
). Viral decay was also higher in eutrophic waters, where it accounted for ca. 40% of viral production, and dropped significantly to 1.3 to 10.7% in oligotrophic waters. These results suggest that viral production and decay rates may not necessarily be balanced in the short term, resulting in a net increase of viruses in the system. In eutrophic waters nanoflagellate grazing, dissolved-colloidal substances, and lysogenic infection were responsible together for the removal of ca. 66% of viral production versus 17% in oligotrophic waters. Our results suggest that different causative agents are primarily responsible for the removal of viruses from the water column in different trophic conditions. Factors other than those considered in the past might shed light on processes responsible for the removal and/or decay of viral particles from the water column.
Ability of Shiga Toxin-Producing
Escherichia coli
and
Salmonella
spp. To Survive in a Desiccation Model System and in Dry Foods
Authors: Hiramatsu Reiji , Matsumoto Masakado , Sakae Kenji , Miyazaki Yutaka 
Published: November 2005

ABSTRACT

In order to determine desiccation tolerances of bacterial strains, the survival of 58 diarrheagenic strains (18 salmonellae, 35 Shiga toxin-producing
Escherichia coli
[STEC], and 5 shigellae) and of 15 nonpathogenic
E. coli
strains was determined after drying at 35°C for 24 h in paper disks. At an inoculum level of 10
7
CFU/disk, most of the salmonellae (14/18) and the STEC strains (31/35) survived with a population of 10
3
to 10
4
CFU/disk, whereas all of the shigellae (5/5) and the majority of the nonpathogenic
E. coli
strains (9/15) did not survive (the population was decreased to less than the detection limit of 10
2
CFU/disk). After 22 to 24 months of subsequent storage at 4°C, all of the selected salmonellae (4/4) and most of the selected STEC strains (12/15) survived, keeping the original populations (10
3
to 10
4
CFU/disk). In contrast to the case for storage at 4°C, all of 15 selected strains (5 strains each of
Salmonella
spp., STEC O157, and STEC O26) died after 35 to 70 days of storage at 25°C and 35°C. The survival rates of all of these 15 strains in paper disks after the 24 h of drying were substantially increased (10 to 79 times) by the presence of sucrose (12% to 36%). All of these 15 desiccated strains in paper disks survived after exposure to 70°C for 5 h. The populations of these 15 strains inoculated in dried foods containing sucrose and/or fat (e.g., chocolate) were 100 times higher than those in the dried paper disks after drying for 24 h at 25°C.
Intervening Sequence Acquired by Lateral Gene Transfer in
Tropheryma whipplei
Results in 23S rRNA Fragmentation
Authors: Crapoulet Nicolas , Robineau Sylvianne , Raoult Didier , Renesto Patricia 
Published: November 2005

ABSTRACT

Completion of
Tropheryma whipplei
genome sequencing may provide insights into the evolution of the molecular mechanisms underlying the pathogenicity of this microorganism. The first postgenomic application was the successful design of a comprehensive culture medium that allows axenic growth of this bacterium, which is particularly recalcitrant to cultivation. This achievement in turn permitted analysis of
T. whipplei
RNA without contaminating eukaryotic nucleic acids. To obtain high-quality RNA, several extraction methods were compared, but under all conditions tested an atypical profile was observed. By using a Northern blot assay we demonstrated that an insertion sequence previously described in
T. whipplei
23S rRNA is in fact an intervening sequence excised during maturation. This cleavage could involve an RNase III identified in the genome of this microorganism. Among the bacteria with a 23S rRNA insertion sequence,
T. whipplei
is the only gram-positive microorganism. We present phylogenetic evidence that this mobile genetic element was acquired by lateral gene transfer from another enteric bacterium.
Enhanced Hydrogen Production from Formic Acid by Formate Hydrogen Lyase-Overexpressing
Escherichia coli
Strains
Authors: Yoshida Akihito , Nishimura Taku , Kawaguchi Hideo , Inui Masayuki , Yukawa Hideaki 
Published: November 2005

ABSTRACT

Genetic recombination of
Escherichia coli
in conjunction with process manipulation was employed to elevate the efficiency of hydrogen production in the resultant strain SR13 2 orders of magnitude above that of conventional methods. The formate hydrogen lyase (FHL)-overexpressing strain SR13 was constructed by combining FHL repressor (
hycA
) inactivation with FHL activator (
fhlA
) overexpression. Transcription of large-subunit formate dehydrogenase,
fdhF
, and large-subunit hydrogenase,
hycE
, in strain SR13 increased 6.5- and 7.0-fold, respectively, compared to the wild-type strain. On its own, this genetic modification effectively resulted in a 2.8-fold increase in hydrogen productivity of SR13 compared to the wild-type strain. Further enhancement of productivity was attained by using a novel method involving the induction of the FHL complex with high-cell-density filling of a reactor under anaerobic conditions. Continuous hydrogen production was achieved by maintaining the reactor concentration of the substrate (free formic acid) under 25 mM. An initial productivity of 23.6 g hydrogen h
−1
liter
−1
(300 liters h
−1
liter
−1
at 37°C) was achieved using strain SR13 at a cell density of 93 g (dry weight) cells/liter. The hydrogen productivity reported in this work has great potential for practical application.
Expression of Rumen Microbial Fibrolytic Enzyme Genes in Probiotic
Lactobacillus reuteri
Authors: Liu Je-Ruei , Yu Bi , Liu Fu-Hwa , Cheng Kuo-Joan , Zhao Xin 
Published: November 2005

ABSTRACT

This study was aimed at evaluating the cloning and expression of three rumen microbial fibrolytic enzyme genes in a strain of
Lactobacillus reuteri
and investigating the probiotic characteristics of these genetically modified lactobacilli. The
Neocallimastix patriciarum
xylanase gene
xynCDBFV
, the
Fibrobacter succinogenes
β-glucanase (1,3-1,4-β-
d
-glucan 4-glucanohydrolase [EC 3.2.1.73]) gene, and the
Piromyces rhizinflata
cellulase gene
eglA
were cloned in a strain of
L. reuteri
isolated from the gastrointestinal tract of broilers. The enzymes were expressed and secreted under the control of the
Lactococcus lactis lacA
promoter and its secretion signal. The
L. reuteri
transformed strains not only acquired the capacity to break down soluble carboxymethyl cellulose, β-glucan, or xylan but also showed high adhesion efficiency to mucin and mucus and resistance to bile salt and acid.
Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques
Authors: Nunan Naoise , Daniell Timothy J. , Singh Brajesh K. , Papert Artemis , McNicol James W. , Prosser James I. 
Published: November 2005

ABSTRACTMolecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.
Polyphenol Oxidase Activity Expression in
Ralstonia solanacearum
Authors: Hernández-Romero Diana , Solano Francisco , Sanchez-Amat Antonio 
Published: November 2005

ABSTRACT

Sequencing of the genome of
Ralstonia solanacearum
revealed several genes that putatively code for polyphenol oxidases (PPOs). To study the actual expression of these genes, we looked for and detected all kinds of PPO activities, including laccase, cresolase, and catechol oxidase activities, in cellular extracts of this microorganism. The conditions for the PPO assays were optimized for the phenolic substrate, pH, and sodium dodecyl sulfate concentration used. It was demonstrated that three different PPOs are expressed. The genes coding for the enzymes were unambiguously correlated with the enzymatic activities detected by generation of null mutations in the genes by using insertional mutagenesis with a suicide plasmid and estimating the changes in the levels of enzymatic activities compared to the levels in the wild-type strain. The protein encoded by the RSp1530 locus is a multicopper protein with laccase activity. Two other genes, RSc0337 and RSc1501, code for nonblue copper proteins exhibiting homology to tyrosinases. The product of RSc0337 has strong tyrosine hydroxylase activity, and it has been shown that this enzyme is involved in melanin synthesis by
R. solanacearum
. The product of the RSc1501 gene is an enzyme that shows a clear preference for oxidation of
o
-diphenols. Preliminary characterization of the mutants obtained indicated that PPOs expressed by
R. solanacearum
may participate in resistance to phenolic compounds since the mutants exhibited higher sensitivity to
l
-tyrosine than the wild-type strain. These results suggest a possible role in the pathogenic process to avoid plant resistance mechanisms involving the participation of phenolic compounds.
Escherichia coli
O157:H7 in Environments of Culture-Positive Cattle
Authors: Davis Margaret A. , Cloud-Hansen Karen A. , Carpenter John , Hovde Carolyn J. 
Published: November 2005

ABSTRACT

Outbreaks of
Escherichia coli
O157:H7 disease associated with animal exhibits have been reported with increasing frequency. Transmission can occur through contact with contaminated haircoats, bedding, farm structures, or water. We investigated the distribution and survival of
E. coli
O157:H7 in the immediate environments of individually housed, experimentally inoculated cattle by systematically culturing feed, bedding, water, haircoat, and feed bunk walls for
E. coli
O157:H7 for 3 months. Cedar chip bedding was the most frequently culture-positive environmental sample tested (27/96 or 28.15%). Among these, 12 (44.0%) of positive bedding samples were collected when the penned animal was fecal culture negative. Survival of
E. coli
O157:H7 in experimentally inoculated cedar chip bedding and in grass hay feed was determined at different temperatures. Survival was longest in feed at room temperature (60 days), but bacterial counts decreased over time. The possibility that urine plays a role in the environmental survival of
E. coli
O157:H7 was investigated. Cedar chip bedding moistened with sterile water or bovine urine was inoculated with
E. coli
O157:H7. Bedding moistened with urine supported growth of
E. coli
O157:H7, whereas inoculated bedding moistened with only water yielded decreasing numbers of bacteria over time. The findings that environmental samples were frequently positive for
E. coli
O157:H7 at times when animals were culture negative and that urine provided a substrate for
E. coli
O157:H7 growth have implications for understanding the on-farm ecology of this pathogen and for the safety of ruminant animal exhibits, particularly petting zoos and farms where children may enter animal pens.
Monitoring Stress-Related Genes during the Process of Biomass Propagation of
Saccharomyces cerevisiae
Strains Used for Wine Making
Authors: Pérez-Torrado Roberto , Bruno-Bárcena Jose M. , Matallana Emilia 
Published: November 2005

ABSTRACT

Physiological capabilities and fermentation performance of
Saccharomyces cerevisiae
strains to be employed during industrial wine fermentations are critical for the quality of the final product. During the process of biomass propagation, yeast cells are dynamically exposed to a mixed and interrelated group of known stresses such as osmotic, oxidative, thermic, and/or starvation. These stressing conditions can dramatically affect the parameters of the fermentation process and the technological abilities of the yeast, e.g., the biomass yield and its fermentative capacity. Although a good knowledge exists of the behavior of
S. cerevisiae
under laboratory conditions, insufficient knowledge is available about yeast stress responses under the specific media and growth conditions during industrial processes. We performed growth experiments using bench-top fermentors and employed a molecular marker approach (changes in expression levels of five stress-related genes) to investigate how the cells respond to environmental changes during the process of yeast biomass production. The data show that in addition to the general stress response pathway, using the
HSP12
gene as a marker, other specific stress response pathways were induced, as indicated by the changes detected in the mRNA levels of two stress-related genes,
GPD1
and
TRX2
. These results suggest that the cells were affected by osmotic and oxidative stresses, demonstrating that these are the major causes of the stress response throughout the process of wine yeast biomass production.