bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Silico Reconstruction of the Metabolic Pathways of
Lactobacillus plantarum
: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments
Authors: Teusink Bas , van Enckevort Frank H. J. , Francke Christof , Wiersma Anne , Wegkamp Arno , Smid Eddy J. , Siezen Roland J. 
Published: November 2005

ABSTRACT

On the basis of the annotated genome we reconstructed the metabolic pathways of the lactic acid bacterium
Lactobacillus plantarum
WCFS1. After automatic reconstruction by the Pathologic tool of Pathway Tools (
http://bioinformatics.ai.sri.com/ptools/
), the resulting pathway-genome database, LacplantCyc, was manually curated extensively. The current database contains refinements to existing routes and new gram-positive bacterium-specific reactions that were not present in the MetaCyc database. These reactions include, for example, reactions related to cell wall biosynthesis, molybdopterin biosynthesis, and transport. At present, LacplantCyc includes 129 pathways and 704 predicted reactions involving some 670 chemical species and 710 enzymes. We tested vitamin and amino acid requirements of
L. plantarum
experimentally and compared the results with the pathways present in LacplantCyc. In the majority of cases (32 of 37 cases) the experimental results agreed with the final reconstruction. LacplantCyc is the most extensively curated pathway-genome database for gram-positive bacteria and is open to the microbiology community via the World Wide Web (
www.lacplantcyc.nl
). It can be used as a reference pathway-genome database for gram-positive microbes in general and lactic acid bacteria in particular.
Ecology, Inhibitory Activity, and Morphogenesis of a Marine Antagonistic Bacterium Belonging to the
Roseobacter
Clade
Authors: Bruhn Jesper Bartholin , Nielsen Kristian Fog , Hjelm Mette , Hansen Michael , Bresciani José , Schulz Stefan , Gram Lone 
Published: November 2005

ABSTRACT

Roseobacter
strain 27-4 has been isolated from a turbot larval rearing unit and is capable of reducing mortality in turbot egg yolk sac larvae. Here, we demonstrate that the supernatant of
Roseobacter
27-4 is lethal to the larval pathogens
Vibrio anguillarum
and
Vibrio splendidus
in a buffer system and inhibited their growth in marine broth. Liquid chromatography (LC) with both UV spectral detection and high-resolution mass spectrometry (HR-MS) identified the known antibacterial compound thiotropocin or its closely related precursor tropodithietic acid in the bioactive fractions. Antibacterial activity correlated with the appearance of a brownish pigment and was only formed in marine broth under static growth conditions. A thick biofilm of multicellular star-shaped aggregated cells formed at the air-liquid interface under static growth conditions. Here, the bioactive compound was the base peak in the LC-UV chromatograms of the extracts where it constituted 15% of the total peak area. Aerated conditions results in 10-fold-higher cell yield, however, cultures were nonpigmented, did not produce antibacterial activity, and grew as single cells. Production of antibacterial compounds may be quorum regulated, and we identified the acylated homoserine lactone (3-hydroxy-decanoyl homoserine lactone) from cultures of
Roseobacter
27-4 using LC-HR-MS. The signal molecule was primarily detected in stagnant cultures.
Roseobacter
27-4 grew between 10 and 30°C but died rapidly at 37°C. Also, the antibacterial compounds was sensitive to heat and was inactivated at 37°C in less than 2 days and at 25°C in 8 days. Using
Roseobacter
27-4 as a probiotic culture will require that is be established in stagnant or adhered conditions and, due to the temperature sensitivity of the active compound, constant production must be ensured.
Ascending Migration of Endophytic Rhizobia, from Roots to Leaves, inside Rice Plants and Assessment of Benefits to Rice Growth Physiology
Authors: Chi Feng , Shen Shi-Hua , Cheng Hai-Ping , Jing Yu-Xiang , Yanni Youssef G. , Dazzo Frank B. 
Published: November 2005

ABSTRACT

Rhizobia, the root-nodule endosymbionts of leguminous plants, also form natural endophytic associations with roots of important cereal plants. Despite its widespread occurrence, much remains unknown about colonization of cereals by rhizobia. We examined the infection, dissemination, and colonization of healthy rice plant tissues by four species of
gfp-
tagged rhizobia and their influence on the growth physiology of rice. The results indicated a dynamic infection process beginning with surface colonization of the rhizoplane (especially at lateral root emergence), followed by endophytic colonization within roots, and then ascending endophytic migration into the stem base, leaf sheath, and leaves where they developed high populations. In situ CMEIAS image analysis indicated local endophytic population densities reaching as high as 9 × 10
10
rhizobia per cm
3
of infected host tissues, whereas plating experiments indicated rapid, transient or persistent growth depending on the rhizobial strain and rice tissue examined. Rice plants inoculated with certain test strains of
gfp
-tagged rhizobia produced significantly higher root and shoot biomass; increased their photosynthetic rate, stomatal conductance, transpiration velocity, water utilization efficiency, and flag leaf area (considered to possess the highest photosynthetic activity); and accumulated higher levels of indoleacetic acid and gibberellin growth-regulating phytohormones. Considered collectively, the results indicate that this endophytic plant-bacterium association is far more inclusive, invasive, and dynamic than previously thought, including dissemination in both below-ground and above-ground tissues and enhancement of growth physiology by several rhizobial species, therefore heightening its interest and potential value as a biofertilizer strategy for sustainable agriculture to produce the world's most important cereal crops.
Copper-Adapted
Suillus luteus
, a Symbiotic Solution for Pines Colonizing Cu Mine Spoils
Authors: Adriaensen K. , Vrålstad T. , Noben J.-P. , Vangronsveld J. , Colpaert J. V. 
Published: November 2005

ABSTRACT

Natural populations thriving in heavy-metal-contaminated ecosystems are often subjected to selective pressures for increased resistance to toxic metals. In the present study we describe a population of the ectomycorrhizal fungus
Suillus luteus
that colonized a toxic Cu mine spoil in Norway. We hypothesized that this population had developed adaptive Cu tolerance and was able to protect pine trees against Cu toxicity. We also tested for the existence of cotolerance to Cu and Zn in
S. luteus
. Isolates from Cu-polluted, Zn-polluted, and nonpolluted sites were grown in vitro on Cu- or Zn-supplemented medium. The Cu mine isolates exhibited high Cu tolerance, whereas the Zn-tolerant isolates were shown to be Cu sensitive, and vice versa. This indicates the evolution of metal-specific tolerance mechanisms is strongly triggered by the pollution in the local environment. Cotolerance does not occur in the
S. luteus
isolates studied. In a dose-response experiment, the Cu sensitivity of nonmycorrhizal
Pinus sylvestris
seedlings was compared to the sensitivity of mycorrhizal seedlings colonized either by a Cu-sensitive or Cu-tolerant
S. luteus
isolate. In nonmycorrhizal plants and plants colonized by the Cu-sensitive isolate, root growth and nutrient uptake were strongly inhibited under Cu stress conditions. In contrast, plants colonized by the Cu-tolerant isolate were hardly affected. The Cu-adapted
S. luteus
isolate provided excellent insurance against Cu toxicity in pine seedlings exposed to elevated Cu levels. Such a metal-adapted
Suillus
-
Pinus
combination might be suitable for large-scale land reclamation at phytotoxic metalliferous and industrial sites.
Detection of Carp Interstitial Nephritis and Gill Necrosis Virus in Fish Droppings
Authors: Dishon Arnon , Perelberg Ayana , Bishara-Shieban Janette , Ilouze Maya , Davidovich Maya , Werker Shlomit , Kotler Moshe 
Published: November 2005

ABSTRACT

Carp interstitial nephritis and gill necrosis virus (CNGV) is an unclassified large DNA virus that morphologically resembles members of the
Herpesviridae
but contains a large (ca. ∼280-kbp) linear double-stranded DNA. This virus has also been named koi herpesvirus, koi herpes-like virus, and cyprinid herpesvirus 3. CNGV is the cause of a lethal disease that afflicts common carp and koi. By using immunohistochemistry, molecular analysis, and electron microscopy we previously demonstrated that this virus is present mainly in the intestine and kidney of infected fish. Based on these observations, we postulated that viruses and/or viral components may appear in droppings of infected carp. Here we report that (i) by using PCR we demonstrated that fish droppings contain viral DNA, (ii) fish droppings contain viral antigens which are useful for CNGV diagnosis, and (iii) fish droppings contain active virus which can infect cultured common carp brain cells and induce the disease in naïve fish following inoculation. Thus, our findings show that CNGV can be identified by using droppings without taking biopsies or killing fish and that infectious CNGV is present in the stools of sick fish. The possibility that fish droppings preserve viable CNGV during the nonpermissive seasons is discussed.
Crucial Role of Extracellular Polysaccharides in Desiccation and Freezing Tolerance in the Terrestrial Cyanobacterium
Nostoc commune
Authors: Tamaru Yoshiyuki , Takani Yayoi , Yoshida Takayuki , Sakamoto Toshio 
Published: November 2005

ABSTRACT

The cyanobacterium
Nostoc commune
is adapted to the terrestrial environment and has a cosmopolitan distribution. In this study, the role of extracellular polysaccharides (EPS) in the desiccation tolerance of photosynthesis in
N. commune
was examined. Although photosynthetic O
2
evolution was not detected in desiccated colonies, the ability of the cells to evolve O
2
rapidly recovered after rehydration. The air-dried colonies contained approximately 10% (wt/wt) water, and field-isolated, natural colonies with EPS were highly water absorbent and were rapidly hydrated by atmospheric moisture. The cells embedded in EPS in
Nostoc
colonies were highly desiccation tolerant, and O
2
evolution was not damaged by air drying. Although
N. commune
was determined to be a mesophilic cyanobacterium, the cells with EPS were heat tolerant in a desiccated state. EPS could be removed from cells by homogenizing colonies with a blender and filtering with coarse filter paper. This treatment to remove EPS did not damage
Nostoc
cells or their ability to evolve O
2
, but O
2
evolution was significantly damaged by desiccation treatment of the EPS-depleted cells. Similar to the EPS-depleted cells, the laboratory culture strain KU002 had only small amount of EPS and was highly sensitive to desiccation. In the EPS-depleted cells, O
2
evolution was also sensitive to freeze-thaw treatment. These results strongly suggest that EPS of
N. commune
is crucial for the stress tolerance of photosynthesis during desiccation and during freezing and thawing.
Antagonists of Hsp16.3, a Low-Molecular-Weight Mycobacterial Chaperone and Virulence Factor, Derived from Phage-Displayed Peptide Libraries
Authors: Saha Abhik , Sharma Archna , Dhar Amlanjyoti , Bhattacharyya Bhabatarak , Roy Siddhartha , Das Gupta Sujoy K. 
Published: November 2005

ABSTRACTThe persistence ofMycobacterium tuberculosisis a major cause of concern in tuberculosis (TB) therapy. In the persistent mode the pathogen can resist drug therapy, allowing the possibility of reactivation of the disease. Several protein factors have been identified that contribute to persistence, one of them being the 16-kDa low-molecular-weight mycobacterial heat shock protein Hsp16.3, a homologue of the mammalian eye lens protein alpha-crystallin. It is believed that Hsp16.3 plays a key role in the persistence phase by protecting essential proteins from being irreversibly denatured. Because of the close association of Hsp16.3 with persistence, an attempt has been made to develop inhibitors against it. Random peptide libraries displayed on bacteriophage M13 were screened for Hsp16.3 binding. Two phage clones were identified that bind to the Hsp16.3 protein. The corresponding synthetic peptides, an 11-mer and a 16-mer, were able to bind Hsp16.3 and inhibit its chaperone activity in vitro in a dose-dependent manner. Little or no effect of these peptides was observed on alphaB-crystallin, a homologous protein that is a key component of human eye lens, indicating that there is an element of specificity in the observed inhibition. Two histidine residues appear to be common to the selected peptides. Nuclear magnetic resonance studies performed with the 11-mer peptide indicate that in this case these two histidines may be the crucial binding determinants. The peptide inhibitors of Hsp16.3 thus obtained could serve as the basis for developing potent drugs against persistent TB.
Capsular Polysaccharide Surrounds Smooth and Rugose Types ofSalmonella entericaserovar Typhimurium DT104
Authors: de Rezende C. Eriksson , Anriany Y. , Carr L. E. , Joseph S. W. , Weiner R. M. 
Published: November 2005

ABSTRACTThe biofilms and rugose colony morphology ofSalmonella entericaserovar Typhimurium strains are usually associated with at least two different exopolymeric substances (EPS), curli and cellulose. In this study, another EPS, a capsular polysaccharide (CP) synthesized constitutively inS. entericaserovar Typhimurium strain DT104 at 25 and 37°C, has been recognized as a biofilm matrix component as well. Fluorophore-assisted carbohydrate electrophoresis (FACE) analysis indicated that the CP is comprised principally of glucose and mannose, with galactose as a minor constituent. The composition differs from that of known colanic acid-containing CP that is isolated from cells ofEscherichia coliand other enteric bacteria grown at 37°C. The reactivity of carbohydrate-specific lectins conjugated to fluorescein isothiocyanate or gold particles with cellular carbohydrates demonstrated the cell surface localization of CP. Further, lectin binding also correlated with the FACE analysis of CP. Immunoelectron microscopy, using specific antibodies against CP, confirmed that CP surrounds the cells. Confocal microscopy of antibody-labeled cells showed greater biofilm formation at 25°C than at 37°C. Since the CP was shown to be produced at both 37°C and 25°C, it does not appear to be significantly involved in attachment during the early formation of the biofilm matrix. Although the attachment ofS. entericaserovar Typhimurium DT104 does not appear to be mediated by its CP, the capsule does contribute to the biofilm matrix and may have a role in other features of this organism, such as virulence, as has been shown previously for the capsules of other gram-negative and gram-positive bacteria.
Community Composition of a Hypersaline Endoevaporitic Microbial Mat
Authors: Sørensen Ketil Bernt , Canfield Donald E. , Teske Andreas P. , Oren Aharon 
Published: November 2005

ABSTRACT

A hypersaline, endoevaporitic microbial community in Eilat, Israel, was studied by microscopy and by PCR amplification of genes for 16S rRNA from different layers. In terms of biomass, the oxygenic layers of the community were dominated by
Cyanobacteria
of the
Halothece
,
Spirulina
, and
Phormidium
types, but cell counts (based on 4′,6′-diamidino-2-phenylindole staining) and molecular surveys (clone libraries of PCR-amplified genes for 16S rRNA) showed that oxygenic phototrophs were outnumbered by the other constituents of the community, including chemotrophs and anoxygenic phototrophs. Bacterial clone libraries were dominated by phylotypes affiliated with the
Bacteroidetes
group and both photo- and chemotrophic groups of α-proteobacteria. Green filaments related to the
Chloroflexi
were less abundant than reported from hypersaline microbial mats growing at lower salinities and were only detected in the deepest part of the anoxygenic phototrophic zone. Also detected were nonphototrophic γ- and δ-proteobacteria,
Planctomycetes
, the TM6 group,
Firmicutes
, and
Spirochetes
. Several of the phylotypes showed a distinct vertical distribution in the crust, suggesting specific adaptations to the presence or absence of oxygen and light.
Archaea
were less abundant than
Bacteria
, their diversity was lower, and the community was less stratified. Detected archaeal groups included organisms affiliated with the
Methanosarcinales
, the
Halobacteriales
, and uncultured groups of
Euryarchaeota
.
Detection of AirborneStachybotrys chartarumMacrocyclic Trichothecene Mycotoxins in the Indoor Environment
Authors: Brasel T. L. , Martin J. M. , Carriker C. G. , Wilson S. C. , Straus D. C. 
Published: November 2005

ABSTRACTThe existence of airborne mycotoxins in mold-contaminated buildings has long been hypothesized to be a potential occupant health risk. However, little work has been done to demonstrate the presence of these compounds in such environments. The presence of airborne macrocyclic trichothecene mycotoxins in indoor environments with knownStachybotrys chartarumcontamination was therefore investigated. In seven buildings, air was collected using a high-volume liquid impaction bioaerosol sampler (SpinCon PAS 450-10) under static or disturbed conditions. An additional building was sampled using an Andersen GPS-1 PUF sampler modified to separate and collect particulates smaller than conidia. Four control buildings (i.e., no detectableS. chartarumgrowth or history of water damage) and outdoor air were also tested. Samples were analyzed using a macrocyclic trichothecene-specific enzyme-linked immunosorbent assay (ELISA). ELISA specificity was tested using phosphate-buffered saline extracts of the fungal generaAspergillus,Chaetomium,Cladosporium,Fusarium,Memnoniella,Penicillium,Rhizopus, andTrichoderma, fiveStachybotrysstrains, and the indoor air allergens Can f 1, Der p 1, and Fel d 1. For test buildings, the results showed that detectable toxin concentrations increased with the sampling time and short periods of air disturbance. Trichothecene values ranged from <10 to >1,300 pg/m3of sampled air. The control environments demonstrated statistically significantly (P< 0.001) lower levels of airborne trichothecenes. ELISA specificity experiments demonstrated a high specificity for the trichothecene-producing strain ofS. chartarum. Our data indicate that airborne macrocyclic trichothecenes can exist inStachybotrys-contaminated buildings, and this should be taken into consideration in future indoor air quality investigations.
Distribution and Diversity of Natural Product Genes in Marine and Freshwater Cyanobacterial Cultures and Genomes
Authors: Ehrenreich Ian M. , Waterbury John B. , Webb Eric A. 
Published: November 2005

ABSTRACT
Natural products are a functionally diverse class of biochemically synthesized compounds, which include antibiotics, toxins, and siderophores. In this paper, we describe both the detection of natural product activities and the sequence identification of gene fragments from two molecular systems that have previously been implicated in natural product production, i.e., nonribosomal peptide synthetases (NRPSs) and modular polyketide synthases (PKSs), in diverse marine and freshwater cyanobacterial cultures. Using degenerate PCR and the sequencing of cloned products, we show that NRPSs and PKSs are common among the cyanobacteria tested. Our molecular data, when combined with genomic searches of finished and progressing cyanobacterial genomes, demonstrate that not all cyanobacteria contain NRPS and PKS genes and that the filamentous and heterocystous cyanobacteria are the richest sources of these genes and the most likely sources of novel natural products within the phylum. In addition to validating the use of degenerate primers for the identification of PKS and NRPS genes in cyanobacteria, this study also defines numerous gene fragments that will be useful as probes for future studies of the synthesis of natural products in cyanobacteria. Phylogenetic analyses of the cyanobacterial NRPS and PKS fragments sequenced in this study, as well as those from the cyanobacterial genome projects, demonstrate that there is remarkable diversity and likely novelty of these genes within the cyanobacteria. These results underscore the potential variety of novel products being produced by these ubiquitous organisms.
Identification and Molecular Characterization of the Chromosomal Exopolysaccharide Biosynthesis Gene Cluster from
Lactococcus lactis
subsp.
cremoris
SMQ-461
Authors: Dabour N. , LaPointe G. 
Published: November 2005

ABSTRACT

The exopolysaccharide (EPS) capsule-forming strain SMQ-461 of
Lactococcus lactis
subsp.
cremoris
, isolated from raw milk, produces EPS with an apparent molecular mass of >1.6 × 10
6
Da. The EPS biosynthetic genes are located on the chromosome in a 13.2-kb region consisting of 15 open reading frames. This region is flanked by three IS
1077
-related
tnp
genes (
L. lactis
) at the 5′ end and
orfY
, along with an IS
981
-related
tnp
gene, at the 3′ end. The
eps
genes are organized in specific regions involved in regulation, chain length determination, biosynthesis of the repeat unit, polymerization, and export. Three (
epsGIK
) of the six predicted glycosyltransferase gene products showed low amino acid similarity with known glycosyltransferases. The structure of the repeat unit could thus be different from those known to date for
Lactococcus
. Reverse transcription-PCR analysis revealed that the
eps
locus is transcribed as a single mRNA. The function of the
eps
gene cluster was confirmed by disrupting the priming glycosyltransferase gene (
epsD
) in
Lactococcus cremoris
SMQ-461, generating non-EPS-producing reversible mutants. This is the first report of a chromosomal location for EPS genetic elements in
Lactococcus cremoris
, with novel glycosyltransferases not encountered before in lactic acid bacteria.
Real-Time PCR Quantification of Human Adenoviruses in Urban Rivers Indicates Genome Prevalence but Low Infectivity
Authors: Choi Samuel , Jiang Sunny C. 
Published: November 2005

ABSTRACT

Real-time PCR was applied to quantify the abundance of human adenoviruses in two southern California urban rivers, the San Gabriel and Los Angeles. A total of 114 river samples from five different locations were collected over a 1-year period and analyzed for human adenoviruses, along with fecal indicator bacteria and coliphages. Adenoviruses were detected by real-time PCR in ∼16% of the samples, with concentrations ranging from 10
2
to 10
4
genomes per liter. However, a plaque assay using two human tissue culture cell lines, HEK-293A and A549, yielded negative results, suggesting that adenoviruses detected by real-time PCR are likely noninfectious. Enterovirus genome was detected in ∼7% of the samples by reverse transcription-PCR. Analysis by Spearman's rho rank order correlation showed significant correlations between fecal indicator bacteria and indicator virus (total coliform, fecal coliform, enterococcus, and coliphage values). However, no significant correlations were found between human adenoviruses quantified by real-time PCR and culturable coliphages or fecal indicator bacteria. Kruskal-Wallis chi-square analysis showed significant seasonal variability of all fecal indicator bacteria and coliphages, while no significant variability was observed for adenoviruses or enteroviruses. This study presents the first quantitative measurement of human adenovirus genomes in urban rivers and their statistical relationship to fecal indicator bacteria and coliphages. The uncoupling between high-number genome copies of adenoviruses detected by real-time PCR and the absence of infectivity detected by tissue culture suggests that genome-based detection methods are inadequate for direct assessment of human health risk.