bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Dietary Zinc Oxide and Copper Sulfate on the Gastrointestinal Ecosystem in Newly Weaned Piglets
Authors: Højberg Ole , Canibe Nuria , Poulsen Hanne Damgaard , Hedemann Mette Skou , Jensen Bent Borg 
Published: May 2005

ABSTRACT

Dietary doses of 2,500 ppm ZnO-Zn reduced bacterial activity (ATP accumulation) in digesta from the gastrointestinal tracts of newly weaned piglets compared to that in animals receiving 100 ppm ZnO-Zn. The amounts of lactic acid bacteria (MRS counts) and lactobacilli (Rogosa counts) were reduced, whereas coliforms (MacConkey counts) and enterococci (Slanetz counts, red colonies) were more numerous in animals receiving the high ZnO dose. Based on 16S rRNA gene sequencing, the colonies on MRS were dominated by three phylotypes, tentatively identified as
Lactobacillus amylovorus
(OTU171),
Lactobacillus reuteri
(OTU173), and
Streptococcus alactolyticus
(OTU180). The colonies on Rogosa plates were dominated by the two
Lactobacillus
phylotypes only. Terminal restriction fragment length polymorphism analysis supported the observations of three phylotypes of lactic acid bacteria dominating in piglets receiving the low ZnO dose and of coliforms and enterococci dominating in piglets receiving the high ZnO dose. Dietary doses of 175 ppm CuSO
4
-Cu also reduced MRS and Rogosa counts of stomach contents, but for these animals, the numbers of coliforms were reduced in the cecum and the colon. The influence of ZnO on the gastrointestinal microbiota resembles the working mechanism suggested for some growth-promoting antibiotics, namely, the suppression of gram-positive commensals rather than potentially pathogenic gram-negative organisms. Reduced fermentation of digestible nutrients in the proximal part of the gastrointestinal tract may render more energy available for the host animal and contribute to the growth-promoting effect of high dietary ZnO doses. Dietary CuSO
4
inhibited the coliforms and thus potential pathogens as well, but overall the observed effect of CuSO
4
was limited compared to that of ZnO.
Quantitative Real-Time PCR Assays To Identify and Quantify Fecal
Bifidobacterium
Species in Infants Receiving a Prebiotic Infant Formula
Authors: Haarman Monique , Knol Jan 
Published: May 2005

ABSTRACT

A healthy intestinal microbiota is considered to be important for priming of the infants' mucosal and systemic immunity. Breast-fed infants typically have an intestinal microbiota dominated by different
Bifidobacterium
species. It has been described that allergic infants have different levels of specific
Bifidobacterium
species than healthy infants. For the accurate quantification of
Bifidobacterium adolescentis
,
Bifidobacterium angulatum
,
Bifidobacterium bifidum
,
Bifidobacterium breve
,
Bifidobacterium catenulatum
,
Bifidobacterium dentium
,
Bifidobacterium infantis
, and
Bifidobacterium longum
in fecal samples, duplex 5′ nuclease assays were developed. The assays, targeting rRNA gene intergenic spacer regions, were validated and compared with conventional PCR and fluorescent in situ hybridization methods. The 5′ nuclease assays were subsequently used to determine the relative amounts of different
Bifidobacterium
species in fecal samples from infants receiving a standard formula or a standard formula supplemented with galacto- and fructo-oligosaccharides (OSF). A breast-fed group was studied in parallel as a reference. The results showed a significant increase in the total amount of fecal bifidobacteria (54.8% ± 9.8% to 73.4% ± 4.0%) in infants receiving the prebiotic formula (OSF), with a diversity of
Bifidobacterium
species similar to breast-fed infants. The intestinal microbiota of infants who received a standard formula seems to resemble a more adult-like distribution of bifidobacteria and contains relatively more
B. catenulatum
and
B. adolescentis
(2.71% ± 1.92% and 8.11% ± 4.12%, respectively, versus 0.15% ± 0.11% and 1.38% ± 0.98% for the OSF group). In conclusion, the specific prebiotic infant formula used induces a fecal microbiota that closely resembles the microbiota of breast-fed infants also at the level of the different
Bifidobacterium
species.
Influence of Top-Down and Bottom-Up Manipulations on the R-BT065 Subcluster of β-Proteobacteria, an Abundant Group in Bacterioplankton of a Freshwater Reservoir
Authors: Šimek Karel , Horňák Karel , Jezbera Jan , Mašín Michal , Nedoma Jiří , Gasol Josep M. , Schauer Michael 
Published: May 2005

ABSTRACT

We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Římov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 μm), bacteria and heterotrophic nanoflagellates (<5 μm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of β-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class
Actinobacteria
, which profited from the enhanced protistan bacterivory.
Potential Role of
Diploscapter
sp. Strain LKC25, a Bacterivorous Nematode from Soil, as a Vector of Food-Borne Pathogenic Bacteria to Preharvest Fruits and Vegetables
Authors: Gibbs Daunte S. , Anderson Gary L. , Beuchat Larry R. , Carta Lynn K. , Williams Phillip L. 
Published: May 2005

ABSTRACT

Diploscapter
, a thermotolerant, free-living soil bacterial-feeding nematode commonly found in compost, sewage, and agricultural soil in the United States, was studied to determine its potential role as a vehicle of
Salmonella enterica
serotype Poona, enterohemorrhagic
Escherichia coli
O157:H7, and
Listeria monocytogenes
in contaminating preharvest fruits and vegetables. The ability of
Diploscapter
sp. strain LKC25 to survive on agar media, in cow manure, and in composted turkey manure and to be attracted to, ingest, and disperse food-borne pathogens inoculated into soil or a mixture of soil and composted turkey manure was investigated.
Diploscapter
sp. strain LKC25 survived and reproduced in lawns of
S. enterica
serotype Poona,
E. coli
O157:H7, and
L. monocytogenes
on agar media and in cow manure and composted turkey manure. Attraction of
Diploscapter
sp. strain LKC25 to colonies of pathogenic bacteria on tryptic soy agar within 10, 20, 30, and 60 min and 24 h was determined. At least 85% of the worms initially placed 0.5 to 1 cm away from bacterial colonies migrated to the colonies within 1 h. Within 24 h, ≥90% of the worms were embedded in colonies. The potential of
Diploscapter
sp. strain LKC25 to shed pathogenic bacteria after exposure to bacteria inoculated into soil or a mixture of soil and composted turkey manure was investigated. Results indicate that
Diploscapter
sp. strain LKC25 can shed pathogenic bacteria after exposure to pathogens in these milieus. They also demonstrate its potential to serve as a vector of food-borne pathogenic bacteria in soil, with or without amendment with compost, to the surface of preharvest fruits and vegetables in contact with soil.
Antimicrobial Resistance Profiles of
Campylobacter jejuni
Isolates from Wild Birds in Sweden
Authors: Waldenström Jonas , Mevius Dik , Veldman Kees , Broman Tina , Hasselquist Dennis , Olsen Björn 
Published: May 2005

ABSTRACT

In order to determine the occurrence and frequency of resistant strains of the bacterium
Campylobacter jejuni
and to establish baseline MICs in isolates from an environmental reservoir, the resistance profiles of 10 antimicrobial substances were determined for 137
C. jejuni
isolates from wild birds in Sweden. Observed MICs were generally low, with only low to moderate incidence of resistance to the tested compounds. One isolate, however, was resistant to nalidixic acid and ciprofloxacin, indicating that quinolone-resistant genotypes of
C. jejuni
have the potential to spread to wild bird hosts.
Heterologous Expression of Novobiocin and Clorobiocin Biosynthetic Gene Clusters
Authors: Eustáquio Alessandra S. , Gust Bertolt , Galm Ute , Li Shu-Ming , Chater Keith F. , Heide Lutz 
Published: May 2005

ABSTRACT

A method was developed for the heterologous expression of biosynthetic gene clusters in different
Streptomyces
strains and for the modification of these clusters by single or multiple gene replacements or gene deletions with unprecedented speed and versatility. λ-Red-mediated homologous recombination was used for genetic modification of the gene clusters, and the attachment site and integrase of phage φC31 were employed for the integration of these clusters into the heterologous hosts. This method was used to express the gene clusters of the aminocoumarin antibiotics novobiocin and clorobiocin in the well-studied strains
Streptomyces coelicolor
and
Streptomyces lividans
, which, in contrast to the natural producers, can be easily genetically manipulated.
S. coelicolor
M512 derivatives produced the respective antibiotic in yields comparable to those of natural producer strains, whereas
S. lividans
TK24 derivatives were at least five times less productive. This method could also be used to carry out functional investigations. Shortening of the cosmids' inserts showed which genes are essential for antibiotic production.
Heme-Dependent Rubber Oxygenase RoxA ofXanthomonassp. Cleaves the Carbon Backbone of Poly(cis-1,4-Isoprene) by a Dioxygenase Mechanism
Authors: Braaz Reinhard , Armbruster Wolfgang , Jendrossek Dieter 
Published: May 2005

ABSTRACTOxidative cleavage of poly(cis-1,4-isoprene) by rubber oxygenase RoxA purified fromXanthomonassp. was investigated in the presence of different combinations of16O2,18O2, H216O, and H218O. 12-Oxo-4,8-dimethyl-trideca-4,8-diene-1-al (ODTD;m/z236) was the main cleavage product in the absence of18O-compounds. Incorporation of one18O atom in ODTD was found if the cleavage reaction was performed in the presence of18O2and H216O. Incubation of poly(cis-1,4-isoprene) (with RoxA) or of isolated unlabeled ODTD (without RoxA) with H218O in the presence of16O2indicated that the carbonyl oxygen atoms of ODTD significantly exchanged with oxygen atoms derived from water. The isotope exchange was avoided by simultaneous enzymatic reduction of both carbonyl functions of ODTD to the corresponding dialcohol (12-hydroxy-4,8-dimethyl-trideca-4,8-diene-1-ol (HDTD;m/z240) during RoxA-mediated in vitro cleavage of poly(cis-1,4-isoprene). In the presence of18O2, H216O, and alcohol dehydrogenase/NADH, incorporation of two atoms of18O into the reduced metabolite HDTD was found (m/z244), revealing that RoxA cleaves rubber by a dioxygenase mechanism. Based on the labeling results and the presence of two hemes in RoxA, a model of the enzymatic cleavage mechanism of poly(cis-1,4-isoprene) is proposed.
Uptake of CdSe and CdSe/ZnS Quantum Dots into Bacteria via Purine-Dependent Mechanisms
Authors: Kloepfer J. A. , Mielke R. E. , Nadeau J. L. 
Published: May 2005

ABSTRACT

Quantum dots (QDs) rendered water soluble for biological applications are usually passivated by several inorganic and/or organic layers in order to increase fluorescence yield. However, these coatings greatly increase the size of the particle, making uptake by microorganisms impossible. We find that adenine- and AMP-conjugated QDs are able to label bacteria only if the particles are <5 nm in diameter. Labeling is dependent upon purine-processing mechanisms, as mutants lacking single enzymes demonstrate a qualitatively different signal than do wild-type strains. This is shown for two example species, one gram negative and one gram positive. Wild-type
Bacillus subtilis
incubated with QDs conjugated to adenine are strongly fluorescent; very weak signal is seen in mutant cells lacking either adenine deaminase or adenosine phosphoribosyltransferase. Conversely, QD-AMP conjugates label mutant strains more efficiently than the wild type. In
Escherichia coli
, QD conjugates are taken up most strongly by adenine auxotrophs and are extruded from the cells over a time course of hours. No fluorescent labeling is seen in killed bacteria or in the presence of EDTA or an excess of unlabeled adenine, AMP, or hypoxanthine. Spectroscopy and electron microscopy suggest that QDs of <5 nm can enter the cells whole, probably by means of oxidative damage to the cell membrane which is aided by light.
Identification of Extracellular
N
-Acylhomoserine Lactone Acylase from a
Streptomyces
sp. and Its Application to Quorum Quenching
Authors: Park Sun-Yang , Kang Hye-Ok , Jang Hak-Sun , Lee Jung-Kee , Koo Bon-Tag , Yum Do-Young 
Published: May 2005

ABSTRACT

N
-Acylhomoserine lactones (AHLs) play an important role in regulating virulence factors in pathogenic bacteria. Recently, the enzymatic inactivation of AHLs, which can be used as antibacterial targets, has been identified in several soil bacteria. In this study, strain M664, identified as a
Streptomyces
sp., was found to secrete an AHL-degrading enzyme into a culture medium. The
ahlM
gene for AHL degradation from
Streptomyces
sp. strain M664 was cloned, expressed heterologously in
Streptomyces lividans
, and purified. The enzyme was found to be a heterodimeric protein with subunits of approximately 60 kDa and 23 kDa. A comparison of AhlM with known AHL-acylases,
Ralstonia
strain XJ12B AiiD and
Pseudomonas aeruginosa
PAO1 PvdQ, revealed 35% and 32% identities in the deduced amino acid sequences, respectively. However, AhlM was most similar to the cyclic lipopeptide acylase from
Streptomyces
sp. strain FERM BP-5809, exhibiting 93% identity. A mass spectrometry analysis demonstrated that AhlM hydrolyzed the amide bond of AHL, releasing homoserine lactone. AhlM exhibited a higher deacylation activity toward AHLs with long acyl chains rather than short acyl chains. Interestingly, AhlM was also found to be capable of degrading penicillin G by deacylation, showing that AhlM has a broad substrate specificity. The addition of AhlM to the growth medium reduced the accumulation of AHLs and decreased the production of virulence factors, including elastase, total protease, and LasA, in
P. aeruginosa
. Accordingly, these results suggest that AHL-acylase, AhlM could be effectively applied to the control of AHL-mediated pathogenicity.
Persistence of
Enterococcus faecalis
in Aquatic Environments via Surface Interactions with Copepods
Authors: Signoretto Caterina , Burlacchini Gloria , Pruzzo Carla , Canepari Pietro 
Published: May 2005

ABSTRACT

Several human pathogens and fecal-pollution indicators may persist as viable organisms in natural environments, owing to their ability to activate different types of survival strategies. These strategies include adhesion on both abiotic and biotic surfaces and the entrance to the so-called viable but nonculturable (VBNC) state. In an 18-month survey for the detection of enterococci in both lake water and seawater, C. Signoretto et al. (Appl. Environ. Microbiol. 70:6892-6896, 2004) have shown that
Enterococcus faecalis
was detected mostly bound to plankton and in the VBNC state. In the present study, we show that in vitro adhesion of
E. faecalis
to copepods accelerated the entry of cells into the VBNC state relative to that of planktonic bacteria. VBNC
E. faecalis
cells maintained their adhesive properties to copepods and chitin (the main component of the copepod carapace), though to a reduced extent in comparison with growing cells. Sugar competition experiments showed interference with adhesion to both copepods and chitin by GlcNAc and only to copepods by
d
-mannose. Four enterococcal cell wall proteins present in both growing and VBNC cells and lipoteichoic acid were shown to be capable of binding chitin. The results indicate that copepods may represent an additional environmental reservoir of enterococci, thus suggesting the advisability of redesigning the protocols currently used for microbial detection during the evaluation of the microbiological quality of environmental samples.
Homologous and Heterologous Overexpression in
Clostridium acetobutylicum
and Characterization of Purified Clostridial and Algal Fe-Only Hydrogenases with High Specific Activities
Authors: Girbal Laurence , von Abendroth Gregory , Winkler Martin , Benton Paul M. C. , Meynial-Salles Isabelle , Croux Christian , Peters John W. , Happe Thomas , Soucaille Philippe 
Published: May 2005

ABSTRACT

Clostridium acetobutylicum
ATCC 824 was selected for the homologous overexpression of its Fe-only hydrogenase and for the heterologous expressions of the
Chlamydomonas reinhardtii
and
Scenedesmus obliquus
HydA1 Fe-only hydrogenases. The three
Strep
tag II-tagged Fe-only hydrogenases were isolated with high specific activities by two-step column chromatography. The purified algal hydrogenases evolve hydrogen with rates of around 700 μmol H
2
min
−1
mg
−1
, while HydA from
C. acetobutylicum
(HydA
Ca
) shows the highest activity (5,522 μmol H
2
min
−1
mg
−1
) in the direction of hydrogen uptake. Further, kinetic parameters and substrate specificity were reported. An electron paramagnetic resonance (EPR) analysis of the thionin-oxidized HydA
Ca
protein indicates a characteristic rhombic EPR signal that is typical for the oxidized H cluster of Fe-only hydrogenases.
Honokiol overcomes conventional drug resistance in human multiple myeloma by induction of caspase-dependent and -independent apoptosis
Authors: Ishitsuka Kenji , Hideshima Teru , Hamasaki Makoto , Raje Noopur , Kumar Shaji , Hideshima Hiromasa , Shiraishi Norihiko , Yasui Hiroshi , Roccaro Aldo M. , Richardson Paul , Podar Klaus , Le Gouill Steven , Chauhan Dharminder , Tamura Kazuo , Arbiser Jack , Anderson Kenneth C. 
Published: May 2005

Abstract
Honokiol (HNK) is an active component purified from magnolia, a plant used in traditional Chinese and Japanese medicine. Here we show that HNK significantly induces cytotoxicity in human multiple myeloma (MM) cell lines and tumor cells from patients with relapsed refractory MM. Neither coculture with bone marrow stromal cells nor cytokines (interleukin-6 and insulin-like growth factor-1) protect against HNK-induced cytotoxicity. Although activation of caspases 3, 7, 8, and 9 is triggered by HNK, the pan-caspase inhibitor z-VAD-fmk does not abrogate HNK-induced apoptosis. Importantly, release of an executioner of caspase-independent apoptosis, apoptosis-inducing factor (AIF), from mitochondria is induced by HNK treatment. HNK induces apoptosis in the SU-DHL4 cell line, which has low levels of caspase 3 and 8 associated with resistance to both conventional and novel drugs. These results suggest that HNK induces apoptosis via both caspase-dependent and -independent pathways. Furthermore, HNK enhances MM cell cytotoxicity and apoptosis induced by bortezomib. In addition to its direct cytotoxicity to MM cells, HNK also represses tube formation by endothelial cells, suggesting that HNK inhibits neovascurization in the bone marrow microenvironment. Taken together, our results provide the preclinical rationale for clinical protocols of HNK to improve patient outcome in MM. (Blood. 2005;106:1794-1800)
Ab initio identification of putative human transcription factor binding sites by comparative genomics
Authors: Corà D , Herrmann C , Dieterich C , Di Cunto F , Provero P , Caselle M 
Published: May 2005

Abstract
Background
Understanding transcriptional regulation of gene expression is one of the greatest challenges of modern molecular biology. A central role in this mechanism is played by transcription factors, which typically bind to specific, short DNA sequence motifs usually located in the upstream region of the regulated genes. We discuss here a simple and powerful approach for the ab initio identification of these cis-regulatory motifs. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome.

Results
By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence) in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets looking for two types of evidence of coregulation: first, we analyze the Gene Ontology annotation of the genes in the set, searching for statistically significant common annotations; second, we analyze the expression profiles of the genes in the set as measured by microarray experiments, searching for evidence of coexpression. The sets which pass one or both filters are conjectured to contain a significant fraction of coregulated genes, and the upstream motifs characterizing the sets are thus good candidates to be the binding sites of the TF's involved in such regulation.
In this way we find various known motifs and also some new candidate binding sites.

Conclusion
We have discussed a new integrated algorithm for the "ab initio" identification of transcription factor binding sites in the human genome. The method is based on three ingredients: comparative genomics, overrepresentation, different types of coregulation. The method is applied to a full-scan of the human genome, giving satisfactory results.