bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression of
Lactobacillus casei
d
-Hydroxyisocaproic Acid Dehydrogenase in Cheddar Cheese
Authors: Broadbent Jeffery R. , Gummalla Sanjay , Hughes Joanne E. , Johnson Mark E. , Rankin Scott A. , Drake Mary Anne 
Published: August 2004

ABSTRACT

Metabolism of aromatic amino acids by lactic acid bacteria is an important source of off-flavor compounds in Cheddar cheese. Previous work has shown that α-keto acids produced from Trp, Tyr, and Phe by aminotransferase enzymes are chemically labile and may degrade spontaneously into a variety of off-flavor compounds. However, dairy lactobacilli can convert unstable α-keto acids to more-stable α-hydroxy acids via the action of α-keto acid dehydrogenases such as
d
-hydroxyisocaproic acid dehydrogenase. To further characterize the role of this enzyme in cheese flavor, the
Lactobacillus casei
d
-hydroxyisocaproic acid dehydrogenase gene was cloned into the high-copy-number vector pTRKH2 and transformed into
L. casei
ATCC 334. Enzyme assays confirmed that α-keto acid dehydrogenase activity was significantly higher in pTRKH2:
dhic
transformants than in wild-type cells. Reduced-fat Cheddar cheeses were made with
Lactococcus lactis
starter only, starter plus
L. casei
ATCC 334, and starter plus
L. casei
ATCC 334 transformed with pTRKH2:
dhic
. After 3 months of aging, the cheese chemistry and flavor attributes were evaluated instrumentally by gas chromatography-mass spectrometry and by descriptive sensory analysis. The culture system used significantly affected the concentrations of various ketones, aldehydes, alcohols, and esters and one sulfur compound in cheese. Results further indicated that enhanced expression of
d
-hydroxyisocaproic acid dehydrogenase suppressed spontaneous degradation of α-keto acids, but sensory work indicated that this effect retarded cheese flavor development.
Influence of Humic Substances on Bacterial and Viral Dynamics in Freshwaters
Authors: Anesio Alexandre M. , Hollas Christin , Granéli Wilhelm , Laybourn-Parry Johanna 
Published: August 2004

ABSTRACTBacterial and viral abundances were measured in 24 lakes with dissolved organic carbon (DOC) concentrations ranging from 3 to 19 mg of C liter−1. In addition, a laboratory experiment was performed to test the effects of different sources of carbon (i.e., glucose and fulvic acids) and nutrients on the dynamics of viruses and bacteria. In the lake survey, no correlation was found between virus abundance and DOC concentration, yet there was a significant positive correlation between bacterial abundance and DOC concentration. A negative correlation was found between the virus-to-bacteria ratio and DOC level. These results are in agreement with our findings in the laboratory, where virus counts were significantly lower in treatments with fulvic acid additions than in a control (mean, 67.4% ± 6.5% of the control). Virus counts did not differ significantly among the control and treatments with glucose, indicating that it was the type of organic carbon and not quantity which had an impact on viruses. Results from this study suggest that the way viruses control bacterial assemblages in humic lakes is different from the mechanism in clear water systems.
Cloning and Characterization of Three Fatty Alcohol Oxidase Genes from
Candida tropicalis
Strain ATCC 20336
Authors: Eirich L. Dudley , Craft David L. , Steinberg Lisa , Asif Afreen , Eschenfeldt William H. , Stols Lucy , Donnelly Mark I. , Wilson C. Ron 
Published: August 2004

ABSTRACT

Candida
tropicalis
(ATCC 20336) converts fatty acids to long-chain
dicarboxylic acids via a pathway that includes among other reactions
the oxidation of ω-hydroxy fatty acids to ω-aldehydes
by a fatty alcohol oxidase (FAO). Three
FAO
genes (one gene
designated
FAO1
and two putative allelic genes designated
FAO2a
and
FAO2b
), have been cloned and sequenced from
this strain. A comparison of the DNA sequence homology and derived
amino acid sequence homology between these three genes and previously
published
Candida FAO
genes indicates that
FAO1
and
FAO2
are distinct genes. Both genes were
individually cloned and expressed in
Escherichia coli
. The
substrate specificity and
K

m

values for
the recombinant FAO1 and FAO2 were significantly different.
Particularly striking is the fact that FAO1 oxidizes ω-hydroxy
fatty acids but not 2-alkanols, whereas FAO2 oxidizes 2-alkanols but
not ω-hydroxy fatty acids. Analysis of extracts of strain H5343
during growth on fatty acids indicated that only FAO1 was highly
induced under these conditions.
FAO2
contains one CTG codon,
which codes for serine (amino acid 177) in
C. tropicalis
but
codes for leucine in
E. coli
. An
FAO2a
construct,
with a TCG codon (codes for serine in
E. coli
) substituted for
the CTG codon, was prepared and expressed in
E. coli
. Neither
the substrate specificity nor the
K

m

values for the FAO2a variant with a serine at position 177 were
radically different from those of the variant with a leucine at that
position.
Binary Toxins from
Bacillus thuringiensis
Active against the Western Corn Rootworm,
Diabrotica virgifera virgifera
LeConte
Authors: Baum James A. , Chu Chi-Rei , Rupar Mark , Brown Gregory R. , Donovan William P. , Huesing Joseph E. , Ilagan Oliver , Malvar Thomas M. , Pleau Michael , Walters Matthew , Vaughn Ty 
Published: August 2004

ABSTRACT

The western corn rootworm,
Diabrotica virgifera virgifera
LeConte, is a significant pest of corn in the United States. The development of transgenic corn hybrids resistant to rootworm feeding damage depends on the identification of genes encoding insecticidal proteins toxic to rootworm larvae. In this study, a bioassay screen was used to identify several isolates of the bacterium
Bacillus thuringiensis
active against rootworm. These bacterial isolates each produce distinct crystal proteins with approximate molecular masses of 13 to 15 kDa and 44 kDa. Insect bioassays demonstrated that both protein classes are required for insecticidal activity against this rootworm species. The genes encoding these proteins are organized in apparent operons and are associated with other genes encoding crystal proteins of unknown function. The antirootworm proteins produced by
B. thuringiensis
strains EG5899 and EG9444 closely resemble previously described crystal proteins of the Cry34A and Cry35A classes. The antirootworm proteins produced by strain EG4851, designated Cry34Ba1 and Cry35Ba1, represent a new binary toxin. Genes encoding these proteins could become an important component of a sustainable resistance management strategy against this insect pest.
Investigation of Spa Pools Associated with Lung Disorders Caused by
Mycobacterium avium
Complex in Immunocompetent Adults
Authors: Lumb Richard , Stapledon Richard , Scroop Andrew , Bond Peter , Cunliffe David , Goodwin Allan , Doyle Robyn , Bastian Ivan 
Published: August 2004

ABSTRACT

Three cases of
Mycobacterium avium
complex-related lung disorders were associated with two poorly maintained spa pools by genotypic investigations. Inadequate disinfection of the two spas had reduced the load of environmental bacteria to less than 1 CFU/ml but allowed levels of
M. avium
complex of 4.3 × 10
4
and 4.5 × 10
3
CFU/ml. Persistence of the disease-associated genotype was demonstrated in one spa pool for over 5 months until repeated treatments with greater than 10 mg of chlorine per liter for 1-h intervals eliminated
M. avium
complex from the spa pool. A fourth case of
Mycobacterium avium
complex-related lung disease was associated epidemiologically but not genotypically with another spa pool that had had no maintenance undertaken. This spa pool contained low numbers of mycobacteria by smear and was culture positive for
M. avium
complex, and the nonmycobacterial organism count was 5.2 × 10
6
CFU/ml. Public awareness about the proper maintenance of private (residential) spa pools must be promoted by health departments in partnership with spa pool retailers.
“
Candidatus
Endobugula glebosa,” a Specific Bacterial Symbiont of the Marine Bryozoan
Bugula simplex
Authors: Lim Grace E. , Haygood Margo G. 
Published: August 2004

ABSTRACT

The bryozoans
Bugula neritina
and
Bugula simplex
harbor bacteria in the pallial sinuses of their larvae as seen by electron microscopy. In
B. neritina
, the bacterial symbiont has been characterized as a gamma-proteobacterium, “
Candidatus
Endobugula sertula.” “
Candidatus
E. sertula” has been implicated as the source of the bryostatins, polyketides that provide chemical defense to the host and are also being tested for use in human cancer treatments. In this study, the bacterial symbiont in
B. simplex
larvae was identified by 16S rRNA-targeted PCR and sequencing as a gamma-proteobacterium closely related to and forming a monophyletic group with “
Candidatus
E. sertula.” In a fluorescence in situ hybridization, a 16S ribosomal DNA probe specific to the
B. simplex
symbiont hybridized to long rod-shaped bacteria in the pallial sinus of a
B. simplex
larva. The taxonomic status “
Candidatus
Endobugula glebosa” is proposed for the
B. simplex
larval symbiont. Degenerate polyketide synthase (PKS) primers amplified a gene fragment from
B. simplex
that closely matched a PKS gene fragment from the bryostatin PKS cluster. PCR surveys show that the symbiont and this PKS gene fragment are consistently and uniquely associated with
B. simplex
. Bryostatin activity assays and chemical analyses of
B. simplex
extracts reveal the presence of compounds similar to bryostatins. Taken together, these findings demonstrate a symbiosis in
B. simplex
that is similar and evolutionarily related to that in
B. neritina
.
Correspondence between Community Structure and Function during Succession in Phenol- and Phenol-plus-Trichloroethene-Fed Sequencing Batch Reactors
Authors: Ayala-del-Río Héctor L. , Callister Stephen J. , Criddle Craig S. , Tiedje James M. 
Published: August 2004

ABSTRACT

The effects of more than 2 years of trichloroethene (TCE) application on community succession and function were studied in two aerobic sequencing batch reactors. One reactor was fed phenol, and the second reactor was fed both phenol and TCE in sequence twice per day. After initiation of TCE loading in the second reactor, the TCE transformation rates initially decreased, but they stabilized with an average second-order rate coefficient of 0.044 liter mg
−1
day
−1
for 2 years. In contrast, the phenol-fed reactor showed higher and unstable TCE transformation rates, with an average rate coefficient of 0.093 liter mg
−1
day
−1
. Community analysis by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes showed that the phenol-plus-TCE-fed reactor had marked changes in community structure during the first 100 days and remained relatively stable afterwards, corresponding to the period of stable function. In contrast, the community structure of the phenol-fed reactor changed periodically, and the changes coincided with the periodicity observed in the TCE transformation rates. Correspondence analysis of each reactor community showed that different community structures corresponded with function (TCE degradation rate). Furthermore, the phenol hydroxylase genotypes, as determined by restriction fragment length polymorphism analysis, corresponded to community structure patterns identified by T-RFLP analysis and to periods when the TCE transformation rates were high. Long-term TCE stress appeared to select for a different and stable community structure, with lower but stable TCE degradation rates. In contrast, the community under no stress exhibited a dynamic structure and dynamic function.
Development and Application of a Real-Time PCR Approach for Quantification of Uncultured Bacteria in the Central Baltic Sea
Authors: Labrenz Matthias , Brettar Ingrid , Christen Richard , Flavier Sebastien , Bötel Julia , Höfle Manfred G. 
Published: August 2004

ABSTRACT

We have developed a highly sensitive approach to assess the abundance of uncultured bacteria in water samples from the central Baltic Sea by using a noncultured member of the “
Epsilonproteobacteria
” related to
Thiomicrospira denitrificans
as an example. Environmental seawater samples and samples enriched for the target taxon provided a unique opportunity to test the approach over a broad range of abundances. The approach is based on a combination of taxon- and domain-specific real-time PCR measurements determining the relative
T. denitrificans-
like 16S rRNA gene and 16S rRNA abundances, as well as the determination of total cell counts and environmental RNA content. It allowed quantification of
T. denitrificans
-like 16S rRNA molecules or 16S rRNA genes as well as calculation of the number of ribosomes per
T. denitrificans
-like cell. Every real-time measurement and its specific primer system were calibrated using environmental nucleic acids obtained from the original habitat for external standardization. These standards, as well as the respective samples to be measured, were prepared from the same DNA or RNA extract. Enrichment samples could be analyzed directly, whereas environmental templates had to be preamplified with general bacterial primers before quantification. Preamplification increased the sensitivity of the assay by more than 4 orders of magnitude. Quantification of enrichments with or without a preamplification step yielded comparable results.
T. denitrificans-
like 16S rRNA molecules ranged from 7.1 × 10
3
to 4.4 × 10
9
copies ml
−1
or 0.002 to 49.7% relative abundance.
T. denitrificans
-like 16S rRNA genes ranged from 9.0 × 10
1
to 2.2 ×10
6
copies ml
−1
or 0.01 to 49.7% relative abundance. Detection limits of this real-time-PCR approach were 20 16S rRNA molecules or 0.2 16S rRNA gene ml
−1
. The number of ribosomes per
T. denitrificans-
like cell was estimated to range from 20 to 200 in seawater and reached up to 2,000 in the enrichments. The results indicate that our real-time PCR approach can be used to determine cellular and relative abundances of uncultured marine bacterial taxa and to provide information about their levels of activity in their natural environment.
Biological Effects of
Trichoderma harzianum
Peptaibols on Mammalian Cells
Authors: Peltola Joanna , Ritieni Alberto , Mikkola Raimo , Grigoriev Pavel A. , Pócsfalvi Gabriella , Andersson Maria A. , Salkinoja-Salonen Mirja S. 
Published: August 2004

ABSTRACT

Trichoderma
species isolated from water-damaged buildings were screened for toxicity by using boar sperm cells as indicator cells. The crude methanolic cell extract from
Trichoderma harzianum
strain ES39 inhibited the boar sperm cell motility at a low exposure concentration (50% effective concentration, 1 to 5 μg [dry weight] ml of extended boar semen
−1
). The same exposure concentration depleted the boar sperm cells of NADH
2
. Inspection of the exposed boar sperm cells by transmission electron microscopy revealed damage to the plasma membrane. By using the black lipid membrane technique, it was shown that the semipurified metabolites (eluted from a SepPak C
18
cartridge) of
T. harzianum
strain ES39 induced voltage-dependent conductivity. The high-performance liquid chromatography-purified metabolites of
T. harzianum
strain ES39 dissipated the mitochondrial membrane potential (Δψ
m
) of human lung epithelial carcinoma cells (cell line A549). The semipurified metabolites (eluted from a SepPak C
18
cartridge) of
T. harzianum
strain ES39 were analyzed by mass spectrometry (MS). Matrix-assisted laser desorption ionization and nanoflow electrospray ionization MS revealed five major peptaibols, each of which contained 18 residues and had a mass ranging from 1,719 to 1,775 Da. Their partial amino acid sequences were determined by collision-induced dissociation tandem MS.
Host Physiology and Pathogenic Variation of
Cochliobolus heterostrophus
Strains with Mutations in the G Protein Alpha Subunit, CGA1
Authors: Degani Ofir , Maor Rudy , Hadar Ruthi , Sharon Amir , Horwitz Benjamin A. 
Published: August 2004

ABSTRACT

Conserved eukaryotic signaling proteins participate in development and disease in plant-pathogenic fungi. Strains with mutations in
CGA1
, a heterotrimeric G protein G alpha subunit gene of the maize pathogen
Cochliobolus heterostrophus
, are defective in several developmental pathways. Conidia from
CGA1
mutants germinate as abnormal, straight-growing germ tubes that form few appressoria, and the mutants are female sterile. Nevertheless, these mutants can cause normal lesions on plants, unlike other filamentous fungal plant pathogens in which functional homologues of
CGA1
are required for full virulence. Δ
cga1
mutants of
C. heterostrophus
were less infective of several maize varieties under most conditions, but not all, as virulence was nearly normal on detached leaves. This difference could be related to the rapid senescence of detached leaves, since delaying senescence with cytokinin also had differential effects on the virulence of the wild type and the Δ
cga1
mutant. In particular, detached leaves may provide a more readily available nutrient source than attached leaves. Decreased fitness of Δ
cga1
as a pathogen may reflect conditions under which full virulence requires signal transduction through CGA1-mediated pathways. The virulence of these signal transduction mutants is thus affected differentially by the physiological state of the host.
Two Morphological Types of Cell Appendages on a Strongly Adhesive Bacterium, Acinetobactersp. Strain Tol 5
Authors: Ishii Shun'ichi , Koki Jun , Unno Hajime , Hori Katsutoshi 
Published: August 2004

ABSTRACTTwo morphological types of appendages, an anchor-like appendage and a peritrichate fibril-type appendage, have been observed on cells of an adhesive bacterium,Acinetobactersp. strain Tol 5, by use of recently developed electron microscopic techniques. The anchor extends straight to the substratum without branching and tethers the cell body at its end at distances of several hundred nanometers, whereas the peritrichate fibril attaches to the substratum in multiple places, fixing the cell at much shorter distances.
Translational Features of Human Alpha 2b Interferon Production in
Escherichia coli
Authors: Valente C. A. , Prazeres D. M. F. , Cabral J. M. S. , Monteiro G. A. 
Published: August 2004

ABSTRACT

The yield of human alpha 2b interferon in
Escherichia coli
was optimized by replacement of low-usage arginine codons located in the mRNA 5′ end. The differences observed among the various gene variants suggest that codon usage, Shine-Dalgarno-like sequences, and mRNA secondary structure contribute to the performance of
E. coli
translation machinery.
Cyanobacterial Protease Inhibitor Microviridin J Causes a Lethal Molting Disruption in
Daphnia pulicaria
Authors: Rohrlack Thomas , Christoffersen Kirsten , Kaebernick Melanie , Neilan Brett A. 
Published: August 2004

ABSTRACT

Laboratory experiments identified microviridin J as the source of a fatal molting disruption in
Daphnia
species organisms feeding on
Microcystis
cells. The molting disruption was presumably linked to the inhibitory effect of microviridin J on daphnid proteases, suggesting that hundreds of further cyanobacterial protease inhibitors must be considered potentially toxic to zooplankton.
Flowing cells through pulsed electric fields efficiently purges stem cell preparations of contaminating myeloma cells while preserving stem cell function
Authors: Craiu Abie , Saito Yoriko , Limon Ana , Eppich Henry M. , Olson Douglas P. , Rodrigues Neil , Adams Gregor B. , Dombkowski David , Richardson Paul , Schlossman Robert , Choi Peter S. , Grogins Jonathan , O'Connor Paula G. , Cohen Kenneth , Attar Eyal C. , Freshman Jay , Rich Rebecca , Mangano Joseph A. , Gribben John G. , Anderson Kenneth C. , Scadden David T. 
Published: August 2004

AbstractAutologous stem cell transplantation, in the setting of hematologic malignancies such as lymphoma, improves disease-free survival if the graft has undergone tumor purging. Here we show that flowing hematopoietic cells through pulsed electric fields (PEFs) effectively purges myeloma cells without sacrificing functional stem cells. Electric fields can induce irreversible cell membrane pores in direct relation to cell diameter, an effect we exploit in a flowing system appropriate for clinical scale. Multiple myeloma (MM) cell lines admixed with human bone marrow (BM) or peripheral blood (PB) cells were passed through PEFs at 1.35 kV/cm to 1.4 kV/cm, resulting in 3- to 4-log tumor cell depletion by flow cytometry and 4.5- to 6-log depletion by tumor regrowth cultures. Samples from patients with MM gave similar results by cytometry. Stem cell engraftment into nonobese diabetic–severe combined immunodeficient (NOD/SCID)/β2m-/- mice was unperturbed by PEFs. Flowing cells through PEFs is a promising technology for rapid tumor cell purging of clinical progenitor cell preparations.
Enhanced tumorigenesis in HTLV-1 Tax-transgenic mice deficient in interferon-gamma
Authors: Mitra-Kaushik Shibani , Harding John , Hess Jay , Schreiber Robert , Ratner Lee 
Published: August 2004

AbstractThe oncoprotein Tax of human T-cell leukemia virus type I (HTLV-1) is the major mediator of viral pathogenesis in infected individuals. Expression of Tax under the regulation of the human granzyme B promoter in mice results in a lymphoproliferative disorder resembling adult T-cell leukemia/lymphoma (ATL). Tax expression is associated with the production of high levels interferon-γ (IFN-γ) in HTLV-1-infected CD4+ cells and Tax-transgenic tumors. We examined the role of IFN-γ in tumorigenesis, by mating Tax-transgenic mice with a gene-specific knockout for IFN-γ. IFN-γ-/- Tax+-transgenic mice show accelerated tumor onset (median, 4 versus 6 months), dissemination (median, 5 versus 7 months), and death (median, 7 versus 10 months), compared with IFN-γ+/- or IFN-γ+/+ Tax+ mice. Pathologic and immunophenotypic characteristics of tumors from all genotypes are indistinguishable, except for enhanced interleukin 2 receptor-β (IL-2Rβ) and suppressed intercellular adhesion molecule-1 (ICAM-1) expression on tumors from IFN-γ-/- Tax+ transgenic mice. IFN-γ-/- tumors demonstrate enhanced CD31 (platelet-endothelial CAM-1 [PECAM-1]) staining compared with those from IFN-γ+/- or IFN-γ+/+ Tax+ mice. Angiogenesis-specific cDNA microarray analysis identified 4 mediators of angiogenic growth differentially expressed in tumors from Tax+IFN-γ-/- mice compared with Tax+IFN-γ+/+ littermates. As confirmed by reverse transcription-polymerase chain reaction (RT-PCR), loss of IFN-γ results in down-regulation of tumor necrosis factor-α (TNF-α) and tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) while up-regulating expression of vascular endothelial growth factor (VEGF) and tenascin C. These results provide insight into a possible mechanism by which IFN-γ contributes to host resistance against HTLV-induced tumors through an angiostatic effect. (Blood. 2004;104:3305-3311)