bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Lipid Rafts from Medicago truncatula Root Plasma Membranes: A Proteomic Study Reveals the Presence of a Raft-Associated Redox System
Authors: Lefebvre Benoit , Furt Fabienne , Hartmann Marie-Andrée , Michaelson Louise V. , Carde Jean-Pierre , Sargueil-Boiron Françoise , Rossignol Michel , Napier Johnathan A. , Cullimore Julie , Bessoule Jean-Jacques , Mongrand Sébastien 
Published: March 2007

Abstract
Several studies have provided new insights into the role of sphingolipid/sterol-rich domains so-called lipid rafts of the plasma membrane (PM) from mammalian cells, and more recently from leaves, cell cultures, and seedlings of higher plants. Here we show that lipid raft domains, defined as Triton X-100-insoluble membranes, can also be prepared from Medicago truncatula root PMs. These domains have been extensively characterized by ultrastructural studies as well as by analysis of their content in lipids and proteins. M. truncatula lipid domains are shown to be enriched in sphingolipids and Δ7-sterols, with spinasterol as the major compound, but also in steryl glycosides and acyl-steryl glycosides. A large number of proteins (i.e. 270) have been identified. Among them, receptor kinases and proteins related to signaling, cellular trafficking, and cell wall functioning were well represented whereas those involved in transport and metabolism were poorly represented. Evidence is also given for the presence of a complete PM redox system in the lipid rafts.
New Method for Evaluation of Genotoxicity, Based on the Use of Real-Time PCR and Lysogenic Gram-Positive and Gram-Negative Bacteria
Authors: Soberón Nora , Martín Rebeca , Suárez Juan E. 
Published: March 2007

ABSTRACT

A method for the detection of the SOS response as measured by the liberation of resident prophages from the genomes of their hosts is described. It is based on the use of two converging oligonucleotides that flank the
attP
attachment site of the phage as primers for real-time PCR. Amplification was observed only after the phage DNA became excised. The system responds to both chemicals and physical conditions. Quantitative data on the concentration and/or potency of the genotoxic condition were obtained. Results can be achieved within 1 day and are less susceptible to possible toxic effects than phage generation or other methods that require DNA synthesis. The use of both gram-positive and gram-negative bacteria widens the range of compounds that can be tested because it eliminates impermeability problems derived from the particular composition of each cell wall type.
Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space
Authors: Rudi Knut , Zimonja Monika , Kvenshagen Bente , Rugtveit Jarle , Midtvedt Tore , Eggesbø Merete 
Published: March 2007

ABSTRACT
We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities.
Role of Cystathionine β-Lyase in Catabolism of Amino Acids to Sulfur Volatiles by Genetic Variants of
Lactobacillus helveticus
CNRZ 32
Authors: Lee Won-Jae , Banavara Dattatreya S. , Hughes Joanne E. , Christiansen Jason K. , Steele James L. , Broadbent Jeffery R. , Rankin Scott A. 
Published: March 2007

ABSTRACT

Catabolism of sulfur-containing amino acids plays an important role in the development of cheese flavor. During ripening, cystathionine β-lyase (CBL) is believed to contribute to the formation of volatile sulfur compounds (VSCs) such as methanethiol and dimethyl disulfide. However, the role of CBL in the generation of VSCs from the catabolism of specific sulfur-containing amino acids is not well characterized. The objective of this study was to investigate the role of CBL in VSC formation by
Lactobacillus helveticus
CNRZ 32 using genetic variants of
L. helveticus
CNRZ 32 including the CBL-null mutant, complementation of the CBL-null mutant, and the CBL overexpression mutant. The formation of VSCs from methionine, cystathionine, and cysteine was determined in a model system using gas chromatography-mass spectrometry with solid-phase microextraction. With methionine as a substrate, CBL overexpression resulted in higher VSC production than that of wild-type
L. helveticus
CNRZ 32 or the CBL-null mutant. However, there were no differences in VSC production between the wild type and the CBL-null mutant. With cystathionine, methanethiol production was detected from the CBL overexpression variant and complementation of the CBL-null mutant, implying that CBL may be involved in the conversion of cystathionine to methanethiol. With cysteine, no differences in VSC formation were observed between the wild type and genetic variants, indicating that CBL does not contribute to the conversion of cysteine.
Biofilm Cohesiveness Measurement Using a Novel Atomic Force Microscopy Methodology
Authors: Ahimou Francois , Semmens Michael J. , Novak Paige J. , Haugstad Greg 
Published: March 2007

ABSTRACT

Biofilms can be undesirable, as in those covering medical implants, and beneficial, such as when they are used for waste treatment. Because cohesive strength is a primary factor affecting the balance between growth and detachment, its quantification is essential in understanding, predicting, and modeling biofilm development. In this study, we developed a novel atomic force microscopy (AFM) method for reproducibly measuring, in situ, the cohesive energy levels of moist 1-day biofilms. The biofilm was grown from an undefined mixed culture taken from activated sludge. The volume of biofilm displaced and the corresponding frictional energy dissipated were determined as a function of biofilm depth, resulting in the calculation of the cohesive energy. Our results showed that cohesive energy increased with biofilm depth, from 0.10 ± 0.07 nJ/μm
3
to 2.05 ± 0.62 nJ/μm
3
. This observation was reproducible, with four different biofilms showing the same behavior. Cohesive energy also increased from 0.10 ± 0.07 nJ/μm
3
to 1.98 ± 0.34 nJ/μm
3
when calcium (10 mM) was added to the reactor during biofilm cultivation. These results agree with previous reports on calcium increasing the cohesiveness of biofilms. This AFM-based technique can be performed with available off-the-shelf instrumentation. It could therefore be widely used to examine biofilm cohesion under a variety of conditions.
Influence of Vitamin B
12
and Cocultures on the Growth of
Dehalococcoides
Isolates in Defined Medium
Authors: He Jianzhong , Holmes Victor F. , Lee Patrick K. H. , Alvarez-Cohen Lisa 
Published: March 2007

ABSTRACT

Bacteria belonging to the genus
Dehalococcoides
play a key role in the complete detoxification of chloroethenes as these organisms are the only microbes known to be capable of dechlorination beyond dichloroethenes to vinyl chloride (VC) and ethene. However,
Dehalococcoides
strains usually grow slowly with a doubling time of 1 to 2 days and have complex nutritional requirements. Here we describe the growth of
Dehalococcoides ethenogenes
195 in a defined mineral salts medium, improved growth of strain 195 when the medium was amended with high concentrations of vitamin B
12
, and a strategy for maintaining
Dehalococcoides
strains on lactate by growing them in consortia. Although strain 195 could grow in defined medium spiked with ∼0.5 mM trichloroethene (TCE) and 0.001 mg/liter vitamin B
12
, the TCE dechlorination and cellular growth rates doubled when the vitamin B
12
concentration was increased 25-fold to 0.025 mg/liter. In addition, the final ratios of ethene to VC increased when the higher vitamin concentration was used, which reflected the key role that cobalamin plays in dechlorination reactions. No further improvement in dechlorination or growth was observed when the vitamin B
12
concentration was increased to more than 0.025 mg/liter. In defined consortia containing strain 195 along with
Desulfovibrio desulfuricans
and/or
Acetobacterium woodii
and containing lactate as the electron donor, tetrachloroethene (∼0.4 mM) was completely dechlorinated to VC and ethene and there was concomitant growth of
Dehalococcoides
cells. In the cultures that also contained
D. desulfuricans
and/or
A. woodii
, strain 195 cells grew to densities that were 1.5 times greater than the densities obtained when the isolate was grown alone. The ratio of ethene to VC was highest in the presence of
A. woodii
, an organism that generates cobalamin de novo during metabolism. These findings demonstrate that the growth of
D. ethenogenes
strain 195 in defined medium can be optimized by providing high concentrations of vitamin B
12
and that this strain can be grown to higher densities in cocultures with fermenters that convert lactate to generate the required hydrogen and acetate and that may enhance the availability of vitamin B
12
.
Biogeography of Actinomycete Communities and Type II Polyketide Synthase Genes in Soils Collected in New Jersey and Central Asia
Authors: Wawrik Boris , Kutliev Djumaniyaz , Abdivasievna Urinova A. , Kukor Jerome J. , Zylstra Gerben J. , Kerkhof Lee 
Published: March 2007

ABSTRACT

Soil microbial communities are believed to be comprised of thousands of different bacterial species. One prevailing idea is that “everything is everywhere, and the environment selects,” implying that all types of bacteria are present in all environments where their growth requirements are met. We tested this hypothesis using actinomycete communities and type II polyketide synthase (PKS) genes found in soils collected from New Jersey and Uzbekistan (
n
= 91). Terminal restriction fragment length polymorphism analysis using actinomycete 16S rRNA and type II PKS genes was employed to determine community profiles. The terminal fragment frequencies in soil samples had a lognormal distribution, indicating that the majority of actinomycete phylotypes and PKS pathways are present infrequently in the environment. Less than 1% of peaks were detected in more than 50% of samples, and as many as 18% of the fragments were unique and detected in only one sample. Actinomycete 16S rRNA fingerprints clustered by country of origin, indicating that unique populations are present in North America and Central Asia. Sequence analysis of type II PKS gene fragments cloned from Uzbek soil revealed 35 novel sequence clades whose levels of identity to genes in the GenBank database ranged from 68 to 92%. The data indicate that actinomycetes are patchily distributed but that distinct populations are present in North American and Central Asia. These results have implications for microbial bioprospecting and indicate that the cosmopolitan actinomycete species and PKS pathways may account for only a small proportion of the total diversity in soil.
Role of Lipid Composition and Lipid Peroxidation in the Sensitivity of Fungal Plant Pathogens to Aluminum Chloride and Sodium Metabisulfite
Authors: Avis Tyler J. , Michaud Mélanie , Tweddell Russell J. 
Published: March 2007

ABSTRACT
Aluminum chloride and sodium metabisulfite have shown high efficacy at low doses in controlling postharvest pathogens on potato tubers. Direct effects of these two salts included the loss of cell membrane integrity in exposed pathogens. In this work, four fungal potato pathogens were studied in order to elucidate the role of membrane lipids and lipid peroxidation in the relative sensitivity of microorganisms exposed to these salts. Inhibition of mycelial growth in these fungi varied considerably and revealed sensitivity groups within the tested fungi. Analysis of fatty acids in these fungi demonstrated that sensitivity was related to high intrinsic fatty acid unsaturation. When exposed to the antifungal salts, sensitive fungi demonstrated a loss of fatty acid unsaturation, which was accompanied by an elevation in malondialdehyde content (a biochemical marker of lipid peroxidation). Our data suggest that aluminum chloride and sodium metabisulfite could induce lipid peroxidation in sensitive fungi, which may promote the ensuing loss of integrity in the plasma membrane. This direct effect on fungal membranes may contribute, at least in part, to the observed antimicrobial effects of these two salts.
Mg2+Deprivation Elicits Rapid Ca2+Uptake and Activates Ca2+/Calcineurin Signaling inSaccharomyces cerevisiae
Authors: Wiesenberger Gerlinde , Steinleitner Katarina , Malli Roland , Graier Wolfgang F. , Vormann Jürgen , Schweyen Rudolf J. , Stadler Jochen A. 
Published: March 2007

ABSTRACTTo learn about the cellular processes involved in Mg2+homeostasis and the mechanisms allowing cells to cope with low Mg2+availability, we performed RNA expression-profiling experiments and followed changes in gene activity upon Mg2+depletion on a genome-wide scale. A striking portion of genes up-regulated under Mg2+depletion are also induced by high Ca2+and/or alkalinization. Among the genes significantly up-regulated by Mg2+starvation, Ca2+stress, and alkalinization areENA1(encoding a P-type ATPase sodium pump) andPHO89(encoding a sodium/phosphate cotransporter). We show that up-regulation of these genes is dependent on the calcineurin/Crz1p (calcineurin-responsive zinc finger protein) signaling pathway. Similarly to Ca2+stress, Mg2+starvation induces translocation of the transcription factor Crz1p from the cytoplasm into the nucleus. The up-regulation ofENA1andPHO89upon Mg2+starvation depends on extracellular Ca2+. Using fluorescence resonance energy transfer microscopy, we demonstrate that removal of Mg2+results in an immediate increase in free cytoplasmic Ca2+. This effect is dependent on external Ca2+. The results presented indicate that Mg2+depletion in yeast cells leads to enhanced cellular Ca2+concentrations, which activate the Crz1p/calcineurin pathway. We provide evidence that calcineurin/Crz1p signaling is crucial for yeast cells to cope with Mg2+depletion stress.
Parallel β-Helix Proteins Required for Accurate Capsule Polysaccharide Synthesis and Virulence in the Yeast
Cryptococcus neoformans
Authors: Liu Oliver W. , Kelly Mark J. S. , Chow Eric D. , Madhani Hiten D. 
Published: March 2007

ABSTRACT

The principal capsular polysaccharide of the opportunistic fungal pathogen
Cryptococcus neoformans
consists of an α-1,3-linked mannose backbone decorated with a repeating pattern of glucuronyl and xylosyl side groups. This structure is critical for virulence, yet little is known about how the polymer, called glucuronoxylomannan (GXM), is faithfully synthesized and assembled. We have generated deletions in two genes encoding predicted parallel β-helix repeat proteins, which we have designated
PBX1
and
PBX2
. Deletion of either gene results in a dry-colony morphology, clumpy cells, and decreased capsule integrity. Two-dimensional nuclear magnetic resonance spectroscopy of purified GXM from the mutants indicated that both the wild-type GXM structure and novel, aberrant linkages were present. Carbohydrate composition and linkage analysis determined that these aberrant structures are correlated with the incorporation of terminal glucose residues that are not found in wild-type capsule polysaccharide. We conclude that Pbx1 and Pbx2 are required for the fidelity of GXM synthesis and may be involved in editing incorrectly added glucose residues.
PBX1
and
PBX2
knockout mutants showed severely attenuated virulence in a murine inhalation model of cryptococcosis. Unlike acapsular strains, these mutant strains induced delayed symptoms of cryptococcosis, though the infected animals eventually contained the infection and recovered.
A-Factor and Phosphate Depletion Signals Are Transmitted to the Grixazone Biosynthesis Genes via the Pathway-Specific Transcriptional Activator GriR
Authors: Higashi Tatsuichiro , Iwasaki Yuko , Ohnishi Yasuo , Horinouchi Sueharu 
Published: March 2007

ABSTRACT

Grixazone (GX), which is a diffusible yellow pigment containing a phenoxazinone chromophore, is one of the secondary metabolites under the control of A-factor (2-isocapryloyl-3
R
-hydroxymethyl-γ-butyrolactone) in
Streptomyces griseus
. GX production is also induced by phosphate starvation. The whole biosynthesis gene cluster for GX was cloned and characterized. The gene cluster consisting of 13 genes contained six transcriptional units,
griT
,
griSR
,
griR
,
griAB
,
griCDEFG
, and
griJIH
. During cultivation in a phosphate-depleted medium, the six promoters were activated in the order (i)
griR
, (ii)
griC
and
griJ
, and (iii)
griT
,
griS
, and
griA
. Disruption of
griR
, which encodes a SARP family transcriptional regulator, abolished the transcriptional activation of all other genes in the cluster. In addition, ectopic expression of
griR
from a constitutively active promoter resulted in GX overproduction even in the absence of AdpA, a key transcriptional activator in the A-factor regulatory cascade, and in the presence of phosphate at a high concentration. GriR monomers bound direct repeat sequences in the
griC
and
griJ
promoters in a cooperative manner. Therefore, the early active genes (
griCDEFG
and
griJIH
), all of which, except for
griG
(which encodes a transporter-like protein), encode the GX biosynthesis enzymes, were directly activated by GriR. The transcription of
griR
was greatly reduced in the presence of phosphate at a high concentration and was hardly detected in the absence of AdpA. These findings showed that both A-factor and phosphate depletion signals were required for
griR
transcription and both signals were transmitted to the GX biosynthesis genes solely via the
griR
promoter.
Complete Nucleotide Sequence of the 113-Kilobase Linear Catabolic Plasmid pAL1 of
Arthrobacter nitroguajacolicus
Rü61a and Transcriptional Analysis of Genes Involved in Quinaldine Degradation
Authors: Parschat Katja , Overhage Jörg , Strittmatter Axel W. , Henne Anke , Gottschalk Gerhard , Fetzner Susanne 
Published: March 2007

ABSTRACT

The nucleotide sequence of the linear catabolic plasmid pAL1 from the 2-methylquinoline (quinaldine)-degrading strain
Arthrobacter nitroguajacolicus
Rü61a comprises 112,992 bp. A total of 103 open reading frames (ORFs) were identified on pAL1, 49 of which had no annotatable function. The ORFs were assigned to the following functional groups: (i) catabolism of quinaldine and anthranilate, (ii) conjugation, and (iii) plasmid maintenance and DNA replication and repair. The genes for conversion of quinaldine to anthranilate are organized in two operons that include ORFs presumed to code for proteins involved in assembly of the quinaldine-4-oxidase holoenzyme, namely, a MobA-like putative molybdopterin cytosine dinucleotide synthase and an XdhC-like protein that could be required for insertion of the molybdenum cofactor. Genes possibly coding for enzymes involved in anthranilate degradation via 2-aminobenzoyl coenzyme A form another operon. These operons were expressed when cells were grown on quinaldine or on aromatic compounds downstream in the catabolic pathway. Single-stranded 3′ overhangs of putative replication intermediates of pAL1 were predicted to form elaborate secondary structures due to palindromic and superpalindromic terminal sequences; however, the two telomeres appear to form different structures. Sequence analysis of ORFs 101 to 103 suggested that pAL1 codes for one or two putative terminal proteins, presumed to be covalently bound to the 5′ termini, and a multidomain telomere-associated protein (Tap) comprising 1,707 amino acids. Even if the putative proteins encoded by ORFs 101 to 103 share motifs with the Tap and terminal proteins involved in telomere patching of
Streptomyces
linear replicons, their overall sequences and domain structures differ significantly.
Identification of NovelEscherichia coliRibosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques
Authors: Jiang M. , Sullivan S. M. , Walker A. K. , Strahler J. R. , Andrews P. C. , Maddock J. R. 
Published: March 2007

ABSTRACTBiogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16°C and 37°C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.
A Putative Gene Cluster for Aminoarabinose Biosynthesis Is Essential for
Burkholderia cenocepacia
Viability
Authors: Ortega Ximena P. , Cardona Silvia T. , Brown Alan R. , Loutet Slade A. , Flannagan Ronald S. , Campopiano Dominic J. , Govan John R. W. , Valvano Miguel A. 
Published: March 2007

ABSTRACT

Using a conditional mutagenesis strategy we demonstrate here that a gene cluster encoding putative aminoarabinose (Ara4N) biosynthesis enzymes is essential for the viability of
Burkholderia cenocepacia
. Loss of viability is associated with dramatic changes in bacterial cell morphology and ultrastructure, increased permeability to propidium iodide, and sensitivity to sodium dodecyl sulfate, suggesting a general cell envelope defect caused by the lack of Ara4N.