bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Mechanism of Biocatalyst Inhibition in Microbial Desulfurization
Authors: Abin-Fuentes Andres , Mohamed Magdy El-Said , Wang Daniel I. C. , Prather Kristala L. J. 
Published: October 2013

ABSTRACT

Microbial desulfurization, or biodesulfurization (BDS), of fuels is a promising technology because it can desulfurize compounds that are recalcitrant to the current standard technology in the oil industry. One of the obstacles to the commercialization of BDS is the reduction in biocatalyst activity concomitant with the accumulation of the end product, 2-hydroxybiphenyl (HBP), during the process. BDS experiments were performed by incubating
Rhodococcus erythropolis
IGTS8 resting-cell suspensions with hexadecane at 0.50 (vol/vol) containing 10 mM dibenzothiophene. The resin Dowex Optipore SD-2 was added to the BDS experiments at resin concentrations of 0, 10, or 50 g resin/liter total volume. The HBP concentration within the cytoplasm was estimated to decrease from 1,100 to 260 μM with increasing resin concentration. Despite this finding, productivity did not increase with the resin concentration. This led us to focus on the susceptibility of the desulfurization enzymes toward HBP. Dose-response experiments were performed to identify major inhibitory interactions in the most common BDS pathway, the 4S pathway. HBP was responsible for three of the four major inhibitory interactions identified. The concentrations of HBP that led to a 50% reduction in the enzymes' activities (IC
50
s) for DszA, DszB, and DszC were measured to be 60 ± 5 μM, 110 ± 10 μM, and 50 ± 5 μM, respectively. The fact that the IC
50
s for HBP are all significantly lower than the cytoplasmic HBP concentration suggests that the inhibition of the desulfurization enzymes by HBP is responsible for the observed reduction in biocatalyst activity concomitant with HBP generation.
Release of Free DNA by Membrane-Impaired Bacterial Aerosols Due to Aerosolization and Air Sampling
Authors: Zhen Huajun , Han Taewon , Fennell Donna E. , Mainelis Gediminas 
Published: October 2013

ABSTRACT

We report here that stress experienced by bacteria due to aerosolization and air sampling can result in severe membrane impairment, leading to the release of DNA as free molecules.
Escherichia coli
and
Bacillus atrophaeus
bacteria were aerosolized and then either collected directly into liquid or collected using other collection media and then transferred into liquid. The amount of DNA released was quantified as the cell membrane damage index (

I
D

), i.e., the number of 16S rRNA gene copies in the supernatant liquid relative to the total number in the bioaerosol sample. During aerosolization by a Collison nebulizer, the

I
D

of
E. coli
and
B. atrophaeus
in the nebulizer suspension gradually increased during 60 min of continuous aerosolization. We found that the

I
D

of bacteria during aerosolization was statistically significantly affected by the material of the Collison jar (glass > polycarbonate;
P
< 0.001) and by the bacterial species (
E. coli
>
B. atrophaeus
;
P
< 0.001). When
E. coli
was collected for 5 min by filtration, impaction, and impingement, its

I
D

values were within the following ranges: 0.051 to 0.085, 0.16 to 0.37, and 0.068 to 0.23, respectively; when it was collected by electrostatic precipitation, the

I
D

values (0.011 to 0.034) were significantly lower (
P
< 0.05) than those with other sampling methods. Air samples collected inside an equine facility for 2 h by filtration and impingement exhibited

I
D

values in the range of 0.30 to 0.54. The data indicate that the amount of cell damage during bioaerosol sampling and the resulting release of DNA can be substantial and that this should be taken into account when analyzing bioaerosol samples.
Anaerobic Benzene Oxidation via Phenol in Geobacter metallireducens
Authors: Zhang Tian , Tremblay Pier-Luc , Chaurasia Akhilesh Kumar , Smith Jessica A. , Bain Timothy S. , Lovley Derek R. 
Published: October 2013

ABSTRACTAnaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated inGeobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (<0.5 μM) of phenol accumulated in cultures ofGeobacter metallireducensanaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures ofGeobacter sulfurreducens, aGeobacterspecies that cannot metabolize benzene. The phenol produced inG. metallireducenscultures was labeled with18O during growth in H218O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in whichGeobacterspecies are considered to play an important role in anaerobic benzene degradation.
Involvement of Botrytis cinerea Small GTPases BcRAS1 and BcRAC in Differentiation, Virulence, and the Cell Cycle
Authors: Minz Dub Anna , Kokkelink Leonie , Tudzynski Bettina , Tudzynski Paul , Sharon Amir 
Published: October 2013

ABSTRACTSmall GTPases of the Ras superfamily are highly conserved proteins that are involved in various cellular processes, in particular morphogenesis, differentiation, and polar growth. Here we report on the analysis of RAS1 and RAC homologues from the gray mold fungusBotrytis cinerea. We show that these small GTPases are individually necessary for polar growth, reproduction, and pathogenicity, required for cell cycle progression through mitosis (BcRAC), and may lie upstream of the stress-related mitogen-activated protein kinase (MAPK) signaling pathway.bcras1andbcracdeletion strains had reduced growth rates, and their hyphae were hyperbranched and deformed. In addition, both strains were vegetatively sterile and nonpathogenic. A strain expressing a constitutively active (CA) allele of the BcRAC protein had partially similar but milder phenotypes. Similar to the deletion strains, the CA-BcRAC strain did not produce any conidia and had swollen hyphae. In contrast to the two deletion strains, however, the growth rate of the CA-BcRAC strain was normal, and it caused delayed but well-developed disease symptoms. Microscopic examination revealed an increased number of nuclei and disturbance of actin localization in the CA-BcRAC strain. Further work with cell cycle- and RAC-specific inhibitory compounds associated the BcRAC protein with progression of the cell cycle through mitosis, possibly via an effect on microtubules. Together, these results show that the multinucleate phenotype of the CA-BcRAC strain could result from at least two defects: disruption of polar growth through disturbed actin localization and uncontrolled nuclear division due to constitutive activity of BcRAC.
Strategies To Discover the Structural Components of Cyst and Oocyst Walls
Authors: Samuelson John , Bushkin G. Guy , Chatterjee Aparajita , Robbins Phillips W. 
Published: October 2013

ABSTRACT

Cysts of
Giardia lamblia
and
Entamoeba histolytica
and oocysts of
Toxoplasma gondii
and
Cryptosporidium parvum
are the infectious and sometimes diagnostic forms of these parasites. To discover the structural components of cyst and oocyst walls, we have developed strategies based upon a few simple assumptions. Briefly, the most abundant wall proteins are identified by monoclonal antibodies or mass spectrometry. Structural components include a sugar polysaccharide (chitin for
Entamoeba
, β-1,3-linked glucose for
Toxoplasma
, and β-1,3-linked GalNAc for
Giardia
) and/or acid-fast lipids (
Toxoplasma
and
Cryptosporidium
). Because
Entamoeba
cysts and
Toxoplasma
oocysts are difficult to obtain, studies of walls of nonhuman pathogens (
E. invadens
and
Eimeria
, respectively) accelerate discovery. Biochemical methods to dissect fungal walls work well for cyst and oocyst walls, although the results are often unexpected. For example, echinocandins, which inhibit glucan synthases and kill fungi, arrest the development of oocyst walls and block their release into the intestinal lumen.
Candida
walls are coated with mannans, while
Entamoeba
cysts are coated in a dextran-like glucose polymer. Models for cyst and oocyst walls derive from their structural components and organization within the wall. Cyst walls are composed of chitin fibrils and lectins that bind chitin (
Entamoeba
) or fibrils of the β-1,3-GalNAc polymer and lectins that bind the polymer (
Giardia
). Oocyst walls of
Toxoplasma
have two distinct layers that resemble those of fungi (β-1,3-glucan in the inner layer) or mycobacteria (acid-fast lipids in the outer layer). Oocyst walls of
Cryptosporidium
have a rigid bilayer of acid-fast lipids and inner layer of oocyst wall proteins.
The Conserved DNA-Binding Protein WhiA Is Involved in Cell Division in Bacillus subtilis
Authors: Surdova Katarina , Gamba Pamela , Claessen Dennis , Siersma Tjalling , Jonker Martijs J. , Errington Jeff , Hamoen Leendert W. 
Published: October 2013

ABSTRACTBacterial cell division is a highly coordinated process that begins with the polymerization of the tubulin-like protein FtsZ at midcell. FtsZ polymerization is regulated by a set of conserved cell division proteins, including ZapA. However, azapAmutation does not result in a clear phenotype inBacillus subtilis. In this study, we used a synthetic-lethal screen to find genes that become essential when ZapA is mutated. Three transposon insertions were found inyvcL. The deletion ofyvcLin a wild-type background had only a mild effect on growth, but ayvcL zapAdouble mutant is very filamentous and sick. This filamentation is caused by a strong reduction in FtsZ-ring assembly, suggesting that YvcL is involved in an early stage of cell division. YvcL is 25% identical and 50% similar to theStreptomyces coelicolortranscription factor WhiA, which inducesftsZand is required for septation of aerial hyphae during sporulation. Using green fluorescent protein fusions, we show that YvcL localizes at the nucleoid. Surprisingly, transcriptome analyses in combination with a ChIP-on-chip assay gave no indication that YvcL functions as a transcription factor. To gain more insight into the function of YvcL, we searched for suppressors of the filamentous phenotype of ayvcL zapAdouble mutant. Transposon insertions ingtaBandpgcArestored normal cell division of the double mutant. The corresponding proteins have been implicated in the metabolic sensing of cell division. We conclude that YvcL (WhiA) is involved in cell division inB. subtilisthrough an as-yet-unknown mechanism.
Conserved Pyridoxal Protein That Regulates Ile and Val Metabolism
Authors: Ito Tomokazu , Iimori Jumpei , Takayama Sayuri , Moriyama Akihito , Yamauchi Ayako , Hemmi Hisashi , Yoshimura Tohru 
Published: October 2013

ABSTRACT

Escherichia coli
YggS is a member of the highly conserved uncharacterized protein family that binds pyridoxal 5′-phosphate (PLP). To assist with the functional assignment of the YggS family,
in vivo
and
in vitro
analyses were performed using a
yggS
-deficient
E. coli
strain (Δ
yggS
) and a purified form of YggS, respectively. In the stationary phase, the Δ
yggS
strain exhibited a completely different intracellular pool of amino acids and produced a significant amount of
l
-Val in the culture medium. The log-phase Δ
yggS
strain accumulated 2-ketobutyrate, its aminated compound 2-aminobutyrate, and, to a lesser extent,
l
-Val. It also exhibited a 1.3- to 2.6-fold increase in the levels of Ile and Val metabolic enzymes. The fact that similar phenotypes were induced in wild-type
E. coli
by the exogenous addition of 2-ketobutyrate and 2-aminobutyrate indicates that the 2 compounds contribute to the Δ
yggS
phenotypes. We showed that the initial cause of the keto acid imbalance was the reduced availability of coenzyme A (CoA); supplementation with pantothenate, which is a CoA precursor, fully reversed phenotypes conferred by the
yggS
mutation. The plasmid-borne expression of YggS and orthologs from
Bacillus subtilis
,
Saccharomyces cerevisiae
, and humans fully rescued the Δ
yggS
phenotypes. Expression of a mutant YggS lacking PLP-binding ability, however, did not reverse the Δ
yggS
phenotypes. These results demonstrate for the first time that YggS controls Ile and Val metabolism by modulating 2-ketobutyrate and CoA availability. Its function depends on PLP, and it is highly conserved in a wide range species, from bacteria to humans.
Description of a Riboflavin Biosynthetic Gene Variant Prevalent in the Phylum Proteobacteria
Authors: Brutinel Evan D. , Dean Antony M. , Gralnick Jeffrey A. 
Published: October 2013

ABSTRACT

Riboflavin (vitamin B
2
) is the precursor of flavin mononucleotide and flavin adenine dinucleotide, which are cofactors essential for a host of intracellular redox reactions. Microorganisms synthesize flavins
de novo
to fulfill nutritional requirements, but it is becoming increasingly clear that flavins play a wider role in cellular physiology than was previously appreciated. Flavins mediate diverse processes beyond the cytoplasmic membrane, including iron acquisition, extracellular respiration, and interspecies interactions. While investigating the regulation of flavin electron shuttle biosynthesis in the Gram-negative gammaproteobacterium
Shewanella oneidensis
, we discovered that a riboflavin biosynthetic gene (
ribBA
) annotated as encoding a bifunctional 3,4-dihydroxy-2-butanone 4-phosphate (DHBP) synthase/GTP cyclohydrolase II does not possess both functions. The novel gene, renamed
ribBX
here, encodes an amino-terminal DHBP synthase domain. The carboxy-terminal end of RibBX not only lacks GTP cyclohydrolase II activity but also has evolved a different function altogether in
S. oneidensis
, regulating the activity of the DHBP synthase domain. Phylogenetic analysis revealed that the misannotation of
ribBX
as
ribBA
is rampant throughout the phylum
Proteobacteria
(40% of 2,173 annotated
ribBA
genes) and that
ribBX
emerged early in the evolution of this group of microorganisms. We examined the functionality of representative
ribBX
genes from
Beta
-,
Gamma
-, and
Epsilonproteobacteria
and found that, consistent with sequence-based predictions, the encoded GTP cyclohydrolase II domains lack catalytic activity. The persistence of
ribBX
in the genomes of so many phylogenetically divergent bacterial species lends weight to the argument that
ribBX
has evolved a function which lends a selective advantage to the host.
Biochemical Activities of Streptococcus pneumoniae Serotype 2 Capsular Glycosyltransferases and Significance of Suppressor Mutations Affecting the Initiating Glycosyltransferase Cps2E
Authors: James David B. A. , Gupta Kanupriya , Hauser Jocelyn R. , Yother Janet 
Published: October 2013

ABSTRACT

The capsular polysaccharide (CPS) is essential for
Streptococcus pneumoniae
virulence. Its synthesis requires multiple enzymes, and defects that block completion of the pathway can be lethal in the absence of secondary suppressor mutations. In this study, we examined the functions of three capsular glycosyltransferases (Cps2F, Cps2G, and Cps2I) involved in serotype 2 CPS synthesis, whose deletions select for secondary mutations. We demonstrate that Cps2F is a rhamnosyltransferase that catalyzes addition of the third and fourth sugars in the capsule repeat unit, while Cps2G adds the fifth sugar (glucose). Addition of the terminal residue (glucuronic acid) could not be detected; however, activities of the other glycosyltransferases together with bioinformatic analyses suggest that this step is mediated by Cps2I. Most of the secondary suppressor mutations resulting from loss of these enzymes occur in
cps2E
, the gene encoding the initiating glycosyltransferase. Examination of the 69
S. pneumoniae
serotypes containing Cps2E homologues yielded a consensus amino acid sequence for this protein and demonstrated that there is a highly significant association between the residues that are 100% conserved and those altered by suppressor mutations. Cps2E contains an extracytoplasmic loop whose function is unknown. Among our collection of mutants, six contained missense mutations affecting amino acids in the extracytoplasmic loop. These residues are highly conserved among
S. pneumoniae
Cps2E homologues, and mutations therein severely reduced CPS synthesis and Cps2E activity. The critical functions of these amino acids suggest a role for the Cps2E extracytoplasmic loop in initiation, and possibly regulation, of capsule synthesis.
Pseudomonas aeruginosa AlgR Phosphorylation Modulates Rhamnolipid Production and Motility
Authors: Okkotsu Yuta , Tieku Prince , Fitzsimmons Liam F. , Churchill Mair E. , Schurr Michael J. 
Published: October 2013

ABSTRACT

AlgR is a key
Pseudomonas aeruginosa
transcriptional response regulator required for virulence. AlgR activates alginate production and twitching motility but represses the Rhl quorum-sensing (QS) system, including rhamnolipid production. The role of AlgR phosphorylation is enigmatic, since phosphorylated AlgR (AlgR-P) is required for twitching motility through the
fimU
promoter but is not required for the activation of alginate production. In order to examine the role of AlgR phosphorylation
in vivo
, a PAO1
algR
D54E strain (with
algR
encoding a D-to-E change at position 54), which constitutively activates
fimU
transcription and exhibits twitching motility, was created. A corresponding PAO1
algR
D54N strain (with
algR
encoding a D-to-N change at position 54) that does not activate
fimU
or twitching motility was compared to PAO1, PAO1
algR
D54E, PAO1 Δ
algZ
(deletion of the
algZ
[
fimS
] gene, encoding a putative histidine kinase), and PAO1 Δ
algR
for swarming motility, rhamnolipid production, and
rhlA
transcription. PAO1 and PAO1
algR
D54E produced approximately 2-fold-higher levels of rhamnolipids than PAO1
algR
D54N and PAO1 Δ
algZ
, thereby indicating that phosphorylated AlgR is required for normal rhamnolipid production. Examination of purified AlgR, AlgR-P, AlgR D54N, and AlgR D54E showed that AlgR-P and AlgR D54E bound preferentially to the
fimU
and
rhlA
promoters. Additionally, AlgR-P bound specifically to two sites within the
rhlA
promoter that were not bound by unphosphorylated AlgR. Taken together, these results indicate that phosphorylated AlgR-P has increased affinity for the
rhlA
promoter and is required for the coordinate activation of twitching motility, rhamnolipid production, and swarming motility in
P. aeruginosa
.
Cellulose as an Architectural Element in Spatially Structured Escherichia coli Biofilms
Authors: Serra Diego O. , Richter Anja M. , Hengge Regine 
Published: October 2013

ABSTRACT

Morphological form in multicellular aggregates emerges from the interplay of genetic constitution and environmental signals. Bacterial macrocolony biofilms, which form intricate three-dimensional structures, such as large and often radially oriented ridges, concentric rings, and elaborate wrinkles, provide a unique opportunity to understand this interplay of “nature and nurture” in morphogenesis at the molecular level. Macrocolony morphology depends on self-produced extracellular matrix components. In
Escherichia coli
, these are stationary phase-induced amyloid curli fibers and cellulose. While the widely used “domesticated”
E. coli
K-12 laboratory strains are unable to generate cellulose, we could restore cellulose production and macrocolony morphology of
E. coli
K-12 strain W3110 by “repairing” a single chromosomal SNP in the
bcs
operon. Using scanning electron and fluorescence microscopy, cellulose filaments, sheets and nanocomposites with curli fibers were localized
in situ
at cellular resolution within the physiologically two-layered macrocolony biofilms of this “de-domesticated” strain. As an architectural element, cellulose confers cohesion and elasticity, i.e., tissue-like properties that—together with the cell-encasing curli fiber network and geometrical constraints in a growing colony—explain the formation of long and high ridges and elaborate wrinkles of wild-type macrocolonies. In contrast, a biofilm matrix consisting of the curli fiber network only is brittle and breaks into a pattern of concentric dome-shaped rings separated by deep crevices. These studies now set the stage for clarifying how regulatory networks and in particular c-di-GMP signaling operate in the three-dimensional space of highly structured and “tissue-like” bacterial biofilms.
Injury rate and injury pattern among elite World Cup snowboarders: a 6-year cohort study
Authors: Major D H , Steenstrup S E , Bere T , Bahr R , Nordsletten L 
Published: October 2013

BackgroundThere is limited knowledge on the injury rate and injury pattern in the different disciplines among elite snowboarders.ObjectiveThe aim of this study was to describe and compare the injury rate and injury pattern among the different International Ski Federation (Fédération Internationale de Ski, FIS) World Cup (WC) snowboard disciplines.MethodsWe conducted retrospective interviews with FIS WC snowboard athletes at the end of each season in the period 2007–2012, to register all acute injuries sustained during training or competition during the competitive season requiring attention by medical personnel. To calculate the exposure, we obtained information from result lists from the FIS competition database for all WC competitions for each of the interviewed athletes.ResultsWe registered a total of 574 injuries among 1432 athletes, accounting for an overall injury rate of 40.1 injuries/100 athlete/season. A total of 171 injuries occurred during the FIS WC competitions, corresponding to 6.4 injuries/1000 runs. During competition, injury risk was highest in snowboard cross with 11.9/1000 runs, followed by 6.3 in halfpipe, 3.6 in big air and 2.8 in parallel giant slalom/parallel slalom (PGS/PSL). Snowboard cross also had the highest risk of severe injuries (>28 days absence). No differences in injury risk were detected between male and female snowboarders. The most commonly injured body part was the knee (17.8%), followed by the shoulder/clavicle (13.4%) and head/face (13.2%). The risk of knee injury (the most common injury type) and head injury was significantly higher in snowboard cross and halfpipe compared to PGS/PSL.ConclusionsThe risk of injuries was higher in snowboard cross than in halfpipe, big air and PGS/PSL. The most commonly injured body part was the knee. Prevention of snowboard injuries among elite snowboarders should focus on knee injuries, severe injuries and snowboard cross athletes.