bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Known and Novel Adenoviruses in Cattle Wastes via Broad-Spectrum Primers
Authors: Sibley Samuel D. , Goldberg Tony L. , Pedersen Joel A. 
Published: May 2011

ABSTRACTThe critical assessment of bovine adenoviruses (BAdV) as indicators of environmental fecal contamination requires improved knowledge of their prevalence, shedding dynamics, and genetic diversity. We examined DNA extracted from bovine and other animal waste samples collected in Wisconsin for atadenoviruses and mastadenoviruses using novel, broad-spectrum PCR primer sets. BAdV were detected in 13% of cattle fecal samples, 90% of cattle urine samples, and 100% of cattle manure samples; 44 percent of BAdV-positive samples contained bothAtadenovirusandMastadenovirusDNA. Additionally, BAdV were detected in soil, runoff water from a cattle feedlot, and residential well water. Overall, we detected 8 of 11 prototype BAdV, plus bovine, rabbit, and porcine mastadenoviruses that diverged significantly from previously reported genotypes. The prevalence of BAdV shedding by cattle supports targeting AdV broadly as indicators of the presence of fecal contamination in aqueous environments. Conversely, several factors complicate the use of AdV for fecal source attribution. Animal AdV infecting a given livestock host were not monophyletic, recombination among livestock mastadenoviruses was detected, and the genetic diversity of animal AdV is still underreported. These caveats highlight the need for continuing genetic surveillance for animal AdV and for supporting data when BAdV detection is invoked for fecal source attribution in environmental samples. To our knowledge, this is the first study to report natural BAdV excretion in urine, BAdV detection in groundwater, and recombination in AdV of livestock origin.
Control of Bacterial Persister Cells by Trp/Arg-Containing Antimicrobial Peptides
Authors: Chen Xi , Zhang Mi , Zhou Chunhui , Kallenbach Neville R. , Ren Dacheng 
Published: May 2011

ABSTRACT

Persister cells are dormant phenotypic variants inherent in a bacterial population. They play important roles in chronic infections and present great challenges to therapy due to extremely enhanced tolerance to antibiotics compared to that of normal cells of the same genotype. In this study, we report that cationic membrane-penetrating peptides containing various numbers of arginine and tryptophan repeats are effective in killing persister cells of
Escherichia coli
HM22, a hyper-persister producer. The activities of three linear peptides [(RW)

n

-NH
2
, where
n
is 2, 3, or 4] and a dendrimeric peptide, (RW)
4D
, in killing bacterial persisters were compared. Although the dendrimeric peptide (RW)
4D
requires a lower threshold to kill planktonic persisters, octameric peptide (RW)
4
-NH
2
is the most effective against planktonic persister cells at high concentrations. For example, treatment with 80 μM (RW)
4
-NH
2
for 60 min led to a 99.7% reduction in the number of viable persister cells. The viability of persister cells residing in surface-attached biofilms was also significantly reduced by (RW)
4
-NH
2
and (RW)
4D
. These two peptides were also found to significantly enhance the susceptibility of biofilm cells to ofloxacin. The potency of (RW)
4
-NH
2
was further marked by its ability to disperse and kill preformed biofilms harboring high percentages of persister cells. Interestingly, approximately 70% of the dispersed cells were found to have lost their intrinsic tolerance and become susceptible to ampicillin if not killed directly by this peptide. These results are helpful for better understanding the activities of these peptides and may aid in future development of more effective therapies of chronic infections.
Assembly of Minicellulosomes on the Surface of Bacillus subtilis
Authors: Anderson Timothy D. , Robson Scott A. , Jiang Xiao Wen , Malmirchegini G. Reza , Fierobe Henri-Pierre , Lazazzera Beth A. , Clubb Robert T. 
Published: May 2011

ABSTRACT

To cost-efficiently produce biofuels, new methods are needed to convert lignocellulosic biomass into fermentable sugars. One promising approach is to degrade biomass using cellulosomes, which are surface-displayed multicellulase-containing complexes present in cellulolytic
Clostridium
and
Ruminococcus
species. In this study we created cellulolytic strains of
Bacillus subtilis
that display one or more cellulase enzymes. Proteins containing the appropriate cell wall sorting signal are covalently anchored to the peptidoglycan by coexpressing them with the
Bacillus anthracis
sortase A (SrtA) transpeptidase. This approach was used to covalently attach the Cel8A endoglucanase from
Clostridium thermocellum
to the cell wall. In addition, a Cel8A-dockerin fusion protein was anchored on the surface of
B. subtilis
via noncovalent interactions with a cell wall-attached cohesin module. We also demonstrate that it is possible to assemble multienzyme complexes on the cell surface. A three-enzyme-containing minicellulosome was displayed on the cell surface; it consisted of a cell wall-attached scaffoldin protein noncovalently bound to three cellulase-dockerin fusion proteins that were produced in
Escherichia coli
.
B. subtilis
has a robust genetic system and is currently used in a wide range of industrial processes. Thus, grafting larger, more elaborate minicellulosomes onto the surface of
B. subtilis
may yield cellulolytic bacteria with increased potency that can be used to degrade biomass.
Saccharomyces cerevisiae Genome Shuffling through Recursive Population Mating Leads to Improved Tolerance to Spent Sulfite Liquor
Authors: Pinel Dominic , D'Aoust Frédéric , del Cardayre Stephen B. , Bajwa Paramjit K. , Lee Hung , Martin Vincent J. J. 
Published: May 2011

ABSTRACT

Spent sulfite liquor (SSL) is a waste effluent from sulfite pulping that contains monomeric sugars which can be fermented to ethanol. However, fermentative yeasts used for the fermentation of the sugars in SSL are adversely affected by the inhibitory substances in this complex feedstock. To overcome this limitation, evolutionary engineering of
Saccharomyces cerevisiae
was carried out using genome-shuffling technology based on large-scale population cross mating. Populations of UV-light-induced yeast mutants more tolerant than the wild type to hardwood spent sulfite liquor (HWSSL) were first isolated and then recursively mated and enriched for more-tolerant populations. After five rounds of genome shuffling, three strains were isolated that were able to grow on undiluted HWSSL and to support efficient ethanol production from the sugars therein for prolonged fermentation of HWSSL. Analyses showed that greater HWSSL tolerance is associated with improved viability in the presence of salt, sorbitol, peroxide, and acetic acid. Our results showed that evolutionary engineering through genome shuffling will yield robust yeasts capable of fermenting the sugars present in HWSSL, which is a complex substrate containing multiple sources of inhibitors. These strains may not be obtainable through classical evolutionary engineering and can serve as a model for further understanding of the mechanism behind simultaneous tolerance to multiple inhibitors.
Development of a Multilocus Sequence Typing Tool for High-Resolution Genotyping of Enterocytozoon bieneusi
Authors: Feng Yaoyu , Li Na , Dearen Theresa , Lobo Maria L. , Matos Olga , Cama Vitaliano , Xiao Lihua 
Published: May 2011

ABSTRACT

Thus far, genotyping of
Enterocytozoon bieneusi
has been based solely on DNA sequence analysis of the internal transcribed spacer (ITS) of the rRNA gene. Both host-adapted and zoonotic (human-pathogenic) genotypes of
E. bieneusi
have been identified. In this study, we searched for microsatellite and minisatellite sequences in the whole-genome sequence database of
E. bieneusi
isolate H348. Seven potential targets (MS1 to MS7) were identified. Testing of the seven targets by PCR using two human-pathogenic
E. bieneusi
genotypes (A and Peru10) led to the selection of four targets (MS1, MS3, MS4, and MS7). Further analysis of the four loci with an additional 24 specimens of both host-adapted and zoonotic
E. bieneusi
genotypes indicated that most host-adapted genotypes were not amplified by PCR targeting these loci. In contrast, 10 or 11 of the 13 specimens of the zoonotic genotypes were amplified by PCR at each locus. Altogether, 12, 8, 7, and 11 genotypes of were identified at MS1, MS3, MS4, and MS7, respectively. Phylogenetic analysis of the nucleotide sequences obtained produced a genetic relationship that was similar to the one at the ITS locus, with the formation of a large group of zoonotic genotypes that included most
E. bieneusi
genotypes in humans. Thus, a multilocus sequence typing tool was developed for high-resolution genotyping of
E. bieneusi.
Data obtained in the study should also have implications for understanding the taxonomy of
Enterocytozoon
spp., the public health significance of
E. bieneusi
in animals, and the sources of human
E. bieneusi
infections.
Role Played by Exosporium Glycoproteins in the Surface Properties of Bacillus cereus Spores and in Their Adhesion to Stainless Steel
Authors: Lequette Yannick , Garénaux Estelle , Tauveron Grégoire , Dumez Sylvain , Perchat Stéphane , Slomianny Christian , Lereclus Didier , Guérardel Yann , Faille Christine 
Published: May 2011

ABSTRACT

Bacillus cereus
spores are surrounded by a loose-fitting layer called the exosporium, whose distal part is mainly formed from glycoproteins. The role played by the exosporium glycoproteins of
B. cereus
ATCC 14579 (BclA and ExsH) was investigated by considering hydrophobicity and charge, as well as the properties of spore adhesion to stainless steel. The absence of BclA increased both the isoelectric point (IEP) and hydrophobicity of whole spores while simultaneously reducing the interaction between spores and stainless steel. However, neither the hydrophobicity nor the charge associated with BclA could explain the differences in the adhesion properties. Conversely, ExsH, another exosporium glycoprotein, did not play a significant role in spore surface properties. The monosaccharide analysis of
B. cereus
ATCC 14579 showed different glycosylation patterns on ExsH and BclA. Moreover, two specific glycosyl residues, namely, 2-
O
-methyl-rhamnose (2-Me-Rha) and 2,4-
O
-methyl-rhamnose (2,4-Me-Rha), were attached to BclA, in addition to the glycosyl residues already reported in
B. anthracis
.
Evaluation of Physical Coverings Used To Control Escherichia coli O157:H7 at the Compost Heap Surface
Authors: Shepherd Marion W. , Kim Jinkyung , Jiang Xiuping , Doyle Michael P. , Erickson Marilyn C. 
Published: May 2011

ABSTRACT

Throughout four field trials, compost heaps covered with finished compost maintained temperatures under the physical covering that were ca. 7 to 15.5°C higher, resulting in rapid
Escherichia coli
O157:H7 reduction, than those of the heaps covered with fresh straw or left uncovered. Our results validated recommendations made by the U.S. Environmental Protection Agency for covering fresh compost.
Cholesterol Degradation by Gordonia cholesterolivorans
Authors: Drzyzga O. , Fernández de las Heras L. , Morales V. , Navarro Llorens J. M. , Perera J. 
Published: May 2011

ABSTRACT

This paper reports physiological and genetic data about the type strain
Gordonia cholesterolivorans
, a strain that is able to degrade steroid compounds containing a long carbon side chain such as cholesterol (C
27
), cholestenone (C
27
), ergosterol (C
28
), and stigmasterol (C
29
). The length of the carbon side chain appears to be of great importance for this bacterium, as the strain is unable to grow using steroids with a shorter or nonaliphatic carbon side chain such as cholic acid (C
24
), progesterone (C
21
), testosterone, androsterone, 4-androstene-3,17-dione (all C
19
), and further steroids. This study also demonstrates that the degradation of cholesterol is a quite common feature of the genus
Gordonia
by comparing
Gordonia
cholesterolivorans
with some other species of this genus (e.g.,
G. sihwensis
,
G. hydrophobica
,
G. australis
, and
G. neofelifaecis
). Pyrosequencing of the genome of
G. cholesterolivorans
led to the identification of two conventional cholesterol oxidase genes on an 8-kb and a 12.8-kb genomic fragment with genetic organizations that are quite unique as compared to the genomes of other cholesterol-degrading bacteria sequenced so far. The identified two putative cholesterol oxidases of
G. cholesterolivorans
are both intracellularly acting enzymes of the class I type. Whereas one of these two cholesterol oxidases (ChoOx-1) shows high identity with an oxidoreductase of the opportunistic pathogen
G. bronchialis
and is not transcribed during growth with cholesterol, the other one (ChoOx-2) appears phylogenetically closer to cholesterol oxidases from members of the genus
Rhodococcus
and is transcribed constitutively. By using targeted gene disruption, a
G. cholesterolivorans
ChoOx-2 gene mutant strain that was unable to grow with steroids was obtained.
Role of Hsl7 in Morphology and Pathogenicity and Its Interaction with Other Signaling Components in the Plant Pathogen Ustilago maydis
Authors: Lovely C. Ben , Aulakh Kavita Burman , Perlin Michael H. 
Published: May 2011

ABSTRACT

The phytopathogenic fungus
Ustilago maydis
undergoes a dimorphic transition in response to mating pheromone, host, and environmental cues. On a solid medium deficient in ammonium (SLAD [0.17% yeast nitrogen base without ammonium sulfate or amino acids, 2% dextrose, 50 μM ammonium sulfate]),
U. maydis
produces a filamentous colony morphology, while in liquid SLAD, the cells do not form filaments. The p21-activated protein kinases (PAKs) play a substantial role in regulating the dimorphic transition in fungi. The PAK-like Ste20 homologue Smu1 is required for a normal response to pheromone, via upregulation of pheromone expression, and virulence, and its disruption affects both processes. Our experiments suggest that Smu1 also regulates cell length and the filamentous response on solid SLAD medium. Yeast two-hybrid analysis suggested an Hsl7 homologue as a potential interacting partner of Smu1, and a unique open reading frame for such an arginine methyltransferase was detected in the
U. maydis
genome sequence. Hsl7 regulates cell length and the filamentous response to solid SLAD in a fashion opposite to that of Smu1, but neither overexpression nor disruption of
hsl7
attenuates virulence. Simultaneous disruption of
hsl7
and overexpression of
smu1
lead to a hyperfilamentous response on solid SLAD. Moreover, only this double mutant strain forms filaments in liquid SLAD. The double mutant strain was also significantly reduced in virulence. A similar filamentous response in both solid and liquid SLAD was observed in strains lacking another PAK-like protein kinase involved in cytokinesis and polar growth, Cla4. Our data suggest that Hsl7 may regulate cell cycle progression, while both Smu1 and Cla4 appear to be involved in the filamentous response in
U. maydis
.
Do Red and Green Make Brown?: Perspectives on Plastid Acquisitions within Chromalveolates
Authors: Dorrell Richard G. , Smith Alison G. 
Published: May 2011

ABSTRACT
The chromalveolate “supergroup” is of key interest in contemporary phycology, as it contains the overwhelming majority of extant algal species, including several phyla of key importance to oceanic net primary productivity such as diatoms, kelps, and dinoflagellates. There is also intense current interest in the exploitation of these algae for industrial purposes, such as biodiesel production. However, the evolution of the constituent species, and in particular the origin and radiation of the chloroplast genomes, remains poorly understood. In this review, we discuss current theories of the origins of the extant red alga-derived chloroplast lineages in the chromalveolates and the potential ramifications of the recent discovery of large numbers of green algal genes in chromalveolate genomes. We consider that the best explanation for this is that chromalveolates historically possessed a cryptic green algal endosymbiont that was subsequently replaced by a red algal chloroplast. We consider how changing selective pressures acting on ancient chromalveolate lineages may have selectively favored the serial endosymbioses of green and red algae and whether a complex endosymbiotic history facilitated the rise of chromalveolates to their current position of ecological prominence.
Effects of Fluconazole on the Secretome, the Wall Proteome, and Wall Integrity of the Clinical Fungus Candida albicans
Authors: Sorgo Alice G. , Heilmann Clemens J. , Dekker Henk L. , Bekker Martijn , Brul Stanley , de Koster Chris G. , de Koning Leo J. , Klis Frans M. 
Published: May 2011

ABSTRACT

Fluconazole is a commonly used antifungal drug that inhibits Erg11, a protein responsible for 14α-demethylation during ergosterol synthesis. Consequently, ergosterol is depleted from cellular membranes and replaced by toxic 14α-methylated sterols, which causes increased membrane fluidity and drug permeability. Surface-grown and planktonic cultures of
Candida albicans
responded similarly to fluconazole at 0.5 mg/liter, showing reduced biomass formation, severely reduced ergosterol levels, and almost complete inhibition of hyphal growth. There was no evidence of cell leakage. Mass spectrometric analysis of the secretome showed that its composition was strongly affected and included 17 fluconazole-specific secretory proteins. Relative quantification of
14
N-labeled query walls relative to a reference standard mixture of
15
N-labeled yeast and hyphal walls in combination with immunological analysis revealed considerable fluconazole-induced changes in the wall proteome as well. They were, however, similar for both surface-grown and planktonic cultures. Two major trends emerged: (i) decreased incorporation of hypha-associated wall proteins (Als3, Hwp1, and Plb5), consistent with inhibition of hyphal growth, and (ii) increased incorporation of putative wall repair-related proteins (Crh11, Pga4, Phr1, Phr2, Pir1, and Sap9). As exposure to the wall-perturbing drug Congo red led to a similar response, these observations suggested that fluconazole affects the wall. In keeping with this, the resistance of fluconazole-treated cells to wall-perturbing compounds decreased. We propose that fluconazole affects the integrity of both the cellular membranes and the fungal wall and discuss its potential consequences for antifungal therapy. We also present candidate proteins from the secretome for clinical marker development.
Activity Control of the ClpC Adaptor McsB in Bacillus subtilis
Authors: Elsholz A. K. W. , Hempel K. , Michalik S. , Gronau K. , Becher D. , Hecker M. , Gerth U. 
Published: May 2011

ABSTRACT

Controlled protein degradation is an important cellular reaction for the fast and efficient adaptation of bacteria to ever-changing environmental conditions. In the low-GC, Gram-positive model organism
Bacillus subtilis
, the AAA+ protein ClpC requires specific adaptor proteins not only for substrate recognition but also for chaperone activity. The McsB adaptor is activated particularly during heat stress, allowing the controlled degradation of the CtsR repressor by the ClpCP protease. Here we report how the McsB adaptor becomes activated by autophosphorylation on specific arginine residues during heat stress. In nonstressed cells McsB activity is inhibited by ClpC as well as YwlE.
Comparative Genomic Analysis of the Hexuronate Metabolism Genes and Their Regulation in Gammaproteobacteria
Authors: Suvorova Inna A. , Tutukina Maria N. , Ravcheev Dmitry A. , Rodionov Dmitry A. , Ozoline Olga N. , Gelfand Mikhail S. 
Published: May 2011

ABSTRACT

The hexuronate metabolism in
Escherichia coli
is regulated by two related transcription factors from the FadR subfamily of the GntR family, UxuR and ExuR. UxuR controls the
d
-glucuronate metabolism, while ExuR represses genes involved in the metabolism of all hexuronates. We use a comparative genomics approach to reconstruct the hexuronate metabolic pathways and transcriptional regulons in gammaproteobacteria. We demonstrate differences in the binding motifs of UxuR and ExuR, identify new candidate members of the UxuR/ExuR regulons, and describe the links between the UxuR/ExuR regulons and the adjacent regulons UidR, KdgR, and YjjM. We provide experimental evidence that two predicted members of the UxuR regulon,
yjjM
and
yjjN
, are the subject of complex regulation by this transcription factor in
E. coli
.
TdaA Regulates Tropodithietic Acid Synthesis by Binding to the
tdaC
Promoter Region
Authors: Geng Haifeng , Belas Robert 
Published: May 2011

ABSTRACT

Silicibacter
sp. TM1040, a member of the marine
Roseobacter
clade, produces the antibiotic and quorum signaling molecule tropodithietic acid (TDA), encoded by
tdaABCDEF
. Here, we showed that an LysR-type transcriptional regulator, TdaA, is a positive regulator of
tdaCDE
gene expression and binds to the
tdaC
promoter region.
Genetic Variation of Adenylation Domains of the Anabaenopeptin Synthesis Operon and Evolution of Substrate Promiscuity
Authors: Christiansen Guntram , Philmus Benjamin , Hemscheidt Thomas , Kurmayer Rainer 
Published: May 2011

ABSTRACT

Anabaenopeptins (AP) are bioactive cyclic hexapeptides synthesized nonribosomally in cyanobacteria. APs are characterized by several conserved motifs, including the ureido bond, N-methylation in position 5, and
d
-Lys in position 2. All other positions of the AP molecule are variable, resulting in numerous structural variants. We have identified a nonribosomal peptide synthetase (NRPS) operon from
Planktothrix agardhii
strain CYA126/8 consisting of five genes (
apnA
to
apnE
) encoding six NRPS modules and have confirmed its role in AP synthesis by the generation of a mutant via insertional inactivation of
apnC
. In order to correlate the genetic diversity among adenylation domains (A domains) with AP structure variation, we sequenced the A domains of all six NRPS modules from seven
Planktothrix
strains differing in the production of AP congeners. It is remarkable that single strains coproduce APs bearing either of the chemically divergent amino acids Arg and Tyr in exocyclic position 1. Since the A domain of the initiation module (the ApnA A
1
domain) has been proposed to activate the amino acid incorporated into exocyclic position 1, we decided to analyze this domain both biochemically and phylogenetically. Only ApnA A
1
enzymes from strains producing AP molecules containing Arg or Tyr in position 1 were found to activate these two chemically divergent amino acids
in vitro
. Phylogenetic analysis of
apn
A domain sequences revealed that strains with a promiscuous ApnA A
1
domain are derived from an ancestor that activates only Arg. Surprisingly, positive selection appears to affect only three codons within the
apnA
A
1
gene, suggesting that this remarkable promiscuity has evolved from point mutations only.