bluuebunny/crossref_metadata_2025 huggingface dataset:
Polyphasic Characterization of a Thermotolerant Siderophilic Filamentous Cyanobacterium That Produces Intracellular Iron Deposits
Authors: Brown Igor I. , Bryant Donald A. , Casamatta Dale , Thomas-Keprta Kathie L. , Sarkisova Svetlana A. , Shen Gaozhong , Graham Joel E. , Boyd Eric S. , Peters John W. , Garrison Daniel H. , McKay David S.
Published: August 2010

Despite the high potential for oxidative stress stimulated by reduced iron, contemporary iron-depositing hot springs with circum-neutral pH are intensively populated with cyanobacteria. Therefore, studies of the physiology, diversity, and phylogeny of cyanobacteria inhabiting iron-depositing hot springs may provide insights into the contribution of cyanobacteria to iron redox cycling in these environments and new mechanisms of oxidative stress mitigation. In this study the morphology, ultrastructure, physiology, and phylogeny of a novel cyanobacterial taxon, JSC-1, isolated from an iron-depositing hot spring, were determined. The JSC-1 strain has been deposited in ATCC under the name
Marsacia ferruginose
, accession number BAA-2121. Strain JSC-1 represents a new operational taxonomical unit (OTU) within
Leptolyngbya
sensu lato. Strain JSC-1 exhibited an unusually high ratio between photosystem (PS) I and PS II, was capable of complementary chromatic adaptation, and is apparently capable of nitrogen fixation. Furthermore, it synthesized a unique set of carotenoids, but only chlorophyll
a
. Strain JSC-1 not only required high levels of Fe for growth (≥40 μM), but it also accumulated large amounts of extracellular iron in the form of ferrihydrite and intracellular iron in the form of ferric phosphates. Collectively, these observations provide insights into the physiological strategies that might have allowed cyanobacteria to develop and proliferate in Fe-rich, circum-neutral environments.
Improving Biocatalyst Performance by Integrating Statistical Methods into Protein Engineering
Authors: Brouk Moran , Nov Yuval , Fishman Ayelet
Published: August 2010

Directed evolution and rational design were used to generate active variants of toluene-4-monooxygenase (T4MO) on 2-phenylethanol (PEA), with the aim of producing hydroxytyrosol, a potent antioxidant. Due to the complexity of the enzymatic system—four proteins encoded by six genes—mutagenesis is labor-intensive and time-consuming. Therefore, the statistical model of Nov and Wein (J. Comput. Biol. 12:247-282) was used to reduce the number of variants produced and evaluated in a lab. From an initial data set of 24 variants, with mutations at nine positions, seven double or triple mutants were identified through statistical analysis. The average activity of these mutants was 4.6-fold higher than the average activity of the initial data set. In an attempt to further improve the enzyme activity to obtain PEA hydroxylation, a second round of statistical analysis was performed. Nine variants were considered, with 3, 4, and 5 point mutations. The average activity of the variants obtained in the second statistical round was 1.6-fold higher than in the first round and 7.3-fold higher than that of the initial data set. The best variant discovered, TmoA I100A E214G D285Q, exhibited an initial oxidation rate of 4.4 ± 0.3 nmol/min/mg protein, which is 190-fold higher than the rate obtained by the wild type. This rate was also 2.6-fold higher than the activity of the wild type on the natural substrate toluene. By considering only 16 preselected mutants (out of ∼13,000 possible combinations), a highly active variant was discovered with minimum time and effort.
A Targeted Multilocus Genotyping Assay for Lineage, Serogroup, and Epidemic Clone Typing of
Listeria monocytogenes
Authors: Ward Todd J. , Usgaard Thomas , Evans Peter
Published: August 2010

A 30-probe assay was developed for simultaneous classification of
Listeria monocytogenes
isolates by lineage (I to IV), major serogroup (4b, 1/2b, 1/2a, and 1/2c), and epidemic clone (EC) type (ECI, ECIa, ECII, and ECIII). The assay was designed to facilitate rapid strain characterization and the integration of subtype data into risk-based inspection programs.
High Stability and Fast Recovery of Expression of the TOL Plasmid-Carried Toluene Catabolism Genes of
Pseudomonas putida
mt-2 under Conditions of Oxygen Limitation and Oscillation
Authors: Martínez-Lavanchy Paula M. , Müller Christina , Nijenhuis Ivonne , Kappelmeyer Uwe , Buffing Marieke , McPherson Kyle , Heipieper Hermann J.
Published: August 2010

Pseudomonas putida
mt-2 harbors the TOL plasmid (pWWO), which contains the genes encoding the enzymes necessary to degrade toluene aerobically. The
xyl
genes are clustered in the upper operon and encode the enzymes of the upper pathway that degrade toluene to benzoate, while the genes encoding the enzymes of the lower pathway (
meta
-cleavage pathway) that are necessary for the conversion of benzoate to tricarboxylic acid cycle intermediates, are encoded in a separate operon. In this study, the effects of oxygen availability and oscillation on the expression of catabolic genes for enzymes involved in toluene degradation were studied by using
P. putida
mt-2 as model bacterium. Quantitative reverse transcription-PCR was used to detect and quantify the expression of the catabolic genes
xylM
(a key gene of the upper pathway) and
xylE
(a key gene of the lower pathway) in cultures of
P. putida
mt-2 that were grown with toluene as a carbon source. Toluene degradation was shown to have a direct dependency on oxygen concentration, where gene expression of
xylM
and
xylE
decreased due to oxygen depletion during degradation. Under oscillating oxygen concentrations,
P. putida
mt-2 induced or downregulated
xylM
and
xylE
genes according to the O
2
availability in the media. During anoxic periods,
P. putida
mt-2 decreased the expression of
xylM
and
xylE
genes, while the expression of both
xylM
and
xylE
genes was immediately increased after oxygen became available again in the medium. These results suggest that oxygen is not only necessary as a cosubstrate for enzyme activity during the degradation of toluene but also that oxygen modulates the expression of the catabolic genes encoded by the TOL plasmid.
Decontamination Options for
Bacillus anthracis
-Contaminated Drinking Water Determined from Spore Surrogate Studies
Authors: Raber Ellen , Burklund Alison
Published: August 2010

Five parameters were evaluated with surrogates of
Bacillus anthracis
spores to determine effective decontamination alternatives for use in a contaminated drinking water supply. The parameters were as follows: (i) type of
Bacillus
spore surrogate (
B. thuringiensis
or
B. atrophaeus
), (ii) spore concentration in suspension (10
2
and 10
6
spores/ml), (iii) chemical characteristics of the decontaminant (sodium dichloro-
S
-triazinetrione dihydrate [Dichlor], hydrogen peroxide, potassium peroxymonosulfate [Oxone], sodium hypochlorite, and VirkonS), (iv) decontaminant concentration (0.01% to 5%), and (v) exposure time to decontaminant (10 min to 1 h). Results from 138 suspension tests with appropriate controls are reported. Hydrogen peroxide at a concentration of 5% and Dichlor or sodium hypochlorite at a concentration of 2% were highly effective at spore inactivation regardless of spore type tested, spore exposure time, or spore concentration evaluated. This is the first reported study of Dichlor as an effective decontaminant for
B. anthracis
spore surrogates. Dichlor's desirable characteristics of high oxidation potential, high level of free chlorine, and a more neutral pH than that of other oxidizers evaluated appear to make it an excellent alternative. All three oxidizers were effective against
B. atrophaeus
spores in meeting the EPA biocide standard of greater than a 6-log kill after a 10-min exposure time and at lower concentrations than typically reported for biocide use. Solutions of 5% VirkonS and Oxone were less effective as decontaminants than other options evaluated in this study and did not meet the EPA's efficacy standard for a biocide, although they were found to be as effective for concentrations of 10
2
spores/ml. Differences in methods and procedures reported by other investigators make quantitative comparisons among studies difficult.
Functional Characterization of pGKT2, a 182-Kilobase Plasmid Containing the
xplAB
Genes, Which Are Involved in the Degradation of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine by
Gordonia
sp. Strain KTR9
Authors: Indest Karl J. , Jung Carina M. , Chen Hao-Ping , Hancock Dawn , Florizone Christine , Eltis Lindsay D. , Crocker Fiona H.
Published: August 2010

Several microorganisms have been isolated that can transform hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a cyclic nitramine explosive. To better characterize the microbial genes that facilitate this transformation, we sequenced and annotated a 182-kb plasmid, pGKT2, from the RDX-degrading strain
Gordonia
sp. KTR9. This plasmid carries
xplA
, encoding a protein sharing up to 99% amino acid sequence identity with characterized RDX-degrading cytochromes P450. Other genes that cluster with
xplA
are predicted to encode a glutamine synthase-XplB fusion protein, a second cytochrome P450, Cyp151C, and XplR, a GntR-type regulator.
Rhodococcus jostii
RHA1 expressing
xplA
from KTR9 degraded RDX but did not utilize RDX as a nitrogen source. Moreover, an
Escherichia coli
strain producing XplA degraded RDX but a strain producing Cyp151C did not. KTR9 strains cured of pGKT2 did not transform RDX. Physiological studies examining the effects of exogenous nitrogen sources on RDX degradation in strain KTR9 revealed that ammonium, nitrite, and nitrate each inhibited RDX degradation by up to 79%. Quantitative real-time PCR analysis of
glnA-xplB
,
xplA
, and
xplR
showed that transcript levels were 3.7-fold higher during growth on RDX than during growth on ammonium and that this upregulation was repressed in the presence of various inorganic nitrogen sources. Overall, the results indicate that RDX degradation by KTR9 is integrated with central nitrogen metabolism and that the uptake of RDX by bacterial cells does not require a dedicated transporter.
Comparison of Single- and Multilocus Genetic Diversity in the Protozoan Parasites
Cryptosporidium parvum
and
C. hominis
Authors: Widmer Giovanni , Lee Yongsun
Published: August 2010

The genotyping of numerous isolates of
Cryptosporidium
parasites has led to the definition of new species and a better understanding of the epidemiology of cryptosporidiosis. A single-locus genotyping method based on the partial sequence of a polymorphic sporozoite surface glycoprotein gene (
GP60
) has been favored by many for surveying
Cryptosporidium parvum
and
C. hominis
populations. Since genetically distinct
Cryptosporidium
parasites recombine in nature, it is unclear whether single-locus classifications can adequately represent intraspecies diversity. To address this question, we investigated whether multilocus genotypes of
C. parvum
and
C. hominis
cluster according to the
GP60
genotype.
C. hominis
multilocus genotypes did not segregate according to this marker, indicating that for this species the
GP60
sequence is not a valid surrogate for multilocus typing methods. In contrast, in
C. parvum
the previously described “anthroponotic” genotype was confirmed as a genetically distinct subspecies cluster characterized by a diagnostic GP60 allele. However, as in
C. hominis
, several
C. parvum
GP60 alleles did not correlate with distinct subpopulations. Given the rarity of some
C. parvum
GP60 alleles in our sample, the existence of additional
C. parvum
subgroups with unique GP60 alleles cannot be ruled out. We conclude that with the exception of genotypically distinct
C. parvum
subgroups, multilocus genotyping methods are needed to characterize
C. parvum
and
C. hominis
populations. Unless parasite virulence is controlled at the GP60 locus, attempts to find associations within species or subspecies between GP60 and phenotype are unlikely to be successful.
Transcriptomic Analysis of
Escherichia coli
O157:H7 and K-12 Cultures Exposed to Inorganic and Organic Acids in Stationary Phase Reveals Acidulant- and Strain-Specific Acid Tolerance Responses
Authors: King Thea , Lucchini Sacha , Hinton Jay C. D. , Gobius Kari
Published: August 2010

The food-borne pathogen
Escherichia coli
O157:H7 is commonly exposed to organic acid in processed and preserved foods, allowing adaptation and the development of tolerance to pH levels otherwise lethal. Since little is known about the molecular basis of adaptation of
E. coli
to organic acids, we studied K-12 MG1655 and O157:H7 Sakai during exposure to acetic, lactic, and hydrochloric acid at pH 5.5. This is the first analysis of the pH-dependent transcriptomic response of stationary-phase
E. coli.
Thirty-four genes and three intergenic regions were upregulated by both strains during exposure to all acids. This universal acid response included genes involved in oxidative, envelope, and cold stress resistance and iron and manganese uptake, as well as 10 genes of unknown function. Acidulant- and strain-specific responses were also revealed. The acidulant-specific response reflects differences in the modes of microbial inactivation, even between weak organic acids. The two strains exhibited similar responses to lactic and hydrochloric acid, while the response to acetic acid was distinct. Acidulant-dependent differences between the strains involved induction of genes involved in the heat shock response, osmoregulation, inorganic ion and nucleotide transport and metabolism, translation, and energy production.
E. coli
O157:H7-specific acid-inducible genes were identified, suggesting that the enterohemorrhagic
E. coli
strain possesses additional molecular mechanisms contributing to acid resistance that are absent in K-12. While
E. coli
K-12 was most resistant to lactic and hydrochloric acid, O157:H7 may have a greater ability to survive in more complex acidic environments, such as those encountered in the host and during food processing.
The Saccharomyces cerevisiae Anaphase-Promoting Complex Interacts with Multiple Histone-Modifying Enzymes To Regulate Cell Cycle Progression
Authors: Turner Emma L. , Malo Mackenzie E. , Pisclevich Marnie G. , Dash Megan D. , Davies Gerald F. , Arnason Terra G. , Harkness Troy A. A.
Published: August 2010

The anaphase-promoting complex (APC), a large evolutionarily conserved ubiquitin ligase complex, regulates cell cycle progression through mitosis and G
1
. Here, we present data suggesting that APC-dependent cell cycle progression relies on a specific set of posttranslational histone-modifying enzymes. Multiple APC subunit mutants were impaired in total and modified histone H3 protein content. Acetylated H3K56 (H3K56
Ac
) levels were as reduced as those of total H3, indicating that loading histones with H3K56
Ac
is unaffected in APC mutants. However, under restrictive conditions, H3K9
Ac
and dimethylated H3K79 (H3K79
me2
) levels were more greatly reduced than those of total H3. In a screen for histone acetyltransferase (HAT) and histone deacetylase (HDAC) mutants that genetically interact with the
apc5

CA

(chromatin assembly) mutant, we found that deletion of
GCN5
or
ELP3
severely hampered
apc5

CA

temperature-sensitive (ts) growth. Further analyses showed that (i) the
elp3
Δ
gcn5
Δ double mutant ts defect was epistatic to that observed in
apc5

CA

cells; (ii)
gcn5
Δ and
elp3
Δ mutants accumulate in mitosis; and (iii) turnover of the APC substrate Clb2 is not impaired in
elp3
Δ
gcn5
Δ cells. Increased expression of
ELP3
and
GCN5
, as well as genes encoding the HAT Rtt109 and the chromatin assembly factors Msi1 and Asf1, suppressed
apc5

CA

defects, while increased
APC5
expression partially suppressed
elp3
Δ
gcn5
Δ growth defects. Finally, we demonstrate that Gcn5 is unstable during G
1
and following G
1
arrest and is stabilized in APC mutants. We present our working model in which Elp3/Gcn5 and the APC work together to facilitate passage through mitosis and G
1
. To progress into S, we propose that at least Gcn5 must then be targeted for degradation in an APC-dependent fashion.
Heterologous Expression of Candida albicans Cell Wall-Associated Adhesins in Saccharomyces cerevisiae Reveals Differential Specificities in Adherence and Biofilm Formation and in Binding Oral Streptococcus gordonii
Authors: Nobbs Angela H. , Vickerman M. Margaret , Jenkinson Howard F.
Published: August 2010

Colonization and infection of the human host by opportunistic pathogen
Candida albicans
derive from an ability of this fungus to colonize mucosal tissues and prosthetic devices within the polymicrobial communities present. To determine the functions of
C. albicans
cell wall proteins in interactions with host or bacterial molecules,
Saccharomyces cerevisiae
was utilized as a surrogate host to express
C. albicans
cell wall proteins Als3p, Eap1p, Hwp1p, and Rbt1p. Salivary pellicle and fibrinogen were identified as novel substrata for Als3p and Hwp1p, while only Als3p mediated adherence of
S. cerevisiae
to basement membrane collagen type IV. Parental
S. cerevisiae
cells failed to form biofilms on salivary pellicle, polystyrene, or silicone, but cells expressing Als3p or Hwp1p exhibited significant attachment to each surface. Virulence factor Rbt1p also conferred lower-level binding to salivary pellicle and polystyrene.
S. cerevisiae
cells expressing Eap1p formed robust biofilms upon polystyrene surfaces but not salivary pellicle. Proteins Als3p and Eap1p, and to a lesser degree Hwp1p, conferred upon
S. cerevisiae
the ability to bind cells of the oral primary colonizing bacterium
Streptococcus gordonii
. These interactions, which occurred independently of amyloid aggregate formation, provide the first examples of specific
C. albicans
surface proteins serving as receptors for bacterial adhesins.
Streptococcus gordonii
did not bind parental
S. cerevisiae
or cells expressing Rbt1p. Taken collectively, these data suggest that a network of cell wall proteins comprising Als3p, Hwp1p, and Eap1p, with complementary adhesive functions, promotes interactions of
C. albicans
with host and bacterial molecules, thus leading to effective colonization within polymicrobial communities.
The ROCO Kinase QkgA Is Necessary for Proliferation Inhibition by Autocrine Signals in Dictyostelium discoideum
Authors: Phillips Jonathan E. , Gomer Richard H.
Published: August 2010

AprA and CfaD are secreted proteins that function as autocrine signals to inhibit cell proliferation in
Dictyostelium discoideum.
Cells lacking AprA or CfaD proliferate rapidly, and adding AprA or CfaD to cells slows proliferation. Cells lacking the ROCO kinase QkgA proliferate rapidly, with a doubling time 83% of that of the wild type, and overexpression of a QkgA-green fluorescent protein (GFP) fusion protein slows cell proliferation. We found that
qkgA
−
cells accumulate normal levels of extracellular AprA and CfaD. Exogenous AprA or CfaD does not slow the proliferation of cells lacking
qkgA
, and expression of QkgA-GFP in
qkgA
−
cells rescues this insensitivity. Like cells lacking AprA or CfaD, cells lacking QkgA tend to be multinucleate, accumulate nuclei rapidly, and show a mass and protein accumulation per nucleus like those of the wild type, suggesting that QkgA negatively regulates proliferation but not growth. Despite their rapid proliferation, cells lacking AprA, CfaD, or QkgA expand as a colony on bacteria less rapidly than the wild type. Unlike AprA and CfaD, QkgA does not affect spore viability following multicellular development. Together, these results indicate that QkgA is necessary for proliferation inhibition by AprA and CfaD, that QkgA mediates some but not all of the effects of AprA and CfaD, and that QkgA may function downstream of these proteins in a signal transduction pathway regulating proliferation.
Phosphatidylinositol 3-Phosphate, an Essential Lipid in Plasmodium, Localizes to the Food Vacuole Membrane and the Apicoplast
Authors: Tawk Lina , Chicanne Gaëtan , Dubremetz Jean-François , Richard Véronique , Payrastre Bernard , Vial Henri J. , Roy Christian , Wengelnik Kai
Published: August 2010

Phosphoinositides are important regulators of diverse cellular functions, and phosphatidylinositol 3-monophosphate (PI3P) is a key element in vesicular trafficking processes. During its intraerythrocytic development, the malaria parasitePlasmodium falciparumestablishes a sophisticated but poorly characterized protein and lipid trafficking system. Here we established the detailed phosphoinositide profile ofP. falciparum-infected erythrocytes and found abundant amounts of PI3P, while phosphatidylinositol 3,5-bisphosphate was not detected. PI3P production was parasite dependent, sensitive to a phosphatidylinositol-3-kinase (PI3-kinase) inhibitor, and predominant in late parasite stages. ThePlasmodiumgenome encodes a class III PI3-kinase of unusual size, containing large insertions and several repetitive sequence motifs. The gene could not be deleted inPlasmodium berghei, andin vitrogrowth ofP. falciparumwas sensitive to a PI3-kinase inhibitor, indicating that PI3-kinase is essential inPlasmodiumblood stages. For intraparasitic PI3P localization, transgenicP. falciparumthat expressed a PI3P-specific fluorescent probe was generated. Fluorescence was associated mainly with the membrane of the food vacuole and with the apicoplast, a four-membrane bounded plastid-like organelle derived from an ancestral secondary endosymbiosis event. Electron microscopy analysis confirmed these findings and revealed, in addition, the presence of PI3P-positive single-membrane vesicles. We hypothesize that these vesicles might be involved in transport processes, likely of proteins and lipids, toward the essential and peculiar parasite compartment, which is the apicoplast. The fact that PI3P metabolism and function inPlasmodiumappear to be substantially different from those in its human host could offer new possibilities for antimalarial chemotherapy.
Ccq1p and the Condensin Proteins Cut3p and Cut14p Prevent Telomere Entanglements in the Fission Yeast Schizosaccharomyces pombe
Authors: Motwani Tina , Doris Rosemarie , Holmes Scott G. , Flory Mark R.
Published: August 2010

The
Schizosaccharomyces pombe
telomere-associated protein Ccq1p has previously been shown to participate in telomerase recruitment, heterochromatin formation, and suppression of checkpoint activation. Here we characterize a critical role for Ccq1p in mitotic transit. We show that mitotic cells lacking Ccq1p lose minichromosomes at high frequencies but that conditional knockdown of Ccq1p expression results in telomere bridging within one cell cycle. Elevating Ccq1p expression resolves the telomere entanglements caused by decreased Taz1p activity. Ccq1p affects telomere resolution in the absence of changes in telomere size, indicating a role for Ccq1p that is independent of telomere length regulation. Using affinity purification, we identify the condensin proteins Cut3p and Cut14p as candidate Ccq1p interactors in this activity. Condensin loss-of-function disrupts Ccq1p telomeric localization and normal intertelomere clustering, while condensin overexpression relieves the chromosome segregation defects associated with conditional Ccq1p knockdown. These data suggest that Ccq1p and condensins collaborate to mediate resolution of telomeres in mitosis and regulate intertelomeric clustering during interphase.
Integration of Metabolism and Virulence by
Clostridium difficile
CodY
Authors: Dineen Sean S. , McBride Shonna M. , Sonenshein Abraham L.
Published: August 2010

CodY, a global regulatory protein that monitors the nutrient sufficiency of the environment by responding to the intracellular levels of GTP and the branched-chain amino acids, was previously shown to be a potent repressor of toxin gene expression in
Clostridium difficile
during growth in rich medium. In the intestinal tract, such derepression of toxin synthesis would lead to destruction of epithelial cells and the liberation of potential nutrients for the bacterium. CodY is likely to play an important role in regulating overall cellular physiology as well. In this study, DNA microarray analysis and affinity purification of CodY-DNA complexes were used to identify and distinguish the direct and indirect effects of CodY on global gene transcription. A
codY
null mutation resulted in >4-fold overexpression of 146 genes (organized in 82 apparent transcription units) and underexpression of 19 genes. In addition to the toxin genes, genes for amino acid biosynthesis, nutrient transport, fermentation pathways, membrane components, and surface proteins were overexpressed in the
codY
mutant. Genome-wide analysis identified more than 350 CodY binding regions, many of which are likely to correspond to sites of direct CodY-mediated regulation. About 60% of the CodY-repressed transcription units were associated with binding regions. Several of these genes were confirmed to be direct targets of CodY by gel mobility shift and DNase I footprinting assays.
CztR, a LysR-Type Transcriptional Regulator Involved in Zinc Homeostasis and Oxidative Stress Defense in
Caulobacter crescentus
Authors: Braz Vânia S. , da Silva Neto José F. , Italiani Valéria C. S. , Marques Marilis V.
Published: August 2010

Caulobacter crescentus
is a free-living alphaproteobacterium that has 11 predicted LysR-type transcriptional regulators (LTTRs). Previously, a
C. crescentus
mutant strain with a mini-Tn
5lacZ
transposon inserted into a gene encoding an LTTR was isolated; this mutant was sensitive to cadmium. In this work, a mutant strain with a deletion was obtained, and the role of this LTTR (called CztR here) was evaluated. The transcriptional start site of this gene was determined by primer extension analysis, and its promoter was cloned in front of a
lacZ
reporter gene. β-Galactosidase activity assays, performed with the wild-type and mutant strains, indicated that this gene is 2-fold induced when cells enter stationary phase and that it is negatively autoregulated. Moreover, this regulator is essential for the expression of the divergent
cztA
gene at stationary phase, in minimal medium, and in response to zinc depletion. This gene encodes a hypothetical protein containing 10 predicted transmembrane segments, and its expression pattern suggests that it encodes a putative zinc transporter. The
cztR
strain was also shown to be sensitive to superoxide (generated by paraquat) and to hydrogen peroxide but not to
tert
-butyl hydroperoxide. The expression of
katG
and
ahpC
, but not that of the superoxide dismutase genes, was increased in the
cztR
mutant. A model is proposed to explain how CztR binding to the divergent regulatory regions could activate
cztA
expression and repress its own transcription.
Domain Analysis of a Modular α-
l
-Arabinofuranosidase with a Unique Carbohydrate Binding Strategy from the Fiber-Degrading Bacterium
Fibrobacter succinogenes
S85
Authors: Yoshida Shosuke , Hespen Charles W. , Beverly Robert L. , Mackie Roderick I. , Cann Isaac K. O.
Published: August 2010

Family 43 glycoside hydrolases (GH43s) are known to exhibit various activities involved in hemicellulose hydrolysis. Thus, these enzymes contribute to efficient plant cell wall degradation, a topic of much interest for biofuel production. In this study, we characterized a unique GH43 protein from
Fibrobacter succinogenes
S85. The recombinant protein showed α-
l
-arabinofuranosidase activity, specifically with arabinoxylan. The enzyme is, therefore, an arabinoxylan arabinofuranohydrolase (AXH). The
F. succinogenes
AXH (FSUAXH1) is a modular protein that is composed of a signal peptide, a GH43 catalytic module, a unique β-sandwich module (XX domain), a family 6 carbohydrate-binding module (CBM6), and
F. succinogenes
-specific paralogous module 1 (FPm-1). Truncational analysis and site-directed mutagenesis of the protein revealed that the GH43 domain/XX domain constitute a new form of carbohydrate-binding module and that residue Y484 in the XX domain is essential for binding to arabinoxylan, although protein structural analyses may be required to confirm some of the observations. Kinetic studies demonstrated that the Y484A mutation leads to a higher
k
cat
for a truncated derivative of FSUAXH1 composed of only the GH43 catalytic module and the XX domain. However, an increase in the

K
m

for arabinoxylan led to a 3-fold decrease in catalytic efficiency. Based on the knowledge that most XX domains are found only in GH43 proteins, the evolutionary relationships within the GH43 family were investigated. These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity.
Small Genes under Sporulation Control in the
Bacillus subtilis
genome
Authors: Schmalisch Matthias , Maiques Elisa , Nikolov Lachezar , Camp Amy H. , Chevreux Bastien , Muffler Andrea , Rodriguez Sabrina , Perkins John , Losick Richard
Published: August 2010

Using an oligonucleotide microarray, we searched for previously unrecognized transcription units in intergenic regions in the genome of
Bacillus subtilis
, with an emphasis on identifying small genes activated during spore formation. Nineteen transcription units were identified, 11 of which were shown to depend on one or more sporulation-regulatory proteins for their expression. A high proportion of the transcription units contained small, functional open reading frames (ORFs). One such newly identified ORF is a member of a family of six structurally similar genes that are transcribed under the control of sporulation transcription factor σ
E
or σ
K
. A multiple mutant lacking all six genes was found to sporulate with slightly higher efficiency than the wild type, suggesting that under standard laboratory conditions the expression of these genes imposes a small cost on the production of heat-resistant spores. Finally, three of the transcription units specified small, noncoding RNAs; one of these was under the control of the sporulation transcription factor σ
E
, and another was under the control of the motility sigma factor σ
D
.
Brochothrix thermosphactaBacteriophages Feature Heterogeneous and Highly Mosaic Genomes and Utilize Unique Prophage Insertion Sites
Authors: Kilcher Samuel , Loessner Martin J. , Klumpp Jochen
Published: August 2010

Brochothrixbelongs to the low-GC branch of Gram-positive bacteria (Firmicutes), closely related toListeria,Staphylococcus,Clostridium, andBacillus. Brochothrix thermosphactais a nonproteolytic food spoilage organism, adapted to growth in vacuum-packaged meats. We report the first genome sequences and characterization ofBrochothrixbacteriophages. Phage A9 is a myovirus with an 89-nm capsid diameter and a 171-nm contractile tail; it belongs to theSpounavirinaesubfamily and shares significant homologies withListeriaphage A511,Staphylococcusphage Twort, and others. The A9 unit genome is 127 kb long with 11-kb terminal redundancy; it encodes 198 proteins and 6 tRNAs. Phages BL3 and NF5 are temperate siphoviruses with a head diameter of 56 to 59 nm. The BL3 tail is 270 nm long, whereas NF5 features a short tail of only 94 nm. The NF5 genome (36.95 kb) encodes 57 gene products, BL3 (41.52 kb) encodes 65 products, and both are arranged in life cycle-specific modules. Surprisingly, BL3 and NF5 show little relatedness toListeriaphages but rather demonstrate relatedness to lactococcal phages. Peptide mass fingerprinting of viral proteins indicate programmed −1 translational frameshifts in the NF5 capsid and the BL3 major tail protein. Both NF5 and BL3 feature circularly permuted, terminally redundant genomes, packaged by a headful mechanism, and integrases of the serine (BL3) and tyrosine (NF5) types. They utilize unique target sequences not previously described: BL3 inserts into the 3′ end of a RNA methyltransferase, whereas NF5 integrates into the 5′-terminal part of a putative histidinol-phosphatase. Interestingly, both genes are reconstituted by phage sequence.
AmrZ Beta-Sheet Residues Are Essential for DNA Binding and Transcriptional Control of
Pseudomonas aeruginosa
Virulence Genes
Authors: Waligora Elizabeth A. , Ramsey Deborah M. , Pryor Edward E. , Lu Haiping , Hollis Thomas , Sloan Gina P. , Deora Rajendar , Wozniak Daniel J.
Published: August 2010

AmrZ is a putative ribbon-helix-helix (RHH) transcriptional regulator. RHH proteins utilize residues within the β-sheet for DNA binding, while the α-helices promote oligomerization. AmrZ is of interest due to its dual roles as a transcriptional activator and as a repressor, regulating genes encoding virulence factors associated with both chronic and acute
Pseudomonas aeruginosa
infection. In this study, cross-linking revealed that AmrZ forms oligomers in solution but that the amino terminus, containing an unordered region and a β-sheet, were not required for oligomerization. The first 12 unordered residues (extended amino terminus) contributed minimally to DNA binding. Mutagenesis of the AmrZ β-sheet demonstrated that residues 18, 20, and 22 were essential for DNA binding at both activation and repressor sites, suggesting that AmrZ utilizes a similar mechanism for binding to these sites. Mice infected with
amrZ
mutants exhibited reduced bacterial burden, morbidity, and mortality. Direct
in vivo
competition assays showed a 5-fold competitive advantage for the wild type over an isogenic
amrZ
mutant. Finally, the reduced infection phenotype of the
amrZ
-null strain was similar to that of a strain expressing a DNA-binding-deficient AmrZ variant, indicating that DNA binding and transcriptional regulation by AmrZ is responsible for the
in vivo
virulence defect. These recent infection data, along with previously identified AmrZ-regulated virulence factors, suggest the necessity of AmrZ transcriptional regulation for optimal virulence during acute infection.
Identification, Source, and Metabolism of
N
-Ethylglutamate in
Escherichia coli
Authors: White Robert H.
Published: August 2010

N
-Ethylglutamate (NEG) was detected in
Escherichia coli
BL21 cells grown on LB broth, and it was found to occur at a concentration of ∼4 mM in these cells under these conditions. The same cells grown on M9 glucose medium contained no detectable amount of NEG. Analysis of the LB broth showed the presence of NEG, a compound never before reported as a natural product. Isotope dilution analysis showed that it occurred at a concentration of 160 μM in LB broth. Analyses of yeast extract and tryptone, the organic components of LB broth, both showed the presence NEG. It was demonstrated that NEG can be generated during the autolysis of the yeast used in the preparation of the yeast extract. Growth of these
E. coli
cells in LB broth prepared in deuterated water showed no incorporation of deuterium into NEG, demonstrating that
E. coli
cells did not generate the NEG. Cell growth rates were not affected by the addition of 5 mM NEG to either LB or M9 glucose medium.
l
-[
ethyl
-
2
H
4
]NEG was found to be readily incorporated into the cells and metabolized by the cells. From these results, it was concluded that all of the NEG present in the cells was taken up from the medium. NEG could serve as the sole nitrogen source for
E. coli
when grown on M9 glucose medium in the presence of glucose but could not serve as the sole carbon source on M9 medium in the absence of glucose.
Both A2a and A2b adenosine receptors at reperfusion are necessary to reduce infarct size in mouse hearts
Authors: Methner Carmen , Schmidt Katharina , Cohen Michael V. , Downey James M. , Krieg Thomas
Published: August 2010

Pre- and postconditioning depend on the activation of adenosine receptors (ARs) at the end of the index ischemia. The aim of this study was to determine which receptor subtypes must be activated. In situ mouse hearts underwent 30 min of regional ischemia, followed by 2 h of reperfusion. As expected, either ischemic postconditioning (6 cycles of 10 s of reperfusion and 10 s of coronary occlusion) or infusion of the selective A2b adenosine receptor (A2bAR) agonist BAY60-6583 (BAY60) for 60 min, starting 5 min before reperfusion reduced infarct size in wild-type C57Bl/6N mice. Protection from either was abolished by the selective A2bAR antagonist MRS-1754, confirming a role for A2bAR. Additionally, the coadministration of ischemic postconditioning and a selective A2aAR antagonist led to the loss of protection as well. 5′-Ectonucleotidase (CD73) is thought to be necessary for the production of adenosine during ischemia. As predicted, ischemic postconditioning did not protect CD73 knockout mice. Selective agonists of either A2bAR (BAY60) or A2aAR (CGS-21680), as well as the coadministration of ischemic postconditioning and BAY60, also failed to protect hearts of the CD73 knockout mice. But the nonselective A1/A2AR agonist 5′-( N-ethylcarboxamido)adenosine (NECA) was protective, suggesting that the activation of multiple AR subtypes might be required. The coadministration of CGS-21680 and BAY60 also elicited profound protection, indicating that two AR subtypes, A2a and A2b, must be simultaneously activated for protection to occur.
Suppression of circulating free fatty acids with acipimox in chronic heart failure patients changes whole body metabolism but does not affect cardiac function
Authors: Halbirk Mads , Nørrelund Helene , Møller Niels , Schmitz Ole , Gøtzsche Liv , Nielsen Roni , Nielsen-Kudsk Jens Erik , Nielsen Søren Steen , Nielsen Torsten Toftegaard , Eiskjær Hans , Bøtker Hans Erik , Wiggers Henrik
Published: August 2010

Circulating free fatty acids (FFAs) may worsen heart failure (HF) due to myocardial lipotoxicity and impaired energy generation. We studied cardiac and whole body effects of 28 days of suppression of circulating FFAs with acipimox in patients with chronic HF. In a randomized double-blind crossover design, 24 HF patients with ischemic heart disease [left ventricular ejection fraction: 26 ± 2%; New York Heart Association classes II ( n = 13) and III ( n = 5)] received 28 days of acipimox treatment (250 mg, 4 times/day) and placebo. Left ventricular ejection fraction, diastolic function, tissue-Doppler regional myocardial function, exercise capacity, noninvasive cardiac index, NH2-terminal pro-brain natriuretic peptide (NT-pro-BNP), and whole body metabolic parameters were measured. Eighteen patients were included for analysis. FFAs were reduced by 27% in the acipimox-treated group [acipimox vs. placebo ( day 28 − day 0): −0.10 ± 0.03 vs. +0.01 ± 0.03 mmol/l, P < 0.01]. Glucose and insulin levels did not change. Acipimox tended to increase glucose and decrease lipid utilization rates at the whole body level and significantly changed the effect of insulin on substrate utilization. The hyperinsulinemic euglycemic clamp M value did not differ. Global and regional myocardial function did not differ. Exercise capacity, cardiac index, systemic vascular resistance, and NT-pro-BNP were not affected by treatment. In conclusion, acipimox caused minor changes in whole body metabolism and decreased the FFA supply, but a long-term reduction in circulating FFAs with acipimox did not change systolic or diastolic cardiac function or exercise capacity in patients with HF.
Isotope Effect on the Thermal Conductivity of Graphene
Authors: Zhang Hengji , Lee Geunsik , Fonseca Alexandre F. , Borders Tammie L. , Cho Kyeongjae
Published: August 2010

The thermal conductivity (TC) of isolated graphene with different concentrations of isotope (C13) is studied with equilibrium molecular dynamics method at 300 K. In the limit of pure C12 or C13 graphene, TC of graphene in zigzag and armchair directions are ~630 W/mK and ~1000W/mK, respectively. We find that the TC of graphene can be maximally reduced by ~80%, in both armchair and zigzag directions, when a random distribution of C12 and C13 is assumed at different doping concentrations. Therefore, our simulation results suggest an effective way to tune the TC of graphene without changing its atomic and electronic structure, thus yielding a promising application for nanoelectronics and thermoelectricity of graphene‐based nano device.
Ex uno homine tota haec animarum redundantia. Ursprung, Entstehung und Weitergabe der individuellen Seele nach Tertullian
Authors: Kitzler Petr
Published: August 2010

The purpose of this article is to examine Tertullian’s opinions on the origin, beginning and transmission of the human soul. These opinions cannot be considered as representing a coherent and systematic doctrine which is evidenced not only by some inner inconsequences and contradictions but also by the fact that Tertullian’s reasoning is to a great extent motivated by the efforts to refute the arguments of his opponents. The core of Tertullian’s “doctrine”—the distinction between the Spirit of God (spiritus) and his breath ( flatus), the latter being the very substance of the human soul, transmitted by the act of procreation and deriving, ultimately, from the original soul of Adam (traducianism)—was intended by him as the main weapon against the alternative concepts of the soul as presented by Hermogenes and Marcion.
The Fortunes and Misfortunes of the Gospel of John in Egypt
Authors: Chapa Juan
Published: August 2010

The numerous manuscripts of John among the earliest Christian papyri have given rise to discussion and speculation. It has been suggested, on the grounds of an alleged preference for the Fourth Gospel among gnostics, that the high number of papyri of John compared to other gospels would favour Walter Bauer’s thesis of the ‘heterodox’ character of early Christian Egypt. The obscurity which veils the origins of the early Egyptian Church allows for conjectures of this kind. However, recent studies on the reception of the Fourth Gospel in the early Church and newly published papyri show that the abundance of early manuscripts of John is not necessarily indicative of the gnostic nature of early Christianity in Egypt. This paper attempts to shed additional light on the issue by comparing early papyri of John with other pieces of Christian evidence.
The Paradox of China’s Policy in Africa
Authors: Adem Seifudein
Published: August 2010

In many cases it was China’s longstanding solidarity with several liberation movements in Africa in the colonial period which was later upgraded to bilateral and state-level diplomatic relations in the postcolonial era. However, the twenty-first century has also brought about quantitative and potentially qualitative changes in Sino-African relations which are more complex than what the advocates of stronger Sino-African relations (Sino-optimists) and proponents of disengagement (Sino-pessimists) seem to suggest. The defining patterns of China’s influence in Africa are either not yet fully crystallized or they come in paradoxical pairs. The essay spells out the manifestations of these paradoxes and what can be done under the circumstances to improve the African condition. The divergent schools of thought about the possible impacts of China’s increased activities in Africa seem not to be totally unrelated to their underlying assumptions about the causes of Africa’s unsuccessful modernization. The essay also explores these intellectual issues by focusing on the contradictory dimensions of Afro-Chinese relations.
Regimes of Piety Revisited: Zaydī Political Moralities in Republican Yemen
Authors: vom Bruck Gabriele
Published: August 2010

The gradual decline of Zaydī-Shī'ī Islam in Yemen occurred within contexts of state transformation over the past three centuries, culminating in the revolution of 1962 that abolished the imāmate. It has since lost its institutional framework and struggled to define its location in the newly established republic. The republic's commitment to an Islam which transcends the schools of law (madhāhib) has become part of Yemen's nationalist project and of the state's political agenda. At the intersection of nation-building and Saudi Arabia's assertion of its hegemony over the Arabian Peninsula, the Salafī da'wa—consonant with the teachings of the 18th/19th century scholar Muhammad al-Shawkānī—has twinned with Hanbalī-'Wahhābī' doctrine. The establishment of educational institutions and mosques propagating anti-Shī'ī schools of thought have provoked a Zaydī revival movement that gained momentum after Yemen's 'unification' in 1990. The movement has led to increased polarisation between the Zaydīs and the Salafīs, and demonstrated profound tensions among Zaydīs who subscribe to diverse political moralities. The article explores how categories of legitimisation have been modulated, and what recent Zaydī political activism reveals about the conflicting meanings people attach to 'being Zaydī'.
Sayyid Ni'mat Allāh al-Jazā'irī and his Anthologies: Anti-Sufism, Shi'ism and Jokes in the Safavid World
Authors: Rizvi Sajjad
Published: August 2010

The paper examines an important Arabic anthology of literary material of mixed content, the al-Anwār al-nu'māniyya of Sayyid Ni'matullāh al-Jazā'irī (d. 1701) to ascertain its value as a source for intellectual and cultural history of the Safavid period. Al-Jazā'irī was a prominent transnational Shi'i intellectual who was born in the marshlands of Southern Iraq, a leading light of the Akhbārī movement of his time, and major scholar associated with the hadīth-based Shi'i revival of Mullā Muhammad Bāqir Majlisī (d. 1699). Literary anthologies are of critical importance for understanding, on the one hand, the anthropology of what it meant to be human as well as the wider contours of the cultural, literary and intellectual history of the Safavid period. They represent both a serious engagement and demonstration of literary excellence in the pre-modern and post-classical period, contrary to rather dated notions of the stagnation of the period. Three themes from the text are analysed: the nature of philosophy, attitudes towards Sufism and mysticism, and the formation of a Safavid Shi'i cultural identity that was reactive and anti-Sunni and articulated through jokes and light-hearted anecdotes.
Adriaan Schoonebeek's Etching Manual (1698): Edition, Translation, Comments
Authors: Stijnman Ad , Janssen Frans , Leeflang Huigen , Markus Adri
Published: August 2010

One of the many practitioners of trades and techniques engaged by Tsar Peter the Great during his visit to the Dutch Republic in 1697-8, was the Amsterdam printmaker Adriaan Schoonebeek (1661-1705). Within the framework of this appointment Schoonebeek wrote a concise manual of the technique of etching. This article presents an edition of this oldest complete Dutch etching manual, together with a modern English translation.
On the occurrence of a myxozoan parasite, Thelohanellus anilae sp. n. from a fresh water fish of India
Authors: Hemananda Thounaojam , Bandyopadhyay Probir , Mohilal Naorem , Mitra Amlan Kumar
Published: August 2010

A new species of the genus Thelohanellus Kudo, 1933 is described from the gills of Labeo rohita. Thelohanellus anilae sp. n. occurs in two morphometrically dissimilar forms which are described as microspore and macrospore of the same species.
The Oxford Calculators’ Middle Degree Theorem in Context
Authors: Sylla Edith Dudley
Published: August 2010

The core Oxford Calculators (here William Heytesbury, John Dumbleton, and Richard Swineshead) developed a science of kinematics in which the key concept was the “latitude of velocity.” Based upon the concept of “latitude,” the Calculators developed parts of a mathematical physics in deductive format that could be applied to quite various situations.