bluuebunny/crossref_metadata_2025_split huggingface dataset:
GROWTH, EMPLOYMENT AND DISTRIBUTION IMPACTS OF MINERALS DEPENDENCY: FOUR CASE STUDIES
Authors: Berry Albert 
Published: October 2008

AbstractCross‐country evidence on the direct and indirect impacts of minerals dependency on growth suggests that the typical effect may be negative, and the experience in some countries implies large negative effects. The impact on employment and income distribution is even more likely to be adverse, since many minerals generate few jobs directly and may destroy more indirectly. Thus, countries heavily endowed with exportable natural resources cannot take it for granted that this condition will put them on a sustained and equitable development path. This study focuses on four countries – Indonesia, Chile, Venezuela and Nigeria – and looks at how they have handled export bonanzas, with focus on the employment as well as the growth fall‐out. The big policy questions are: what is the best way for a country to use its mineral resources to achieve equitable development, and is there a significant role for industrial strategy in identifying new comparative advantages or can markets do a better job relatively unimpeded? The four case studies reviewed here suggest that, depending on the specifics of the country, promising new comparative advantages can emerge in the primary, secondary and tertiary sectors, while the role of service tradables should not be discounted. It is intriguing that the great majority of minerals‐dependent countries to achieve sustained growth have also made significant progress in manufacturing. In a world that now penalises trade protectionism, the exchange rate can be a powerful tool to provide more neutral incentives for new tradables; indeed, one of the most striking features of the two success stories related here has been these countries' timely use of currency devaluations to achieve highly competitive exchange rates. The experiences of the four countries further confirm the risks of focusing on capital‐intensive industries in labour‐surplus countries, as well as the risk of lodging such activities in the public sector. Only Indonesia of the four countries was able to achieve good enough employment growth under mineral dependency to avoid a high or rising level of inequality. Clearly the challenge on the employment/distribution front is severe.
Phylogenetic Relationships and Functional Genes: Distribution of a Gene (
mnxG
) Encoding a Putative Manganese-Oxidizing Enzyme in
Bacillus
Species
Authors: Mayhew Lisa E. , Swanner Elizabeth D. , Martin Andy P. , Templeton Alexis S. 
Published: October 2008

ABSTRACT

Several
Bacillus
and
Paenibacillus
species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the
mnxG
gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in
Bacillus
species. Seven of eight
Bacillus
species were capable of Mn(II) oxidation; however, the
mnxG
gene was detected in only one isolate. Using sequences of known
Bacillus
species both with and without amplifiable
mnxG
genes and Henderson Mine isolates, the 16S rRNA and
mnxG
gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable
mnxG
gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable
mnxG
gene in the isolates. The data revealed a complex phylogenetic distribution of the
mnxG
gene in which vertical inheritance and gene loss influence the distribution of the gene among the
Bacillus
species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the
mnxG
gene within the
Bacillus
clade.
Identification of
Bacillus cereus
Group Species Associated with Food Poisoning Outbreaks in British Columbia, Canada
Authors: McIntyre Lorraine , Bernard Kathryn , Beniac Daniel , Isaac-Renton Judith L. , Naseby David Craig 
Published: October 2008

ABSTRACT

Food poisoning laboratories identify
Bacillus cereus
using routine methods that may not differentiate all
Bacillus cereus
group species. We recharacterized
Bacillus
food-poisoning strains from 39 outbreaks and identified
B. cereus
in 23 outbreaks,
B. thuringiensis
in 4,
B. mycoides
in 1, and mixed strains of
Bacillus
in 11 outbreaks.
Use of Flow Cytometry To Monitor
Legionella
Viability
Authors: Allegra Séverine , Berger Françoise , Berthelot Philippe , Grattard Florence , Pozzetto Bruno , Riffard Serge 
Published: October 2008

ABSTRACT

Legionella
viability was monitored during heat shock treatment at 70°C by a flow cytometric assay (FCA). After 30 min of treatment, for 6 of the 12 strains tested, the FCA still detected 10 to 25% of cells that were viable but nonculturable (VBNC). These VBNC cells were able to produce ATP and to be resuscitated after culture on amoebae.
Transcriptional Analysis of
Clostridium beijerinckii
NCIMB 8052 and the Hyper-Butanol-Producing Mutant BA101 during the Shift from Acidogenesis to Solventogenesis
Authors: Shi Zhen , Blaschek Hans P. 
Published: October 2008

ABSTRACT

Clostridium beijerinckii
is an anaerobic bacterium used for the fermentative production of acetone and butanol. The recent availability of genomic sequence information for
C. beijerinckii
NCIMB 8052 has allowed for an examination of gene expression during the shift from acidogenesis to solventogenesis over the time course of a batch fermentation using a ca. 500-gene set DNA microarray. The microarray was constructed using a collection of genes which are orthologs of members of gene families previously found to be important to the physiology of
C. acetobutylicum
ATCC 824. Similar to the onset of solventogenesis in
C. acetobutylicum
824, the onset of solventogenesis in
C. beijerinckii
8052 was concurrent with the initiation of sporulation. However, forespores and endospores developed more rapidly in
C. beijerinckii
8052 than in
C. acetobutylicum
824, consistent with the accelerated expression of the
sigE
- and
sigG
-regulated genes in
C. beijerinckii
8052. The comparison of gene expression patterns and morphological changes in
C. beijerinckii
8052 and the hyper-butanol-producing
C. beijerinckii
strain BA101 indicated that BA101 was less efficient in sporulation and phosphotransferase system-mediated sugar transport than 8052 but that it exhibited elevated expression of several primary metabolic genes and chemotaxis/motility genes.
Differential Expression in
Phanerochaete chrysosporium
of Membrane-Associated Proteins Relevant to Lignin Degradation
Authors: Shary Semarjit , Kapich Alexander N. , Panisko Ellen A. , Magnuson Jon K. , Cullen Daniel , Hammel Kenneth E. 
Published: October 2008

ABSTRACT

Fungal lignin-degrading systems likely include membrane-associated proteins that participate in diverse processes such as uptake and oxidation of lignin fragments, production of ligninolytic secondary metabolites, and defense of the mycelium against ligninolytic oxidants. Little is known about the nature or regulation of these membrane-associated components. We grew the white rot basidiomycete
Phanerochaete chrysosporium
on cellulose or glucose as the carbon source and monitored the mineralization of a
14
C-labeled synthetic lignin by these cultures to assess their ligninolytic competence. The results showed that the cellulose-grown cultures were ligninolytic, whereas the glucose-grown ones were not. We isolated microsomal membrane fractions from both types of culture and analyzed tryptic digests of their proteins by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the results against the predicted
P. chrysosporium
proteome showed that a catalase (Joint Genome Institute
P. chrysosporium
protein identification number [I.D.] 124398), an alcohol oxidase (126879), two transporters (137220 and 132234), and two cytochrome P450s (5011 and 8912) were upregulated under ligninolytic conditions. Quantitative reverse transcription-PCR assays showed that RNA transcripts encoding all of these proteins were also more abundant in ligninolytic cultures. Catalase 124398, alcohol oxidase 126879, and transporter 137220 were found in a proteomic analysis of partially purified plasma membranes from ligninolytic
P. chrysosporium
and are therefore most likely associated with the outer envelope of the fungus.
Case Series Study of Traveler's Diarrhea in U.S. Military Personnel at Incirlik Air Base, Turkey
Authors: Porter C. K. , El Mohammady H. , Baqar S. , Rockabrand D. M. , Putnam S. D. , Tribble D. R. , Riddle M. S. , Frenck R. W. , Rozmajzl P. , Kilbane E. , Fox A. , Ruck R. , Lim M. , Johnston Y. J. , Murphy E. , Sanders J. W. 
Published: October 2008

ABSTRACT

Military personnel with traveler's diarrhea (
n
= 202) while deployed to Incirlik Air Base, Turkey, from June to September 2002 were evaluated for pathogen-specific immune responses. Serologic and fecal immunoglobulin A (IgA) titers to enterotoxigenic
Escherichia coli
antigens (CS6, CS3, and LT) were quite low. In contrast, subjects with
Campylobacter
infections had high serologic and fecal IgA responses.
Characterization of the Genomes of a Diverse Collection of
Salmonella enterica
Serovar Typhimurium Definitive Phage Type 104
Authors: Cooke Fiona J. , Brown Derek J. , Fookes Maria , Pickard Derek , Ivens Alasdair , Wain John , Roberts Mark , Kingsley Robert A. , Thomson Nicholas R. , Dougan Gordon 
Published: October 2008

ABSTRACT

Salmonella enterica
serovar Typhimurium definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We completed the full DNA sequence of one DT104 strain, NCTC13348, and showed that significant differences between the genome of this isolate and the genome of the previously sequenced strain
Salmonella
serovar Typhimurium LT2 are due to integrated prophage elements and
Salmonella
genomic island 1 encoding antibiotic resistance genes. Thirteen isolates of
Salmonella
serovar Typhimurium DT104 with different pulsed-field gel electrophoresis (PFGE) profiles were analyzed by using multilocus sequence typing (MLST), plasmid profiling, hybridization to a pan-
Salmonella
DNA microarray, and prophage-based multiplex PCR. All the isolates belonged to a single MLST type, sequence type ST19. Microarray data demonstrated that the gene contents of the 13 DT104 isolates were remarkably conserved. The PFGE DNA fragment size differences in these isolates could be explained to a great extent by differences in the prophage and plasmid contents. Thus, here the nature of variation in different
Salmonella
serovar Typhimurium DT104 isolates is further defined at the gene and whole-genome levels, illustrating how this phage type evolves over time.
The
Mycobacterium avium
Complex
gtfTB
Gene Encodes a Glucosyltransferase Required for the Biosynthesis of Serovar 8-Specific Glycopeptidolipid
Authors: Miyamoto Yuji , Mukai Tetsu , Maeda Yumi , Kai Masanori , Naka Takashi , Yano Ikuya , Makino Masahiko 
Published: October 2008

ABSTRACT

Mycobacterium avium
complex (MAC) is one of the most common opportunistic pathogens widely distributed in the natural environment. The 28 serovars of MAC are defined by variable oligosaccharide portions of glycopeptidolipids (GPLs) that are abundant on the surface of the cell envelope. These GPLs are also known to contribute to the virulence of MAC. Serovar 8 is one of the dominant serovars isolated from AIDS patients, but the biosynthesis of serovar 8-specific GPL remains unknown. To clarify this, we compared gene clusters involved in the biosynthesis of several serovar-specific GPLs and identified the genomic region predicted to be responsible for GPL biosynthesis in a serovar 8 strain. Sequencing of this region revealed the presence of four open reading frames, three unnamed genes and
gtfTB
, the function of which has not been elucidated. The simultaneous expression of
gtfTB
and two downstream genes in a recombinant
Mycobacterium smegmatis
strain genetically modified to produce serovar 1-specific GPL resulted in the appearance of 4,6-
O
-(1-carboxyethylidene)-3-
O
-methyl-glucose, which is unique to serovar 8-specific GPL, suggesting that these three genes participate in its biosynthesis. Furthermore, functional analyses of
gtfTB
indicated that it encodes a glucosyltransferase that transfers a glucose residue via 1→3 linkage to a rhamnose residue of serovar 1-specific GPL, which is critical to the formation of the oligosaccharide portion of serovar 8-specific GPL. Our findings might provide a clue to understanding the biosynthetic regulation that modulates the biological functions of GPLs in MAC.
DNA Repair of 8-Oxo-7,8-Dihydroguanine Lesions in
Porphyromonas gingivalis
Authors: Henry Leroy G. , Sandberg Lawrence , Zhang Kangling , Fletcher Hansel M. 
Published: October 2008

ABSTRACT

The persistence of
Porphyromonas gingivalis
in the inflammatory environment of the periodontal pocket requires an ability to overcome oxidative stress. DNA damage is a major consequence of oxidative stress. Unlike the case for other organisms, our previous report suggests a role for a non-base excision repair mechanism for the removal of 8-oxo-7,8-dihydroguanine (8-oxo-G) in
P. gingivalis
. Because the
uvrB
gene is known to be important in nucleotide excision repair, the role of this gene in the repair of oxidative stress-induced DNA damage was investigated. A 3.1-kb fragment containing the
uvrB
gene was PCR amplified from the chromosomal DNA of
P. gingivalis
W83. This gene was insertionally inactivated using the
ermF-ermAM
antibiotic cassette and used to create a
uvrB
-deficient mutant by allelic exchange. When plated on brucella blood agar, the mutant strain, designated
P. gingivalis
FLL144, was similar in black pigmentation and beta-hemolysis to the parent strain. In addition,
P. gingivalis
FLL144 demonstrated no significant difference in growth rate, proteolytic activity, or sensitivity to hydrogen peroxide from that of the parent strain. However, in contrast to the wild type,
P. gingivalis
FLL144 was significantly sensitive to UV irradiation. The enzymatic removal of 8-oxo-G from duplex DNA was unaffected by the inactivation of the
uvrB
gene. DNA affinity fractionation identified unique proteins that preferentially bound to the oligonucleotide fragment carrying the 8-oxo-G lesion. Collectively, these results suggest that the repair of oxidative stress-induced DNA damage involving 8-oxo-G may occur by a still undescribed mechanism in
P. gingivalis
.
The
hpx
Genetic System for Hypoxanthine Assimilation as a Nitrogen Source in
Klebsiella pneumoniae
: Gene Organization and Transcriptional Regulation
Authors: de la Riva Lucia , Badia Josefa , Aguilar Juan , Bender Robert A. , Baldoma Laura 
Published: October 2008

ABSTRACT

Growth experiments showed that adenine and hypoxanthine can be used as nitrogen sources by several strains of
K. pneumoniae
under aerobic conditions. The assimilation of all nitrogens from these purines indicates that the catabolic pathway is complete and proceeds past allantoin. Here we identify the genetic system responsible for the oxidation of hypoxanthine to allantoin in
K. pneumoniae.
The
hpx
cluster consists of seven genes, for which an organization in four transcriptional units,
hpxDE
,
hpxR
,
hpxO
, and
hpxPQT
, is proposed. The proteins involved in the oxidation of hypoxanthine (HpxDE) or uric acid (HpxO) did not display any similarity to other reported enzymes known to catalyze these reactions but instead are similar to oxygenases acting on aromatic compounds. Expression of the
hpx
system is activated by nitrogen limitation and by the presence of specific substrates, with
hpxDE
and
hpxPQT
controlled by both signals. Nitrogen control of
hpxPQT
transcription, which depends on σ
54
, is mediated by the Ntr system. In contrast, neither NtrC nor the nitrogen assimilation control protein is involved in the nitrogen control of
hpxDE
, which is dependent on σ
70
for transcription. Activation of these operons by the specific substrates is also mediated by different effectors and regulatory proteins. Induction of
hpxPQT
requires uric acid formation, whereas expression of
hpxDE
is induced by the presence of hypoxanthine through the regulatory protein HpxR. This LysR-type regulator binds to a TCTGC-N
4
-GCAAA site in the intergenic
hpxD-hpxR
region. When bound to this site for
hpxDE
activation, HpxR negatively controls its own transcription.
Genetic Adaptation of
Pseudomonas aeruginosa
to the Airways of Cystic Fibrosis Patients Is Catalyzed by Hypermutation
Authors: Mena A. , Smith E. E. , Burns J. L. , Speert D. P. , Moskowitz S. M. , Perez J. L. , Oliver A. 
Published: October 2008

ABSTRACT

In previous work (E. E. Smith, D. G. Buckley, Z. Wu, C. Saenphimmachack, L. R. Hoffman, D. A. D'Argenio, S. I. Miller, B. W. Ramsey, D. P. Speert, S. M. Moskowitz, J. L. Burns, R. Kaul, and M. V. Olson, Proc. Natl. Acad. Sci. USA
103:
8487-8492, 2006) it was shown that
Pseudomonas aeruginosa
undergoes intense genetic adaptation during chronic respiratory infection (CRI) in cystic fibrosis (CF) patients. We used the same collection of isolates to explore the role of hypermutation in this process, since one of the hallmarks of CRI is the high prevalence of DNA mismatch repair (MMR) system-deficient mutator strains. The presence of mutations in 34 genes (many of them positively linked to adaptation in CF patients) in the study collection of 90
P. aeruginosa
isolates obtained longitudinally from 29 CF patients was not homogeneous; on the contrary, mutations were significantly concentrated in the mutator lineages, which represented 17% of the isolates (87% MMR deficient). While sequential nonmutator lineages acquired a median of only 0.25 mutation per year of infection, mutator lineages accumulated more than 3 mutations per year. On the whole-genome scale, data for the first fully sequenced late CF isolate, which was also shown to be an MMR-deficient mutator, also support these findings. Moreover, for the first time the predicted amplification of mutator populations due to hitchhiking with adaptive mutations in the course of natural human infections is clearly documented. Interestingly, increased accumulation of mutations in mutator lineages was not a consequence of overrepresentation of mutations in genes involved in antimicrobial resistance, the only adaptive trait linked so far to hypermutation in CF patients, demonstrating that hypermutation also plays a major role in
P. aeruginosa
genome evolution and adaptation during CRI.
Extended-Spectrum Beta-Lactamase Detection with Different Panels for Automated Susceptibility Testing and with a Chromogenic Medium
Authors: Färber J. , Moder K.-A. , Layer F. , Tammer I. , König W. , König B. 
Published: October 2008

ABSTRACT

Infections caused by extended-spectrum beta-lactamase (ESBL)- and
ampC
beta-lactamase-producing gram-negative bacteria complicate therapy and limit treatment options. Several different panels for ESBL detection with automated systems exist. In addition, a chromogenic agar medium is available for ESBL screening. We compared two automated identification and susceptibility testing systems with regard to their effectiveness in detecting ESBL production in
Enterobacteriaceae
: the BD Phoenix system (BD Diagnostic Systems, Sparks, MD) and the Vitek 2 system (bioMerieux, Marcy l'Etoile, France). We tested 114 strains using the Etest as the standard, various available panels for both automated systems (for BD Phoenix, the NMIC/ID-50 and NMIC/ID-70 GN Combo panels for combined identification and susceptibility testing of gram-negative bacilli, and for Vitek 2, the ID-GNB panel for identification of gram-negative bacilli and the AST-N020, AST-N041, and AST-N062 panels for susceptibility testing), and a chromogenic agar medium (bioMérieux, Marcy l'Etoile, France). PCR for common ESBL gene families (encoding TEM, SHV, OXA, and CTX-M) and for chromosomal or plasmid-mediated
ampC
beta-lactamase genes was conducted to complete the study design. For the tested specimens overall, the chromID ESBL agar showed the highest sensitivity (95.8%) but the lowest specificity (10.5%) compared to the sensitivity and specificity of the Etest (chosen as reference by the authors) for the detection of ESBL-producing strains. The BD Phoenix system showed sensitivities of 77.1% and 84.2% and specificities of 61.5% and 75.0%, respectively, for the NMIC/ID-50 andNMIC/ID-70 panels. The sensitivity of the Vitek 2 system ranged from 78.8% (AST-N020) to 80.6% (AST-N062) and up to 84.2% (AST-N041). The specificities of the respective panels were 50.0% (AST-N041 and AST-N062) and 55.6% (AST-N020). In conclusion, the sensitivities and specificities of ESBL detection by the different methods differ depending on the microorganisms under study.
Evaluation of Repeat
Clostridium difficile
Enzyme Immunoassay Testing
Authors: Cardona Diana M. , Rand Kenneth H. 
Published: October 2008

ABSTRACT

Clostridium difficile
is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis, which have significant morbidity and mortality. Accurate and timely diagnosis is critical. Repeat enzyme immunoassay testing for
C. difficile
toxin has been recommended because of <100% sensitivity. All
C. difficile
tests between 1 January 2006 and 31 December 2006 were retrospectively analyzed for results and testing patterns. The Wampole
C. difficile
Tox A/B II enzyme immunoassay kit was used. There were a total of 8,256 tests from 3,112 patients; 49% of tests were repeated. Of the 3,749 initially negative patient tests, 96 were positive upon repeat testing within 10 days of the first test. Of repeat tests, 0.9% repeated on day 0 (same day as the first test), 1.8% on day 1, 3.8% on day 2, 2.6% on day 3, 5.4% on days 4 to 6, and 10.6% on days 7 to 10 were positive. Thirty-eight patients had a positive test within 48 h of an initial negative test, and based on chart review, 18 patients were treated empirically while 16 were treated following the new result. None had evidence of medical complications. Of initially positive patients, 91% were positive upon repeat testing on day 0, 75% on day 1, and 58% on day 2, to a low of 14% on days 7 to 10. Depending on the clinical setting, these data support not repeating
C. difficile
tests within 2 days of a negative result and limiting repeat testing to ≥1 week of a positive result.