bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Better Local Governance Improve District Growth Performance in Indonesia?
Authors: McCulloch Neil , Malesky Edmund 
Published: August 2011

SummaryA large literature suggests that countries with better governance have higher growth rates. We explore whether this is also true at the sub‐national level in Indonesia. We exploit a new dataset of firm perceptions of the quality of economic governance in 243 districts across Indonesia to estimate the impact of nine different dimensions of governance on district growth. Surprisingly, we find relatively little evidence of a robust relationship between the quality of governance and economic performance. However, we do find support for the idea that structural variables, such as economic size, natural resource endowments and population, have a direct influence on the quality of local governance as well as on economic growth. This suggests that efforts to improve local governance should pay greater attention to understanding how such structural characteristics shape the local political economy and how this in turn influences economic performance.
Two Novel Alkane Hydroxylase-Rubredoxin Fusion Genes Isolated from a Dietzia Bacterium and the Functions of Fused Rubredoxin Domains in Long-Chain
n
-Alkane Degradation
Authors: Nie Yong , Liang Jieliang , Fang Hui , Tang Yue-Qin , Wu Xiao-Lei 
Published: August 2011

ABSTRACT

Two alkane hydroxylase-rubredoxin fusion gene homologs (
alkW1
and
alkW2
) were cloned from a
Dietzia
strain, designated DQ12-45-1b, which can grow on crude oil and
n
-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the
alkW1
gene in DQ12-45-1b was induced when cells were grown on C
8
to C
32
n
-alkanes as sole carbon sources, but expression of the
alkW2
gene was not detected. Functional heterologous expression in an
alkB
deletion mutant of
Pseudomonas fluorescens
KOB2Δ1 suggested the
alkW1
could restore the growth of KOB2Δ1 on C
14
and C
16
n
-alkanes and induce faster growth on C
18
to C
32
n
-alkanes than
alkW1
ΔRd, the Rd domain deletion mutant gene of
alkW1
, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative
P. fluorescens
CHA0 and the Rds from both Gram-negative
P. fluorescens
CHA0 and Gram-positive
Dietzia
sp. DQ12-45-1b significantly increased the degradation of C
32
alkane compared to that seen with AlkB itself. In conclusion, the
alkW1
gene cloned from
Dietzia
species encoded an alkane hydroxylase which increased growth on and degradation of
n
-alkanes up to C
32
in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain
n
-alkanes (such as C
32
) in the Gram-negative bacterium.
Niche Partitioning of Marine Group I Crenarchaeota in the Euphotic and Upper Mesopelagic Zones of the East China Sea
Authors: Hu Anyi , Jiao Nianzhi , Zhang Rui , Yang Zao 
Published: August 2011

ABSTRACT

Marine group I
Crenarchaeota
(MGI) represents a ubiquitous and numerically predominant microbial population in marine environments. An understanding of the spatial dynamics of MGI and its controlling mechanisms is essential for an understanding of the role of MGI in energy and element cycling in the ocean. In the present study, we investigated the diversity and abundance of MGI in the East China Sea (ECS) by analysis of crenarchaeal 16S rRNA gene, the ammonia monooxygenase gene
amoA
, and the biotin carboxylase gene
accA
. Quantitative PCR analyses revealed that these genes were higher in abundance in the mesopelagic than in the euphotic zone. In addition, the crenarchaeal
amoA
gene was positively correlated with the copy number of the MGI 16S rRNA gene, suggesting that most of the MGI in the ECS are nitrifiers. Furthermore, the ratios of crenarchaeal
accA
to
amoA
or to MGI 16S rRNA genes increased from the euphotic to the mesopelagic zone, suggesting that the role of MGI in carbon cycling may change from the epipelagic to the mesopelagic zones. Denaturing gradient gel electrophoretic profiling of the 16S rRNA genes revealed depth partitioning in MGI community structures. Clone libraries of the crenarchaeal
amoA
and
accA
genes showed both “shallow” and “deep” groups, and their relative abundances varied in the water column. Ecotype simulation analysis revealed that MGI in the upper ocean could diverge into special ecotypes associated with depth to adapt to the light gradient across the water column. Overall, our results showed niche partitioning of the MGI population and suggested a shift in their ecological functions between the euphotic and mesopelagic zones of the ECS.
Merging Taxonomy with Ecological Population Prediction in a Case Study of Vibrionaceae
Authors: Preheim Sarah P. , Timberlake Sonia , Polz Martin F. 
Published: August 2011

ABSTRACT

We synthesized population structure data from three studies that assessed the fine-scale distribution of
Vibrionaceae
among temporally and spatially distinct environmental categories in coastal seawater and animals. All studies used a dynamic model (AdaptML) to identify phylogenetically cohesive and ecologically distinct bacterial populations and their predicted habitats without relying on a predefined genetic cutoff or relationships to previously named species. Across the three studies, populations were highly overlapping, displaying similar phylogenetic characteristics (identity and diversity), and were predominantly congruent with taxonomic
Vibrio
species previously characterized as genotypic clusters by multilocus sequence analysis (MLSA). The environmental fidelity of these populations appears high, with 9 out of 12 reproducibly associating with the same predicted (micro)habitats when similar environmental categories were sampled. Overall, this meta-analysis provides information on the habitat predictability and structure of previously described species, demonstrating that MLSA-based taxonomy can, at least in some cases, serve to approximate ecologically cohesive populations.
Alga-Derived Substrates Select for Distinct Betaproteobacterial Lineages and Contribute to Niche Separation in Limnohabitans Strains
Authors: Šimek Karel , Kasalický Vojtěch , Zapomělová Eliška , Horňák Karel 
Published: August 2011

ABSTRACT

We examined the proportions of major Betaproteobacteria subgroups within bacterial communities in diverse nonaxenic, monospecific cultures of algae or cyanobacteria: four species of cryptophyta (genera
Cryptomonas
and
Rhodomonas
), four species of chlorophyta (genera
Pediastrum
,
Staurastrum
, and
Chlamydomonas
), and two species of cyanobacteria (genera
Dolichospermum
and
Aphanizomenon
). In the cryptophyta cultures,
Betaproteobacteria
represented 48 to 71% of total bacteria, the genus
Limnohabitans
represented 18 to 26%, and the
Polynucleobacter
B subcluster represented 5 to 16%. In the taxonomically diverse chlorophyta group, the genus
Limnohabitans
accounted for 7 to 45% of total bacteria. In contrast, cyanobacterial cultures contained significantly lower proportions of the
Limnohabitans
bacteria (1 to 3% of the total) than the cryptophyta and chlorophyta cultures. Notably, largely absent in all of the cultures was
Polynucleobacter necessarius
(
Polynucleobacter
C subcluster). Subsequently, we examined the growth of
Limnohabitans
strains in the presence of different algae or their extracellular products (EPP). Two strains, affiliated with
Limnohabitans
planktonicus
and
Limnohabitans
parvus
, were separately inoculated into axenic cultures of three algal species growing in an inorganic medium:
Cryptomonas
sp.,
Chlamydomonas noctigama
, and
Pediastrum boryanum
. The
Limnohabitans
strains cocultured with these algae or inoculated into their EPP consistently showed (i) pronounced population growth compared to the control without the algae or EPP and (ii) stronger growth stimulation of
L. planktonicus
than of
L. parvus.
Overall, growth responses of the
Limnohabitans
strains cultured with algae were highly species specific, which suggests a pronounced niche separation between two closely related
Limnohabitans
species likely mediated by different abilities to utilize the substrates produced by different algal species.
Comparison of the Gut Microbiotas of Healthy Adult Twins Living in South Korea and the United States
Authors: Lee Sunghee , Sung Joohon , Lee JungEun , Ko GwangPyo 
Published: August 2011

ABSTRACT
We compared the composition of the fecal microbiotas of Korean and U.S. adult twins. Our data indicated that the gut microbiota shows some signature of biogeography, potentially mediated by differences in diet and/or other environmental factors; however, these regional differences may be masked by other phenotypic variations, such as obesity.
Relationships between Free-Living Protozoa, Cultivable Legionella spp., and Water Quality Characteristics in Three Drinking Water Supplies in the Caribbean
Authors: Valster Rinske M. , Wullings Bart A. , van den Berg Riemsdijk , van der Kooij Dick 
Published: August 2011

ABSTRACT

The study whose results are presented here aimed at identifying free-living protozoa (FLP) and conditions favoring the growth of these organisms and cultivable
Legionella
spp. in drinking water supplies in a tropical region. Treated and distributed water (±30°C) of the water supplies of three Caribbean islands were sampled and investigated with molecular techniques, based on the 18S rRNA gene. The protozoan host
Hartmannella vermiformis
and cultivable
Legionella pneumophila
were observed in all three supplies. Operational taxonomic units (OTUs) with the highest similarity to the potential or candidate hosts
Acanthamoeba
spp.,
Echinamoeba exundans
,
E. thermarum
, and an
Neoparamoeba
sp. were detected as well. In total, 59 OTUs of FLP were identified. The estimated protozoan richness did not differ significantly between the three supplies. In supply CA-1, the concentration of
H. vermiformis
correlated with the concentration of
Legionella
spp. and clones related to Amoebozoa predominated (82%) in the protozoan community. These observations, the low turbidity (<0.2 nephelometric turbidity units [NTU]), and the varying ATP concentrations (1 to 12 ng liter
−1
) suggest that biofilms promoted protozoan growth in this supply. Ciliophora represented 25% of the protozoan OTUs in supply CA-2 with elevated ATP concentrations (maximum, 55 ng liter
−1
) correlating with turbidity (maximum, 62 NTU) caused by corroding iron pipes. Cercozoan types represented 70% of the protozoan clones in supply CA-3 with ATP concentrations of <1 ng liter
−1
and turbidity of <0.5 NTU in most samples of distributed water. The absence of
H. vermiformis
in most samples from supply CA-3 suggests that growth of this protozoan is limited at ATP concentrations of <1 ng liter
−1
.
Identification and Targeted Cultivation of Abundant Novel Freshwater Sphingomonads and Analysis of Their Population Substructure
Authors: Jogler Mareike , Siemens Helge , Chen Hong , Bunk Boyke , Sikorski Johannes , Overmann Jörg 
Published: August 2011

ABSTRACTLittle is known with respect to bacterial population structures in freshwater environments. Using complementary culture-based, cloning, and high-throughput Illumina sequencing approaches, we investigated microdiverse clusters of bacteria that comprise members with identical or very similar 16S rRNA gene sequences. Two 16S rRNA phylotypes could be recovered by cultivation in low-nutrient-strength liquid media from two lakes of different trophic status. Both phylotypes were found to be physiologically activein situthroughout most of the year, as indicated by the presence of their rRNA sequences in the samples. Analyses of internal transcribed spacer (ITS1) sequences revealed the presence of seven different sequence types among cultured representatives and the clonedrrnfragments. Illumina sequencing yielded 8,576 ITS1 sequences that encompassed 15 major and numerous rare sequence types. The major ITS1 types exhibited distinct temporal patterns, suggesting that the correspondingSphingomonadaceaelineages occupy different ecological niches. However, since strains of the same ITS1 type showed highly variable substrate utilization patterns, the potential mechanism of niche separation inSphingomonadaceaecannot be explained by substrate utilization alone and may be related to other traits.
Anatoxin-a Synthetase Gene Cluster of the Cyanobacterium Anabaena sp. Strain 37 and Molecular Methods To Detect Potential Producers
Authors: Rantala-Ylinen Anne , Känä Suvi , Wang Hao , Rouhiainen Leo , Wahlsten Matti , Rizzi Ermanno , Berg Katri , Gugger Muriel , Sivonen Kaarina 
Published: August 2011

ABSTRACT

Cyanobacterial mass occurrences are common in fresh and brackish waters. They pose a threat to water users due to toxins frequently produced by the cyanobacterial species present. Anatoxin-a and homoanatoxin-a are neurotoxins synthesized by various cyanobacteria, e.g.,
Anabaena
,
Oscillatoria
, and
Aphanizomenon
. The biosynthesis of these toxins and the genes involved in anatoxin production were recently described for
Oscillatoria
sp. strain PCC 6506 (A. Méjean et al., J. Am. Chem. Soc.
131:
7512-7513, 2009). In this study, we identified the anatoxin synthetase gene cluster (
anaA
to
anaG
and
orf1
; 29 kb) in
Anabaena
sp. strain 37. The gene (81.6% to 89.2%) and amino acid (78.8% to 86.9%) sequences were highly similar to those of
Oscillatoria
sp. PCC 6506, while the organization of the genes differed. Molecular detection methods for potential anatoxin-a and homoanatoxin-a producers of the genera
Anabaena
,
Aphanizomenon
, and
Oscillatoria
were developed by designing primers to recognize the
anaC
gene.
Anabaena
and
Oscillatoria anaC
genes were specifically identified in several cyanobacterial strains by PCR. Restriction fragment length polymorphism (RFLP) analysis of the
anaC
amplicons enabled simultaneous identification of three producer genera:
Anabaena
,
Oscillatoria
, and
Aphanizomenon
. The molecular methods developed in this study revealed the presence of both
Anabaena
and
Oscillatoria
as potential anatoxin producers in Finnish fresh waters and the Baltic Sea; they could be applied for surveys of these neurotoxin producers in other aquatic environments.
Directed Chromosomal Integration and Expression of the Reporter Gene
gusA3
in Lactobacillus acidophilus NCFM
Authors: Douglas Grace L. , Klaenhammer Todd R. 
Published: August 2011

ABSTRACT

Lactobacillus acidophilus
NCFM is a probiotic microbe that survives passage through the human gastrointestinal tract and interacts with the host epithelium and mucosal immune cells. The potential for
L. acidophilus
to express antigens at mucosal surfaces has been investigated with various antigens and plasmid expression vectors. Plasmid instability and antibiotic selection complicate the possibility of testing these constructs in human clinical trials. Integrating antigen encoding genes into the chromosome for expression is expected to eliminate selection requirements and provide genetic stability. In this work, a reporter gene encoding a β-glucuronidase (GusA3) was integrated into four intergenic chromosomal locations. The integrants were tested for genetic stability and GusA3 activity. Two locations were selected for insertion downstream of constitutively highly expressed genes, one downstream of
slpA
(LBA0169), encoding a highly expressed surface-layer protein, and one downstream of phosphopyruvate hydratase (LBA0889), a highly expressed gene with homologs in other lactic acid bacteria. An inducible location was selected downstream of
lacZ
(LBA1462), encoding a β-galactosidase. A fourth location was selected in a low-expression region. The expression of
gusA3
was evaluated from each location by measuring GusA3 activity on 4-methyl-umbelliferyl-β-
d
-glucuronide (MUG). GusA3 activity from both highly expressed loci was more than three logs higher than the
gusA3
-negative parent,
L. acidophilus
NCK1909. GusA3 activity from the
lacZ
locus was one log higher in cells grown in lactose than in glucose. The differences in expression levels between integration locations highlights the importance of rational targeting with gene cassettes intended for chromosomal expression.
Occurrence of Intestinal and Extraintestinal Virulence Genes in Escherichia coli Isolates from Rainwater Tanks in Southeast Queensland, Australia
Authors: Ahmed W. , Hodgers L. , Masters N. , Sidhu J. P. S. , Katouli M. , Toze S. 
Published: August 2011

ABSTRACT

In this study, 200
Escherichia coli
isolates from 22 rainwater tank samples in Southeast Queensland, Australia, were tested for the presence of 20 virulence genes (VGs) associated with intestinal and extraintestinal pathotypes. In addition,
E. coli
isolates were also classified into phylogenetic groups based on the detection of the
chuA
,
yjaA
, and TSPE4.C2 genes. Of the 22 rainwater tanks, 8 (36%) and 5 (23%) were positive for the
eaeA
(belonging to enteropathogenic
E. coli
[EPEC] and Shiga-toxigenic
E. coli
[STEC]) and ST1 (belonging to enterotoxigenic
E. coli
[ETEC]) genes, respectively. VGs (
cdtB
,
cvaC
,
ibeA
,
kpsMT
allele III, PAI,
papAH
, and
traT
) belonging to extraintestinal pathogenic
E. coli
(ExPEC) were detected in 15 (68%) of the 22 rainwater tanks. Of the 22 samples, 17 (77%) and 11 (50%) contained
E. coli
belonging to phylogenetic groups A and B1, respectively. Similarly, 10 (45%) and 16 (72%) contained
E. coli
belonging to phylogenetic groups B2 and D, respectively. Of the 96 of the 200 strains from 22 tanks that were VG positive, 40 (42%) were carrying a single VG, 36 (37.5%) were carrying two VGs, 17 (18%) were carrying three VGs, and 3 (3%) had four or more VGs. This study reports the presence of multiple VGs in
E. coli
strains belonging to the STEC, EPEC, ETEC, and ExPEC pathotypes in rainwater tanks. The public health risks associated with potentially clinically significant
E. coli
in rainwater tanks should be assessed, as the water is used for drinking and other, nonpotable purposes. It is recommended that rainwater be disinfected using effective treatment procedures such as filtration, UV disinfection, or simply boiling prior to drinking.
The Paf1 Complex Represses
SER3
Transcription in Saccharomyces cerevisiae by Facilitating Intergenic Transcription-Dependent Nucleosome Occupancy of the
SER3
Promoter
Authors: Pruneski Justin A. , Hainer Sarah J. , Petrov Kostadin O. , Martens Joseph A. 
Published: August 2011

ABSTRACT

Previous studies have shown that repression of the
Saccharomyces cerevisiae
SER3
gene is dependent on transcription of
SRG1
from noncoding DNA initiating within the intergenic region 5′ of
SER3
and extending across the
SER3
promoter region. By a mechanism dependent on the activities of the Swi/Snf chromatin remodeling factor, the HMG-like factor Spt2, and the Spt6 and Spt16 histone chaperones,
SRG1
transcription deposits nucleosomes over the
SER3
promoter to prevent transcription factors from binding and activating
SER3
. In this study, we uncover a role for the Paf1 transcription elongation complex in
SER3
repression. We find that
SER3
repression is primarily dependent on the Paf1 and Ctr9 subunits of this complex, with minor contributions by the Rtf1, Cdc73, and Leo1 subunits. We show that the Paf1 complex localizes to the
SRG1
transcribed region under conditions that repress
SER3
, consistent with it having a direct role in mediating
SRG1
transcription-dependent
SER3
repression. Importantly, we show that the defect in
SER3
repression in strains lacking Paf1 subunits is not a result of reduced
SRG1
transcription or reduced levels of known Paf1 complex-dependent histone modifications. Rather, we find that strains lacking subunits of the Paf1 complex exhibit reduced nucleosome occupancy and reduced recruitment of Spt16 and, to a lesser extent, Spt6 at the
SER3
promoter. Taken together, our results suggest that Paf1 and Ctr9 repress
SER3
by maintaining
SRG1
transcription-dependent nucleosome occupancy.
RNA-Binding Protein Khd1 and Ccr4 Deadenylase Play Overlapping Roles in the Cell Wall Integrity Pathway in Saccharomyces cerevisiae
Authors: Ito Wataru , Li Xia , Irie Kaoru , Mizuno Tomoaki , Irie Kenji 
Published: August 2011

ABSTRACT

The
Saccharomyces cerevisiae
RNA-binding protein Khd1/Hek2 associates with hundreds of potential mRNA targets preferentially, including the mRNAs encoding proteins localized to the cell wall and plasma membrane. We have previously revealed that Khd1 positively regulates expression of
MTL1
mRNA encoding a membrane sensor in the cell wall integrity (CWI) pathway. However, a
khd1
Δ mutation has no detectable phenotype on cell wall synthesis. Here we show that the
khd1
Δ mutation causes a severe cell lysis when combined with the deletion of the
CCR4
gene encoding a cytoplasmic deadenylase. We identified the
ROM2
mRNA, encoding a guanine nucleotide exchange factor (GEF) for Rho1, as a target for Khd1 and Ccr4. The
ROM2
mRNA level was decreased in the
khd1
Δ
ccr4
Δ mutant, and
ROM2
overexpression suppressed the cell lysis of the
khd1
Δ
ccr4
Δ mutant. We also found that Ccr4 negatively regulates expression of the
LRG1
mRNA encoding a GTPase-activating protein (GAP) for Rho1. The
LRG1
mRNA level was increased in the
ccr4
Δ and
khd1
Δ
ccr4
Δ mutants, and deletion of
LRG1
suppressed the cell lysis of the
khd1
Δ
ccr4
Δ mutant. Our results presented here suggest that Khd1 and Ccr4 modulate a signal from Rho1 in the CWI pathway by regulating the expression of RhoGEF and RhoGAP.
XoxF Is Required for Expression of Methanol Dehydrogenase in Methylobacterium extorquens AM1
Authors: Skovran Elizabeth , Palmer Alexander D. , Rountree Austin M. , Good Nathan M. , Lidstrom Mary E. 
Published: August 2011

ABSTRACT

In Gram-negative methylotrophic bacteria, the first step in methylotrophic growth is the oxidation of methanol to formaldehyde in the periplasm by methanol dehydrogenase. In most organisms studied to date, this enzyme consists of the MxaF and MxaI proteins, which make up the large and small subunits of this heterotetrameric enzyme. The
Methylobacterium extorquens
AM1 genome contains two homologs of MxaF, XoxF1 and XoxF2, which are ∼50% identical to MxaF and ∼90% identical to each other. It was previously reported that
xoxF
is not required for methanol growth in
M. extorquens
AM1, but here we show that when both
xoxF
homologs are absent, strains are unable to grow in methanol medium and lack methanol dehydrogenase activity. We demonstrate that these defects result from the loss of gene expression from the
mxa
promoter and suggest that XoxF is part of a complex regulatory cascade involving the 2-component systems MxcQE and MxbDM, which are required for the expression of the methanol dehydrogenase genes.