bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial Triple
Wolbachia
Infection in
Aedes albopictus
Yields a New Pattern of Unidirectional Cytoplasmic Incompatibility
Authors: Fu Yuqing , Gavotte Laurent , Mercer David R. , Dobson Stephen L. 
Published: July 2010

ABSTRACT

Obligately intracellular
Wolbachia
bacteria infect numerous invertebrates and often manipulate host reproduction to facilitate the spread of infection. An example of reproductive manipulation is
Wolbachia
-induced cytoplasmic incompatibility (CI), which occurs commonly in insects. This CI has been the focus both of basic scientific studies of naturally occurring invasion events and of applied investigations on the use of
Wolbachia
as a vehicle to drive desired genotypes into insect populations (“gene drive” or “population replacement” strategies). The latter application requires an ability to generate artificial infections that cause a pattern of unidirectional incompatibility with the targeted host population. A suggested target of population replacement strategies is the mosquito
Aedes albopictus
(Asian tiger mosquito), an important invasive pest and disease vector.
Aedes albopictus
individuals are naturally “superinfected” with two
Wolbachia
types:
w
AlbA and
w
AlbB. Thus, generating a strain that is unidirectionally incompatible with field populations requires the introduction of an additional infection into the preexisting superinfection. Although prior reports demonstrate an ability to transfer
Wolbachia
infections to
A. albopictus
artificially, including both intra- and interspecific
Wolbachia
transfers, previous efforts have not generated a strain capable of invading natural populations. Here we describe the generation of a stable triple infection by introducing
Wolbachia w
Ri from
Drosophila simulans
into a naturally superinfected
A. albopictus
strain. The triple-infected strain displays a pattern of unidirectional incompatibility with the naturally infected strain. This unidirectional CI, combined with a high fidelity of maternal inheritance and low fecundity effects, suggests that the artificial cytotype could serve as an appropriate vehicle for gene drive.
Molecular Detection of Hepatitis E Virus in Sewage Samples
Authors: La Rosa Giuseppina , Pourshaban Manoochehr , Iaconelli Marcello , Spuri Vennarucci Valentina , Muscillo Michele 
Published: July 2010

ABSTRACT
Human hepatitis E virus (HEV) is considered an emerging pathogen in industrialized countries. In Italy, the true burden of HEV infection is unknown. Molecular HEV screening of raw sewage samples from 11 wastewater treatment plants yielded 19 positives (16%; 18 genotype I, 1 genotype III) evenly distributed throughout Italy. Evidence that HEV could be establishing itself in our region is accumulating and may justify more active surveillance to monitor its spread.
Proteorhodopsin-Bearing Bacteria in Antarctic Sea Ice
Authors: Koh Eileen Y. , Atamna-Ismaeel Nof , Martin Andrew , Cowie Rebecca O. M. , Beja Oded , Davy Simon K. , Maas Elizabeth W. , Ryan Ken G. 
Published: July 2010

ABSTRACT

Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes
Alphaproteobacteria
,
Gammaproteobacteria
, and
Flavobacteria
. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the protein's ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.
Expression of a
Bacillus
Phytase C Gene in
Pichia pastoris
and Properties of the Recombinant Enzyme
Authors: Guerrero-Olazarán Martha , Rodríguez-Blanco Lilí , Carreon-Treviño J. Gerardo , Gallegos-López Juan A. , Viader-Salvadó José M. 
Published: July 2010

ABSTRACT

The cloning and expression of a native gene encoding a
Bacillus subtilis
phytase using
Pichia pastoris
as the host is described. In addition, the influence of N-glycosylation on the biochemical properties of the
B. subtilis
phytase, the influence of pH on the thermostability of the recombinant and native
B. subtilis
phytases, and the resistance of both phytases to shrimp digestive enzymes and porcine trypsin are also described. After 48 h of methanol induction in shake flasks, a selected recombinant strain produced and secreted 0.82 U/ml (71 mg/liter) recombinant phytase. This phytase was N-glycosylated, had a molecular mass of 39 kDa after N-deglycosylation, exhibited activity within a pH range of 2.5 to 9 and at temperatures of 25 to 70°C, had high residual activity (85% ± 2%) after 10 min of heat treatment at 80°C and pH 5.5 in the presence of 5 mM CaCl
2
, and was resistant to shrimp digestive enzymes and porcine trypsin. Although the recombinant
Bacillus
phytase had pH and temperature activity profiles that were similar to those of the corresponding nonglycosylated native phytase, the thermal stabilities of the recombinant and native phytases were different, although both were calcium concentration and pH dependent.
Isolation from
Ochrobactrum anthropi
of a Novel Class II 5-Enopyruvylshikimate-3-Phosphate Synthase with High Tolerance to Glyphosate
Authors: Tian Yong-Sheng , Xiong Ai-Sheng , Xu Jing , Zhao Wei , Gao Feng , Fu Xiao-Yan , Xu Hu , Zheng Jian-Li , Peng Ri-He , Yao Quan-Hong 
Published: July 2010

ABSTRACT

Applying the genomic library construction process and colony screening, a novel
aro
A
gene encoding 5-enopyruvylshikimate-3-phosphate synthase from
Ochrobactrum anthropi
was identified, cloned, and overexpressed, and the enzyme was purified to homogeneity. Furthermore, site-directed mutagenesis was employed to assess the role of single amino acid residues in glyphosate resistance.
Regulation of the Expression of Genes Involved in NAD
De Novo
Biosynthesis in
Corynebacterium glutamicum
Authors: Teramoto Haruhiko , Suda Masako , Inui Masayuki , Yukawa Hideaki 
Published: July 2010

ABSTRACT

Three genes,
nadA
,
nadB
, and
nadC
, involved in NAD
de novo
biosynthesis are broadly conserved in the genomes of numerous bacterial species. In the genome of
Corynebacterium glutamicum
,
nadA
and
nadC
but not
nadB
are annotated. The
nadA
and
nadC
genes are located in a gene cluster containing two other genes, designated
ndnR
and
nadS
herein.
ndnR
encodes a member of the Nudix-related transcriptional regulator (NrtR) family.
nadS
encodes a homologue of cysteine desulfurase involved in Fe-S cluster assembly. The gene cluster
ndnR
-
nadA
-
nadC
-
nadS
is genetically characterized herein. Mutant strains deficient in
nadA
,
nadC
, or
nadS
required exogenous nicotinate for growth, and the nicotinate auxotrophy was complemented by introduction of the corresponding gene in
trans
, indicating that each of these genes is essential for growth in the absence of an exogenous source of NAD biosynthesis. The results of reverse transcriptase PCR analyses and
ndnR
promoter-
lacZ
expression analyses revealed that the expression of
ndnR
,
nadA
,
nadC
, and
nadS
genes was markedly and coordinately repressed by nicotinate. The expression of these genes was enhanced by the disruption of
ndnR
, resulting in the loss of the nicotinate-responsive regulation of gene expression. These results suggest that NdnR acts as a transcriptional repressor of NAD
de novo
biosynthesis genes and plays an essential role in the regulation of the response to nicotinate.
The Abundance of Microbial Functional Genes in Grassy Woodlands Is Influenced More by Soil Nutrient Enrichment than by Recent Weed Invasion or Livestock Exclusion
Authors: Lindsay Elizabeth A. , Colloff Matthew J. , Gibb Nerida L. , Wakelin Steven A. 
Published: July 2010

ABSTRACT

A diverse soil microbial community is involved in nitrogen cycling, and these microbes can be affected by land management practices and weed invasion. We surveyed 20 woodlands with a history of livestock grazing, with livestock recently excluded from 10 sites. We investigated whether soil nutrients were lower when grazing was excluded and higher when exotic grasses dominated the understory. Second, using quantitative real-time PCR, we investigated whether microbial nitrogen functional gene (NFG) abundance was altered with soil nutrient enrichment, livestock exclusion, and exotic grass invasion. The target genes were
chiA
(decomposition-ammonification),
nifH
(nitrogen fixation),
nirK
and
narG
(denitrification), and bacterial
amoA
(nitrification). Woodland soils were enriched in phosphorus and nitrogen compared to reference condition sites, but soil nutrients were not lower following livestock exclusion. Total nitrogen and
nifH
were negatively correlated in grazed woodlands, suggesting that aboveground herbivory reduces the capacity for belowground nitrogen fixation. Woodlands dominated by exotic grasses had higher levels of nitrate,
narG
, and
nirK
than those dominated by native grasses. We hypothesize that the increase in potential for denitrification was due to increases in soil nitrate, rather than changes in plant composition. Overall, soil physicochemistry explained more variation in NFG abundance than livestock presence or plant invasion, particularly for
chiA
and bacterial
amoA
, with significant relationships between the abundance of all five NFGs and total nitrogen or nitrate. All woodlands investigated had a history of anthropogenic disturbance and nutrification, and soil nutrient levels and the abundance of NFGs are likely to be related to long-term land management practices.
Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems
Authors: Nowrousian Minou 
Published: July 2010

ABSTRACT

Over the past 5 years, large-scale sequencing has been revolutionized by the development of several so-called next-generation sequencing (NGS) technologies. These have drastically increased the number of bases obtained per sequencing run while at the same time decreasing the costs per base. Compared to Sanger sequencing, NGS technologies yield shorter read lengths; however, despite this drawback, they have greatly facilitated genome sequencing, first for prokaryotic genomes and within the last year also for eukaryotic ones. This advance was possible due to a concomitant development of software that allows the
de novo
assembly of draft genomes from large numbers of short reads. In addition, NGS can be used for metagenomics studies as well as for the detection of sequence variations within individual genomes, e.g., single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), or structural variants. Furthermore, NGS technologies have quickly been adopted for other high-throughput studies that were previously performed mostly by hybridization-based methods like microarrays. This includes the use of NGS for transcriptomics (RNA-seq) or the genome-wide analysis of DNA/protein interactions (ChIP-seq). This review provides an overview of NGS technologies that are currently available and the bioinformatics analyses that are necessary to obtain information from the flood of sequencing data as well as applications of NGS to address biological questions in eukaryotic microorganisms.
A Systems Biology Approach To Modeling
Vibrio cholerae
Gene Expression under Virulence-Inducing Conditions
Authors: Kanjilal Sanjat , Citorik Robert , LaRocque Regina C. , Ramoni Marco F. , Calderwood Stephen B. 
Published: July 2010

ABSTRACT

Vibrio cholerae
is a Gram-negative bacillus that is the causative agent of cholera. Pathogenesis
in vivo
occurs through a series of spatiotemporally controlled events under the control of a gene cascade termed the ToxR regulon. Major genes in the ToxR regulon include the master regulators
toxRS
and
tcpPH
, the downstream regulator
toxT
, and virulence factors, the
ctxAB
and
tcpA
operons. Our current understanding of the dynamics of virulence gene expression is limited to microarray analyses of expression at selected time points. To better understand this process, we utilized a systems biology approach to examine the temporal regulation of gene expression in El Tor
V. cholerae
grown under virulence-inducing conditions
in vitro
(AKI medium), using high-resolution time series genomic profiling. Results showed that overall gene expression in AKI medium mimics that of
in vivo
studies but with less clear temporal separation between upstream regulators and downstream targets. Expression of
toxRS
was unaffected by growth under virulence-inducing conditions, but expression of
toxT
was activated shortly after switching from stationary to aerating conditions. The
tcpA
operon was also activated early during mid-exponential-phase growth, while the
ctxAB
operon was turned on later, after the rise in
toxT
expression. Expression of
ctxAB
continued to rise despite an eventual decrease in
toxT
. Cluster analysis of gene expression highlighted 15 hypothetical genes and six genes related to environmental information processing that represent potential new members of the ToxR regulon. This study applies systems biology tools to analysis of gene expression of
V. cholerae
in vitro
and provides an important comparator for future studies done
in vivo
.
Structural Study of the
Serratia entomophila
Antifeeding Prophage: Three-Dimensional Structure of the Helical Sheath
Authors: Sen Anindito , Rybakova Daria , Hurst Mark R. H. , Mitra Alok K. 
Published: July 2010

ABSTRACT

The sheath of the
Serratia entomophila
antifeeding prophage, which is pathogenic to the New Zealand grass grub
Costelytra zealandica
, is a 3-fold helix formed by a 4-fold symmetric repeating motif disposed around a helical inner tube. This structure, determined by electron microscopy and image processing, is distinct from that of the other known morphologically similar bacteriophage sheaths.
A Monoacylglycerol Lipase from
Mycobacterium smegmatis
Involved in Bacterial Cell Interaction
Authors: Dhouib Rabeb , Laval Françoise , Carrière Frédéric , Daffé Mamadou , Canaan Stéphane 
Published: July 2010

ABSTRACT

MSMEG
_
0220
from
Mycobacterium smegmatis
, the ortholog of the
Rv0183
gene from
M. tuberculosis
, recently identified and characterized as encoding a monoacylglycerol lipase, was cloned and expressed in
Escherichia coli
. The recombinant protein (rMSMEG_0220), which exhibits 68% amino acid sequence identity with Rv0183, showed the same substrate specificity and similar patterns of pH-dependent activity and stability as the
M. tuberculosis
enzyme. rMSMEG_0220 was found to hydrolyze long-chain monoacylglycerol with a specific activity of 143 ± 6 U mg
−1
. Like Rv0183 in
M. tuberculosis
, MSMEG_0220 was found to be located in the cell wall. To assess the
in vivo
role of the homologous proteins, an
MSMEG
_
0220
disrupted mutant of
M. smegmatis
(MsΔ0220) was produced. An intriguing change in the colony morphology and in the cell interaction, which were partly restored in the complemented mutant containing either an active (ComMsΔ0220) or an inactive (ComMsΔ0220S111A) enzyme, was observed. Growth studies performed in media supplemented with monoolein showed that the ability of both MsΔ0220 and ComMsΔ0220S111A to grow in the presence of this lipid was impaired. Moreover, studies of the antimicrobial susceptibility of the MsΔ0220 strain showed that this mutant is more sensitive to rifampin and more resistant to isoniazid than the wild-type strain, pointing to a critical structural role of this enzyme in mycobacterial physiology, in addition to its function in the hydrolysis of exogenous lipids.
Expression of Tropodithietic Acid Biosynthesis Is Controlled by a Novel Autoinducer
Authors: Geng Haifeng , Belas Robert 
Published: July 2010

ABSTRACT

The interactions between marine prokaryotic and eukaryotic microorganisms are crucial to many biological and biogeochemical processes in the oceans. Often the interactions are mutualistic, as in the symbiosis between phytoplankton, e.g., the dinoflagellate
Pfiesteria piscicida
and
Silicibacter
sp. TM1040, a member of the
Roseobacter
taxonomic lineage. It is hypothesized that an important component of this symbiosis is bacterial production of tropodithietic acid (TDA), a biologically active tropolone compound whose synthesis requires the expression of
tda
ABCDEF
(
tdaA-F
), as well as six additional genes (
cysI
,
malY
,
paaIJK
, and
tdaH
). The factors controlling
tda
gene expression are not known, although growth in laboratory standing liquid cultures drastically increases TDA levels. In this report, we measured the transcription of
tda
genes to gain a greater understanding of the factors controlling their expression. While the expression of
tdaAB
was constitutive,
tdaCDE
and
tdaF
mRNA increased significantly (3.7- and 17.4-fold, respectively) when cells were grown in standing liquid broth compared to their levels with shaking liquid culturing. No transcription of
tdaC
was detected when a
tdaC
p
::
lacZ
transcriptional fusion was placed in 11 of the 12 Tda
−
mutant backgrounds, with
cysI
being the sole exception. The expression of
tdaC
could be restored to 9 of the remaining 11 Tda
−
mutants—
tdaA
and
tdaH
failed to respond—by placing wild-type (Tda
+
) strains in close proximity or by supplying exogenous TDA to the mutant, suggesting that TDA induces
tda
gene expression. These results indicate that TDA acts as an autoinducer of its own synthesis and suggest that roseobacters may use TDA as a quorum signal.
DNA Uptake Sequence-Mediated Enhancement of Transformation in
Neisseria gonorrhoeae
Is Strain Dependent
Authors: Duffin Paul M. , Seifert H. Steven 
Published: July 2010

ABSTRACT

Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen
Neisseria gonorrhoeae. Neisseria
spp. have been shown to preferentially take up and transform their own DNA by recognizing the nonpalindromic 10- or 12-nucleotide sequence 5′-

AT

GCCGTCTGAA-3′ (additional semiconserved nucleotides are underlined), termed the DNA uptake sequence (DUS10 or DUS12). Here we investigated the effects of the DUS on transformation and DNA uptake for several laboratory strains of
N. gonorrhoeae
. We found that all strains showed efficient transformation of DUS containing DNA (DUS10 and DUS12) but that the level of transformation with DNA lacking a DUS (DUS0) was variable in different strains. The DUS-enhanced transformation was 20-fold in two strains, FA1090 and FA19, but was approximately 150-fold in strains MS11 and 1291. All strains tested provide some level of DUS0 transformation, and DUS0 transformation was type IV pilus dependent. Competition with plasmid DNA revealed that transformation of MS11 was enhanced by the addition of excess plasmid DNA containing a DUS while FA1090 transformation was competitively inhibited. Although FA1090 was able to mediate much more efficient transformation of DNA lacking a DUS than was MS11, DNA uptake experiments showed similar levels of uptake of DNA containing and lacking a DUS in FA1090 and MS11. Finally, DNA uptake was competitively inhibited in both FA1090 and MS11. Taken together, our data indicate that the role of the DUS during DNA transformation is variable between strains of
N. gonorrhoeae
and may influence multiple steps during transformation.
Complete Genome Sequence of
Halalkalicoccus jeotgali
B3
T
, an Extremely Halophilic Archaeon
Authors: Roh Seong Woon , Nam Young-Do , Nam Seong-Hyeuk , Choi Sang-Haeng , Park Hong-Seog , Bae Jin-Woo 
Published: July 2010

ABSTRACT

Halalkalicoccus jeotgali
B3
T
, isolated from salt-fermented seafood from South Korea, is an extremely halophilic archaeon belonging to the family
Halobacteriaceae
. Here, we present the complete genome sequence of the type strain
H. jeotgali
B3
T
(3,698,650 bp, with a G+C content of 62.5%), which consists of one chromosome and six plasmids. This is the first complete genome sequence of the
Halalkalicoccus
species.
U.S. Food and Drug Administration Approval: Ofatumumab for the Treatment of Patients with Chronic Lymphocytic Leukemia Refractory to Fludarabine and Alemtuzumab
Authors: Lemery Steven J. , Zhang Jenny , Rothmann Mark D. , Yang Jun , Earp Justin , Zhao Hong , McDougal Andrew , Pilaro Anne , Chiang Raymond , Gootenberg Joseph E. , Keegan Patricia , Pazdur Richard 
Published: July 2010

Abstract
Purpose: To describe the data and analyses that led to the U.S. Food and Drug Administration (FDA) approval of ofatumumab (Arzerra, GlaxoSmithKline) for the treatment of patients with chronic lymphocytic leukemia (CLL) refractory to fludarabine and alemtuzumab.
Experimental Design: The FDA reviewed the results of a planned interim analysis of a single-arm trial, enrolling 154 patients with CLL refractory to fludarabine, and a supportive dose-finding, activity-estimating trial in 33 patients with CLL. Patients in the primary efficacy study received ofatumumab weekly for eight doses, then every 4 weeks for an additional four doses; patients in the supportive trial received four weekly doses. In the primary efficacy study, endpoints were objective response rate and response duration.
Results: For regulatory purposes, the primary efficacy population consisted of 59 patients with CLL refractory to fludarabine and alemtuzumab. In this subgroup, the investigator-determined objective response rate was 42% [99% confidence interval (CI), 26–60], with a median duration of response of 6.5 months (95% CI, 5.8–8.3); all were partial responses. The most common adverse reactions in the primary efficacy study were neutropenia, pneumonia, pyrexia, cough, diarrhea, anemia, fatigue, dyspnea, rash, nausea, bronchitis, and upper respiratory tract infections. Infusion reactions occurred in 44% of patients with the first infusion (300 mg) and 29% with the second infusion (2,000 mg). The most common serious adverse reactions were infections, neutropenia, and pyrexia.
Conclusions: On October 26, 2009, the FDA granted accelerated approval to ofatumumab for the treatment of patients with CLL refractory to fludarabine and alemtuzumab, on the basis of demonstration of durable tumor shrinkage. Clin Cancer Res; 16(17); 4331–8. ©2010 AACR.