bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Detection and Enumeration of Giardia lamblia Cysts in Water Samples by Immunomagnetic Separation and Flow Cytometric Analysis
Authors: Keserue Hans-Anton , Füchslin Hans Peter , Egli Thomas 
Published: June 2011

ABSTRACT

Giardia lamblia
is an important waterborne pathogen and is among the most common intestinal parasites of humans worldwide. Its fecal-oral transmission leads to the presence of cysts of this pathogen in the environment, and so far, quantitative rapid screening methods are not available for various matrices, such as surface waters, wastewater, or food. Thus, it is necessary to establish methods that enable reliable rapid detection of a single cyst in 10 to 100 liters of drinking water. Conventional detection relies on cyst concentration, isolation, and confirmation by immunofluorescence microscopy (IFM), resulting in low recoveries and high detection limits. Many different immunomagnetic separation (IMS) procedures have been developed for separation and cyst purification, so far with variable but high losses of cysts. A method was developed that requires less than 100 min and consists of filtration, resuspension, IMS, and flow cytometric (FCM) detection. MACS MicroBeads were used for IMS, and a reliable flow cytometric detection approach was established employing 3 different parameters for discrimination from background signals, i.e., green and red fluorescence (resulting from the distinct pattern emitted by the fluorescein dye) and sideward scatter for size discrimination. With spiked samples, recoveries exceeding 90% were obtained, and false-positive results were never encountered for negative samples. Additionally, the method was applicable to naturally occurring cysts in wastewater and has the potential to be automated.
Analysis of
bla
CTX-M
-Carrying Plasmids from Escherichia coli Isolates Collected in the BfT-GermVet Study
Authors: Schink Anne-Kathrin , Kadlec Kristina , Schwarz Stefan 
Published: June 2011

ABSTRACT

In this study, 417
Escherichia coli
isolates from defined disease conditions of companion and farm animals collected in the BfT-GermVet study were investigated for the presence of extended-spectrum β-lactamase (ESBL) genes. Three ESBL-producing
E. coli
isolates were identified among the 100 ampicillin-resistant isolates. The
E. coli
isolates 168 and 246, of canine and porcine origins, respectively, harbored
bla
CTX-M-1
, and the canine isolate 913 harbored
bla
CTX-M-15
, as confirmed by PCR and sequence analysis. The isolates 168 and 246 belonged to the novel multilocus sequence typing (MLST) types ST1576 and ST1153, respectively, while isolate 913 had the MLST type ST410. The ESBL genes were located on structurally related IncN plasmids in isolates 168 and 246 and on an IncF plasmid in isolate 913. The
bla
CTX-M-1
upstream regions of plasmids pCTX168 and pCTX246 were similar, whereas the downstream regions showed structural differences. The genetic environment of the
bla
CTX-M-15
gene on plasmid pCTX913 differed distinctly from that of both
bla
CTX-M-1
genes. Detailed sequence analysis showed that the integration of insertion sequences, as well as interplasmid recombination events, accounted for the structural variability in the
bla
CTX-M
gene regions.
Environmental, Biogeographic, and Biochemical Patterns of Archaea of the Family Ferroplasmaceae
Authors: Golyshina Olga V. 
Published: June 2011

ABSTRACT

About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea,
Ferroplasmaceae
, within the large archaeal phylum
Euryarchaeota
, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.
Systematic Search for Cultivatable Fungi That Best Deconstruct Cell Walls of Miscanthus and Sugarcane in the Field
Authors: Shrestha Prachand , Szaro Timothy M. , Bruns Thomas D. , Taylor John W. 
Published: June 2011

ABSTRACT

The goals of our project were to document the diversity and distributions of cultivable fungi associated with decaying
Miscanthus
and sugarcane plants in nature and to further assess biodegradation of host plant cell walls by these fungi in pure cultures. Late in 2008 and early in 2009 we collected decaying
Miscanthus
and
Saccharum
from 8 sites in Illinois and 11 sites in Louisiana, respectively. To recover fungi that truly decay plants and to recover slow-growing fungi, we washed the plant material repeatedly to remove spores and cultivated fungi from plant fragments small enough to harbor at most one mycelium. We randomly selected 950 fungal colonies out of 4,560 microwell colonies and used molecular identification to discover that the most frequently recovered fungal species resided in
Hypocreales
(
Sordariomycetes
),
Pleosporales
(
Dothideomycetes
), and
Chaetothryiales
(
Eurotiomycetes
) and that only a few weedy species were recovered. We were particularly interested in
Pleosporales
and
Chaetothyriales
, groups that have not been mined for plant decay fungi. To confirm that we had truly recovered fungi that deconstruct plant cell walls, we assayed the capacity of the fungi to consume whole, alkali-pretreated, ground
Miscanthus
. Solid substrate cultures of the nine most commonly encountered
Ascomycota
resulted in
Miscanthus
weight loss of 8 to 13% over 4 weeks. This is the first systematic, high-throughput, isolation and biodegradation assessment of fungi isolated from decaying bioenergy grasses.
Increased Furfural Tolerance Due to Overexpression of NADH-Dependent Oxidoreductase FucO in Escherichia coli Strains Engineered for the Production of Ethanol and Lactate
Authors: Wang X. , Miller E. N. , Yomano L. P. , Zhang X. , Shanmugam K. T. , Ingram L. O. 
Published: June 2011

ABSTRACT

Furfural is an important fermentation inhibitor in hemicellulose sugar syrups derived from woody biomass. The metabolism of furfural by NADPH-dependent oxidoreductases, such as YqhD (low

K
m

for NADPH), is proposed to inhibit the growth and fermentation of xylose in
Escherichia coli
by competing with biosynthesis for NADPH. The discovery that the NADH-dependent propanediol oxidoreductase (FucO) can reduce furfural provided a new approach to improve furfural tolerance. Strains that produced ethanol or lactate efficiently as primary products from xylose were developed. These strains included chromosomal mutations in
yqhD
expression that permitted the fermentation of xylose broths containing up to 10 mM furfural. Expression of
fucO
from plasmids was shown to increase furfural tolerance by 50% and to permit the fermentation of 15 mM furfural. Product yields with 15 mM furfural were equivalent to those of control strains without added furfural (85% to 90% of the theoretical maximum). These two defined genetic traits can be readily transferred to enteric biocatalysts designed to produce other products. A similar strategy that minimizes the depletion of NADPH pools by native detoxification enzymes may be generally useful for other inhibitory compounds in lignocellulosic sugar streams and with other organisms.
Rickettsia monteiroi sp. nov., Infecting the Tick Amblyomma incisum in Brazil
Authors: Pacheco Richard C. , Moraes-Filho Jonas , Marcili Arlei , Richtzenhain Leonardo J. , Szabó Matias P. J. , Catroxo Márcia H. B. , Bouyer Donald H. , Labruna Marcelo B. 
Published: June 2011

ABSTRACTFree-living adultAmblyomma incisumticks were collected in an Atlantic rainforest area at Intervales State Park, State of São Paulo, Brazil. From anA. incisumspecimen, rickettsiae were successfully isolated in Vero cell culture by the shell vial technique. Rickettsial isolation was confirmed by optical microscopy, transmission electron microscopy, and PCRs targeting portions of the rickettsial genesgltA,htrA,rrs, andsca1on infected cells. Fragments of 1,089, 457, 1,362, and 443 nucleotides of thegltA,htrA,rrs, andsca1genes, respectively, were sequenced. By BLAST analysis, the partial sequence ofrrsof theA. incisumrickettsial isolate was closest to the corresponding sequence ofRickettsia bellii(99.1% similarity). ThegltApartial sequence was closest to the corresponding sequences of “CandidatusRickettsia tarasevichiae” (96.1% similarity) andRickettsia canadensis(95.8% similarity). ThehtrApartial sequence was closest to the corresponding sequence ofR. canadensis(89.8% similarity). Thesca1partial sequence was closest to the corresponding sequence ofR. canadensis(95.2% similarity). Since our rickettsial isolate was genetically distinct from otherRickettsiaspecies, we propose a new species designatedRickettsia monteiroisp. nov. Phylogenetic analyses indicated thatR. monteiroibelongs to the canadensis group within the genusRickettsia, together with the speciesR. canadensisand “CandidatusR. tarasevichiae”. Little or no antibody cross-reaction was observed between sera ofR. monteiroi-inoculated guinea pigs andR. bellii-,Rickettsia rickettsii-, orR. canadensis-inoculated guinea pigs.
Variation among Plasmodium falciparum Strains in Their Reliance on Mitochondrial Electron Transport Chain Function
Authors: Ke Hangjun , Morrisey Joanne M. , Ganesan Suresh M. , Painter Heather J. , Mather Michael W. , Vaidya Akhil B. 
Published: June 2011

ABSTRACT

Previous studies demonstrated that
Plasmodium falciparum
strain D10 became highly resistant to the mitochondrial electron transport chain (mtETC) inhibitor atovaquone when the mtETC was decoupled from the pyrimidine biosynthesis pathway by expressing the fumarate-dependent (ubiquinone-independent) yeast dihydroorotate dehydrogenase (yDHODH) in parasites. To investigate the requirement for decoupled mtETC activity in
P. falciparum
with different genetic backgrounds, we integrated a single copy of the yDHODH gene into the genomes of D10attB, 3D7attB, Dd2attB, and HB3attB strains of the parasite. The yDHODH gene was equally expressed in all of the transgenic lines. All four yDHODH transgenic lines showed strong resistance to atovaquone in standard short-term growth inhibition assays. During longer term growth with atovaquone, D10attB-yDHODH and 3D7attB-yDHODH parasites remained fully resistant, but Dd2attB-yDHODH and HB3attB-yDHODH parasites lost their tolerance to the drug after 3 to 4 days of exposure. No differences were found, however, in growth responses among all of these strains to the
Plasmodium
-specific DHODH inhibitor DSM1 in either short- or long-term exposures. Thus, DSM1 works well as a selective agent in all parasite lines transfected with the yDHODH gene, whereas atovaquone works for some lines. We found that the ubiquinone analog decylubiquinone substantially reversed the atovaquone inhibition of Dd2attB-yDHODH and HB3attB-yDHODH transgenic parasites during extended growth. Thus, we conclude that there are strain-specific differences in the requirement for mtETC activity among
P. falciparum
strains, suggesting that, in erythrocytic stages of the parasite, ubiquinone-dependent dehydrogenase activities other than those of DHODH are dispensable in some strains but are essential in others.
Genetic and Biochemical Analysis of PadR-
padC
Promoter Interactions during the Phenolic Acid Stress Response in Bacillus subtilis 168
Authors: Nguyen Thi Kim Chi , Tran Ngoc Phuong , Cavin Jean-François 
Published: June 2011

ABSTRACT

Bacillus subtilis
168 is resistant to phenolic acids by expression of an inducible enzyme, the phenolic acid decarboxylase (PadC), that decarboxylates these acids into less toxic vinyl derivatives. In the phenolic acid stress response (PASR), the repressor of
padC
, PadR, is inactivated by these acids. Inactivation of PadR is followed by a strong expression of
padC
. To elucidate the functional interaction between PadR and the
padC
promoter, we performed (i) footprinting assays to identify the region protected by PadR, (ii) electrophoretic mobility shift assays (EMSAs) with a modified
padC
promoter protected region to determine the interacting sequences, and (iii) random mutagenesis of
padR
to identify amino acid residues essential for the function of PadR. We identified an important consensus dyad sequence called IR1-2 (ATGT-8N-ACAT) overlapping a second dyad element (GTGT-8N-ACAT) that we named dIR1-2bis. The entire dIR1-2bis/IR1-2 sequence permits binding of two PadR dimers in EMSAs, which may be observed for bacteria grown under noninduced conditions where the
padC
promoter is completely repressed. Three groups of modified PadRs giving a PASR phenotype were characterized
in vivo
. The DNA sequences of certain mutant
padR
alleles indicate that important residues are all located in the region containing the coiled-coil leucine zipper domain that is involved in dimerization. These substitutions reduce the affinity of PadR binding to the
padC
promoter. Of particular interest are residue L128, located at the center of the putative coiled-coil leucine zipper domain, and residue E97, which is conserved among all PadRs.
Refining the Binding of the Escherichia coli Flagellar Master Regulator, FlhD
4
C
2
, on a Base-Specific Level
Authors: Lee Yi-Ying , Barker Clive S. , Matsumura Philip , Belas Robert 
Published: June 2011

ABSTRACT

The
Escherichia coli
flagellar master regulator, FlhD
4
C
2
, binds to the promoter regions of flagellar class II genes, yet, despite extensive analysis of the FlhD
4
C
2
-regulated promoter region, a detailed consensus sequence has not emerged. We used
in vitro
and
in vivo
experimental approaches to determine the nucleotides in the class II promoter,
fliAp
, required for the binding and function of FlhD
4
C
2
. FlhD
4
C
2
protects 48 bp (positions −76 to −29 relative to the σ
70
-dependent transcriptional start site) in the
fliA
promoter. We divided the 48-bp footprint region into 5 sections to determine the requirement of each DNA segment for the binding and function of FlhD
4
C
2
. Results from an
in vitro
binding competition assay between the wild-type FlhD
4
C
2
-protected fragment and DNA fragments possessing mutations in one section of the 48-bp protected region showed that only one-third of the 48 bp protected by FlhD
4
C
2
is required for FlhD
4
C
2
binding and
fliA
promoter activity. This
in vitro
binding result was also seen
in vivo
with
fliA
promoter-
lacZ
fusions carrying the same mutations. Only seven bases (A
12
, A
15
, T
34
, A
36
, T
37
, A
44
, and T
45
) are absolutely required for the promoter activity. Moreover, A
12
, A
15
, T
34
, T
37
, and T
45
within the 7 bases are highly specific to
fliA
promoter activity, and those bases form an asymmetric recognition site for FlhD
4
C
2
. The implications of the asymmetry of the FlhD
4
C
2
binding site and its potential impact on FlhD
4
C
2
are discussed.
Cooperativity and Interference of Germination Pathways in Bacillus anthracis Spores
Authors: Luu Helen , Akoachere Monique , Patra Manomita , Abel-Santos Ernesto 
Published: June 2011

ABSTRACT

Spore germination is the first step to
Bacillus anthracis
pathogenicity. Previous work has shown that
B. anthracis
spores use germination (Ger) receptors to recognize amino acids and nucleosides as germinants. Genetic analysis has putatively paired each individual Ger receptor with a specific germinant. However, Ger receptors seem to be able to partially compensate for each other and recognize alternative germinants. Using kinetic analysis of
B. anthracis
spores germinated with inosine and
l
-alanine, we previously determined kinetic parameters for this germination process and showed binding synergy between the cogerminants. In this work, we expanded our kinetic analysis to determine kinetic parameters and binding order for every
B. anthracis
spore germinant pair. Our results show that germinant binding can exhibit positive, neutral, or negative cooperativity. Furthermore, different germinants can bind spores by either a random or an ordered mechanism. Finally, simultaneous triggering of multiple germination pathways shows that germinants can either cooperate or interfere with each other during the spore germination process. We postulate that the complexity of germination responses may allow
B. anthracis
spores to respond to different environments by activating different germination pathways.
The Requirement for Pneumococcal MreC and MreD Is Relieved by Inactivation of the Gene Encoding PBP1a
Authors: Land Adrian D. , Winkler Malcolm E. 
Published: June 2011

ABSTRACT

MreC and MreD, along with the actin homologue MreB, are required to maintain the shape of rod-shaped bacteria. The depletion of MreCD in rod-shaped bacteria leads to the formation of spherical cells and the accumulation of suppressor mutations. Ovococcus bacteria, such as
Streptococcus pneumoniae
, lack MreB homologues, and the functions of the
S. pneumoniae
MreCD (MreCD

Spn

) proteins are unknown.
mreCD
are located upstream from the
pcsB
cell division gene in most
Streptococcus
species, but we found that
mreCD
and
pcsB
are transcribed independently. Similarly to rod-shaped bacteria, we show that
mreCD
are essential in the virulent serotype 2 D39 strain of
S. pneumoniae
, and the depletion of MreCD results in cell rounding and lysis. In contrast, laboratory strain R6 contains suppressors that allow the growth of Δ
mreCD
mutants, and bypass suppressors accumulate in D39 Δ
mreCD
mutants. One class of suppressors eliminates the function of class A penicillin binding protein 1a (PBP1a). Unencapsulated Δ
pbp1a
D39 mutants have smaller diameters than their
pbp1a
+
parent or Δ
pbp2a
and Δ
pbp1b
mutants, which lack other class A PBPs and do not show the suppression of Δ
mreCD
mutations. Suppressed Δ
mreCD
Δ
pbp1a
double mutants form aberrantly shaped cells, some with misplaced peptidoglycan (PG) biosynthesis compared to that of single Δ
pbp1a
mutants. Quantitative Western blotting showed that MreC

Spn

is abundant (≈8,500 dimers per cell), and immunofluorescent microscopy (IFM) located MreCD

Spn

to the equators and septa of dividing cells, similarly to the PBPs and PG pentapeptides indicative of PG synthesis. These combined results are consistent with a model in which MreCD

Spn

direct peripheral PG synthesis and control PBP1a localization or activity.
Structure-Based Functional Studies of the Effects of Amino Acid Substitutions in GerBC, the C Subunit of the Bacillus subtilis GerB Spore Germinant Receptor
Authors: Li Yunfeng , Catta Parvathimadhavi , Stewart Kerry-Ann V. , Dufner Matthew , Setlow Peter , Hao Bing 
Published: June 2011

ABSTRACT

Highly conserved amino acid residues in the C subunits of the germinant receptors (GRs) of spores of
Bacillus
and
Clostridium
species have been identified by amino acid sequence comparisons, as well as structural predictions based on the high-resolution structure recently determined for the C subunit of the
Bacillus subtilis
GerB GR (GerBC). Single and multiple alanine substitutions were made in these conserved residues in three regions of GerBC, and the effects of these changes on
B. subtilis
spore germination via the GerB GR alone or in concert with the GerK GR, as well as on germination via the GerA GR, were determined. In addition, levels of the GerBC variants in the spore inner membrane were measured, and a number of the GerBC proteins were expressed and purified and their solubility and aggregation status were assessed. This work has done the following: (i) identified a number of conserved amino acids that are crucial for GerBC function in spore germination via the GerB GR and that do not alter spores' levels of these GerBC variants; (ii) identified other conserved GerBC amino acid essential for the proper folding of the protein and/or for assembly of GerBC in the spore inner membrane; (iii) shown that some alanine substitutions in GerBC significantly decrease the GerA GR's responsiveness to its germinant
l
-valine, consistent with there being some type of interaction between GerA and GerB GR subunits in spores; and (iv) found no alanine substitutions that specifically affect interaction between the GerB and GerK GRs.
Draft Genome Sequence of Streptomyces Strain S4, a Symbiont of the Leaf-Cutting Ant Acromyrmex octospinosus
Authors: Seipke Ryan F. , Crossman Lisa , Drou Nizar , Heavens Darren , Bibb Mervyn J. , Caccamo Mario , Hutchings Matthew I. 
Published: June 2011

ABSTRACT

Streptomyces
spp. are common symbionts of the leaf-cutting ant species
Acromyrmex octospinosus
, which feeds on basidiomycete fungus leaf matter and harvests the lipid- and carbohydrate-rich gongylidia as a food source.
A. octospinosus
and other ant genera use antifungal compounds produced by
Streptomyces
spp. and other actinomycetes in order to help defend their fungal gardens from parasitic fungi. Herein, we report the draft genome sequence of
Streptomyces
strain S4, an antifungal-producing symbiont of
A. octospinosus
.
Complete Genome Sequence of a Novel Clinical Isolate, the Nontuberculous Mycobacterium Strain JDM601
Authors: Zhang Zhuo-Yang , Sun Zhan-Qiang , Wang Zi-Ling , Wen Zi-Lu , Sun Qing-Wen , Zhu Zhao-Qin , Song Yan-Zheng , Zhao Jun-Wei , Wang Hong-Hai , Zhang Shu-Lin , Guo Xiao-Kui 
Published: June 2011

ABSTRACT

Mycobacteriosis is on the increase. Nontuberculous mycobacteria (NTM) are resistant to most antituberculosis drugs naturally. We determined the complete genome sequence of a novel NTM strain, JDM601, of the
Mycobacterium terrae
complex, which was isolated from a patient with tuberculosis-like disease and with various antibiotic resistances.
Genome Sequence of Lactococcus garvieae 8831, Isolated from Rainbow Trout Lactococcosis Outbreaks in Spain
Authors: Aguado-Urda Mónica , López-Campos Guillermo H. , Gibello Alicia , Cutuli M. Teresa , López-Alonso Victoria , Fernández-Garayzábal José F. , Blanco M. Mar 
Published: June 2011

ABSTRACT

Lactococcus garvieae
is the etiological agent of lactococcosis, one of the most important disease threats to the sustainability of the rainbow trout farming industry. Here, we present the draft genome sequence of
Lactococcus garvieae
strain 8831, isolated from diseased rainbow trout, which is composed of 2,087,276 bp with a G+C content of 38%.
Genome Sequence of Acinetobacter sp. Strain P8-3-8, Isolated from Fistularia commersonii in Vietnam
Authors: Kim Young-Ok , Kim Woo-Jin , Choi Sang-Haeng , Kim Dae-Soo , Kim Dong-Wook , Lee Jun-Seo , Kong Hee Jeong , Nam Bo-Hye , Kim Bong-Seok , Lee Sang-Jun , Park Hong-Seog , Chae Sung-Hwa 
Published: June 2011

ABSTRACT

Acinetobacter
sp. strain P8-3-8 is an aerobic, Gram-negative marine bacterium isolated from the intestine of the bluespotted cornetfish (
Fistularia commersonii
). Here, we present the draft genome sequence of
Acinetobacter
sp. P8-3-8 (3,905,565 bp, with a G+C content of 37.6%) containing 3,621 putative coding sequences. The genome data reveal a high density of genes encoding transcriptional regulators involved in anaerobic respiration.
Draft Genome Sequence of Kocuria rhizophila P7-4
Authors: Kim Woo-Jin , Kim Young-Ok , Kim Dae-Soo , Choi Sang-Haeng , Kim Dong-Wook , Lee Jun-Seo , Kong Hee Jeong , Nam Bo-Hye , Kim Bong-Seok , Lee Sang-Jun , Park Hong-Seog , Chae Sung-Hwa 
Published: June 2011

ABSTRACT

We report the draft genome sequence of
Kocuria rhizophila
P7-4, which was isolated from the intestine of
Siganus doliatus
caught in the Pacific Ocean. The 2.83-Mb genome sequence consists of 75 large contigs (>100 bp in size) and contains 2,462 predicted protein-coding genes.