bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability in Protist Grazing and Growth on Different Marine Synechococcus Isolates
Authors: Apple Jude K. , Strom Suzanne L. , Palenik Brian , Brahamsha Bianca 
Published: March 2011

ABSTRACTGrazing mortality of the marine phytoplanktonSynechococcusis dominated by planktonic protists, yet rates of consumption and factors regulating grazer-Synechococcusinteractions are poorly understood. One aspect of predator-prey interactions for which little is known are the mechanisms by whichSynechococcusavoids or resists predation and, in turn, how this relates to the ability ofSynechococcusto support growth of protist grazer populations. Grazing experiments conducted with the raptorial dinoflagellateOxyrrhis marinaand phylogenetically diverseSynechococcusisolates (strains WH8102, CC9605, CC9311, and CC9902) revealed marked differences in grazing rates—specifically that WH8102 was grazed at significantly lower rates than all other isolates. Additional experiments using the heterotrophic nanoflagellateGoniomonas pacificaand the filter-feeding tintinnid ciliateEutintinnissp. revealed that this pattern in grazing susceptibility among the isolates transcended feeding guilds and grazer taxon.Synechococcuscell size, elemental ratios, and motility were not able to explain differences in grazing rates, indicating that other features play a primary role in grazing resistance. Growth of heterotrophic protists was poorly coupled to prey ingestion and was influenced by the strain ofSynechococcusbeing consumed. AlthoughSynechococcuswas generally a poor-quality food source, it tended to support higher growth and survival ofG. pacificaandO. marinarelative toEutintinnissp., indicating that suitability ofSynechococcusvaries among grazer taxa and may be a more suitable food source for the smaller protist grazers. This work has developed tractable model systems for further studies of grazer-Synechococcusinteractions in marine microbial food webs.
Persistence of Mycobacterium avium subsp. paratuberculosis at a Farm-Scale Biogas Plant Supplied with Manure from Paratuberculosis-Affected Dairy Cattle
Authors: Slana I. , Pribylova R. , Kralova A. , Pavlik I. 
Published: March 2011

ABSTRACT

In this study, products from all steps of anaerobic digestion at a farm-scale biogas plant supplied with manure from paratuberculosis-affected dairy cattle were examined and quantified for the presence of the causal agent of paratuberculosis,
Mycobacterium avium
subsp.
paratuberculosis
, using culture and quantitative real-time PCR (qPCR). Viable
M. avium
subsp.
paratuberculosis
cells were detected using culture in fermentors for up to 2 months; the presence of
M. avium
subsp.
paratuberculosis
DNA (10
1
cells/g) was demonstrated in all anaerobic fermentors and digestate 16 months after initiation of work at a biogas plant, using IS
900
qPCR.
F57
qPCR was able to detect
M. avium
subsp.
paratuberculosis
DNA (10
2
cells/g) at up to 12 months. According to these results, a fermentation process that extended beyond 2 months removed all viable
M. avium
subsp.
paratuberculosis
cells and therefore rendered its product
M. avium
subsp.
paratuberculosis
free. However,
M. avium
subsp.
paratuberculosis
DNA was found during all the examined periods (more than 1 year), which could be explained by either residual DNA being released from dead cells or by the presence of viable cells whose amount was under the limit of cultivability. As the latter hypothesis cannot be excluded, the safety of the final products of digestion used for fertilization or animal bedding cannot be defined, and further investigation is necessary to confirm or refute this risk.
Production of Poly(3-Hydroxybutyrate-
co
-3-Hydroxyhexanoate) from Plant Oil by Engineered Ralstonia eutropha Strains
Authors: Budde Charles F. , Riedel Sebastian L. , Willis Laura B. , Rha ChoKyun , Sinskey Anthony J. 
Published: March 2011

ABSTRACT

The polyhydroxyalkanoate (PHA) copolymer poly(3-hydroxybutyrate-
co
-3-hydroxyhexanoate) [P(HB-
co
-HHx)] has been shown to have potential to serve as a commercial bioplastic. Synthesis of P(HB-
co
-HHx) from plant oil has been demonstrated with recombinant
Ralstonia eutropha
strains expressing heterologous PHA synthases capable of incorporating HB and HHx into the polymer. With these strains, however, short-chain-length fatty acids had to be included in the medium to generate PHA with high HHx content. Our group has engineered two
R. eutropha
strains that accumulate high levels of P(HB-
co
-HHx) with significant HHx content directly from palm oil, one of the world's most abundant plant oils. The strains express a newly characterized PHA synthase gene from the bacterium
Rhodococcus aetherivorans
I24. Expression of an enoyl coenzyme A (enoyl-CoA) hydratase gene (
phaJ
) from
Pseudomonas aeruginosa
was shown to increase PHA accumulation. Furthermore, varying the activity of acetoacetyl-CoA reductase (encoded by
phaB
) altered the level of HHx in the polymer. The strains with the highest PHA titers utilized plasmids for recombinant gene expression, so an
R. eutropha
plasmid stability system was developed. In this system, the essential pyrroline-5-carboxylate reductase gene
proC
was deleted from strain genomes and expressed from a plasmid, making the plasmid necessary for growth in minimal media. This study resulted in two engineered strains for production of P(HB-
co
-HHx) from palm oil. In palm oil fermentations, one strain accumulated 71% of its cell dry weight as PHA with 17 mol% HHx, while the other strain accumulated 66% of its cell dry weight as PHA with 30 mol% HHx.
Importance of Porins for Biocide Efficacy against Mycobacterium smegmatis
Authors: Frenzel Elrike , Schmidt Stefan , Niederweis Michael , Steinhauer Katrin 
Published: March 2011

ABSTRACT

Mycobacteria are among the microorganisms least susceptible to biocides but cause devastating diseases, such as tuberculosis, and increasingly opportunistic infections. The exceptional resistance of mycobacteria to toxic solutes is due to an unusual outer membrane, which acts as an efficient permeability barrier, in synergy with other resistance mechanisms. Porins are channel-forming proteins in the outer membrane of mycobacteria. In this study we used the alamarBlue assay to show that the deletion of Msp porins in isogenic mutants increased the resistance of
Mycobacterium smegmatis
to isothiazolinones (methylchloroisothiazolinone [MCI]/methylisothiazolinone [MI] and octylisothiazolinone [2-
n
-octyl-4-isothiazolin-3-one; OIT]), formaldehyde-releasing biocides {hexahydrotriazine [1,3,5-tris (2-hydroxyethyl)-hexahydrotriazine; HHT] and methylenbisoxazolidine [
N
,
N
′-methylene-bis-5-(methyloxazolidine); MBO]}, and the lipophilic biocides polyhexamethylene biguanide and octenidine dihydrochloride 2- to 16-fold. Furthermore, the susceptibility of the porin triple mutant against a complex disinfectant was decreased 8-fold compared to wild-type (wt)
M. smegmatis
. Efficacy testing in the quantitative suspension test EN 14348 revealed 100-fold improved survival of the porin mutant in the presence of this biocide. These findings underline the importance of porins for the susceptibility of
M. smegmatis
to biocides.
Genetic Control of Amadori Product Degradation in Bacillus subtilis via Regulation of
frlBONMD
Expression by FrlR
Authors: Deppe Veronika Maria , Klatte Stephanie , Bongaerts Johannes , Maurer Karl-Heinz , O'Connell Timothy , Meinhardt Friedhelm 
Published: March 2011

ABSTRACT

Bacillus subtilis
is capable of degrading fructosamines. The phosphorylation and the cleavage of the resulting fructosamine 6-phosphates is catalyzed by the
frlD
and
frlB
gene products, respectively. This study addresses the physiological importance of the
frlBONMD
genes (formerly
yurPONML
), revealing the necessity of their expression for growth on fructosamines and focusing on the complex regulation of the corresponding transcription unit. In addition to the known regulation by the global transcriptional regulator CodY, the
frl
genes are repressed by the convergently transcribed FrlR (formerly YurK). The latter causes repression during growth on substrates other than fructosamines. Additionally, we identified in the first intergenic region of the operon an FrlR binding site which is centrally located within a 38-bp perfect palindromic sequence. There is genetic evidence that this sequence, in combination with FrlR, contributes to the remarkable decrease in the transcription downstream of the first gene of the
frl
operon.
Involvement of the SmeAB Multidrug Efflux Pump in Resistance to Plant Antimicrobials and Contribution to Nodulation Competitiveness in Sinorhizobium meliloti
Authors: Eda Shima , Mitsui Hisayuki , Minamisawa Kiwamu 
Published: March 2011

ABSTRACT

The contributions of multicomponent-type multidrug efflux pumps to antimicrobial resistance and nodulation ability in
Sinorhizobium meliloti
were comprehensively analyzed. Computational searches identified genes in the
S. meliloti
strain 1021 genome encoding 1 pump from the ATP-binding cassette family, 3 pumps from the major facilitator superfamily, and 10 pumps from the resistance-nodulation-cell division family, and subsequently, these genes were deleted either individually or simultaneously. Antimicrobial susceptibility tests demonstrated that deletion of the
smeAB
pump genes resulted in increased susceptibility to a range of antibiotics, dyes, detergents, and plant-derived compounds and, further, that specific deletion of the
smeCD
or
smeEF
genes in a Δ
smeAB
background caused a further increase in susceptibility to certain antibiotics. Competitive nodulation experiments revealed that the
smeAB
mutant was defective in competing with the wild-type strain for nodulation. The introduction of a plasmid carrying
smeAB
into the
smeAB
mutant restored antimicrobial resistance and nodulation competitiveness. These findings suggest that the SmeAB pump, which is a major multidrug efflux system of
S. meliloti
, plays an important role in nodulation competitiveness by mediating resistance toward antimicrobial compounds produced by the host plant.
Enzymatic Dysfunction of Mitochondrial Complex I of the Candida albicansgoa1Mutant Is Associated with Increased Reactive Oxidants and Cell Death
Authors: Li Dongmei , Chen Hui , Florentino Abigail , Alex Deepu , Sikorski Patricia , Fonzi William A. , Calderone Richard 
Published: March 2011

ABSTRACTWe have previously shown that deletion ofGOA1(growth andoxidantadaptation) ofCandida albicansresults in a loss of mitochondrial membrane potential, ATP synthesis, increased sensitivity to oxidants and killing by human neutrophils, and avirulence in a systemic model of candidiasis. We established that translocation of Goa1p to mitochondria occurred during peroxide stress. In this report, we show that thegoa1Δ (GOA31), compared to the wild type (WT) and a gene-reconstituted (GOA32) strain, exhibits sensitivity to inhibitors of the classical respiratory chain (CRC), including especially rotenone (complex I [CI]) and salicylhydroxamic acid (SHAM), an inhibitor of the alternative oxidase pathway (AOX), while potassium cyanide (KCN; CIV) causes a partial inhibition of respiration. In the presence of SHAM, however, GOA31 has an enhanced respiration, which we attribute to the parallel respiratory (PAR) pathway and alternative NADH dehydrogenases. Interestingly, deletion ofGOA1also results in a decrease in transcription of the alternative oxidase geneAOX1in untreated cells as well as negligibleAOX1andAOX2transcription in peroxide-treated cells. To explain the rotenone sensitivity, we measured enzyme activities of complexes I to IV (CI to CIV) and observed a major loss of CI activity in GOA31 but not in control strains. Enzymatic data of CI were supported by blue native polyacrylamide gel electrophoresis (BN-PAGE) experiments which demonstrated less CI protein and reduced enzyme activity. The consequence of a defective CI in GOA31 is an increase in reactive oxidant species (ROS), loss of chronological aging, and programmed cell death ([PCD] apoptosis)in vitrocompared to control strains. The increase in PCD was indicated by an increase in caspase activity and DNA fragmentation in GOA31. Thus,GOA1is required for a functional CI and partially for the AOX pathway; loss ofGOA1compromises cell survival. Further, the loss of chronological aging is new to studies ofCandidaspecies and may offer an insight into therapies to control these pathogens. Our observation of increased ROS production associated with a defective CI and PCD is reminiscent of mitochondrial studies of patients with some types of neurodegenerative diseases where CI and/or CIII dysfunctions lead to increased ROS and apoptosis.
Two Major Inositol Transporters and Their Role in Cryptococcal Virulence
Authors: Wang Yina , Liu Tong-bao , Delmas Guillaume , Park Steven , Perlin David , Xue Chaoyang 
Published: March 2011

ABSTRACT

Cryptococcus neoformans
is an AIDS-associated human fungal pathogen and the most common cause of fungal meningitis, with a mortality rate over 40% in AIDS patients. Significant advances have been achieved in understanding its disease mechanisms. Yet the underlying mechanism of a high frequency of cryptococcal meningitis remains unclear. The existence of high inositol concentrations in brain and our earlier discovery of a large inositol transporter (
ITR
) gene family in
C. neoformans
led us to investigate the potential role of inositol in
Cryptococcus
-host interactions. In this study, we focus on functional analyses of two major
ITR
genes to understand their role in virulence of
C. neoformans
. Our results show that
ITR1A
and
ITR3C
are the only two
ITR
genes among 10 candidates that can complement the growth defect of a
Saccharomyces cerevisiae
strain lacking inositol transporters. Both
S. cerevisiae
strains heterologously expressing
ITR1A
or
ITR3C
showed high inositol uptake activity, an indication that they are major inositol transporters. Significantly,
itr1a itr3c
double mutants showed significant virulence attenuation in murine infection models. Mutating both
ITR1A
and
ITR3C
in an
ino1
mutant background activates the expression of several remaining
ITR
candidates and does not show more severe virulence attenuation, suggesting that both inositol uptake and biosynthetic pathways are important for inositol acquisition. Overall, our study provides evidence that host inositol and fungal inositol transporters are important for
Cryptococcus
pathogenicity.
Catabolite Repression of the Bacillus subtilis FadR Regulon, Which Is Involved in Fatty Acid Catabolism
Authors: Tojo Shigeo , Satomura Takenori , Matsuoka Hiroshi , Hirooka Kazutake , Fujita Yasutaro 
Published: March 2011

ABSTRACT

The
Bacillus subtilis fadR
regulon involved in fatty acid degradation comprises five operons,
lcfA-fadR-fadB-etfB-etfA
,
lcfB
,
fadN-fadA-fadE
,
fadH-fadG
, and
fadF-acdA-rpoE
. Since the
lcfA-fadRB-etfBA
,
lcfB
, and
fadNAE
operons, whose gene products directly participate in the β-oxidation cycle, had been found to be probably catabolite repressed upon genome-wide transcript analysis, we performed Northern blotting, which indicated that they are clearly under CcpA-dependent catabolite repression. So, we searched for catabolite-responsive elements (
cre
's) to which the complex of CcpA and P-Ser-HPr binds to exert catabolite repression by means of a web-based
cis
-element search in the
B. subtilis
genome using known
cre
sequences, which revealed the respective candidate
cre
sequences in the
lcfA
,
lcfB
, and
fadN
genes. DNA footprinting indicated that the complex actually interacted with these
cre
's
in vitro
. Deletion analysis of each
cre
using the
lacZ
fusions with the respective promoter regions of the three operons with and without it, indicated that these
cre
's are involved in the CcpA-dependent catabolite repression of the operons
in vivo
.
More than One Way To Control Hair Growth: Regulatory Mechanisms in Enterobacteria That Affect Fimbriae Assembled by the Chaperone/Usher Pathway
Authors: Clegg Steven , Wilson Janet , Johnson Jeremiah 
Published: March 2011

ABSTRACT
Many Gram-negative enterobacteria produce surface-associated fimbriae that facilitate attachment and adherence to eucaryotic cells and tissues. These organelles are believed to play an important role during infection by enabling bacteria to colonize specific niches within their hosts. One class of these fimbriae is assembled using a periplasmic chaperone and membrane-associated scaffolding protein that has been referred to as an usher because of its function in fimbrial biogenesis. The presence of multiple types of fimbriae assembled by the chaperone/usher pathway can be found both within a single bacterial species and also among different genera. One way of controlling fimbrial assembly in these bacteria is at the genetic level by positively or negatively regulating fimbrial gene expression. This minireview considers the mechanisms that have been described to control fimbrial gene expression and uses specific examples to demonstrate both unique and shared properties of such regulatory mechanisms.
Complete Genome Sequence of Streptococcus suis Serotype 14 Strain JS14
Authors: Hu Pan , Yang Ming , Zhang Anding , Wu Jiayan , Chen Bo , Hua Yafeng , Yu Jun , Xiao Jingfa , Jin Meilin 
Published: March 2011

ABSTRACT

Streptococcus suis
is an important zoonotic agent leading to a variety of diseases in swine and can be transmitted to human beings upon close contact. Here, we report the complete genome sequence of
S. suis
serotype 14 strain JS14 which was isolated from a diseased pig in Jiangsu Province, China.
Biosynthesis of the RNA Polymerase Inhibitor Streptolydigin in Streptomyces lydicus: Tailoring Modification of 3-Methyl-Aspartate
Authors: Horna Dina H. , Gómez Cristina , Olano Carlos , Palomino-Schätzlein Martina , Pineda-Lucena Antonio , Carbajo Rodrigo J. , Braña Alfredo F. , Méndez Carmen , Salas José A. 
Published: March 2011

ABSTRACT

The asparaginyl-tRNA synthetase-like SlgZ and methyltransferase SlgM enzymes are involved in the biosynthesis of the tetramic acid streptolydigin in
Streptomyces lydicus
. Inactivation of
slgZ
led to a novel streptolydigin derivative. Overexpression of
slgZ
,
slgM
, or both in
S. lydicus
led to a considerable increase in streptolydigin production.
Complete Genome Sequence of the Hemotrophic Mycoplasma suis Strain KI3806
Authors: Oehlerking Joern , Kube Michael , Felder Kathrin M. , Matter Denise , Wittenbrink Max M. , Schwarzenbach Sarah , Kramer Manuela M. , Hoelzle Katharina , Hoelzle Ludwig E. 
Published: March 2011

ABSTRACT

Mycoplasma suis
, a member of the hemotrophic mycoplasma (HM) group, parasitize erythrocytes of pigs. Increasing evidence suggests that
M. suis
is also a zoonotic agent. Highly pathogenic strains of
M. suis
(e.g.,
M. suis
KI3806) have been demonstrated to invade erythrocytes. This complete sequenced and manually annotated genome of
M. suis
KI3806 is the first available from this species and from the HM group. The DNA was isolated from blood samples of experimentally infected pigs due to the lack of an
in vitro
cultivation system. The small circular chromosome of 709,270 bp, encoding an unexpectedly high number of hypothetical proteins and limited transport and metabolic capacities, could reflect the unique lifestyle of HM on the surface of erythrocytes.
Genome Sequence of Acinetobacter baumannii MDR-TJ
Authors: Gao Feng , Wang Yue , Liu Yan-Jie , Wu Xiao-Meng , Lv Xing , Gan Yi-Ru , Song Shi-Duo , Huang He 
Published: March 2011

ABSTRACT

Acinetobacter baumannii
is a pathogenic species of bacteria, identified as an aerobic Gram-negative bacterium, that is resistant to most antibiotics. In this study, the MDR-TJ strain was isolated at the Second Hospital of Tianjin Medical University, China, and was found to be resistant to penicillin, cephalosporins, aminoglycosides, quinolones, and also imipenem. The genome sequence of
Acinetobacter baumannii
strain MDR-TJ was determined by using a combination of 454 pyrosequencing and paired-end sequencing performed with the Roche Genome Sequencer FLX system to generate a scaffolded assembly.
Genome Sequence of the Verrucomicrobium Opitutus terrae PB90-1, an Abundant Inhabitant of Rice Paddy Soil Ecosystems
Authors: van Passel Mark W. J. , Kant Ravi , Palva Airi , Copeland Alex , Lucas Susan , Lapidus Alla , Glavina del Rio Tijana , Pitluck Sam , Goltsman Eugene , Clum Alicia , Sun Hui , Schmutz Jeremy , Larimer Frank W. , Land Miriam L. , Hauser Loren , Kyrpides Nikolaos , Mikhailova Natalia , Richardson P. Paul , Janssen Peter H. , de Vos Willem M. , Smidt Hauke 
Published: March 2011

ABSTRACT

Bacteria of the deeply branching phylum
Verrucomicrobia
are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. We have sequenced the genome of
Opitutus terrae
PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides.
Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum
Authors: Miller David A. , Suen Garret , Bruce David , Copeland Alex , Cheng Jan-Feng , Detter Chris , Goodwin Lynne A. , Han Cliff S. , Hauser Loren J. , Land Miriam L. , Lapidus Alla , Lucas Susan , Meincke Linda , Pitluck Sam , Tapia Roxanne , Teshima Hazuki , Woyke Tanja , Fox Brian G. , Angert Esther R. , Currie Cameron R. 
Published: March 2011

ABSTRACT

Cellulosilyticum lentocellum
DSM 5427 is an anaerobic, endospore-forming member of the
Firmicutes
. We describe the complete genome sequence of this cellulose-degrading bacterium, which was originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.
Genome Sequence of a Dominant, Multidrug-Resistant Acinetobacter baumannii Strain, TCDC-AB0715
Authors: Chen Chun-Chen , Lin Yu-Chi , Sheng Wang-Huei , Chen Yee-Chun , Chang Shan-Chwen , Hsia Ko-Chiang , Liao Mei-Hui , Li Shu-Ying 
Published: March 2011

ABSTRACT

Acinetobacter baumannii
has emerged as a significant nosocomial pathogen worldwide. The increasing trend of carbapenem and fluoroquinolone resistance in
A. baumannii
severely limits the usage of therapeutic antimicrobial agents. Here we report the genome sequence of a multidrug-resistant
A. baumannii
strain, TCDC-AB0715, harboring both
bla
OXA-23
and
bla
OXA-66
.
Regulation of Cytotoxicity by Quorum-Sensing Signaling in Vibrio vulnificus Is Mediated by SmcR, a Repressor of hlyU
Authors: Shao Chung-Ping , Lo Horng-Ren , Lin Jen-Hsing , Hor Lien-I 
Published: March 2011

ABSTRACT

Cytotoxicity is an important virulence determinant in the pathogenesis of
Vibrio vulnificus
, and two cytotoxins, RTX (encoded by
rtxA1
) and cytolysin/hemolysin (encoded by
vvhA
), have been identified in this organism. We showed that the quorum-sensing regulator LuxO controlled the cytotoxicity of this organism: a Δ
luxO
mutant exhibited low cytotoxicity, whereas a constitutively activated
luxO
mutant,
luxO(D47E)
, remained highly cytotoxic. The cytotoxicity of the Δ
luxO
mutant was restored when
smcR
, a
Vibrio harveyi luxR
homologue repressed by
luxO
, was further deleted. SmcR then was shown to repress the expression of both
rtxA1
and
vvhA
. A DNA library of
V. vulnificus
was screened in
Escherichia coli
for clones that upregulated
vvhA
in the presence of SmcR, and
hlyU
, which has been shown to positively regulate
rtxA1
and
vvhA
, was identified. We demonstrated that SmcR repressed the expression of
hlyU
and bound to a region upstream of
hlyU
in
V. vulnificus
. The deletion of
hlyU
resulted in the loss of cytotoxicity and reduced cytolysin/hemolysin production in the Δ
smcR
mutant. The Δ
smcR
Δ
hlyU
mutant regained cytotoxicity and cytolysin/hemolysin activity when
hns
, which has been shown to repress the transcription of
rtxA1
and interfere with
hlyU
, was further removed. Collectively, our data suggest that SmcR mediates the regulation of cytotoxicity by quorum-sensing signaling in
V. vulnificus
by repressing
hlyU
, an activator of
rtxA1
and
vvhA
.