bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor
Authors: Kashefi Kazem , Shelobolina Evgenya S. , Elliott W. Crawford , Lovley Derek R. 
Published: November 2007

ABSTRACTRecent studies have suggested that the structural Fe(III) within phyllosilicate minerals, including smectite and illite, is an important electron acceptor for Fe(III)-reducing microorganisms in sedimentary environments at moderate temperatures. The reduction of structural Fe(III) by thermophiles, however, has not previously been described. A wide range of thermophilic and hyperthermophilicArchaeaandBacteriafrom marine and freshwater environments that are known to reduce poorly crystalline Fe(III) oxides were tested for their ability to reduce structural (octahedrally coordinated) Fe(III) in smectite (SWa-1) as the sole electron acceptor. Two out of the 10 organisms tested,Geoglobus ahangariandGeothermobacterium ferrireducens, were not able to conserve energy to support growth by reduction of Fe(III) in SWa-1 despite the fact that both organisms were originally isolated with solid-phase Fe(III) as the electron acceptor. The other organisms tested were able to grow on SWa-1 and reduced 6.3 to 15.1% of the Fe(III). This is 20 to 50% less than the reported amounts of Fe(III) reduced in the same smectite (SWa-1) by mesophilic Fe(III) reducers. Two organisms,Geothermobacter ehrlichiiand archaeal strain 140, produced copious amounts of an exopolysaccharide material, which may have played an active role in the dissolution of the structural iron in SWa-1 smectite. The reduction of structural Fe(III) in SWa-1 by archaeal strain 140 was studied in detail. Microbial Fe(III) reduction was accompanied by an increase in interlayer and octahedral charges and some incorporation of potassium and magnesium into the smectite structure. However, these changes in the major element chemistry of SWa-1 smectite did not result in the formation of an illite-like structure, as reported for a mesophilic Fe(III) reducer. These results suggest that thermophilic Fe(III)-reducing organisms differ in their ability to reduce and solubilize structural Fe(III) in SWa-1 smectite and that SWa-1 is not easily transformed to illite by these organisms.
Utilization of Molasses Sugar for Lactic Acid Production by
Lactobacillus delbrueckii
subsp.
delbrueckii
Mutant Uc-3 in Batch Fermentation
Authors: Dumbrepatil Arti , Adsul Mukund , Chaudhari Shivani , Khire Jayant , Gokhale Digambar 
Published: November 2007

ABSTRACT

Efficient lactic acid production from cane sugar molasses by
Lactobacillus delbrueckii
mutant Uc-3 in batch fermentation process is demonstrated. Lactic acid fermentation using molasses was not significantly affected by yeast extract concentrations. The final lactic acid concentration increased with increases of molasses sugar concentrations up to 190 g/liter. The maximum lactic acid concentration of 166 g/liter was obtained at a molasses sugar concentration of 190 g/liter with a productivity of 4.15 g/liter/h. Such a high concentration of lactic acid with high productivity from molasses has not been reported previously, and hence mutant Uc-3 could be a potential candidate for economical production of lactic acid from molasses at a commercial scale.
(Per)chlorate Reduction by the Thermophilic BacteriumMoorella perchloratireducenssp. nov., Isolated from Underground Gas Storage
Authors: Balk Melike , van Gelder Ton , Weelink Sander A. , Stams Alfons J. M. 
Published: November 2007

ABSTRACTA thermophilic bacterium, strain An10, was isolated from underground gas storage with methanol as a substrate and perchlorate as an electron acceptor. Cells were gram-positive straight rods, 0.4 to 0.6 μm in diameter and 2 to 8 μm in length, growing as single cells or in pairs. Spores were terminal with a bulged sporangium. The temperature range for growth was 40 to 70°C, with an optimum at 55 to 60°C. The pH optimum was around 7. The salinity range for growth was between 0 and 40 g NaCl liter−1with an optimum at 10 g liter−1. Strain An10 was able to grow on CO, methanol, pyruvate, glucose, fructose, cellobiose, mannose, xylose, and pectin. The isolate was able to respire with (per)chlorate, nitrate, thiosulfate, neutralized Fe(III) complexes, and anthraquinone-2,6-disulfonate. The G+C content of the DNA was 57.6 mol%. On the basis of 16S rRNA analysis, strain An10 was most closely related toMoorella thermoaceticaandMoorella thermoautotrophica. The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell extracts. Strain An10 is the first thermophilic and gram-positive bacterium with the ability to use (per)chlorate as a terminal electron acceptor.
In Situ Activity of Suspended and Immobilized Microbial Communities as Measured by Fluorescence Lifetime Imaging
Authors: Walczysko Petr , Kuhlicke Ute , Knappe Sabine , Cordes Christiana , Neu Thomas R. 
Published: November 2007

ABSTRACTIn this study, the feasibility of fluorescence lifetime imaging (FLIM) for measurement of RNA:DNA ratios in microorganisms was assessed. The fluorescence lifetime of a nucleic acid-specific probe (SYTO 13) was used to directly measure the RNA:DNA ratio inside living bacterial cells. In vitro, SYTO 13 showed shorter fluorescence lifetimes in DNA solutions than in RNA solutions. Growth experiments with bacterial monocultures were performed in liquid media. The results demonstrated the suitability of SYTO 13 for measuring the growth-phase-dependent RNA:DNA ratio inEscherichia colicells. The fluorescence lifetime of SYTO 13 reflected the known changes of the RNA:DNA ratio in microbial cells during different growth phases. As a result, the growth rate ofE. colicells strongly correlated with the fluorescence lifetime. Finally, the fluorescence lifetimes of SYTO 13 in slow- and fast-growing biofilms were compared. For this purpose, biofilms developed from activated sludge were grown as autotrophic and heterotrophic communities. The FLIM data clearly showed a longer fluorescence lifetime for the fast-growing heterotrophic biofilms and a shorter fluorescence lifetime for the slow-growing autotrophic biofilms. Furthermore, starved biofilms showed shorter lifetimes than biofilms supplied with glucose, indicating a lower RNA:DNA ratio in starved biofilms. It is suggested that FLIM in combination with SYTO 13 represents a useful tool for the in situ differentiation of active and inactive bacteria. The technique does not require radioactive chemicals and may be applied to a broad range of sample types, including suspended and immobilized microorganisms.
Comparison and Validation of Methods To Quantify Cry1Ab Toxin from
Bacillus thuringiensis
for Standardization of Insect Bioassays
Authors: Crespo André L. B. , Spencer Terence A. , Nekl Emily , Pusztai-Carey Marianne , Moar William J. , Siegfried Blair D. 
Published: November 2007

ABSTRACT

Standardization of toxin preparations derived from
Bacillus thuringiensis
(Berliner) used in laboratory bioassays is critical for accurately assessing possible changes in the susceptibility of field populations of target pests. Different methods were evaluated to quantify Cry1Ab, the toxin expressed by 80% of the commercially available transgenic maize that targets the European corn borer,
Ostrinia nubilalis
(Hübner). We compared three methods of quantification on three different toxin preparations from independent sources: enzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfate-polyacrylamide gel electrophoresis and densitometry (SDS-PAGE/densitometry), and the Bradford assay for total protein. The results were compared to those obtained by immunoblot analysis and with the results of toxin bioassays against susceptible laboratory colonies of
O. nubilalis
. The Bradford method resulted in statistically higher estimates than either ELISA or SDS-PAGE/densitometry but also provided the lowest coefficients of variation (CVs) for estimates of the Cry1Ab concentration (from 2.4 to 5.4%). The CV of estimates obtained by ELISA ranged from 12.8 to 26.5%, whereas the CV of estimates obtained by SDS-PAGE/densitometry ranged from 0.2 to 15.4%. We standardized toxin concentration by using SDS-PAGE/densitometry, which is the only method specific for the 65-kDa Cry1Ab protein and is not confounded by impurities detected by ELISA and Bradford assay for total protein. Bioassays with standardized Cry1Ab preparations based on SDS-PAGE/densitometry showed no significant differences in LC
50
values, although there were significant differences in growth inhibition for two of the three Cry1Ab preparations. However, the variation in larval weight caused by toxin source was only 4% of the total variation, and we conclude that standardization of Cry1Ab production and quantification by SDS-PAGE/densitometry may improve data consistency in monitoring efforts to identify changes in insect susceptibility to Cry1Ab.
Thickness and Surface Density of Extracellular Polymers on
Acidithiobacillus ferrooxidans
Authors: Taylor Eric S. , Lower Steven K. 
Published: November 2007

ABSTRACT

In vivo force microscopy measurements of
Acidithiobacillus ferrooxidans
revealed a repulsive force that was due to the presence of extracellular polymers on the bacterium's surface. Measured force-distance profiles were fit to steric force theory to estimate the density and thickness values of these exopolymers. The polymer densities were 3.4 × 10
16
to 7.1 × 10
16
molecules m
−2
, and the equilibrium thickness was 29 nm.
Recycling of Shiga Toxin 2 Genes in Sorbitol-Fermenting Enterohemorrhagic
Escherichia coli
O157:NM
Authors: Mellmann Alexander , Lu Shan , Karch Helge , Xu Jian-guo , Harmsen Dag , Schmidt M. Alexander , Bielaszewska Martina 
Published: November 2007

ABSTRACT

Using colony blot hybridization with
stx
2
and
eae
probes and agglutination in anti-O157 lipopolysaccharide serum, we isolated
stx
2
-positive and
eae
-positive sorbitol-fermenting (SF) enterohemorrhagic
Escherichia coli
(EHEC) O157:NM (nonmotile) strains from initial stool specimens and
stx
-negative and
eae
-positive SF
E. coli
O157:NM strains from follow-up specimens (collected 3 to 8 days later) from three children. The
stx
-negative isolates from each patient shared with the corresponding
stx
2
-positive isolates
fliC
H7
, non-
stx
virulence traits, and multilocus sequence types, which indicates that they arose from the
stx
2
-positive strains by loss of
stx
2
during infection. Analysis of the integrity of the
yecE
gene, a possible
stx
phage integration site in EHEC O157, in the consecutive
stx
2
-positive and
stx
-negative isolates demonstrated that
yecE
was occupied in
stx
2
-positive but intact in
stx
-negative strains. It was possible to infect and lysogenize the
stx
-negative
E. coli
O157 strains in vitro using an
stx
2
-harboring bacteriophage from one of the SF EHEC O157:NM isolates. The acquisition of the
stx
2
-containing phage resulted in the occupation of
yecE
and production of biologically active Shiga toxin 2. We conclude that the
yecE
gene in SF
E. coli
O157:NM is a hot spot for excision and integration of Shiga toxin 2-encoding bacteriophages. SF EHEC O157:NM strains and their
stx
-negative derivatives thus represent a highly dynamic system that can convert in both directions by the loss and gain of
stx
2
-harboring phages. The ability to recycle
stx
2
, a critical virulence trait, makes SF
E. coli
O157:NM strains ephemeral EHEC that can exist as
stx
-negative variants during certain phases of their life cycle.
Carbon Source Dependence and Photostimulation of Conidiation in
Hypocrea atroviridis
Authors: Friedl Martina A. , Kubicek Christian P. , Druzhinina Irina S. 
Published: November 2007

ABSTRACT

Hypocrea atroviridis
is frequently used as a photomorphogenetic model due to its ability to conidiate upon exposure to light. Light is thereby believed to be the primary trigger for spore formation. In contrast, we show here that conidiation is primarily carbon source dependent and that illumination plays a catalytic role; of a total of 95 tested carbon sources, only a small set of carbohydrates, polyols, and sugar acids allowed conidiation in darkness, and on most of them, conidiation was significantly more strongly expressed in light. In addition, there are also a number of carbon sources on which
H. atroviridis
conidiates in darkness, but light does not further stimulate the process. Yet on another small set of carbon sources (
l
-sorbitol,
d
-fucose,
d
- and
l
-arabinose, and erythritol),
H. atroviridis
shows better sporulation in darkness than in light. No sporulation was observed on organic acids and amino acids. Mutants with deletions in the two blue-light receptor proteins BLR-1 and BLR-2 generally showed weaker conidiation on a smaller number of carbon sources than did the parental strain, yet they clearly sporulated on 15 and 27 of the 95 carbon sources tested, respectively. Of the carbon sources supporting sporulation, only 11 supported the conidiation of both mutants, suggesting that the BLR-1 and BLR-2 receptors are variously involved in the carbon source-dependent regulation of spore formation. The addition of cyclic AMP, which has been reported to lead to conidiation in darkness, both positively and negatively affected sporulation and resulted in different effects in the parental strain and the two Δ
blr
mutants. Our data show that the carbon source is the prime determinant for conidiation and that it influences the organism's regulation of conidiation by means of BLR-1 and BLR-2 and their cross talk with cyclic AMP.
Characterization of Plasmacytoid Dendritic Cells in Bone Marrow of Pig-Tailed Macaques
Authors: Reeves R. Keith , Fultz Patricia N. 
Published: November 2007

ABSTRACTPlasmacytoid dendritic cells (pDCs), one of two types of bone marrow (BM)-derived blood DCs, play an important role in linking innate and adaptive immune responses. However, little is known about the nature of pDCs that reside in the BM. Because the simian immunodeficiency virus-macaque model closely mimics human immunodeficiency virus disease in humans, with both infections inducing a decrease in pDCs, we characterized and compared pDCs in the BM with those in peripheral blood (PB) of healthy pig-tailed macaques. The results revealed that pDCs from both compartments had the same CD123++HLA-DR+Lin−phenotype and were similar in size. Although BM-derived pDCs (BM-pDCs) were 3-fold greater in frequency and 10-fold greater in number, they had lower cell surface expression of both HLA-DR and the costimulatory molecule CD86 than did PB-pDCs. Both BM- and PB-pDCs responded ex vivo to synthetic CpG oligodeoxynucleotides and inactivated influenza virus by upregulating HLA-DR and CD86 and secreting cytokines; however, stimulated BM-pDCs secreted less alpha interferon and tumor necrosis factor alpha per cell than did PB-pDCs. These results suggest that while BM-pDCs appear to be phenotypically less mature than PB-pDCs, they do respond to pathogens. Thus, during acute infections, these cells could initiate immune responses either in the BM or after rapidly migrating from the BM into the periphery. A better characterization of pDCs in blood and tissues will be beneficial for future studies of macaques that focus on either pathogenesis or vaccine development.
Mycobacterium bovisBacillus Calmette-Guérin Induces CCL5 Secretion via the Toll-Like Receptor 2-NF-κB and -Jun N-Terminal Kinase Signaling Pathways
Authors: Méndez-Samperio Patricia , Trejo Artemisa , Pérez Aline 
Published: November 2007

ABSTRACTIn response toMycobacterium bovisbacillus Calmette-Guérin (BCG), CC chemokines are secreted from host cells to attract components of the innate and adaptive immune systems to the site of infection. Toll-like receptor 2 (TLR2) has been shown to recognizeM. bovisBCG and to initiate signaling pathways that result in enhanced secretion of CC chemokines. Despite the essential requirement of TLR2 inM. bovisBCG infection, the mechanisms by which it induces secretion of CC chemokines are not well defined. In this study, we report that stimulation of HEK293 cells expressing human TLR2 withM. bovisBCG resulted in increased CCL2 and CCL5 secretion, as determined by an enzyme-linked immunosorbent assay.M. bovisBCG infection resulted in the activation of c-Jun N-terminal kinase (JNK), and the inhibition of JNK activity had a significant effect onM. bovisBCG-dependent CCL5 secretion in TLR2-expressing cells but no effect onM. bovisBCG-dependent CCL2 secretion from infected HEK293 cells expressing human TLR2. TheM. bovisBCG-induced CCL5 release was attenuated by sulfasalazine (a well-described inhibitor of NF-κB activity), BAY 11-7082 (an IκB phosphorylation inhibitor), and ALLN (a well-described inhibitor of NF-κB activation that prevents degradation of IκB and eventually results in a lack of translocated NF-κB in the nucleus). In addition, stimulation of TLR2-expressing cells withM. bovisBCG resulted in translocation of NF-κB subunits from the cytoplasmic to the nuclear fraction, and stimulation of cells withM. bovisBCG activated IκB kinase αβ. These findings indicate thatM. bovisBCG induces CCL5 production through mechanisms that include a TLR2-dependent component that requires JNK and NF-κB activities.
Elucidating the Role of C/D snoRNA in rRNA Processing and Modification inTrypanosoma brucei
Authors: Barth Sarit , Shalem Boaz , Hury Avraham , Tkacz Itai Dov , Liang Xue-hai , Uliel Shai , Myslyuk Inna , Doniger Tirza , Salmon-Divon Mali , Unger Ron , Michaeli Shulamit 
Published: November 2007

ABSTRACTMost eukaryotic C/D small nucleolar RNAs (snoRNAs) guide 2′-O methylation (Nm) on rRNA and are also involved in rRNA processing. The four core proteins that bind C/D snoRNA inTrypanosoma bruceiare fibrillarin (NOP1), NOP56, NOP58, and SNU13. Silencing of NOP1 by RNA interference identified rRNA-processing and modification defects that caused lethality. Systematic mapping of 2′-O-methyls on rRNA revealed the existence of hypermethylation at certain positions of the rRNA in the bloodstream form of the parasites, suggesting that this modification may assist the parasites in coping with the major temperature changes during cycling between their insect and mammalian hosts. The rRNA-processing defects of NOP1-depleted cells suggest the involvement of C/D snoRNA in trypanosome-specific rRNA-processing events to generate the small rRNA fragments. MRP RNA, which is involved in rRNA processing, was identified in this study in one of the snoRNA gene clusters, suggesting that trypanosomes utilize a combination of unique C/D snoRNAs and conserved snoRNAs for rRNA processing.
Morphogenesis Control in
Candida albicans
and
Candida dubliniensis
through Signaling Molecules Produced by Planktonic and Biofilm Cells
Authors: Martins Margarida , Henriques Mariana , Azeredo Joana , Rocha Sílvia M. , Coimbra Manuel A. , Oliveira Rosário 
Published: November 2007

ABSTRACT

Morphogenesis control by chemical signaling molecules is beginning to be highlighted in
Candida
biology. The present study focuses on morphogenic compounds produced in situ by
Candida albicans
and
Candida dubliniensis
during planktonic and biofilm growth that may at least partially substantiate the effect promoted by supernatants in morphogenesis. For both species, planktonic versus biofilm supernatants were analyzed by headspace-solid-phase microextraction and gas chromatography-mass spectrometry. Both planktonic cells and biofilm supernatants of
C. albicans
and
C. dubliniensis
contained isoamyl alcohol, 2-phenylethanol, 1-dodecanol,
E
-nerolidol, and
E
,
E
-farnesol. Alcohol secretion profiles were species, culture mode, and growth time specific. The addition of exogenous alcohols to the cultures of both species inhibited the morphological transition from the yeast to the filamentous form by up to 50%. The physiological role of these alcohols was put to evidence by comparing the effects of a 96-h cultured supernatant with synthetic mixtures containing isoamyl alcohol, 2-phenylethanol,
E
-nerolidol, and
E
,
E
-farnesol at concentrations determined herein. All synthetic mixtures elicited a morphological effect similar to that observed for the corresponding supernatants when used to treat
C. albicans
and
C. dubliniensis
cultures, except for the effect of the 96-h
C. dubliniensis
planktonic supernatant culture on
C. albicans
. Overall, these results reveal a group of alcohol extracellular signaling molecules that are biologically active with
C. albicans
and
C. dubliniensis
morphogenesis.
Novel 44-Kilodalton Subunit of Axonemal Dynein Conserved from
Chlamydomonas
to Mammals
Authors: Yamamoto Ryosuke , Yanagisawa Haru-aki , Yagi Toshiki , Kamiya Ritsu 
Published: November 2007

ABSTRACT

Cilia and flagella have multiple dyneins in their inner and outer arms.
Chlamydomonas
inner-arm dynein contains at least seven major subspecies (dynein a to dynein g), of which all but dynein f (also called dynein I1) are the single-headed type that are composed of a single heavy chain, actin, and either centrin or a 28-kDa protein (p28). Dynein d was found to associate with two additional proteins of 38 kDa (p38) and 44 kDa (p44). Following the characterization of the p38 protein (R. Yamamoto, H. A. Yanagisawa, T. Yagi, and R. Kamiya, FEBS Lett.
580
:6357-6360, 2006), we have identified p44 as a novel component of dynein d by using an immunoprecipitation approach. p44 is present along the length of the axonemes and is diminished, but not absent, in the
ida4
and
ida5
mutants, both lacking this dynein. In the
ida5
axoneme, p44 and p38 appear to form a complex, suggesting that they constitute the docking site of dynein d on the outer doublet. p44 has potential homologues in other ciliated organisms. For example, the mouse homologue of p44, NYD-SP14, was found to be strongly expressed in tissues with motile cilia and flagella. These results suggest that inner-arm dynein d and its subunit organization are widely conserved.
Regulation of Rot Expression in
Staphylococcus aureus
Authors: Hsieh Hsin-Yeh , Tseng Ching Wen , Stewart George C. 
Published: November 2007

ABSTRACT

Repressor of toxins (Rot) is known to be a global regulator of virulence gene expression in
Staphylococcus aureus
. The function of Rot, but not the transcription of
rot
, is regulated by the staphylococcal accessory gene regulator (Agr) quorum-sensing system. In addition, the alternative sigma factor (σ
B
) has a repressive effect on
rot
expression during the postexponential phase of growth. The transcriptional profiles of Rot in σ
B
-positive and σ
B
-negative strains in the postexponential and stationary phases of growth were compared. An upregulation of
rot
expression was observed during the stationary phase of growth, and this upregulation occurred in a σ
B
-dependent manner. The effects of other staphylococcal transcriptional factors were also investigated. Electrophoretic mobility shift assays revealed that proteins present in staphylococcal lysates retarded the mobility of the
rot
promoter fragment and that the effect was reduced, but not eliminated, with lysates from strains lacking a functional SarS protein. A modest upregulation of
rot
expression was also observed in
sarS
-negative strains. Affinity purification of proteins binding to the
rot
promoter fragment, followed by N-terminal protein sequencing, identified the SarA and SarR proteins. Primer extension analysis of the
rot
promoter revealed a number of discreet products. However, these RNA species were not associated with identifiable promoter activity and likely represented RNA breakdown products. Loss of Rot function during the postexponential phase of growth likely involves degradation of the
rot
mRNA but not the inhibition of
rot
transcription.