bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Biotransformation of Fluoranthene by Intertidally Derived Cunninghamella elegans under Biofilm-Based and Niche-Mimicking Conditions
Authors: Mitra Sayani , Pramanik Arnab , Banerjee Srijoni , Haldar Saubhik , Gachhui Ratan , Mukherjee Joydeep 
Published: September 2013

ABSTRACT

The aims of the investigation were to ascertain if surface attachment of
Cunninghamella elegans
and niche intertidal conditions provided in a bioreactor influenced biotransformation of fluoranthene by
C. elegans
. A newly designed polymethylmethacrylate (PMMA) conico-cylindrical flask (CCF) holding eight equidistantly spaced rectangular strips mounted radially on a circular disc allowed comparison of fluoranthene biotransformation between CCFs with a hydrophobic surface (PMMA-CCF) and a hydrophilic glass surface (GS-CCF) and a 500-ml Erlenmeyer flask (EF). Fluoranthene biotransformation was higher by 22-fold, biofilm growth was higher by 3-fold, and cytochrome P450 gene expression was higher by 2.1-fold when
C. elegans
was cultivated with 2% inoculum as biofilm culture in PMMA-CCF compared to planktonic culture in EF. Biotransformation was enhanced by 7-fold with 10% inoculum. The temporal pattern of biofilm progression based on three-channel fluorescence detection by confocal laser scanning microscopy demonstrated well-developed, stable biofilm with greater colocalization of fluoranthene within extracellular polymeric substances and filaments of the biofilm grown on PMMA in contrast to a glass surface. A bioreactor with discs rotating at 2 revolutions per day affording 6-hourly emersion and immersion mimicked the niche intertidal habitat of
C. elegans
and supported biofilm formation and transformation of fluoranthene. The amount of transformed metabolite was 3.5-fold, biofilm growth was 3-fold, and cytochrome P450 gene expression was 1.9-fold higher in the process mimicking the intertidal conditions than in a submerged process without disc rotation. In the CCF and reactor, where biofilm formation was comparatively greater, higher concentration of exopolysaccharides allowed increased mobilization of fluoranthene within the biofilm with consequential higher gene expression leading to enhanced volumetric productivity.
Acquired Genetic Mechanisms of a Multiresistant Bacterium Isolated from a Treatment Plant Receiving Wastewater from Antibiotic Production
Authors: Johnning Anna , Moore Edward R. B. , Svensson-Stadler Liselott , Shouche Yogesh S. , Larsson D. G. Joakim , Kristiansson Erik 
Published: September 2013

ABSTRACT

The external environment, particularly wastewater treatment plants (WWTPs), where environmental bacteria meet human commensals and pathogens in large numbers, has been highlighted as a potential breeding ground for antibiotic resistance. We have isolated the extensively drug-resistant
Ochrobactrum intermedium
CCUG 57381 from an Indian WWTP receiving industrial wastewater from pharmaceutical production contaminated with high levels of quinolones. Antibiotic susceptibility testing against 47 antibiotics showed that the strain was 4 to >500 times more resistant to sulfonamides, quinolones, tetracyclines, macrolides, and the aminoglycoside streptomycin than the type strain
O. intermedium
LMG 3301
T
. Whole-genome sequencing identified mutations in the Indian strain causing amino acid substitutions in the target enzymes of quinolones. We also characterized three acquired regions containing resistance genes to sulfonamides (
sul1
), tetracyclines [
tet
(
G
) and
tetR
], and chloramphenicol/florfenicol (
floR
). Furthermore, the Indian strain harbored acquired mechanisms for horizontal gene transfer, including a type I mating pair-forming system (MPF
I
), a MOB
P
relaxase, and insertion sequence transposons. Our results highlight that WWTPs serving antibiotic manufacturing may provide nearly ideal conditions for the recruitment of resistance genes into human commensal and pathogenic bacteria.
CelR, an Ortholog of the Diguanylate Cyclase PleD of Caulobacter, Regulates Cellulose Synthesis in Agrobacterium tumefaciens
Authors: Barnhart D. Michael , Su Shengchang , Baccaro Brenna E. , Banta Lois M. , Farrand Stephen K. 
Published: September 2013

ABSTRACT

Cellulose fibrils play a role in attachment of
Agrobacterium tumefaciens
to its plant host. While the genes for cellulose biosynthesis in the bacterium have been identified, little is known concerning the regulation of the process. The signal molecule cyclic di-GMP (c-di-GMP) has been linked to the regulation of exopolysaccharide biosynthesis in many bacterial species, including
A. tumefaciens
. In this study, we identified two putative diguanylate cyclase genes,
celR
(
atu1297
) and
atu1060
, that influence production of cellulose in
A. tumefaciens
. Overexpression of either gene resulted in increased cellulose production, while deletion of
celR
, but not
atu1060
, resulted in decreased cellulose biosynthesis.
celR
overexpression also affected other phenotypes, including biofilm formation, formation of a polar adhesion structure, plant surface attachment, and virulence, suggesting that the gene plays a role in regulating these processes. Analysis of
celR
and Δ
cel
mutants allowed differentiation between phenotypes associated with cellulose production, such as biofilm formation, and phenotypes probably resulting from c-di-GMP signaling, which include polar adhesion, attachment to plant tissue, and virulence. Phylogenetic comparisons suggest that species containing both
celR
and
celA
, which encodes the catalytic subunit of cellulose synthase, adapted the CelR protein to regulate cellulose production while those that lack
celA
use CelR, called PleD, to regulate specific processes associated with polar localization and cell division.
The Sinorhizobium meliloti
ntrX
Gene Is Involved in Succinoglycan Production, Motility, and Symbiotic Nodulation on Alfalfa
Authors: Wang Dong , Xue Haiying , Wang Yiwen , Yin Ruochun , Xie Fang , Luo Li 
Published: September 2013

ABSTRACT

Rhizobia establish a symbiotic relationship with their host legumes to induce the formation of nitrogen-fixing nodules. This process is regulated by many rhizobium regulators, including some two-component regulatory systems (TCSs). NtrY/NtrX, a TCS that was first identified in
Azorhizobium caulinodans
, is required for free-living nitrogen metabolism and symbiotic nodulation on
Sesbania rostrata
. However, its functions in a typical rhizobium such as
Sinorhizobium meliloti
remain unclear. Here we found that the
S. meliloti
response regulator NtrX but not the histidine kinase NtrY is involved in the regulation of exopolysaccharide production, motility, and symbiosis with alfalfa. A plasmid insertion mutant of
ntrX
formed mucous colonies, which overproduced succinoglycan, an exopolysaccharide, by upregulating its biosynthesis genes. This mutant also exhibited motility defects due to reduced flagella and decreased expression of flagellins and regulatory genes. The regulation is independent of the known regulatory systems of ExoR/ExoS/ChvI, EmmABC, and ExpR. Alfalfa plants inoculated with the
ntrX
mutant were small and displayed symptoms of nitrogen starvation. Interestingly, the deletion mutant of
ntrY
showed a phenotype similar to that of the parent strain. These findings demonstrate that the
S. meliloti
NtrX is a new regulator of succinoglycan production and motility that is not genetically coupled with NtrY.
Overexpression of
fetA
(
ybbL
) and
fetB
(
ybbM
), Encoding an Iron Exporter, Enhances Resistance to Oxidative Stress in Escherichia coli
Authors: Nicolaou Sergios A. , Fast Alan G. , Nakamaru-Ogiso Eiko , Papoutsakis Eleftherios T. 
Published: September 2013

ABSTRACT

Reactive oxygen species are generated by redox reactions and the Fenton reaction of H
2
O
2
and iron that generates the hydroxyl radical that causes severe DNA, protein, and lipid damage. We screened
Escherichia coli
genomic libraries to identify a fragment, containing
cueR
,
ybbJ
,
qmcA
,
ybbL
, and
ybbM
, which enhanced resistance to H
2
O
2
stress. We report that the Δ
ybbL
and Δ
ybbM
strains are more susceptible to H
2
O
2
stress than the parent strain and that
ybbL
and
ybbM
overexpression overcomes H
2
O
2
sensitivity. The
ybbL
and
ybbM
genes are predicted to code for an ATP-binding cassette metal transporter, and we demonstrate that YbbM is a membrane protein. We investigated various metals to identify iron as the likely substrate of this transporter. We propose the gene names
fetA
and
fetB
(for Fe transport) and the gene product names FetA and FetB. FetAB allows for increased resistance to oxidative stress in the presence of iron, revealing a role in iron homeostasis. We show that iron overload coupled with H
2
O
2
stress is abrogated by
fetA
and
fetB
overexpression in the parent strain and in the Δ
fur
strain, where iron uptake is deregulated. Furthermore, we utilized whole-cell electron paramagnetic resonance to show that intracellular iron levels in the Δ
fur
strain are decreased by 37% by
fetA
and
fetB
overexpression. Combined, these findings show that
fetA
and
fetB
encode an iron exporter that has a role in enhancing resistance to H
2
O
2
-mediated oxidative stress and can minimize oxidative stress under conditions of iron overload and suggest that FetAB facilitates iron homeostasis to decrease oxidative stress.
Characterization of CpdC, a Large-Ring Lactone-Hydrolyzing Enzyme from Pseudomonas sp. Strain HI-70, and Its Use as a Fusion Tag Facilitating Overproduction of Proteins in Escherichia coli
Authors: Xu Yali , Grosse Stephan , Iwaki Hiroaki , Hasegawa Yoshie , Lau Peter C. K. 
Published: September 2013

ABSTRACT

There are few entries of carbon-carbon bond hydrolases (EC 3.7.1.-) in the ExPASy database. In microbes, these enzymes play an essential role in the metabolism of alicyclic or aromatic compounds as part of the global carbon cycle. CpdC is a ω-pentadecalactone hydrolase derived from the degradation pathway of cyclopentadecanol or cyclopentadecanone by
Pseudomonas
sp. strain HI-70. CpdC was purified to homogeneity and characterized. It is active as a dimer of 56,000 Da with a subunit molecular mass of 33,349. Although CpdC has the highest activity and reaction rate (
k
cat
) toward ω-pentadecalactone, its catalytic efficiency favors lauryl lactone as a substrate. The melting temperature (

T
m

) of CpdC was estimated to be 50.9 ± 0.1°C. The half-life of CpdC at 35°C is several days. By virtue of its high level of expression in
Escherichia coli
, the intact CpdC-encoding gene and progressive 3′-end deletions were employed in the construction of a series of fusion plasmid system. Although we found them in inclusion bodies, proof-of-concept of overproduction of three microbial cutinases of which the genes were otherwise expressed poorly or not at all in
E. coli
was demonstrated. On the other hand, two antigenic proteins, azurin and MPT63, were readily produced in soluble form.
Influence of Habitat and Climate Variables on Arbuscular Mycorrhizal Fungus Community Distribution, as Revealed by a Case Study of Facultative Plant Epiphytism under Semiarid Conditions
Authors: Torrecillas E. , Torres P. , Alguacil M. M. , Querejeta J. I. , Roldán A. 
Published: September 2013

ABSTRACT

In semiarid Mediterranean ecosystems, epiphytic plant species are practically absent, and only some species of palm trees can support epiphytes growing in their lower crown area, such as
Phoenix dactylifera
L. (date palm). In this study, we focused on
Sonchus tenerrimus
L. plants growing as facultative epiphytes in
P. dactylifera
and its terrestrial forms growing in adjacent soils. Our aim was to determine the possible presence of arbuscular mycorrhizal fungi (AMF) in these peculiar habitats and to relate AMF communities with climatic variations. We investigated the AMF community composition of epiphytic and terrestrial
S. tenerrimus
plants along a temperature and precipitation gradient across 12 localities. Epiphytic roots were colonized by AMF, as determined by microscopic observation; all of the epiphytic and terrestrial samples analyzed showed AMF sequences from taxa belonging to the phylum
Glomeromycota
, which were grouped in 30 AMF operational taxonomic units. The AMF community composition was clearly different between epiphytic and terrestrial root samples, and this could be attributable to dispersal constraints and/or the contrasting environmental and ecophysiological conditions prevailing in each habitat. Across sites, the richness and diversity of terrestrial AMF communities was positively correlated with rainfall amount during the most recent growing season. In contrast, there was no significant correlation between climate variables and AMF richness and diversity for epiphytic AMF communities, which suggests that the composition of AMF communities in epiphytic habitats appears to be largely determined by the availability and dispersion of fungal propagules from adjacent terrestrial habitats.
Noninvasive High-Throughput Single-Cell Analysis of the Intracellular pH of Saccharomyces cerevisiae by Ratiometric Flow Cytometry
Authors: Valkonen Mari , Mojzita Dominik , Penttilä Merja , Benčina Mojca 
Published: September 2013

ABSTRACTThe ability of cells to maintain pH homeostasis in response to environmental changes has elicited interest in basic and applied research and has prompted the development of methods for intracellular pH measurements. Many traditional methods provide information at population level and thus the average values of the studied cell physiological phenomena, excluding the fact that cell cultures are very heterogeneous. Single-cell analysis, on the other hand, offers more detailed insight into population variability, thereby facilitating a considerably deeper understanding of cell physiology. Although microscopy methods can address this issue, they suffer from limitations in terms of the small number of individual cells that can be studied and complicated image processing. We developed a noninvasive high-throughput method that employs flow cytometry to analyze large populations of cells that express pHluorin, a genetically encoded ratiometric fluorescent probe that is sensitive to pH. The method described here enables measurement of the intracellular pH of single cells with high sensitivity and speed, which is a clear improvement compared to previously published methods that either require pretreatment of the cells, measure cell populations, or require complex data analysis. The ratios of fluorescence intensities, which correlate to the intracellular pH, are independent of the expression levels of the pH probe, making the use of transiently or extrachromosomally expressed probes possible. We conducted an experiment on the kinetics of the pH homeostasis ofSaccharomyces cerevisiaecultures grown to a stationary phase after ethanol or glucose addition and after exposure to weak acid stress and glucose pulse. Minor populations with pH homeostasis behaving differently upon treatments were identified.
Changing Dietary Calcium-Phosphorus Level and Cereal Source Selectively Alters Abundance of Bacteria and Metabolites in the Upper Gastrointestinal Tracts of Weaned Pigs
Authors: Metzler-Zebeli Barbara U. , Mann Evelyne , Schmitz-Esser Stephan , Wagner Martin , Ritzmann Mathias , Zebeli Qendrim 
Published: September 2013

ABSTRACT

Several dietary ingredients may affect the bacterial community structure and metabolism in the porcine gut and may therefore influence animals' health and performance. This study investigated the effects of cereal source and calcium-phosphorus (CaP) level in the diet on bacterial microbiota and metabolites, nutrient intake, and gut environment in weaned pigs. Pigs (
n
= 8/treatment) were fed wheat-barley- or corn-based diets with an adequate or high CaP level for 14 days. Effects on microbiota in the stomach, ileum, and midcolon were assessed using quantitative PCR. Data showed that
Enterobacteriaceae
,
Campylobacter
spp., and
Helicobacter
spp., which all contain highly immune reactive lipopolysaccharide (LPS), were abundant at all gut sites. Diet effects on bacteria and metabolites were moderate and occurred mainly in the upper gut, whereas no effects on bacteria, fermentation products, and LPS could be observed in the colon. Differences in carbohydrate intake with corn versus wheat-barley diets selectively stimulated
Bifidobacterium
in the stomach and ileum. There was a growth advantage for a few bacterial groups in the stomach and ileum of pigs fed the high versus adequate CaP level (i.e., gastric
Enterobacteriaceae
and ileal
Enterococcus
,
Bacteroides-Prevotella-Porphyromonas
, and
Campylobacter
). Interestingly, gastrointestinal pH was not affected by dietary CaP level. The present findings demonstrate the stability of the bacterial community and gut environment toward dietary changes even in young pigs. The results on stimulation of gastric and ileal
Bifidobacterium
by corn diets may be employed in nutritional strategies to support gut health after weaning.
Termites Facilitate Methane Oxidation and Shape the Methanotrophic Community
Authors: Ho Adrian , Erens Hans , Mujinya Basile Bazirake , Boeckx Pascal , Baert Geert , Schneider Bellinda , Frenzel Peter , Boon Nico , Van Ranst Eric 
Published: September 2013

ABSTRACT

Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of the methane produced can be consumed by methanotrophs that inhabit the mound material, yet the methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and
in situ
(∼0.004%) methane concentrations through a vertical profile of a termite (
Macrotermes falciger
) mound and a reference soil. Interestingly, the mound material showed higher methanotrophic activity. The methanotroph community structure was determined by means of a
pmoA
-based diagnostic microarray. Although the methanotrophs in the mound were derived from populations in the reference soil, it appears that termite activity selected for a distinct community. Applying an indicator species analysis revealed that putative atmospheric methane oxidizers (high-indicator-value probes specific for the JR3 cluster) were indicative of the active nest area, whereas methanotrophs belonging to both type I and type II were indicative of the reference soil. We conclude that termites modify their environment, resulting in higher methane oxidation and selecting and/or enriching for a distinct methanotroph population.
Abi Is Required for Modulation and Stability but Not Localization or Activation of the SCAR/WAVE Complex
Authors: Davidson Andrew J. , Ura Seiji , Thomason Peter A. , Kalna Gabriela , Insall Robert H. 
Published: September 2013

ABSTRACT

The SCAR/WAVE complex drives actin-based protrusion, cell migration, and cell separation during cytokinesis. However, the contribution of the individual complex members to the activity of the whole remains a mystery. This is primarily because complex members depend on one another for stability, which limits the scope for experimental manipulation. Several studies suggest that Abi, a relatively small complex member, connects signaling to SCAR/WAVE complex localization and activation through its polyproline C-terminal tail. We generated a deletion series of the
Dictyostelium discoideum
Abi to investigate its exact role in regulation of the SCAR complex and identified a minimal fragment that would stabilize the complex. Surprisingly, loss of either the N terminus of Abi or the C-terminal polyproline tail conferred no detectable defect in complex recruitment to the leading edge or the formation of pseudopods. A fragment containing approximately 20% Abi—and none of the sites that couple to known signaling pathways—allowed the SCAR complex to function with normal localization and kinetics. However, expression of N-terminal Abi deletions exacerbated the cytokinesis defect of the
Dictyostelium abi
mutant, which was earlier shown to be caused by the inappropriate activation of SCAR. This demonstrates, unexpectedly, that Abi does not mediate the SCAR complex's ability to make pseudopods, beyond its role in complex stability. Instead, we propose that Abi has a modulatory role when the SCAR complex is activated through other mechanisms.
Dictyostelium Lipid Droplets Host Novel Proteins
Authors: Du Xiaoli , Barisch Caroline , Paschke Peggy , Herrfurth Cornelia , Bertinetti Oliver , Pawolleck Nadine , Otto Heike , Rühling Harald , Feussner Ivo , Herberg Friedrich W. , Maniak Markus 
Published: September 2013

ABSTRACT

Across all kingdoms of life, cells store energy in a specialized organelle, the lipid droplet. In general, it consists of a hydrophobic core of triglycerides and steryl esters surrounded by only one leaflet derived from the endoplasmic reticulum membrane to which a specific set of proteins is bound. We have chosen the unicellular organism
Dictyostelium discoideum
to establish kinetics of lipid droplet formation and degradation and to further identify the lipid constituents and proteins of lipid droplets. Here, we show that the lipid composition is similar to what is found in mammalian lipid droplets. In addition, phospholipids preferentially consist of mainly saturated fatty acids, whereas neutral lipids are enriched in unsaturated fatty acids. Among the novel protein components are LdpA, a protein specific to
Dictyostelium
, and Net4, which has strong homologies to mammalian DUF829/Tmem53/NET4 that was previously only known as a constituent of the mammalian nuclear envelope. The proteins analyzed so far appear to move from the endoplasmic reticulum to the lipid droplets, supporting the concept that lipid droplets are formed on this membrane.
SPO71
Encodes a Developmental Stage-Specific Partner for Vps13 in Saccharomyces cerevisiae
Authors: Park Jae-Sook , Okumura Yuuya , Tachikawa Hiroyuki , Neiman Aaron M. 
Published: September 2013

ABSTRACT

The creation of haploid gametes in yeast, termed spores, requires the
de novo
formation of membranes within the cytoplasm. These membranes, called prospore membranes, enclose the daughter nuclei generated by meiosis. Proper growth and closure of prospore membranes require the highly conserved Vps13 protein. Mutation of
SPO71
, a meiosis-specific gene first identified as defective in spore formation, was found to display defects in membrane morphogenesis very similar to those seen in
vps13
Δ cells. Specifically, prospore membranes are smaller than in the wild type, they fail to close, and membrane vesicles are present within the prospore membrane lumen. As in
vps13
Δ cells, the levels of phophatidylinositol-4-phosphate are reduced in the prospore membranes of
spo71
Δ cells.
SPO71
is required for the translocation of Vps13 from the endosome to the prospore membrane, and ectopic expression of
SPO71
in vegetative cells results in mislocalization of Vps13. Finally, the two proteins can be coprecipitated from sporulating cells. We propose that Spo71 is a sporulation-specific partner for Vps13 and that they act in concert to regulate prospore membrane morphogenesis.
Complete Genome Sequences of Two Bovine Viral Diarrhea Viruses Isolated from Brain Tissues of Nonambulatory (Downer) Cattle
Authors: Oem Jae-Ku , Joo Soo-Kyung , An Dong-Jun 
Published: September 2013

ABSTRACT
Here, we report the complete genome sequences of two bovine viral diarrhea viruses (BVDVs) (strains 11F011 and 12F004) isolated from brain tissues from nonambulatory (downer) cattle. The complete genomes of strains 11F011 and 12F004 contain 12,287 nucleotides (nt) with a single large open reading frame and 12,301 nt with a single large open reading frame, respectively. Phylogenetic analysis indicated that these strains belong to the BVDV-2a and -1b genotypes, respectively.