bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of Aeromonas Strains with Lactic Acid Bacteria via Caco-2 Cells
Authors: Hatje E. , Neuman C. , Katouli M. 
Published: November 2013

ABSTRACT

The genus
Aeromonas
includes some species that have now been identified as human pathogens of significant medical importance. We investigated the ability of 13 selected
Aeromonas
strains belonging to nine species isolated from clinical cases (
n
= 5), environmental waters (
n
= 5), and fish (
n
= 3) to adhere to and translocate Caco-2 cells in the absence and presence of two lactic acid bacteria (LAB), i.e.,
Lactobacillus acidophilus
and
Bifidobacterium breve
.
Aeromonas
isolates were also assessed for their cytotoxicity, the presence of virulence genes, and hemolysin production. Among the clinical isolates, one strain of
Aeromonas veronii
biovar veronii and two strains of
Aeromonas hydrophila
carried cytotoxin (
act
), heat-labile toxin (
alt
), hemolysin (
hlyA
), and aerolysin (
aerA
) genes, were cytotoxic to Vero cells, produced hemolysin, and showed higher adherence to Caco-2 cells. In contrast, this was seen in only one environmental strain, a strain of
A. veronii
biovar sobria. When
Aeromonas
strains were coinoculated with LAB onto Caco-2 cells, their level of adhesion was reduced. However, their rate of translocation in the presence of LAB increased and was significantly (
P
< 0.05) higher among fish strains. We suggest that either the interaction between
Aeromonas
and LAB strains could have a detrimental effect on the Caco-2 cells, allowing the
Aeromonas
to translocate more readily, or the presence of the LAB stimulated the
Aeromonas
strains to produce more toxins and/or increase their translocation rate.
Bifidobacterium bifidum PRL2010 Modulates the Host Innate Immune Response
Authors: Turroni Francesca , Taverniti Valentina , Ruas-Madiedo Patricia , Duranti Sabrina , Guglielmetti Simone , Lugli Gabriele Andrea , Gioiosa Laura , Palanza Paola , Margolles Abelardo , van Sinderen Douwe , Ventura Marco 
Published: November 2013

ABSTRACTHere, we describe data obtained from transcriptome profiling of human cell lines and intestinal cells of a murine model upon exposure and colonization, respectively, withBifidobacterium bifidumPRL2010. Significant changes were detected in the transcription of genes that are known to be involved in innate immunity. Furthermore, results from enzyme-linked immunosorbent assays (ELISAs) showed that exposure toB. bifidumPRL2010 causes enhanced production of interleukin 6 (IL-6) and IL-8 cytokines, presumably through NF-κB activation. The obtained global transcription profiles strongly suggest thatBifidobacterium bifidumPRL2010 modulates the innate immune response of the host.
The Fitness Advantage of Commercial Wine Yeasts in Relation to the Nitrogen Concentration, Temperature, and Ethanol Content under Microvinification Conditions
Authors: García-Ríos Estéfani , Gutiérrez Alicia , Salvadó Zoel , Arroyo-López Francisco Noé , Guillamon José Manuel 
Published: November 2013

ABSTRACTThe effect of the main environmental factors governing wine fermentation on the fitness of industrial yeast strains has barely received attention. In this study, we used the concept of fitness advantage to measure how increasing nitrogen concentrations (0 to 200 mg N/liter), ethanol (0 to 20%), and temperature (4 to 45°C) affects competition among four commercial wine yeast strains (PDM, ARM, RVA, and TTA). We used a mathematical approach to model the hypothetical time needed for the control strain (PDM) to out-compete the other three strains in a theoretical mixed population. The theoretical values obtained were subsequently verified by competitive mixed fermentations in both synthetic and natural musts, which showed a good fit between the theoretical and experimental data. Specifically, the data show that the increase in nitrogen concentration and temperature values improved the fitness advantage of the PDM strain, whereas the presence of ethanol significantly reduced its competitiveness. However, the RVA strain proved to be the most competitive yeast for the three enological parameters assayed. The study of the fitness of these industrial strains is of paramount interest for the wine industry, which uses them as starters of their fermentations. Here, we propose a very simple method to model the fitness advantage, which allows the prediction of the competitiveness of one strain with respect to different abiotic factors.
The Secreted Esterase of Propionibacterium freudenreichii Has a Major Role in Cheese Lipolysis
Authors: Abeijón Mukdsi María Claudia , Falentin Hélène , Maillard Marie-Bernadette , Chuat Victoria , Medina Roxana Beatriz , Parayre Sandrine , Thierry Anne 
Published: November 2013

ABSTRACT

Free fatty acids are important flavor compounds in cheese.
Propionibacterium freudenreichii
is the main agent of their release through lipolysis in Swiss cheese. Our aim was to identify the esterase(s) involved in lipolysis by
P. freudenreichii
. We targeted two previously identified esterases: one secreted esterase, PF#279, and one putative cell wall-anchored esterase, PF#774. To evaluate their role in lipolysis, we constructed overexpression and knockout mutants of
P. freudenreichii
CIRM-BIA1
T
for each corresponding gene. The sequences of both genes were also compared in 21 wild-type strains. All strains were assessed for their lipolytic activity on milk fat. The lipolytic activity observed matched data previously reported in cheese, thus validating the relevance of the method used. The mutants overexpressing PF#279 or PF#774 released four times more fatty acids than the wild-type strain, demonstrating that both enzymes are lipolytic esterases. However, inactivation of the
pf279
gene induced a 75% reduction in the lipolytic activity compared to that of the wild-type strain, whereas inactivation of the
pf774
gene did not modify the phenotype. Two of the 21 wild-type strains tested did not display any detectable lipolytic activity. Interestingly, these two strains exhibited the same single-nucleotide deletion at the beginning of the
pf279
gene sequence, leading to a premature stop codon, whereas they harbored a
pf774
gene highly similar to that of the other strains. Taken together, these results clearly demonstrate that PF#279 is the main lipolytic esterase in
P. freudenreichii
and a key agent of Swiss cheese lipolysis.
Aeromonas hydrophila and Aeromonas veronii Predominate among Potentially Pathogenic Ciprofloxacin- and Tetracycline-Resistant Aeromonas Isolates from Lake Erie
Authors: Skwor Troy , Shinko Jasmine , Augustyniak Alexander , Gee Christopher , Andraso Greg 
Published: November 2013

ABSTRACT

Members of the genus
Aeromonas
are ubiquitous in nature and have increasingly been implicated in numerous diseases of humans and other animal taxa. Although some species of aeromonads are human pathogens, their presence, density, and relative abundance are rarely considered in assessing water quality. The objectives of this study were to identify
Aeromonas
species within Lake Erie, determine their antibiotic resistance patterns, and assess their potential pathogenicity.
Aeromonas
strains were isolated from Lake Erie water by use of
Aeromonas
selective agar with and without tetracycline and ciprofloxacin. All isolates were analyzed for hemolytic ability and cytotoxicity against human epithelial cells and were identified to the species level by using 16S rRNA gene restriction fragment length polymorphisms and phylogenetic analysis based on
gyrB
gene sequences. A molecular virulence profile was identified for each isolate, using multiplex PCR analysis of six virulence genes. We demonstrated that
Aeromonas
comprised 16% of all culturable bacteria from Lake Erie. Among 119
Aeromonas
isolates, six species were identified, though only two species (
Aeromonas hydrophila
and
A. veronii
) predominated among tetracycline- and ciprofloxacin-resistant isolates. Additionally, both of these species demonstrated pathogenic phenotypes
in vitro
. Virulence gene profiles demonstrated a high prevalence of aerolysin and serine protease genes among
A. hydrophila
and
A. veronii
isolates, a genetic profile which corresponded with pathogenic phenotypes. Together, our findings demonstrate increased antibiotic resistance among potentially pathogenic strains of aeromonads, illustrating an emerging potential health concern.
Sex Determination Directs Uniparental Mitochondrial Inheritance in Phycomyces
Authors: Shakya Viplendra P. S. , Idnurm Alexander 
Published: November 2013

ABSTRACT

Uniparental inheritance (UPI) of mitochondria is common among eukaryotes. The underlying molecular basis by which the sexes of the parents control this non-Mendelian pattern of inheritance is yet to be fully understood. Two major factors have complicated the understanding of the role of sex-specific genes in the UPI phenomenon: in many cases (i) fusion occurs between cells of unequal size or (ii) mating requires a large region of the genome or chromosome that includes genes unrelated to sex determination. The fungus
Phycomyces blakesleeanus
is a member of the Mucoromycotina and has a simple mating type locus encoding only one high-mobility group (HMG) domain protein, and mating occurs by fusion of isogamous cells, thus providing a model system without the limitations mentioned above. Analysis of more than 250 progeny from a series of genetic crosses between wild-type strains of
Phycomyces
revealed a correlation between the individual genes in the mating type locus and UPI of mitochondria. Inheritance is from the plus (+) sex type and is associated with degradation of the mtDNA from the minus (−) parent. These findings suggest that UPI can be directly controlled by genes that determine sex identity, independent of cell size or the complexity of the genetic composition of a sex chromosome.
PakD, a Putative p21-Activated Protein Kinase in Dictyostelium discoideum, Regulates Actin
Authors: Garcia Miguel , Ray Sibnath , Brown Isaiah , Irom Jon , Brazill Derrick 
Published: November 2013

ABSTRACT

Proper regulation of the actin cytoskeleton is essential for cell function and ultimately for survival. Tight control of actin dynamics is required for many cellular processes, including differentiation, proliferation, adhesion, chemotaxis, endocytosis, exocytosis, and multicellular development. Here we describe a putative p21-activated protein kinase, PakD, that regulates the actin cytoskeleton in
Dictyostelium discoideum
. We found that cells lacking
pakD
are unable to aggregate and thus unable to develop. Compared to the wild type, cells lacking PakD have decreased membrane extensions, suggesting defective regulation of the actin cytoskeleton.
pakD
−
cells show poor chemotaxis toward cyclic AMP (cAMP) but normal chemotaxis toward folate, suggesting that PakD mediates some but not all chemotaxis responses.
pakD
−
cells have decreased polarity when placed in a cAMP gradient, indicating that the chemotactic defects of the
pakD
−
cells may be due to an impaired cytoskeletal response to cAMP. In addition, while wild-type cells polymerize actin in response to global stimulation by cAMP,
pakD
−
cells exhibit F-actin depolymerization under the same conditions. Taken together, the results suggest that PakD is part of a pathway coordinating F-actin organization during development.
Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa
Authors: Wang Zheng , Lopez-Giraldez Francesc , Lehr Nina , Farré Marta , Common Ralph , Trail Frances , Townsend Jeffrey P. 
Published: November 2013

ABSTRACT

Fungi can serve as highly tractable models for understanding genetic basis of sexual development in multicellular organisms. Applying a reverse-genetic approach to advance such a model, we used random and multitargeted primers to assay gene expression across perithecial development in
Neurospora crassa
. We found that functionally unclassified proteins accounted for most upregulated genes, whereas downregulated genes were enriched for diverse functions. Moreover, genes associated with developmental traits exhibited stage-specific peaks of expression. Expression increased significantly across sexual development for mating type gene
mat a-1
and for
mat A-1
specific pheromone precursor
ccg-4
. In addition, expression of a gene encoding a protein similar to zinc finger,
stc1
, was highly upregulated early in perithecial development, and a strain with a knockout of this gene exhibited arrest at the same developmental stage. A similar expression pattern was observed for genes in RNA silencing and signaling pathways, and strains with knockouts of these genes were also arrested at stages of perithecial development that paralleled their peak in expression. The observed stage specificity allowed us to correlate expression upregulation and developmental progression and to identify regulators of sexual development. Bayesian networks inferred from our expression data revealed previously known and new putative interactions between RNA silencing genes and pathways. Overall, our analysis provides a fine-scale transcriptomic landscape and novel inferences regarding the control of the multistage development process of sexual crossing and fruiting body development in
N. crassa
.
Cell Wall-Related Bionumbers and Bioestimates of Saccharomyces cerevisiae and Candida albicans
Authors: Klis Frans M. , de Koster Chris G. , Brul Stanley 
Published: November 2013

ABSTRACT

Bionumbers and bioestimates are valuable tools in biological research. Here we focus on cell wall-related bionumbers and bioestimates of the budding yeast
Saccharomyces cerevisiae
and the polymorphic, pathogenic fungus
Candida albicans
. We discuss the linear relationship between cell size and cell ploidy, the correlation between cell size and specific growth rate, the effect of turgor pressure on cell size, and the reason why using fixed cells for measuring cellular dimensions can result in serious underestimation of
in vivo
values. We further consider the evidence that individual buds and hyphae grow linearly and that exponential growth of the population results from regular formation of new daughter cells and regular hyphal branching. Our calculations show that hyphal growth allows
C. albicans
to cover much larger distances per unit of time than the yeast mode of growth and that this is accompanied by strongly increased surface expansion rates. We therefore predict that the transcript levels of genes involved in wall formation increase during hyphal growth. Interestingly, wall proteins and polysaccharides seem barely, if at all, subject to turnover and replacement. A general lesson is how strongly most bionumbers and bioestimates depend on environmental conditions and genetic background, thus reemphasizing the importance of well-defined and carefully chosen culture conditions and experimental approaches. Finally, we propose that the numbers and estimates described here offer a solid starting point for similar studies of other cell compartments and other yeast species.
Identification of New Residues Involved in Intramolecular Signal Transmission in a Prokaryotic Transcriptional Repressor
Authors: Molina-Santiago Carlos , Daddaoua Abdelali , Fillet Sandy , Krell Tino , Morel Bertrand , Duque Estrella , Ramos Juan L. 
Published: November 2013

ABSTRACT

TtgV is a member of the IclR family of transcriptional regulators. This regulator controls its own expression and that of the
ttgGHI
operon, which encodes an RND efflux pump. TtgV has two domains: a GAF-like domain harboring the effector-binding pocket and a helix-turn-helix (HTH) DNA-binding domain, which are linked by a long extended helix. When TtgV is bound to DNA, a kink at residue 86 in the extended helix gives rise to 2 helices. TtgV contacts DNA mainly through a canonical recognition helix, but its three-dimensional structure bound to DNA revealed that two residues, R19 and S35, outside the HTH motif, directly contact DNA. Effector binding to TtgV releases it from DNA; when this occurs, the kink at Q86 is lost and residues R19 and S35 are displaced due to the reorganization of the turn involving residues G44 and P46. Mutants of TtgV were generated at positions 19, 35, 44, 46, and 86 by site-directed mutagenesis to further analyze their role. Mutant proteins were purified to homogeneity, and differential scanning calorimetry (DSC) studies revealed that all mutants, except the Q86N mutant, unfold in a single event, suggesting conservation of the three-dimensional organization. All mutant variants bound effectors with an affinity similar to that of the parental protein. R19A, S35A, G44A, Q86N, and Q86E mutants did not bind DNA. The Q86A mutant was able to bind to DNA but was only partially released from its target operator in response to effectors. These results are discussed in the context of intramolecular signal transmission from the effector binding pocket to the DNA binding domain.
Hypersensitive Photic Responses and Intact Genome-Wide Transcriptional Control without the KaiC Phosphorylation Cycle in the Synechococcus Circadian System
Authors: Umetani Miki , Hosokawa Norimune , Kitayama Yohko , Iwasaki Hideo 
Published: November 2013

ABSTRACT

Cyanobacteria are unique organisms with remarkably stable circadian oscillations. These are controlled by a network architecture that comprises two regulatory factors: posttranslational oscillation (PTO) and a transcription/translation feedback loop (TTFL). The clock proteins KaiA, KaiB, and KaiC are essential for the circadian rhythm of the unicellular species
Synechococcus elongatus
PCC 7942. Temperature-compensated autonomous cycling of KaiC phosphorylation has been proposed as the primary oscillator mechanism that maintains the circadian clock, even in the dark, and it controls genome-wide gene expression rhythms under continuous-light conditions (LL). However, the
kaiC

EE

mutation (where “EE” represents the amino acid changes Ser431Glu and Thr432Glu), where phosphorylation cycling does not occur
in vivo
, has a damped but clear
kaiBC
expression rhythm with a long period. This suggests that there must be coupling between the robust PTO and the “slave” unstable TTFL. Here, we found that the
kaiC

EE

mutant strain in LL was hypersensitive to the dark acclimation required for phase shifting. Twenty-three percent of the genes in the
kaiC

EE

mutant strain exhibited genome-wide transcriptional rhythms with a period of 48 h in LL. The circadian phase distribution was also conserved significantly in most of the wild-type and
kaiC

EE

mutant strain cycling genes, which suggests that the output mechanism was not damaged severely even in the absence of KaiC phosphorylation cycles. These results strongly suggest that the KaiC phosphorylation cycle is not essential for generating the genome-wide rhythm under light conditions, whereas it is important for appropriate circadian timing in the light and dark.
PrgK, a Multidomain Peptidoglycan Hydrolase, Is Essential for Conjugative Transfer of the Pheromone-Responsive Plasmid pCF10
Authors: Laverde Gomez Jenny A. , Bhatty Minny , Christie Peter J. 
Published: November 2013

ABSTRACT

Peptidoglycan (PG) hydrolases associated with bacterial type IV secretion systems (T4SSs) are thought to generate localized lesions in the PG layer to facilitate assembly of the translocation channel. The pheromone-responsive plasmid pCF10 of
Enterococcus faecalis
encodes a putative cell wall hydrolase, PrgK, and here we report that a
prgK
deletion abolished functionality of the pCF10-encoded T4SS as monitored by pCF10 conjugative transfer. Expression in
trans
of wild-type
prgK
fully complemented this mutation. PrgK has three potential hydrolase motifs resembling staphylococcal LytM, soluble lytic transglycosylase (SLT), and cysteine-, histidine-dependent amidohydrolase/peptidase (CHAP) domains. Complementation analyses with mutant alleles established that PrgK bearing two hydrolase domains in any combination supported near-wild-type plasmid transfer, and PrgK bearing a single hydrolase domain supported at least a low level of transfer in filter matings. When exported to the
Escherichia coli
periplasm, each domain disrupted cell growth, and combinations of domains additionally induced cell rounding and blebbing and conferred enhanced sensitivity to osmotic shock. Each domain bound PG
in vitro
, but only the SLT domain exhibited detectable hydrolase activity, as shown by zymographic analyses and release of fluorescent PG fragments. Genes encoding three T4SS-associated, putative hydrolases,
Lactococcus lactis
CsiA, Tn
925
Orf14, and pIP501 TraG, partially complemented the Δ
prgK
mutation. Our findings establish that PrgK is an essential component of the pCF10-encoded Prg/Pcf T4SS and that its hydrolase domains coordinate their activities for full PrgK function. PrgK is indispensable for plasmid transfer in liquid matings, suggestive of a role in formation or stabilization of mating junctions.
Transcriptional Analysis of the Streptococcus pyogenes Salivaricin Locus
Authors: Namprachan-Frantz Phanramphoei , Rowe Hannah M. , Runft Donna L. , Neely Melody N. 
Published: November 2013

ABSTRACT

The
sal
lantibiotic locus plays an important role in the virulence of
Streptococcus pyogenes
. Our transcriptional analysis of the
sal
locus provides new information on the complex regulation of this operon. Transcription of the operon is regulated by a promoter upstream of the operon and by a second internal promoter upstream of the
salKRZ
genes. Here we identify the location of the internal promoter and provide information on how this promoter is autoregulated by proteins within the locus. We determined by primer extension that the
salKR
promoter is located within the
salY
gene and identified several regulatory regions important for expression. The higher activity of the promoter in a
salKR
deletion strain indicates a role in repression by the SalR response regulator. Further, this promoter had higher activity in a
salA
deletion strain, implicating corepression or a signaling role for the SalA peptide. Finally, we demonstrate that this promoter can be controlled by host factors. Analysis of transcriptional regulation of this locus provides a better understanding of the function of the
sal
locus in
S. pyogenes
pathogenesis.