bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Wild, Novel Nisin A-Producing Lactococcus Strain with an L. lactis subsp.
cremoris
Genotype and an L. lactis subsp.
lactis
Phenotype, Isolated from Greek Raw Milk
Authors: Parapouli Maria , Delbès-Paus Céline , Kakouri Athanasia , Koukkou Anna-Irini , Montel Marie-Christine , Samelis John 
Published: March 2013

ABSTRACT

Several molecular taxonomic studies have revealed that many natural (wild)
Lactococcus lactis
strains of dairy origin which are phenotypically representative of the
L. lactis
subspecies
lactis
cluster genotypically within subspecies
cremoris
and
vice versa
. Recently, we isolated two wild nisin-producing (Nis
+
)
L. lactis
strains, M78 and M104, of the
lactis
phenotype from Greek raw milk (J. Samelis, A. Lianou, A. Kakouri, C. Delbès, I. Rogelj, B. B. Matijašic, and M. C. Montel, J. Food Prot. 72:783–790, 2009); strain M78 possess a novel nisin A sequence (GenBank accession number
HM219853
). In this study, the actual subspecies identity of M78 and M104 isolates was elucidated, using 16S rRNA and
acmA
(encoding lactococcal
N
-acetylmuramidase) gene and histidine biosynthesis operon polymorphisms and 16S rRNA and
ldh
(encoding lactate dehydrogenase) gene phylogenies. Except the
acmA
gene analysis, molecular tools revealed that isolates M78 and M104 clustered with strains of the
cremoris
genotype, including the LMG 6897
T
strain, while they were distant from strains of the
lactis
genotype, including the LMG 6890
T
strain. The two wild isolates had identical repetitive sequence-based PCR (rep-PCR), randomly amplified polymorphic DNA (RAPD), plasmid, and whole-cell protein profiles and shared high 16S rRNA (99.9%) and
ldh
(100%) gene sequence homologies. In contrast, they exhibited identical sugar fermentation and enzymatic patterns which were similar to those of the subspecies
lactis
LMG 6890
T
strain. To our knowledge, this is the first complete identification report on a wild
L. lactis
subsp.
cremoris
genotype of the
lactis
phenotype which is capable of nisin A production and, thus, has strong potential for use as a novel dairy starter and/or protective culture.
Physiological and Transcriptional Responses of Saccharomyces cerevisiae to
d
-Limonene Show Changes to the Cell Wall but Not to the Plasma Membrane
Authors: Brennan Timothy C. R. , Krï¿½mer Jens O. , Nielsen Lars K. 
Published: March 2013

ABSTRACT

Monoterpenes can, upon hydrogenation, be used as light-fraction components of sustainable aviation fuels. Fermentative production of monoterpenes in engineered microorganisms, such as
Saccharomyces cerevisiae
, has gained attention as a potential route to deliver these next-generation fuels from renewable biomass. However, end product toxicity presents a formidable problem for microbial synthesis. Due to their hydrophobicity, monoterpene inhibition has long been attributed to membrane interference, but the molecular mechanism remains largely unsolved. In order to gain a better understanding of the mode of action, we analyzed the composition and structural integrity of the cell envelope as well as the transcriptional response of yeast cells treated with an inhibitory amount of
d
-limonene (107 mg/liter). We found no alterations in membrane fluidity, structural membrane integrity, or fatty acid composition after the solvent challenge. A 4-fold increase in the mean fluorescence intensity per cell (using calcofluor white stain) and increased sensitivity to cell wall-degrading enzymes demonstrated that limonene disrupts cell wall properties. Global transcript measurements confirmed the membrane integrity observations by showing no upregulation of ergosterol or fatty acid biosynthesis pathways, which are commonly overexpressed in yeast to reinforce membrane rigidity during ethanol exposure. Limonene shock did cause a compensatory response to cell wall damage through overexpression of several genes (
ROM1
,
RLM1
,
PIR3
,
CTT1
,
YGP1
,
MLP1
,
PST1
, and
CWP1
) involved with the cell wall integrity signaling pathway. This is the first report demonstrating that cell wall, rather than plasma membrane, deterioration is the main source of monoterpene inhibition. We show that limonene can alter the structure and function of the cell wall, which has a clear effect on cytokinesis.
Genotypic Diversity and Virulence Characteristics of Clinical and Environmental Vibrio vulnificus Isolates from the Baltic Sea Region
Authors: Bier Nadja , Bechlars Silke , Diescher Susanne , Klein Florian , Hauk Gerhard , Duty Oliver , Strauch Eckhard , Dieckmann Ralf 
Published: March 2013

ABSTRACT

The genetic diversity of
Vibrio vulnificus
isolates from clinical and environmental sources originating from the Baltic Sea region was evaluated by multilocus sequence typing (MLST), and possible relationships between MLST clusters, potential genotypic and phenotypic traits associated with pathogenicity, and source of isolation were investigated. The studied traits included genotyping of polymorphic loci (16S rRNA,
vcg
, and
pilF
), presence/absence of potential virulence genes, including
nanA
,
nab
, and genes of pathogenicity regions, metabolic features, hemolytic activity, resistance to human serum, and cytotoxicity to human intestinal cells. MLST generated 35 (27 new) sequence types and divided the 53 isolates (including four reference strains) into two main clusters, with cluster I containing biotype 1 and 2 isolates of mainly environmental origin and cluster II containing biotype 1 isolates of mainly clinical origin. Cluster II isolates were further subdivided into two branches. Branch IIB included isolates from recent cases of wound infections that were acquired at the German Baltic Sea coastline between 2010 and 2011 and isolates from seawater samples of the same regions isolated between 1994 and 2010. Comparing the MLST data with the results of genotyping and phenotyping showed that strains of MLST cluster II possess a number of additional pathogenicity-associated traits compared to cluster I strains. Rapid microbiological methods such as matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry combined with typing of selected virulence-associated traits (e.g., serum resistance, mannitol fermentation,
nanA
, and pathogenicity region XII) could be used for risk assessment purposes regarding
V. vulnificus
strains isolated from the Baltic Sea region.
Identification and Expression of Genes Involved in the Conversion of Daidzein and Genistein by the Equol-Forming Bacterium Slackia isoflavoniconvertens
Authors: Schröder Christine , Matthies Anastasia , Engst Wolfram , Blaut Michael , Braune Annett 
Published: March 2013

ABSTRACT

Gut bacteria play a key role in the metabolism of dietary isoflavones, thereby influencing the availability and bioactivation of these polyphenols in the intestine. The human intestinal bacterium
Slackia isoflavoniconvertens
converts the main soybean isoflavones daidzein and genistein to equol and 5-hydroxy-equol, respectively. Cell extracts of
S. isoflavoniconvertens
catalyzed the conversion of daidzein via dihydrodaidzein to equol and that of genistein to dihydrogenistein. Growth of
S. isoflavoniconvertens
in the presence of daidzein led to the induction of several proteins as observed by two-dimensional difference gel electrophoresis. Based on determined peptide sequences, we identified a cluster of eight genes encoding the daidzein-induced proteins. Heterologous expression of three of these genes in
Escherichia coli
and enzyme activity tests with the resulting cell extracts identified the corresponding gene products as a daidzein reductase (DZNR), a dihydrodaidzein reductase (DHDR), and a tetrahydrodaidzein reductase (THDR). The recombinant DZNR also converted genistein to dihydrogenistein at higher rates than were observed for the conversion of daidzein to dihydrodaidzein. Higher rates were also observed with cell extracts of
S. isoflavoniconvertens
. The recombinant DHDR and THDR catalyzed the reduction of dihydrodaidzein to equol, while the corresponding conversion of dihydrogenistein to 5-hydroxy-equol was not observed. The DZNR, DHDR, and THDR were expressed as
Strep
-tag fusion proteins and subsequently purified by affinity chromatography. The purified enzymes were further characterized with regard to their activity, stereochemistry, quaternary structure, and content of flavin cofactors.
Importance of Relating Efficacy Measures to Unbound Drug Concentrations for Anti-Infective Agents
Authors: Gonzalez Daniel , Schmidt Stephan , Derendorf Hartmut 
Published: April 2013

SUMMARY
For the optimization of dosing regimens of anti-infective agents, it is imperative to have a good understanding of pharmacokinetics (PK) and pharmacodynamics (PD). Whenever possible, drug efficacy needs to be related to unbound concentrations at the site of action. For anti-infective drugs, the infection site is typically located outside plasma, and a drug must diffuse through capillary membranes to reach its target. Disease- and drug-related factors can contribute to differential tissue distribution. As a result, the assumption that the plasma concentration of drugs represents a suitable surrogate of tissue concentrations may lead to erroneous conclusions. Quantifying drug exposure in tissues represents an opportunity to relate the pharmacologically active concentrations to an observed pharmacodynamic parameter, such as the MIC. Selection of an appropriate specimen to sample and the advantages and limitations of the available sampling techniques require careful consideration. Ultimately, the goal will be to assess the appropriateness of a drug and dosing regimen for a specific pathogen and infection.
Detection and Characterization of Megasatellites in Orthologous and Nonorthologous Genes of 21 Fungal Genomes
Authors: Tekaia Fredj , Dujon Bernard , Richard Guy-Franck 
Published: March 2013

ABSTRACTMegasatellites are large DNA tandem repeats, originally described inCandida glabrata, in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
Diverse Hap43-Independent Functions of the Candida albicans CCAAT-Binding Complex
Authors: Hsu Po-Chen , Chao Chun-Cheih , Yang Cheng-Yao , Ye Ya-Ling , Liu Fu-Chen , Chuang Yung-Jen , Lan Chung-Yu 
Published: March 2013

ABSTRACT

The CCAAT motif is ubiquitous in promoters of eukaryotic genomes. The CCAAT-binding complex (CBC) is conserved across a wide range of organisms, specifically recognizes the CCAAT motif, and modulates transcription directly or in cooperation with other transcription factors. In
Candida albicans
, CBC is known to interact with the repressor Hap43 to negatively regulate iron utilization genes in response to iron deprivation. However, the extent of additional functions of CBC is unclear. In this study, we explored new roles of CBC in
C. albicans
and found that CBC pleiotropically regulates many virulence traits
in vitro
, including negative control of genes responsible for ribosome biogenesis and translation and positive regulation of low-nitrogen-induced filamentation. In addition,
C. albicans
CBC is involved in utilization of host proteins as nitrogen sources and in repression of cellular flocculation and adhesin gene expression. Moreover, our epistasis analyses suggest that CBC acts as a downstream effector of Rhb1-TOR signaling and controls low-nitrogen-induced filamentation via the Mep2-Ras1-protein kinase A (PKA)/mitogen-activated protein kinase (MAPK) pathway. Importantly, the phenotypes identified here are all independent of Hap43. Finally, deletion of genes encoding CBC components slightly attenuated
C. albicans
virulence in both zebrafish and murine models of infection. Our results thus highlight new roles of
C. albicans
CBC in regulating multiple virulence traits in response to environmental perturbations and, finally, suggest potential targets for antifungal therapies as well as extending our understanding of the pathogenesis of other fungal pathogens.
Multiple Roles of RNase Y in Streptococcus pyogenes mRNA Processing and Degradation
Authors: Chen Zhiyun , Itzek Andreas , Malke Horst , Ferretti Joseph J. , Kreth Jens 
Published: March 2013

ABSTRACT

Control over mRNA stability is an essential part of gene regulation that involves both endo- and exoribonucleases. RNase Y is a recently identified endoribonuclease in Gram-positive bacteria, and an RNase Y ortholog has been identified in
Streptococcus pyogenes
(group A streptococcus [GAS]). In this study, we used microarray and Northern blot analyses to determine the
S. pyogenes
mRNA half-life of the transcriptome and to understand the role of RNase Y in global mRNA degradation and processing. We demonstrated that
S. pyogenes
has an unusually high mRNA turnover rate, with median and mean half-lives of 0.88 min and 1.26 min, respectively. A mutation of the RNase Y-encoding gene (
rny
) led to a 2-fold increase in overall mRNA stability. RNase Y was also found to play a significant role in the mRNA processing of virulence-associated genes as well as in the rapid degradation of
rnpB
read-through transcripts. From these results, we conclude that RNase Y is a pleiotropic regulator required for mRNA stability, mRNA processing, and removal of read-through transcripts in
S. pyogenes
.
Three of Four GlnR Binding Sites Are Essential for GlnR-Mediated Activation of Transcription of the
Amycolatopsis mediterranei nas
Operon
Authors: Wang Ying , Wang Jing-Zhi , Shao Zhi-Hui , Yuan Hua , Lu Yin-Hua , Jiang Wei-Hong , Zhao Guo-Ping , Wang Jin 
Published: March 2013

ABSTRACT

In
Amycolatopsis mediterranei
U32, genes responsible for nitrate assimilation formed one operon,
nasACKBDEF
, whose transcription is induced by the addition of nitrate. Here, we characterized GlnR as a direct transcriptional activator for the
nas
operon. The GlnR-protected DNA sequences in the promoter region of the
nas
operon were characterized by DNase I footprinting assay, the previously deduced
Streptomyces coelicolor
double 22-bp GlnR binding consensus sequences comprising
a1
,
b1
,
a2
, and
b2
sites were identified, and the sites were then mutated individually to test their roles in both the binding of GlnR
in vitro
and the GlnR-mediated transcriptional activation
in vivo
. The results clearly showed that only three GlnR binding sites (
a1
,
b1
, and
b2
sites) were required by GlnR for its specific binding to the
nas
promoter region and efficient activation of the transcription of the
nas
operon in U32, while the
a2
site seemed unnecessary.
Characterization of the
ospZ
Promoter in Shigella flexneri and Its Regulation by VirB and H-NS
Authors: Basta David W. , Pew Krystle L. , Immak Joy A. , Park Hiromichi S. , Picker Michael A. , Wigley Amanda F. , Hensley Christopher T. , Pearson Jaclyn S. , Hartland Elizabeth L. , Wing Helen J. 
Published: March 2013

ABSTRACT

OspZ is an effector protein of the type III secretion system in
Shigella
spp. that downregulates the human inflammatory response during bacterial infection. The
ospZ
gene is located on the large virulence plasmid of
Shigella
. Many genes on this plasmid are transcriptionally repressed by the nucleoid structuring protein H-NS and derepressed by VirB, a DNA-binding protein that displays homology to the plasmid partitioning proteins ParB and SopB. In this study, we characterized the
ospZ
promoter and investigated its regulation by H-NS and VirB in
Shigella flexneri
. We show that H-NS represses and VirB partially derepresses the
ospZ
promoter. H-NS-mediated repression requires sequences located between −731 and −412 relative to the beginning of the
ospZ
gene. Notably, the VirB-dependent derepression of
ospZ
requires the same VirB binding sites as are required for the VirB-dependent derepression of the divergent
icsP
gene. These sites are centered 425 bp upstream of the
ospZ
gene but over 1 kb upstream of the
icsP
transcription start site. Although these VirB binding sites lie closer to
ospZ
than
icsP
, the VirB-dependent increase in
ospZ
promoter activity is lower than that observed at the
icsP
promoter. This indicates that the proximity of VirB binding sites to
Shigella
promoters does not necessarily correlate with the level of VirB-dependent derepression. These findings have implications for virulence gene regulation in
Shigella
and other pathogens that control gene expression using mechanisms of transcriptional repression and derepression.
Rapid Detection of HIV-1 Proviral DNA for Early Infant Diagnosis Using Recombinase Polymerase Amplification
Authors: Boyle David S. , Lehman Dara A. , Lillis Lorraine , Peterson Dylan , Singhal Mitra , Armes Niall , Parker Mathew , Piepenburg Olaf , Overbaugh Julie 
Published: April 2013

ABSTRACTEarly diagnosis and treatment of human immunodeficiency virus type 1 (HIV-1) infection in infants can greatly reduce mortality rates. However, current infant HIV-1 diagnostics cannot reliably be performed at the point of care, often delaying treatment and compromising its efficacy. Recombinase polymerase amplification (RPA) is a novel technology that is ideal for an HIV-1 diagnostic, as it amplifies target DNA in <20 min at a constant temperature, without the need for complex thermocycling equipment. Here we tested 63 HIV-1-specific primer and probe combinations and identified two RPA assays that target distinct regions of the HIV-1 genome (long terminal repeat [LTR] andpol) and can reliably detect 3 copies of proviral DNA by the use of fluorescence detection and lateral-flow strip detection. Thesepoland LTR primers amplified 98.6% and 93%, respectively, of the diverse HIV-1 variants tested. This is the first example of an isothermal assay that consistently detects all of the major HIV-1 global subtypes.IMPORTANCEDiagnosis of HIV-1 infection in infants cannot rely on the antibody-based tests used in adults because of the transfer of maternal HIV-1 antibodies from mother to child. Therefore, infant diagnostics rely on detection of the virus itself. However, current infant HIV-1 diagnostic methods require a laboratory setting with complex equipment. Here we describe the initial development of an HIV-1 diagnostic for infants that may be performed at the point of care in rural health clinics. We utilize a method that can amplify and detect HIV-1 DNA at an incubation temperature within the range of 25 to 42°C, eliminating the need for thermocycling equipment. HIV-1 diagnostics are challenging to develop due to the high diversity seen in HIV-1 strains worldwide. Here we show that this method detects the major HIV-1 strains circulating globally.
Bacterial Bioluminescence Regulates Expression of a Host Cryptochrome Gene in the Squid-Vibrio Symbiosis
Authors: Heath-Heckman Elizabeth A. C. , Peyer Suzanne M. , Whistler Cheryl A. , Apicella Michael A. , Goldman William E. , McFall-Ngai Margaret J. 
Published: April 2013

ABSTRACTThe symbiosis between the squidEuprymna scolopesand its luminous symbiont,Vibrio fischeri, is characterized by daily transcriptional rhythms in both partners and daily fluctuations in symbiont luminescence. In this study, we sought to determine whether symbionts affect host transcriptional rhythms. We identified two transcripts in host tissues (E. scolopes cry1[escry1] andescry2) that encode cryptochromes, proteins that influence circadian rhythms in other systems. Both genes cycled daily in the head of the squid, with a pattern similar to that of other animals, in which expression of certaincrygenes is entrained by environmental light. In contrast,escry1expression cycled in the symbiont-colonized light organ with 8-fold upregulation coincident with the rhythms of bacterial luminescence, which are offset from the day/night light regime. Colonization of the juvenile light organ by symbionts was required for induction ofescry1cycling. Further, analysis with a mutant strain defective in light production showed that symbiont luminescence is essential for cycling ofescry1; this defect could be complemented by presentation of exogenous blue light. However, blue-light exposure alone did not induce cycling in nonsymbiotic animals, but addition of molecules of the symbiont cell envelope to light-exposed animals did recover significant cycling activity, showing that light acts in synergy with other symbiont features to induce cycling. While symbiont luminescence may be a character specific to rhythms of the squid-vibrio association, resident microbial partners could similarly influence well-documented daily rhythms in other systems, such as the mammalian gut.IMPORTANCEIn mammals, biological rhythms of the intestinal epithelium and the associated mucosal immune system regulate such diverse processes as lipid trafficking and the immune response to pathogens. While these same processes are affected by the diverse resident microbiota, the extent to which these microbial communities control or are controlled by these rhythms has not been addressed. This study provides evidence that the presentation of three bacterial products (lipid A, peptidoglycan monomer, and blue light) is required for cyclic expression of a cryptochrome gene in the symbiotic organ. The finding that bacteria can directly influence the transcription of a gene encoding a protein implicated in the entrainment of circadian rhythms provides the first evidence for the role of bacterial symbionts in influencing, and perhaps driving, peripheral circadian oscillators in the host.