bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endless Hide‐and‐Seek: Dynamic Co‐evolution in Plant‐Bacterium Warfare
Authors: Shan Libo , He Ping , Sheen Jen 
Published: January 2007

AbstractPlants possess innate immune systems to prevent most potential infections. The ancient and conserved innate immune responses are triggered by microbe‐associated molecular patterns (MAMPs) and play important roles in broad‐spectrum defenses. However, successful bacterial pathogens evolved type III virulence effectors to suppress MAMP‐mediated immunity. To survive, plants further developed highly specific resistance (R) genes to trigger gene‐for‐gene‐mediated immunity and turn the virulent pathogens into avirulent ones. We summarize here the very recent advances in this dynamic coevolution of plant‐bacterium interaction.
A Role for Auxin in Flower Development
Authors: Cheng Youfa , Zhao Yunde 
Published: January 2007

AbstractAuxin has long been implicated in many aspects of plant growth and development including flower development. However, the exact roles of auxin in flower development have not been well defined until the recent identification of auxin biosynthesis mutants. Auxin is necessary for the initiation of floral primordia, and the disruption of auxin biosynthesis, polar auxin transport or auxin signaling leads to the failure of flower formation. Auxin also plays an essential role in specifying the number and identity of floral organs. Further analysis of the relationship between the auxin pathways and the known flower development genes will provide critical information regarding mechanisms of organogenesis and pattern formation in plants.
Jasmonate Signal Pathway in Arabidopsis
Authors: Shan Xiao‐Yi , Wang Zhi‐Long , Xie Daoxin 
Published: January 2007

AbstractJasmonates (JAs), which include jasmonic acid and its cyclopentane derivatives are synthesized from the octadecanoid pathway and widely distributed throughout the plant kingdom. JAs modulate the expression of numerous genes and mediate responses to stress, wounding, insect attack, pathogen infection, and UV damage. They also affect a variety of processes in many plant developmental processes. The JA signal pathway involves two important events: the biosynthesis of JA and the transduction of JA signal. Several important Arabidopsis mutants in jasmonate signal pathway were described in this review.
Ubiquitination in Abscisic Acid‐Related Pathway
Authors: Zhang Yi‐Yue , Xie Qi 
Published: January 2007

AbstractUbiquitination is emerging as a tight regulatory mechanism that is necessary for all aspects of development and survival of all eukaryotes. Recent genomic and genetic analysis in Arabidopsis suggests that ubiquitination may also play important roles in plant response to the phytohormone abscisic acid (ABA). Many components of the ubiquitination pathway, such as ubiquitin‐conjugating enzyme E2, ubiquitin ligase E3 and components of the proteasome, have been identified or predicted to be essential in ABA biosynthesis, catabolism and signaling. In addition, the ubiquitination‐related pathway, sumoylation, is also involved in ABA signaling. We summarize in this report recent developments to elucidate their roles in the ABA‐related pathway.
Roles of Pectin Methylesterases in Pollen‐Tube Growth
Authors: Chen Li‐Qun , Ye De 
Published: January 2007

AbstractElongation of the pollen tube in pistil is essential for delivering sperms into the female gametophyte in sexual plant reproduction. Recently, a group of cell wall enzymes, pectin methylesterases (PMEs), have been identified as playing an important role in this process. This article reviews the new understanding of the roles of PMEs in regulating pollen tube growth.
Characterization of the Ubiquitin E2 Enzyme Variant Gene Family in Arabidopsis
Authors: Zhang Yu , Wen Pei , Lau On‐Sun , Deng Xing‐Wang 
Published: January 2007

AbstractUbiquitin E2 enzyme variant (UEV) proteins are similar to ubiquitin‐conjugating enzyme (E2) in both sequence and structure, but the lack of a catalytic cysteine residue renders them incapable of forming a thiol‐ester linkage with ubiquitin. While the functional roles of several UEVs have been defined in yeast and animal systems, Arabidopsis COP10, a photomorphogenesis repressor, is the only UEV characterized in plants. Phylogenetic analysis revealed that the eight Arabidopsis UEV genes belong to three subfamilies. The expression of those genes is supported by either the presence of ESTs or RT‐PCR analysis. We also characterized the other members of the COP10 subfamily, UEV2. Semi‐quantitative RT‐PCR analysis indicated that the UEV2 transcripts can be detected in most organs of Arabidopsis. Analysis of UEV2::GUS transgenic lines also showed its ubiquitous expression in nearly all the developmental stages of Arabidopsis. Transient expression analysis indicated that the sGFP‐UEV2 fusion protein can localize to both the cytoplasm and nucleus. A T‐DNA insertion mutant, uev2‐1, which abolished the transcription of UEV2, displays no visible phenotype. Further, the cop10‐4 uev2‐1 double mutant exhibits the same phenotype as the cop10‐4 mutant in darkness. UEV2 is therefore not functionally redundant with COP10.
Barriers to immunizations: Multiethnic parents of under‐ and unimmunized children speak
Authors: Niederhauser Victoria P. , Markowitz Malama 
Published: January 2007

AbstractPurpose: Childhood immunizations are one of the greatest pubic health success stories. Despite the fact that many children receive immunizations according to the recommended schedule, there are many that lag behind. The purpose of this study was to explore the barriers to immunizations in parents whose children are not fully immunized by age 2.Data source: Thirteen focus groups, on four different islands (Oahu, Kauai, Maui, Hawaii) were held with a total of 64 parents. Verbatim transcripts were utilized for content analysis.Conclusion: Five core themes emerged as barriers to childhood immunizations, parental, transportation, financial, child, and organization. The majority of responses were in the parental core theme, which included the sub‐themes of issues, beliefs, knowledge, and fears.Implications for practice: Recommendations included identification of specific barriers to target immunization interventions strategies, public policy changes, identification and case management of high risk families, and minimization of organizational barriers.
Reduced Contamination by the
Fusarium
Mycotoxin Zearalenone in Maize Kernels through Genetic Modification with a Detoxification Gene
Authors: Igawa Tomoko , Takahashi-Ando Naoko , Ochiai Noriyuki , Ohsato Shuichi , Shimizu Tsutomu , Kudo Toshiaki , Yamaguchi Isamu , Kimura Makoto 
Published: January 2007

ABSTRACT

Maize is subject to ear rot caused by toxigenic
Aspergillus
and
Fusarium
species, resulting in contamination with aflatoxins, fumonisins, trichothecenes, and zearalenone (ZEN). The trichothecene group and ZEN mycotoxins are produced by the cereal pathogen
Fusarium graminearum
. A transgenic detoxification system for the elimination of ZEN was previously developed using an
egfp
::
zhd101
gene (
gfzhd101
), encoding an enhanced green fluorescent protein fused to a ZEN-degrading enzyme. In this study, we produced a transgenic maize line expressing an intact copy of
gfzhd101
and examined the feasibility of transgene-mediated detoxification in the kernels. ZEN-degrading activity has been detected in transgenic kernels during seed maturation (for a period of 6 weeks after pollination). The level of detoxification activity was unaltered after an additional storage period of 16 weeks at 6°C. When the seeds were artificially contaminated by immersion in a ZEN solution for 48 h at 28°C, the total amount of the mycotoxin in the transgenic seeds was uniformly reduced to less than 1/10 of that in the wild type. The ZEN in the transgenic maize kernels was also efficiently decontaminated under conditions of lower water activity (a
w
) and temperature; e.g., 16.9 μg of ZEN was removed per gram of seed within 48 h at an a
w
of 0.90 at 20°C.
F. graminearum
infection assays demonstrated an absence of ZEN in the transgenic maize seeds, while the mycotoxin accumulated in wild-type kernels under the same conditions. Transgene-mediated detoxification may offer simple solutions to the problems of mycotoxin contamination in maize.
Air-Liquid Interface Biofilms of
Bacillus cereus
: Formation, Sporulation, and Dispersion
Authors: Wijman Janneke G. E. , de Leeuw Patrick P. L. A. , Moezelaar Roy , Zwietering Marcel H. , Abee Tjakko 
Published: January 2007

ABSTRACT

Biofilm formation by
Bacillus cereus
was assessed using 56 strains of
B. cereus
, including the two sequenced strains, ATCC 14579 and ATCC 10987. Biofilm production in microtiter plates was found to be strongly dependent on incubation time, temperature, and medium, as well as the strain used, with some strains showing biofilm formation within 24 h and subsequent dispersion within the next 24 h. A selection of strains was used for quantitative analysis of biofilm formation on stainless steel coupons. Thick biofilms of
B. cereus
developed at the air-liquid interface, while the amount of biofilm formed was much lower in submerged systems. This suggests that
B. cereus
biofilms may develop particularly in industrial storage and piping systems that are partly filled during operation or where residual liquid has remained after a production cycle. Moreover, depending on the strain and culture conditions, spores constituted up to 90% of the total biofilm counts. This indicates that
B. cereus
biofilms can act as a nidus for spore formation and subsequently can release their spores into food production environments.
Expression of Plant Flavor Genes in
Lactococcus lactis
Authors: Hernández Igor , Molenaar Douwe , Beekwilder Jules , Bouwmeester Harro , van Hylckama Vlieg Johan E. T. 
Published: January 2007

ABSTRACT

Lactic acid bacteria, such as
Lactococcus lactis
, are attractive hosts for the production of plant-bioactive compounds because of their food grade status, efficient expression, and metabolic engineering tools. Two genes from strawberry (
Fragaria x ananassa
), encoding an alcohol acyltransferase (SAAT) and a linalool/nerolidol synthase (FaNES), were cloned in
L. lactis
and actively expressed using the nisin-induced expression system. The specific activity of SAAT could be improved threefold (up to 564 pmol octyl acetate h
−1
mg protein
−1
) by increasing the concentration of tRNA
1
Arg
, which is a rare tRNA molecule in
L. lactis
. Fermentation tests with GM17 medium and milk with recombinant
L. lactis
strains expressing SAAT or FaNES resulted in the production of octyl acetate (1.9 μM) and linalool (85 nM) to levels above their odor thresholds in water. The results illustrate the potential of the application of
L. lactis
as a food grade expression platform for the recombinant production of proteins and bioactive compounds from plants.
Analysis of the Mechanism and Regulation of Lactose Transport and Metabolism in
Clostridium acetobutylicum
ATCC 824
Authors: Yu Yang , Tangney Martin , Aass Hans C. , Mitchell Wilfrid J. 
Published: January 2007

ABSTRACT

Although the acetone-butanol-ethanol fermentation of
Clostridium acetobutylicum
is currently uneconomic, the ability of the bacterium to metabolize a wide range of carbohydrates offers the potential for revival based on the use of cheap, low-grade substrates. We have investigated the uptake and metabolism of lactose, the major sugar in industrial whey waste, by
C. acetobutylicum
ATCC 824. Lactose is taken up via a phosphoenolpyruvate-dependent phosphotransferase system (PTS) comprising both soluble and membrane-associated components, and the resulting phosphorylated derivative is hydrolyzed by a phospho-β-galactosidase. These activities are induced during growth on lactose but are absent in glucose-grown cells. Analysis of the
C. acetobutylicum
genome sequence identified a gene system,
lacRFEG
, encoding a transcriptional regulator of the DeoR family, IIA and IICB components of a lactose PTS, and phospho-β-galactosidase. During growth in medium containing both glucose and lactose,
C. acetobutylicum
exhibited a classical diauxic growth, and the
lac
operon was not expressed until glucose was exhausted from the medium. The presence upstream of
lacR
of a potential catabolite responsive element (
cre
) encompassing the transcriptional start site is indicative of the mechanism of carbon catabolite repression characteristic of low-GC gram-positive bacteria. A pathway for the uptake and metabolism of lactose by this industrially important organism is proposed.
Changing a Single Amino Acid in
Clostridium perfringens
β-Toxin Affects the Efficiency of Heterologous Secretion by
Bacillus subtilis
Authors: Nijland Reindert , Heerlien René , Hamoen Leendert W. , Kuipers Oscar P. 
Published: January 2007

ABSTRACT

Achieving efficient heterologous protein production and secretion by
Bacillus subtilis
is an attractive prospect, although often disappointingly low yields are reached. The expression of detoxified
Clostridium perfringens
β-toxin (β-toxoid) is exemplary for this. Although β-toxin can be efficiently expressed and secreted by
Bacillus subtilis
, the genetically detoxified, and industrially interesting, β-toxoid variant is difficult to obtain in high amounts. To optimize the expression of this putative vaccine component, we studied the differences in the global gene regulation responses of
B. subtilis
to overproduction of either β-toxin or β-toxoid by transcriptomics. A clear difference was the upregulation of the CssRS regulon, known to be induced upon secretion stress, when β-toxoid is produced. YkoJ, a protein of unknown function, was also upregulated, and we show that its expression is dependent on
cssS
. We then focused on the heterologous protein itself and found that the major secretion bottleneck can be traced back to a single amino acid substitution between the β-toxin and the β-toxoid, which results in the rapid degradation of β-toxoid following secretion across the cytoplasmic membrane. In contrast to β-toxin, β-toxoid protein is more prone to degradation directly after secretion, most likely due to poor folding characteristics introduced with point mutations. Our results show that although the host can be adapted in many ways, the intrinsic properties of a heterologous protein can play a decisive role when optimizing heterologous protein production.
Efficient Extraction of Thioreodoxin from
Saccharomyces cerevisiae
by Ethanol
Authors: Inoue Yoshiharu , Nomura Wataru , Takeuchi Yoko , Ohdate Takumi , Tamasu Shogo , Kitaoka Atsushi , Kiyokawa Yoshifumi , Masutani Hiroshi , Murata Kazuo , Wakai Yoshinori , Izawa Shingo , Yodoi Junji 
Published: January 2007

ABSTRACT

Thioredoxin, an antioxidant protein, is a promising molecule for development of functional foods because it protects the gastric mucosa and reduces the allergenicity of allergens. To establish a method for obtaining an ample amount of yeast thioredoxin, we found here that thioredoxin is released from
Saccharomyces cerevisiae
by treatment with 20% ethanol. We also found that Japanese sake contains a considerable amount of thioredoxin.
Identification and Characterization of
MFA1
, the Gene Encoding
Candida albicans
a
-Factor Pheromone
Authors: Dignard Daniel , El-Naggar Ahmed L. , Logue Mary E. , Butler Geraldine , Whiteway Malcolm 
Published: January 2007

ABSTRACT

In the opaque state,
MTL
a
and
MTL
α strains of
Candida albicans
are able to mate, and this mating is directed by a pheromone-mediated signaling process. We have used comparisons of genome sequences to identify a
C. albicans
gene encoding a candidate
a
-specific mating factor. This gene is conserved in
Candida dubliniensis
and is similar to a three-gene family in the related fungus
Candida parapsilosis
but has extremely limited similarity to the
Saccharomyces cerevisiae MFA1
(Sc
MFA1
) and Sc
MFA2
genes. All these genes encode C-terminal CAAX box motifs characteristic of prenylated proteins. The
C. albicans
gene, designated Ca
MFA1
, is found on chromosome 2 between ORF19.2165 and ORF19.2219.
MFA1
encodes an open reading frame of 42 amino acids that is predicted to be processed to a 14-amino-acid prenylated mature pheromone. Microarray analysis shows that
MFA1
is poorly expressed in opaque
MTL
a
cells but is induced when the cells are treated with α-factor. Disruption of this
C. albicans
gene blocks the mating of
MTL
a
cells but not
MTL
α cells, while the reintegration of the gene suppresses this cell-type-specific mating defect.
A Possible Heterodimeric Prophage-Like Element in the Genome of the Insect EndosymbiontSodalis glossinidius
Authors: Clark Alvin J. , Pontes Mauricio , Jones Tait , Dale Colin 
Published: January 2007

ABSTRACTExtrachromosomal element pSOG3 (52,162 nucleotides) in the genome ofSodalis glossinidiuscontains redundant phage-related gene pairs, indicating that it may have been formed by the fusion of two ancestral phage genomes followed by gene degradation. We suggest that pSOG3 is a prophage that has undergone genome degeneration accompanying host adaptation to symbiosis.
Enzyme Diversity of the Cellulolytic System Produced by
Clostridium cellulolyticum
Explored by Two-Dimensional Analysis: Identification of Seven Genes Encoding New Dockerin-Containing Proteins
Authors: Blouzard Jean-Charles , Bourgeois Caroline , de Philip Pascale , Valette Odile , Bélaïch Anne , Tardif Chantal , Bélaïch Jean-Pierre , Pagès Sandrine 
Published: January 2007

ABSTRACT

The enzyme diversity of the cellulolytic system produced by
Clostridium cellulolyticum
grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of
C. cellulolyticum
is composed of at least 30 dockerin-containing proteins (designated cellulosomal proteins) and 30 noncellulosomal components. Most of the known cellulosomal proteins, including CipC, Cel48F, Cel8C, Cel9G, Cel9E, Man5K, Cel9M, and Cel5A, were identified by using two-dimensional Western blot analysis with specific antibodies, whereas Cel5N, Cel9J, and Cel44O were identified by using N-terminal sequencing. Unknown enzymes having carboxymethyl cellulase or xylanase activities were detected by zymogram analysis of two-dimensional gels. Some of these enzymes were identified by N-terminal sequencing as homologs of proteins listed in the NCBI database. Using Trap-Dock PCR and DNA walking, seven genes encoding new dockerin-containing proteins were cloned and sequenced. Some of these genes are clustered. Enzymes encoded by these genes belong to glycoside hydrolase families GH2, GH9, GH10, GH26, GH27, and GH59. Except for members of family GH9, which contains only cellulases, the new modular glycoside hydrolases discovered in this work could be involved in the degradation of different hemicellulosic substrates, such as xylan or galactomannan.
CadC Has a Global Translational Effect during Acid Adaptation in
Salmonella enterica
Serovar Typhimurium
Authors: Lee Yong Heon , Kim Bae Hoon , Kim Ji Hye , Yoon Won Suck , Bang Seong Ho , Park Yong Keun 
Published: January 2007

ABSTRACT

In
Salmonella enterica
serovar Typhimurium, the membrane-localized CadC is a transcriptional activator of the
cadBA
operon, which contributes to the acid tolerance response. Unlike in
Escherichia coli
, in which transcription of
cadC
is constitutive, in
S. enterica
serovar Typhimurium
cadC
expression is induced by low pH and lysine. Inactivation of
cadC
suppresses the acid-sensitive phenotype of a
cadA
mutation, suggesting the existence of other CadC-dependent genes in addition to the
cadBA
operon. Using a proteomic approach, we identified 8 of the putative CadC-induced proteins and 15 of the putative CadC-repressed proteins. The former include porin proteins OmpC and OmpF. The latter include proteins involved in glycolysis, energy production, and stress tolerance. To better understand the altered levels of OmpC and OmpF, we compared expression of
ompR
in
S. enterica
serovar Typhimurium wild-type and
cadC
mutant strains and determined that CadC exerted a negative influence on
ompR
transcription. Taken together, our findings strongly suggest that CadC may be a global regulator involved in the OmpR regulatory system during acid adaptation.
The Lysine Decarboxylase CadA Protects
Escherichia coli
Starved of Phosphate against Fermentation Acids
Authors: Moreau Patrice L. 
Published: January 2007

ABSTRACT

Conflicting results have been reported for the rate and extent of cell death during a prolonged stationary phase. It is shown here that the viability of wild-type cells (MG1655) could decrease ≥10
8
-fold between days 1 and 14 and between days 1 and 6 of incubation under aerobic and anaerobic phosphate (P
i
) starvation conditions, respectively, whereas the cell viability decreased moderately under ammonium and glucose starvation conditions. Several lines of evidence indicated that the loss of viability of P
i
-starved cells resulted primarily from the catabolism of glucose into organic acids through pyruvate oxidase (PoxB) and pyruvate-formate lyase (PflB) under aerobic and anaerobic conditions, respectively. Weak organic acids that are excreted into the medium can reenter the cell and dissociate into protons and anions, thereby triggering cell death. However, P
i
-starved cells were efficiently protected by the activity of the inducible GadABC glutamate-dependent acid resistance system. Glutamate decarboxylation consumes one proton, which contributes to the internal pH homeostasis, and removes one intracellular negative charge, which might compensate for the accumulated weak acid anions. Unexpectedly, the tolerance of P
i
-starved cells to fermentation acids was markedly increased as a result of the activity of the inducible CadBA lysine-dependent acid resistance system that consumes one proton and produces the diamine cadaverine. CadA plays a key role in the defense of
Salmonella
at pH 3 but was thought to be ineffective in
Escherichia coli
since the protection of
E. coli
challenged at pH 2.5 by lysine is much weaker than the protection by glutamate. CadA activity was favored in P
i
-starved cells probably because weak organic acids slowly reenter cells fermenting glucose. Since the environmental conditions that trigger the death of P
i
-starved cells are strikingly similar to the conditions that are thought to prevail in the human colon (i.e., a combination of low levels of P
i
and oxygen and high levels of carbohydrates, inducing the microbiota to excrete high levels of organic acids), it is tempting to speculate that
E. coli
can survive in the gut because of the activity of the GadABC and CadBA glutamate- and lysine-dependent acid resistance systems.
Metabolism of Linoleic Acid by Human Gut Bacteria: Different Routes for Biosynthesis of Conjugated Linoleic Acid
Authors: Devillard Estelle , McIntosh Freda M. , Duncan Sylvia H. , Wallace R. John 
Published: January 2007

ABSTRACT

A survey of 30 representative strains of human gram-positive intestinal bacteria indicated that
Roseburia
species were among the most active in metabolizing linoleic acid (
cis
-9,
cis-
12-18:2). Different
Roseburia
spp. formed either vaccenic acid (
trans-
11-18:1) or a 10-hydroxy-18:1; these compounds are precursors of the health-promoting conjugated linoleic acid
cis-
9,
trans-
11-18:2 in human tissues and the intestine, respectively.