bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated levels of gene expression for collagen and decorin in human gingival overgrowth
Authors: Dannewitz Bettina , Edrich Christina , Tomakidi Pascal , Kohl Annette , Gabbert Olaf , Staehle Hans‐Jörg , Steinberg Thorsten 
Published: June 2006

AbstractObjectives: It has been demonstrated that extracellular matrix molecules are involved in cyclosporine‐induced gingival overgrowth (GO). However, for many of these molecules, it remains unclear whether their abundance is modulated on the protein and gene expression level.Material and Methods: To contribute to this clarification, we have analysed the protein and mRNA expression of type‐I collagen (COL1) and decorin (DC) in native specimens obtained from five patients with GO, and matched normal tissue using indirect immunofluorescence (IIM), in situ hybridization (ISH) and quantitative polymerase chain reaction (PCR).Results: IIF revealed a largely co‐localized although remarkably increased abundance for COL1 and DC in GO. This increase coincided with an up‐regulated gene expression observed for both molecules, as detected by ISH and quantitative PCR.Conclusions: Analysis of our data clearly demonstrates elevated levels for COL1 and DC and shows for the first time in native human tissue that involvement of these genes in GO is not confined to the protein level but also includes the transcriptional level.
Acceptability, feasibility and affordability of infant feeding options for HIV‐infected women: a qualitative study in south‐west Nigeria
Authors: Abiona Titilayo C. , Onayade Adedeji A. , Ijadunola Kayode T. , Obiajunwa Perpetua O. , Aina Olabisi I. , Thairu Lucy N. 
Published: June 2006

AbstractThe objective of this study was to explore the acceptability, feasibility, affordability, safety and sustainability of replacement feeding options for HIV‐infected mothers in Ile‐Ife, in south‐west Nigeria. Six focus group discussions were conducted with a purposive sample of mothers, fathers and grandmothers. The HIV status of all participants was unknown to investigators. All text data were analysed using the Text‐based Beta Software program. With regard to the acceptability of replacement feeds, respondents perceived the stigma associated with not breastfeeding to be an important consideration. In this community, breastfeeding is the norm – even though it is not necessarily exclusive. For infected mothers who choose to breastfeed exclusively and then to wean their infants before 6 months of age, respondents did not anticipate early cessation of breastfeeding to be problematic. Respondents noted that acceptable replacement foods included infant formula, soy milk and cow’s milk. Barriers to replacement feeding that were mentioned included: the high costs of replacement foods and fuel for cooking; an unreliable supply of electrical power; poor access to safe water; and poor access to storage facilities. The research confirms the difficulty of replacement feeding for HIV‐infected mothers in sub‐Saharan Africa. The results also provide the basis for new issues and hypothesis for future research in other communities with similar socio‐cultural and economic characteristics.
Relative validity of a dietary interview for assessing infant diet and compliance in a dietary intervention trial
Authors: Vähätalo Liisa , Bärlund Sonja , Hannila Marja‐Leena , Uusitalo Ulla , Pigg Hanna‐Mari , Salonen Marja , Nucci Anita , Krischer Jeffrey P. , Knip Mikael , Åkerblom Hans K. , Virtanen Suvi M. ,   the TRIGR Study Group
Published: June 2006

AbstractThe objective of this study was to assess the relative validity of a dietary interview method for use in an infant population. A dietary interview covering a 1‐month period was completed during a study visit at 3 or 6 months of age. It included structured questions and a short food frequency questionnaire (FFQ). The information was compared with data from two 48‐h recall interviews conducted during the month previous to the study visit. The agreement between the FFQ and 48‐h recalls was analysed as proportion of subjects classified into the same categories of consumption frequency and by the kappa analysis. A total of 100 subjects, at the age of 2–3 months (n = 50) and 5–6 months (n = 50), were included. The kappa values for breastmilk and study formula ranged from 0.82 to 0.95, indicating very good agreement. The agreement for other foods and vitamin D supplementation ranged from fair to very good. We also found a strong correlation for the reported amount of study formula consumed per feeding at 3 months (rs = 0.87, n = 24) and 6 months of age (rs = 0.73, n = 35) between the questionnaire and 48‐h recall data. However, the average amount of study formula per feeding was significantly higher when estimated for a 1‐month period, compared with a mean calculated from the two 48‐h recalls. As a conclusion, the interview was found to be a useful tool for assessing diet and compliance in a dietary intervention for infants.
Physiological and biochemical response of potato (Solanum tuberosum L. cv. Kara) to O3 and antioxidant chemicals: possible roles of antioxidant enzymes
Authors: Hassan I.A. 
Published: June 2006

AbstractAn Egyptian cultivar of potato (Solanum tuberosum L. cv. Kara) was grown in the field at two locations in northern Egypt: a ‘rural’ and a ‘suburban’ site, from October 2000 and November 2002. The antiozonant ethylenediurea (EDU) and the fungicide chlorothalonil (1,3‐benzenedicarbonitrile‐2,4,5,6 tetrachloroisophthalnitrile) were applied as a foliar spray to plants at both sites. It was found that foliar injury symptoms were reduced greatly in plants treated with EDU and/or chlorothalonil, and the yield of treated plants was higher than that of the untreated ones, with the EDU having a greater protection than chlorothalonil. Antiozonant (EDU) and fungicide (chlorothalonil) combination sprays were even more effective in reducing O3 injury. Moreover, the percentage of protection was higher in the rural area than in the suburban one, and this was associated with higher levels of O3 recorded in the rural area. The response to O3, EDU, and chlorothalonil of the leaf antioxidant scavenger system was examined. Antiozonant‐treated plants had the highest reduced glutathione/oxidised glutathione ratio. The results suggest that EDU and chlorothalonil do not act directly as antiozonant to inhibit O3 injury but act through maintaining some antioxidant enzymes during O3 exposure. To the best of knowledge, this is the first report demonstrating the marked enhancement of yield and plant oxidative enzymes by fungicides as a mechanism of protecting plants against noxious oxidative stress from the environment in the developing world.
Pathotypes of Plasmodiophora brassicae, the cause of clubroot, in Australia
Authors: Donald E.C. , Cross S.J. , Lawrence J.M. , Porter I.J. 
Published: June 2006

AbstractVariation in pathogenicity of Plasmodiophora brassicae in Australia was studied using the European Clubroot Differential series of brassica hosts. From 41 collections of P. brassicae originating from important vegetable brassica production regions in Victoria, Western Australia, Tasmania, Queensland and New South Wales, 23 triplet codes were generated. These were more similar to populations of P. brassicae reported from the USA than those from Europe. The most common Australian pathotypes had triplet codes of 16/3/12 and 16/3/31 and were each assigned seven times to pathogen collections originating from three states of Australia. Other codes that occurred more than once were 16/2/31, which was assigned to six collections from four states of Australia, and 16/19/31, which was assigned twice to collections originating from Western Australia.
Insight into the Binding Mode for Cyclopentapeptide Antagonists of the CXCR4 Receptor
Authors: Våbenø Jon , Nikiforovich Gregory V. , Marshall Garland R. 
Published: June 2006

The finding that the chemokine receptor CXCR4 is involved in T‐cell HIV entry has encouraged the development of antiretroviral drugs targeting this receptor. Additional evidence that CXCR4 plays a crucial role in both angiogenesis and metastasis provides further motivation for the development of a CXCR4 inhibitor for therapeutic applications in oncology. To facilitate the design of such ligands, we have investigated the possible binding modes for cyclopentapeptide CXCR4 antagonists by docking 11 high/medium affinity cyclopentapeptides to a developed three‐dimensional model of the CXCR4 G‐protein‐coupled receptor's transmembrane region. These ligands, expected to bind in the same mode to the receptor, were docked in the previously deduced receptor‐bound conformation [Våbenøet al., in press; doi 10.1002/bip.20508]. Ligand–receptor complexes were generated using an automated docking procedure that allowed ligand flexibility. By comparing the resulting ligand poses, only two binding modes common for all 11 compounds were identified. Inspection of these two ligand–receptor complexes identified several CXCR4 contact residues shown by mutation to be interaction sites for ligands and important for HIV gp120 binding. Thus, the results provide further insight into the mechanism by which these cyclopentapeptides block HIV entry as well as a basis for rational design of CXCR4 mutants to map potential contacts with small peptide ligands.
Replication Control of Staphylococcal Multiresistance Plasmid pSK41: an Antisense RNA Mediates Dual-Level Regulation of Rep Expression
Authors: Kwong Stephen M. , Skurray Ronald A. , Firth Neville 
Published: June 2006

ABSTRACT

Replication of staphylococcal multiresistance plasmid pSK41 is negatively regulated by the antisense transcript RNAI. pSK41 minireplicons bearing
rnaI
promoter (P

rnaI

) mutations exhibited dramatic increases in copy number, approximately 40-fold higher than the copy number for the wild-type replicon. The effects of RNAI mutations on expression of the replication initiator protein (Rep) were evaluated using transcriptional and translational fusions between the
rep
control region and the
cat
reporter gene. The results suggested that when P

rnaI

is disrupted, the amount of
rep
mRNA increases and it becomes derepressed for translation. These effects were reversed when RNAI was provided in
trans
, demonstrating that it is responsible for significant negative regulation at two levels, with the greatest repression exerted on
rep
translation initiation. Mutagenesis provided no evidence for RNAI-mediated transcriptional attenuation as a basis for the observed reduction in
rep
message associated with expression of RNAI. However, RNA secondary-structure predictions and supporting mutagenesis data suggest a novel mechanism for RNAI-mediated repression of
rep
translation initiation, where RNAI binding promotes a steric transition in the
rep
mRNA leader to an alternative thermodynamically stable stem-loop structure that sequesters the
rep
translation initiation region, thereby preventing translation.
Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic ArchaeonSulfolobus solfataricus
Authors: Tachdjian Sabrina , Kelly Robert M. 
Published: June 2006

ABSTRACTApproximately one-third of the open reading frames encoded in theSulfolobus solfataricusgenome were differentially expressed within 5 min following an 80 to 90°C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.
Crystal Structure of Pyridoxal Kinase from the
Escherichia coli pdxK
Gene: Implications for the Classification of Pyridoxal Kinases
Authors: Safo Martin K. , Musayev Faik N. , di Salvo Martino L. , Hunt Sharyn , Claude Jean-Baptiste , Schirch Verne 
Published: June 2006

ABSTRACT

The
pdxK
and
pdxY
genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including
Escherichia coli
pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the
pdxY
and
pdxK
genes, respectively. We now report the crystal structure of
E. coli
pyridoxal kinase 1 (ePL kinase 1), encoded by a
pdxK
gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-Å resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4′ substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4′ of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.
The Orphan Response Regulator DigR Is Required for Synthesis of Extracellular Matrix Fibrils inMyxococcus xanthus
Authors: Overgaard Martin , Wegener-Feldbrügge Sigrun , Søgaard-Andersen Lotte 
Published: June 2006

ABSTRACTInMyxococcus xanthus, two-component systems have crucial roles in regulating motility behavior and development. Here we describe an orphan response regulator, consisting of an N-terminal receiver domain and a C-terminal DNA binding domain, which is required for A and type IV pilus-dependent gliding motility. Genetic evidence suggests that phosphorylation of the conserved, phosphorylatable aspartate residue in the receiver domain is required for DigR activity. Consistent with the defect in type IV pilus-dependent motility, adigRmutant is slightly reduced in type IV pilus biosynthesis, and the composition of the extracellular matrix fibrils is abnormal, with an increased content of polysaccharides and decreased accumulation of the FibA metalloprotease. By using genome-wide transcriptional profiling, 118 genes were identified that are directly or indirectly regulated by DigR. These 118 genes include only 2,agmQandcheY4, previously implicated in A and type IV pilus-dependent motility, respectively. In silico analyses showed that 36% of the differentially expressed genes are likely to encode exported proteins. Moreover, four genes encoding homologs of extracytoplasmic function (ECF) sigma factors, which typically control aspects of cell envelope homeostasis, are differentially expressed in adigRmutant. We suggest that the DigR response regulator has an important function in cell envelope homeostasis and that the motility defects in adigRmutant are instigated by the abnormal cell envelope and abnormal expression ofagmQandcheY4.
Lesions in Teichoic Acid Biosynthesis in
Staphylococcus aureus
Lead to a Lethal Gain of Function in the Otherwise Dispensable Pathway
Authors: D'Elia Michael A. , Pereira Mark P. , Chung Yu Seon , Zhao Wenjun , Chau Andrew , Kenney Teresa J. , Sulavik Mark C. , Black Todd A. , Brown Eric D. 
Published: June 2006

ABSTRACT

An extensive study of teichoic acid biosynthesis in the model organism
Bacillus subtilis
has established teichoic acid polymers as essential components of the gram-positive cell wall. However, similar studies pertaining to therapeutically relevant organisms, such as
Staphylococcus aureus
, are scarce. In this study we have carried out a meticulous examination of the dispensability of teichoic acid biosynthetic enzymes in
S. aureus
. By use of an allelic replacement methodology, we examined all facets of teichoic acid assembly, including intracellular polymer production and export. Using this approach we confirmed that the first-acting enzyme (TarO) was dispensable for growth, in contrast to dispensability studies in
B. subtilis
. Upon further characterization, we demonstrated that later-acting gene products (TarB, TarD, TarF, TarIJ, and TarH) responsible for polymer formation and export were essential for viability. We resolved this paradox by demonstrating that all of the apparently indispensable genes became dispensable in a
tarO
null genetic background. This work suggests a lethal gain-of-function mechanism where lesions beyond the initial step in wall teichoic acid biosynthesis render
S. aureus
nonviable. This discovery poses questions regarding the conventional understanding of essential gene sets, garnered through single-gene knockout experiments in bacteria and higher organisms, and points to a novel drug development strategy targeting late steps in teichoic acid synthesis for the infectious pathogen
S. aureus
.
Cohesion-Defective Mutants ofMyxococcus xanthus
Authors: Bonner Pamela J. , Shimkets Lawrence J. 
Published: June 2006

ABSTRACTCohesion ofMyxococcus xanthuscells involves interaction of a cell surface cohesin with a component of the extracellular matrix. In this work, two previously isolated cohesion-defective (fbd) mutants were characterized. ThefbdAandfbdBgenes do not encode the cohesins but are necessary for their production. Both mutants produce type IV pili, suggesting that PilA is not a major cohesin.
Expression of SarX, a Negative Regulator of
agr
and Exoprotein Synthesis, Is Activated by MgrA in
Staphylococcus aureus
Authors: Manna Adhar C. , Cheung Ambrose L. 
Published: June 2006

ABSTRACT

The expression of genes involved in the pathogenesis of
Staphylococcus aureus
is known to be controlled by global regulatory loci, including
agr
,
sarA
,
saeRS
,
arlRS
, and
sarA
-like genes. As part of our continuing efforts to understand the regulatory mechanisms that involve
sarA
-like genes, we describe here the characterization of a novel transcriptional regulator called SarX, a member of the SarA protein family. The transcription of
sarX
was growth phase dependent and was expressed maximally during the stationary phase of growth, which was significantly decreased in the
mgrA
mutant. MgrA acted as an activator of
sarX
expression as confirmed by transcriptional fusion and Northern blot analyses. Purified MgrA protein bound to the upstream region of the
sarX
promoter as demonstrated by gel shift assay. The expression levels of various potential target genes involved in virulence and regulation, specifically those affected by
sarA
and
mgrA
, were analyzed with isogenic
sarX
mutant strains. Our data indicated that SarX acted as a repressor of the
agr
locus and consequently target genes regulated by the
agr
system. We propose that SarX is an important regulator in the SarA protein family and may be part of the common pathway by which
agr
and members of the
sarA
gene family control virulence in
S. aureus
.
The BBA01 Protein, a Member of Paralog Family 48 fromBorrelia burgdorferi, Is Potentially Interchangeable with the Channel-Forming Protein P13
Authors: Pinne Marija , Denker Katrin , Nilsson Elin , Benz Roland , Bergström Sven 
Published: June 2006

ABSTRACTTheBorrelia burgdorferigenome exhibits redundancy, with many plasmid-carried genes belonging to paralogous gene families. It has been suggested that certain paralogs may be necessary in various environments and that they are differentially expressed in response to different conditions. The chromosomally locatedp13gene which codes for a channel-forming protein belongs to paralog family 48, which consists of eight additional genes. Of the paralogous genes from family 48, the BBA01 gene has the highest homology top13. Herein, we have inactivated the BBA01 gene inB. burgdorferistrain B31-A. This mutant shows no apparent phenotypic difference compared to the wild type. However, analysis of BBA01 in a C-terminal protease A (CtpA)-deficient background revealed that like P13, BBA01 is posttranslationally processed at its C terminus. Elevated BBA01 expression was obtained in strains with the BBA01 gene introduced on the shuttle vector compared to the wild-type strain. We could further demonstrate that BBA01 is a channel-forming protein with properties surprisingly similar to those of P13. The single-channel conductance, of about 3.5 nS, formed by BBA01 is comparable to that of P13, which together with the high degree of sequence similarity suggests that the two proteins may have similar and interchangeable functions. This is further strengthened by the up-regulation of the BBA01 protein and its possible localization in the outer membrane in ap13knockout strain, thus suggesting that P13 can be replaced by BBA01.
Chromosome Condensation in the Absence of the Non-SMC Subunits of MukBEF
Authors: Wang Qinhong , Mordukhova Elena A. , Edwards Andrea L. , Rybenkov Valentin V. 
Published: June 2006

ABSTRACTMukBEF is a bacterial SMC (structural maintenance of chromosome) complex required for chromosome partitioning inEscherichia coli. We report that overproduction of MukBEF results in marked chromosome condensation. This condensation is rapid and precedes the effects of overproduction on macromolecular synthesis. Condensed nucleoids are often mispositioned; however, cell viability is only mildly affected. The overproduction of MukB leads to a similar chromosome condensation, even in the absence of MukE and MukF. Thus, the non-SMC subunits of MukBEF play only an auxiliary role in chromosome condensation. MukBEF, however, was often a better condensin than MukB. Furthermore, the chromosome condensation by MukB did not rescue the temperature sensitivity of MukEF-deficient cells, nor did it suppress the high frequency of anucleate cell formation. We infer that the role of MukBEF in stabilizing chromatin architecture is more versatile than its role in controlling chromosome size. We further propose that MukBEF could be directly involved in chromosome segregation.
Expression of Genes Coding for GerA and GerK Spore Germination Receptors Is Dependent on the Protein Phosphatase PrpE
Authors: Hinc Krzysztof , Nagórska Krzysztofa , Iwanicki Adam , Węgrzyn Grzegorz , Séror Simone J. , Obuchowski Michał 
Published: June 2006

ABSTRACT

The ability of
Bacillus subtilis
to form spores is a strategy for survival under unfavorable environmental conditions. It is equally crucial to break spore dormancy and return to vegetative growth at the appropriate time. Here we present data showing that the PrpE phosphatase is involved in the control of expression of genes coding for GerA receptors, which are necessary for
l
-alanine-induced spore germination. Moreover, PrpE is also involved in aspartic acid, glucose, fructose, and potassium (AGFK)-induced spore germination by controlling expression of genes coding for GerK receptors. In the absence of PrpE, the production of spores was essentially normal. However,
l
-alanine-induced spore germination and, to a lesser extent, the AGFK-induced pathway were abolished. In contrast, the germination pathway dependent on Ca
2+
-dipicolinate or dodecylamine remained intact. A protein phosphatase PrpE-green fluorescent protein fusion was localized to the prespore and to the dormant spore, consistent with a role in controlling expression of genes coding for GerA receptors. We propose that PrpE is an important element in a signal transduction pathway in
Bacillus subtilis
that controls the expression of genes coding for germination receptors.