bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation at two flowering time genes within and among populations of Arabidopsis thaliana: comparison with markers and traits
Authors: CORRE V. LE 
Published: September 2005

Abstract Flowering Locus C (FLC) and Frigida are two interacting genes controlling flowering time variation in Arabidopsis thaliana. Variation at these genes was surveyed in 12 A. thaliana populations sampled in France. These populations were also screened for variation at molecular markers [12 microsatellites and 19 cleaved amplified polymorphic sequence (CAPS) markers] and at seven quantitative traits measured with and without vernalization. Seven populations were highly polymorphic at markers (HS = 0.57 at microsatellites, 0.24 at CAPS) and showed heritable variation for bolting time and some other traits. Five populations were genetically fixed or nearly fixed. QST for bolting time without vernalization was significantly higher than FST, suggesting local divergent selection. One of the two haplotype groups at FLC (FLCA) was very predominant (frequency of 99%). The first exon of Frigida showed elevated nonsynonymous variation, and nine loss‐of‐function mutations were found throughout the gene. The association between loss‐of‐function and earlier bolting was confirmed. Overall, 18 Frigida haplotypes were detected. The pattern of variation at Frigida was largely similar to that found at markers and traits, with the same populations being fixed or highly diverse. Metapopulation dynamics is thus probably the main factor shaping genetic variation in A. thaliana. However, FST for functional (FRI) vs. nonfunctional (FRIΔ) haplotypes was significantly higher than FST at markers. This suggested that loss‐of‐function at Frigida is under local selection for flowering time.
Historical colonization and demography of the Mediterranean damselfish, Chromis chromis
Authors: DOMINGUES VERA S. , BUCCIARELLI GIUSEPPE , ALMADA VITOR C. , BERNARDI GIACOMO 
Published: September 2005

AbstractThe desiccation of the Mediterranean Sea during the Messinian Salinity Crisis 6.0–5.3 million years ago (Ma), caused a major extinction of the marine ichthyofauna of the Mediterranean. This was followed by an abrupt replenishment of the Mediterranean from the Atlantic after the opening of the Strait of Gibraltar. In this study, we combined demographic and phylogeographic approaches using mitochondrial and nuclear DNA markers to test the alternative hypotheses of where (Atlantic or Mediterranean) and when (before or after the Messinian Salinity Crisis) speciation occurred in the Mediterranean damselfish, Chromis chromis. The closely related geminate transisthmian pair Chromis multilineata and Chromis atrilobata was used as a way of obtaining an internally calibrated molecular clock. We estimated C. chromis speciation timing both by determining the time of divergence between C. chromis and its Atlantic sister species Chromis limbata (0.93–3.26 Ma depending on the molecular marker used, e.g. 1.23–1.39 Ma for the control region), and by determining the time of coalescence for C. chromis based on mitochondrial control region sequences (0.14–0.21 Ma). The time of speciation of C. chromis was always posterior to the replenishment of the Mediterranean basin, after the Messinian Salinity Crisis. Within the Mediterranean, C. chromis population structure and demographic characteristics revealed a genetic break at the Peloponnese, Greece, with directional and eastbound gene flow between western and eastern groups. The eastern group was found to be more recent and with a faster growing population (coalescent time = 0.09–0.13 Ma, growth = 485.3) than the western group (coalescent time = 0.13–0.20 Ma, growth = 325.6). Our data thus suggested a western origin of C. chromis, most likely within the Mediterranean. Low sea water levels during the glacial periods, the hydrographic regime of the Mediterranean and dispersal restriction during the short pelagic larval phase of C. chromis (18–19 days) have probably played an important role in C. chromis historical colonization.
Nitrogen‐fixing nodules from rose wood legume trees (Dalbergia spp.) endemic to Madagascar host seven different genera belonging to α‐ and β‐Proteobacteria
Authors: RASOLOMAMPIANINA R. , BAILLY X. , FETIARISON R. , RABEVOHITRA R. , BÉNA G. , RAMAROSON L. , RAHERIMANDIMBY M. , MOULIN L. , DE LAJUDIE P. , DREYFUS B. , AVARRE J.‐C. 
Published: September 2005

AbstractAlthough legume biodiversity is concentrated in tropical regions, the majority of studies on legume nodulating bacteria (LNB) are focused on cultivated leguminous plants from temperate regions. However, recent works on tropical regions tend to indicate that the actual diversity of LNB is largely underestimated. In this study, we report the isolation and characterization of 68 nitrogen‐fixing root nodule bacteria collected from eight endemic tree species of Dalbergia in Madagascar. The isolates were characterized by (i) restriction fragment length polymorphism (RFLP) analysis of 16S‐IGS rDNA, (ii) 16S rDNA gene sequencing and (iii) nodulation tests. Results revealed a wide diversity of bacteria present in the nodules of Dalbergia. Among the 68 isolated bacteria, 65 belonged to Bradyrhizobium, Mesorhizobium, Rhizobium, Azorhizobium and Phyllobacterium from the α‐class of Proteobacteria, and three isolates belonged to Burkholderia and Ralstonia from the β‐class of Proteobacteria. Our results also show for the first time that a strain belonging to the Burkholderia cepacia complex is able to induce efficient nodules on a legume plant.
Identification of a protein Ser/Thr kinase cascade that regulates essential transcriptional activators in Myxococcus xanthus development
Authors: Nariya Hirofumi , Inouye Sumiko 
Published: September 2005

SummaryPkn8 is a membrane‐associated protein Ser/Thr kinase (PSTK) of Myxoccocus xanthus that was previously found to associate with a novel cytoplasmic kinase, Pkn14. In the present study, MrpC, an essential transcription factor for fruA expression during fruiting body development, was identified using a genomic yeast two‐hybrid screen with Pkn14 as bait. Our biochemical studies demonstrated that purified Pkn8 and Pkn14 are active kinases and that Pkn8 is able to phosphorylate Pkn14 that forms a tetramer via its C‐terminal 41 residues. Moreover, Pkn14 phosphorylated purified MrpC, indicating that Pkn8 is a Pkn14 kinase and Pkn14 is an MrpC kinase. The pkn8 and pkn14 deletion strains (Δpkn8 and Δpkn14) developed into fruiting bodies significantly faster than that of the parent strain, DZF1. While mrpC expression was at a low level in DZF1 during vegetative growth, it was highly elevated in Δpkn8 and Δpkn14 during vegetative growth and development. Furthermore, FruA, usually induced at 6 h of development, was instead detected at the early stationary phase and accumulated faster during development in Δpkn8 and Δpkn14. Therefore, the developmental phenotype of Δpkn8 and Δpkn14 seems to be due to untimely FruA production mediated by elevated levels of MrpC in Δpkn8 and Δpkn14 during vegetative growth. As pkn14 expression was increased at the mid‐ and late‐log. phases in DZF1 but decreased during development, the Pkn8–Pkn14 kinase cascade appears to negatively regulate mrpC expression by phosphorylating MrpC during vegetative growth. This is the first demonstration of a functional PSTK cascade in prokaryotes. mrpC expression has been proposed to be activated by MrpA and MrpB which belong to a two‐component His‐Asp phosphorelay signal transduction system and that MrpC autoregulate its own expression (Sun H. and Shi W., 2001 J Bacteriol 183: 4786–4795). Therefore, M. xanthus seems to utilize both eukaryotic PSTK cascade and prokaryotic His‐Asp phosphorelay system to precisely regulate mrpC expression with specific timing during development.
The transcriptome response of Neisseria gonorrhoeae to hydrogen peroxide reveals genes with previously uncharacterized roles in oxidative damage protection
Authors: Stohl Elizabeth A. , Criss Alison K. , Seifert H. Steven 
Published: September 2005

SummarySymptomatic gonococcal infection, caused by the pathogen Neisseria gonorrhoeae (Gc), is characterized by the influx of polymorphonuclear leukocytes (PMNs) to the site of infection. Although PMNs possess several mechanisms of oxidative killing, intact Gc can be found associated with PMNs, suggesting that gonococcal defences against oxidative stress are crucial for its ability to evade killing by PMNs. We used microarrays to identify genes that were differentially expressed after transient exposure of Gc to hydrogen peroxide (H2O2). Of the 75 genes found to be upregulated after H2O2 treatment, over one‐quarter, including two of the most highly upregulated genes (NGO1686 and NGO554), were predicted to encode proteins with unknown functions. Further characterization of a subset of these upregulated genes demonstrated that NGO1686, a putative zinc metalloprotease, protects against oxidative damage caused by both H2O2 and cumene hydroperoxide, and that NGO554, a Gc‐specific protein, acts to protect against damage caused by high levels of H2O2. Our current study also ascribes a role in H2O2 damage protection to recN, a gene previously characterized for its role in DNA repair. A PMN survival assay demonstrated that the recN and NGO1686 mutants were more susceptible to killing than the parent strain FA1090. These results define for the first time the robust transcriptional response to H2O2 by this strict human pathogen and underscore the importance of this system for survival to host defences.
Fluorescence thiol modification assay: oxidatively modified proteins in Bacillus subtilis
Authors: Hochgräfe Falko , Mostertz Jörg , Albrecht Dirk , Hecker Michael 
Published: September 2005

SummaryOxidatively modified thiol groups of cysteine residues are known to modulate the activity of a growing number of proteins. In this study, we developed a fluorescence‐based thiol modification assay and combined it with two‐dimensional gel electrophoresis and mass spectrometry to monitor the in vivo thiol state of cytoplasmic proteins. For the Gram‐positive model organism Bacillus subtilis our results show that protein thiols of growing cells are mainly present in the reduced state. Only a few proteins were found to be thiol‐modified, e.g. enzymes that include oxidized thiols in their catalytic cycle. To detect proteins that are particularly sensitive to oxidative stress we exposed growing B. subtilis cells to diamide, hydrogen peroxide or to the superoxide generating agent paraquat. Diamide mediated a significant increase of oxidized thiols in a variety of metabolic enzymes, whereas treatment with paraquat affected only a few proteins. Exposure to hydrogen peroxide forced the oxidation especially of proteins with active site cysteines, e.g. of cysteine‐based peroxidases and glutamine amidotransferase‐like proteins. Moreover, high levels of hydrogen peroxide were observed to influence the isoelectric point of proteins of this group indicating the generation of irreversibly oxidated thiols. From the overlapping set of oxidatively modified proteins, also enzymes necessary for methionine biosynthesis were identified, e.g. cobalamin‐independent methionine synthase MetE. Growth experiments revealed a methionine limitation after diamide and hydrogen peroxide stress, which suggests a thiol‐oxidation‐dependent inactivation of MetE. Finally, evidence is presented that the antibiotic nitrofurantoin mediates the formation of oxidized thiols in B. subtilis.
Agrobacterium tumefaciens oncogenic suppressors inhibit T‐DNA and VirE2 protein substrate binding to the VirD4 coupling protein
Authors: Cascales Eric , Atmakuri Krishnamohan , Liu Zhenying , Binns Andrew N. , Christie Peter J. 
Published: September 2005

SummaryAgrobacterium tumefaciens uses a type IV secretion (T4S) system composed of VirB proteins and VirD4 to deliver oncogenic DNA (T‐DNA) and protein substrates to susceptible plant cells during the course of infection. Here, by use of the Transfer DNA ImmunoPrecipitation (TrIP) assay, we present evidence that the mobilizable plasmid RSF1010 (IncQ) follows the same translocation pathway through the VirB/D4 secretion channel as described previously for the T‐DNA. The RSF1010 transfer intermediate and the Osa protein of plasmid pSa (IncW), related in sequence to the FiwA fertility inhibition factor of plasmid RP1 (IncPα), render A. tumefaciens host cells nearly avirulent. By use of a semi‐quantitative TrIP assay, we show that both of these ‘oncogenic suppressor factors’ inhibit binding of T‐DNA to the VirD4 substrate receptor. Both factors also inhibit binding of the VirE2 protein substrate to VirD4, as shown by coimmunoprecipitation and bimolecular fluorescence complementation assays. Osa fused to the green fluorescent protein (GFP) also blocks T‐DNA and VirE2 binding to VirD4, and Osa‐GFP colocalizes with VirD4 at A. tumefaciens cell poles. RSF1010 and Osa interfere specifically with VirD4 receptor function and not with VirB channel activity, as shown by (i) TrIP and (ii) a genetic screen for effects of the oncogenic suppressors on pCloDF13 translocation through a chimeric secretion channel composed of the pCloDF13‐encoded MobB receptor and VirB channel subunits. Our findings establish that a competing plasmid substrate and a plasmid fertility inhibition factor act on a common target, the T4S receptor, to inhibit docking of DNA and protein substrates to the translocation apparatus.
A novel bacterial signalling system with a combination of a Ser/Thr kinase cascade and a His/Asp two‐component system
Authors: Lux Renate , Shi Wenyuan 
Published: September 2005

SummaryProkaryotes and eukaryotes have long been thought to use very different types of kinases (the His kinases of the ‘bacterial’ two‐component systems versus the ‘eukaryotic’ Ser/Thr/Tyr kinases) to carry out signal transduction. This paradigm no longer holds true, because both systems are now found together in an increasing number of prokaryotic organisms and ‘two‐component’ His kinase are present in eukaryotes. Pioneering work on bacterial protein serine threonine kinases (PSTKs) has been performed in Myxococcus xanthus, a soil bacterium with a complex life cycle that possesses orthologues of signalling‐related kinases ‘typical’ of both the prokaryotic and the eukaryotic kingdoms. In the work reported in this volume of Molecular Microbiology, Nariya and Inouye describe a PSTK cascade that modulates the biochemical activity of MrpC, a CRP‐like transcriptional regulator for essential developmental signalling pathways in M. xanthus whose transcription is under the control of a two‐component system. This is the first report of both a functional PSTK cascade in bacteria and the use of both PSTK and two‐component systems to control a single complex bacterial signalling event.
Evidence for functional overlap among multiple bacterial cell division proteins: compensating for the loss of FtsK
Authors: Geissler Brett , Margolin William 
Published: September 2005

SummaryIn Escherichia coli, at least 12 proteins colocalize to the cell midpoint, assembling into a membrane‐associated protein machine that forms the division septum. Many of these proteins, including FtsK, are essential for viability but their functions in cell division are unknown. Here we show that the essential function of FtsK in cell division can be partially bypassed. Cells containing either the ftsA R286W mutation or a plasmid carrying the ftsQAZ genes suppressed a ftsK44(ts) allele efficiently. Moreover, ftsA R286W or multicopy ftsQAZ, which can largely bypass the requirement for the essential cell division gene zipA, allowed cells with a complete deletion of ftsK to survive and divide, although many of these ftsK null cells formed multiseptate chains. Green fluorescent protein (GFP) fusions to FtsI and FtsN, which normally depend on FtsK to localize to division sites, localized to division sites in the absence of FtsK, indicating that FtsK is not directly involved in their recruitment. Cells expressing additional ftsQ, and to a lesser extent ftsB and ftsN, were able to survive and divide in the absence of ftsK, although cell chains were often formed. Surprisingly, the cytoplasmic and transmembrane domains of FtsQ, while not sufficient to complement an ftsQ null mutant, conferred viability and septum formation in the absence of ftsK. These findings suggest that the N‐terminal domain of FtsK is normally involved in stability of the division protein machine and shares functional overlap with FtsQ, FtsB, FtsA, ZipA and FtsN.
Ketolide resistance in Streptococcus pyogenes correlates with the degree of rRNA dimethylation by Erm
Authors: Douthwaite Stephen , Jalava Jari , Jakobsen Lene 
Published: September 2005

SummaryMacrolide and ketolide antibiotics inhibit protein synthesis on the bacterial ribosome. Resistance to these antibiotics is conferred by dimethylation at 23S rRNA nucleotide A2058 within the ribosomal binding site. This form of resistance is encoded by erm dimethyltransferase genes, and is found in many pathogenic bacteria. Clinical isolates of Streptococcus pneumoniae with constitutive erm(B) and Streptococcus pyogenes with constitutive erm(A) subtype (TR) are resistant to macrolides, but remain susceptible to ketolides such as telithromycin. Paradoxically, some strains of S. pyogenes that possess an identical erm(B) gene are clinically resistant to ketolides as well as macrolides. Here we explore the molecular basis for the differences in these streptococcal strains using mass spectrometry to determine the methylation status of their rRNAs. We find a correlation between the levels of A2058‐dimethylation and ketolide resistance, and dimethylation is greatest in S. pyogenes strains expressing erm(B). In constitutive erm strains that are ketolide‐sensitive, appreciable proportions of the rRNA remain monomethylated. Incubation of these strains with subinhibitory amounts of the macrolide erythromycin increases the proportion of dimethylated A2058 (in a manner comparable with inducible erm strains) and reduces ketolide susceptibility. The designation ‘constitutive’ should thus be applied with some reservation for most streptococcal erm strains. One strain worthy of the constitutive designation is S. pyogenes isolate KuoR21, which has lost part of the regulatory region upstream of erm(B). In S. pyogenes KuoR21, nucleotide A2058 is fully dimethylated under all growth conditions, and this strain displays the highest resistance to telithromycin (MIC > 64 µg ml−1).
Subcutaneous Angiolipoma of Abdomen in a Golden Hamster (Mesocrietus auratus)
Authors: Kondo H. , Sato T. , Shibuya H. , Onuma M. 
Published: September 2005

SummaryThis is a single case report of an angiolipoma located in the subcutis of a 2‐year‐old golden hamster. The histological appearance of the tumour resembled that described in other species. The hamster died 1 month following removal of tumour and a necropsy was not performed. This is apparently the first recorded case of angiolipoma in a hamster.
Dual‐energy X‐ray Absorptiometry in Canine Legg‐Calvé‐Perthes Disease
Authors: Isola M. , Zotti A. , Carnier P. , Baroni E. , Busetto R. 
Published: September 2005

SummaryRadiographic examination and subsequent dual‐energy X‐ray absorptiometry scans of the hips were performed in seven dogs with monolateral Legg‐Perthes‐Calvé disease to quantify bone changes produced by osteonecrosis in the proximal femur on the affected and unaffected side. All dogs were found to be affected with grade 2 and 3 of the radiographic classification proposed by Ljunggren [Acta Orthop. Scand.(1967) vol. 95]. Bone mineral density (g/cm2) of the femoral neck and proximal femoral metaphysis were evaluated on the affected and unaffected side; we detected no differences in bone mineral density for both regions of interest within the population studied in relation to gender, body weight and side analysed nor between the affected and the unaffected limb. We therefore assume that radiographic areas of decreased density in the proximal femoral epiphysis during chronic stages of Legg‐Calvé‐Perthes disease do not alter the global mineral content of the scanned region.
Locomotive Disorders Associated with Sow Mortality in Danish Pig Herds
Authors: Kirk R. K. , Svensmark B. , Ellegaard L. P. , Jensen H. E. 
Published: September 2005

SummaryGiven the increase in sow mortality in Danish pig herds over the last 10 years, we have investigated the causes of spontaneous death and killing of sows, especially those due to locomotive disorders. A total of 265 culled sows (93 spontaneously dead sows and 172 killed sows) from 10 different herds were sent for complete necropsy, and grouped according to primary diagnoses. From 35 of these sows, tissue for histological evaluation and samples for bacteriological cultivation were also collected, and secondary diagnoses and body condition were recorded. The main causes for killing were related to the locomotive system (72%), arthritis (24%) and fractures (16%) being the most frequent lesions. The main causes of spontaneous death were related to the gastrointestinal system and spleen (45%) and the reproductive system (24%). Arthrosis was a secondary diagnosis in 88% of the killed sows and in 92.5% of the spontaneously dead sows. Arcanobacterium pyogenes was the main cause of arthritis. The killed sows had significantly lower body condition compared with spontaneously dead sows. The first two parities and the time around farrowing were associated with the highest mortality in both groups. Hopefully, these observations can guide breeding units attempting to monitor, control and reduce sow mortality.
Plasma Concentrations of 15‐Ketodihydro‐PGF2α, Cortisol and Progesterone during Manual Twin Reduction in Thoroughbred Mares
Authors: Veronesi M. C. , Faustini M. , Villani M. , Kindahl H. , Galeati G. , Battocchio M. 
Published: September 2005

SummaryThe aim of the present study was to highlight the effect of two different techniques of one embryo crushing on some hormonal changes. Ten twinning mares were submitted to the mobile or fixed manual crushing of one blastocyst within day 19 after the last mating. Blood sample was collected from 20 min before to 90 min, 24 and 72 h after the procedure was performed to analyse 15‐ketodihydro‐PGF2α, cortisol and progesterone plasma concentrations. Singleton pregnancy diagnosis was checked 72 h after crushing and at term of pregnancy. Because the unwanted crushing of both embryos occurred in one mare during the attempt of manual separation of the twins, that mare was not included in the evaluation of crushing‐induced hormonal changes. No significant differences in hormonal concentrations were observed after one embryo crushing and also when the effect of the mobile (n = 6) or fixed (n = 3) technique was specifically evaluated. When the effect of the two techniques on each post‐crushing sampling time hormonal levels was analysed, only a higher cortisol level 30 min after the fixed compared with the mobile technique was observed. The crushing performed within 19 days of gestation does not induce significant changes in 15‐ketodihydro‐PGF2α, cortisol or progesterone plasma concentrations. When the fixed technique was performed, only a temporary higher cortisol concentration was seen 30 min after crushing, suggesting that the fixed technique might be responsible for a slight level of stress for the mare.
A Rare Case of Odontogenic Myxoma in a Dog
Authors: Gupta K. , Singh A. , Sood N. , Mohindroo J. , Sood N. K. 
Published: September 2005

SummaryA case of odontogenic myxoma in an old Doberman bitch involving the periodontal region of the mandible was recorded. Grossly, the tumour mass was soft and slimy, having brownish‐black foci on cut surface. Histopathologically, the tumour predominantly consisted of mesenchyme‐like cells with prominent nuclei and nucleoli. The tumour had abundant ground substance, rich in acid mucopolysaccharides.