bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia
Authors: WHITTALL JUSTEN B. , VOELCKEL CLAUDIA , KLIEBENSTEIN DANIEL J. , HODGES SCOTT A. 
Published: September 2006

AbstractConvergent phenotypes are testament to the role of natural selection in evolution. However, little is known about whether convergence in phenotype extends to convergence at the molecular level. We use the independent losses of floral anthocyanins in columbines (Aquilegia) to determine the degree of molecular convergence in gene expression across the anthocyanin biosynthetic pathway (ABP). Using a phylogeny of the North American Aquilegia clade, we inferred six independent losses of floral anthocyanins. Via semiquantitative reverse transcriptase–polymerase chain reaction (RT–PCR), we monitored developmental and tissue‐specific variation in expression of the six major structural ABP loci in three Aquilegia species, two that produce anthocyanins (A+) and one that does not (A−). We then compared ABP expression in petals of old‐bud and pre‐anthesis flowers of 13 Aquilegia species, eight wild species and two horticultural lines representing seven independent A− lineages as well as three wild A+ species. We only found evidence of down‐regulation of ABP loci in A− lineages and losses of expression were significantly more prevalent for genes late in the pathway. Independent contrast analysis indicates that changes in expression of dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS) are strongly phylogenetically correlated consistent with the multilocus targets of trans‐regulatory elements in the ABP of other systems. Our findings strongly suggest that pleiotropy constrains the evolution of loss of floral anthocyanins to mutations affecting genes late in the ABP mostly through convergent changes in regulatory genes. These patterns support the hypothesis that rapid evolutionary change occurs largely through regulatory rather than structural mutations.
The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism
Authors: Heidrich Nadja , Chinali Alberto , Gerth Ulf , Brantl Sabine 
Published: September 2006

SummaryWhereas about 70 small non‐coding RNAs have been found in the Escherichia coli genome, relatively little is known about regulatory RNAs from Gram‐positive bacteria. Here, we demonstrate that the recently identified small untranslated RNA SR1 from the Bacillus subtilis genome is a regulatory RNA involved in fine‐tuning of arginine catabolism. 2D protein gel electrophoresis indicated three possible SR1 targets that are regulated by the transcriptional activator AhrC, which was shown to be the primary target of SR1. In vitro pairing studies and an in vivo reporter gene test demonstrated a specific interaction between SR1 and ahrC mRNA. This interaction did not lead to degradation of ahrC mRNA, but inhibited translation at a post‐initiation stage. Our data show that the Hfq chaperone was not required for the stabilization of SR1 in vivo. The amount of SR1 was increased upon addition of l‐arginine and l‐ornithine, but not l‐citrulline or l‐proline.
Two higBA loci in the Vibrio cholerae superintegron encode mRNA cleaving enzymes and can stabilize plasmids
Authors: Christensen‐Dalsgaard Mikkel , Gerdes Kenn 
Published: September 2006

SummaryVibrio cholerae codes for 13 toxin–antitoxin (TA) loci all located within the superintegron on chromosome II. We show here that the two higBA TA loci of V. cholerae encode functional toxins, HigB‐1 and HigB‐2, whose ectopic expression inhibits cell growth of Escherichia coli, and functional antitoxins, HigA‐1 and HigA‐2, which counteract the toxicity of the cognate toxins. Three hours of ectopic expression of the HigB toxins resulted in bacteriostasis without any detectable loss of cell viability. The HigB toxins inhibited translation by cleavage of mRNA. Efficient mRNA cleavage occurred preferentially within the translated part of a model mRNA and only when the mRNA was translatable. Promoter analysis in V. cholerae and E. coli showed that the two higBA loci are both transcribed into bi‐cistronic mRNAs and that the higBA‐2 mRNA is leaderless. Transcription of the two higBA loci was strongly induced by amino acid (aa) starvation in V. cholerae and E. coli, indicating that the regulatory mechanisms of transcriptional induction are conserved across the two species. Both higBA loci stabilized a test‐plasmid very efficiently in E. coli, raising the possibility that the loci contribute to maintain genetic stability of the V. cholerae superintegron. Based on these results we discuss the possible biological functions of the TA loci of V. cholerae.
The HD‐GYP domain of RpfG mediates a direct linkage between the Rpf quorum‐sensing pathway and a subset of diguanylate cyclase proteins in the phytopathogen Xanthomonas axonopodis pv citri
Authors: Andrade Maxuel O. , Alegria Marcos Castanheira , Guzzo Cristiane R. , Docena Cassia , Pareda Rosa Maria Claudia , Ramos Carlos H. I. , Farah Chuck S. 
Published: September 2006

SummaryBacteria use extracellular levels of small diffusible autoinducers to estimate local cell‐density (quorum‐sensing) and to regulate complex physiological processes. The quorum‐sensing signal transduction pathway of Xanthomonas spp. phytopathogens has special features that distinguish it from that of other pathogens. This pathway consists of RpfF, necessary for the production of the unique autoinducer ‘diffusible signalling factor’ (DSF), and RpfC and RpfG, a two‐component system necessary for the DSF‐dependent production of extracellular pathogenicity factors and cellular dispersion. Yeast two‐hybrid and direct in vitro assays were used to identify interactions involving the Rpf group of proteins. We show that RpfC, a protein consisting of N‐terminal transmembrane, histidine kinase, response‐regulator and C‐terminal histidine phosphotransfer domains interacts with both RpfG, a protein consisting of an N‐terminal response regulator domain and a C‐terminal HD‐GYP domain, and with RpfF. We also show that RpfC interacts with the only known homologue of ‘conditioned medium factor’, which is involved in quorum‐sensing in Dictyostelium discoideum under conditions of nutritional stress. Furthermore, RpfCG is shown to interact with a second two‐component system made up of NtrB and NtrC homologues. Finally we show that the recently characterized HD‐GYP phosphodiesterase domain of RpfG interacts directly with diguanylate cyclase GGDEF domain‐containing proteins coded by the Xanthomonas axonopodis pv. citri genome, which in other bacteria produce cyclic diGMP, an important second messenger involved in the regulation of complex bacterial processes including biofilm production, virulence and motility. These results demonstrate a direct physical linkage between quorum‐sensing and cyclic diGMP signalling pathways in bacteria.
YpdC determines site‐1 degradation in regulated intramembrane proteolysis of the RsiW anti‐sigma factor of Bacillus subtilis
Authors: Heinrich Janine , Wiegert Thomas 
Published: September 2006

SummaryGenes of Bacillus subtilis controlled by the alternative extracytoplasmic function family sigma factor σW constitute an antibiosis regulon. Its activity is modulated by RsiW, a transmembrane anti‐sigma factor that sequesters and inactivates σW. Upon a stress signal, RsiW is degraded by a mechanism of regulated intramembrane proteolysis. To identify genes which influence RsiW degradation, a transposon screen with a reporter fusion of the green fluorescent protein to RsiW was performed. Among several gene loci identified, the ypdC (prsW) gene displayed a strong effect on RsiW stability. In a ypdC null mutant, induction of σW‐controlled genes is abolished and site‐1 proteolysis of RsiW is completely blocked. Transcriptional analysis revealed that ypdC is a monocistronic gene, and the defect of σW induction of the null mutant was complemented by ectopically integrated ypdC under xylose control. Orthologues of YpdC can be found in a variety of different bacteria. Its membrane topology was analysed by alkaline phosphatase fusions, revealing that YpdC contains five transmembrane segments and two larger extracytoplasmic loops. In the first loop, two invariantly conserved glutamate residues can be found. In an Escherichia coli system, the cloned ypdC is the only determinant of efficient degradation of RsiW; however, YpdC does not display plain similarities to known proteases, suggesting that it either controls the activity of site‐1 proteolysis of RsiW or represents a new type of protease.
Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS
Authors: Ramsay Joshua P. , Sullivan John T. , Stuart Gabriella S. , Lamont Iain L. , Ronson Clive W. 
Published: September 2006

SummaryThe Mesorhizobium loti strain R7A symbiosis island is an Integrative Conjugative Element (ICE), herein termed ICEMlSymR7A, which integrates into a phetRNA gene. Integration reconstructs the phetRNA gene at one junction with the core chromosome, and a direct repeat of the 3‐prime 17 bp of the gene is formed at the other junction. We show that the ICEMlSymR7AintS gene, which encodes an integrase of the phage P4 family, is required for integration and excision of the island. Excision also depended on a novel recombination directionality factor encoded by msi109 (rdfS). Constitutive expression of rdfS resulted in curing of ICEMlSymR7A. The rdfS gene is part of an operon with genes required for conjugative transfer, allowing co‐ordinate regulation of ICEMlSymR7A excision and transfer. The excised form of ICEMlSymR7A was detectable during exponential growth but occurred at higher frequency during stationary phase. ICEMlSymR7A encodes homologues of the traR and traI genes of Agrobacterium tumefaciens that regulate Ti plasmid transfer via quorum sensing. The presence of a plasmid with cloned island traR traI2 genes resulted in excision of ICEMlSymR7A in all cells regardless of culture density, indicating that excision may be similarly regulated. Maintenance of ICEMlSymR7A in these cells depended on msi106 (rlxS) that encodes a putative relaxase. Transfer of the island to non‐symbiotic mesorhizobia required intS, rlxS and rdfS. The rdfS and rlxS genes are conserved across a diverse range of α‐, β‐ and γ‐proteobacteria and identify a large family of genomic islands with a common transfer mechanism.
Regulated intramembrane proteolysis of FtsL protein and the control of cell division in Bacillus subtilis
Authors: Bramkamp Marc , Weston Louise , Daniel Richard A. , Errington Jeff 
Published: September 2006

SummaryThe small bitopic division protein FtsL is an essential part of the division machinery (divisome) in most eubacteria. In Bacillus subtilis FtsL is a highly unstable protein and the turnover has been implicated in regulation of division in response to DNA damage. N‐terminal deletions and a domain swap experiment identified the short cytoplasmic domain of FtsL as being required for instability. We then identified a zinc metalloprotease, YluC, required for turnover, and likely sequence motifs involved in substrate recognition. YluC belongs to the site‐2‐protease (S2P) family of proteases involved in regulated intramembrane proteolysis (RIP), which plays a role in diverse regulatory phenomena from bacteria to man. The yluC mutant, and strains with N‐terminal truncations of ftsL have a short cell phenotype, indicating that that FtsL is normally rate‐limiting for division. Coexpression experiments of FtsL and YluC in Escherichia coli corroborated a model in which FtsL is directly cleaved by the membrane metalloprotease. The results shed new light on the regulation of cell division in B. subtilis and identify a novel class of targets for RIP.
Measurement of anti‐CD154 monoclonal antibody in primate sera by competitive inhibition ELISA
Authors: Tai Hao‐Chih , Campanile Nathalie , Ezzelarab Mohamed , Cooper David K. C. , Phelps Carol 
Published: September 2006

Abstract:  Background:  Anti‐human CD154 monoclonal antibody (mAb)‐based regimens have been demonstrated to prevent T cell‐dependent elicited antibody response in baboon recipients of pig hematopoietic progenitor cells, organs and islets. Monitoring of anti‐CD154 mAb in serum is important to ensure maintenance of adequate levels and for adjusting dosage of the anti‐CD154 mAb. We describe a method for measuring the level in primate sera.Methods:  The anti‐CD154 mAb level in primate serum was measured with a competitive inhibition enzyme linked immunosorbent assay in which the extent of inhibition of binding by anti‐CD154 mAb conjugated to horseradish peroxidase (anti‐CD154‐HRP) to soluble CD154 was used to determine the serum level. Briefly, a 96‐well maxisorb plate coated with soluble human CD154, and blocked with bovine serum albumin, was loaded with graded doses of anti‐CD154 mAb or primate sera containing anti‐CD154 mAb. Both were mixed with a known dosage of anti‐CD154‐HRP before loading. Bound anti‐CD154‐HRP was detected by color developed using 3,3′,5,5′ tetramethyl‐benzidine as substrate. Absorbance was measured in a SynergyTM HT Multi‐Detection Microplate Reader at a wavelength of 450 nm. Data analysis was carried out using BioTek's KC4TM Data Analysis Software. The standard curve was generated from the wells loaded with the mixture of anti‐CD154 mAb and anti‐CD154‐HRP.Results and conclusions:  The assay has been used successfully to measure anti‐CD154 mAb levels in the serum of both baboons and monkeys.
Protective effects of volatile agents against acetylcholine‐induced bronchoconstriction in isolated perfused rat lungs
Authors: Lele E. , Petak F. , Fontao F. , Morel D. R. , Habre W. 
Published: September 2006

Background:  Bronchoactive properties of volatile agents against lung constriction are well established. The purpose of this study was to investigate the ability of halothane (Hal), isoflurane (Iso), sevoflurane (Sev) and desflurane (Des) to alter the lung mechanics in the absence of an airway tone and during acetylcholine (Ach)‐induced bronchoconstriction.Methods:  Low‐frequency pulmonary impedance data (ZL) were collected from isolated, normo‐perfused rat lungs under baseline conditions and following the injection of Ach (0.1 mg/kg) into the pulmonary artery. Measurements were performed without the administration of any anaesthetic agent in the first phase of the experiments and during inhalation without any volatile agent (control group, n = 6) or during inhalation of Hal (n = 6), Iso (n = 9), Sev (n = 6) or Des (n = 8) at 1 minimum alveolar concentration (MAC). The airway resistance (Raw) and parenchymal damping and elastance were estimated from the ZL data by model fitting.Results:  Under baseline conditions, the basic value of Raw was significantly decreased by Des (− 31.2 ± 3.8%) and Sev (− 18.0 ± 4.5%) administration, whereas Hal and Iso did not have a statistically significant effect on Raw (− 3.3 ± 5.1% and − 8.6 ± 2.4%, respectively). Moreover, all four inhalation anaesthetics prevented the increase in Raw following Ach administration, the findings ranging between − 14.3 ± 11.4% for Hal and − 37.5 ± 10.9% for Sev.Conclusions:  Our results on a denervated isolated perfused lung model demonstrate the potential of Des and Sev to decrease the basal airway tone, whereas Iso and Hal are ineffective in this regard. All of these volatile agents markedly protect against Ach‐induced bronchoconstriction.
Effects of two different hydroxyethyl starch solutions (HES200/0.5 vs. HES130/0.4) on the expression of platelet membrane glycoprotein
Authors: Chen G. , Yan M. , Lu Q. H. , Gong M. 
Published: September 2006

Background:  There are various hydroxyethyl starch (HES) solutions with different degrees of hydroxylation and different molecular weights. HES200/0.5 solution is most commonly used. HES130/0.4 is a new HES solution and is the ‘state‐of‐the‐art’ in volume substitution. However, the mechanism of the observed anticoagulation action of HES has not been fully delineated. The objective of this study was to further investigate the effect of HES200/0.5 and HES130/0.4 on platelet coagulation.Methods:  Sixty ASA I–II patients undergoing elective minor surgery were randomly allocated to receive an intravenous infusion (20 ml/kg) of lactated Ringer’s solution (group L), HES200/0.5 (group H) or HES130/0.4 (group V) after the induction of anesthesia. The expression of CD42b, CD41/61 and CD62p in vivo was assessed on non‐stimulated platelets and adenosine diphosphate (ADP) agonist‐activated platelets using flow cytometry.Results:  Resting glycoprotein expression of the non‐stimulated platelets was observed. HES200/0.5 and HES130/0.4 reduced the CD42b, CD41/61 and CD62p expression of ADP‐agonist‐activated platelets at 15 min after intravenous infusion. At 6 h after intravenous infusion, the trend of decreasing expression of activated CD42b, CD41/61 and CD62p was maintained in group H. However, CD42b, CD41/61 and CD62p expression returned to the pre‐operative level in group V.Conclusion:  This study showed that both HES200/0.5 and HES130/0.4 can inhibit platelet coagulation. Platelet dysfunction experienced a faster recovery after the infusion of HES130/0.4 than after HES200/0.5. Liquid resuscitation with HES130/0.4 may decrease the risk of hemorrhage in the operative period.
Can We Increase the Estimative Value of Semen Assessment?*
Authors: Rodríguez‐Martínez H 
Published: September 2006

ContentsEstimating the fertility of a semen sample or of the male from where it has been collected by simple assessment of in vitro sperm characteristics is still difficult, owing to the variable correlations that laboratory results achieve with in vivo fertility. A major reason behind these variations is the fact that the ejaculate and the artificial insemination (AI)‐doses it generates are composed of a diverse sperm population. Such heterogeneity is reflected both in differences of intactness of attributes needed for fertilization, such as motility or morphology, but also in the relative ability of spermatozoa to prevail fertile over time, handling and exposure to different stimuli, all of which account for innate variations in fertilizing ability among doses, ejaculates and sires. However, methods are already available to select sub‐populations of intact spermatozoa which can be tested for their degree of competence for fertilization and whose estimative power is promising, allowing the elimination of cases of sub‐fertility, particularly in bovine. Examples of these methods are the separation of viable spermatozoa by swim‐up or discontinuous gradient centrifugation, followed by testing the ability of the selected spermatozoa to dose‐response/time sustain capacitation and acrosome reaction induction. Finding how large a sperm population with non‐compensable attributes for fertilization and ability to display and sustain stimuli is, perhaps by a quick screening of membrane integrity and stability by multi‐parametric methods, would allow, provided the particular male produces this sub‐population in a repeatable manner, for a better estimation of fertility.
Mammalian Sperm Energy Resources Management and Survival during Conservation in Refrigeration
Authors: Rodriguez‐Gil JE 
Published: September 2006

ContentsThe present review has as its main aim to present an overview regarding the mechanisms utilized by mammalian sperm to manage its intracellular energy levels. This management will strongly influence the sperm's ability to maintain its overall function during its entire life span. Thus, the precise knowledge of these mechanisms will be of the utmost interest to optimize the systems utilized to conserve mammalian sperm for a medium‐to‐long time‐lapse. Briefly, utilization of hexoses as energy substrates by mammalian sperm is very finely regulated from the very first step of its metabolization. Furthermore, the equilibrium among the separate, monosaccharide metabolization pathways in mammalian sperm depends on many factors. This prevents the possibility to draw a general vision of sperm energy utilization, which explains the results of all mammalian species in all points of the sperm life‐cycle. To complicate the matter further, there are separate energy phenotypes among mammalian spermatozoa. The precise knowledge of these phenotypes is of the greatest importance in order to optimize the design of new extenders for sperm conservation in refrigerated conditions. Moreover, sugars can act on sperm not only as passive metabolic substrates, but also as direct function activators through mechanisms like specific changes in the tyrosine phosphorylation status of distinct proteins. Finally, mammalian sperm utilizes non‐glucidic substrates like citrate and lactate to obtain energy in a regular form. This utilization is also finely regulated and of importance to maintain overall sperm function. This implies that the exact proportion of glucidic and non‐glucidic energy substrates could be very important to optimize the survival ability of these cells in conservation.
Developmental Consequences of Sexual Dimorphism During Pre‐implantation Embryonic Development
Authors: Gutiérrez‐Adán A , Perez‐Crespo M , Fernandez‐Gonzalez R , Ramirez MA , Moreira P , Pintado B , Lonergan P , Rizos D 
Published: September 2006

ContentsAbnormalities of development potential arising from pre‐implantation environment are not limited to in vitro culture (IVC) (for, i.e. in ruminants the large offspring syndrome produced by IVC), they may also be consequence of specific stress conditions experienced in vivo, like maternal diet, toxins, etc. A complex group of mechanisms (gene expression, epigenetic, metabolic, etc.) may operate to link early embryo environment with future health. Furthermore, during the pre‐implantation period, in vitro produced male embryos have a higher metabolic rate, they grow faster than females, and they also have differential gene transcription of genes located in the Y‐, X‐, or in autosomal‐chromosomes. As a consequence of these differences embryos may be affected differentially by natural or artificial environmental conditions, depending on their gender. It has been suggested that under some stress conditions male embryos are more vulnerable than females; however the biological fragility of male embryos is poorly understood. Evidences suggest that epigenetic differences produced by the presence of one or two X‐chromosomes are the principal cause of the male and female pre‐implantation differences, and we put forward the possible role of these early sex differences to control sex ratio of the offspring under different environmental conditions in Nature. By following the differences between male and female early embryos not only may be possible to manipulate sex ratio in farm animals, we can also gain further insight into aspects of early embryo development, X inactivation, and epigenetic and genetic processes related with early development that may have a long‐term effect on the offspring.