bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor
Authors: Navarro‐Avilés Gloria , Jiménez María Angeles , Pérez‐Marín Mari Cruz , González Carlos , Rico Manuel , Murillo Francisco Jose , Elías‐Arnanz Montserrat , Padmanabhan S. 
Published: January 2007

SummaryBlue light induces carotenogenesis in Myxococcus xanthus. The carB operon encodes all but one of the structural genes involved, and its expression is regulated by the CarA‐CarS repressor‐antirepressor pair. In the dark, CarA‐operator binding represses carB. CarS, produced on illumination, interacts physically with CarA to dismantle the CarA‐operator complex and activate carB. Both operator and CarS bind to the autonomously folded N‐terminal domain of CarA, CarA(Nter), which in excess represses carB. Here, we report the NMR structure of CarA(Nter), and map residues that interact with operator and CarS by NMR chemical shift perturbations, and in vivo and in vitro analyses of site‐directed mutants. We show CarA(Nter) adopts the winged‐helix topology of MerR‐family DNA‐binding domains, and conserves the majority of the helix‐turn‐helix and wing contacts with DNA. Tellingly, helix α2 in CarA, a key element in operator DNA recognition, is also critical for interaction with CarS, implying that the CarA‐CarS protein‐protein and the CarA‐operator protein–DNA interfaces overlap. Thus, binding of CarA to operator and to antirepressor are mutually exclusive, and CarA may discern structural features in the acidic CarS protein that resemble operator DNA. Repressor inactivation by occluding the DNA‐binding region may be a recurrent mechanism of action for acidic antirepressors.
Smooth to rugose phase variation in Vibrio cholerae can be mediated by a single nucleotide change that targets c‐di‐GMP signalling pathway
Authors: Beyhan Sinem , Yildiz Fitnat H. 
Published: January 2007

SummaryMicroorganisms use phase variation to increase population diversity to maximize evolutionary success. One such variation is the smooth to rugose phenotype change in Vibrio cholerae. We determined that the variation between smooth and rugose phenotypes can be controlled by a single nucleotide change in a gene (vpvC) predicted to encode a diguanylate cyclase. The vpvC allele found in the rugose genetic background is more active at producing c‐di‐GMP while that in smooth genetic background is less active. In support of this finding, disruption of vpvC in the rugose genetic variant decreases cellular c‐di‐GMP levels, diminishes rugose‐associated phenotypes and yields a smooth variant. Furthermore, the frequency of phase variation decreases dramatically when the vpvC locus is deleted in the smooth genetic background. Evidence is presented that the rugose variant is less susceptible to phage infection than the smooth variant. As phage infection is known to control populations of V. cholerae and thus outbreaks of cholera, phase variation may increase the evolutionary success of the pathogen.
A novel interaction between N‐myristoylation and the 26S proteasome during cell morphogenesis
Authors: Lee Soo Chan , Shaw Brian D. 
Published: January 2007

SummaryN‐myristoylation is a protein lipidation event in which myristate is covalently linked to the N‐terminal glycine of target proteins. In Aspergillus nidulans, the N‐myristoylation deficient swoF1 mutant was previously shown to lose cell polarity during the early morphogenic event of germ tube emergence. To further investigate this defect, we mutagenized swoF1 and recovered six partial suppressors designated ssf (suppressor of swoF1). The secondary mutations enabled swoF1 to partially bypass its growth defect. We characterized a frame‐shift mutation in ssfA1, which encodes an alpha subunit of the 20S core particle of the 26S proteasome. Fewer ubiquitinated proteins accumulated in the swoF1 mutant compared with wild‐type. In contrast, the swoF1;ssfA1 mutant accumulated higher levels of ubiquitinated proteins than wild‐type. The swoF1 mutant was bypassed in the presence of the proteasome inhibitor, MG132. These results demonstrate that the swoF1 phenotype was caused, at least in part, by an increased activity of 26S proteasome‐dependent proteolysis and suppression occurred by attenuating the 26S proteasome activity. This is the first report linking N‐myristoylation and ubiquitin–proteasome‐dependent proteolysis during morphogenesis.
A novel phospholipase from Trypanosoma brucei
Authors: Richmond Gregory S. , Smith Terry K. 
Published: January 2007

SummaryPhospholipase A1 activities have been detected in most cells where they have been sought and yet their characterization lags far behind that of the phospholipases A2, C and D. The study presented here details the first cloning and characterization of a cytosolic PLA1 that exhibits preference for phosphatidylcholine (GPCho) substrates. Trypanosoma brucei phospholipase A1 (TbPLA1) is unique from previously identified eukaryotic PLA1 because it is evolutionarily related to bacterial secreted PLA1. A T. brucei ancestor most likely acquired the PLA1 from a horizontal gene transfer of a PLA1 from Sodalis glossinidius, a bacterial endosymbiont of tsetse flies. Nano‐electrospray ionization tandem mass spectrometry analysis of TbPLA1 mutants established that the enzyme functions in vivo to synthesize lysoGPCho metabolites containing long‐chain mostly polyunsaturated and highly unsaturated fatty acids. Analysis of purified mutated recombinant forms of TbPLA1 revealed that this enzyme is a serine hydrolase whose catalytic mechanism involves a triad consisting of the amino acid residues Ser‐131, His‐234 and Asp‐183. The TbPLA1 homozygous null mutants generated here constitute the only PLA1 double knockouts from any organism.
AtNHX8, a member of the monovalent cation:proton antiporter‐1 family in Arabidopsis thaliana, encodes a putative Li+/H+ antiporter
Authors: An Rui , Chen Qi‐Jun , Chai Mao‐Feng , Lu Ping‐Li , Su Zhao , Qin Zhi‐Xiang , Chen Jia , Wang Xue‐Chen 
Published: January 2007

SummaryThe Arabidopsis monovalent cation:proton antiporter‐1 (CPA1) family includes eight members, AtNHX1–8. AtNHX1 and AtNHX7/SOS1 have been well characterized as tonoplast and plasma membrane Na+/H+ antiporters, respectively. The proteins AtNHX2–6 have been phylogenetically linked to AtNHX1, while AtNHX8 appears to be related to AtNHX7/SOS1. Here we report functional characterization of AtNHX8. AtNHX8 T‐DNA insertion mutants are hypersensitive to lithium ions (Li+) relative to wild‐type plants, but not to the other metal ions such as sodium (Na+), potassium (K+) and caesium (Cs+). AtNHX8 overexpression in a triple‐deletion yeast mutant AXT3 that exhibits defective Na+/Li+ transport specifically suppresses sensitivity to Li+, but does not affect Na+ sensitivity. Likewise, AtNHX8 overexpression complemented sensitivity to Li+, but not Na+, in sos1‐1 mutant seedlings, and increased Li+ tolerance of both the sos1‐1 mutant and wild‐type seedlings. Results of Li+ and K+ measurement of loss‐of‐function and gain‐of‐function mutants indicate that AtNHX8 may be responsible for Li+ extrusion, and may be able to maintain K+ acquisition and intracellular ion homeostasis. Subcellular localization of the AtNHX8–enhanced green fluorescent protein (EGFP) fusion protein suggested that AtNHX8 protein is targeted to the plasma membrane. Taken together, our findings suggest that AtNHX8 encodes a putative plasma membrane Li+/H+ antiporter that functions in Li detoxification and ion homeostasis in Arabidopsis.
Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation
Authors: Bossolini Eligio , Wicker Thomas , Knobel Philip A. , Keller Beat 
Published: January 2007

Summary Brachypodium sylvaticum and Brachypodium distachyon were recently proposed as new model plants because of their small genomes and their phylogenetic position between rice and Triticeae crops. We sequenced a 371‐kb region in B. sylvaticum, the largest genomic sequence available so far from this species, providing quantitative data on gene conservation, collinearity and phylogeny. We compared it with orthologous regions from rice and wheat. Brachypodium and wheat show perfect macro‐collinearity of genetic markers, whereas rice contains an approximately 220‐kb inversion. Rice contains almost twice as many genes as Brachypodium in the region studied, whereas wheat has about 40% more. Through comparative annotation, we identified alternative transcripts and improved the annotation for several rice genes, indicating that approximately 15% of rice genes might require re‐annotation. Surprisingly, our data suggest that 10–15% of functional sequences in small grass genomes may not encode any proteins. From available genomic and expressed sequence tag sequences, we estimated Brachypodium to have diverged from wheat about 35–40 Mya, significantly more recently than the divergence of rice and wheat. However, our data also indicate that orthologous regions from Brachypodium and wheat differ considerably in gene content, thus the Brachypodium genome sequence probably cannot replace genomic studies in the large Triticeae genomes.
Molecular and family analyses revealed two novel RHD alleles in a survey of a Chinese RhD‐negative population
Authors: Ye L.‐Y. , Guo Z.‐H. , Li Q. , Zhu Z.‐Y. 
Published: January 2007

Background and Objectives  RHD alleles are considered variable in the Chinese RhD‐negative persons. The purpose of the present work was to elucidate the molecular bases of two novel RHD alleles identified in a survey of a Chinese RhD‐negative population.Materials and Methods  A total of 163 RhD‐negative blood samples were investigated. The sequences of RHD exons were examined by RHD exon specific multiplex polymerase chain reaction (PCR) and PCR with sequence‐specific primers (PCR‐SSP). Characterizations of RHD intron 2 and Rhesus box were performed by PCR‐PstI digestion. The DNA and cDNA sequences of the novel alleles were determined by PCR and reverse transcriptase‐PCR (RT‐PCR) sequencing analysis. A family study was performed to investigate the segregation of a novel RHD allele.Results  One hundred and twenty‐nine samples (79·1%) had no RHD gene. Twenty‐seven samples (16·6%) carried RHD‐CE‐D hybrid alleles. The remainder seven samples (4·3%) appeared to have an intact RHD gene. Three of them were sequenced for RHD gene and two novel alleles, RHD 325del and RHD intron 2 1A, were identified. The deletion of a nucleotide A at position 325 in the allele RHD 325del resulted in a stop codon at amino acid position 118. The RHD intron 2 1A allele was generated from a splice mutation and its transcript sequence had no exon 2. Family study indicated that the RHD 325del allele was inherited with a Ce haplotype.Conclusion  This study provides the molecular bases of RHD alleles RHD 325del and RHD intron 2 1A. The existences of RHD 711del, RH (D1 CE2‐9 D10), and RH (D1 CE2‐9 D10) alleles in the Chinese population were confirmed. A PCR‐SSP‐based assay for rapid detection of RHD 325del and RHD intron 2 1A alleles was established and it could be used to predict the RHD genotype in the Chinese RhD‐negative subjects.
White‐blood‐cell‐containing allogeneic blood transfusion and postoperative infection or mortality: an updated meta‐analysis
Authors: Vamvakas E. C. 
Published: January 2007

Background  Additional randomized controlled trials (RCTs) comparing recipients of non‐white‐blood‐cell‐(WBC)‐reduced and WBC‐reduced allogeneic red blood cells (RBCs) have been reported since the undertaking of previous meta‐analyses of the association of allogeneic blood transfusion (ABT) with postoperative infection and/or mortality. Because no further RCTs are underway, a final meta‐analysis of all available RCTs was conducted.Methods  RCTs reporting on the association of ABT with postoperative infection and/or short‐term (up to 3‐month post‐transfusion), all‐cause mortality were retrieved. Twelve RCTs reporting on infection and 11 RCTs reporting on mortality were eligible for meta‐analysis. Summary odds ratios (ORs) of infection or mortality in recipients of WBC‐containing ABT vs. WBC‐reduced ABT were calculated across the studies.Results  An association of ABT with postoperative infection was demonstrated across RCTs transfusing RBCs WBC‐reduced after storage [summary OR = 2·25; 95% confidence interval (CI), 1·12–4·25] but not before storage (summary OR = 1·06; 95% CI, 0·91–1·24). An association of ABT with mortality was demonstrated across RCTs conducted in cardiac surgery (summary OR = 1·72, 95% CI, 1·05–2·81) and across RCTs transfusing buffy‐coat‐reduced RBCs vs. RBCs WBC‐reduced before storage (summary OR = 1·60; 95% CI, 1·14–2·24), but not across RCTs transfusing non‐buffy‐coat‐reduced RBCs vs. RBCs WBC‐reduced before storage (summary OR = 1·01; 95% CI, 0·73–1·40).Conclusions  An association between ABT and postoperative infection or short‐term mortality is not detected across all clinical settings and transfused RBC products. An association between ABT and mortality is detected in cardiac surgery, but the other associations found in subgroup analyses contradict current theories about mechanism(s) of the ABT effect.
Food intake and ingredient profile affect viscosity of ileal digesta of dogs
Authors: Dikeman C. L. , Murphy M. R. , Fahey G. C. 
Published: January 2007

SummaryTwo experiments were conducted to determine dietary factors affecting digesta viscosity. In experiment 1, six ileal‐cannulated dogs were either full (607.1 kJ/BW0.67) or restricted (303.5 kJ/BW0.67) fed. In experiment 2, four dog foods were surveyed for effects on digesta viscosity based on protein source [animal protein (AP) or plant protein (PP)] or dietary fibre source [soluble dietary fibre (SDF) or insoluble dietary fibre (IDF)]. Dry matter (DM) intake was higher (p < 0.05) when dogs were full (11.4 g/kg) compared with restricted fed (5.98 g/kg). Ileal digesta viscosity tended to be higher (p = 0.07) for full fed [10 251 centipoise (cP)] compared with restricted‐fed dogs (6677 cP). Ileal digesta viscosities were 6561, 11 074, 13 830 and 15 967 cP for dogs consuming IDF, SDF, AP and PP treatments respectively. Ileal DM concentrations were 11.4%, 13.6%, 14.8% and 14.8% for SDF, IDF, AP and PP treatments respectively. DM digestibility coefficients were lowest (71.2%) for the PP treatment and highest (88.7%) for the IDF treatment. Organic matter digestibilities followed a similar pattern. Ileal digesta viscosity of dogs appears to increase with increased diet intake, and increased ileal DM concentration. More digestible diets result in less ileal DM and lower viscosity constants.
Effect of linseed cake supplementation on digestibility and faecal and haematological parameters in dogs
Authors: Kempe R. , Saastamoinen M. 
Published: January 2007

SummaryThe experiment was conducted with a 6 × 4 cyclic changeover design. Six adult Alaskan huskies were assigned to diets containing 0%, 2%, 4%, 6% and 8% linseed cake. A linear decrease in the apparent digestibilities of organic matter (OM) (p < 0.020), ether extract (EE) (p < 0.003), neutral detergent fibre (p < 0.015), nitrogen‐free extract (NFE) (p < 0.001) and crude carbohydrates (p < 0.001) was noted. Digestibilities of dry matter (DM) and crude protein (CP) were unaffected by the treatment. Wet weight of faeces increased (p < 0.001) and DM of faeces decreased (p < 0.001) linearly as the percentage of dietary linseed cake increased. Serum cholesterol concentration tended to decrease (p = 0.094) as the proportion of linseed cake increased. Apparent OM, EE, CP and NFE digestibility coefficients for linseed cake were 52%, 77%, 54% and 37%, respectively, and the digestible energy (DE) value was 13.22 MJ/kg DM. Our results showed that working and racing dogs fed the extruded and kibbled diet can utilize up to 4.2% linseed cake of diet DM as a fibre source without severe reductions in nutrient digestibility or feed consumption. Even higher levels of linseed cake, up to 8.5% of diet DM, can be used for normal or obese dogs, but more faeces will be excreted.
Effect of exogenous growth‐hormone‐releasing factor on blood metabolites and minerals in late maturing buffalo heifers (Bubalus bubalis)
Authors: Haldar A. , Prakash B. S. 
Published: January 2007

SummaryPrevious studies have suggested that growth‐hormone‐releasing factor (GRF) enhanced growth and advanced puberty onset along with hormonal changes in buffalo heifers (Bubalus bubalis). However, it is not known to what extent exogenous GRF could influence blood metabolites and minerals to bring about puberty in buffalo heifers. Therefore, we planned to investigate the effect of exogenous bovine GRF (bGRF) on blood metabolites and minerals in buffalo heifers during a 3‐month pre‐treatment period, 9‐month treatment period and 1‐month post‐treatment period. Six buffalo heifers were treated intravenously with bGRF (10 μg per 100 kg body weight) at 15‐day interval for 9 months. Another six buffalo heifers of weight‐ and age‐matched received requisite amount of vehicle (0.9% NaCl solution) during the same period. Exogenous bGRF enhanced (p < 0.01) plasma non‐esterified fatty acids (NEFA) concentrations in treatment group when compared with control group during the treatment and post‐treatment period, while plasma alpha‐amino nitrogen (AAN) concentrations showed a decreasing trend (p < 0.05) in the treatment group when compared with the control group during the treatment and post‐treatment periods. The plasma inorganic phosphorus (Pi) was found to be higher (p < 0.05) in the treatment group animals in comparison with the levels recorded in the control group animals during the treatment as well as post‐treatment periods. However, there was no change (p > 0.05) in plasma glucose and calcium concentrations between the two groups. Plasma NEFA was found to be positively correlated with plasma growth hormone (GH); however, it was only significant for the treatment group (r = + 0.76; p < 0.05). Plasma AAN in the treatment group exhibited negative correlation with plasma GH (r = 0.72; p < 0.05), while plasma AAN and GH were recorded to be positively correlated in the control group (r = 0.47; p < 0.05). The present findings suggest that exogenous bGRF induces GH release that increases plasma NEFA and Pi and decreases AAN concentrations, which probably help to reach a certain physiological state that initiates events necessary for bringing about puberty in buffalo heifers.
Rate of metabolic decarboxylation of leucine as assessed by a l[1‐13C1]leucine breath test combined with indirect calorimetry of broiler chickens fed isocaloric diets with different protein:fat ratio
Authors: Swennen Q. , Laroye C. , Janssens G. , Verbeke K. , Decuypere E. , Buyse J. 
Published: January 2007

SummaryResearch has shown that broiler chickens reared on a low‐protein diet have a more efficient protein digestion. However, information on the fate of absorbed amino acids in relation to the dietary crude protein level in poultry is sparse. Therefore, this study aimed at developing a methodology for a 1‐13C1‐leucine breath test combined with indirect calorimetry, and to apply this technique using broiler diets known to induce differences in protein retention. From 14 days of age onwards, broiler chickens were reared on one of two isocaloric diets with substitutions between fat and protein [low‐protein (LP) vs. high‐protein (HP) diet: 130.4 vs. 269 g protein/kg; and 101.8 vs. 27.9 g fat/kg]. Every 4 or 5 days, three chickens per diet were placed in the respiratory cells for 48 h. The broilers were intubated with 40 mg 1‐13C1‐leucine/kg body weight, followed by breath sampling for 4 h at 15‐min intervals and mass spectrometric analysis of the 13C:12C ratio in the samples. The CO2 level in the respiratory cell air was monitored and excreta samples were collected. The methodology to study l[1‐13C1]leucine decarboxyation in chickens using a breath test combined with indirect calorimetry was accomplished. Results of the nitrogen balance test indicated that the LP broilers had an improved dietary protein retention compared with the HP animals. Moreover, LP chickens decarboxylated a significantly lower percentage of l[1‐13C1]leucine, demonstrating several ‘protein‐ or amino acid‐sparing’ mechanisms in animals reared on a diet with lower protein level, both at the digestive and at the postabsorptive level.
Colonization of Female Watermelon Blossoms by Acidovorax avenae ssp. citrulli and the Relationship between Blossom Inoculum Dosage and Seed Infestation
Authors: Lessl J. T. , Fessehaie A. , Walcott R. R. 
Published: January 2007

AbstractThe aim of this work was to investigate the ability of Acidovorax avenae ssp. citrulli, the causal agent of bacterial fruit blotch of cucurbits (BFB), to colonize female watermelon blossoms, and to explore the relationship between blossom inoculum dosage and seed infestation. Under greenhouse conditions A. avenae ssp. citrulli colonized stigmas and styles of female watermelon blossoms reaching populations of ≈107 to 108 colony‐forming units (CFU) per blossom for 96 h after inoculation. Acidovorax avenae ssp. citrulli growth on stigmas was slower than that of Pseudomonas syringae Cit7, a non‐pathogenic, foliar epiphyte of tomato. While pollination reduced growth of A. avenae ssp. citrulli, but P. syringae Cit7 was unaffected. Both bacteria colonized style tissues but bacterial growth in the style was significantly less than the stigma. Blossom inoculation with ≈1 × 103A. avenae ssp. citrulli CFU/blossom led to 36–55% infested seedlots within symptomless fruits. On average 14% of the seedlings produced from these seedlots displayed BFB symptoms. There was a strong positive correlation between A. avenae ssp. citrulli inoculum concentration applied to blossoms and the percentage of infested seedlots, as determined by the seedling grow‐out assay (R2 = 0.94). However, this relationship was weaker when seedlot infestation was determined by a polymerase chain reaction‐based assay (R2 = 0.34). There was also a strong positive linear relationship between A. avenae ssp. citrulli blossom inoculum dose and the mean percentage of BFB‐infected seedlings (R2 = 0.99) produced in seedling grow‐out assays. These data support the hypothesis that blossom colonization might be involved in seed infestation under field conditions.
Clinical usage of the squamous cell carcinoma antigen in patients with penile cancer
Authors: Touloupidis Stavros , Zisimopoulos Athanasios , Giannakopoulos Stylianos , Papatsoris Athanasios G , Kalaitzis Christos , Thanos Anastasios 
Published: January 2007

Background:  We present our initial experience with the use of the squamous cell carcinoma (SCC) antigen (SCCAg) in 16 men with penile SCC (SCC group), in four men with condyloma acuminatum (benign group), and in 32 blood donors (control group).Methods:  The SCCAg levels were measured at presentation and every 6 months (upper limit was 2 ng/mL). The mean follow‐up time was 4 years.Results:  All non‐SCC patients had normal SSCAg serum levels in contrast with the SCC patients. The presence of nodal and/or distant metastases resulted in statistically significant higher SCCAg levels, both at presentation and during the follow‐up. In patients undergoing lymph node dissection with elevated SCCAg levels prior to the procedure, there was a statistically significant decrease of the SCCAg levels after the operation.Conclusion:  The SCCAg level could be a serum marker that holds promise for clinical use in penile SCC. Sequential monitoring of SCCAg level might indicate developing of nodal and/or distant metastases and could be useful in following the response to treatment.