bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microcolinearity and genome evolution in theAdhAregion of diploid and polyploid cotton (Gossypium)
Authors: Grover Corrinne E. , Kim HyeRan , Wing Rod A. , Paterson Andrew H. , Wendel Jonathan F. 
Published: May 2007

SummaryGenome sizes vary by several orders of magnitude, driven by mechanisms such as illegitimate recombination and transposable element proliferation. Prior analysis of theCesAregion in two cotton genomes that diverged 5–10 million years ago (Ma), and acquired a twofold difference in genome size, revealed extensive local conservation of genic and intergenic regions, with no evidence of the global genome size difference. The present study extends the comparison to include BAC sequences surrounding the gene encoding alcohol dehydrogenase A (AdhA) from four cotton genomes: the two co‐resident genomes (ATand DT) of the allotetraploid,Gossypium hirsutum, as well as the model diploid progenitors,Gossypium arboreum(A) andGossypium raimondii(D). In contrast to earlier work, evolution in theAdhAregion reflects, in a microcosm, the overall difference in genome size, with a nearly twofold difference in aligned sequence length. Most size differences may be attributed to differential accumulation of retroelements during divergence of the genome diploids from their common ancestor, but in addition there has been a biased accumulation of small deletions, such that those in the smaller D genome are on average twice as large as those in the larger A genome. The data also provide evidence for the global phenomenon of ‘genomic downsizing’ in polyploids shortly after formation. This in part reflects a higher frequency of small deletions post‐polyploidization, and increased illegitimate recombination. In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions.
Purification of the M flax‐rust resistance protein expressed in Pichia pastoris
Authors: Schmidt Simon A. , Williams Simon J. , Wang Ching‐I A. , Sornaraj Pradeep , James Ben , Kobe Bostjan , Dodds Peter N. , Ellis Jeffrey G. , Anderson Peter A. 
Published: May 2007

SummaryThe M flax‐rust resistance (R) gene is predicted to encode a 150‐kDa protein of the Toll‐interleukin‐like receptor‐nucleotide binding site‐leucine rich repeat (TIR‐NBS‐LRR) class of plant disease resistance proteins and provides resistance against the Melampsora lini (flax rust) fungus carrying the AvrM avirulence gene. The extremely low level of this class of R proteins found in plant tissue has precluded their biochemical and structural analysis, and the study of these proteins has been largely restricted to genetic analyses and in vivo investigations. Here we report the production and purification of the M protein in the methalotrophic yeast, Pichia pastoris. Expression trials with five different constructs reveals optimum levels of soluble native M protein can be obtained as an N‐terminally 9× His‐tagged protein, in which the first 21 amino acids of the predicted wild‐type protein are deleted. Expression was achieved using a high cell density fed‐batch bioreactor culture at low temperature. M protein was purified to near homogeneity from whole‐cell lysates using cation exchange, immobilised metal ion affinity chromatography and gel filtration with a final yield of approximately 3 mg of protein/1000 g wet weight of yeast cells lysed. The successful expression and purification of soluble M protein opens the way for biochemical and structural analysis of this class of important plant proteins.
ABA‐Hypersensitive Germination1 encodes a protein phosphatase 2C, an essential component of abscisic acid signaling in Arabidopsis seed
Authors: Nishimura Noriyuki , Yoshida Tomo , Kitahata Nobutaka , Asami Tadao , Shinozaki Kazuo , Hirayama Takashi 
Published: May 2007

SummaryThe phytohormone abscisic acid (ABA) regulates physiologically important stress and developmental responses in plants. To reveal the mechanism of response to ABA, we isolated several novel ABA‐hypersensitive Arabidopsis thaliana mutants, named ahg (ABA‐hypersensitive germination). ahg1‐1 mutants showed hypersensitivity to ABA, NaCl, KCl, mannitol, glucose and sucrose during germination and post‐germination growth, but did not display any significant phenotypes in adult plants. ahg1‐1 seeds accumulated slightly more ABA before stratification and showed increased seed dormancy. Map‐based cloning of AHG1 revealed that ahg1‐1 has a nonsense mutation in a gene encoding a novel protein phosphatase 2C (PP2C). We previously showed that the ahg3‐1 mutant has a point mutation in the AtPP2CA gene, which encodes another PP2C that has a major role in the ABA response in seeds (Yoshida et al., 2006b). The levels of AHG1 mRNA were higher in dry seeds and increased during late seed maturation – an expression pattern similar to that of ABI5. Transcriptome analysis revealed that, in ABA‐treated germinating seeds, many seed‐specific genes and ABA‐inducible genes were highly expressed in ahg1‐1 and ahg3‐1 mutants compared with the wild‐type. Detailed analysis suggested differences between the functions of AHG1 and AHG3. Dozens of genes were expressed more strongly in the ahg1‐1 mutant than in ahg3‐1. Promoter–GUS analyses demonstrated both overlapping and distinct expression patterns in seed. In addition, the ahg1‐1 ahg3‐1 double mutant was more hypersensitive than either monogenic mutant. These results suggest that AHG1 has specific functions in seed development and germination, shared partly with AHG3.
Members of the PHO1 gene family show limited functional redundancy in phosphate transfer to the shoot, and are regulated by phosphate deficiency via distinct pathways
Authors: Stefanovic Aleksandra , Ribot Cécile , Rouached Hatem , Wang Yong , Chong Julie , Belbahri Lassaad , Delessert Syndie , Poirier Yves 
Published: May 2007

SummaryThe PHO1 family comprises 11 members in Arabidopsis thaliana. In order to decipher the role of these genes in inorganic phosphate (Pi) transport and homeostasis, complementation of the pho1 mutant, deficient in loading Pi to the root xylem, was determined by the expression of the PHO1 homologous genes under the control of the PHO1 promoter. Only PHO1 and the homologue PHO1;H1 could complement pho1. The PHO1;H1 promoter was active in the vascular cylinder of roots and shoots. Expression of PHO1;H1 was very low in Pi‐sufficient plants, but was strongly induced under Pi‐deficient conditions. T‐DNA knock‐out mutants of PHO1;H1 neither showed growth defects nor alteration in Pi transport dynamics, or Pi content, compared with wild type. However, the double mutant pho1/pho1;h1 showed a strong reduction in growth and in the capacity to transfer Pi from the root to the shoot compared with pho1. Grafting experiments revealed that phenotypes associated with the pho1 and pho1/pho1;h1 mutants were linked to the lack of gene expression in the root. The increased expression of PHO1;H1 under Pi deficiency was largely controlled by the transcription factor PHR1 and was suppressed by the phosphate analogue phosphite, whereas the increase of PHO1 expression was independent of PHR1 and was not influenced by phosphite. Together, these data reveal that although transfer of Pi to the root xylem vessel is primarily mediated by PHO1, the homologue PHO1;H1 also contributes to Pi loading to the xylem, and that the two corresponding genes are regulated by Pi deficiency by distinct signal transduction pathways.
Immunogenic tagging of chloroplasts allows their isolation from defined cell types
Authors: Truernit Elisabeth , Hibberd Julian M. 
Published: May 2007

SummaryChloroplast structure varies depending on cell type. Currently it is difficult to obtain insight into how differences in chloroplast structure relate to function, as it is often not possible to isolate chloroplasts from specific cells. To address this, we have developed an approach that involves labelling chloroplasts from individual cell types by placing the foreign yellow fluorescent protein (YFP) on their outer surface, and then isolating those labelled chloroplasts immunogenically. Cell specificity is achieved through the use of enhancer trap lines. When whole leaves are homogenized, a mixture of labelled and unlabelled chloroplasts is released, but magnetic beads coated with antibodies to the green fluorescent protein (GFP) allow the labelled chloroplasts to be isolated. Chloroplasts from spongy mesophyll, vascular and epidermal cells of Arabidopsis thaliana were obtained in this way, and semi‐quantitative RT‐PCR showed that the abundance of various chloroplast transcripts differed between these three cell types. The approach is based on genetic logic, and so could be applied to the isolation of various organelles or subcellular compartments from transformable organisms other than A. thaliana.
Deficiency of mitochondrial fumarase activity in tomato plants impairs photosynthesis via an effect on stomatal function
Authors: Nunes‐Nesi Adriano , Carrari Fernando , Gibon Yves , Sulpice Ronan , Lytovchenko Anna , Fisahn Joachim , Graham James , Ratcliffe R. George , Sweetlove Lee J. , Fernie Alisdair R. 
Published: May 2007

AbstractTransgenic tomato (Solanum lycopersicum) plants expressing a fragment of a fumarate hydratase (fumarase) gene in the antisense orientation and exhibiting considerable reductions in the mitochondrial activity of this enzyme show impaired photosynthesis. The rate of the tricarboxylic acid cycle was reduced in the transformants relative to the other major pathways of carbohydrate oxidation and the plants were characterized by a restricted rate of dark respiration. However, biochemical analyses revealed relatively little alteration in leaf metabolism as a consequence of reducing the fumarase activity. That said, in comparison to wild‐type plants, CO2 assimilation was reduced by up to 50% under atmospheric conditions and plants were characterized by a reduced biomass on a whole plant basis. Analysis of further photosynthetic parameters revealed that there was little difference in pigment content in the transformants but that the rate of transpiration and stomatal conductance was markedly reduced. Analysis of the response of the rate of photosynthesis to variation in the concentration of CO2 confirmed that this restriction was due to a deficiency in stomatal function.
Seed dormancy release in Arabidopsis Cvi by dry after‐ripening, low temperature, nitrate and light shows common quantitative patterns of gene expression directed by environmentally specific sensing
Authors: Finch‐Savage William E. , Cadman Cassandra S. C. , Toorop Peter E. , Lynn James R. , Hilhorst Henk W. M. 
Published: May 2007

SummaryThe depth of seed dormancy can be influenced by a number of different environmental signals, but whether a common mechanism underlies this apparently similar response has yet to be investigated. Full‐genome microarrays were used for a global transcript analysis of Arabidopsis thaliana Cape Verde Island accession seeds exposed to dry after‐ripening (AR), or low temperature, nitrate and light when imbibed. Germination studies showed that the sensitivity of imbibed seeds to low temperature, nitrate and light was dependant upon the length of time spent AR following harvest. Seeds had an absolute requirement for light to complete dormancy release in all conditions, but this effect required an exposure to a prior dormancy relieving environment. Principal component analyses of the expression patterns observed grouped physiological states in a way that related to the depth of seed dormancy, rather than the type of environmental exposure. Furthermore, opposite changes in transcript abundance of genes in sets associated with dormancy, or dormancy relief through AR, were also related to the depth of dormancy and common to different environments. Besides these common quantitative changes, environment‐specific gene expression patterns during dormancy relief are also described. For example, higher transcript abundance for genes linked to the process of nitrate accumulation, and nitrate reduction was associated with dormancy relief. The quantity of GA3ox1 transcripts increased during dormancy relief in all conditions, in particular when dormancy relief was completed by exposure to light. This contrasts with transcripts linked to abscisic acid (ABA) synthesis, which declined. The results are consistent with a role for the ABA/gibberellic acid balance in integrating dormancy‐relieving environmental signals.
TheTUMOROUS SHOOT DEVELOPMENT2gene of Arabidopsis encoding a putative methyltransferase is required for cell adhesion and co‐ordinated plant development
Authors: Krupková Eva , Immerzeel Peter , Pauly Markus , Schmülling Thomas 
Published: May 2007

SummaryMutations in theTUMOROUS SHOOT DEVELOPMENT2(TSD2) gene reduce cell adhesion, and in strongly affected individuals cause non‐coordinated shoot development that leads to disorganized tumor‐like growthin vitro.tsd2mutants showed increased activity of axial meristems, reduced root growth and enhanced de‐etiolation. The expression domains of the shoot meristem marker genesKNAT1andKNAT2were enlarged in the mutant background. Soil‐growntsd2mutants were dwarfed, but overall showed morphology similar to that of the wild‐type (WT). TheTSD2gene was identified by map‐based cloning. It encodes a novel 684 amino acid polypeptide containing a single membrane‐spanning domain in the N‐terminal part andS‐adenosyl‐l‐methionine binding and methyltransferase domains in the C‐terminal part. Expression of aTSD2:GUSreporter gene was detected mainly in meristems and young tissues. A green fluorescent protein‐tagged TSD2 protein localized to the Golgi apparatus. The cell‐adhesion defects indicated altered pectin properties, and we hypothesize that TSD2 acts as a pectin methyltransferase. However, analyses of the cell‐wall composition revealed no significant differences of the monosaccharide composition, the uronic acid content and the overall degree of pectin methylesterification betweentsd2and WT. The findings support a function of TSD2 as a methyltransferase, with an essential role in cell adhesion and coordinated plant development.
Accuracy in identifying patients with loss of consciousness in a police‐operated emergency call centre – first step in the chain of survival
Authors: Bach A. , Christensen E. F. 
Published: May 2007

Background:  The first link in the ‘chain of survival’ is the activation of Emergency Medical Services (EMS). In the major part of Denmark, police officers operate the alarm 1‐1‐2 centre, including calls for EMS. Our aim was to study the police 1‐1‐2 operators’ accuracy in identifying calls concerning patients with loss of consciousness as a key symptom of life‐threatening conditions. ‘Unconsciousness’ was defined as patients with a Glasgow Coma Scale (GCS) score of < 9, scored by the on‐scene anaesthesiologist from the Mobile Emergency Care Unit (MECU).Methods:  This study was an observational cohort study based on data from the Police 1‐1‐2 Database and the Aarhus County Pre‐hospital Database containing data from MECU cases during 6 months in 2004–05.Results:  Two thousand, three hundred and forty‐three emergency calls with MECU dispatch were identified. In 1655 cases, both 1‐1‐2 data and the GCS score were recorded. Two hundred and ninety‐five patients were found with a GCS score of < 9 at MECU arrival, 243 of whom were reported ‘unconscious’ by 1‐1‐2, giving a sensitivity of 82%. One thousand, three hundred and sixty patients were found with a GCS score of ≥ 9, 972 of whom were reported ‘awake’, giving a specificity of 72%. The positive predictive value (percentage of patients found with a GCS score of < 9 at MECU arrival amongst patients reported as ‘unconscious’) was 39%.Conclusions:  The accuracy was moderate with room for improvement. The positive predictive value was low, indicating over‐triage of MECU.
Effect of age on pulmonary gas exchange during laparoscopy in the Trendelenburg lithotomy position
Authors: Takahata O. , Kunisawa T. , Nagashima M. , Mamiya K. , Sakurai K. , Fujita S. , Fujimoto K. , Iwasaki H. 
Published: May 2007

Background:  Physiological changes in respiratory mechanics caused by aging may lead to a deterioration in pulmonary gas exchange, an increase in the alveolar–arterial oxygen gradient [(A–a)Do2] and a difference between the arterial carbon dioxide (CO2) tension (Paco2) and expired end‐tidal CO2 tension (PETco2) [P(a–ET)co2] during laparoscopy in the Trendelenburg lithotomy position (TLP).Methods:  The subjects were 51 gynecologic patients. Pressure‐controlled ventilation was used to maintain PETco2, measured by the side stream method, within the range 4–4.67 kPa. During laparoscopy with CO2 insufflation in TLP, the tidal volume was increased to keep PETco2 within ± 20% of the pre‐insufflation value. The subjects were divided into three groups by age: young group (< 45 years); middle‐aged group (45–64 years); and elderly group (≥ 65 years).Results:  Before pneumoperitoneum (PPN), significant differences were found between the young and elderly groups in the arterial oxygen tension (Pao2), (A–a)Do2, Paco2 and P(a–ET)co2. In all groups, the peak inspiratory pressure and Paco2 increased progressively during PPN in TLP. P(a–ET)co2 increased gradually after starting CO2 insufflation in TLP only in the elderly group.Conclusions:  An increase in P(a–ET)co2 was seen during PPN in TLP in the elderly group. With CO2 insufflation in TLP, the setting of mechanical ventilation based on the value of PETco2 (measured by the side stream method) should be determined with caution in elderly patients.
Oral naproxen but not oral paracetamol reduces the need for rescue analgesic after adenoidectomy in children
Authors: Korpela R. , Silvola J. , Laakso E. , Meretoja O. A. 
Published: May 2007

Background:  Our aim was to show the efficacy of naproxen and paracetamol with and without pethidine on pain and nausea and vomiting after adenoidectomy. The primary outcome was the requirement of rescue analgesic for post‐operative pain and the secondary outcome was post‐operative nausea and vomiting (PONV).Methods:  A randomized, double‐blind, placebo‐controlled study design was used. Thirty minutes before anaesthesia induction, patients (n= 180) received either a single oral dose analgesic (naproxen 10 mg/kg or paracetamol 20 mg/kg) or a placebo. Half of the children received pethidine 1 mg/kg intravenously (i.v.) at the induction of anaesthesia. Post‐operative pain was evaluated using an objective behavioural pain scale (OPS 0–9) and rescue medication, i.v. fentanyl 1 μg/kg, was administered if the child suffered from moderate or severe pain (OPS ≥ 4).Results:  When pethidine was not used, 83% of the children in the naproxen group vs. 97% in the other two groups required rescue fentanyl (P < 0.05). The use of pethidine reduced the incidence of fentanyl requirement by 30% and the number of fentanyl doses by 50% (P < 0.001). It also equalized the effects of naproxen, paracetamol and the placebo making the pain model invalid for this kind of study. The drawback associated with better analgesia was a doubling of the incidence of PONV (P < 0.001).Conclusions:  Oral naproxen (10 mg/kg), but not oral paracetamol (20 mg/kg), reduces the need for rescue analgesic after adenoidectomy in children. The sensitivity of the pain model is crucial for these types of studies.
Pheromonal dominance and the selection of a socially parasitic honeybee worker lineage (Apis mellifera capensis Esch.)
Authors: DIETEMANN V. , NEUMANN P. , HÄRTEL S. , PIRK C. W. W. , CREWE R. M. 
Published: May 2007

AbstractThe recent invasion by self‐replicating socially parasitic Cape honeybee workers, Apis mellifera capensis, of colonies of the neighbouring African subspecies Apis mellifera scutellata represents an opportunity to study evolution of intraspecific parasitism in real time. As honeybee workers compete pheromonally for reproductive dominance, and as A. m. capensis workers readily produce queen‐like pheromones, we hypothesized that these semiochemicals promoted the evolution of intraspecific social parasitism. Remarkably, the offspring of a single worker became established as a parasite in A. m. scutellata's range. This could have resulted from extreme selection among different clonal parasitic worker lineages. Using pheromonal contest experiments, we show that the selected parasitic lineage dominates in the production of mandibular gland pheromones over all other competitors to which it is exposed. Our results suggest that mandibular gland pheromones played a key role in the evolution of intraspecific social parasitism in the honeybee and in the selection of a single genotype of parasitic workers.
Cost of resistance to parasites in digital organisms
Authors: KRAAIJEVELD A. R. 
Published: May 2007

AbstractVirtually all organisms are attacked by parasites and are therefore expected to evolve resistance against these natural enemies. Parasite resistance is costly in a wide range of organisms, although the generality of such costs has been questioned, especially when resistance is not based on reallocation of resources. Digital organisms are increasingly used to explore aspects of life in general. In the Tierra system, there is a trade‐off between resistance against parasites and competitive ability. Because digital organisms are too simple to store resources, the finding that resistance to parasites is costly in digital organisms suggests that costs of parasite resistance can also occur when resistance is not resource based.
Predation by killer whales (Orcinus orca) and the evolution of whistle loss and narrow‐band high frequency clicks in odontocetes
Authors: MORISAKA T. , CONNOR R. C. 
Published: May 2007

AbstractA disparate selection of toothed whales (Odontoceti) share striking features of their acoustic repertoires including the absence of whistles and high frequency but weak (low peak‐to‐peak source level) clicks that have a relatively long duration and a narrow bandwidth. The non‐whistling, high frequency click species include members of the family Phocoenidae, members of one genus of delphinids,Cephalorhynchus, the pygmy sperm whale,Kogia breviceps, and apparently the sole member of the family Pontoporiidae. Our review supports the ‘acoustic crypsis’ hypothesis that killer whale predation risk was the primary selective factor favouring an echolocation and communication system in cephalorhynchids, phocoenids and possibly Pontoporiidae and Kogiidae restricted to sounds that killer whales hear poorly or not at all (< 2 and > 100 kHz).
The origin and colonization history of the barley scald pathogen Rhynchosporium secalis
Authors: BRUNNER P. C. , SCHÜRCH S. , MCDONALD B. A. 
Published: May 2007

AbstractThe origins of pathogens and their past and present migration patterns are often unknown. We used phylogenetic haplotype clustering in conjunction with model‐based coalescent approaches to reconstruct the genetic history of the barley leaf pathogen Rhynchosporium secalis using the avirulence gene NIP1 and its flanking regions. Our results falsify the hypothesis that R. secalis emerged in association with its host during the domestication of barley 10 000 to 15 000 years ago in the Fertile Crescent and was introduced into Europe through the migration of Neolithic farmers. Estimates of time since most recent common ancestor (2500–5000 BP) placed the emergence of R. secalis clearly after the domestication of barley. We propose that modern populations of R. secalis originated in northern Europe following a host switch, most probably from a wild grass onto cultivated barley shortly after barley was introduced into northern Europe. R. secalis subsequently spread southwards into already established European barley‐growing areas.