bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide‐MHC without increasing apparent cross‐reactivity
Authors: Dunn Steven M. , Rizkallah Pierre J. , Baston Emma , Mahon Tara , Cameron Brian , Moysey Ruth , Gao Feng , Sami Malkit , Boulter Jonathan , Li Yi , Jakobsen Bent K. 
Published: April 2006

AbstractThe mammalian α/β T cell receptor (TCR) repertoire plays a pivotal role in adaptive immunity by recognizing short, processed, peptide antigens bound in the context of a highly diverse family of cell‐surface major histocompatibility complexes (pMHCs). Despite the extensive TCR–MHC interaction surface, peptide‐independent cross‐reactivity of native TCRs is generally avoided through cell‐mediated selection of molecules with low inherent affinity for MHC. Here we show that, contrary to expectations, the germ line‐encoded complementarity determining regions (CDRs) of human TCRs, namely the CDR2s, which appear to contact only the MHC surface and not the bound peptide, can be engineered to yield soluble low nanomolar affinity ligands that retain a surprisingly high degree of specificity for the cognate pMHC target. Structural investigation of one such CDR2 mutant implicates shape complementarity of the mutant CDR2 contact interfaces as being a key determinant of the increased affinity. Our results suggest that manipulation of germ line CDR2 loops may provide a useful route to the production of high‐affinity TCRs with therapeutic and diagnostic potential.
Guanidinium derivatives bind preferentially and trigger long‐distance conformational changes in an engineered T4 lysozyme
Authors: Yousef Mohammad S. , Bischoff Nicole , Dyer Collin M. , Baase Walter A. , Matthews Brian W. 
Published: April 2006

AbstractThe binding of guanidinium ion has been shown to promote a large‐scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for the guanidino group of an arginine side chain. Here we determine whether methyl‐ and ethylguani‐dinium provide better mimics. The results show that addition of the hydrophobic moieties to the ligand enhances the binding affinity concomitant with reduction in ligand solubility. Crystallographic analysis confirms that binding of the alternative ligands to the engineered site still drives the large‐scale conformational change. Thermal analysis and NMR data show, in comparison to guanidinium, an increase in protein stability and in ligand affinity. This is presumably due to the successive increase in hydrophobicity in going from guanidinium to ethylguanidinium. A fluorescence‐based optical method was developed to sense the ligand‐triggered helix translation in solution. The results are a first step in the de novo design of a molecular switch that is not related to the normal function of the protein.
TOPOGRAPHY OF CELL DIVISION IN THE STRUCTURALLY COMPLEX DINOFLAGELLATE GENUS ORNITHOCERCUS1
Authors: Taylor F. J. R. 
Published: April 2006

SUMMARYThe dinophysoid dinoflagellates (to which Ornithocercus belongs) achieve growth both by increase in size of individual wall elements and, during rapid lateral expansion associated with cell division, by the formation of a semimeridional band of material termed the megacytic zone (MZ). The MZ maintains mother cell wall integrity during complete cytokinesis of the cell body and enclosure with new wall elements. The lists, extensive wing‐like extensions of the wall, can only be reformed after dissolution of the MZ. Beginning near the ventral region (which is the last region of the wall to be duplicated), the MZ dislocates and its material is apparently resorbed. The last region of attachment is invariably dorsal and in several, but not all species, the daughter cells may remain attached during early list formation by a special remnant of the MZ, termed here the dorsal megacytic bridge (DMB). After full separation of daughter cells remnants of the DMB persist for an unknown but presumably short period.The topography of this process, involving radical ontogenetic alterations in the appearance of the daughter cells and some wall surfaces, is illustrated here by the scanning electron microscope. In addition 2 aberrant types of division are shown, one of which results in a double individual, termed a geminoid.
FERTILIZATION IN OEDOGONIUM. I. PLASMOGAMY12
Authors: Hoffman Larry R. 
Published: April 2006

SUMMARYEvents prior to, during, and immediately following plasmogamy have been investigated in Oedogonium cardiacum using combined techniques of light and electron microscopy. Maturation of the oogonium involves the formation of an oogonial pore and the differentiation of the single egg from the larger oogonial protoplast from which it is formed. The fine structure of the sperm cell at the time of plasmogamy is described as well as the nature of its entrance into the oogonium. Cinematographic films were used to analyze the movements of the spermatozoids prior to plasmogamy and, similarly, 26 complete acts of gametic fusion were recorded and analyzed. Prior to plasmogamy the flagella‐bearing anterior extremity of the spermatozoid typically becomes elongate and is thereafter capable of flexible movements and rapid changes in shape which appear more or less independent of the rest of the cell. The sperm cell always makes initial contact with the egg surface by means of this agile, proboscis‐like, anterior end. Contact results through a combination of thrusting movements of the entire sperm cell and rapid, lateral sweeping movements of its flagellated anterior extremity against the egg surface. Gametic fusion is initiated with violent, vibrational movements of the sperm cell accompanied by loss of its flagella. Apparent fusion of the gamete membranes unites their protoplasts by a narrow cytoplasmic bridge which gradually increases in size as the sperm cell cytoplasm flows into the egg. An average time of 30.5 sec was required for complete fusion as determined from 25 typical sequences of plasmogamy recorded cinematographically. Fusion occurs even more rapidly when diploid oogonia are substituted for daploid oogonia. The entire sperm cell, with the exception of the flagella, fuses with the egg during plasmogamy. The dissimilar gamete nuclei are clearly distinguished ultrastructurally in the binucleate fusion cell. Concentrations of sperm cell mitochondria and remains of the flagellar apparatus (but no flagella) are readily recognized in the fusion cell. The fate of these and other cytoplasmic constituents of the sperm cell is discussed. Immediately after plasmogamy, and prior to karyogamy, a thin, finely fibrous layer is formed us an investment exterior to the fusion cell. Karyogamy follows shortly after plasmogamy, and both events may take place within 15 min after mixing eggs and spermatozoids.
PHOTOASSIMILATION OF 14C‐ACETATE BY ULVA LACTUCA1
Authors: Gemmill Eldon R. , Galloway Raymond A. 
Published: April 2006

SUMMARYThe effect of light on the uptake of 14C‐labeled acetate, glucose, α‐ketoglutarate, mannitol, and glycine was investigated in Ulva lactuca var. rigida. Uptake in the light over that in the dark of 14C‐acetale (8‐fold) was far higher than that of the other compounds tested. Further study of the phenomenon showed that (1) an increase in light intensity from 60 through 1000 ft‐c results in increased 14C‐acetate uptake, the kinetics of which differ from that of 14CO2 uptake versus light intensity over the same range: (2) the action spectrum of acetate uptake, between 450 and 730 nm conforms to the action spectrum for photosynthesis in Ulva; (3) the acetate uptake process is sensitive to photosynthetic poisons including N'‐ (3‐4, dichlorophenyl)‐N, N‐dimethyl urea (DCMU), and phenazine methosulfate (PMS), and inhibitors of the Krebs cycle including sodium monofluoroacetate (MFA) and malonate; (4) uptake of acetate is favored by low CO2 concentrations; (5) uptake of acetate is not sensitive to 10−4 M uranyl nitrate; (6) continuous white light, with and without far‐red radiation, indicates no significant phytochrome involvement in the process.These results point to an intracellular dependence of the assimilation of acetate on the Krebs cycle in some manner (possibly in cooperation with the glyoxylate cycle) other than simply releasing CO2 from the acetate moiety with subsequent fixation via the Calvin cycle, and on some product(s) of photo‐system 2, eg, NADPH+, reduced ferredoxin, or O2.
A cDNA macroarray approach to parasite‐induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum
Authors: WANG ZHENSHAN , FARMER KRISTY , HILL GEOFFREY E. , EDWARDS SCOTT V. 
Published: April 2006

AbstractIn 1994, the bacterial parasite Mycoplasma gallisepticum expanded its host range and swept through populations of a novel host — eastern US populations of the house finch (Carpodacus mexicanus). This epizootic caused a dramatic decline in finch population numbers, has been shown to have caused strong selection on house finch morphology, and presumably caused evolutionary change at the molecular level as finches evolved enhanced resistance. As a first step toward identifying finch genes that respond to infection by Mycoplasma and which may have experienced natural selection by this parasite, we used suppression subtractive hybridization (SSH) and cDNA macroarray approaches to identify differentially expressed genes regulated by the Mycoplasma parasite. Two subtractive cDNA libraries consisting of 16 512 clones were developed from spleen using an experimentally uninfected bird as the ‘tester’ and an infected bird as ‘driver’, and vice versa. Two hundred and twenty cDNA clones corresponding 34 genes with known vertebrate homologues and a large number of novel transcripts were found to be qualitatively up‐ or down‐regulated genes by high‐density filter hybridization. These gene expression changes were further confirmed by a high throughout reverse Northern blot approach and in specific cases by targeted Northern analysis. blast searches show that heat shock protein (HSP) 90, MHC II‐associated invariant chain (CD74), T‐cell immunoglobulin mucin 1 (TIM1), as well as numerous novel expressed genes not found in the databases were up‐ or down‐regulated by the host in response to this parasite. Our results and macroarray resources provide a foundation for molecular co‐evolutionary studies of the Mycoplasma parasite and its recently colonized avian host.
Natural genetic variation in whole‐genome expression in Arabidopsis thaliana: the impact of physiological QTL introgression
Authors: JUENGER THOMAS E. , WAYNE TIERNEY , BOLES SANDRA , SYMONDS V. VAUGHAN , MCKAY JOHN , COUGHLAN SEAN J. 
Published: April 2006

AbstractA long‐standing and fundamental question in biology is how genes influence complex phenotypes. Combining near‐isogenic line mapping with genome expression profiling offers a unique opportunity for exploring the functional relationship between genotype and phenotype and for generating candidate genes for future study. We used a whole‐genome microarray produced with ink‐jet technology to measure the relative expression level of over 21 500 genes from an Arabidopsis thaliana near‐isogenic line (NIL) and its recurrent parent. The NIL material contained two introgressions (bottom of chromosome II and top of chromosome III) of the Cvi‐1 ecotype in a Ler‐2 ecotype genome background. Each introgression ‘captures’ a Cvi allele of a physiological quantitative trait loci (QTL) that our previous studies have shown increases transpiration and reduces water‐use efficiency at the whole‐plant level. We used a mixed model anova framework for assessing sources of expression variability and for evaluating statistical significance in our array experiment. We discovered 25 differentially expressed genes in the introgression at a false‐discovery rate (FDR) cut‐off of 0.20 and identified new candidate genes for both QTL regions. Several differentially expressed genes were confirmed with QRT–PCR (quantitative reverse transcription–polymerase chain reaction) assays. In contrast, we found no statistically significant differentially expressed genes outside of the QTL introgressions after controlling for multiple tests. We discuss these results in the context of candidate genes, cloning QTL, and phenotypic evolution.
Microarray analysis reveals differential gene expression in hybrid sunflower species
Authors: LAI ZHAO , GROSS BRIANA L. , ZOU YI , ANDREWS JUSTEN , RIESEBERG LOREN H. 
Published: April 2006

AbstractThis paper describes the creation of a cDNA microarray for annual sunflowers and its use to elucidate patterns of gene expression inHelianthus annuus,Helianthus petiolaris, and the homoploid hybrid speciesHelianthus deserticola. The array comprises 3743 ESTs (expressed sequence tags) representing approximately 2897 unique genes. It has an average clone/EST identity rate of 91%, is applicable across species boundaries within the annual sunflowers, and shows patterns of gene expression that are highly reproducible according to real‐time RT–PCR (reverse transcription–polymerase chain reaction) results. Overall, 12.8% of genes on the array showed statistically significant differential expression across the three species.Helianthus deserticoladisplayed transgressive, or extreme, expression for 58 genes, with roughly equal numbers exhibiting up‐ or down‐regulation relative to both parental species. Transport‐related proteins were strongly over‐represented among the transgressively expressed genes, which makes functional sense given the extreme desert floor habitat ofH. deserticola. The potential adaptive value of differential gene expression was evaluated for five genes in two populations of early generation (BC2) hybrids between the parental species grown in theH.deserticolahabitat. One gene (a G protein‐coupled receptor) had a significant association with fitness and maps close to a QTL controlling traits that may be adaptive in the desert habitat.
A predicted microsatellite map of the passerine genome based on chicken–passerine sequence similarity
Authors: DAWSON DEBORAH A. , BURKE TERRY , HANSSON BENGT , PANDHAL JAGROOP , HALE MATTHEW C. , HINTEN GAVIN N. , SLATE JON 
Published: April 2006

AbstractWe present a predicted passerine genome map consisting of 196 microsatellite markers distributed across 25 chromosomes. The map was constructed by assigning chromosomal locations based on the sequence similarity between 550 publicly available passerine microsatellites and the draft chicken genome sequence published by the International Chicken Genome Sequencing Consortium. We compared this passerine microsatellite map with a recently published great reed warbler (Acrocephalus arundinaceus) linkage map derived from the segregation of marker alleles in a pedigree of a natural population. Twenty‐four microsatellite markers were shared between the two maps, distributed across ten chromosomes. Synteny was maintained between the predicted passerine microsatellite map and the great reed warbler linkage map, confirming the validity and accuracy of our approach. Possible applications of the predicted passerine microsatellite map include genome mapping; quantitative trait locus (QTL) discovery; understanding heterozygosity–fitness correlations; investigating avian karyotype evolution; understanding microsatellite mutation processes; and for identifying loci conserved in multiple species, unlinked loci for use in genotyping sets and sex‐linked markers.
Genomics of hybrid poplar (Populus trichocarpa× deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full‐length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect‐induced defences in poplar
Authors: RALPH STEVEN , ODDY CLAIRE , COOPER DAWN , YUEH HESTHER , JANCSIK SHARON , KOLOSOVA NATALIA , PHILIPPE RYAN N. , AESCHLIMAN DANA , WHITE RICK , HUBER DEZENE , RITLAND CAROL E. , BENOIT FRANÇOIS , RIGBY TRACEY , NANTEL ANDRÉ , BUTTERFIELD YARON S. N. , KIRKPATRICK ROBERT , CHUN ELIZABETH , LIU JERRY , PALMQUIST DIANA , WYNHOVEN BRIAN , STOTT JEFFREY , YANG GEORGE , BARBER SARAH , HOLT ROBERT A. , SIDDIQUI ASIM , JONES STEVEN J. M. , MARRA MARCO A. , ELLIS BRIAN E. , DOUGLAS CARL J. , RITLAND KERMIT , BOHLMANN JÖRG 
Published: April 2006

AbstractAs part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore‐ and elicitor‐treated tissues and incorporating normalization methods to capture rare transcripts. From a set of 15 standard, normalized or full‐length cDNA libraries, we generated 139 007 3′‐ or 5′‐end sequenced ESTs, representing more than one‐third of the c. 385 000 publicly available Populus ESTs. Clustering and assembly of 107 519 3′‐end ESTs resulted in 14 451 contigs and 20 560 singletons, altogether representing 35 011 putative unique transcripts, or potentially more than three‐quarters of the predicted c. 45 000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15 496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up‐regulated, compared to only 537 down‐regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1‐aminocyclopropane‐1‐carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (–)‐germacrene D synthase] and transcriptional regulation [e.g. leucine‐rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome‐scale approach to characterize insect‐induced defences in a woody perennial providing a solid platform for functional investigation of plant–insect interactions in poplar.
Exposed and concealed antigens as vaccine targets for controlling ticks and tick‐borne diseases
Authors: NUTTALL P. A. , TRIMNELL A. R. , KAZIMIROVA M. , LABUDA M. 
Published: April 2006

SUMMARY Tick vaccines derived from Bm86, a midgut membrane‐bound protein of the cattle tick, Boophilus microplus, are currently the only commercially available ectoparasite vaccines. Despite its introduction to the market in 1994, and the recognized need for alternatives to chemical pesticides, progress in developing effective antitick vaccines (and ectoparasite vaccines in general) is slow. The primary rate‐limiting step is the identification of suitable antigenic targets for vaccine development. Two sources of candidate vaccine antigens have been identified: ‘exposed’ antigens that are secreted in tick saliva during attachment and feeding on a host and ‘concealed’ antigens that are normally hidden from the host. Recently, a third group of antigens has been distinguished that combines the properties of both exposed and concealed antigens. This latter group offers the prospect of a broad‐spectrum vaccine effective against both adults and immature stages of a wide variety of tick species. It also shows transmission‐blocking and protective activity against a tick‐borne pathogen. With the proliferation of molecular techniques and their application to vaccine development, there are high hopes for new and effective antitick vaccines that also control tick‐borne diseases.
Arabidopsis myrosinases TGG1 and TGG2 have redundant function in glucosinolate breakdown and insect defense
Authors: Barth Carina , Jander Georg 
Published: April 2006

SummaryIn Arabidopsis and other Brassicaceae, the enzyme myrosinase (β‐thioglucoside glucohydrolase, TGG) degrades glucosinolates to produce toxins that deter herbivory. A broadly applicable selection for meiotic recombination between tightly linked T‐DNA insertions was developed to generate Arabidopsis tgg1tgg2 double mutants and study myrosinase function. Glucosinolate breakdown in crushed leaves of tgg1 or tgg2 single mutants was comparable to that of wild‐type, indicating redundant enzyme function. In contrast, leaf extracts of tgg1tgg2 double mutants had undetectable myrosinase activity in vitro, and damage‐induced breakdown of endogenous glucosinolates was apparently absent for aliphatic and greatly slowed for indole glucosinolates. Maturing leaves of myrosinase mutants had significantly increased glucosinolate levels. However, developmental decreases in glucosinolate content during senescence and germination were unaffected, showing that these processes occur independently of TGG1 and TGG2. Insect herbivores with different host plant preferences and feeding styles varied in their responses to myrosinase mutations. Weight gain of two Lepidoptera, the generalist Trichoplusia ni and the facultative Solanaceae‐specialist Manduca sexta, was significantly increased on tgg1tgg2 double mutants. Two crucifer‐specialist Lepidoptera had differing responses. Whereas Plutella xylostella was unaffected by myrosinase mutations, Pieris rapae performed better on wild‐type, perhaps due to reduced feeding stimulants in tgg1tgg2 mutants. Reproduction of two Homoptera, Myzus persicae and Brevicoryne brassicae, was unaffected by myrosinase mutations.
Assessment of New Dental Graduates in General Practice Using Seven Key Skills Portfolios
Authors: Grieveson B‐Brigden.D 
Published: April 2006

Aims  To demonstrate a formative assessment process for new dental graduates in general practice which includes seven key skills which are the foundation of good clinical practice and teamwork.Methods and materials  The key skills identified are: clinical record keeping; radiography; infection control; risk management and communication; legislation and good practice guidelines; team training and medical emergencies.Learning is by compilation of portfolios for each key skill for each individual and their practice. Supporting educational material is by a CD Rom for each key skill. Assessment is by external validation (Faculty of General Dental Practitioners) and local evaluation.Results  Each graduate will submit their key skills portfolios for assessment at the end of their vocational training year or agreed period. Support will be from their practices, study groups and tutors with access to the key skills CD Roms. Young graduates will be able to demonstrate knowledge and insight of general practice and show evidence of their own understanding of the seven key skills Satisfactory completion of the key skills portfolios may be used for the MFGDP(UK) coursework module as part of continuing professional development. The seven key skills portfolios CD Roms will contribute to the GDC verifiable CPD requirements.Conclusions  When students make the transition from dental school to general practice it is essential they understand the key requirements for high quality patient care and also the importance of teamwork in providing that care. The seven key skills portfolio learning not only helps new graduates do that but also make them more aware of their own practice and the many requirements of good safe care for patients and their staff. The seven key skills portfolios also contribute to further professional development as part of further professional examinations as well as being a good model of assessment of new dental graduates