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Short Sequences (short + sequence)
Selected AbstractsGPS tracking of the foraging movements of Manx Shearwaters Puffinus puffinus breeding on Skomer Island, WalesIBIS, Issue 3 2008T. C. GUILFORD We report the first successful use of miniature Global Positioning System loggers to track the ocean-going behaviour of a c. 400 g seabird, the Manx Shearwater Puffinus puffinus. Breeding birds were tracked over three field seasons during the incubation and chick-rearing periods on their foraging excursions from the large colony on Skomer Island, Pembrokeshire, UK. Foraging effort was concentrated in the Irish Sea. Likely foraging areas were identified to the north, and more diffusely to the west of the colony. No foraging excursions were recorded significantly to the south of the colony, conflicting with the conclusions of earlier studies based on ringing recoveries and observations. We discuss several explanations including the hypothesis that foraging may have shifted substantially northwards in recent decades. We found no obvious relationship between birds' positions and water depth, although there was a suggestion that observations at night were in shallower water than those during the day. We also found that, despite the fact that Shearwaters can be observed rafting off-shore from their colonies in the hours prior to making landfall at night, breeding birds are usually located much further from the colony in the last 8 h before arrival, a finding that has significance for the likely effectiveness of marine protection areas if they are only local to the colony. Short sequences of precise second-by-second fixes showed that movement speeds were bimodal, corresponding to sitting on the water (most common at night and around midday) and flying (most common in the morning and evening), with flight behaviour separable into erratic (indicative of searching for food) and directional (indicative of travelling). We also provide a first direct measurement of mean flight speed during directional flight (c. 40 km/h), slower than a Shearwater's predicted maximum range velocity, suggesting that birds are exploiting wave or dynamic soaring during long-distance travel. [source] Synthesis of polycyclic polyfunctionalized carbocycles by a cobalt(I)-initiated tandem diels,alder reaction sequence,ISRAEL JOURNAL OF CHEMISTRY, Issue 4 2001Gerhard Hilt The cobalt(I)-catalyzed neutral Diels,Alder reaction of acyclic 1,3-dienes with conjugated enynes can be used to generate secondary dihydroaromatic 1,4,8-trienes containing a 1,3-diene substructure, in good yields under mild reaction conditions. These 1,3-dienes can be converted, with reactive dienophiles in a tandem normal Diels,Alder reaction, into polycyclic compounds. In a similar tandem Diels,Alder sequence, the cobalt-catalyzed neutral homo Diels,Alder reaction of 2,5-norbornadiene can be used to generate polycyclic cycloaddition adducts. A sequential triple Diels,Alder reaction sequence can be realized when norbornadiene is reacted with the excess of the conjugated enynes under cobalt(I) catalysis. In a homo Diels,Alder, neutral Diels,Alder, normal Diels,Alder reaction sequence, the intermediately formed adducts are reacted with activated dienophiles to yield polycyclic compounds in a short sequence. The structures of several products were established by X-ray analysis. This showed that predominantly endo-products are formed in the tandem reaction sequences, while the exo-product becomes predominant in the triple Diels,Alder reaction sequence. [source] Tristetraprolin recruits functional mRNA decay complexes to ARE sequencesJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2007Heidi H. Hau Abstract AU-rich elements (AREs) in the 3, untranslated region (UTR) of numerous mammalian transcripts function as instability elements that promote rapid mRNA degradation. Tristetraprolin (TTP) is an ARE-binding protein that promotes rapid mRNA decay through mechanisms that are poorly understood. A 31 nucleotide ARE sequences from the TNF-alpha 3, UTR promoted TTP-dependent mRNA decay when it was inserted into the 3, UTR of a beta-globin reporter transcript, indicating that this short sequence was sufficient for TTP function. We used a gel shift assay to identify a TTP-containing complex in cytoplasmic extracts from TTP-transfected HeLa cells that bound specifically to short ARE sequences. This TTP-containing complex also contained the 5,,3, exonuclease Xrn1 and the exosome component PM-scl75 because it was super-shifted with anti-Xrn1 or anti-PMscl75 antibodies. RNA affinity purification verified that these proteins associated specifically with ARE sequences in a TTP-dependent manner. Using a competition binding assay, we found that the TTP-containing complex bound with high affinity to short ARE sequences from GM-CSF, IL-3, TNF-alpha, IL-2, and c-fos, but did not bind to a U-rich sequence from c-myc, a 22 nucleotide poly U sequence or a mutated GM-CSF control sequence. High affinity binding by the TTP-containing complex correlated with TTP-dependent deadenylation and decay of capped, polyadenylated transcripts in a cell-free mRNA decay assay, suggesting that the TTP-containing complex was functional. These data support a model whereby TTP functions to enhance mRNA decay by recruiting components of the cellular mRNA decay machinery to the transcript. J. Cell. Biochem. 100: 1477,1492, 2007. © 2006 Wiley-Liss, Inc. [source] Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL systemJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2010Oscar Bertran Abstract The PUPIL system is a combination of software and protocols for the systematic linkage and interoperation of molecular dynamics and quantum mechanics codes to perform QM/MD (sometimes called QM/MM) calculations. The Gaussian03 and Amber packages were added to the PUPIL suite recently. However, efficient parallel QM codes are critical because calculation of the QM forces is the overwhelming majority of the computational load. Here we report details of incorporation of the deMon2k density functional suite as a new parallel QM code. An additional motivation is to add a highly optimized, purely DFT code. We illustrate with a demonstration study of the influence of perchlorate as a dopant ion of the poly(3,4-ethylenedioxythiophene) conducting polymer in explicit acetonitrile solvent using Amber and deMon2k. We discuss unanticipated requirements for use of a scheme for semi-empirical correction of Kohn-Sham eigenvalues to give physically meaningful one-electron gap energies. We provide comparison of both geometric parameters and electronic properties for nondoped and doped systems. We also present results comparing deMon2k and Gaussian03 calculation of forces for a short sequence of steps. We discuss briefly some difficult problems of quantum zone SCF convergence for the anionically doped system. The difficulties seem to be caused by well-know deficiencies in simple approximate exchange-correlation functionals. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Genome-wide SNP detection in the great tit Parus major using high throughput sequencingMOLECULAR ECOLOGY, Issue 2010NIKKIE E. M. VAN BERS Abstract Identifying genes that underlie ecological traits will open exiting possibilities to study gene,environment interactions in shaping phenotypes and in measuring natural selection on genes. Evolutionary ecology has been pursuing these objectives for decades, but they come into reach now that next generation sequencing technologies have dramatically lowered the costs to obtain the genomic sequence information that is currently lacking for most ecologically important species. Here we describe how we generated over 2 billion basepairs of novel sequence information for an ecological model species, the great tit Parus major. We used over 16 million short sequence reads for the de novo assembly of a reference sequence consisting of 550 000 contigs, covering 2.5% of the genome of the great tit. This reference sequence was used as the scaffold for mapping of the sequence reads, which allowed for the detection of over 20 000 novel single nucleotide polymorphisms. Contigs harbouring 4272 of the single nucleotide polymorphisms could be mapped to a unique location on the recently sequenced zebra finch genome. Of all the great tit contigs, significantly more were mapped to the microchromosomes than to the intermediate and the macrochromosomes of the zebra finch, indicating a higher overall level of sequence conservation on the microchromosomes than on the other types of chromosomes. The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines. [source] A basic study design for expedited safety signal evaluation based on electronic healthcare data,PHARMACOEPIDEMIOLOGY AND DRUG SAFETY, Issue 8 2010Sebastian Schneeweiss MD Abstract Active drug safety monitoring based on longitudinal electronic healthcare databases (a Sentinel System), as outlined in recent FDA-commissioned reports, consists of several interlocked processes, including signal generation, signal strengthening, and signal evaluation. Once a signal of a potential drug safety issue is generated, signal strengthening and signal evaluation have to follow in short sequence in order to quickly provide as much information about the triggering drug-event association as possible. This paper proposes a basic study design based on the incident user cohort design for expedited signal evaluation in longitudinal healthcare databases. It will not resolve all methodological issues nor will it fit all study questions arising within the framework of a Sentinel System. It should rather be seen as a guidance that will fit the majority of situations and serve as a starting point for adaptations to specific studies. Such an approach will expedite and structure the process of study development and highlight specific assumptions, which is particularly valuable in a Sentinel System where signals are by definition preliminary and evaluation of signals is time critical. Copyright © 2010 John Wiley & Sons, Ltd. [source] Functional analysis of synaptotagmin gene regulatory regions in two distantly related ascidian speciesDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 7 2008Jun Matsumoto We have studied the structure and function of a promoter region of the Halocynthia synaptotagmin (Hr-Syt) gene, which is abundantly expressed in neuronal cells. Our previous analysis suggested that the expression of Hr-Syt is regulated by at least one epidermal and two neuronal regulatory regions. In this study, the regulatory regions of Hr-Syt promoter were further characterized by using two species of ascidians, Halocynthia roretzi and Ciona intestinalis embryos. A putative GATA transcription factor binding site in the epidermal regulatory region has ectodermal enhancer activity in the Halocynthia embryo. Neuronal expression of Hr-Syt was regulated by multiple redundant enhancer regions. Among these enhancer regions, a 200-bp (,2900/,2700) region drove the reporter expression in neurons in both species of ascidian. Although the synaptotagmin promoter sequences did not show overall similarity between Hr-Syt and Ciona synaptotagmin (Ci-Syt), 5,-upsteream two short sequences of Ci-Syt have similarity to the ,2766/,2732 region of the Hr-Syt promoter. The homeodomain binding sites in this region are required for the neuronal enhancer activity. These results suggest that GATA and homeodomain transcription factors regulate the expression of synaptotagmin. [source] STABILITY AND EVOLUTION OF OVERLAPPING GENESEVOLUTION, Issue 3 2000David C. Krakauer Abstract., When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. Overlap is most common in rapidly evolving genomes with high mutation rates such as viruses, bacteria, and mitochondria. Overlap is thought to be important as: (1) a means of compressing a maximum amount of information into short sequences of structural genes; and (2) as a mechanism for regulating gene expression through translational coupling of functionally related polypeptides. The stability of overlapping codes is examined in relation to the information cost of overlap and the mutation rate of the genome. The degree of overlap in a given population will tend to become monomorphic. Evolution toward partial overlap of genes is shown to depend on a convex cost function of overlap. Overlap does not evolve when expression of overlapping genes is mutually exclusive and produced by rare mutations to the wild-type genome. Assuming overlap increases coupling between functionally related genes, the conditions favoring overlap are explored in relation to the kinetics of gene activation and decay. Coupling is most effective for genes in which the gene overlapping at its 5'end (leading gene) decays rapidly, while the gene overlapping at the 3'end (induced gene) decays slowly. If gene expression can feedback on itself (autocatalysis), then high rates of activation favor overlap. [source] Implementing quality control on a random number stream to improve a stochastic weather generator,,HYDROLOGICAL PROCESSES, Issue 8 2008Charles R. Meyer Abstract For decades, stochastic modellers have used computerized random number generators to produce random numeric sequences fitting a specified statistical distribution. Unfortunately, none of the random number generators we tested satisfactorily produced the target distribution. The result is generated distributions whose mean even diverges from the mean used to generate them, regardless of the length of run. Non-uniform distributions from short sequences of random numbers are a major problem in stochastic climate generation, because truly uniform distributions are required to produce the intended climate parameter distributions. In order to ensure generation of a representative climate with the stochastic weather generator CLIGEN within a 30-year run, we tested the climate output resulting from various random number generators. The resulting distributions of climate parameters showed significant departures from the target distributions in all cases. We traced this failure back to the uniform random number generators themselves. This paper proposes a quality control approach to select only those numbers that conform to the expected distribution being retained for subsequent use. The approach is based on goodness-of-fit analysis applied to the random numbers generated. Normally distributed deviates are further tested with confidence interval tests on their means and standard deviations. The positive effect of the new approach on the climate characteristics generated and the subsequent deterministic process-based hydrology and soil erosion modelling are illustrated for four climatologically diverse sites. Copyright © 2007 John Wiley & Sons, Ltd. [source] Fresh insights into long-term changes in flora, vegetation, land use and soil erosion in the karstic environment of the Burren, western IrelandJOURNAL OF ECOLOGY, Issue 5 2009Ingo Feeser Summary 1. ,The study focuses on species-rich, upland, heathy vegetation with arctic-alpine floristic affinities and Sesleria grasslands in the karstic Burren region, western Ireland. The investigations aimed at reconstructing the long-term development of these high conservation-value communities and the role of farming in their formation and long-term survival. 2. ,The methods used included pollen analysis and 14C-dating of short monoliths and investigation of grykes (fissures in karstic limestone) for evidence of soil erosion. Special attention was paid to fossil, coprophilous fungal spores as indicators of local grazing. The strong local character of the pollen records facilitated identification of inter-site differences as well as regional patterns. It is shown that open pine woodland characterized the Cappanawalla uplands between c. 1500 BC and 500 BC. It is proposed that such woodlands, with floristic affinities to Scandinavian open pine woodlands on calcareous soils, provided a suitable environment for the present-day, open heath vegetation with species such as Dryas octopetala, Arctostaphylos uva-ursi, Geranium sanguineum and Empetrum nigrum. 3. ,Burning of vegetation as a management tool was important in the uplands over most of the last two millennia. Firing seems to have ceased with the onset of more intensive grazing regimes in the 18th century. 4. ,Synthesis. Upland palaeoarchives, derived from shallow peaty deposits, show that the upland Burren supported mainly plagioclimax Corylus -dominated woody vegetation and grasslands from c. 1500 BC (beginning of present record), until possibly as late as the 17th century AD. In the uplands of the north-western Burren, open, species-rich pinewoods with hazel dominated. The northern-arctic elements in the present-day upland flora survived clearances, involving initially Pinus sylvestris (c. 500 BC) and subsequently Corylus avellana (c. AD 1600). Colluvial material retrieved from grykes supports the idea of considerable soil loss occurring as late as the first and early 2nd millennium AD. The investigations highlight the potential of upland palaeoarchives, consisting of short sequences, for elucidating vegetation and land-use dynamics in karstic environments such as the Burren. [source] BARCODING: Assessing the effect of varying sequence length on DNA barcoding of fungiMOLECULAR ECOLOGY RESOURCES, Issue 3 2007XIANG JIA MIN Abstract DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences , of various lengths , and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences (,600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi. [source] A minimalist barcode can identify a specimen whose DNA is degradedMOLECULAR ECOLOGY RESOURCES, Issue 4 2006MEHRDAD HAJIBABAEI Abstract A DNA barcode based on 650 bp of mitochondrial gene cytochrome c oxidase I is proving to be highly functional in species identification for various animal groups. However, DNA degradation complicates the recovery of a full-length barcode from many museum specimens. Here we explore the use of shorter barcode sequences for identification of such specimens. We recovered short sequences , i.e. ,100 bp , with a single PCR pass from more than 90% of the specimens in assemblages of moth and wasp museum specimens from which full barcode recovery was only 50%, and the latter were usually less than 8 years old. Short barcodes were effective in identifying specimens, confirming their utility in circumstances where full barcodes are too expensive to obtain and the identification comparisons are within a confined taxonomic group. [source] New short peptaibols from a marine Trichoderma strainRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2006Mustapha Mohamed-Benkada The production of peptaibols by a marine-related Trichoderma longibrachiatum strain was studied using electrospray ionisation multiple-stage ion trap mass spectrometry (ESI-MSn -IT) and gas chromatography/electron impact mass spectrometry (GC/EI-MS). Two major groups of peptaibols were identified, those with long sequences (20 amino acids) and others with short sequences (11 amino acids). This paper describes the methodology used to establish the sequences of short peptaibols in a mixture without previous individual separation. Nine peptaibols were identified. Among them, eight are new, namely as trichobrachin A I,IV (Aib9 -Pro10 sequence) and as trichobrachin B I,IV (Val9 -Pro10 sequence). Original Pro6 -Val7 and Val9 -Pro10 sequences have to be noted. Copyright © 2006 John Wiley & Sons, Ltd. [source] Structure of human TSG101 UEV domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2006Pedro L. Mateo The UEV domain of the TSG101 protein functions in the vacuolar protein-sorting pathway and in the budding process of HIV-1 and other retroviruses by recognizing ubiquitin in proteins tagged for degradation and short sequences in viral proteins containing an essential and well conserved PTAP motif, respectively. A deep understanding of these interactions is key to the rational design of much-needed novel antivirals. Here, the crystal structure of the TSG101 UEV domain (TSG101-UEV) is presented. TSG101-UEV was crystallized in the presence of PEG 4000 and ammonium sulfate. Under these conditions, crystals were obtained in space group R3, with unit-cell parameters a = b = 97.9, c = 110.6,Å, , = , = 90, , = 120°. Phases were solved by molecular replacement and the crystal structure of TSG101-UEV was refined to an R factor of 18.8% at 2.2,Å resolution. A comparison between the crystal structure and previously reported NMR structures has revealed significant differences in the conformation of one of the loops implicated in ubiquitin recognition. Also, the resulting structure has provided information about the presence of water molecules at the binding interface that could be of relevance for peptide recognition. [source] | |||||||||||||