bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide SNP detection in the great titParus majorusing high throughput sequencing
Authors: BERS NIKKIE E. M. VAN , OERS KEES VAN , KERSTENS HINDRIK H. D. , DIBBITS BERT W. , CROOIJMANS RICHARD P. M. A. , VISSER MARCEL E. , GROENEN MARTIEN A. M. 
Published: February 2010

AbstractIdentifying 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 titParus major.We used over 16 million short sequence reads for thede novoassembly 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.
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
Authors: KÜNSTNER AXEL , WOLF JOCHEN B. W. , BACKSTRÖM NICLAS , WHITNEY OSCEOLA , BALAKRISHNAN CHRISTOPHER N. , DAY LAINY , EDWARDS SCOTT V. , JANES DANIEL E. , SCHLINGER BARNEY A. , WILSON RICHARD K. , JARVIS ERICH D. , WARREN WESLEY C. , ELLEGREN HANS 
Published: February 2010

AbstractNext‐generation sequencing technology provides an attractive means to obtain large‐scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non‐model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with ∼1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male‐biased mutation) and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill–Robertson effect (the effect of selection at linked loci) and point at stochastic problems with ω as an independent measure of selection. Overall, this study demonstrates the usefulness of next‐generation sequencing for obtaining genomic resources for comparative genomic analysis of non‐model organisms.
Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
Authors: ELMER K. R. , FAN S. , GUNTER H. M. , JONES J. C. , BOEKHOFF S. , KURAKU S. , MEYER A. 
Published: February 2010

AbstractCrater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next‐generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthicAmphilophus astorquiiand limneticAmphilophus zaliosus. We obtained 24 174A. astorquiiand 21 382A. zaliosushigh‐quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (Ka/Ks > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based onKs ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10−6per site per year. We conclude that next‐generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.
Genome‐wide analysis of alternative splicing evolution among Mus subspecies
Authors: HARR BETTINA , TURNER LESLIE M. 
Published: February 2010

AbstractAlternative splicing, the combination of different exons to produce a variety of transcripts from a single gene, contributes enormously to transcriptome diversity in mammals, and the majority of genes encode alternatively spliced products. Previous research comparing mouse, rat and human has shown that a significant proportion of splice forms are not conserved across species, suggesting that alternative transcripts are an important source of evolutionary novelty. Here, we studied the evolution of alternative splicing in the early stages of species divergence in the house mouse. We sequenced the testis transcriptomes of three Mus musculus subspecies and Mus spretus using Illumina technology. On the basis of a genome‐wide analysis of read coverage differences among subspecies, we identified several hundred candidate alternatively spliced regions. We conservatively estimate that 6.5% of testis‐expressed genes show alternative splice differences between at least one pair of M. musculus subspecies, a proportion slightly higher than the proportion of genes differentially expressed among subspecies. These results suggest that differences in both the structure and abundance of transcripts contribute to early transcriptome divergence.
On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs
Authors: SANTURE ANNA W. , STAPLEY JESSICA , BALL ALEXANDER D. , BIRKHEAD TIM R. , BURKE TERRY , SLATE JON 
Published: February 2010

AbstractIn recent years there has been a dramatic increase in the availability of high density genetic marker data for both model and non‐model organisms. A potential application of these data is to infer relatedness in the absence of a complete pedigree. Using a marker panel of 771 SNPs genotyped in three generations of an extensive zebra finch pedigree, correlations between pedigree relatedness and seven marker‐based estimates of relatedness were examined, as was the relationship between heterozygosity and inbreeding. Although marker‐based and pedigree relatedness were highly correlated, the variance in estimated relatedness was high. Further, the correlation between heterozygosity and inbreeding was weak, even though mean inbreeding coefficient is typical of that seen in wild vertebrate pedigrees; the weak relationship was in part due to the small variance in inbreeding in the pedigree. Our data suggest that using marker information to reconstruct the pedigree, and then calculating relatedness from the pedigree, is likely to give more accurate relatedness estimates than using marker‐based estimators directly.
The earliest stages of adaptation in an experimental plant population: strong selection on QTLS for seed dormancy
Authors: HUANG XUEQING , SCHMITT JOHANNA , DORN LISA , GRIFFITH CONVERSE , EFFGEN SIGI , TAKAO SHAUN , KOORNNEEF MAARTEN , DONOHUE KATHLEEN 
Published: February 2010

AbstractColonizing species may often encounter strong selection during the initial stages of adaptation to novel environments. Such selection is particularly likely to act on traits expressed early in development since early survival is necessary for the expression of adaptive phenotypes later in life. Genetic studies of fitness under field conditions, however, seldom include the earliest developmental stages. Using a new set of recombinant inbred lines, we present a study of the genetic basis of fitness variation in Arabidopsis thaliana in which genotypes, environments, and geographic location were manipulated to study total lifetime fitness, beginning with the seed stage. Large‐effect quantitative trait loci (QTLs) for fitness changed allele frequency and closely approached 90% in some treatments within a single generation. These QTLs colocated with QTLs for germination phenology when seeds were dispersed following a schedule of a typical winter annual, and they were detected in two geographic locations at different latitudes. Epistatically interacting loci affected both fitness and germination in many cases. QTLs for field germination phenology colocated with known QTLs for primary dormancy induction as assessed in laboratory tests, including the candidate genes DOG1 and DOG6. Therefore fitness, germination phenology, and primary dormancy are genetically associated at the level of specific chromosomal regions and candidate loci. Genes associated with the ability to arrest development at early life stages and assess environmental conditions are thereby likely targets of intense natural selection early in the colonization process.
Distinct subcellular localization in the cytosol and apicoplast, unexpected dimerization and inhibition of Plasmodium falciparum glyoxalases
Authors: Urscher Miriam , Przyborski Jude M. , Imoto Masaya , Deponte Marcel 
Published: February 2010

SummaryThe ubiquitous glyoxalase system removes methylglyoxal as a harmful by‐product of glycolysis. Because malaria parasites have drastically increased glycolytic fluxes, they could be highly susceptible to the inhibition of this detoxification pathway. Here we analysed the intracellular localization, oligomerization and inhibition of the glyoxalases from Plasmodium falciparum. Glyoxalase I (GloI) and one of the two glyoxalases II (cGloII) were located in the cytosol of the blood stages. The second glyoxalase II (tGloII) was detected in the apicoplast pointing to alternative metabolic pathways. Using a variety of methods, cGloII was found to exist in a monomer–dimer equilibrium that might have been overlooked for homologues from other organisms and that could be of physiological importance. The compounds methyl‐gerfelin and curcumin, which were previously shown to inhibit mammalian GloI, also inhibited P. falciparum GloI. Inhibition patterns were predominantly competitive but were complicated because of the two different active sites of the enzyme. This effect was neglected in previous inhibition studies of monomeric glyoxalases I, with consequences for the interpretation of inhibition constants. In summary, the present work reveals novel general glyoxalase properties that future research can build on and provides a significant advance in characterizing the glyoxalase system from P. falciparum.
Estimating Z‐ring radius and contraction in dividing Escherichia coli
Authors: Strömqvist Johan , Skoog Karl , Daley Daniel O. , Widengren Jerker , Von Heijne Gunnar 
Published: February 2010

SummaryWe present a fluorescence recovery after photobleaching‐based method for monitoring the progression of septal Z‐ring contraction in dividing Escherichia coli cells. In a large number of cells undergoing division, we irreversibly bleached cytosolically expressed Enhanced Green Fluorescent Protein on one side of the septal invagination and followed the fluorescence relaxation on both sides of the septum. Since the relaxation time depends on the cross‐sectional area of the septum, it can be used to determine the septal radius r. Assuming that the fraction of the observed cells with r‐values in a given interval reflects the duration of that interval in the division process we could derive an approximate time‐course for the contraction event, as a population average. By applying the method repeatedly on individual cells, the contraction process was also followed in real time. On a population average level, our data are best described by a linear contraction process in time. However, on the single cell level the contraction processes display a complex behaviour, with varying levels of activity. The proposed approach provides a simple yet versatile method for studying Z‐ring contraction in vivo, and will help to elucidate its underlying mechanisms.
Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function
Authors: Bowman Grant R. , Comolli Luis R. , Gaietta Guido M. , Fero Michael , Hong Sun‐Hae , Jones Ying , Lee Julie H. , Downing Kenneth H. , Ellisman Mark H. , McAdams Harley H. , Shapiro Lucy 
Published: February 2010

SummaryThe bacterium Caulobacter crescentus has morphologically and functionally distinct cell poles that undergo sequential changes during the cell cycle. We show that the PopZ oligomeric network forms polar ribosome exclusion zones that change function during cell cycle progression. The parS/ParB chromosomal centromere is tethered to PopZ at one pole prior to the initiation of DNA replication. During polar maturation, the PopZ‐centromere tether is broken, and the PopZ zone at that pole then switches function to act as a recruitment factor for the ordered addition of multiple proteins that promote the transformation of the flagellated pole into a stalked pole. Stalked pole assembly, in turn, triggers the initiation of chromosome replication, which signals the formation of a new PopZ zone at the opposite cell pole, where it functions to anchor the newly duplicated centromere that has traversed the long axis of the cell. We propose that pole‐specific control of PopZ function co‐ordinates polar development and cell cycle progression by enabling independent assembly and tethering activities at the two cell poles.
AglP is a S‐adenosyl‐L‐methionine‐dependent methyltransferase that participates in the N‐glycosylation pathway of Haloferax volcanii
Authors: Magidovich Hilla , Yurist‐Doutsch Sophie , Konrad Zvia , Ventura Valeria V. , Dell Anne , Hitchen Paul G. , Eichler Jerry 
Published: February 2010

SummaryWhile pathways for N‐glycosylation in Eukarya and Bacteria have been solved, considerably less is known of this post‐translational modification in Archaea. In the halophilic archaeon Haloferax volcanii, proteins encoded by the agl genes are involved in the assembly and attachment of a pentasaccharide to select asparagine residues of the S‐layer glycoprotein. AglP, originally identified based on the proximity of its encoding gene to other agl genes whose products were shown to participate in N‐glycosylation, was proposed, based on sequence homology, to serve as a methyltransferase. In the present report, gene deletion and mass spectrometry were employed to reveal that AglP is responsible for adding a 14 Da moiety to a hexuronic acid found at position four of the pentasaccharide decorating the Hfx. volcanii S‐layer glycoprotein. Subsequent purification of a tagged version of AglP and development of an in vitro assay to test the function of the protein confirmed that AglP is a S‐adenosyl‐L‐methionine‐dependent methyltransferase.
Development of Melaleuca oils as effective natural‐based personal insect repellents
Authors: Greive Kerryn A , Staton John A , Miller Peter F , Peters Bryce A , Oppenheim V M Jane 
Published: February 2010

AbstractFor many decades effective insect repellents have relied on synthetic actives such as N,N‐diethyl‐meta‐toluamide. Increasingly, consumers are seeking natural‐based alternatives to many everyday products including insect repellents. While many studies have been published detailing the potential of essential oils to act as insect repellents, few oils have been identified as viable alternatives to synthetic actives. This study details the process involved in the selection of Australian essential oils effective as repellents and the subsequent testing of natural‐based insect repellents using the selected oils. Using a combination of laboratory‐based and field‐based testing, oil from Melaleuca ericifolia was identified as being an effective insect repellent. When formulated into three different bases: an alcohol‐based spray, an emulsion and a gel, these Melaleuca‐based repellents were shown to be as effective at repelling mosquitoes Aedes vigilax (Skuse) (Diptera: Culicidae) and Verrallina carmenti (Edwards) (Diptera: Culicidae), the bush fly Musca vetustissima (Walker) (Diptera: Muscidae), and biting midges Culicoides ornatus (Taylor) (Diptera: Ceratopogonidae) and Culicoides immaculatus (Lee & Reye) (Diptera: Ceratopogonidae) as a synthetic‐based commercial repellent. This study has shown that effective insect repellents based on natural active ingredients can deliver repellency on par with synthetic actives in the field. Three Melaleuca‐based formulations have been registered as repellents and are now commercially available.
Life history traits and foraging behaviour of Cotesia nonagriae (Olliff) (Hymenoptera: Braconidae), a newly recognised member of the Cotesia flavipes complex of stemborer parasitoids
Authors: Muirhead Kate A , Sallam Nader , Austin Andrew D 
Published: February 2010

Abstract Cotesia nonagriae (Olliff) from Australia, a parasitoid of the incidental native pest of sugarcane, Bathytricha truncata (Walker) (Lepidoptera: Noctuidae), was previously thought to be a synonym of Cotesia flavipes Cameron. However, recent studies using DNA sequences, morphology and preliminary biological information show that this parasitoid is clearly a different species than C. flavipes and other members of the species complex. Here we further examine differences in the biology of these species by undertaking a detailed study of the life history traits of C. nonagriae, including adult longevity and the potential and realised fecundity of females. In addition, the influence of learning on microhabitat location and foraging behaviour were investigated. Duration of the larval stages and adult longevity of C. nonagriae were longer than previously recorded for other members of the species complex. The potential fecundity of females was similar to C. flavipes (∼200 eggs); however, C. nonagriae oviposited a average of over 100 eggs into each host, almost three times more than for other species in the C. flavipes complex (30–40). The propensity of C. nonagriae to allocate a large number of eggs to each host may be an evolutionary strategy due to the high mortality rate (50–57%) of ovipositing adult wasps. During microhabitat location, both naïve and experienced females demonstrated a strong response towards the plant host complex, with experienced wasps benefiting by having a more rapid response time to host‐induced volatiles and cues.
Predicting the probability of significant prostate cancer in Japanese men with serum prostate‐specific antigen less than 10 ng/mL: Development of a novel pre‐biopsy nomogram
Authors: Ohigashi Takashi , Kanao Kent , Mizuno Ryuichi , Kikuchi Eiji , Nakashima June , Oya Mototsugu 
Published: February 2010

Objectives:  To develop and assess a new nomogram incorporating pre‐biopsy clinical data to predict significant prostate cancer in Japanese men with a serum prostate‐specific antigen (PSA) level of less than 10 ng/mL.Methods:  We collected pre‐biopsy data from 620 men with a serum total PSA of less than 10 ng/mL. They included 491 men with a negative biopsy and 129 men who were confirmed to have histological prostate cancer and subsequently underwent radical prostatectomy. Clinically significant tumors were defined as those with a tumor volume larger than 0.5 mL and/or a Gleason score of 7 or more.Results:  One hundred and seven prostatectomy patients had clinically significant cancers. Stepwise multivariate logistic regression analysis showed that digital rectal examination findings, PSA adjusted for transition zone volume and free‐to‐total PSA ratio were the significant independent predictors of significant cancers (P < 0.0001). Using these pre‐biopsy independent factors, a nomogram was developed to predict significant cancers. According to a receiver operating characteristics analysis, the nomogram showed an area under the curve of 0.831.Conclusion:  This represents the first nomogram to predict the probability of clinically significant cancers before biopsy. This tool is most likely to be useful in the management of patients with moderate to elevated PSA.
Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’‐enriched enhanced biological phosphorus removal sludge
Authors: He Shaomei , Kunin Victor , Haynes Matthew , Martin Hector Garcia , Ivanova Natalia , Rohwer Forest , Hugenholtz Philip , McMahon Katherine D. 
Published: February 2010

SummaryHere we report the first metatranscriptomic analysis of gene expression and regulation of ‘Candidatus Accumulibacter’‐enriched lab‐scale sludge during enhanced biological phosphorus removal (EBPR). Medium density oligonucleotide microarrays were generated with probes targeting most predicted genes hypothesized to be important for the EBPR phenotype. RNA samples were collected at the early stage of anaerobic and aerobic phases (15 min after acetate addition and switching to aeration respectively). We detected the expression of a number of genes involved in the carbon and phosphate metabolisms, as proposed by EBPR models (e.g. polyhydroxyalkanoate synthesis, a split TCA cycle through methylmalonyl‐CoA pathway, and polyphosphate formation), as well as novel genes discovered through metagenomic analysis. The comparison between the early stage anaerobic and aerobic gene expression profiles showed that expression levels of most genes were not significantly different between the two stages. The majority of upregulated genes in the aerobic sample are predicted to encode functions such as transcription, translation and protein translocation, reflecting the rapid growth phase of Accumulibacter shortly after being switched to aerobic conditions. Components of the TCA cycle and machinery involved in ATP synthesis were also upregulated during the early aerobic phase. These findings support the predictions of EBPR metabolic models that the oxidation of intracellularly stored carbon polymers through the TCA cycle provides ATP for cell growth when oxygen becomes available. Nitrous oxide reductase was among the very few Accumulibacter genes upregulated in the anaerobic sample, suggesting that its expression is likely induced by the deprivation of oxygen.