bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating nitrogen uptake of individual roots in container- and field-grown plants using a 15N-depletion approach
Authors: Volder Astrid , Anderson Laurel J. , Smart David R. , Bloom Arnold J. , Lakso Alan N. , Eissenstat David M.
Published: July 2009

We only have a limited understanding of the nutrient uptake physiology of individual roots as they age. Despite this shortcoming, the importance of nutrient uptake processes to our understanding of plant nutrition and nutrient cycling cannot be underestimated. In this study, we used a 15N depletion method that allowed for the measurement of nitrate-N uptake rates on intact, individual, fine roots of known age. We expected that N uptake would decline rapidly as fine roots aged, regardless of the environmental conditions and species used. We compared age dependent uptake patterns of young grape cuttings with those of mature vines and with those of tomato. Although patterns of declining uptake with increasing root age were similar for all species and conditions tested, large differences in maximum N uptake rates existed between young cuttings and mature vines, and between woody and herbaceous species. Maximum rates were 10-fold higher for tomato and 3-fold higher for the grape cuttings, when compared with uptake rates of fine roots of mature vines. Coefficients of variation ranged from 43 to 122% within root age groups. The large variability in physiological characteristics of fine roots of the same age, diameter and order suggests that there is a functional diversity within fine roots that is still poorly understood.
Phospholipase D family interactions with the cytoskeleton: isoform delta promotes plasma membrane anchoring of cortical microtubules
Authors: Andreeva Zornitza , Ho Angela Y. Y. , Barthet Michelle M. , Potocký Martin , Bezvoda Radek , Žárský Viktor , Marc Jan
Published: July 2009

Phospholipase D (PLD) is a key enzyme in signal transduction – mediating plant responses to various environmental stresses including drought and salinity. Isotype PLDδ interacts with the microtubule cytoskeleton, although it is unclear if, or how, each of the 12 PLD isotypes in Arabidopsis may be involved mechanistically. We employed RNA interference in epidermal cells of Allium porrum L. (leek) leaves, in which the developmental reorientation of cortical microtubule arrays to a longitudinal direction is highly sensitive to experimental manipulation. Using particle bombardment and transient transformation with synthetic siRNAs targeting AtPLDα, β, γ, δ, ॉ and ζ, we examined the effect of ‘cross-target’ silencing orthologous A. porrum genes on microtubule reorientation dynamics during cell elongation. Co-transformation of individual siRNAs together with a GFP-MBD microtubule-reporter gene revealed that siRNAs targeting AtPLDδ promoted, whereas siRNAs targeting AtPLDβ and γ reduced, longitudinal microtubule orientation in A. porrum. These PLD isotypes, therefore, interact, directly or indirectly, with the cytoskeleton and the microtubule-plasma membrane interface. The unique response of PLDδ to silencing, along with its exclusive localisation to the plasma membrane, indicates that this isotype is specifically involved in promoting microtubule-membrane anchorage.
Epigenetic modifications and related mRNA expression during bovine oocyte in vitro maturation
Authors: Racedo S. E. , Wrenzycki C. , Lepikhov K. , Salamone D. , Walter J. , Niemann H.
Published: July 2009

The present study investigated the global pattern of two histone modifications and methylation of DNA during in vitro maturation of bovine oocytes retrieved from follicles of two different sizes (<2 mm and 2–8 mm). The methylation status of histone H3 at position lysine K9 (H3K9 me2), the acetylation status of histone H4 at position lysine K12 (H4K12ac) and the methylation of DNA were assessed by immunocytochemistry. In parallel, the relative abundance of mRNAs coding for proteins specifically involved in reprogramming, including HLA-B associated transcript 8 (G9A), suppressor of variegation 3-9 homolog 1 (SUV39H1), the somatic isoform of DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3b (DNMT3b) and zygote arrest 1 (ZAR1) was determined by RT-PCR. The α-H3K9 me2 signal was present in the GV stage and remained detectable until the end of the maturation period. α-H4K12ac antibody gave a stronger signal in GV and GVBD oocytes and markedly decreased after GVBD. The signal showing the methylation of DNA was present during the entire maturation period. The five transcripts showed a gene-specific expression profile. Results revealed the global patterns of H3K9 me2, H4K12ac, DNA methylation and the mRNA pool profiles of genes critically involved in epigenetic modifications during bovine oocyte maturation and their possible relationship with the acquisition of oocyte developmental competence and follicular development.
DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I
Authors: Whittle Christina M. , Lazakovitch Elena , Gronostajski Richard M. , Lieb Jason D.
Published: July 2009

The conserved nuclear factor I (NFI) family of transcription factors is unique to animals and essential for mammalian development. The
Caenorhabditis elegans
genome encodes a single NFI family member, whereas vertebrate genomes encode 4 distinct NFI protein subtypes (A, B, C, and X). NFI-1-deficient worms exhibit abnormalities, including reduced lifespan, defects in movement and pharyngeal pumping, and delayed egg-laying. To explore the functional basis of these phenotypes, we sought to comprehensively identify NFI-1-bound loci in
C. elegans
. We first established NFI-1 DNA-binding specificity using an in vitro DNA-selection strategy. Analysis yielded a consensus motif of TTGGCA(N)
3
TGCCAA, which occurs 586 times in the genome, a 100-fold higher frequency than expected. We next asked which sites were occupied by NFI-1 in vivo by performing chromatin immunoprecipitation of NFI-1 followed by microarray hybridization. Only 55 genomic locations were identified, an unexpectedly small target set. In vivo NFI-1 binding sites tend to be upstream of genes involved in core cellular processes, such as chromatin remodeling, mRNA splicing, and translation. Remarkably, 59 out of 70 (84%) of the
C. briggsae
orthologs of the identified targets contain conserved NFI binding sites in their promoters. These experiments provide a foundation for understanding how NFI-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif.
Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein
Authors: Davidson Amy , Leeper Thomas C. , Athanassiou Zafiria , Patora-Komisarska Krystyna , Karn Jonathan , Robinson John A. , Varani Gabriele
Published: July 2009

The interaction of the HIV-1 transactivator protein Tat with its transactivation response (TAR) RNA is an essential step in viral replication and therefore an attractive target for developing antivirals with new mechanisms of action. Numerous compounds that bind to the 3-nt bulge responsible for binding Tat have been identified in the past, but none of these molecules had sufficient potency to warrant pharmaceutical development. We have discovered conformationally-constrained cyclic peptide mimetics of Tat that are specific nM inhibitors of the Tat-TAR interaction by using a structure-based approach. The lead peptides are nearly as active as the antiviral drug nevirapine against a variety of clinical isolates in human lymphocytes. The NMR structure of a peptide–RNA complex reveals that these molecules interfere with the recruitment to TAR of both Tat and the essential cellular cofactor transcription elongation factor-b (P-TEFb) by binding simultaneously at the RNA bulge and apical loop, forming an unusually deep pocket. This structure illustrates additional principles in RNA recognition: RNA-binding molecules can achieve specificity by interacting simultaneously with multiple secondary structure elements and by inducing the formation of deep binding pockets in their targets. It also provides insight into the P-TEFb binding site and a rational basis for optimizing the promising antiviral activity observed for these cyclic peptides.
Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
Authors: Chung Hoi Sung , Louis John M. , Eaton William A.
Published: July 2009

Transition paths are a uniquely single-molecule property not yet observed for any molecular process in solution. The duration of transition paths is the tiny fraction of the time in an equilibrium single-molecule trajectory when the process actually happens. Here, we report the determination of an upper bound for the transition path time for protein folding from photon-by-photon trajectories. FRET trajectories were measured on single molecules of the dye-labeled, 56-residue 2-state protein GB1, immobilized on a glass surface via a biotin-streptavidin-biotin linkage. Characterization of individual emitted photons by their wavelength, polarization, and absolute and relative time of arrival after picosecond excitation allowed the determination of distributions of FRET efficiencies, donor and acceptor lifetimes, steady state polarizations, and waiting times in the folded and unfolded states. Comparison with the results for freely diffusing molecules showed that immobilization has no detectable effect on the structure or dynamics of the unfolded protein and only a small effect on the folding/unfolding kinetics. Analysis of the photon-by-photon trajectories yields a transition path time <200 μs, >10,000 times shorter than the mean waiting time in the unfolded state (the inverse of the folding rate coefficient). Szabo's theory for diffusive transition paths shows that this upper bound for the transition path time is consistent with previous estimates of the Kramers preexponential factor for the rate coefficient, and predicts that the transition path time is remarkably insensitive to the folding rate, with only a 2-fold difference for rate coefficients that differ by 10
5
-fold.
Genetic identification of putative remains of the famous astronomer Nicolaus Copernicus
Authors: Bogdanowicz Wiesław , Allen Marie , Branicki Wojciech , Lembring Maria , Gajewska Marta , Kupiec Tomasz
Published: July 2009

We report the results of mitochondrial and nuclear DNA analyses of skeletal remains exhumed in 2005 at Frombork Cathedral in Poland, that are thought to be those of Nicolaus Copernicus (1473–1543). The analyzed bone remains were found close to the altar Nicolaus Copernicus was responsible for during his tenure as priest. The mitochondrial DNA (mtDNA) profiles from 3 upper molars and the femurs were identical, suggesting that the remains originate from the same individual. Identical mtDNA profiles were also determined in 2 hairs discovered in a calendar now exhibited at Museum Gustavianum in Uppsala, Sweden. This calendar was the property of Nicolaus Copernicus for much of his life. These findings, together with anthropological data, support the identification of the human remains found in Frombork Cathedral as those of Nicolaus Copernicus. Up-to-now the particular mtDNA haplotype has been observed only 3 times in Germany and once in Denmark. Moreover, Y-chromosomal and autosomal short tandem repeat markers were analyzed in one of the tooth samples, that was much better preserved than other parts of the skeleton. Molecular sex determination revealed that the skeleton is from a male individual, and this result is consistent with morphological investigations. The minimal Y-chromosomal haplotype determined in the putative remains of Nicolaus Copernicus has been observed previously in many countries, including Austria, Germany, Poland, and the Czech Republic. Finally, an analysis of the SNP located in the
HERC2
gene revealed the C/C genotype that is predominant in blue-eyed humans, suggesting that Copernicus may have had a light iris color.
Concerted proton-coupled electron transfers in aquo/hydroxo/oxo metal complexes: Electrochemistry of [Os
II
(bpy)
2
py(OH
2
)]
2+
in water
Authors: Costentin Cyrille , Robert Marc , Savéant Jean-Michel , Teillout Anne-Lucie
Published: July 2009

Kinetic analysis of the successive oxidative cyclic voltammetric responses of [Os
II
(bpy)
2
py(OH
2
)]
2+
in buffered water, together with determination of H/D isotope effects, has allowed the determination of the mechanisms of the successive proton-coupled electron transfers that convert the Os
II
-aquo complex into the Os
III
-hydroxo complex and the later into the Os
IV
-oxo complex. The stepwise pathways prevail over the concerted pathway in the first case. However, very large concentrations of a base, such as acetate, trigger the beginning of a concerted reaction. The same trend appears, but to a much larger extent, when high local concentration of carboxylates are attached close to the Os complex. The Os
III
-hydroxo/Os
IV
-oxo couple is globally much slower and concerted pathways predominate over the stepwise pathways. Water is, however, not an appropriate proton acceptor in this respect. Other bases, such as citrate or phosphate, are instead quite effective for triggering concerted pathways. Here, we suggest factors causing these contrasting behaviors, providing a practical illustration of the prediction that concerted processes are an efficient way of avoiding high-energy intermediates. Observation of a strong decelerating effect of inactive ions together with the positive role of high local concentrations of carboxylates to initiate a concerted route underscores the variety of structural and medium factors that may operate to modulate and control the occurrence of concerted pathways. These demonstrations and analyses of the occurrence of concerted pathways in an aquo–hydroxo–oxo series are expected to serve as guidelines for studies in term of methodology and factor analysis.
Importance of collisions with the main plasma components for impurity anomalous transport
Authors: Moradi S. , Tokar M.Z. , Singh R. , Weyssow B.
Published: July 2009

The problem of impurity transport in fusion plasmas is of extraordinary importance and has been intensively studied for a long time. Nevertheless the experimentally found behaviour of impurity transport characteristics, such as diffusivity and pinch-velocity and, in particular, their dependence on the impurity ion charge, Z, has not been completely understood yet. In this paper the model for the impurity anomalous transport is developed further by taking into account the effects of impurity ion collisions with the main plasma components which become more and more important with increasing impurity charge. In linearized transport equations these effects are included as friction, thermal forces and collision energy exchange, affecting the perturbations of impurity ion parallel velocity and temperature, correspondingly. New terms can provide significant Z-dependence of the impurity anomalous convection and the density peaking factor. A numerical assessment is done for plasma parameters typical in the tokamak JET, with anomalous transport due to the ion temperature gradient/trapped electron unstable modes.
Identification of distant family relationships
Authors: Skare Øivind , Sheehan Nuala , Egeland Thore
Published: July 2009

Motivation: Family relationships can be estimated from DNA marker data. Applications arise in a large number of areas including evolution and conservation research, genealogical research in human, plant and animal populations, forensic problems and genetic mapping via linkage and association analyses. Traditionally, likelihood-based approaches to relationship estimation have used unlinked genetic markers. Due to the fact that some relationships cannot be distinguished from data at unlinked markers, and given the limited number of such markers available, there are considerable constraints on the type of identification problem that can be satisfactorily addressed with such approaches. The aim of this article is to explore the potential of linked autosomal single nucleotide polymorphism markers in this context. Throughout, we will view the problem of relationship estimation as one of pedigree identification rather than identity-by-descent, and thus focus on applications where determination of the exact relationship is important.

Results: We show that the increase in information obtained by exploiting large sets of linked markers substantially increases the number of problems that can be solved. Results are presented based on simulations as well as on real data.

Availability: The R library FEST is freely available from http://folk.uio.no/thoree/FEST.

Contact:  thore.egeland@medisin.uio.no

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evidence for human microRNA-offset RNAs in small RNA sequencing data
Authors: Langenberger David , Bermudez-Santana Clara , Hertel Jana , Hoffmann Steve , Khaitovich Philipp , Stadler Peter F.
Published: July 2009

MicroRNA-offset-RNAs (moRNAs) were recently detected as highly abundant class of small RNAs in a basal chordate. Using short read sequencing data, we show here that moRNAs are also produced from human microRNA precursors, albeit at quite low expression levels. The expression levels of moRNAs are unrelated to those of the associated microRNAs. Surprisingly, microRNA precursors that also show moRNAs are typically evolutionarily old, comprising more than half of the microRNA families that were present in early Bilateria, while evidence for moRNAs was found only for a relative small fraction of microRNA families of recent origin.

Contact:  studla@bioinf.uni-leipzig.de

Supplementary information:  Supplementary data are available at Bioinformatics online and in machine-readable form at http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/09-015/
Maternal Baicalin Treatment Increases Fetal Lung Surfactant Phospholipids in Rats
Authors: Chen Chung-Ming , Wang Leng-Fang , Cheng Kur-Ta
Published: July 2009

Baicalin is a flavonoid compound purified from the medicinal plant Scutellaria baicalensis Georgi and has been reported to stimulate surfactant protein (SP)‐A gene expression in human lung epithelial cell lines (H441). The aims of this study were to determine whether maternal baicalin treatment could increase lung surfactant production and induce lung maturation in fetal rats. This study was performed with timed pregnant Sprague‐Dawley rats. One‐day baicalin group mothers were injected intraperitoneally with baicalin (5 mg/kg/day) on Day 18 of gestation. Two‐day baicalin group mothers were injected intraperitoneally with baicalin (5 mg/kg/day) on Days 17 and 18 of gestation. Control group mothers were injected with vehicle alone on Day 18 of gestation. On Day 19 of gestation, fetuses were delivered by cesarean section. Maternal treatment with 2‐day baicalin significantly increased saturated phospholipid when compared with control group and total phospholipid in fetal lung tissue when compared with control and 1‐day baicalin groups. Antenatal treatment with 2‐day baicalin significantly increased maternal growth hormone when compared with control group. Fetal lung SP‐A mRNA expression and maternal serum corticosterone levels were comparable among the three experimental groups. Maternal baicalin treatment increases pulmonary surfactant phospholipids of fetal rat lungs and the improvement was associated with increased maternal serum growth hormone. These results suggest that antenatal baicalin treatment might accelerate fetal rat lung maturation.
Bottom temperature and in situ development of chokka squid eggs (Loligo vulgaris reynaudii) on mid-shelf spawning grounds, South Africa
Authors: Oosthuizen Anè , Roberts Mike J.
Published: July 2009

Oosthuizen, A., and Roberts, M. J. 2009. Bottom temperature and in situ development of chokka squid eggs (Loligo vulgaris reynaudii) on mid-shelf spawning grounds, South Africa. – ICES Journal of Marine Science, 66: 1967–1971. The aim of the study was to test the development success of squid eggs on the mid-shelf (60–150 m deep) spawning grounds in relation to previous laboratory results, and to describe the mid-shelf temperature environment and how it could affect egg development. A series of in situ egg incubation experiments was conducted on the mid-shelf (∼119 m deep) spawning grounds using cages, temperature sensors, and acoustic releases for retrieval. Newly spawned eggs were collected by scuba, and continuous temperature data were collected at two points between the known inshore spawning grounds and the mid-shelf areas. Temperature variations followed a seasonal warming and cooling cycle, with superimposed peaks and troughs. Egg development data indicated that warm temperature peaks (10–13°C) are sufficient for normal development of eggs on the mid-shelf. Egg development time on the mid-shelf was 2–3 times longer (50–60 vs. 20–30 d) than inshore. The scarcity of abnormalities (0.45%) disputes previous laboratory results that suggested that ∼50% of eggs would suffer abnormalities in the colder mid-shelf temperature environment.
Cross‐Sectional Staining and Surface Properties of DDGS Particles and Their Influence on Flowability
Authors: Bhadra Rumela , Rosentrater Kurt A. , Muthukumarappan K.
Published: July 2009

With the U.S. fuel ethanol industry projected to grow during the next several years, supplies of distillers dried grains with solubles (DDGS) are anticipated to continue to grow as well. DDGS is used primarily as livestock feed. Much of the DDGS must be shipped, often over large distances, outside the Corn Belt (which is where most of the corn‐based ethanol plants are currently located). Stickiness and caking among particles is a common issue for DDGS, and it often leads to flowability problems. To address this, the objective of this study was to understand the cross‐sectional and surface natures of DDGS particles from five ethanol plants, and how they interact with DDGS properties. This study examined the distribution patterns of chemical components within cross‐sections, within section edges (i.e., surface layers), and on surfaces using standard staining techniques; chemical composition was determined using standard protocols; and physical and flowability properties were also determined. Crude protein in the samples was 28.33–30.65% db, crude fat was 9.40–10.98% db, and neutral detergent fiber (NDF) was 31.84–39.90% db. Moisture contents were 4.61–8.08% db, and geometric mean diameters were 0.37–0.52 mm. Cross‐sectional staining showed protein levels of 19.57–40.39%, and carbohydrate levels of 22.17–43.06%, depending on the particle size examined and the production plant from which the DDGS was sampled. Staining of DDGS particles indicated a higher amount of surface layer protein compared with carbohydrate thickness in DDGS particles that had a lower flow function index (which indicated potential flow issues). Additionally, surface fat staining suggested that higher surface fat also occurred in samples with worse flow problems. This study represents another step toward understanding why DDGS particles stick together during storage and transport, and will hopefully help to improve DDGS material handling strategies.
Clusters and superclusters of phased small RNAs in the developing inflorescence of rice
Authors: Johnson Cameron , Kasprzewska Anna , Tennessen Kristin , Fernandes John , Nan Guo-Ling , Walbot Virginia , Sundaresan Venkatesan , Vance Vicki , Bowman Lewis H.
Published: July 2009

To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from mature leaves and developing roots, shoots, and inflorescences. Using a spatial clustering algorithm, we identified 36,780 genomic groups of small RNAs. Most consisted of 24-nt RNAs that are expressed in all four tissues and enriched in repeat regions of the genome; 1029 clusters were composed primarily of 21-nt small RNAs and, strikingly, 831 of these contained phased RNAs and were preferentially expressed in developing inflorescences. Thirty-eight of the 24-mer clusters were also phased and preferentially expressed in inflorescences. The phased 21-mer clusters derive from nonprotein coding, nonrepeat regions of the genome and are grouped together into superclusters containing 10–46 clusters. The majority of these 21-mer clusters (705/831) are flanked by a degenerate 22-nt motif that is offset by 12 nt from the main phase of the cluster. Small RNAs complementary to these flanking 22-nt motifs define a new miRNA family, which is conserved in maize and expressed in developing reproductive tissues in both plants. These results suggest that the biogenesis of phased inflorescence RNAs resembles that of tasiRNAs and raise the possibility that these novel small RNAs function in early reproductive development in rice and other monocots.
Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences
Authors: Arpanahi Ali , Brinkworth Martin , Iles David , Krawetz Stephen A. , Paradowska Agnieszka , Platts Adrian E. , Saida Myriam , Steger Klaus , Tedder Philip , Miller David
Published: July 2009

During the haploid phase of mammalian spermatogenesis, nucleosomal chromatin is ultimately repackaged by small, highly basic protamines to generate an extremely compact, toroidal chromatin architecture that is critical to normal spermatozoal function. In common with several species, however, the human spermatozoon retains a small proportion of its chromatin packaged in nucleosomes. As nucleosomal chromatin in spermatozoa is structurally more open than protamine-packaged chromatin, we considered it likely to be more accessible to exogenously applied endonucleases. Accordingly, we have used this premise to identify a population of endonuclease-sensitive DNA sequences in human and murine spermatozoa. Our results show unequivocally that, in contrast to the endonuclease-resistant sperm chromatin packaged by protamines, regions of increased endonuclease sensitivity are closely associated with gene regulatory regions, including many promoter sequences and sequences recognized by CCCTC-binding factor (CTCF). Similar differential packaging of promoters is observed in the spermatozoal chromatin of both mouse and man. These observations imply the existence of epigenetic marks that distinguish gene regulatory regions in male germ cells and prevent their repackaging by protamines during spermiogenesis. The ontology of genes under the control of endonuclease-sensitive regulatory regions implies a role for this phenomenon in subsequent embryonic development.
Overexpression of the potential kinase serine/ threonine/tyrosine kinase 1 (STYK 1) in castration‐resistant prostate cancer
Authors: Chung Suyoun , Tamura Kenji , Furihata Mutsuo , Uemura Motohide , Daigo Yataro , Nasu Yasutomo , Miki Tsuneharu , Shuin Taro , Fujioka Tomoaki , Nakamura Yusuke , Nakagawa Hidewaki
Published: July 2009

Despite high response rates and clinical benefits, androgen ablation often fails to cure advanced or relapsed prostate cancer because castration‐resistant prostate cancer (CRPC) cells inevitably emerge. CRPC cells not only grow under castration, but also behave more aggressively, indicating that a number of malignant signaling pathways are activated in CRPC cells as well as androgen receptor signaling. Based on information from the gene expression profiles of clinical CRPC cells, we here identified one overexpressed gene, serine/threonine/tyrosine kinase 1 (STYK1), encoding a potential kinase, as a molecular target for CRPC. RNA and immunohistochemical analyses validated the overexpression of STYK1 in prostate cancer cells, and its expression was distinct in CRPC cells. Knockdown of STYK1 by siRNA resulted in drastic suppression of prostate cancer cell growth and, concordantly, enforced expression of STYK1 promoted cell proliferation, whereas ectopic expression of a kinase‐dead mutant STYK1 did not. An in vitro kinase assay using recombinant STYK1 demonstrated that STYK1 could have some potential as a kinase, although its specific substrates are unknown. These findings suggest that STYK1 could be a possible molecular target for CRPC, and small molecules specifically inhibiting STYK1 kinase could be a possible approach for the development of novel CRPC therapies. (Cancer Sci 2009)
Huntington’s Disease Does Not Appear to Increase the Risk of Diabetes Mellitus
Authors: Boesgaard T. W. , Nielsen T. T. , Josefsen K. , Hansen T. , Jørgensen T. , Pedersen O. , Nørremølle A. , Nielsen J. E. , Hasholt L.
Published: July 2009

Huntington’s disease (HD) is an autosomal, dominantly inherited, neurodegenerative disorder characterised by neurological, cognitive and psychiatric symptoms. HD has been associated with diabetes mellitus, which is, to some extent, supported by studies in transgenic HD mice. In transgenic mice, the severity of the diabetic phenotype appears to correlate with the length of a polyglutamine expansion in the protein huntingtin. In the present study, we investigated the association between diabetes mellitus and HD by performing an oral glucose‐tolerance test (OGTT) to evaluate the glucose‐tolerance status and OGTT‐related insulin release in 14 HD patients. Furthermore, we expressed N‐terminal huntingtin fragments with different polyglutamine lengths in an insulinoma‐cell line (INS‐1E) to investigate how mutant huntingtin influences glucose‐stimulated insulin release in vitro. We found no difference between a group of early‐ and middle‐stage HD patients and a large group of control individuals in any of the assessed variables. However, the glucose‐stimulated induction of insulin release was significantly reduced in the insulinoma‐cell line expressing highly expanded huntingtin compared to cells expressing huntingtin with modestly elongated polyglutamine stretches. These data indicate that insulin release from β‐cells expressing mutant huntingtin appears to be polyglutamine length‐dependent, and that polyglutamine lengths within the range normally found in adult onset HD do not influence insulin release. This challenges the assumption of an increased risk of diabetes among HD patients, although our results do not exclude a changed glucose tolerance in end‐stage HD patients or in patients with juvenile onset HD. It also raises the question of which extent transgenic mice models reflect the pathology of human HD in this regard.
Allonursing in Captive Guanacos, Lama guanicoe: Milk Theft or Misdirected Parental Care?
Authors: Zapata Beatriz , González Benito A. , Ebensperger Luis A.
Published: July 2009

Females in several ungulates transfer milk to non‐filial (NF) offspring, in a process known as allonursing. This behavior is less common in monotocous species, including most ungulates, and it has been associated with parasitic behavior of calves or mothers who have lost their own offspring. To examine whether the calves ‘steal’ milk from the females or whether females fail to discriminate their own calves in guanacos, allonursing behavior was observed. If milk theft drives allonursing, mothers should reject NF offspring, they should search for their own calves, and calves attempting to suckle from alien mothers should adopt parallel (as opposed to the anti‐parallel) position during allonursing. Alternatively, if allonursing is caused by mothers unable to discriminate own offspring, mothers are not expected to reject NF offspring, and alien calves should use parallel and antiparallel position similarly when allonursing. Allonursing was investigated during the first 3 mo of lactation in two groups of captive guanacos composed of 15 and 14 mother‐calf pairs, respectively. While 40% and 62.5% of mothers in groups 1 and 2 performed allonursing, high individual variation prevailed; some females exhibited this behavior infrequently (4.1% and 6.5 % in groups 1 and 2). The rejection rate to NF nursing attempts was threefold higher than the rejection rate to filial nursing attempts. The occurrence of nursing to NF was associated to a parallel posture by the calves. Our findings suggest that ‘milk theft’ is a more plausible hypothesis to explain allonursing in guanacos than ‘misdirected parental care’.
Early Comers Become Owners: Effect of Residency Experience on Territorial Contest Dynamics in a Lycaenid Butterfly
Authors: Takeuchi Tsuyoshi , Honda Keiichi
Published: July 2009

A positive relationship between ownership and contest success is widespread among territorial butterflies. We tested the hypothesis that owners win simply because they have a longer experience occupying a given territory than do intruders in territorial butterflies. Using the lycaenid butterfly Chrysozephyrus smaragdinus, we staged contests between two males that had experienced different residency periods at the same contested territory, similar to owners and intruders in natural contests. We found that males that had occupied the contested territory for a longer period (a day) always defeated the shorter occupancy males (15 min). Therefore, residency period plays a key role in settling territorial contests. As residency confers advantages in a time‐dependent manner, the mechanism of owner dominance could be an increase in motivation to fight as local familiarity increases. Moreover, this result predicts a population‐level territorial dynamics. If residency period per se confers advantages in each contest, males arriving at a territory early in their adult season should acquire territorial dominance because they can remain there for a certain period with only a few rivals; late‐appearing males do not have this advantage. As predicted, we found that males appearing at territory sites early in the season were more likely to hold their territories. This finding provides new evidence for the evolution of protandry in butterflies.
Microstructure variation effects on room temperature fatigue threshold and crack propagation in Udimet 720Li Ni‐base superalloy
Authors: PANG H. T. , REED P. A. S.
Published: July 2009

An assessment of the effects of microstructure on room temperature fatigue threshold and crack propagation behaviour has been carried out on microstructural variants of U720Li, i.e. as‐received U720Li, U720Li‐LG (large grain variant) and U720Li‐LP (large intragranular coherent γ′ variant). Fatigue tests were carried out at room temperature using a 20 Hz sinusoidal cycling waveform at an R‐ratio = 0.1 on 12.5 mm × 12.5 mm square cross‐section SENB specimens with a 60° starter notch. U720Li‐LG showed the highest threshold ΔK (ΔKth), whilst U720Li‐LP showed the lowest ΔKth value. U720Li‐LP also showed higher crack growth rates in the near‐threshold regime and at high ΔK (although at higher ΔK levels the difference was less marked). Crack growth rates of U720Li and U720Li‐LG were relatively similar both in the near‐threshold regime and at high ΔK. The materials showed crystallographic stage I type crack growth in the near‐threshold regime, with U720Li showing distinct crystallographic facets on the fracture surface, while U720Li‐LG and U720Li‐LP showed mostly microfacets and a lower proportion of large facets. At high ΔK, crack growth in the materials becomes flat and featureless indicative of stage II type crack growth. The observed fatigue behaviour, which is an effect of the combined contributions of intrinsic and extrinsic crack growth resistances, is rationalized in terms of the microstructural characteristics of the materials. Enhanced room temperature fatigue threshold and near‐threshold long crack growth resistance are seen for materials with larger grain size and higher degree of planar slip which may be related to increased extrinsic crack growth resistance contributions from crack tip shielding and roughness‐induced crack closure. Differences in the deformation behaviour, either homogeneous or heterogeneous due to microstructural variation in this set of materials may provide approximately equivalent intrinsic crack growth resistance contributions at room temperature.
Analysis of manufacturing effects on fatigue failure of an automotive component using finite element methods
Authors: KANG W. J. , KIM G. H.
Published: July 2009

In this study, the fatigue life of an automotive suspension component was analysed using finite element methods with regard to stamping and welding effects. Because automotive suspension components are produced by forming and welding sheet metal, there are various effects on the final product, such as uneven thickness distribution, residual stresses and weld notches. Manufacturing effects may change the mechanical performance of the automotive components; therefore, it is desirable to consider these effects in the early design stage. Residual stresses due to work hardening and thermal deformation were investigated through process simulation. The redistribution and relaxation of residual stresses in a component were investigated in fatigue life analysis under a cyclic loading condition. Various equivalent relaxation curves were investigated and one was selected after comparisons with test results. The fatigue simulation results were compared to the test results; a good correlation between the two was achieved for the residual stress effects in terms of life cycles and failure locations. The simulation results also show that welding produces more detrimental effects than stamping with regard to the fatigue life of a component.
Comparison of kidney‐ureter‐bladder abdominal radiography and computed tomography scout films for identifying renal calculi
Authors: Johnston Richard , Lin Anthony , Du Jason , Mark Stephen
Published: July 2009

OBJECTIVE

To assess the sensitivity of computed tomography (CT) scout topograms and kidney‐ureter‐bladder abdominal radiography (KUB) in detecting urinary tract stones.

PATIENTS AND METHODS

We assesed films taken on presentation for 163 consecutive patients referred to our service for stone follow‐up. Only those with both CT and KUB imaging on the same day were studied further. Two urology registrars examined the films independently. Location, size and length of stone were recorded. Where there was discordance, the films were examined by an independent radiologist.

RESULTS

In all, 108 of 163 patients had both CT and KUB imaging on the same day. Stones were identified in 63% (68/108) of patients with KUB, with a mean length of 4.93 mm. There were 40/108 radiolucent stones subsequently measured on CT, with a mean length of 4.90 mm. Stones were seen on 47% (51/108) of the CT scouts, with a mean length of 5.22 mm. Importantly, all stones visible on CT scout were also visible on KUB. There was no correlation between stone location and visibility on KUB or CT scout films.

CONCLUSION

KUB could be used for follow‐up in 63% of cases. All stones seen on CT scout were also visible on KUB. Scout detected 75% of stones visible on KUB. We suggest CT scout film should be reported before proceeding to KUB. If the stone is visible on CT scout film, then the decision to use KUB for follow‐up can be made. This minimizes radiation exposure and other costs.
Bacillus Calmette‐Guérin cell‐wall skeleton enhances the killing activity of cytotoxic lymphocyte‐activated human dendritic cells transduced with the prostate‐specific antigen gene
Authors: Fujii Reona , Iwahashi Makoto , Kikkawa Kazuro , Inagaki Takeshi , Kohjimoto Yasuo , Ojima Toshiyasu , Mori Takashi , Kuramoto Tomomi , Nishizawa Satoshi , Azuma Ichiro , Yamaue Hiroki , Shinka Toshiaki , Hara Isao
Published: July 2009

OBJECTIVE

To determine whether dendritic cells (DC) transduced with the prostate‐specific antigen (PSA) gene can induce PSA‐specific cytotoxic lymphocytes (CTL) against prostate cancer cells, and whether bacillus Calmette‐Guérin (BCG) cell‐wall skeleton (CWS) can enhance the maturation of DC‐PSA and the killing activity of subsequently induced PSA‐specific CTL.

MATERIALS AND METHODS

We generated an adenovirus encoding the PSA gene (AxCA‐PSA) using the cosmid‐terminal protein complex method. DC were infected with AxCA‐PSA using the centrifugal method. The ability of CTL to lyse target cells expressing PSA, i.e the PSA‐positive prostate cancer cell line, LNCap, and PSA‐transduced autologous phytohaemagglutinin (PHA) blasts expressing PSA, was assessed using the 51Cr‐release assay. The maturation of DC‐PSA stimulated by BCG‐CWS was assayed by flow cytometry. The cytotoxic activity enhanced by BCG‐CWS was assessed by the 51Cr‐release assay.

RESULTS

DC‐PSA induced PSA‐specific CTL with 85% cytotoxic activity against LNCaP (effector: target ratio, E:T, of 50:1). However, the cytotoxic activity against PSA‐negative cells was very low. Anti‐CD8 and anti‐major histocompatibility (MHC) class I antibodies blocked PSA‐specific cytotoxicity. The PSA‐specific killing was reproducible against autologous PHA blast cells expressing PSA, independently of human leukocyte antigen haplotype. Furthermore, the combination of DC‐PSA with BCG‐CWS remarkably enhanced the PSA‐specific cytotoxicity against PHA blasts expressing PSA (15–30% at an E:T ratio of 50:1).

CONCLUSION

These findings suggest that DC‐PSA can induce MHC class I‐restricted PSA‐specific CD8+ CTL responses and that DC‐PSA matured by BCG‐CWS enhance PSA‐specific cytotoxicity. The combination of DC‐PSA with BCG‐CWS might be a useful approach for treating advanced prostate cancer.
A comparative population‐based analysis of the rate of partial vs radical nephrectomy for clinically localized renal cell carcinoma
Authors: Baillargeon‐Gagné Sara , Jeldres Claudio , Lughezzani Giovanni , Sun Maxine , Isbarn Hendrik , Capitanio Umberto , Shariat Shahrokh F. , Crépel Maxime , Alasker Ahmed , Widmer Hugues , Arjane Philippe , Patard Jean‐Jacques , Perrotte Paul , Montorsi Francesco , Graefen Markus , Karakiewicz Pierre I.
Published: July 2009

Study Type – Prevalence (prospective cohort with good follow up)Level of Evidence 1a

OBJECTIVE

To examine contemporary (1989–2004) trends in partial nephrectomy (PN) within the Surveillance, Epidemiology and End Results (SEER) database, as among other considerations, a survival benefit due to avoidance of surgically induced renal insufficiency distinguishes PN from radical nephrectomy (RN).

PATIENTS AND METHODS

Diagnostic, stage and surgical codes of patients with T1‐2N0M0 renal cell carcinoma treated with either PN or RN were assessed. Proportions, trends and multivariable logistic regression models tested the predictors of the use of PN.

RESULTS

Of 19 733 assessable patients, 2614 (13.2%) and 17 119 (86.8%), respectively, had PN or RN. The use of PN decreased with increasing tumour size, was more frequent in younger patients and increased with more contemporary years of surgery (all P < 0.001). Intriguingly, there was important geographical variability (P < 0.001), e.g. in the San Francisco‐Oakland Metropolitan Area the absolute PN rate was 16.4%, vs 7.6% in New Mexico (P < 0.001). In multivariable analyses, tumour size, age, year of surgery, gender and SEER registries were independent predictors of PN use.

CONCLUSION

Although as expected the rate of PN use increased over time, unexplained variability remained. For example, gender and SEER registries affected the likelihood of PN. These variables warrant further analyses to reduce unnecessary variability and to maximize PN use and its benefit.
Testing the limits of statistical learning for word segmentation
Authors: Johnson Elizabeth K. , Tyler Michael D.
Published: July 2009

Past research has demonstrated that infants can rapidly extract syllable distribution information from an artificial language and use this knowledge to infer likely word boundaries in speech. However, artificial languages are extremely simplified with respect to natural language. In this study, we ask whether infants’ ability to track transitional probabilities between syllables in an artificial language can scale up to the challenge of natural language. We do so by testing both 5.5‐ and 8‐month‐olds’ ability to segment an artificial language containing four words of uniform length (all CVCV) or four words of varying length (two CVCV, two CVCVCV). The transitional probability cues to word boundaries were held equal across the two languages. Both age groups segmented the language containing words of uniform length, demonstrating that even 5.5‐month‐olds are extremely sensitive to the conditional probabilities in their environment. However, neither age group succeeded in segmenting the language containing words of varying length, despite the fact that the transitional probability cues defining word boundaries were equally strong in the two languages. We conclude that infants’ statistical learning abilities may not be as robust as earlier studies have suggested.
Online usage of theory of mind continues to develop in late adolescence
Authors: Dumontheil Iroise , Apperly Ian A. , Blakemore Sarah‐Jayne
Published: July 2009

The development of theory of mind use was investigated by giving a computerized task to 177 female participants divided into five age groups: Child I (7.3–9.7 years); Child II (9.8–11.4); Adolescent I (11.5–13.9); Adolescent II (14.0–17.7); Adults (19.1–27.5). Participants viewed a set of shelves containing objects, which they were instructed to move by a ‘director’ who could see some but not all of the objects. Correct interpretation of critical instructions required participants to use the director’s perspective and only move objects that the director could see. In a control condition, participants were asked to ignore objects in slots with a grey background. Accuracy improved similarly in both conditions between Child I and Adolescent II. However, while performance of the Adolescent II and Adult groups did not differ in the control condition, the Adolescent II group made more errors than the adults in the experimental condition. These results suggest that theory of mind use improves between late adolescence and adulthood. Thus, while theory of mind tasks are passed by age 4, these data indicate that the interaction between theory of mind and executive functions continues to develop in late adolescence.
Age differences in the contribution of recollection and familiarity to false‐memory formation: a new paradigm to examine developmental reversals
Authors: Lyons Kristen E. , Ghetti Simona , Cornoldi Cesare
Published: July 2009

Using a new method for studying the development of false‐memory formation, we examined developmental differences in the rates at which 6‐, 7‐, 9‐, 10‐, and 18‐year‐olds made two types of memory errors: backward causal‐inference errors (i.e. falsely remembering having viewed the non‐viewed cause of a previously viewed effect), and gap‐filling errors (i.e. falsely remembering having viewed a script‐consistent event that was not actually witnessed). Previous research suggests that backward causal‐inference errors are supported by recollection, whereas gap‐filling errors are supported by familiarity. We hypothesized that age differences in these errors would parallel the developmental trajectories of these processes. As predicted, age‐related increases in backward causal‐inference errors were observed, while gap‐filling errors were age‐invariant, suggesting that recollection‐based memory distortions increase with age while familiarity‐based memory distortions are relatively stable from middle childhood through adulthood.