bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti‐Convulsant Activity ofBoerhaavia diffusa: Plausible Role of Calcium Channel Antagonism
Authors: Kaur Mandeep , Goel Rajesh Kumar
Published: December 2009

“Ethnopharmacological” use of roots ofBoerhaavia diffusa(B. diffusa) in the treatment of epilepsy in Nigerian folk medicine and reports showing the presence of a calcium channel antagonistic compound “liriodendrin” in its roots, led us to undertake the present study. The study was designed to investigate the methanolic root extract ofB. diffusaand its different fractions including liriodendrin‐rich fraction for exploring the possible role of liriodendrin in its anti‐convulsant activity. Air‐dried roots ofB. diffusawere extracted with methanol by cold maceration. The methanol soluble fraction of extract thus obtained was successively extracted to obtain liriodendrin‐rich fraction and two side fractions, that is, chloroform fraction and phenolic compound fraction. Anti‐convulsant activity of methanolic extract (1000, 1500 and 2000 mg kg-1, intraperitoneally (i.p.)) and its different fractions, that is, liriodendrin‐rich fraction (10, 20 and 40 mg kg-1, i.p., chloroform fraction (20 mg kg-1, i.p.) and phenolic compound fraction (1 mg kg-1, i.p.) were studied in pentylenetetrazol (PTZ)‐induced seizures (75 mg kg-1, i.p.). The crude methanolic extract ofB. diffusaand only its liriodendrin‐rich fraction showed a dose‐dependent protection against PTZ‐induced convulsions. The liriodendrin‐rich fraction also showed significant protection against seizures induced by BAY k‐8644. These findings reiterated the anti‐convulsant activity of methanolic extract ofB. diffusaroots. Furthermore, it can be concluded that the observed anti‐convulsant activity was due to its calcium channel antagonistic action as this activity was retained only in the liodendrin‐rich fraction, which has additionally been confirmed by significant anti‐convulsant activity of liriodendrin‐rich fraction in BAY k‐8644‐induced seizures.
A Contemporary Treatment Approach to Both Diabetes and Depression by Cordyceps sinensis, Rich in Vanadium
Authors: Guo Jian-You , Han Chun-Chao , Liu Yong-Mei
Published: December 2009

Diabetes mellitus is accompanied by hormonal and neurochemical changes that can be associated with anxiety and depression. Both diabetes and depression negatively interact, in that depression leads to poor metabolic control and hyperglycemia exacerbates depression. We hypothesize one novel vanadium complex of vanadium‐enriched Cordyceps sinensis (VECS), which is beneficial in preventing depression in diabetes, and influences the long‐term course of glycemic control. Vanadium compounds have the ability to imitate the action of insulin, and this mimicry may have further favorable effects on the level of treatment satisfaction and mood. C. sinensis has an antidepressant‐like activity, and attenuates the diabetes‐induced increase in blood glucose concentrations. We suggest that the VECS may be a potential strategy for contemporary treatment of depression and diabetes through the co‐effect of C. sinensis and vanadium. The validity of the hypothesis can most simply be tested by examining blood glucose levels, and swimming and climbing behavior in streptozotocin‐induced hyperglycemic rats.
Slave to the rhythm: how large-scale climate cycles trigger herring (Clupea harengus) regeneration in the North Sea
Authors: Gröger Joachim P. , Kruse Gordon H. , Rohlf Norbert
Published: December 2009

Gröger, J. P., Kruse, G. H., and Rohlf, N. 2010. Slave to the rhythm: how large-scale climate cycles trigger herring (Clupea harengus) regeneration in the North Sea. – ICES Journal of Marine Science, 67: 454–465. Understanding the causes of variability in the recruitment of marine fish stocks has been the “holy grail” of fisheries scientists for more than 100 years. Currently, debate is ongoing about the functionality and performance of traditional stock–recruitment functions used during stock assessments. Additionally, the European Commission requires European fishery scientists to apply the ecosystem approach to fisheries in part by integrating environmental knowledge into stock assessments and forecasts. Motivated to understand better the recent years of reproductive failures of commercially valuable North Sea herring, we studied large-scale climate changes in the North Atlantic Ocean and their potential effects on stock regeneration. Applying traffic light plots and time-series (TS) analyses, it was possible not only to explain the most recent reproductive failures, but also to reconstruct the full TS of recruitment from climate cycles, indexed by the North Atlantic Oscillation and the Atlantic Multidecadal Oscillation. A prognostic model was developed to provide predictions of herring stock changes several years in advance, allowing recruitment forecasts to be incorporated easily into risk assessments and management strategy evaluations, to promote a sustainable herring fishery in the North Sea. Insights gained from the analysis permit reinterpretation of the sharp decline in the North Sea herring stocks in the 1970s.
Ranking the ecological relative status of exploited marine ecosystems
Authors: Coll Marta , Shannon Lynne J. , Yemane Dawit , Link Jason S. , Ojaveer Henn , Neira Sergio , Jouffre Didier , Labrosse Pierre , Heymans Johanna J. , Fulton Elizabeth A. , Shin Yunne-Jai
Published: December 2009

Coll, M., Shannon, L. J., Yemane, D., Link, J. S., Ojaveer, H., Neira, S., Jouffre, D., Labrosse, P., Heymans, J. J., Fulton, E. A., and Shin, Y-J. 2010. Ranking the ecological relative status of exploited marine ecosystems. – ICES Journal of Marine Science, 67: 769–786. A set of simple, data-based ecological indicators was used to rank exploited ecosystems regarding fishing impacts with respect to their status, trends, and ecosystem EAF attributes. Expected theoretical changes in indicators with respect to increasing fishing impacts were considered, and ecosystems were compared by examining the mean values of indicators in the most recent three years for which data were available and over time (1980–2005 and 1996–2005). Systems were classified into nine potential categories according to whether they were most, moderately, or least impacted, and whether they were becoming more or less impacted, or remaining stationary. The responses of ecological indicators to additional environmental and socio-economic explanatory factors were tested. Ecosystems ranked using short- and long-term trends and states differed because of differences in trends, underscoring the importance of analysing both states and trends in ecosystem analyses. The number of ecosystems classified as unclear or intermediately impacted has increased recently, the proportion of ecosystems classified as less strongly impacted has been maintained, but more now fall within the category more strongly impacted in terms of long-term trends and states. Ecosystem type, fisheries enforcement, primary production, sea temperature, and fishing type were important variables explaining the ecological indicators. The results reflect different changes and processes in the ecosystems, demonstrating that information on ecological, environmental, and fishery histories is crucial to interpreting indicators correctly, while disentangling the effects of fishing and of the environment.
The SAND domain protein ULTRAPETALA1 acts as a trithorax group factor to regulate cell fate in plants
Authors: Carles Cristel C. , Fletcher Jennifer C.
Published: December 2009

During development, trithorax group (trxG) chromatin remodeling complexes counteract repression by Polycomb group (PcG) complexes to sustain active expression of key regulatory genes. Although PcG complexes are well characterized in plants, little is known about trxG activities. Here we demonstrate that the Arabidopsis SAND (Sp100, AIRE-1, NucP41/75, DEAF-1) domain protein ULTRAPETALA1 (ULT1) functions as a trxG factor that counteracts the PcG-repressive activity of CURLY LEAF. In floral stem cells, ULT1 protein associates directly with the master homeotic locus AGAMOUS, inducing its expression by regulating its histone methylation status. Our analysis introduces a novel mechanism that mediates epigenetic switches controlling post-embryonic stem cell fates in plants.
Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3′ UTR
Authors: Liu Niankun , Han Hong , Lasko Paul
Published: December 2009

Vasa (Vas) is a DEAD-box RNA-binding protein required in Drosophila at several steps of oogenesis and for primordial germ cell (PGC) specification. Vas associates with eukaryotic initiation factor 5B (eIF5B), and this interaction has been implicated in translational activation of gurken mRNA in the oocyte. Vas is expressed in all ovarian germline cells, and aspects of the vas-null phenotype suggest a function in regulating the balance between germline stem cells (GSCs) and their fate-restricted descendants. We used a biochemical approach to recover Vas-associated mRNAs and obtained mei-P26, whose product represses microRNA activity and promotes GSC differentiation. We found that vas and mei-P26 mutants interact, and that mei-P26 translation is substantially reduced in vas mutant cells. In vitro, Vas protein bound specifically to a (U)-rich motif in the mei-P26 3′ untranslated region (UTR), and Vas-dependent regulation of GFP-mei-P26 transgenes in vivo was dependent on the same (U)-rich 3′ UTR domain. The ability of Vas to activate mei-P26 expression in vivo was abrogated by a mutation that greatly reduces its interaction with eIF5B. Taken together, our data support the conclusion that Vas promotes germ cell differentiation by directly activating mei-P26 translation in early-stage committed cells.
The Drosophila DHR96 nuclear receptor binds cholesterol and regulates cholesterol homeostasis
Authors: Horner Michael A. , Pardee Keith , Liu Suya , King-Jones Kirst , Lajoie Gilles , Edwards Aled , Krause Henry M. , Thummel Carl S.
Published: December 2009

Cholesterol homeostasis is required to maintain normal cellular function and avoid the deleterious effects of hypercholesterolemia. Here we show that the Drosophila DHR96 nuclear receptor binds cholesterol and is required for the coordinate transcriptional response of genes that are regulated by cholesterol and involved in cholesterol uptake, trafficking, and storage. DHR96 mutants die when grown on low levels of cholesterol and accumulate excess cholesterol when maintained on a high-cholesterol diet. The cholesterol accumulation phenotype can be attributed to misregulation of npc1b, an ortholog of the mammalian Niemann-Pick C1-like 1 gene NPC1L1, which is essential for dietary cholesterol uptake. These studies define DHR96 as a central regulator of cholesterol homeostasis.
Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t complex responder
Authors: Véron Nathalie , Bauer Hermann , Weiße Andrea Y. , Lüder Gerhild , Werber Martin , Herrmann Bernhard G.
Published: December 2009

The t complex responder (Tcr) encoded by the mouse t haplotype is able to cause phenotypic differences between t and + sperm derived from t/+ males, leading to non-Mendelian inheritance. This capability of Tcr contradicts the concept of phenotypic equivalence proposed for sperm cells, which develop in a syncytium and actively share gene products. By analyzing a Tcr minigene in hemizygous transgenic mice, we show that Tcr gene products are post-meiotically expressed and are retained in the haploid sperm cells. The wild-type allele of Tcr, sperm motility kinase-1 (Smok1), behaves in the same manner, suggesting that Tcr/Smok reveal a common mechanism prone to evolve non-Mendelian inheritance in mammals.
The Tammar Wallaby,Macropus eugenii: A Model Kangaroo for the Study of Developmental and Reproductive Biology
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

The tammar wallaby(Macropus eugenii)is the best-studied marsupial in terms of its reproduction and development. It fares well in captivity, is large enough to take serial blood samples from, and its young are accessible in the pouch for experimental manipulation. These features have made it an excellent model for both physiological and molecular research. It is a seasonal, monovular breeder, but also has a lactational control of its reproduction, as well as embryonic diapause. As in all marsupials, the composition of the milk changes throughout the lengthy lactation, and the dynamic changes that occur in the genes and secreted proteins of the mammary gland have now been characterized. Studies of the tammar have contributed to our understanding of the control of reproduction in all mammals, and more recently, have helped clarify the endocrine and molecular aspects of sexual differentiation. The completion of the tammar wallaby genome will facilitate further study of this marsupial.
The Sea Squirt Ciona intestinalis: Figure 1.
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

Sea squirts (Ciona intestinalis) are tunicates (or urochordates), the closest living relatives of the vertebrates. Although the adults are simple, sessile filter feeders, the embryos and larvae possess clear chordate features including a prominent notochord and dorsal, hollow neural tube. Tail-bud-stage embryos and mature swimming tadpoles are composed of approximately 1000 and 2600 cells, respectively, with complete lineage information. This cellular simplicity is coupled with a streamlined genome that has not undergone the duplications seen in vertebrates. A variety of molecular tools have been applied to understanding Ciona embryogenesis. Comparisons of the C. intestinalis genome and the related but divergent Ciona savignyi genome have facilitated the identification of conserved non-coding DNAs, including regulatory DNAs such as tissue-specific enhancers. Systematic in situ hybridization assays and gene-disruption experiments using specific morpholino antisense oligonucleotides have led to the elaboration of provisional gene regulatory networks underlying the specification of key chordate tissues, including the notochord, neural tube, and beating heart. These networks provide a foundation for understanding the mechanistic basis of more complex cell-specification processes in vertebrates, and for understanding the evolutionary origins of distinctive vertebrate characteristics such as the neural crest. Because tunicates and vertebrates are sister groups, there is every indication that the developmental mechanisms revealed in the simple Ciona model will be applicable to comparable processes in vertebrates.
In Vitro Transcription Using HeLa Cell Extracts and Primer Extension
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: December 2009

INTRODUCTION

Primer extension is a popular method for measuring transcription. Among the methods for start-site mapping in vivo, it is the one most easily adapted for in vitro transcription. Typically, DNA templates bearing activator binding sites are co-incubated with nuclear extracts (which provide the general transcription factors) and the corresponding activators to synthesize mRNA. In some cases, the activator is present in the extract (e.g., Sp1) and templates lacking or containing sites are compared. In the primer extension assay, a 32P-end-labeled DNA oligonucleotide is annealed to a complementary region in the mRNA and then extended by a reverse transcriptase to the 5′ end of the mRNA. The resulting labeled cDNA is then fractionated and detected on a polyacrylamide/urea gel. The amount of the product is a measure of the transcriptional activation by the activators. Generally, the addition of 0.1 pmol of primer to the extension reaction is sufficient because it will be in vast excess over the amount of mRNA, facilitating quantitative primer hybridization and extension.
Performing Surgery on Tammar Wallaby (Macropus eugenii) Adults
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

Adult tammar wallabies (Macropus eugenii) are very tolerant of surgery if it is conducted with care. Adult females weigh ~4‐5 kg, males ~7‐8 kg. Routine surgery performed in our laboratory and described in this protocol includes castration, laparotomy (to visualize the reproductive tract), ovariectomy, and hysterectomy (for embryo collection). All surgery is conducted under aseptic conditions. For most reproductive surgery on females, the optimum surgical approach is via the inside of the pouch. Any pouch young must be removed before surgery.
Collection, Handling, Fixation, and Processing of Tammar Wallaby (Macropus eugenii) Embryos
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

This protocol describes methods for collecting and handling tammar wallaby (Macropus eugenii) conceptuses. Zygotes, cleavage stages, diapausing blastocysts, and unexpanded blastocysts are ~250 μm in diameter and are collected by flushing either the oviduct or uterus. Later stages are collected by opening the uterus. Late preimplantation stages must be handled carefully because their large size (>2 cm in diameter) results in high surface tension within the yolk sac, especially on the delicate avascular area. When handled too roughly, the embryonic vesicle tends to split and then rapidly collapse; such embryos do not reinflate. If embryos are to be cultured, all steps during collection must be carried out aseptically. In all cases, solutions should be prewarmed to 37°C and embryos should be kept warm by use of a heating stage. Standard fixatives, fixation times, and washing protocols used for mouse embryos are also used for tammar embryos. Methods for embedding tammar conceptuses in paraffin wax depend on the size and stage of the conceptus.
Culturing Tammar Wallaby (Macropus eugenii) Pouch Young Gonads
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

Tammar wallaby (Macropus eugenii) pouch young (PY) gonads are ideal for studies on gonadal differentiation and germ cell proliferation because, in contrast to the mouse, both of these events occur postnatally in the tammar. In the male, testicular cords start developing at day 2 postpartum (pp), whereas in the female the ovarian cortex and medulla differentiate from ~day 8 pp. In females, meiosis starts from day 25 pp and is complete in most germ cells by day 50 pp. The gonads can be cultured either in grooves within agar or flat on a membrane. The former arrangement maintains the close contact of the gonad and mesonephros better than culturing them flat on a membrane. This protocol provides methods for isolation and culturing of PY gonads.
Culturing Tammar Wallaby(Macropus eugenii)Peri-gastrulation Stage Embryos
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

Tammar wallaby(Macropus eugenii)peri-gastrulation stage embryos can be cultured in complete medium in 95% oxygen for up to 3 d. There is little apparent difference in terms of development between tammar peri-gastrulation stage embryos cultured in DMEM versus Medium 199 with Earle’s salts, or between the supplementation of complete medium with either 10% fetal calf serum (FCS) or 10% wallaby serum (WS). The peri-gastrulation marsupial conceptus is hollow, which means that some techniques, such as grafting, cannot be performed on embryos to be cultured whole because, once punctured, the embryo collapses and does not reinflate. This protocol describes both whole embryo culture and an alternative method of culture. In the latter method, the embryonic disc and some adjoining vascular yolk sac are isolated, laid flat on a membrane, and cultured as a flat mount. Embryos cultured in this way develop to a similar stage as those cultured whole.
Whole-Mount Immunohistochemical Staining of Tammar Wallaby (Macropus eugenii) Cleavage Stages and Blastocysts
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

This protocol describes a method for whole-mount immunofluorescence staining of early stages of tammar wallaby (Macropus eugenii) development, including cleavage and unilaminar blastocysts. Conceptuses of these stages are surrounded by a shell coat, which must be removed before staining to ensure proper penetration of all solutions.
Whole-Mount Immunohistochemical Staining of Tammar Wallaby(Macropus eugenii)Peri-gastrulation Embryos
Authors: Hickford Danielle , Frankenberg Stephen , Renfree Marilyn B.
Published: December 2009

INTRODUCTION

This protocol describes a method for whole-mount immunohistochemical staining of tammar wallaby (Macropus eugenii) peri-gastrulation stage embryos using the avidin-biotin complex system. Tammar embryos are ideal for whole-mount immunostaining because of their morphology: They develop in a planar manner on the surface of the embryonic vesicle and are not covered by any extraembryonic membranes until amnion formation (which occurs during mid-somitogenesis). Tammar embryos are surrounded by a transparent shell coat, which must be opened prior to staining to ensure penetration of solutions and reagents.
Biarsenical Labeling of Tetracysteine-Tagged Proteins for Tracking Existing and Newly Synthesized Pools of Proteins
Authors: Pattnaik Asit K. , Panda Debasis
Published: December 2009

INTRODUCTION

Genetically tagging proteins of interest with fluorescent labels such as green fluorescent protein is a valuable technique for studying protein localization and interactions in live cells. However, the relatively large size of fluorescent fusion proteins can limit the utility of this approach, and sometimes the tag can render the protein of interest nonfunctional. Small genetic tagging with tetracysteine (TC) and subsequent labeling with membrane-permeable biarsenical dyes can overcome these limitations. This protocol describes the method to detect TC-tagged proteins by biarsenical labeling in live cells. A small amino acid tag containing four cysteines (CCPGCC) is introduced to a protein of interest. Cells expressing proteins with this tag are then treated with membrane-permeable dyes (FlAsH-EDT2 or ReAsH-EDT2), and the two arsenic groups of the dyes each bind to the two thiols in the TC motif. Once bound, FlAsH and ReAsH are converted to a fluorescent state (green and red fluorescence at excitation maxima of 508 and 593 nm, respectively) and can be detected by fluorescence microscopy. The method is particularly suitable for investigating protein dynamics that are difficult to study using a fluorescent protein tag. It also is a powerful method for visualizing trafficking of newly synthesized proteins in real time, because existing and newly synthesized pools of proteins can be labeled differentially with the red and green dyes. A method for labeling virally produced proteins is also presented.
Microinjection of Morpholino Oligos and RNAs in Sea Squirt (Ciona) Embryos
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

This protocol describes microinjection of morpholino oligos (MOs) and RNAs into sea squirt (Ciona) embryos. This is the method of choice for gene disruption assays. MOs that target the initiating ATG can be used, in addition to those that target splice donor and acceptor sites. The latter method permits the selective inhibition of zygotic mRNAs in cases in which the gene in question is expressed in both the egg and embryo. Although injection is usually performed at the one-cell stage, it is possible to target individual blastomeres, up to the eight-cell stage, thereby permitting lineage-specific knockdown of pleiotropic genes. Injection can also be performed in unfertilized eggs to inhibit maternal genes. Microinjection also permits DiI labeling and lineage tracing.
Isolation of Individual Cells and Tissues from Electroporated Sea Squirt (Ciona) Embryos by Fluorescence-Activated Cell Sorting (FACS)
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

This protocol describes the dissociation of electroporated sea squirt (Ciona) embryos and the subsequent isolation of individual cells, cell lineages, and tissues, using fluorescence-activated cell sorting (FACS). Sorted samples can be used for RNA extraction and reverse transcriptase polymerase chain reaction (RT-PCR) or microarray analysis. Alternatively, dissociated samples can be used for the subsequent culturing and/or chemical treatment of isolated embryonic cells. This method permits the identification of effector genes responsible for changes in cell shape, polarity, or motility in a given tissue.
Fluorescent Protein Tracking and Detection: Fluorescent Protein Structure and Color Variants
Authors: Rizzo Mark A. , Davidson Michael W. , Piston David W.
Published: December 2009

INTRODUCTION

The rapidly growing arsenal of genetically encoded fluorescent proteins (FPs) obtained from sea creatures has launched and fueled a revolution in live cell imaging. The diverse array of applications benefiting from FPs ranges from markers targeted at organelles and protein fusions designed to monitor intracellular dynamics to reporters of transcriptional regulation and in vivo probes for whole-body imaging and detection of cancer. FPs have enabled the creation of highly specific biosensors to monitor a wide range of intracellular phenomena, including pH and metal-ion concentration, protein kinase activity, apoptosis, membrane voltage, cyclic nucleotide signaling, and tracing neuronal pathways. The purpose of this article is to provide a description of the wide variety of FPs that are currently available.
Computational Image Analysis of Cellular Dynamics: A Case Study Based on Particle Tracking
Authors: Jaqaman Khuloud , Danuser Gaudenz
Published: December 2009

INTRODUCTION

Obtaining quantitative data from live cell images is the key to testing mechanistic hypotheses of molecular and cellular processes. The importance of using computer vision-based methods to accomplish this task is well recognized. However, in practice, investigators often encounter obstacles that render the application of computational image processing in cell biology far from routine. First, it is not always clear which measurements are necessary to characterize a molecular system and whether these measurements are sufficient to characterize the cellular process under investigation. Second, even when the requirements for measurements are well defined, it often is difficult to find a software tool to extract these data. It can be even more challenging to find software tools to answer specific questions raised by the hypotheses underlying the experiments. One solution is for investigators to develop their own software tools. This is feasible for some applications with the assistance of commercial and open-source software packages that support the assembly and integration of custom-designed algorithms, even for users with limited computational expertise. Another solution is for investigators to develop interdisciplinary collaborations with computer scientists. Such collaborations require close interaction between the computer scientists and experimental biologists to optimize the data acquisition and analytical procedures, which must be tightly coupled in any project applying computational analysis to biological image data. This article introduces the basic concepts that make the application of computational image processing to live cell image data successful.
Genome-Wide Association Studies
Authors: Al-Chalabi Ammar
Published: December 2009

INTRODUCTION

The goal of association studies is to discover genetic variation that differs in frequency between cases and controls or between individuals with different phenotypic values. Until a few years ago, the only method available for such studies was low-throughput analysis in which a single gene was selected and either genotyped for known genetic variants or sequenced to identify such variants. With the completion of the Human Genome Mapping Project, we have learned that single-nucleotide polymorphisms (SNPs) are frequent in the genome and that variants in physical proximity tend to correlate in genotype. Therefore, a major international effort was started to map this correlation in the form of the International HapMap Project. The concurrent advances in genetic laboratory techniques, statistical methods, and computing power, coupled with the information from the HapMap, have allowed large-scale microchip-based technologies to be used to assay large numbers of SNPs quickly and easily. Thus, truly genome-wide association studies (GWAS) can now be performed, analogous to linkage studies of Mendelian diseases in having no prior hypothesis of the chromosomal location responsible for disease. In this article, we will only discuss case-control studies in which family members are not analyzed, but the principles apply to large-scale family-based association studies as well.
Phylogeny of the large extinct South American Canids (Mammalia, Carnivora, Canidae) using a “total evidence” approach
Authors: Prevosti Francisco J.
Published: December 2009

South America currently possesses a high diversity of canids, comprising mainly small to medium‐sized omnivorous species, but in the Pleistocene there were large hypercarnivorous taxa that were assigned to Protocyon spp., Theriodictis spp., Canis gezi, Canis nehringi and Canis dirus. These fossils have never been included in phylogenies based on quantitative cladistics, but hand‐constructed cladograms published in the 1980s included some of them in the South American canine clade and others in the Canis clade. In this work, the phylogenetic position of the large extinct South American canids was studied using a large sample of living and extinct canids, as well as different sources of characters (e.g. DNA and 133 osteological characters). The phylogenetic analysis corroborates the inclusion of Theriodictis and Protocyon in the “South American clade”, where C. gezi is also included. In addition, the position of C. dirus as a highly derived Canis species is confirmed. The simultaneous analysis supports hypercarnivory having arisen at least three times in Caninae and once in the “South American clade”. The combination of the phylogenetic analyses, the fossil record and divergence dates estimated in previous works suggests that at least three or four independent lineages of the “South American clade” invaded South America after the establishment of the Panama bridge around 3 million years ago, plus other events corresponding to the immigration of Urocyon and Canis dirus. © The Willi Hennig Society 2009.
Parents' views about pre‐school immunization: an interview study in southern England
Authors: Tickner S. , Leman P. J. , Woodcock A.
Published: December 2009

Background  National Health Service immunization statistics for England indicate that uptake of the first plus second dose of measles, mumps and rubella (MMR) vaccine, and pre‐school booster against diphtheria, tetanus, polio and pertussis, is lower than for the primary course alone. This qualitative study aimed to explore parents' views about pre‐school immunization and to identify possible reasons for lower pre‐school uptake compared with the primary course.

Methods  Semi‐structured interviews were conducted with 21 parents of children aged 2–5 years from 19 family units. The parents were recruited from nine playgroups and pre‐schools in three locations in southern England. Data collection and analysis were guided by a modified Grounded Theory approach.

Results  Although most parents believed pre‐school immunization to be important and most intended to immunise, a minority questioned whether it was necessary based on their understanding of the duration of protection provided by the primary course. Compared with primary immunization, parents typically received no information about pre‐school doses prior to their invitation to attend and had little or no contact with healthcare professionals. Other barriers included minor illness, apprehension about taking an older child for vaccinations and work or childcare commitments.

Conclusions  Parents reported uncertainties, anxieties and time constraints, all of which may contribute to poor attendance for pre‐school immunization. These findings have important implications for providing parents with timely information about boosters and the two‐dose MMR programme. They indicate the potential value of playgroup or pre‐school involvement and the need for improved communication with children about immunization.
Active transportation as a way to increase physical activity among children
Authors: Morency C. , Demers M.
Published: December 2009

Background  This study examines how active transportation could help increase the daily physical activity volume of school‐aged children.

Methods  Using data from the 2003 Origin‐Destination Survey carried out among 5% of the 3.5 million residents of the Greater Montreal Area, we determined the proportion of short motorized trips made daily by children 5–14 years old (16 837 children sampled) and estimated the number of steps these trips would account for if they were travelled by foot, taking into account variables such as age, sex and height of children. Modal choice and trip purpose were also examined.

Results  In 2003, 31.2% of the daily trips made by children aged 5–14 years in the Greater Montreal Area were 1 km or less (0.6 mile). Of these, 33.0% were motorized trips. Overall, 13.1% of the children in the area had ‘steps in reserve’, an average of 2238 steps per child per day. If they were performed, these steps would account for 16.6% of the daily recommended volume of physical activity for children.

Conclusion  Replacing short motorized trips with walking could increase the physical activity level of children and contribute to meet the recommended guidelines, as long as these walking trips add to their daily physical activity volume. It could also reduce their dependence towards adults for moving around.
Collaborative transdisciplinary intervention in early years – putting theory into practice
Authors: Bell A. , Corfield M. , Davies J. , Richardson N.
Published: December 2009

Background  Recent government initiatives in the UK encourage collaborative working among professionals and highlight the importance of a co‐ordinated and collaborative approach in early years for families and children. There are many models of collaborative working but the evidence base for its effectiveness in early years (0–2.5 years) in a community setting in the UK is patchy. The aim of this study is to objectively evaluate the transdisciplinary model of collaborative working in this setting.

Methods  This paper describes the development of a transdisciplinary early intervention team providing services to a 0‐ to 2.5‐year‐old age group in a community setting in the UK, between 2004 and 2007. The effects on waiting times, therapy session attendance and caseload were evaluated.

Results  Statistically significant reduction in waiting times from an average 114–35.6 days for the highest priority children was demonstrated. Attendance at therapy sessions increased significantly from 49% in 2005 to 56% in 2006 and 75% 2007, despite an increasing case load from 29 in 2004 to 64 in 2008 through more efficient utilization of time and resources.

Conclusion  It is felt that this paper demonstrates, for the first time, the objective benefits to clients and fundholders/Primary Care Trust (PCT) of practical application of the theory of transdisciplinary working in a community paediatric service setting in the UK.
Family needs of parents of children and youth with cerebral palsy
Authors: Palisano R. J. , Almarsi N. , Chiarello L. A. , Orlin M. N. , Bagley A. , Maggs J.
Published: December 2009

Background  Understanding the needs of families of children and youth with cerebral palsy (CP) is important for family‐centred services. The aims of this study were to identify: (1) differences in the number and types of family needs expressed by parents based on the age and gross motor function level of their children with CP; (2) the most frequent family needs; and (3) needs that differ on gross motor function level.

Methods  A total of 501 parents (77.6% mothers) of children and youth with CP completed a modified version of a Family Needs Survey and a demographic questionnaire. Children's gross motor function level was classified using the Gross Motor Function Classification System.

Results  Total number of family needs differed based on gross motor function level (P < 0.001) but not age. Parents of children/youth who use wheeled mobility expressed the highest number of family needs, while parents of children/youth who walk without restrictions expressed the fewest needs. Family needs for Information (P= 0.001), Support (P= 0.001), Community Services (P < 0.001) and Finances (P < 0.001) differed based on children's gross motor function level. Over 50% of parents expressed family needs for information on current and future services, planning for the future, help in locating community activities and more personal time. Parents of children and youth who use wheeled mobility were more likely to express the need for help in paying for home modifications, equipment, services and locating sitters, respite care providers and community activities.

Conclusions  The gross motor function of children/youth with CP has implications for collaboration with families to identify needs and co‐ordinate services. Health professionals have a role to assist families with information needs and locating community services and leisure activities. Family needs for future planning suggest that health professionals should assist families to prepare for key periods in the lives of their children with CP.
The ConMap approach for terrain‐based digital soil mapping
Authors: Behrens T. , Schmidt K. , Zhu A. X. , Scholten T.
Published: December 2009

We present a new digital terrain analysis framework for digital soil mapping, referred to as contextual elevation mapping (ConMap). In contrast to common regression approaches based on features from digital terrain analysis, ConMap is not based on standard terrain attributes, but on elevation differences from the centre pixel to each pixel in circular neighbourhoods only. These differences are used as features in random forest regressions. We applied and validated the framework by predicting topsoil silt content in a loess region of 1150 km2in Rhineland‐Palatinate and Hesse, Germany. Three hundred and forty‐two samples and a 20‐m resolution digital elevation model were used for this illustration and validation. We compared ConMap with standard and multi‐scale terrain analysis approaches as well as with ordinary kriging interpolations. Cross‐validation root mean square error (RMSE)decreased from 16.1 when the standard digital terrain analysis was used to 11.2 when ConMap was used. This corresponds to an increase in variance explained (R2) from 15 to 61%. Even though ordinary kriging out‐performed standard terrain analysis as well, the variance explained was 6% smaller compared with that using ConMap. The results show that the geomorphic settings in the study area must have induced the spatial trend, which can be accounted for by ConMap over different scales. We conclude that ConMap shows great potential for digital soil mapping studies.
Impact of common European tree species on the chemical and physicochemical properties of fine earth: an unusual pattern
Authors: Mareschal L. , Bonnaud P. , Turpault M. P. , Ranger J.
Published: December 2009

Case studies are necessary to assess the effects of changes to tree species on the physicochemical and chemical properties of soils. To achieve this, the fine earth under five tree species was investigated. This study was performed in the Breuil‐Chenue experimental forest site located in the Morvan Mountains (France). This site contains two adjacent blocks with replicated stands. The native forest (old beech and oak coppice with standards) was partially clear‐felled and replaced in 1976 with mono‐specific plantations of European beech, Norway spruce, Laricio pine and Douglas fir. The same changes in soil properties were revealed in both blocks, thus confirming the tree species effect. The percentage of exchangeable acidity on the cation exchange capacity (CEC) was greater under spruce, Douglas fir and pine than under the other species. Spruce stands, and to a lesser extent those of Douglas fir and pine, had a less acidic soil pH than hardwood stands (which was unusual in view of the data in the literature) and smaller CEC values. The small quantities of carbon added to the soil under these tree species provide an explanation for these effects through a partial control of both CEC and pH. This case study thus demonstrated that the tree species effect was not unequivocal and different criteria are necessary for its interpretation. Tree species significantly influenced certain aspects of the chemical properties of topsoil and have the potential to have an impact on current soil fertility.
Time‐frequency seismic data de‐noising
Authors: Elboth Thomas , Vik Presterud Ida , Hermansen Dag
Published: December 2009

Marine seismic data are always affected by noise. An effective method to handle a broad range of noise problems is a time‐frequency de‐noising algorithm. In this paper we explain details regarding the implementation of such a method. Special emphasis is given to the choice of threshold values, where several different strategies are investigated. In addition we present a number of processing results where time‐frequency de‐noising has been successfully applied to attenuate noise resulting from swell, cavitation, strumming and seismic interference. Our seismic interference noise removal approach applies time‐frequency de‐noising on slowness gathers (τ−p domain). This processing trick represents a novel approach, which efficiently handles certain types of seismic interference noise that otherwise are difficult to attenuate. We show that time‐frequency de‐noising is an effective, amplitude preserving and robust tool that gives superior results compared to many other conventional de‐noising algorithms (for example frequency filtering, τ−p or fx‐prediction). As a background, some of the physical mechanisms responsible for the different types of noise are also explained. Such physical understanding is important because it can provide guidelines for future survey planning and for the actual processing.
Developmental regulation of the pheromone biosynthesis activating neuropeptide‐receptor (PBAN‐R): re‐evaluating the role of juvenile hormone
Authors: Bober R. , Azrielli A. , Rafaeli A.
Published: December 2009

Sex pheromone production in Helicoverpa armigera is regulated by pheromone‐biosynthesis‐activating neuropeptide (PBAN), which binds to a G‐protein coupled receptor at the pheromone gland. We demonstrate the temporal differential expression levels of the PBAN receptor (PBAN‐R) gene, reaching peak levels at a critical period of 5 h post‐eclosion. Previous studies implied a possible regulatory role for juvenile hormone (JH). We herein demonstrate that PBAN‐R expression levels increase normally when females are decapitated or head‐ligated, removing the source of JH, before peak transcript levels are reached. Similarly, sex pheromone production can be induced by PBAN in such decapitated females. These results indicate that up‐regulation, at this critical time, is not dependent on JH originating from the head. Conversely, JH injected in vivo at this critical period significantly inhibits PBAN‐R transcript levels.
Functional analysis of the cis‐acting elements responsible for the induction of the Cyp6a8 and Cyp6g1 genes of Drosophila melanogaster by DDT, phenobarbital and caffeine
Authors: Morra R. , Kuruganti S. , Lam V. , Lucchesi J. C. , Ganguly R.
Published: December 2009

Many Drosophila cytochrome P450 or Cyp genes are induced by caffeine and phenobarbital (PB). To understand the induction mechanism, we created Drosophila S2 cell lines stably transformed with different luciferase reporter plasmids carrying upstream DNAs of Cyp6a8 allele of the resistant 91‐R strain, and the 1.1‐kb upstream DNAs of Cyp6g1 of the 91‐R and the susceptible 91‐C strains. Following 24 h treatment with dichlorodiphenyltrichloroethane (DDT), caffeine or PB, luciferase activity of all cell lines was determined. Results showed that the 0.1‐kb DNA of Cyp6a8 and the upstream DNAs of Cyp6g1 from both strains are not induced by these chemicals in S2 cells. However, the 0.2‐, 0.5‐ and 0.8‐kb DNAs of Cyp6a8 showed 13–24‐, 4–5‐ and 2.2–2.7‐fold induction with caffeine, PB and DDT, respectively. These DNAs also showed a 2–3‐fold synergistic effect of caffeine and PB but not of caffeine and DDT. The results suggest that the cis‐regulatory elements for all three chemicals are located within the ‐11/‐199 DNA of Cyp6a8. Furthermore, caffeine and PB inductions appear to be mediated via different cis‐elements, whereas caffeine and DDT induction may involve common regulatory elements. These stably transformed cell lines should help understand the mechanism of resistance‐associated Cyp gene overexpression in Drosophila.
The use of likelihood ratio methodology to find predictors of treatment outcome in patients with dental injury diagnoses
Authors: EMSHOFF R. , GERHARD S. , ENNEMOSER T. , HÄCHEL O. , SCHERL M. , STROBL H.
Published: December 2009

Summary  The purpose of this prospective, cohort study of patients with dental injuries was to develop prediction rules to predict treatment response related to the management of dental injuries. The study comprised of 130 patients with a single permanent incisor affected by a dental displacement (n = 100) or fracture injury (n = 30). Laser Doppler flowmetry (LDF) measurements of pulpal blood flow (PBF) were taken 6 and 18 weeks after dental injury Treatment response (success or failure) was categorized based on findings of clinical and radiographical evaluation after 9 months. Forty‐four (34%) subjects were categorized as treatment success (absence of loss of sensitivity, periapical radiolucency and grey discolouration of crown), 43 (33%) as treatment failures (loss of sensitivity, and periapical radiolucency and/or grey discolouration of crown) and 43 (33%) as acceptable outcome (loss of sensitivity). After using univariate analysis to determine the association between potential clinical and LDF predictor variables and treatment response status, preliminary prediction rules were developed for prediction of success [positive likelihood ratio (LR), 29·0; 95% confidence interval (CI), 1·7–496·4] and failure (negative LR, 0·55; CI, 0·4–0·7). The most important variables were subluxation, root fracture, baseline PBF level and change in PBF level at 3‐month follow‐up. Outcome following the management of dental injuries may be predicted from variables collected from LDF and physical examination. Predictive modelling may provide clinicians with the opportunity to identify ‘at‐risk’ patients early and initiate specific treatment approaches.