bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and behavior of the barringerite Ni end‐member, Ni2P, at deep Earth conditions and implications for natural Fe‐Ni phosphides in planetary cores
Authors: Dera Przemyslaw , Lavina Barbara , Borkowski Lauren A. , Prakapenka Vitali B. , Sutton Stephen R. , Rivers Mark L. , Downs Robert T. , Boctor Nabil Z. , Prewitt Charles T.
Published: March 2009

High‐pressure and high‐temperature behavior of synthetic Ni2P has been studied in a laser‐heated diamond anvil cell up to 50 GPa and 2200 K. Incongruent melting associated with formation of pyrite‐type NiP2 and amorphous Ni‐P alloy was found at an intermediate pressure range, between 6.5 and 40 GPa. Above 40 GPa, Ni2P melts congruently. At room conditions, Ni2P has hexagonal C22‐type structure, and without heating it remains in this structure to at least 50 GPa. With a bulk modulus K0 = 201(8) GPa and K' = 4.2(6), Ni2P is noticeably less compressible than hcp Fe, as well as all previously described iron phosphides, and its presence in the Earth core would favorably lower the core density. In contrast to Fe2P, the c/a ratio in Ni2P decreases on compression because of the lack of ferromagnetic interaction along the c direction. Lack of the C22→C23 transition in Ni2P rules out a stabilizing effect of Ni on the orthorhombic phase of natural (Fe1−xNix)2P allabogdanite.
Correlations of small cumuli droplet and drizzle drop concentrations with cloud condensation nuclei concentrations
Authors: Hudson James G. , Noble Stephen , Jha Vandana , Mishra Subhashree
Published: March 2009

Aircraft field measurements of cloud condensation nuclei (CCN) and cloud microphysics in maritime air masses showed ubiquitous influence of CCN. Flight averages of CCN concentrations and cloud droplet and drizzle drop concentrations were examined for as many as 17 flights during the Rain in Cumulus over the Ocean (RICO) project. CCN concentrations at only one supersaturation (S) of 1% measured at 100‐m altitude were compared with cloud droplet and drizzle drop concentrations at six altitude bands between 600 and 3000 m. High positive correlations (R) between these CCN concentrations and the small size threshold of the cumulative cloud droplet concentrations (i.e., total activated cloud droplets) were found at all altitudes. These high R values also persisted for cloud parcels with a wide span of liquid water contents (LWCs), most of which were far below adiabatic (unmixed) values. For all but the lowest LWC parcels, R was essentially constant. There was an even more consistent negative R between CCN and large cloud droplet and drizzle drop concentrations. There was a sharp transition from positive to negative R over a small size range. The size at which this R transition occurred increased with altitude and LWC as overall droplet sizes increased with altitude or LWC. Entrainment seemed to show an opposite effect on R, but this was only apparent at the highest altitudes where entrainment was greatest and only for the smallest droplet sizes. These results indicate that the effect of CCN concentrations on cloud microphysics was pervasive with altitude, LWC, cloud droplet, and drizzle drop concentrations. This indicates greater impact of the indirect aerosol effect (IAE) in both of its manifestations, first IAE cloud radiation and second IAE precipitation.
Variability of aerosol optical depth over east Asia and its possible impacts
Authors: Bao Zhenhao , Wen Zhiping , Wu Renguang
Published: March 2009

On the basis of monthly aerosol optical depth (AOD) from the Moderate Resolution Imaging Spectroradiometer data set from March 2000 to May 2006, the present study analyzes the variability of the AOD over east Asia and its plausible relationship with cloud, surface shortwave radiation, and sea surface temperature (SST) over the North Pacific. Climatologically, the AOD over east Asia peaks around April or May, before the start of rainy season. The AOD decreases seasonally during May to August, likely because of the removal of aerosol from the atmosphere by precipitation. The leading mode of interannual AOD variations has large loading from east Asia to the North Pacific north of 30°N, with largest amplitudes often in May–June. The second mode has the same sign loading over eastern China, and the corresponding time series displays an obvious linear trend during the study period. Correlation analyses show that interannual variations of the AOD over east Asia may have important impacts on cloud and shortwave radiation over the western North Pacific, which, in turn, may induce SST anomalies.
Formation dry‐out from CO2 injection into saline aquifers: 2. Analytical model for salt precipitation
Authors: Pruess Karsten
Published: March 2009

From a mass balance for water dissolved into the flowing CO2 stream and a consideration of saturation profiles from the Buckley‐Leverett fractional flow theory, we derive an equation that directly relates gas saturation Sg,d at the dry‐out front to temperature, pressure, and salinity dependence of fluid properties. The equation is easily solved by iteration or interpolation. From gas saturation at the front we derive the average gas saturation in the dry‐out region, from which we obtain the “solid saturation” SS, i.e., the fraction of pore space filled with solid precipitate. Values of SS derived from this theory show excellent agreement with numerical simulations presented in the preceding companion paper. Thus, from relative permeabilities and fluid properties at in situ conditions prior to CO2 injection, it is possible to directly make an accurate estimate of solids precipitation, without having to perform a numerical simulation of the injection process.
Improved Tracking of Research Cruises
Authors: Urban Ed , Sathyendranath Shubha , de Leeuw Jan
Published: March 2009

Every year, several hundred ocean research cruises are conducted by academic institutions and government agencies worldwide, with major expenditures of finances and human resources. Ships may be in the same ocean area at the same time without prior knowledge of one another's activities, missing opportunities for joint work. Some ships go to sea with empty berths, which might have been filled if scientists from other institutions or countries had known about the availability of space. Many scientists using in situ instruments have missed opportunities to deploy them in seldom visited parts of the ocean because the scientists did not realize a ship was going to that area, and opportunities for ”sea truthing“ of satellite observations in remote regions are missed.

In an era of stagnant or shrinking budgets for research and ship operations, and increasing operational costs, it is imperative that scientists and ship operators look for ways to increase the efficiency of research cruises, for example, by reducing transit time and sharing research cruises. In addition, synergy of observations and opportunities for intercalibrations can be achieved in coordinated, multiple‐ship operations.
Improving Environmental Projections in Nonboreal Eastern Europe: Regional Aspects of Climate‐Terrestrial‐Hydrologic Interactions in Non‐boreal Eastern Europe; Odessa, Ukraine, 23–28 August 2008
Authors: Groisman Pavel , Ivanov Sergiy , Gutman Garik , Simmer Clemens
Published: March 2009

Ecosystems in Eastern Europe, in particular environments such as grasslands and semiarid regions, have undergone significant changes during the entire twentieth century due to warming climate and socioeconomic impacts. As a result, the biome boundaries between forests and steppes and between steppes and semideserts have become increasingly volatile, with dramatic changes in phenology and land fertility. Compounding these problems is a dense rural population engaging in intense land use, a population that suffers socioeconomic hardships resulting from recent and still unsettled political changes. Such political problems combined with a lack of local funds have limited the amount of observational data collected in Eastern Europe, leaving climate modelers unable to validate regional climate projections.
Zoback Receives 2008 Walter H. Bucher Medal
Authors: Mooney Walter D. , Zoback Mark D.
Published: March 2009

Mark D. Zoback was awarded the 2008 Walter H. Bucher Medal at the AGU Fall Meeting Honors Ceremony, held 17 December 2008 in San Francisco, Calif. The medal is for “original contributions to the basic knowledge of the Earth's crust.”
Metabolic disturbances in non-alcoholic fatty liver disease
Authors: Byrne Christopher D. , Olufadi Rasaq , Bruce Kimberley D. , Cagampang Felino R. , Ahmed Mohamed H.
Published: March 2009

NAFLD (non-alcoholic fatty liver disease) refers to a wide spectrum of liver damage, ranging from simple steatosis to NASH (non-alcoholic steatohepatitis), advanced fibrosis and cirrhosis. NAFLD is strongly associated with insulin resistance and is defined by accumulation of liver fat >5% per liver weight in the presence of <10 g of daily alcohol consumption. The exact prevalence of NAFLD is uncertain because of the absence of simple non-invasive diagnostic tests to facilitate an estimate of prevalence. In certain subgroups of patients, such as those with Type 2 diabetes, the prevalence of NAFLD, defined by ultrasound, may be as high as 70%. NASH is an important subgroup within the spectrum of NAFLD that progresses over time with worsening fibrosis and cirrhosis, and is associated with increased risk for cardiovascular disease. It is, therefore, important to understand the pathogenesis of NASH and, in particular, to develop strategies for interventions to treat this condition. Currently, the ‘gold standard’ for the diagnosis of NASH is liver biopsy, and the need to undertake a biopsy has impeded research in subjects in this field. Limited results suggest that the prevalence of NASH could be as high as 11% in the general population, suggesting there is a worsening future public health problem in this field of medicine. With a burgeoning epidemic of diabetes in an aging population, it is likely that the prevalence of NASH will continue to increase over time as both factors are important risk factors for liver fibrosis. The purpose of this review is to: (i) briefly discuss the epidemiology of NAFLD to describe the magnitude of the future potential public health problem; and (ii) to discuss extra- and intra-hepatic mechanisms contributing to the pathogenesis of NAFLD, a better understanding of which may help in the development of novel treatments for this condition.
Speech-Language Pathology Assistants Current State of Affairs
Authors: McNeilly Lemmietta
Published: March 2009

The utilization of speech-language pathology assistants (SLPAs) is increasing in the United States particularly in the public schools. The American Speech-Language-Hearing Association provides specific guidelines regarding the training, use, and supervision of (SLPAs; ASHA, 2004). The current state of affairs of SLPAs involves variable requirements across the states to qualify for SLPA credentials. The programs that educate SLPAs have variable technical and curricular requirements, and the educational requirements for regulating SLPAs also vary across the states. School-based SLPs continue to raise questions about the supervision requirements, funding, and reimbursement issues for working with SLPA in schools across the country.
Using What You Have: Training Teacher Assistants as Speech-Language Assistants
Authors: Keane Lisa , Rogers Laura
Published: March 2009

The “Speech-Language Assistant (S/L Assistant or SLA) Model” in Broward County Schools was created to assist the speech-language pathologist (SLP) with the continuing effort to provide quality programs to students with speech and language impairments. Through the perseverance and dedication of a group of SLPs and the organization SPEECH (Speech Language Pathologists Energetically Effecting Change), a 3-year study called The Speech Language Improvement Plan was initiated. The study demonstrated that the use of S/L assistants increased dismissal rates, allowed for better caseload management, and improved the student / SLP ratio. In order to maintain consistency and fidelity of the SLA Model, specific requirements were established. Consideration of the S/L Assistant Model for a school requires that the school administrator and SLP review caseload, workload, and budget factors to determine the needs of the students. There are limitations to the responsibilities of an S/L assistant that must be taken into consideration as well. Training of the S/L assistant includes a variety of activities, readings, and observations along with verification of competencies.
The Evolution of an SLPA Program
Authors: Sparks Susan , Van Horne Lisa
Published: March 2009

There is an increasing demand for qualified individuals available in our profession. One answer to this crisis is to hire trained speech-language pathology assistants (SLPAs) to assist speech language pathologists (SLPs). Shoreline Community College's SLPA program was created in response to the shortage of fully trained SLPs. The program is designed in strict compliance with ASHA's guidelines (ASHA, 2004). Students attend lectures remotely, complete assigned reading, take quizzes, engage in in-class and online discussions, turn in assignments, and take exams without ever having to commute to the Shoreline campus. This allows students from across the state to complete their education while continuing to live and work in their communities.
Relationship between oxidative degradation of 2-mercaptobenzothiazole and physicochemical properties of manganese (hydro)oxides
Authors: Liu C. S. , Zhang L. J. , Feng C. H. , Wu C. A. , Li F. B. , Li X. Z.
Published: March 2009

Environmental context. Manganese (hydro)oxide is one kind of the most important natural minerals that are capable of oxidising organic contaminants with a wide range of functionality. However, the oxidative reactivity of manganese (hydro)oxides for organic pollutant degradation may depend on their individual physicochemical properties. It is important to determine a relationship between their oxidative reactivity and physicochemical properties. Abstract. The oxidative reactivity of manganese (hydro)oxides is important for geochemical transformation of organic pollutants. Here, 2-mercaptobenzothiazole (MBT) degradation by six manganese (hydro)oxides, including γ-MnOOH, β-MnO2, α-MnO2, γ-Mn2O3, δ-MnO2, and MO-700, were investigated with different initial MBT concentrations, manganese (hydro)oxide dosages and pH values. The results show the oxidative reactivity of manganese (hydro)oxides towards MBT degradation strongly depends on their physicochemical properties. Specific surface area and reduction potential of manganese (hydro)oxides were positively correlated with MBT degradation rates, whereas pH at the point of zero charge (pHPZC) of manganese (hydro)oxides and apparent activation energy (Ea) were negatively correlated. A high average oxidation state with the same chemical valence always corresponds to high oxidative reactivity. Such findings provide some insights into understanding the transport and fate of organic pollutants in the presence of different manganese (hydro)oxides in the natural environment.
Perchlorate and ion chemistry of road runoff
Authors: Munster Jennie , Hanson Gilbert N.
Published: March 2009

Environmental context. Recognising that road flares and air bags may contribute perchlorate to road runoff, we analysed perchlorate in runoff from two accident-prone suburban highways during a period of five rain events. This runoff reaches recharge basins where it then infiltrates into the groundwater. The concentrations of perchlorate averaged ~2 μg L–1, high enough to be of concern if the drinking water standard for perchlorate were in the low μg levels.
Abstract. First flush samples of road runoff were sampled in April 2006 corresponding with five rain events at 12 catch basins and two recharge basins in Suffolk County, NY. Most runoff here is directed into recharge basins or sumps that drain directly into the sole source aquifer. Thus, contaminants from road runoff can contaminate groundwater. In addition to ClO4, we present data for Cl, Na, Br, Sr, and nitrogen as nitrate (N-NO3) as they are the dominant ions in the most probable sources of ClO4 to road runoff, presumably road flares, road salt, air bags and road-side fertilizers. Correlations between the ions indicate that road salt elevates concentrations of Na, Br and Cl in road runoff. The average ClO4 value is 2.18 ± 0.66 (standard error of the mean) μg L–1 for the catch basins and 2.98 ± 0.87 μg L–1 for the two recharge basins. Excess ClO4 in the present study appears mainly from road flares. On average, only 47% of the ClO4 in the catch basins and 11% in the recharge basins can be accounted for by bulk precipitation.
Characteristics of perchlorate formation via photodissociation of aqueous chlorite
Authors: Kang Namgoo , Anderson Todd A. , Rao Balaji , Jackson W. Andrew
Published: March 2009

Environmental context. Perchlorate, a well-known thyroid disruptor with both man-made and natural sources represents a major environmental problem in the United States but little information is available concerning the source of natural perchlorate. Previous research has demonstrated that perchlorate can be produced from exposure of some chlorine compounds to ultraviolet radiation, but no information was available how quickly or comparatively how much perchlorate was formed. The results of the present study can be used to evaluate the potential impact of ultraviolet processes on the overall occurrence of perchlorate in the environment.
Abstract. The present study provides new and important information on perchlorate (ClO4–) formation through ultraviolet (UV) photodissociation of unbuffered chlorite (ClO2–) solutions from the standpoint of kinetics under three different wavelength regimes having maximum emissions, λe,max, at 235.7, 300 and 350 nm. ClO4– production rates and yields were in general found to be inversely related, with higher yields and lower rates at higher wavelengths, and vice versa. A simple kinetic model for ClO4– production as a function of the ClO2– first-order decay constant and starting concentration was fitted to the experimental data, resulting in the calculation of a rate constant, k2, which is a function of light-source characteristics. Further, a conceptual scheme for ClO4– formation via photochemical reactions between oxychlorine species was proposed based on the experimental results and available literature. The present study is a further step towards understanding the formation of ClO4– from the photolysis of its precursors.
Perchlorate: a cause for iodine deficiency?
Authors: Dasgupta Purnendu K.
Published: March 2009

Environmental context. Depending on its severity, inadequate iodine nutrition can lead from minor developmental disorders all the way to cretinism. In recent years, the omnipresence of environmental perchlorate, a potent iodine transport inhibitor, has been much in the news but the ultimate issue of iodine nutrition has largely been ignored. There is little consciousness that even many developed nations are putting future generations in peril with vulnerable populations that are barely iodine sufficient, whether or not there is any excessive perchlorate intake.
Seasonality, abundance and breeding biology of one of the largest populations of nesting flatback turtles, Natator depressus: Cape Domett, Western Australia
Authors: Whiting Andrea U. , Thomson Allan , Chaloupka Milani , Limpus Colin J.
Published: March 2009

Cape Domett, located in tropical Western Australia, supports a significant population of flatback turtles, Natator depressus, but the magnitude of this was previously underestimated. We assessed temporal nesting abundance to find that Cape Domett supports one of the largest aggregated nesting flatback turtle populations globally with annual abundance in the order of several thousand individuals (estimated = 3250, 95% CI = 1431–7757). We assessed temporal abundance within a year to find turtles nested throughout the year with peak nesting occurring between August and September. This paper re-evaluates the importance of this major flatback turtle nesting site and shows the first detailed examination of flatback turtle nesting biology in north-western Australia.
Scabies Outbreak in an Intensive Care Unit with 1,659 Exposed Individuals—Key Factors for Controlling the Outbreak
Authors: Buehlmann Manuela , Beltraminelli Helmut , Strub Christoph , Bircher Andreas , Jordan Xavier , Battegay Manuel , Itin Peter , Widmer Andreas F.
Published: March 2009

Objective.

To investigate a large outbreak of scabies in an intensive care unit of a university hospital and an affiliated rehabilitation center, and to establish effective control measures to prevent further transmission.

Design.

Outbreak investigation.

Setting.

The intensive care unit of a 750-bed university hospital and an affiliated 92-bed rehabilitation center.

Methods.

All exposed individuals were screened by a senior staff dermatologist. Scabies was diagnosed on the basis of (1) identification of mites by skin scraping, (2) identification of mites by dermoscopy, or (3) clinical examination of patients without history of prior treatment for typical burrows. During a follow-up period of 6 months, the attack rate was calculated as the number of symptomatic individuals divided by the total number of exposed individuals.

Interventions.

All exposed healthcare workers (HCWs) and their household members underwent preemptive treatment. Initially, the most effective registered drug in Switzerland (ie, topical lindane) was prescribed, but this prescribption was switched to topical permethrin or systemic ivermectin as a result of the progression of the outbreak. Individuals with any signs or symptoms of scabies underwent dermatological examination.

Results.

Within 7 months, 19 cases of scabies were diagnosed, 6 in children with a mean age of 3.1 years after exposure to the index patient with HIV and crusted scabies. A total of 1,640 exposed individuals underwent preemptive treatment. The highest attack rate of 26%–32% was observed among HCWs involved in the care of the index patient. A too-restricted definition of individuals at risk, non-compliance with treatment, and the limited effectiveness of lindane likely led to treatment failure, relapse, and reinfestation within families.

Conclusions.

Crusted scabies resulted in high attack rates among HCWs and household contacts. Timely institution of hygienic precautions with close monitoring and widespread, simultaneous scabicide treatment of all exposed individuals are essential for control of an outbreak.
The Short-Tailed Fruit Bat Carollia perspicillata: A Model for Studies in Reproduction and Development
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R.
Published: March 2009

INTRODUCTION

Carollia perspicillata has proven to be a valuable laboratory model for studies in reproduction and development. We present here an overview of the care and handling of Carollia in captivity and discuss some pertinent studies in reproductive biology. Finally, we describe various features of the genome and some of the genetic manipulations that are now possible.
Darwin’s Finches: Analysis of Beak Morphological Changes During Evolution: Figure 1.
Authors: Abzhanov Arhat
Published: March 2009

INTRODUCTION

Finches of the Galápagos Islands were first described by Charles Darwin during his voyage on the HMS Beagle in 1835. Since then, through the subsequent work of many biologists, Darwin’s finches have become a classic textbook example of many important processes in evolution. Today, this group of birds continues to be a significant source of information on such processes as speciation, niche partitioning, morphological adaptation, and species ecology. The approximately 14 species of Darwin’s finches are closely related to one another and display a remarkable degree of diversity in bill shapes and sizes that are adapted for different food sources (e.g., seeds, insects, and even young leaves or blood from sea birds) in an otherwise scarce environment. For example, the deep and wide bills of the Ground Finches, one of the subgroups of Darwin’s finches, are used to feed on seeds, whereas the Cactus Finches use their elongated and narrow bills to probe cactus fruit and flowers. These differences in bill shapes are not due to their differential usage or other external factors; rather, the differences are genetically and developmentally regulated and can be observed and studied during embryogenesis. Therefore, Darwin’s finches are becoming a very useful non-model animal and avian system in which to investigate the molecular basis of morphological changes during evolution.
PCR Primer Design
Authors: Apte Arun , Daniel Saurabha
Published: March 2009

INTRODUCTION

The objective of a polymerase chain reaction (PCR) is to amplify a specific DNA segment without any nonspecific by-products. In principle, each physical and chemical component of PCR can be modified to produce a potential increase in yield, specificity, or sensitivity. Yet the most critical parameter for successful PCR is optimal primer design. A poorly designed primer can result in little or no product, due to nonspecific amplification and/or primer-dimer formation leading to reaction failure, even when all the other parameters are properly optimized. This article provides general guidelines for PCR primer design, tips for development of primer pairs for more complex applications, and advice on the development of probes for real-time PCR.
Collection of Short-Tailed Fruit Bats (Carollia perspicillata) from the Wild: Figure 1.
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R.
Published: March 2009

INTRODUCTION

Adult female short-tailed fruit bats (Carollia perspicillata) exhibit a relatively high degree of reproductive synchronization in populations sampled carefully in Central America and on Trinidad. On the basis of these studies and temporal data for pregnancies in captive-bred animals, one may be able to sample adult female Carollia from other populations and, during much of the year, predict when different embryonic stages might be prevalent. Most adult female Carollia on Trinidad seem to carry two pregnancies each year, based on the observation that more than 90% are typically pregnant when sampled around the middle of each pregnancy period. For many females, the first pregnancy appears to be established between September and early November, includes a period of post-implantational developmental delay at the primitive streak stage, and is completed in March or April. A peak in births has been observed around April 1. Most parous females then conceive again at a post-partum estrus. In captive animals, this estrus usually occurs between 3 and 6 d after parturition, but sometimes, it is several days later. Using the available temporal data on pregnancies in both captive and wild Carollia, it is possible to predict when embryos at particular stages of development are most likely to be carried by females in the wild population on Trinidad. A similar approach might be used to collect embryos from another population, as outlined in this protocol.
Whole-Mount In Situ Hybridization of Short-Tailed Fruit Bat (Carollia perspicillata) Embryos with RNA Probes
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R.
Published: March 2009

INTRODUCTION

This protocol describes whole-mount in situ hybridization of short-tailed fruit bat (Carollia perspicillata) embryos with RNA probes. This technique allows direct visualization of the mRNA expression pattern of a gene of interest within embryos fixed at a wide range of developmental stages. Due to limitations in probe penetration, the size of the specimen must be considered when using whole-mount procedures. In addition, the preparation of probe is an important step in whole-mount in situ hybridization. Two primary considerations for making a good probe are (1) a good template sequence and (2) an efficient labeling reaction. In our experience, the ideal template sequence for a whole-mount in situ probe should be 300-1000 bp in length. We have had little success using shorter probes, although they can be made to work in a case-by-case (and presumably sequence-dependent) manner. Typically, one begins with a cDNA or coding genomic fragment cloned into an in vitro transcription vector. The linearized vector is purified and used as the template for in vitro transcription. In this protocol, the in situ hybridization procedure is presented as a 3-d schedule: Day 1, Pre-treatment and hybridization; Day 2, Post-hybridization washes and antibody incubation; and Day 3, Post-antibody washes and color reaction.
Alcian Blue Staining of Cartilage of Short-Tailed Fruit Bat (Carollia perspicillata): Figure 1.
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R.
Published: March 2009

INTRODUCTION

This protocol is used to visualize the cartilaginous elements of the developing skeleton using alcian blue. It has been used with excellent results on the fruit bat Carollia perspicillata, as well as several other bat species at stages from CS 14 through CS 22. Staining has been shown to last at least 2 yr in benzyl alcohol:benzyl benzoate (BABB). However, staining has been observed to weaken during the course of months. It is therefore advisable to document results immediately.
Whole-Mount Immunohistochemistry of Short-Tailed Fruit Bat (Carollia perspicillata)
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R.
Published: March 2009

INTRODUCTION

This protocol describes whole-mount immunohistochemistry of short-tailed fruit bat (Carollia perspicillata) embryos. This method is used for direct visualization of the expression pattern of a protein of interest within embryos fixed at a wide range of developmental stages. It has been used with good results on embryos at stages from CS 11 through CS 15.
Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture
Authors: Tiwari Vijay K. , Baylin Stephen B.
Published: March 2009

INTRODUCTION

Progress in technologies to address long-range chromosomal interactions in vivo has extensively revised concepts about different aspects of transcriptional regulation. These methods allow probing physical proximities between chromatin elements without specifically identifying the protein components that mediate such interactions. Here we describe a detailed protocol for Combined 3C-ChIP-Cloning (6C) technology, which combines multiple techniques to identify the proteins that bridge distant genomic regions, while simultaneously identifying such physical proximities. This method is also useful for determining if a candidate protein might mediate long-range interactions, both in cis and in trans in the nucleus. We discuss how the 6C technique can be incorporated with other techniques to discover all the chromatin regions in the nucleus that interact with a given gene or chromatin region of interest in a specific protein-dependent manner. Such information allows complete, cell-type-specific mapping of all the chromatin interactions mediated by specific proteins. The 6C assay advances our understanding of the three-dimensional aspects of the higher-order folding of chromatin and provides an important tool to examine the role of specific proteins in nuclear organization. In addition to providing a detailed protocol of the 6C technique, we discuss how this technology can be used by investigators working in the area of chromatin biology, with special interest in chromatin long-range interactions.
Alcian Blue Staining of the Mouse Fetal Cartilaginous Skeleton: Figure 1.
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard
Published: March 2009

INTRODUCTION

The vertebrate skeleton forms by endochondral and intramembranous bone formation. During endochondral bone formation, mesenchyme condensations give rise to cartilages that are eventually replaced by bone. However, there are some permanent cartilages that do not ossify, such as the cartilage of the trachea and articular cartilage of the joints, and intramembranous bone formation occurs directly without a cartilage template. This protocol is ideal for revealing the cartilaginous skeleton of mouse embryos between 12.5 and 16.5 days post-coitum (dpc). The cartilaginous skeleton is stained dark blue by alcian blue, whereas the other tissues of the embryo are made transparent by a clearing solution, benzyl alcohol/benzyl benzoate (BABB).
Alizarin Red Staining of Post-natal Bone in Mouse
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard
Published: March 2009

INTRODUCTION

The vertebrate skeleton forms by endochondral and intramembranous bone formation. During endochondral bone formation, mesenchyme condensations give rise to cartilages that are eventually replaced by bone. However, there are some permanent cartilages that do not ossify, such as the cartilage of the trachea and articular cartilage of the joints, and intramembranous bone formation occurs directly without a cartilage template. This article describes an abbreviated outline of a technique for staining the bone of newborn and adult mice. Because the ossified skeleton is a robust tissue, even the skeletons of dead animals can be processed using this method.
Regulating Protein Stability in Mammalian Cells Using Small Molecules
Authors: Hagan Emily L. , Banaszynski Laura A. , Chen Ling-chun , Maynard-Smith Lystranne A. , Wandless Thomas J.
Published: March 2009

INTRODUCTION

Regulating protein stability using small molecules provides a rapid, reversible, and tunable method to study a protein of interest’s (POI) role in cells. We recently designed a small protein domain based on the 12-kDa FKBP (FK506 binding protein) that can be fused at either the carboxyl or amino terminus of a protein of interest. This destabilization domain (DD) confers instability to fusion protein partners. The method described here explains how to use a DD fusion to control the biological activity of a POI. In the absence of a small molecule ligand, the DD is unstable and directs the fusion protein for degradation. Addition of the ligand stabilizes the DD, allowing the fusion protein to accumulate in cells and the POI to exert its biological effect. The ligand is specific for the DD and has no detectable off-target effects. By utilizing the specificity of genetic fusion and the speed of small molecule binding, this technique provides an alternative to RNA interference to study a POI’s role in cells.
A General Method for Conditional Regulation of Protein Stability in Living Animals
Authors: Sellmyer Mark A. , Thorne Steve H. , Banaszynski Laura A. , Contag Christopher H. , Wandless Thomas J.
Published: March 2009

INTRODUCTION

The ability to rapidly and reversibly perturb protein levels in living animals is a powerful tool for researchers to determine protein function in complex systems. We recently designed a small protein domain based on the 12-kDa FKBP (FK506 binding protein) that can be fused at either the carboxyl or amino terminus of a protein of interest. This destabilization domain (DD) confers instability to fusion protein partners, allowing targeted degradation of the protein of interest. A small molecule called Shield-1 binds to the DD and protects the fusion protein from degradation. Small-molecule-mediated post-translational regulation of protein stability affords this system rapid, reversible, and tunable control of protein levels and functions in a variety of model systems. Theoretically, a number of transgene delivery methods (e.g., viral, liposomal, or stem cell) can be used for the analysis of a DD fusion protein in an animal model. This protocol uses tumor xenografts in mice as one such mechanism for delivering the fusion protein and presents a method for delivering Shield-1 to regulate the fusion proteins in vivo.
In Situ Hybridization Analysis of Embryonic Beak Tissue from Darwin’s Finches
Authors: Abzhanov Arhat
Published: March 2009

INTRODUCTION

The beaks of Darwin’s finches develop their distinct shapes during embryogenesis. To visualize where and when mRNA transcripts of genes involved in beak development are present during embryogenesis, this protocol describes how to analyze embryonic tissue samples using in situ hybridization. The principle of this technique is to use probes specific to mRNAs coding for proteins of interest to reveal how the corresponding genes are expressed in the beaks of different species of Darwin’s finches.
Microarray Analysis of Embryonic Beak mRNA from Darwin’s Finches
Authors: Abzhanov Arhat
Published: March 2009

INTRODUCTION

In this protocol, microarray technology is used as a very sensitive and rapid method to identify genes that are potentially involved in beak development and morphology in Darwin’s finches. The method allows for the direct comparison between cDNA targets from two different species (each labeled with a different dye). The prevalence of one of the dyes for any of the genes on the resulting scan indicates a higher level of accumulation of transcripts from that gene in a particular beak morphology/species. The obtained expression profiles can be clustered to identify transcripts that are expressed in a species- and/or size-specific manner.
Preparation of Recombinant Baculoviruses with the BVboost System
Authors: Airenne Kari J. , Laitinen Olli H. , Mähönen Anssi J. , Ylä-Herttuala Seppo
Published: March 2009

INTRODUCTION

We have developed an improved transposition-based system (BVboost) for the generation of recombinant baculoviruses. This system bypasses the disadvantages of the original transposition-based generation of baculoviral genomes in Escherichia coli while remaining a simple, rapid, and convenient viral production technique. The method is based on the modified donor vector (pBVboost) and an improved selection scheme of the baculoviral genomes (bacmids) in E. coli with a mutated sacB gene. Recombinant bacmids can be generated at a frequency of ~107/μg of donor vector with a negligible background. The BVboost system also allows efficient setups for high-throughput screening and gene expression purposes. After cloning the desired gene/cDNA/library into a BVboost system-compatible donor plasmid, the recombinant baculoviral genome is prepared simply by transforming electrocompetent DH10BacΔTn7 E. coli cells with the donor. Transfer from the donor vector into the baculoviral genome (bacmid) occurs via a Tn7-mediated site-specific transposition reaction in E. coli cells. The selection scheme guarantees that virtually all colonies are correct. The recombinant baculoviral genome is subsequently extracted from E. coli culture using a modified isolation procedure for large plasmids. To generate the recombinant viruses, insect cells are transfected with the isolated recombinant bacmid. This protocol provides instructions on how to prepare recombinant baculoviruses by the BVboost system in order to express the desired gene(s) in insect and/or vertebrate cells.
Immigrant Communities and Civil War
Authors: Laitin David D.
Published: March 2009

This paper explains why international migrants, who face numerous security and cultural threats in their host societies, are almost never implicated in civil war violence. This is quite different from situations of internal migration, which often set off violence that escalates to civil war proportions. The paper first lays out the stark contrast between the political implications of external and internal migration based on data adapted from the Minorities at Risk (MAR) dataset. It then explores the reasons for the low incidence of civil war violence for international migrants through an examination of three cases: Bahrain, which has a large expatriate community without political rights that has been politically quiescent; Estonia, where some 30 percent of the population are disaffected Russian-speakers linked to post-World War II migrations from other republics of the Soviet Union; and Pakistan, where the immigrant Muhajirs are a partial exception to the general pattern outlined in this paper. It concludes with a general statement of the relationship between immigration and rebellion, where the level of grievances is less consequential than the conditions that make insurgency pay off.
Turkish Immigrants in Sweden: Are They Integrated?
Authors: Bayram Nuran , Nyquist Hans , Thorburn Daniel , Bilgel Nazan
Published: March 2009

Many in Europe believe that large numbers of Turkish immigrants have failed to integrate into their host communities. How is this situation in Sweden? We found that most of the Turkish immigrants felt themselves to be Turkish and Sweden was accepted as a foreign country. Turkish-originated media was followed frequently and strong ties with relatives in Turkey were maintained. Marriage and friendship with native Swedes were not well accepted. We concluded that despite the multicultural aspects of Swedish integration policies, Turkish immigrants in Sweden were not well integrated and they prefer to live within the boundaries of their segregated, closed, small communities.
Gender Stereotyping in the Dutch Asylum Procedure: “Independent” Men versus “Dependent” Women
Authors: Mascini Peter , van Bochove Marjolein
Published: March 2009

Attention for discrimination against women in asylum law has grown considerably during the last few decades. Yet it is male claimants who have had smaller success rates in the asylum procedures of different countries. Using administrative data from the Dutch INS, we show this difference is caused by the traditionally gendered migration pattern of asylum seekers. Men have a smaller success rate than women because they are less likely than women to have a spouse or children, are less likely to follow their spouse to the country of destination, and are more likely to come from countries considered to be safe. This suggests that men are less successful in their attempts to seek asylum because they better fit the image of “bogus” refugees, while women more clearly match the image of “victim of patriarchal domination.”
Migration Plans and Received Remittances: Evidence from Fiji and Tonga
Authors: Leeves Gareth
Published: March 2009

This paper investigates the relationship between remittances and migration intentions in the source country using data from households in the Pacific island countries of Tonga and Fiji. Unlike previous research it accounts for potential endogeneity in the relationship between remittances and intentions and also includes households that receive remittances but do not have current migrants. We find a positive impact of remittances on intentions. The impact of remittances on intentions is stronger in a country with a longer history of migration and stronger in households with current migrants than those without migrants. These results provide new evidence on the role of remittances in the development of migration chains.
Pancreatic adenocarcinoma up‐regulated factor (PAUF), a novel up‐regulated secretory protein in pancreatic ductal adenocarcinoma
Authors: Kim Sun A. , Lee Yangsoon , Jung Dawoon E. , Park Kyung Hwa , Park Jeong Youp , Gang Jingu , Jeon Sun Bok , Park Eui Chul , Kim Young‐Gun , Lee Bogman , Liu Qing , Zeng Wen , Yeramilli Subramanyam , Lee Soojin , Koh Sang Seok , Song Si Young
Published: March 2009

The identification of novel tumor‐specific proteins or antigens is of great importance for diagnostic and therapeutic applications in pancreatic cancer. Using oligonucleotide microarrays, we identified a broad spectrum of differentially expressed pancreatic cancer‐related genes. Of these, we selected an overexpressed expressed sequence taq and cloned a 721‐bp full‐length cDNA with an open reading frame of 196 amino acids. This novel gene was localized on the Homo sapiens 16p13.3 chromosomal locus, and its nucleotide sequence matched the Homo sapiens similar to common salivary protein 1 (LOC124220). We named the gene pancreatic adenocarcinoma up‐regulated factor. The pancreatic adenocarcinoma up‐regulated factor was secreted into the culture medium of pancreatic adenocarcinoma up‐regulated factor‐overexpressing Chinese hamster ovary cells, had an apparent molecular mass of ~25 kDa, and was N‐glycosylated. The induction of pancreatic adenocarcinoma up‐regulated factor in Chinese hamster ovary cells increased cell proliferation, migration, and invasion ability in vitro. Subcutaneous injection of mice with Chinese hamster ovary/pancreatic adenocarcinoma up‐regulated factor cells resulted in 3.8‐fold greater tumor sizes compared to Chinese hamster ovary/mock cells. Reverse transcription–polymerase chain reaction and western blotting with antirecombinant human pancreatic adenocarcinoma up‐regulated factor antibodies confirmed that pancreatic adenocarcinoma up‐regulated factor was highly expressed in six of eight pancreatic cancer cell lines. Immunohistochemical staining of human pancreatic cancer tissues also showed pancreatic adenocarcinoma up‐regulated factor overexpression in the cytoplasm of cancer cells. Transfection with pancreatic adenocarcinoma up‐regulated factor‐specific small‐interfering RNA reduced cancer cell migration and invasion in vitro. Treatment with antirecombinant human pancreatic adenocarcinoma up‐regulated factor in vitro and in vivo reduced proliferation, migration, invasion, and tumorigenic ability. Collectively, our results suggest that pancreatic adenocarcinoma up‐regulated factor is a novel secretory protein involved in pancreatic cancer progression and might be a potential target for the treatment of pancreatic cancer. (Cancer Sci 2009; 100: 828–836)
Down‐regulation of cIAP2 enhances 5‐FU sensitivity through the apoptotic pathway in human colon cancer cells
Authors: Karasawa Hideaki , Miura Koh , Fujibuchi Wataru , Ishida Kazuyuki , Kaneko Naoyuki , Kinouchi Makoto , Okabe Mitsunori , Ando Toshinori , Murata Yukio , Sasaki Hiroyuki , Takami Kazuhiro , Yamamura Akihiro , Shibata Chikashi , Sasaki Iwao
Published: March 2009

Currently 5‐fluorouracil (5‐FU) plays a central role in the chemotherapeutic regimens for colorectal cancers and thus it is important to understand the mechanisms that determine 5‐FU sensitivity. The expression profiles of human colon cancer cell line DLD‐1, its 5‐FU‐resistant subclone DLD‐1/FU and a futher 21 types of colon cancer cell lines were compared to identify the novel genes defining the sensitivity to 5‐FU and to estimate which population of genes is responsible for 5‐FU sensitivity. In the hierarchical clustering, DLD‐1 and DLD‐1/FU were most closely clustered despite over 100 times difference in their 50% inhibitory concentration of 5‐FU. In DLD‐1/FU, the population of genes differentially expressed compared to DLD‐1 was limited to 3.3%, although it ranged from 4.8% to 24.0% in the other 21 cell lines, thus indicating that the difference of 5‐FU sensitivity was defined by a limited number of genes. Next, the role of the cellular inhibitor of apoptosis 2 (cIAP2) gene, which was up‐regulated in DLD‐1/FU, was investigated for 5‐FU resistance using RNA interference. The down‐regulation of cIAP2 efficiently enhanced 5‐FU sensitivity, the activation of caspase 3/7 and apoptosis under exposure to 5‐FU. The immunohistochemistry of cIAP2 in cancer and corresponding normal tissues from colorectal cancer patients in stage III revealed that cIAP2 was more frequently expressed in cancer tissues than in normal tissues, and cIAP2‐positive patients had a trend toward early recurrence after fluorouracil‐based chemotherapy. Although the association between drug sensitivity and the IAP family in colorectal cancer has not yet been discussed, cIAP2 may therefore play an important role as a target therapy in colorectal cancer. (Cancer Sci 2009; 100: 903–913)