bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane‐Based Yeast Two‐Hybrid System to Detect Protein Interactions
Authors: Lentze Nicolas , Auerbach Daniel 
Published: May 2008

AbstractThe classical yeast two‐hybrid system and its modifications have been successfully used over the past decade to investigate interactions between most classes of proteins expressed in a given cell or tissue. However, some proteins (e.g., integral membrane proteins or nuclear proteins) are relatively difficult to investigate by standard yeast two‐hybrid methods either because they are retained at cellular membranes or they activate the system in the absence of a true protein interaction. The membrane‐based yeast two‐hybrid (MbY2H) system presented in this unit overcomes some of these limitations. It is based on the split‐ubiquitin protein complementation assay and detects protein interactions directly at the membrane, thereby allowing the use of full‐length integral membrane proteins and membrane‐associated proteins as baits to hunt for novel interaction partners. A simple modification also allows the use of proteins that are self‐activating in a classical yeast two‐hybrid system (e.g., acidic proteins and many transcription factors). Like the yeast two‐hybrid system, the MbY2H system can also be used for interaction discovery by screening complex cDNA libraries for novel interaction partners. Curr. Protoc. Protein Sci. 52:19.7.1‐19.7.28. © 2008 by John Wiley & Sons, Inc.
Assessment of Lymphocyte Development in Radiation Bone Marrow Chimeras
Authors: Spangrude Gerald J. 
Published: May 2008

AbstractTransplantation of marrow between mouse strains congenic for CD45 after lethal irradiation establishes hematopoiesis driven by genetically marked cells in recipient animals. After several weeks, peripheral blood or primary and secondary lymphoid organs of transplant recipients can be evaluated for the presence of donor‐derived cells. Two‐ or three‐color flow cytometry can be used to identify the progeny of transplanted cells, to document their cell‐surface phenotypes, and to follow development of T, B, and myeloid lineages in vivo. Curr. Protoc. Immunol. 81:4.6.1‐4.6.9. © 2008 by John Wiley & Sons, Inc.
Creation of “Humanized” Mice to Study Human Immunity
Authors: Pearson Todd , Greiner Dale L. , Shultz Leonard D. 
Published: May 2008

Abstract“Humanized” mice are a promising translational model for studying human hematopoiesis and immunity. Their utility has been enhanced by the development of new stocks of immunodeficient hosts, most notably mouse strains such as NOD‐scid IL2rγnull mice that lack the IL‐2 receptor common gamma chain. These stocks of mice lack adaptive immune function, display multiple defects in innate immunity, and support heightened levels of human hematolymphoid engraftment. Humanized mice can support studies in many areas of immunology, including autoimmunity, transplantation, infectious diseases, and cancer. These models are particularly valuable in experimentation where there is no appropriate small animal model of the human disease, as in the case of certain viral infections. This unit details the creation of humanized mice by engraftment of immunodeficient mice with hematopoietic stem cells or peripheral blood mononuclear cells, provides methods for evaluating engraftment, and discusses considerations for choosing the appropriate model system to meet specific goals. Curr. Protoc. Immunol. 81:15.21.1‐15.21.21. © 2008 by John Wiley & Sons, Inc.
The K/BxN Arthritis Model
Authors: Monach Paul A. , Mathis Diane , Benoist Christophe 
Published: May 2008

AbstractMice expressing both the T cell receptor (TCR) transgene KRN and the MHC class II molecule Ag7 (K/BxN mice) develop severe inflammatory arthritis, and serum from these mice causes a similar arthritis in a wide range of mouse strains, due to autoantibodies recognizing glucose‐6‐phosphate isomerase (GPI). K/BxN transgenic mice have been useful for investigating the development of autoimmunity, and the serum transfer model has been particularly valuable in eliciting mechanisms by which anti‐GPI autoantibodies induce joint‐specific inflammation. This unit describes detailed methods for the maintenance of a K/BxN colony, induction of arthritis by serum transfer, clinical evaluation of arthritis, and measurement of anti‐GPI antibodies. Curr. Protoc. Immunol. 81:15.22.1‐15.22.12. © 2008 by John Wiley & Sons, Inc.
Paired Receptor Systems of the Innate Immune System
Authors: Yamada Eriko , McVicar Daniel W. 
Published: May 2008

AbstractThis appendix describes paired receptors involved in the innate immune system. “Paired Receptors” are defined as families of related membrane proteins that show the following characteristics: (1) they are encoded by different genes, but located as a gene cluster on a given chromosome; (2) they have significant homology within their extracellular domains; (3) they are expressed on overlapping immune populations; and (4) they are confirmed to have both activating and inhibitory members. For simplicity in nomenclature, the authors used the official gene nomenclature provided by NCBI and listed all other names in the alias field. Paired receptor information related to both mouse and human systems is included, as some families exist in both species whereas others are important in the study of either human or murine models of disease. Curr. Protoc. Immunol. 81:A.1X.1‐A.1X.25. © 2008 by John Wiley & Sons, Inc.
Expansion of Human Embryonic Stem Cells In Vitro
Authors: Costa Magdaline , Sourris Koula , Hatzistavrou Tanya , Elefanty Andrew G. , Stanley Edouard G. 
Published: May 2008

AbstractThis unit describes a protocol for the large‐scale expansion of karyotypically normal human embryonic stem cells (hESCs). hESCs can be maintained indefinitely as dense colonies that are mechanically cut into pieces, which are subsequently transferred to fresh organ culture dishes seeded with primary mouse embryonic fibroblasts (MEFs). hESCs can also be enzymatically passaged (bulk culture); however, over time, this style of culturing may lead to the acquisition of chromosomal abnormalities. Nevertheless, enzymatic passaging can be used for short periods (up to 25 passages) without the appearance of cells with abnormal karyotypes. Curr. Protoc. Stem Cell Biol. 5:1C.1.1‐1C.1.7. © 2008 by John Wiley & Sons, Inc.
Differentiation of Mouse Embryonic Stem Cells to Spinal Motor Neurons
Authors: Wichterle Hynek , Peljto Mirza 
Published: May 2008

AbstractControlled differentiation of embryonic stem (ES) cells into clinically relevant cell types is a fundamental goal of stem cell research. This unit describes one of the most efficient protocols for conversion of mouse ES cells into a defined type of nerve cells, the spinal motor neurons. ES cells are separated from feeder mouse embryonic fibroblasts and aggregated to form embryoid bodies (EBs). Two days after the withdrawal of growth factors, EBs reach a stage at which they are responsive to patterning signals and can be effectively induced with retinoic acid (RA) to differentiate into spinal nerve cells. Nascent neural cells become responsive to the ventralizing signal sonic hedgehog (Hh) that controls expression of ventral spinal progenitor markers and initiates the genetic program of motor neuron differentiation. Curr. Protoc. Stem Cell Biol. 5:1H.1.1‐1H.1.9. © 2008 by John Wiley & Sons, Inc.
Biological Sand Filters: Low‐Cost Bioremediation Technique for Production of Clean Drinking Water
Authors: Lea Michael 
Published: May 2008

AbstractApproximately 1.1 billion people in rural and peri‐urban communities of developing countries do not have access to safe drinking water. The mortality from diarrheal‐related diseases amounts to ∼2.2 million people each year from the consumption of unsafe water. Most of them are children under 5 years of age—250 deaths an hour from microbiologically contaminated water. There is conclusive evidence that one low‐cost household bioremediation intervention, biological sand filters, are capable of dramatically improving the microbiological quality of drinking water. This unit will describe this relatively new and proven bioremediation technology's ability to empower at‐risk populations to use naturally occurring biology and readily available materials as a sustainable way to achieve the health benefits of safe drinking water. Curr. Protoc. Microbiol. 9:1G.1.1‐1G.1.28. © 2008 by John Wiley & Sons, Inc.
Laboratory Maintenance of Ehrlichia chaffeensis and Ehrlichia canis and Recovery of Organisms for Molecular Biology and Proteomics Studies
Authors: Cheng Chuanmin , Ganta Roman R. 
Published: May 2008

AbstractTick‐borne illnesses are emerging as a major concern for human health in recent years. These include the human monocytic ehrlichiosis caused by the Amblyomma americanum tick‐transmitted bacterium, Ehrlichia chaffeensis; human ewingii ehrlichiosis caused by Ehrlichia ewingii (also transmitted by A. americanum ticks); and human granulocytic anaplasmosis caused by the Ixodes scapularis tick‐transmitted pathogen, Anaplasma phagocytophilum. Likewise, tick‐borne rickettsial pathogens are also a major concern to the health of various vertebrates including dogs, cattle, and several wild animals. In vitro–cultured pathogens grown in a vertebrate host cell and a tick cell culture system will be useful in studies to understand the pathogenic differences as well as to perform experimental infection studies and to generate large quantities of purified antigens. In this unit, methods for culturing E. chaffeensis and Ehrlichia canis (a canine monocytic ehrlichiosis pathogen) in cell lines to represent vertebrate and tick hosts are described. The unit also includes methods useful in purifying bacteria from the host cells and to evaluate proteins by 2‐D gel electrophoresis and western blotting. Curr. Protoc. Microbiol. 9:3A.1.1‐3A.1.21. © 2008 by John Wiley & Sons, Inc.
Analysis of Bacterial Membrane Proteins Produced During Mammalian Infection Using Hydrophobic Antigen Tissue Triton Extraction (HATTREX)
Authors: Crother Timothy R. , Nally Jarlath E. 
Published: May 2008

AbstractHydrophobic antigen tissue Triton extraction (HATTREX) provides a method to extract and identify hydrophobic bacterial membrane proteins from host‐infected tissues. The non‐ionic detergent Triton X‐114 is used to solubilize host‐infected tissues at 4°C. Subsequent phase partitioning of Triton X‐114 extracted material at 37°C results in a “detergent poor” aqueous phase and a “detergent rich” detergent phase. While soluble proteins partition to the aqueous phase, hydrophobic proteins, such as proteins of the outer and inner membranes, can be found in the detergent phase. Characterization of the detergent phase sample provides insights into the proteome of bacterial membranes during infection. Curr. Protoc. Microbiol. 9:12.1.1‐12.1.5. © 2008 by John Wiley & Sons, Inc.
Laboratory Maintenance and Cultivation of Bacteroides Species
Authors: Bacic Melissa K. , Smith C. Jeffrey 
Published: May 2008

AbstractBacteroides species are Gram‐negative, obligate anaerobic bacteria. They are the predominant indigenous bacterial species in the human intestinal tract, where they play an important role in the normal physiology of the host, but they can also be significant opportunistic pathogens. The fact that these are obligate anaerobes is the prevailing feature that affects the methodology used for their cultivation. Several techniques are described for anaerobic culturing; the anaerobic glove box and anaerobic jars are the two techniques most adaptable to a range of research needs. Straightforward methods are presented for propagation on solid media and in broth cultures, and for the long‐term storage and maintenance of stock cultures. The Bacteroides species are saccharolytic, which is the second feature of their physiology that impacts cultivation methodology. Several flexible media formulations, including a defined minimal media, are provided that allow the researcher to choose the carbon source best suited for his or her work. Curr. Protoc. Microbiol. 9:13C.1.1‐13C.1.21. © 2008 by John Wiley & Sons, Inc.
Studies on Electrophilic Interaction of 2,3‐Allenols with Electrophilic Halogen Reagents: Selective Synthesis of 2,5‐Dihydrofurans, 3‐Halo‐3‐alkenals, or 2‐Halo‐2‐alkenyl Ketones
Authors: Li Jing , Fu Chunling , Chen Guofei , Chai Guobi , Ma Shengming 
Published: May 2008

AbstractThe reaction of primary 2,3‐allenols with iodine (I2) afforded 2,5‐dihydrofurans while that of readily available 1‐aryl or 1‐methyl substituted 2,3‐allenols with bromine (Br2), N‐bromosuccinimide (NBS), I2 or N‐iodosuccinimide (NIS) formed the not easily available but synthetically useful 3‐halo‐3‐alkenals and 2‐halo‐2‐alkenyl ketones with good selectivity and yields via a sequential electrophilic interaction of X+ with the allene moiety, 1,2‐aryl or 1,2‐proton shift, and H+ elimination process.
Chiral 1,2,3,4‐Tetrahydro‐1‐naphthylamine‐Derived Phosphine‐Phosphoramidite Ligand (THNAPhos): Application in Highly Enantioselective Hydrogenations of Functionalized CC Bonds
Authors: Qiu Min , Hu Xiang‐Ping , Wang Dao‐Yong , Deng Jun , Huang Jia‐Di , Yu Sai‐Bo , Duan Zheng‐Chao , Zheng Zhuo 
Published: May 2008

AbstractWe have recently reported a new chiral 1,2,3,4‐tetrahydro‐1‐naphthylamine‐derived phosphine‐phosphoramidite ligand, (Rc,Ra)‐THNAPhos, that is highly efficient in the rhodium‐catalyzed asymmetric hydrogenation of a broad range of α‐enol ester phosphonates. To further demonstrate the utility of THNAPhos in asymmetric hydrogenation, in this paper, we describe its new application in the asymmetric hydrogenation of α‐dehydroamino acid esters, enamides, dimethyl itaconate and α‐enamido phosphonates. The results disclosed that the Rh/(Rc,Ra)‐THNAPhos complex is highly effective for the enantioselective hydrogenation of these kinds of functionalized CC olefins, affording the corresponding hydrogenation product in excellent enantioselectivities (normally over 99% ee).
Dietary intake, overweight status, and perceptions of food insecurity among homeless Minnesotan youth
Authors: Smith Chery , Richards Rickelle 
Published: May 2008

AbstractYouth, 9–18 years (n = 202), living in homeless shelters in Minneapolis, Minnesota, were assessed for height, weight, dietary intake, and perceptions of food insecurity. Perceptions of food security were measured by asking youth to respond to the statements (1) “There are times when we do not have enough food in the house,” (2) “I go to bed hungry at night,” (3) “I do not get enough to eat at home,” and (4) “Have you ever had to miss a meal (or not been able to eat) because there was no food at home?” Additionally, questions evaluated coping mechanisms used by children to ward off hunger. Fifty‐five percent of the children reported not enough food in the house and 25% reported going to bed hungry. Youth had inadequate intakes of vitamin D, calcium, and potassium and the majority consumed less than the estimated average requirements (EAR) for vitamins A, C, and E, phosphorus, folate, and zinc. Fruits, vegetables, and dairy were also consumed below recommended levels. Forty‐five percent of boys and 50% of girls were at risk‐for‐overweight or were overweight. Overeating, eating anything, eating disliked foods, and eating at the homes of family and friends were identified as strategies to cope with food insecurity. Overeating when food is available may explain why we see a hunger‐obesity paradigm to the magnitude that we do among the poorest Americans. These strategies protect children from the immediate negative associations of poverty and hunger, but they may contribute to long‐term weight problems currently found in the US. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.
The effect of menarcheal age on anthropometric, limb length, and bone measures in Hutterite and non‐Hutterite women
Authors: Grimsrud Courtney , Binkley Teresa , Specker Bonny 
Published: May 2008

AbstractThe age women reach menarche may affect bone length and mass. Some studies show an earlier menarcheal age (MA) results in a shorter stature and increased body fat. We hypothesized that Hutterite women have a shorter height and limb length, but greater bone mass and areal bone mineral density (aBMD) than non‐Hutterites. Results are from a secondary analysis of 344 (198 Hutterite) healthy, pre‐menopausal women aged 20−40 years who participated in the South Dakota Rural Bone Health Study. Bone measures were obtained by DXA (spine, hip and total body) and pQCT (4 and 20% distal radius). MA correlated with year of birth (r = −0.10, P = 0.08) indicating a trend toward a younger MA for women born in more recent years. MA was inversely associated with current weight (r = −0.11, P < 0.05), percent body fat (r = −0.16, P < 0.01), femoral neck BMC (r = −0.18, P = 0.003), femoral neck aBMD (r = −0.21, P < 0.001), hip aBMD (r = −0.22, P < 0.001) and trabecular volumetric BMD (vBMD) (r = −0.14, P = 0.03). Hutterite women had a younger MA than non‐Hutterite women (12.3 ± 1.3 vs. 13.0 ± 1.3 yr, P < 0.001). In final regression models controlling for diet and activity patterns, Hutterite compared to non‐Hutterite women had shorter standing height (162 ± 0.4 vs. 166 ± 0.4 cm, P < 0.001), forearm length (258 ± 0.8 vs. 261 ± 0.9 mm, P = 0.04); and leg length (76 ± 0.2 vs. 77 ± 0.3 cm, P < 0.01) as hypothesized, but MA did not predict these outcomes. In conclusion, younger MA in Hutterite women did not explain their shorter standing height and limb lengths, but total hip aBMD was inversely associated with MA and greater in Hutterite than non‐Hutterite women. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.
Workplace violence against adolescent workers in the US
Authors: Rauscher Kimberly J. 
Published: May 2008

AbstractBackgroundWorkplace violence is a significant problem yet most research on this topic has focused on adults. Despite facing numerous employment conditions that raise their risk for workplace violence, adolescent workers have received inadequate attention.MethodsSurvey data from 1,171 US students ages 14–17 were analyzed using descriptive statistics to investigate the incidence and perpetrators of physical attacks, verbal threats, and sexual harassment.ResultsNearly one‐third of respondents experienced some form of workplace violence: 25% verbally threatened, 10% physically attacked, and 10% sexually harassed. Significant demographic differences were found. The most common perpetrators of physical attacks and verbal threats were customers while sexual harassment most often came from co‐workers.ConclusionsMany working adolescents, most with only a fewyears work experience, have already suffered workplace violence. As youth are likely to be more vulnerable to its effects, developing workplace violence prevention strategies that target adolescent workers should be made a priority. Am. J. Ind. Med. 51:539–544, 2008. © 2008 Wiley‐Liss, Inc.
Thermally stimulated depolarization current and space charge measurements on low‐density polyethylene: Influence of the presence of antioxidant
Authors: Tebani M. , Boudou L. , Guastavino J. 
Published: May 2008

AbstractThe purpose of this study is an investigation upstream of polymer insulator ageing and rupture. We studied the electrical and physicochemical properties of a low‐density polyethylene (LDPE) used in high‐power insulated cables. Space charge measurements using pulsed electroacoustic method and thermally stimulated depolarization current (TSDC) were carried out on LDPE samples, with and without antioxidant, at different temperatures. TSDC peaks were observed only in the presence of an antioxidant. Furthermore, a TSDC anomalous peak was revealed for the sample containing an antioxidant and polarized at 50°C. All the TSDC peaks are interpreted as trapped charges and can be explained by measuring the space charge distribution within the sample bulk. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Synthesis and FTIR spectroscopic investigation of the UV curing kinetics of telechelic urethane methacrylate crosslinkers based on the renewable resource—Cardanol
Authors: Rekha N. , Asha S. K. 
Published: May 2008

AbstractUV curable telechelic urethane–methacrylate crosslinkers based on the natural resource—cardanol was synthesized in a one pot synthetic step involving end capping of isophorone diisocyanate with one equivalent of hydroxyethyl methacrylate followed by condensation with cardanol. The structures of the resins were characterized by 1H and 13C NMR, fourier transform infrared (FTIR) and Matrix‐assisted laser desorption/ionization time of flight (MALDI‐TOF) spectroscopies and size exclusion chromatography (SEC). The curing process and double bond conversion in presence of 2,2‐diethoxy acetophenone as photoinitiator upon UV irradiation was followed by Fourier transform infrared spectroscopy. These hydrogen bonded crosslinkers based on cardanol and its derivatives had higher double bond conversion when compared to a nonhydrogen bonding standard such as hexanediol diacrylate (HDDA) under identical conditions. The temperature effects on the hydrogen bonding were investigated, and a decrease in the extent of double bond conversion with increase in temperature was observed for the telechelic urethane–methacrylate crosslinkers whereas a steady increase in the curing rate was observed for HDDA. This gives direct indication of the influence of hydrogen bonding on the curing process. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
On adapting PQPFs to fit hydrological needs: the case of flash flood forecasting
Authors: Marty R. , Zin I. , Obled Ch. 
Published: May 2008

AbstractA simple, but rather complete hydro‐meteorological system for ensemble flash flood forecasting is described. Special focus is put on the use of precipitation forecasts, essentially quantitative and overall probabilistic (PQPFs). A first issue addressed concerns the matching of the time‐step used by the meteorological forecasts providers (12 or 24 h) with the appropriate hydrological time‐step for quick responding catchments (1 h or less). A second issue concerns the forecasts management between two updating cycles of the PQPFs. Finally, ensemble discharge forecasts for a case‐study event observed in Vogüé (South‐eastern France) are illustrated as an application of our flood forecasting system. Copyright © 2008 Royal Meteorological Society
Guanine quadruplex formation by RNA/DNA hybrid analogs of Oxytricha telomere G4T4G4 fragment
Authors: Vondrušková Jitka , Kypr Jaroslav , Kejnovská Iva , Fialová Markéta , Vorlíčková Michaela 
Published: May 2008

AbstractUsing circular dichroism spectroscopy, gel electrophoresis, and ultraviolet absorption spectroscopy, we have studied quadruplex folding of RNA/DNA analogs of the Oxytricha telomere fragment, G4T4G4, which forms the well‐known basket‐type, antiparallel quadruplex. We have substituted riboguanines (g) for deoxyriboguanines (G) in the positions G1, G9, G4, and G12; these positions form the terminal tetrads of the G4T4G4 quadruplex and adopt syn, syn, anti, and anti glycosidic geometries, respectively. We show that substitution of a single sugar was able to change the quadruplex topology. With the exception of G4T4G3g, which adopted an antiparallel structure, all the RNA/DNA hybrid analogs formed parallel, bimolecular quadruplexes in concentrated solution at low salt. In dilute solutions (∼0.1 mM nucleoside), the RNA/DNA hybrids substituted at positions 4 or 12 adopted antiparallel quadruplexes, which were especially stable in Na+ solutions. The hybrids substituted at positions 1 and 9 preferably formed parallel quadruplexes, which were more stable than the nonmodified G4T4G4 quadruplex in K+ solutions. Substitutions near the 3′end of the molecule affected folding more than substitutions near the 5′end. The ability to control quadruplex folding will allow further studies of biophysical and biological properties of the various folding topologies. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 797–806, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com