bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Forward Genetic Screen for Identifying Mutations Affecting Larval Neuronal Dendrite Development in Drosophila melanogaster
Authors: Medina Paul Mark B , Swick Lance L , Andersen Ryan , Blalock Zachary , Brenman Jay E 
Published: January 2006

Abstract
Vertebrate and invertebrate dendrites are information-processing compartments that can be found on both central and peripheral neurons. Elucidating the molecular underpinnings of information processing in the nervous system ultimately requires an understanding of the genetic pathways that regulate dendrite formation and maintenance. Despite the importance of dendrite development, few forward genetic approaches have been used to analyze the latest stages of dendrite development, including the formation of F-actin-rich dendritic filopodia or dendritic spines. We developed a forward genetic screen utilizing transgenic Drosophila second instar larvae expressing an actin, green fluorescent protein (GFP) fusion protein (actin∷GFP) in subsets of sensory neurons. Utilizing this fluorescent transgenic reporter, we conducted a forward genetic screen of &gt;4000 mutagenized chromosomes bearing lethal mutations that affected multiple aspects of larval dendrite development. We isolated 13 mutations on the X and second chromosomes composing 11 complementation groups affecting dendrite outgrowth/branching, dendritic filopodia formation, or actin∷GFP localization within dendrites in vivo. In a fortuitous observation, we observed that the structure of dendritic arborization (da) neuron dendritic filopodia changes in response to a changing environment.
Genetically Engineered Underdominance for Manipulation of Pest Populations: A Deterministic Model
Authors: Magori Krisztian , Gould Fred 
Published: January 2006

Abstract
We theoretically investigate the potential for introgressing a desired engineered gene into a pest population by linking the desired gene to DNA constructs that exhibit underdominance properties. Our deterministic model includes two independently segregating engineered constructs that both carry a lethal gene, but suppress each other. Only genotypes containing both or neither construct are viable. Both constructs also carry the desired gene with an independent regulatory mechanism. We examine the minimal number of individuals of an engineered strain that must be released into a natural population to successfully introgress the desired gene. We compare results for strains carrying single and multiple insertions of the constructs. When there are no fitness costs associated with the inserted constructs (when the lethal sequences are not expressed), the number of individuals that must be released decreases as the number of insertions in the genome of the released strain increases. As fitness costs increase, the number of individuals that must be released increases at a greater rate for release strains with more insertions. Under specific conditions this results in the strain with only a single insertion of each construct being the most efficient for introgressing the desired gene. We discuss practical implications of our findings.
Origin and Evolution of Processed Pseudogenes That Stabilize Functional Makorin1 mRNAs in Mice, Primates and Other Mammals
Authors: Kaneko Satoko , Aki Ikuko , Tsuda Kaoru , Mekada Kazuyuki , Moriwaki Kazuo , Takahata Naoyuki , Satta Yoko 
Published: January 2006

Abstract
We investigate the origin and evolution of a mouse processed pseudogene, Makorin1-p1, whose transcripts stabilize functional Makorin1 mRNAs. It is shown that Makorin1-p1 originated almost immediately before the musculus and cervicolor species groups diverged from each other some 4 million years ago and that the Makorin1-p1 orthologs in various Mus species are transcribed. However, Mus caroli in the cervicolor species group expresses not only Makorin1-p1, but also another older Makorin1-derived processed pseudogene, demonstrating the rapid generation and turnover in subgenus Mus. Under this circumstance, transcribed processed pseudogenes (TPPs) of Makorin1 evolved in a strictly neutral fashion even with an enhanced substitution rate at CpG dinucleotide sites. Next, we extend our analyses to rats and other mammals. It is shown that although these species also possess their own Makorin1-derived TPPs, they occur rather infrequently in simian primates. Under this circumstance, it is hypothesized that already existing TPPs must be prevented from accumulating detrimental mutations by negative selection. This hypothesis is substantiated by the presence of two rather old TPPs, MKRNP1 and MKRN4, in humans and New World monkeys. The evolutionary rate and pattern of Makorin1-derived processed pseudogenes depend heavily on how frequently they are disseminated in the genome.
Hos2 and Set3 Promote Integration of Ty1 Retrotransposons at tRNA Genes in Saccharomyces cerevisiae
Authors: Mou Zhongming , Kenny Alison E , Curcio M Joan 
Published: January 2006

Abstract
The yeast LTR retrotransposon Ty1 integrates preferentially into regions upstream of tRNA genes. The chromatin structure of transcriptionally active tRNA genes is known to be important for Ty1 integration, but specific chromatin factors that enhance integration at tRNA genes have not been identified. Here we report that the histone deacetylase, Hos2, and the Trithorax-group protein, Set3, both components of the Set3 complex (Set3C), enhance transposition of chromosomal Ty1 elements by promoting integration into the upstream region of tRNA genes. Deletion of HOS2 or SET3 reduced the mobility of a chromosomal Ty1his3AI element about sevenfold. Despite the fact that Ty1his3AI RNA, total Ty1 RNA, and total Ty1 cDNA levels were not reduced in hos2Δ or set3Δ mutants, transposition of endogenous Ty1 elements into the upstream regions of tRNAGly genes was substantially decreased. Furthermore, when equivalent numbers of Ty1HIS3 mobility events launched from a pGAL1:Ty1his3AI plasmid were analyzed, only one-quarter to one-half as many were found upstream of tRNAGly genes in a hos2Δ or set3Δ mutant than in a wild-type strain. Chromatin immunoprecipitation analysis revealed that Hos2 is physically associated with tRNA genes. Taken together, our results support the hypothesis that Hos2 and Set3 function at tRNA genes to promote Ty1 integration.
Overview of Signal Transduction
Authors: Esbenshade Timothy A. , Duzic Emir 
Published: January 2006

AbstractReceptor‐ and ion channel‐coupled signal transduction mechanisms are downstream communication processes used by regulatory molecules to modulate the essential cell processes of growth, differentiation and survival. Knowledge of signal transduction processes has dramatically increased in the past decade, and the basic principles of intracellular signaling are now quite well established. Cell signaling in higher organisms is a major, highly complex, phenomena that occupies a central position in current biomedical research. The complex machinery of intracellular signaling also has the potential to provide a wealth of novel drug discovery targets, from protein kinases, adaptor proteins, lipases, and cytoskeletal proteins, to nuclear effectors. This overview describes common features of cellular signaling pathways, including their interactions and responses to environmental stimuli. In particular, the overview focuses on the regulation of signaling pathways by protein functional‐domain interactions as well as the intracellular proteins that mediate signal transduction.
Nucleoside Phosphoramidites Containing Cleavable Linkers
Authors: Pon Richard T. 
Published: January 2006

AbstractPhosphoramidite reagents (linker phosphoramidites) containing a cleavable 3′‐ester linkage between the nucleoside and the phosphoramidite group can be used to attach the first nucleoside to a solid‐phase support. Inexpensive underivatized supports such as LCAA‐CPG can then be used as universal supports for oligonucleotide synthesis. No modifications to synthesis coupling conditions and no 3′‐dephosphorylation are required. Only oligonucleotides with terminal 3′‐OH ends are produced. Phosphoramidites containing both a succinate and a sulfonyldiethanol linkage are particularly useful and create oligonucleotides with both a 3′‐OH and 5′‐phosphate. In addition, by using these reagents, one oligonucleotide sequence can be added onto the 5′‐end of another (tandem synthesis) to produce a string of multiple oligonucleotides linked end‐to‐end. Deprotection releases the oligonucleotides from each other to yield a mixture of oligonucleotides. This approach is particularly useful for making pairs of PCR primers or both strands of a double‐stranded sequence in a single operation.
Microwave‐Assisted Functionalization of Solid Supports for Rapid Loading of Nucleosides
Authors: Iyer Radhakrishnan P. , Padmanabhan Seetharamaiyer , Coughlin John E. 
Published: January 2006

AbstractUltra‐fast and efficient functionalization of solid supports such as controlled‐pore glass (CPG), amino methyl polystyrene, and Tentagel has been achieved using microwave‐assisted procedures. Both amino‐ and carboxy‐terminated supports are easily prepared within minutes, in a reproducible manner, using microwave‐assisted methodologies. The resulting functionalized supports are efficiently coupled to nucleosides using dimethylformamide as a solvent in conjunction with a specially designed reactor and workstation called LOTUS. Using these improved protocols, CPG with loadings of 75 to 85 µmol/g can be prepared on a large scale within 3 to 4 days starting from native CPG, as opposed to traditional methods that require 10 to 15 days to achieve the same objective. In addition, the methods described here can potentially be employed for rapid functionalization of other solid matrices such as beads, slides, and pins for applications in microarrays or combinatorial chemistry.
Nucleoside‐5′‐Phosphoimidazolides: Reagents for Facile Synthesis of Dinucleoside Pyrophosphates
Authors: Chen Liqiang , Rejman Dominik , Bonnac Laurent , Pankiewicz Krzysztof W. , Patterson Steven E. 
Published: January 2006

AbstractA facile method is presented for preparation of dinucleoside pyrophosphate derivatives based on reaction of a nucleoside 5′‐monophosphate with carbonyldiimidazole followed by treatment of the resulting nucleoside 5′‐phosphoimidazolide with a nucleoside 5′‐phosphate. This method is suitable for preparation of pyrophosphates analogous to NAD, FAD, and related natural pyrophosphates. The resulting compounds are useful for mechanistic studies of enzymes that use natural pyrophosphates as co‐factors or substrates, and in development of inhibitors that have potential applications as therapeutic agents.
Detection Assays for HIV Proteins
Authors: Ostrowski Mario A. , Chun Tae‐Wook , Cheseboro Bruce , Stanley Sharilyn K. , Tremblay Michel 
Published: January 2006

AbstractThis updated unit describes four assays for detection of HIV proteins including: (1) a quantitative ELISA, (2) a quantitative immunoblotting assay, (3) a qualitative immunofluorescence assay, and (4) a functional assay to measure virus‐associated reverse transcriptase activity as an indicator of viral production.
Immunoisolation of Centrosomes from Drosophila melanogaster
Authors: Lehmann Verena , Müller Hannah , Lange Bodo M.H. 
Published: January 2006

AbstractClassical protocols for the isolation of centrosomes from higher eukaryotic cells are based on enrichment of cell organelles by density gradient centrifugation. Various successful protocols have been described that isolate centrosomes from mammalian tissue culture cells, tissue, clam oocytes, Drosophila, and yeast, to mention only some of the more frequently used sources. The material produced is subsequently used in various assays. These include functional tests such as the microtubule nucleation assay, electron microscopic study of centrosome morphology, and antigen localization; the organelles may also be used for the generation of antibodies. Furthermore, centrosomal preparations have been used for the characterization of their protein composition. The method described here focuses on the isolation of centrosomes from the syncytial stages of the early Drosophila embryo. This is a particularly attractive system because these organelles are not bounded by cellular membranes. Moreover, the abundance of pericentriolar material of these centrosomes produces excellent total protein yields.
Using Apollo to Browse and Edit Genome Annotations
Authors: Misra Sima , Harris Nomi 
Published: January 2006

AbstractAn annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. As biological knowledge increases, annotations of different types need to be added and modified, and links to other sources of information need to be incorporated, to allow biologists to easily access all of the available sequence analysis data and design appropriate experiments. The Apollo genome browser and editor offers biologists these capabilities. Apollo can display many different types of computational evidence, such as alignments and similarities based on BLAST searches (UNITS & ), and enables biologists to utilize computational evidence to create and edit gene models and other genomic features, e.g., using experimental evidence to refine exon‐intron structures predicted by gene prediction algorithms. This protocol describes simple ways to browse genome annotation data, as well as techniques for editing annotations and loading data from different sources.
Eye and respiratory symptoms in poultry processing workers exposed to chlorine by‐products
Authors: King Bradley S. , Page Elena H. , Mueller Charles A. , Dollberg Donald D. , Gomez Katherine E. , Warren Angela M. 
Published: January 2006

AbstractBackgroundCDC/NIOSH responded to a request to investigate complaints of eye and respiratory irritation among workers in a poultry processing facility's evisceration department.MethodsInvestigators administered symptom questionnaires and sampled for chlorine and chloramines. Spirometry was performed on workers before and after their work shift.ResultsSymptoms were significantly more prevalent in evisceration workers than in dark meat workers (a control group). Air concentrations of chloramine compounds (i.e., trichloramine and ‘soluble chlorine’) were significantly higher in the evisceration area than the dark meat area. Exposure levels were significantly higher for employees reporting various symptoms compared to employees not reporting those symptoms. Mean trichloramine exposure concentrations were significantly higher in workers with significant cross‐shift declines in lung function; air concentrations of ‘soluble chlorine’ were higher as well, however, not significantly so.ConclusionsResults of this evaluation suggest a health hazard may exist from exposure to chloramines. Am. J. Ind. Med. 49:119–126, 2006. Published 2006 Wiley‐Liss, Inc.
Polymeric Sensor Materials: Toward an Alliance of Combinatorial and Rational Design Tools?
Authors: Potyrailo Radislav A. 
Published: January 2006

AbstractIncreased selectivity, response speed, and sensitivity in the chemical and biological determinations of gases and liquids are of great interest. Particular attention is paid to polymeric sensor materials, which are applicable to sensors exploiting various energy transduction principles, such as radiant, electrical, mechanical, and thermal energy. Ideally, numerous functional parameters of sensor materials can be tailored to meet specific needs using rational design approaches. However, increasing the structural and functional complexity of polymeric sensor materials makes it more difficult to predict the desired properties. Combinatorial and high‐throughput methods have had an impact on all areas of research on polymer‐based sensor materials including homo‐ and copolymers, formulated materials, polymeric structures with engineered morphology, and molecular shape‐recognition materials. Herein we report on the state‐of‐the‐art, the development trends, and the remaining knowledge gaps in the area of combinatorial polymeric sensor materials design.
Central visual system of the naked mole‐rat (Heterocephalus glaber)
Authors: Crish Samuel D. , Dengler‐Crish Christine M. , Catania Kenneth C. 
Published: January 2006

AbstractNaked mole‐rats are fossorial rodents native to eastern Africa that spend their lives in extensive subterranean burrows where visual cues are poor. Not surprisingly, they have a degenerated eye and optic nerve, suggesting they have poor visual abilities. However, little is known about their central visual system. To investigate the organization of their central visual system, we injected a neuronal tracer into the eyes of naked mole‐rats and mice to compare the neural structures mediating vision. We found that the superior colliculus and lateral geniculate nucleus were severely atrophied in the naked mole‐rat. The olivary pretectal nucleus was reduced but still retained its characteristic morphology, possibly indicating a role in light detection. In addition, the suprachiasmatic nucleus is well innervated and resembles the same structure in other rodents. The naked mole‐rat appears to have selectively lost structures that mediate form vision while retaining structures needed for minimal entrainment of circadian rhythms. Similar results have been reported for other mole‐rat species. Taken together, these data suggest that light detection may still play an important role in the lives of these “blind” animals: most likely for circadian entrainment or setting seasonal rhythms. © 2006 Wiley‐Liss, Inc.
Flow‐injection chemiluminescence determination of catecholamines based on their enhancing effects on the luminol–potassium periodate system
Authors: Yao Hong , Sun Yuan Yuan , Lin Xinhua , Cheng Jinghua , Huang Liying 
Published: January 2006

AbstractA rapid and sensitive chemiluminescence (CL) method using flow injection analysis is described for the determination of four catecholamines, dopamine, adrenaline, isoprenaline and noradrenaline, based on their greatly enhancing effects on the CL reaction of luminol–potassium periodate in basic solutions. The optimized chemical conditions for the chemiluminescence reaction were 1.0 × 10−4 mol/L luminol and 1.0 × 10−5 mol/L potassium periodate in 0.2 mol/L sodium hydroxide (NaOH). Under the optimized conditions, the calibration graphs relating the CL signal intensity (peak height) to the concentration of the analytes were curvilinear and they were suitable for determining dopamine, adrenaline, isoprenaline, and noradrenaline in the range 0.1–10 ng/mL, 0.1–100 ng/mL, 1–100 ng/mL and 5–50 ng/mL, respectively, with the relative standard deviations of 0.8–1.7%. The detection limits of the method are 0.02 ng/mL for dopamine, 0.01 ng/mL for adrenaline, 0.1 ng/mL for isoprenaline and 2.0 ng/mL for noradrenaline. The sampling frequency was calculated to be about 60/h. The selectivity of the method was good, because a series of common ions or excipients, such as K+, Ba2+, CO32−, NO3−, SO42−, PO43−, sodium citrate, sodium bisulphite, oxidate dopamine, starch, lactose, carbamide and gelatin, could not produce interference when their concentrations were 1000‐fold than those of dopamine. The present method was successfully applied to the determination of the four catecholamines in pharmaceutical injections. Copyright © 2006 John Wiley & Sons, Ltd.
Competition of cytarabine and aspirin in binding to serum albumin in multidrug therapy
Authors: Sułkowska Anna , Bojko Barbara , Równicka Joanna , Sułkowski Wiesław W. 
Published: January 2006

AbstractThe aim of this study was to describe a competition between cytarabine (araC) and aspirin (ASA) in binding with bovine serum albumin (BSA). High‐affinity binding sites for both drugs were determined using a spectrofluorimetric method. Cytarabine as well as aspirin binds in the IIA hydrophobic subdomain of the transporting protein. Binding constants for araC–BSA and ASA–BSA were calculated by the Scatchard method. Analysis of ultraviolet (UV) difference spectra showed that araC, which has a higher affinity to BSA in comparison to ASA [Ka(araC) > Ka(ASA)] displaces ASA in high‐affinity binding sites.The competition between drugs in low‐affinity binding sites was investigated using 1H nuclear magnetic resonance (NMR) and 13C‐NMR spectra. We concluded that in the low‐affinity binding sites cytarabine decreases the affinity of albumin toward aspirin. However, the interaction between araC and BSA becomes more difficult in the presence of aspirin. © 2006 Wiley Periodicals, Inc. Biopolymers 81: 464–472, 2006This 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
Percutaneous edge‐to‐edge mitral valve repair: 2‐year follow‐up in the first human case
Authors: Condado José Antonio , Acquatella Harry , Rodriguez Leonardo , Whitlow Patrick , Vélez‐Gimo Manuel , St. Goar Frederick G. 
Published: January 2006

AbstractWe report the first‐in–human mitral valve repair using percutaneous technology that creates a “surgical‐like” edge‐to‐edge repair. A catheter‐delivered clip was introduced transseptally from the femoral vein, advanced through the mitral orifice, retracted to grasp the leaflets, and detached to create a functional double‐orifice valve. The patient had an uncomplicated post‐procedural course. Echocardiography at 1‐ and 2‐years post procedure showed mild mitral regurgitation and positive ventricular remodeling. The success of this case suggests that percutaneous mitral valve repair may be a feasible therapy for certain patients suffering from mitral regurgitation. © 2006 Wiley‐Liss, Inc.
Scope and Mechanism of the PdII‐Catalyzed Arylation/Carboalkoxylation of Unactivated Olefins with Indoles
Authors: Liu Cong , Widenhoefer Ross A. 
Published: January 2006

AbstractTreatment of 1‐methyl‐2‐(4‐pentenyl)indole (5) with a catalytic amount of [PdCl2(MeCN)2] (2; 5 mol %) and a stoichiometric amount of CuCl2 (3 equiv) in methanol under CO (1 atm) at room temperature for 30 min gives methyl (9‐methyl‐2,3,4,9‐tetrahydro‐4‐carbazolyl)acetate (6), which was isolated in 83 % yield. A number of 2‐ and 3‐alkenyl indoles undergo a similar palladium‐catalyzed cyclization/carboalkoxylation to give the corresponding polycyclic indole derivatives in moderate to excellent yields with excellent regio‐ and diastereoselectivity. Under similar conditions, vinyl arenes undergo intermolecular arylation/carboalkoxylation with indoles to give 3‐(1‐aryl‐2‐carbomethoxyethyl) indoles in moderate yield with high regioselectivity. Stereochemical analyses of the palladium‐catalyzed cyclization/carboalkoxylation of both 2‐ and 3‐alkenyl indoles are in agreement with mechanisms involving outer‐sphere attack of the indole on a palladium–olefin complex followed by α‐migratory insertion of CO and methanolysis of the resulting acyl palladium intermediate. CuCl2 functions as the terminal oxidant in this palladium‐catalyzed cyclization/carboalkoxylation of alkenyl indoles and also significantly increases the rate of reaction of 2 with the alkenyl indole to form the corresponding acyl palladium complex. Spectroscopic studies are in agreement with the intermediacy of a heterobimetallic Pd/Cu complex as the active catalyst in this reaction.