bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular epidemiological investigation of Ascaris genotypes in China based on single‐strand conformation polymorphism analysis of ribosomal DNA
Authors: Peng Weidong , Yuan Keng , Zhou Xianmin , Hu Min , Abs EL‐Osta Youssef G. , Gasser Robin B.
Published: July 2003

Using a single‐strand conformation polymorphism‐based approach, we investigated nucleotide variation in part of the first internal transcribed spacer (pITS‐1) of nuclear ribosomal DNA within and among a large number of Ascaris individuals from humans and pigs from six endemic regions in China, and examined the frequency of the different genotypes of Ascaris in relation to host species and geographical origin. Five different SSCP genotypes (G1–G5) were recorded for human Ascaris (n = 486), of which three (genotypes G1–G3) were detected for pig Ascaris (n = 329). Of the five Ascaris genotypes detected, genotype G1 predominantly infected humans (∼63–74%) whereas genotype G3 infected mainly pigs (∼79–86%), indicating that each of these genotypes has a particular host affiliation. In contrast, the frequencies of the other three genotypes was substantially lower for each of the two host species. The findings also suggested that the rate of cross infection of Ascaris between humans and pigs is relatively low and that gene flow between the predominant genotypes is limited, consistent with previous proposals for endemic regions in other countries. While the nature and extent of nucleotide variation in the pITS‐1 (and the proposal of host affiliated Ascaris populations) may relate to “introgression” or “lineage sorting and retention of ancentral polymorphism”, other explanations are possible. Evidence of multiple pITS‐1 sequence types in some Ascaris individuals representing particular genotypes (e.g., G2 and G5) may suggest hybridization between human‐ and pig‐affiliated Ascaris. This aspect and the species status of Ascaris (from each host species) warrant future experimental testing, employing the pig/Ascaris model and the present electrophoretic approach.*
Study of the development of chemoresistance in melanoma cell lines using proteome analysis
Authors: Sinha Pranav , Poland Julia , Kohl Sandro , Schnölzer Martina , Helmbach Heike , Hütter Gero , Lage Hermann , Schadendorf Dirk
Published: July 2003

Malignant melanomas have poor prognosis since treatment with anti‐neoplastic agents is mostly ineffective. The biological mechanisms of this strong intrinsic therapy resistance are unknown. In order to identify new molecular factors potentially associated with the drug‐resistant phenotype of malignant melanoma, a panel of human melanoma cell variants exhibiting low and high levels of resistance to four commonly used anticancer drugs in melanoma treatment, i.e., vindesine, etoposide, cisplatin, and fotemustine, was characterized using proteomic tools (two‐dimensional electrophoresis for protein fractionation and matrix assisted laser desorption/ionization‐time of flight (MALDI‐TOF)‐mass spectrometry for protein identification). In the neutral and weak acidic milieu (pH 4.0–8.0) a total number of 14 proteins showed alterations in expression whereas 20 proteins were differentially expressed in the basic milieu (pH 8.0–11.0). Besides proteins with unknown physiologic function, several factors were identified that show chaperone activity. Moreover, proteins involved in drug detoxification, metabolism, and regulation of apoptotic pathways could be identified. The possible role of these proteins in the development of chemoresistance is discussed, although detailed functional tests with these proteins have still to be performed. Nevertheless, it is clear that this proteomic approach for studying chemoresistance phenomena is a prerequisite before further investigation can yield insight into the biology and development of drug resistance in malignant melanoma.
Polyacrylamide gel electrophoresis followed by sodium dodecyl sulfate gradient polyacrylamide gel electrophoresis for the study of the dimer to monomer transition of human transthyretin
Authors: Altland Klaus , Winter Pia
Published: July 2003

Familial amyloidotic polyneuropathy (FAP) is caused by mutations which destabilize transthyretin (TTR) and facilitate the aggregation into extracellular amyloid fibrils preferentially in peripheral nerve and heart tissues. Therapeutic and preventive trials for FAP at the plasma TTR level require a careful study of the destabilization of TTR under variable conditions. We have developed a simple double one‐dimensional (D1‐D) electrophoretic procedure with polyacrylamide gel electrophoresis (PAGE) followed by sodium dodecylsulfate (SDS) gradient PAGE to study the dimer to monomer transition. TTR is first isolated by PAGE from other plasma proteins. The gel strip containing the TTR fraction is incubated in 2% SDS under varying conditions of temperature, buffer composition, pH, and additives like urea and/or a sulfhydryl‐reactive agent, followed by SDS‐gradient PAGE for the separation of TTR dimers and monomers. We demonstrate that an unidirectional dimer to monomer transition of normal TTR is achieved at 70–80°C in neutral to mild alkaline buffers or at 37°C and slightly acidic pH (6–7). Addition of urea favors the transition into monomers. Amyloidogenic mutations like amyloidogenic TTR (ATTR)‐V30M or ATTR‐I107V favor the transition into monomers in buffer systems close to the physiological pH of human plasma. We conclude that this finding has to be considered by any hypothesis on ATTR‐derived amyloidogenesis.
Thiol‐reactive dyes for fluorescence labeling of proteomic samples
Authors: Tyagarajan Kamala , Pretzer Elizabeth , Wiktorowicz John E.
Published: July 2003

Covalent derivatization of proteins with fluorescent dyes prior to separation is increasingly used in proteomic research. This paper examines the properties of several commercially available iodoacetamide and maleimide dyes and discusses the conditions and caveats for their use in labeling of proteomic samples. The iodoacetamide dyes BODIPY TMR cadaverine IA and BODIPY Fl C1‐IA were highly specific for cysteine residues and showed little or no nonspecific labeling even at very high dye:thiol ratios. These dyes also showed minimal effects on pI's of standard proteins. Some iodoacetamide dyes, (5‐TMRIA and eosin‐5‐iodoacetamide) and some maleimide dyes (ThioGlo I and Rhodamine Red C2 maleimide) exhibited nonspecific labeling at high dye:thiol ratios. Labeling by both iodoacetamide and maleimide dyes was inhibited by tris(2‐carboxyethyl)phosphine (TCEP); interactions between TCEP and dye were also observed. Thiourea, an important component of sample solubilization cocktails, inhibited labeling of proteins with iodoacetamide dyes but not with maleimide dyes. Maleimide dyes may serve as an alternative for labeling proteins where it is essential to have thiourea in the solubilization buffer. Covalent derivatization by BODIPY TMR cadaverine IA, BODIPY Fl C1‐IA or Rhodamine Red C2 maleimide was also demonstrated to be compatible with in‐gel digestion and peptide mass fingerprinting by matrix assisted laser desorption/ionization‐mass spectrometry and allowed successful protein identification.
Nonconventional synthesis and characterization of ultrahigh‐molar‐mass polyacrylamides
Authors: Cretich Marina , Chelaru Carmen , Pirri Giovanna , Levi Marinella , Clerici Gigliola , Chiari Marcella
Published: July 2003

In spite of the significant progresses in the field of replaceable sieving matrices for separating DNA in capillary electrophoresis (CE), an intense research activity is still going on to improve the separation of large size DNA sequencing fragments. There are evidences, both from experimental and theoretical sides that the resolution of these fragments, at the single base, requires the use of sieving matrices comprised of long chain linear polymers. In the separation of DNA fragments by CE are of upmost importance: (i) the complete solubility of the polymer, (ii) the linearity of the chain, (iii) the achievement of ultrahigh viscosity in dilute solutions. The aim of this work is the synthesis of ultrahigh‐molecular‐weight polymers which possess the three requirements mentioned above by employing a nonconventional method. We demonstrate that the sieving performance of polyacrylamide is directly correlated to its intrinsic viscosity.
Protein extraction for two‐dimensional electrophoresis from olive leaf, a plant tissue containing high levels of interfering compounds
Authors: Wang Wei , Scali Monica , Vignani Rita , Spadafora Antonia , Sensi Elisabetta , Mazzuca Silvia , Cresti Mauro
Published: July 2003

The purpose of this research is to establish a routine procedure for the application of proteomic analysis to olive tree. Olive leaf tissue is notoriously recalcitrant to common protein extraction methods due to high levels of interfering compounds. We developed a protocol for isolating proteins suitable for two‐dimensional electrophoresis (2‐DE) from olive leaf. The remarkable characteristics of the protocol include: (i) additional grinding dry acetone powder of leaf tissue to a finer extent, (ii) after extensive organic solvent washes to remove pigments, lipids etc., using aqueous tricholoroacetic acid washes to remove water‐soluble contaminants, and (iii) phenol extraction of proteins in the presence of sodium dodecyl sulfate. The final protein preparation is free of interfering compounds based on its well‐resolved 2‐DE patterns. The protocol can be completed within 3 h, and protein yield is approximately 2.49 mg⋅g−1 of aged leaf. We also evaluated the protocol by immunoblotting with anti‐tyrosinate α‐tubulin antibody. To our knowledge, this is the first time that a protocol for protein extraction from olive leaf appears to give satisfactory and reproducible results. The protocol is expected to be applicable to other recalcitrant plant tissues and could be of interest to laboratories involved in plant proteomics.
Electrophoretic analysis of the cleaved form of serpin, squamous cell carcinoma antigen‐1 in normal and malignant squamous epithelial tissues
Authors: Nawata Shugo , Nakamura Kazuyuki , Hirakawa Hiroshi , Sueoka Kotaro , Emoto Tomoko , Murakami Akihiro , Umayahara Kenji , Ogata Hidenobu , Suminami Yoshinori , Numa Fumitaka , Kato Hiroshi
Published: July 2003

The aim of this study was to detect the cleaved form of serine proteinase inhibitor (serpin), squamous cell carcinoma (SCC) antigen‐1 in normal and malignant squamous epithelial tissues, which implies the presence of its target proteinase. The cleaved SCC antigen‐1 in normal squamous epithelium was identified as a single spot with pI 6.35 and Mr 40 000 by two‐dimensional electrophoresis (2‐DE) combined with immunoblotting. Interestingly, the cleaved form showed different biochemical properties in heat stability or immunoreactivity with a monoclonal antibody for SCC antigen (Mab 426) compared to intact SCC antigen‐1. Furthermore, sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) analysis of tissue extracts showed an abundant 40 kDa band of cleaved SCC antigen‐1 in tumor tissue compared to normal tissue. Among the potential target proteinase of SCC antigen‐1, immunoblotting analyses revealed that cathepsin L2 was remarkably overexpressed in tumor tissue, while cathepsin L was expressed in both normal and tumor tissues. These findings indicate that SCC antigen‐1 interacts with specific endogenous proteinases such as cathepsins L and L2 in physiological and pathological states of squamous epithelium.
Estimation of the optimal electrophoretic temperature of DNA single‐strand conformation polymorphism by DNA base composition
Authors: Li Wei , Gao Feng , Liang Junlin , Li Chensheng , Zhang Haitian , Tang Zongjiang , Chen Lisheng , Jin Qi , Tang Weizhong
Published: July 2003

To explore the relation between DNA base composition and the optimal single‐strand conformation polymorphism (SSCP) electrophoretic temperature (Ts), we analyzed DNA base composition and Ts of 24 DNA fragments from different genes and found that Ts was positively correlative with the ratio of base C/base A. Ts could be estimated by the formula Ts = [80×C/(A+1)]/{2.71 + [C/(A+1)]}. Ts could be increased dramatically by the complementary sequences in both 5'‐and 3'‐ends of a DNA single‐strand.
Determining eosin as a groundwater migration tracer by capillary electrophoresis/laser‐induced fluorescence using a multiwavelength laser
Authors: Brumley William C. , Farley John W.
Published: July 2003

Measurements for determining of the path of groundwater migration remain an important tool in the overall assessment of environmental processes and transport of pollutants. This paper examines a multiwavelength laser for the determination of eosin, a groundwater tracer, using capillary electrophoresis/laser‐induced fluorescence (CE‐LIF) at excitation wavelength 514.5 nm. Eosin was one of four dyes used in a study of adjacent resource conservation and recovery act (RCRA) and Superfund sites (created by the comprehensive environmental response, compensation, and liability act) that routinely relied on spectrofluorimetry for determination as we have previously reported. However, the improved specificity of CE‐LIF is further illustrated in this work applied to the analysis of adsorbent pads placed in monitoring wells after dye injection and flushing from injection wells. The multiwavelength laser provided the capability to analyze for several dyes with one laser. The advantages/disadvantages of CE‐LIF versus spectrofluorimetry are discussed. Spectrofluorimetry is fast and sensitive and will likely continue to be the primary workhorse technique. CE‐LIF could provide confirmation when greater specificity is needed in a regulatory context.
Drosophila S3 ribosomal protein accelerates repair of 8‐oxoguanine performed by human and mouse cell extracts
Authors: Cappelli Enrico , D'Osualdo Andrea , Bogliolo Massimo , Kelley Mark R. , Frosina Guido
Published: July 2003

The S3 ribosomal protein of Drosophila melanogaster possesses various DNA repair activities, including the capacity to incise at apurinic/apyrimidinic (AP) sites and 8‐oxo‐7,8‐dihydroguanine (8‐oxoG) residues. We have recently hypothesized that this multifunctional protein may improve the efficiency of DNA base excision repair (BER) in mammalian cells. We have investigated the effect of pure GST‐tagged Drosophila S3 on BER of different endogenous lesions performed by human and mouse cell extracts. Drosophila S3 significantly accelerated the BER of 8‐oxoG (initiated by the bifunctional glycosylase OGG1). The stimulating effect was linked to the capacity of S3 to remove the 8‐oxoG lesion and cleave the resulting AP site, rather than acceleration of downstream steps of the BER pathway (e.g., removal of 3′ blocking fragments). No stimulating effect was observed on the BER of uracil, natural AP sites, and β‐lyase‐cleaved AP sites. Heterologous expression of Drosophila S3 may be used to enhance 8‐oxoG repair in human cells. Environ. Mol. Mutagen. 42:50–58, 2003. © 2003 Wiley‐Liss, Inc.
Quantitation of aberrant interlocus T‐cell receptor rearrangements in mouse thymocytes and the effect of the herbicide 2,4‐dichlorophenoxyacetic acid
Authors: Knapp Geremy W. , Setzer R. Woodrow , Fuscoe James C.
Published: July 2003

Small studies in human populations have suggested a correlation between the frequency of errors in antigen receptor gene assembly and lymphoid malignancy risk. In particular, agricultural workers exposed to pesticides have both an increased risk for lymphoma and an increased frequency of errors in antigen receptor gene assembly. In order to further investigate the potential of such errors to serve as a mechanistically based biomarker of lymphoid cancer risk, we have developed a sensitive PCR assay for quantifying errors of V(D)J recombination in the thymocytes of mice. This assay measures interlocus rearrangements between two T‐cell receptor loci, V‐gamma and J‐beta, located on chromosomes 13 and 6, respectively. The baseline frequency in four strains of mice was determined at several ages (2–8 weeks of age) and was found to be stable at ∼1.5 × 10‐5 per thymocyte. Strain AKR, which has a high susceptibility to T‐cell lymphomas, did not show an elevated frequency of aberrant V(D)J events. We used this assay to examine the effects of the herbicide 2,4‐dichlorophenoxyacetic acid (2,4‐D) on the frequency of these events. Female B6C3F1 mice, 27 days of age, were exposed to 2,4‐D by gavage at doses of 0, 3, 10, 30, and 100 mg/kg/day for 4 successive days and sacrificed on day 5. Thymus DNA was isolated and examined for illegitimate V(D)J recombination‐mediated gene rearrangements. In addition, pregnant mice were exposed to 2,4‐D and thymocytes from the offspring examined at 2 weeks of age. No significant increase in aberrant V(D)J rearrangements was found, indicating that under these conditions 2,4‐D does not appear to effect this important mechanism of carcinogenesis. Environ. Mol. Mutagen. 42: 37–43, 2003. Published 2003 Wiley‐Liss, Inc.
Identification of transcriptome profiles for the DNA‐damaging agents bleomycin and hydrogen peroxide in L5178Y mouse lymphoma cells
Authors: Seidel Shawn D. , Kan H. Lynn , Stott William T. , Schisler Melissa R. , Gollapudi B. Bhaskar
Published: July 2003

It is believed that some aspects of genotoxicity are associated with changes in the transcription levels of certain genes, especially those involved in DNA repair and cell cycle control. Additionally, it is hypothesized that chemicals sharing a common mode of genotoxicity should exhibit similar changes in gene expression. We have evaluated these hypotheses by analyzing transcriptome profiles of mouse lymphoma L5178Y/TK+/− cells treated with bleomycin and hydrogen peroxide, two mutagens that produce genotoxicity by generating reactive free radicals. The cells were treated for 4 hr and RNA was isolated at the end of the treatment and after a 20 hr recovery. Transcriptome analyses were performed using the Clontech Mouse 1.2K cDNA microarray (1,185 genes) and hybridization with a 32[P]‐labeled probe. Of the genes examined, each mutagen altered the expression (1.5‐fold or greater) of only two genes after the 4 hr treatment. In cells allowed to recover for 20 hr after treatment, bleomycin and hydrogen peroxide altered the expression of 8 and 5 genes, respectively. Many of the altered genes have some association with apoptosis. Of these genes, three (the genes encoding granzyme A, integrin beta 7, and 45 kDa calcium‐binding protein precursor) were in common between chemical treatments. The expression of DNA repair and cell cycle controlling genes present on the array was not affected by the treatments. These results show that bleomycin and hydrogen peroxide both have unique and commonly regulated genes that have the potential to serve as biomarkers of exposure to agents causing DNA damage by free radical mechanisms. Environ. Mol. Mutagen. 42:19–25, 2003. © 2003 Wiley‐Liss, Inc.
Comparison of mutagenicity and calf thymus DNA adducts formed by the particulate and semivolatile fractions of vehicle exhausts
Authors: Pohjola Sanna K. , Lappi Maija , Honkanen Markku , Savela Kirsti
Published: July 2003

In this study we compared the ability of extractable organic material from particulate and semivolatile fractions of gasoline emission to induce mutations in bacteria and form adducts with calf thymus (CT) DNA with corresponding data obtained from diesel exhaust. Exhaust particles from gasoline‐powered passenger cars were collected on filters and semivolatile compounds were collected on polyurethane foam (PUF). The mutagenicity of the soluble organic fraction (SOF) was determined in Salmonella typhimurium strain TA98 and the DNA binding of aromatic compounds in the extracts was assessed by in vitro incubations with CT DNA and rat liver S9 (oxidative activation) or xanthine oxidase (reductive activation) followed by butanol‐enhanced 32P‐postlabeling analysis. Semivolatile fractions of gasoline emission collected on PUF formed more CT DNA adducts than filter extracts under all reaction conditions, but showed a lower mutagenic potential than the corresponding particulate samples. This suggests that the capacity of PUF to collect exhaust particle‐derived compounds and/or the efficiency of xanthine oxidase and enzymes in the rat liver S9 to activate these compounds to DNA binding metabolites was higher than expected. Gasoline extracts, benzo[a]pyrene and diesel particulate matter (SRM 1650) formed more S9‐mediated DNA adducts as their dose increased, although a linear dose–response was not observed for the gasoline exhausts. Lower concentrations of gasoline and diesel extracts bound to DNA with greater efficiency than did 8‐fold higher doses, suggesting complex interactions and/or an inhibition of S9 enzyme activities by the high doses. Diesel extracts formed higher levels of adducts than gasoline extracts, especially with the reductive activation system, suggesting that diesel extracts contain high levels of nitro‐polycyclic aromatic hydrocarbons (nitro‐PAHs). The higher direct‐acting Salmonella mutagenicity in diesel extracts in comparison with gasoline extracts is consistent with diesel extracts containing higher concentrations of nitro‐PAHs. The results of this study indicate that diesel extracts are more mutagenic and form more DNA adducts than gasoline extracts and that the effects of extract dose on DNA adduct formation are complex. Environ. Mol. Mutagen. 42:26–36, 2003. © 2003 Wiley‐Liss, Inc.
Basic consultation requirements of NAGPRA for federal land managers: What's a manager to do?
Authors: Wilde James D. , Brown Clifford
Published: July 2003

This article introduces the Native American Graves Protection and Repatriation Act of 1990 (NAGPRA)
and outlines basic compliance procedures for most federal agency land managers. NAGPRA is actually civil rights
law, but federal cultural or natural resource managers generally are assigned responsibility for NAGPRA compliance
within affected agencies. The Act deals only with “NAGPRA objects,” defined in NAGPRA as Native
American human remains, funerary objects, sacred objects, and objects of cultural patrimony. NAGPRA has three
basic parts. The first deals with collections under federal control or in museums prior to 1990. The second deals
with intentional removal or inadvertent discovery of NAGPRA objects. The third deals with criminal penalties for
illegal trafficking in NAGPRA objects. This article addresses only the first two parts, with the primary focus on
the second part; that is, processes required and recommended for intentional removal and inadvertent
discovery of NAGPRA objects on federal lands. © 2003 Wiley Periodicals, Inc.
Health risk assessment at the Oklahoma City Air Logistics Center industrial wastewater treatment facility
Authors: Hall Freddie E.
Published: July 2003

During production and maintenance operations at the Oklahoma City Air Logistics Center
(OC‐ALC), industrial wastewater streams are generated which contain organic compounds
(primarily phenol and methylene chloride). These streams result from both direct and indirect contact
with organic compounds via chemical depainting operations, chemical cleaning processes, and electroplating
operations. Organic materials in the combined wastewater are treated at the on‐site industrial wastewater
treatment facility (IWTF) with unit processes including open surface basins. Some of these treatment
processes result in the release of semi‐volatile and volatile organic compounds (VOCs) from the
wastewater to the ambient air. Because emitted VOCs can create potential health risks for treatment facility
workers and the general public in the immediate surrounding areas, Tinker AFB is required to quantify (and
report) VOCs released into the atmosphere. Such regulatory reporting can encompass identifying VOC emission
sources, estimating emissions from the IWTF, quantifying ambient air concentrations surrounding the facility via
dispersion modeling, and evaluating computer‐generated numerical concentration estimates with respect to
discontinuous field data and an open‐path optical remote monitoring system. The focus of this paper is to
identify and quantify health risks associated with phenol and methylene chloride releases surrounding the IWTF. The
risk assessment will include calculation of an equivalent human dose (based on animal mortality studies),
the maximum risk for individuals in the general population, excess number of cases of cancer, the average excess
number of cases of cancer generated per year, and loss of life expectancy for the general population. © 2003
Wiley Periodicals, Inc.
An updated cost study for enhanced sludge washing of radioactive waste
Authors: DeMuth Scott F. , Thayer Gary R.
Published: July 2003

This article updates previous cost savings studies conducted to evaluate the use of enhanced sludge washing
(ESW) of high‐level radioactive waste at the United States Department of Energy Hanford Site.
The cost savings estimate was updated using stochastic analysis based on new information from the Independent
Review of Hanford High Level Waste Volume and the more recent Tank Waste Remediation System Operation and
Utilization Plan. It is estimated that implementation of ESW in the tank waste remediation system
(TWRS) at the Hanford Site can save approximately $4.8 billion compared to the use of an
alternative, simpler water wash. The simpler water wash dissolution was found to be 85 percent as effective as
the ESW dissolution. Further, the updated remediation cost estimate of $4.8 billion savings is uncertain
only within ±$1.6 billion at the 95 percent confidence interval. © 2003 Wiley Periodicals,
Inc. Reprinted from Remediation Volume 12, Number 2.
EMS success story at Naval Air Station in Willow Grove, Pennsylvania: How an EIMS supports effective EMS implementation
Authors: Turner Russell , Greco Paul
Published: July 2003

This is a success story about a U.S. Navy concurrent implementation of an ISO 14001 environmental management
system (EMS) and a World Wide Web (Web)‐based environmental information management
system (EIMS) under a pilot program at Naval Air Station Joint Reserve Base (NASJRB) in
Willow Grove, Pennsylvania. The EIMS is a unique approach within DOD to take advantage of Knowledge Management
(i.e., the collaborative sharing of work products, data, procedures, reports, and communications to make
better business decisions faster).

The challenge of complying with Executive Order (E.O.) 13148, requiring EMS implementation by
October 2005, was complemented by the desire to capture and leverage knowledge to improve systems accuracy,
reliability, and accessibility so business decisions could be made better and faster. Working with the NASJRB
Willow Grove Environmental Division, the project team developed a concurrent approach to the EMS and EIMS
implementation as a pilot program for the U.S. Navy Reserve Force Command (COMNAVRESFOR) based in New
Orleans, Louisiana. The EMS implementation followed the approach used by industry to comply with ISO 14001.
Modifications to a typical ISO 14001 EMS implementation approach were made to adapt to Navy
chain‐of‐command issues and to comply with a well‐developed institutional environmental
program (Navy Operations Instructions and Regulations‐OPNAVINST 5090.1B).

The EIMS consists of several components housed in one moderately powerful Web server at the Air Station. One
part of the system taps unwieldy “legacy” databases to prepare routine and ad hoc management reports
for users on demand via a simple Web browser approach. Another component of the EIMS consists of a
knowledge‐based decision support system using commercial‐off‐the‐shelf
(COTS) software to perform Environmental Division task assignment and tracking, project financial
control, document management, and scheduling/planning on a shared calendar. Information housed in the EIMS,
including administrative/management functions, is available to Environmental Division employees and can be
made available to collaborators and higher level Command users over the Internet using simple Web browser access.
© 2003 Wiley Periodicals, Inc.
Transitory real‐time property rights and exchange intellectual property
Authors: Webb Robert I.
Published: July 2003

American exchanges own the price quotations they generate. Access to real‐time price information is
highly valued by most market participants. This enables exchanges to exact royalties from the sale of such
market information. In this sense, an exchange's ownership of its price quotations is akin to owning a
property right in a perishable commodity (i.e., fresh market price quotations) that
is most valuable for only a transitory or limited period of time. The implications of exchange
ownership of price data extend beyond financial markets. Recently, Woodard (2000) has noted that some
internet auction operators have asserted ownership over the prices they generate. This study reviews the legal
origin and nature of the property right to price quotations generated on U.S. futures exchanges and assesses
whether exchange ownership should be transitory. The legal basis for transitory real‐time (real and
personal) property rights is discussed and the economic implications are considered. © 2003 Wiley
Periodicals, Inc. Jrl Fut Mark 23:891–913, 2003
MLL/SEPTIN6 chimeric transcript from inv ins(X;11)(q24;q23q13) in acute monocytic leukemia: Report of a case and review of the literature
Authors: Kim Hee‐Jin , Ki Chang‐Seok , Park Quehn , Koo Hong‐Hoe , Yoo Keon‐Hee , Kim Eun‐Jeong , Kim Sun‐Hee
Published: July 2003

Rearrangements of the MLL gene on chromosome 11, band q23, are one of the most common genetic changes in acute leukemia. Reciprocal translocation is the most common form of MLL rearrangement, and the partner genes in MLL translocation are notably diverse. Involvement of the SEPTIN6 gene on Xq24 in MLL rearrangements occurs very rarely, with only six cases having been documented in the literature. Of note, the MLL/SEPTIN6 rearrangements in these cases were cryptic or complex, and it was shown that the 5′‐MLL/SEPTIN6‐3′ transcript resides on the derivative X chromosome rather than on the derivative chromosome 11 as in the majority of cases of MLL translocations. These observations suggested that MLL and SEPTIN6 reside on their respective chromosome loci in reverse orientation, that is, centromere‐to‐telomere and telomere‐to‐centromere, respectively. We here report a case of acute monocytic leukemia with inv ins(X;11)(q24;q23q13) in a 29‐month‐old child. Fluorescence in situ hybridization study revealed the break‐apart 5′‐MLL segment to be translocated to the derivative X chromosome, and reverse transcriptase–polymerase chain reaction followed by sequencing analysis confirmed the 5′‐MLL/SEPTIN6‐3′ chimeric transcript. This case is the first to provide direct cytogenetic evidence for the salient nature of the MLL/SEPTIN6 rearrangement. We reviewed clinical and cytogenetic features of all cases of 11q23 and Xq22–24 rearrangements reported up to now, including six cases where the involvement of the SEPTIN6 gene was confirmed by molecular techniques. © 2003 Wiley‐Liss, Inc.
Characterization of FRA6E and its potential role in autosomal recessive juvenile parkinsonism and ovarian cancer
Authors: Denison Stacy R. , Callahan Gwen , Becker Nicole A. , Phillips Leslie A. , Smith David I.
Published: July 2003

Characterization of FRA6E (6q26), the third most frequently observed common fragile site (CFS) in the human population, determined that aphidicolin‐induced instability at FRA6E extends over a very large region (3.6 Mb). Sequence analysis identified eight genes (IGF2R, SLC22A1, SLC22A2, SLC22A3, PLG, LPA, MAP3K4, and PARK2) as mapping within the large FRA6E region. PARK2, the gene associated with autosomal recessive juvenile parkinsonism (ARJP), accounts for more than half of the CFS. Homozygous deletions and large heterozygous deletions have been observed in PARK2 in ARJP patients. RT‐PCR analysis of the eight genes localizing to FRA6E indicated that 50% of the genes, including PARK2, were down‐regulated in one or more of the primary ovarian tumors analyzed. PARK2 expression was down‐regulated in 60.0% of the primary ovarian tumors analyzed. Additionally, we found tumor‐specific alternative transcripts of PARK2. Loss of heterozygosity analysis of primary ovarian tumors by use of polymorphic markers in the 6q26 region demonstrated 72% LOH in the center of the PARK2 gene, the highest of any of the markers tested. FRA6E shares many similarities with FRA3B (3p14.2) and FRA16D (16q23.2) in representing a large region of genomic instability and containing an extremely large gene that may play a role in the development of ovarian and many other cancers. © 2003 Wiley‐Liss, Inc.
Aneuploidy in oncocytic lesions of the thyroid gland: Diffuse accumulation of mitochondria within the cell is associated with trisomy 7 and progressive numerical chromosomal alterations
Authors: Dettori Tinuccia , Frau Daniela V. , Lai Maria L. , Mariotti Stefano , Uccheddu Alessandro , Daniele Giovanni M. , Tallini Giovanni , Faa Gavino , Vanni Roberta
Published: July 2003

Oncocytic cells are characterized by a greatly increased number of mitochondria that distend the cell cytoplasm and result in a distinctive granular appearance of the cell on conventional histology sections. Oncocytes are frequently found in metabolically active human tissues including the thyroid gland, and, as a general rule, when their proportion in a thyroid tumor is greater than 75% the tumor is referred to as oncocytic (Hürthle cell) adenoma or carcinoma. Such tumors represent a subset of thyroid lesions, and recently, both interphase fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) studies reported that they may show aneuploidy, with widespread numerical chromosomal alterations. In contrast, very few cases have been studied by conventional cytogenetic analysis. Whether the cells with chromosomal changes are the same as those with mitochondrial accumulation or whether lesions only partially composed of oncocytic cells also have cytogenetic alterations is unclear. To investigate the relationship between acquisition of the oncocytic phenotype and numerical chromosomal changes, we analyzed a random selection of thyroid lesions with (18 cases) and without (11 cases) morphological evidence of oncocytic differentiation. Lesions with oncocytes included hyperplastic nodules, adenomas, Hürthle cell tumors, and papillary carcinomas with lymphocytic stroma (Whartin‐like tumors of the thyroid). Karyotypic changes were analyzed by cytogenetic analysis, FISH, or CGH, and the results were compared with in situ analysis of mitochondrial accumulation by immunofluorescence. A striking correlation between the presence of oncocytes and the presence of aneuploid katyotypes was seen in the oncocytic follicular thyroid nodules, but not in the oncocytic papillary tumors. Structural chromosome changes or normal karyotypes were observed in the lesions lacking oncocytic features. Extending the FICTION technique to the evaluation of a cytoplasmic antigen (mitochondrial membrane antigen), we pursued the simultaneous visualization of both mitochondrial increase and numerical chromosomal alterations, and showed that oncocytes of follicular lesions are prone to become aneuploid. Our data support the contention that follicular tumors composed of oncocytes should be regarded as a distinct subset. © 2003 Wiley‐Liss, Inc.
By‐products of immunoglobulin somatic hypermutation
Authors: Bemark Mats , Neuberger Michael S.
Published: July 2003

The antigen receptor loci are the only loci in humans to undergo programmed somatic gene modification. Although aberrant V(D)J integration and class switch recombination can both give rise to chromosomal translocations, a role for somatic hypermutation in such genomic rearrangements has been suggested but is less clearly established. To characterize the types of by‐products of somatic hypermutation, we analyzed aberrant rearrangements involving the immunoglobulin loci in a human B‐cell line (Ramos) that performs Ig V gene hypermutation constitutively during culture. Single‐nucleotide substitutions account for 95% of the mutational events in the VH gene, with small deletions and duplications accounting for most of the remaining mutations. However, larger genetic alterations can be detected at low frequency, accounting for 0.5% of VH‐inactivating mutations. Examples include a large (13 kb) deletion, which entirely removes the expressed VH gene; a 3‐kb deletion extending from the functional VHDJH into an upstream VH (generating a hybrid VHDJH gene reminiscent of VH replacement); and an ectopic insertion into the VH from chromosome 1. The results support the proposal that aberrant antibody hypermutation can lead to gross genomic alterations but indicate that such events are rare. © 2003 Wiley‐Liss, Inc.
Synovial fibroblasts and synovial macrophages from patients with rheumatoid arthritis and other inflammatory joint diseases show chromosomal aberrations
Authors: Kinne Raimund W. , Kunisch Elke , Beensen Volkmar , Zimmermann Thomas , Emmrich Frank , Petrow Peter , Lungershausen Wolfgang , Hein Gert , Braun Rudolf K. , Foerster Martin , Kroegel Claus , Winter Rando , Liesaus Eckehard , Fuhrmann Renée A. , Roth Andreas , Claussen Uwe , Liehr Thomas
Published: July 2003

Chromosomal aberrations were investigated in nuclei extracted from synovial tissue and first‐passage synovial fibroblasts (P‐1 SFB, 98% enrichment) or macrophages (P‐1 Mϕ) from patients with rheumatoid arthritis (n = 10). The findings were compared with those in other rheumatic diseases (osteoarthritis, n = 14; reactive arthritis, n = 1), as well as with those in chronic obstructive pulmonary disease (n = 8). Controls were paired peripheral blood lymphocytes from arthritic patients, synovial tissue or SFB/Mϕ from joint trauma/normals (n = 9), and peripheral blood monocytes from normal donors (n = 10). GTG banding of metaphase chromosomes and interphase fluorescence in situ hybridization with centromere‐specific probes were used. Comparable chromosomal aberrations were observed in synovial tissue and P‐1 SFB of patients with rheumatoid arthritis, osteoarthritis, and reactive arthritis (polysomy 7 and aneusomies of chromosomes 4, 8, 9, 12, and 18). Notably, aneusomies of chromosomes 4, 6, 7, 8, 9, 11, 12, and/or X were also detected in P‐1 synovial Mϕ from rheumatoid arthritis (90% of the cases), osteoarthritis (93%), and reactive arthritis (1/1), as well as bronchial Mϕ from chronic obstructive pulmonary disease (25%). No aberrations were detected in paired peripheral blood lymphocytes (except for one osteoarthritis case with a karyotype 45,X[10]/46,XX[17]), or in peripheral blood monocytes and synovial tissue of normals/joint trauma. Because Mϕ aberrations were common to chronic joint and pulmonary disease, chronic inflammatory stress may induce chromosomal aberrations with potential functional relevance in local mesenchymal cells and infiltrating leukocytes in an organ‐independent fashion. © 2003 Wiley‐Liss, Inc.
Identification of tissue‐specific genes in nasopharyngeal epithelial tissue and differentially expressed genes in nasopharyngeal carcinoma by suppression subtractive hybridization and cDNA microarray
Authors: Zhang Bicheng , Nie Xinmin , Xiao Bingyi , Xiang Juanjuan , Shen Shourong , Gong Jialei , Zhou Ming , Zhu Shiguo , Zhou Jie , Qian Jun , Lu Hongbin , He Xianfeng , Li Xiaoling , Hu Gengxi , Li Guiyuan
Published: July 2003

Suppression subtractive hybridization (SSH) was performed for isolation of tissue‐specific genes in nasopharyngeal epithelial tissue, by use of cDNAs from human adult nasopharyngeal epithelial tissue as tester and mixed cDNAs from esophagus, lung, liver, heart, stomach, spleen, skeletal muscle, kidney, and skin as drivers. Fourteen differentially expressed genes in nasopharyngeal epithelial tissue were obtained. Among these genes, LPLUNC1 and SPLUNC1 were confirmed to be specifically expressed in nasopharyngeal epithelial tissue and the trachea. A novel transcript of SPLUNC1, which we designate NASG, was found. We also combined SSH and cDNA microarray hybridization to identify genes whose expressions were altered in nasopharyngeal carcinoma (NPC). We used NPC cell line HNE1 and primary human embryo nasopharyngeal epithelial cells in one SSH experiment, and NPC biopsies and normal adult nasopharyngeal epithelial tissue in another. Some 1,200 SSH inserts from four subtractive cDNA libraries were arrayed onto nylon membranes by use of robotic printing. Differential gene expression was verified by hybridizing of the membranes with radioactively labeled first‐strand cDNA from NPC cell line HNE1, primary human embryo nasopharyngeal epithelial cells, NPC biopsies, and normal adult nasopharyngeal epithelial tissue. Seventeen differentially expressed genes in NPC were obtained. Among these genes, we identified SPLUNC1 and LPLUNC1 to be down‐expressed in NPC biopsies (34/48, 33/48). © 2003 Wiley‐Liss, Inc.
Mutations and aberrant DNA methylation of the PROX1 gene in hematologic malignancies
Authors: Nagai Hirokazu , Li Yinghua , Hatano Sonoko , Toshihito Ohno , Yuge Masayuki , Ito Etsuro , Utsumi Makoto , Saito Hidehiko , Kinoshita Tomohiro
Published: July 2003

The homeobox gene PROX1 is related to the Drosophila prospero gene, which is expressed in the developing central nervous system and lens‐secreting cone cells. We found that the PROX1 gene had missense and nonsense mutations in 4 of 29 hematologic cell lines analyzed. Decreased mRNA expression was also observed in half of these cell lines by RT‐PCR. The restoration of PROX1 gene expression after treatment with the demethylating agent 5‐aza‐2′‐deoxycytidine, as well as bisulfite sequencing analysis, indicated that gene silencing is caused by DNA hypermethylation at intron 1. Such hypermethylation was also seen in primary lymphomas (56.3%, 18/32) in a tumor‐specific manner. These findings indicate that the profile of the PROX1 gene corresponds to that of a candidate tumor‐suppressor gene. © 2003 Wiley‐Liss, Inc.
Cross‐modal sensory processing in the anterior cingulate and medial prefrontal cortices
Authors: Laurienti Paul J. , Wallace Mark T. , Maldjian Joseph A. , Susi Christina M. , Stein Barry E. , Burdette Jonathan H.
Published: July 2003

One of the principal functions of the nervous system is to synthesize information from multiple sensory channels into a coherent behavioral and perceptual gestalt. A critical feature of this multisensory synthesis is the sorting and coupling of information derived from the same event. One of the singular features of stimuli conveying such information is their contextual or semantic congruence. Illustrating this fact, subjects are typically faster and more accurate when performing tasks that include congruent compared to incongruent cross‐modal stimuli. Using functional magnetic resonance imaging, we demonstrate that activity in select brain areas is sensitive to the contextual congruence among cross‐modal cues and to task difficulty. The anterior cingulate gyrus and adjacent medial prefrontal cortices showed significantly greater activity when visual and auditory stimuli were contextually congruent (i.e., matching) than when they were nonmatching. Although activity in these regions was also dependent on task difficulty, showing decreased activity with decreasing task difficulty, the activity changes associated with stimulus congruence predominated. Hum. Brain Mapping 19:213–223, 2003. © 2003 Wiley‐Liss, Inc.
Aperiodic phase re‐setting in scalp EEG of beta–gamma oscillations by state transitions at alpha–theta rates
Authors: Freeman Walter J. , Burke Brian C. , Holmes Mark D.
Published: July 2003

We evaluated the rapid changes in regional scalp EEG synchronization in normal subjects with spatial and temporal resolution exceeding prior art 10‐fold with a high spatial density array and the Hilbert transform. A curvilinear array of 64 electrodes 3 mm apart extending 18.9 cm across the scalp was used to record EEG at 200/sec. Analytic amplitude (AA) and phase (AP) were calculated at each time step for the 64 traces in the analog pass band of 0.5–120 Hz. AP differences approximated the AP derivative (instantaneous frequency). The AP from unfiltered EEG revealed no reproducible patterns. Filtering was necessary in the β and gamma ranges according to a technique that optimized the correlation of the AP differences with the activity band pass filtered in the alpha range. The sizes of temporal AP differences were usually within ±0.5 radian from the average step corresponding to the center frequency of the pass band. Large AP differences were often synchronized over distances of 6 to 19 cm. An optimal pass band to detect and measure these recurring jumps in AP in the β and γ ranges was found by maximizing the α peak in the cospectrum of the correlation between unfiltered EEG and the band pass AP differences. Synchronized AP jumps recurred in clusters (CAP) at α and theta rates in resting subjects and with EMG. Cortex functions by serial changes in state. The Hilbert transform of EEG from high‐density arrays can visualize these state transitions with high temporal and spatial resolution and should be useful in relating EEG to cognition. Hum. Brain Mapping 19:248–272, 2003. © 2003 Wiley‐Liss, Inc.
Three‐dimensional maximum probability atlas of the human brain, with particular reference to the temporal lobe
Authors: Hammers Alexander , Allom Richard , Koepp Matthias J. , Free Samantha L. , Myers Ralph , Lemieux Louis , Mitchell Tejal N. , Brooks David J. , Duncan John S.
Published: July 2003

Probabilistic atlases of neuroanatomy are more representative of population anatomy than single brain atlases. They allow anatomical labeling of the results of group studies in stereotaxic space, automated anatomical labeling of individual brain imaging datasets, and the statistical assessment of normal ranges for structure volumes and extents. No such manually constructed atlas is currently available for the frequently studied group of young adults. We studied 20 normal subjects (10 women, median age 31 years) with high‐resolution magnetic resonance imaging (MRI) scanning. Images were nonuniformity corrected and reoriented along both the anterior‐posterior commissure (AC–PC) line horizontally and the midsagittal plane sagittally. Building on our previous work, we have expanded and refined existing algorithms for the subdivision of MRI datasets into anatomical structures. The resulting algorithm is presented in the Appendix. Forty‐nine structures were interactively defined as three‐dimensional volumes‐of‐interest (VOIs). The resulting 20 individual atlases were spatially transformed (normalized) into standard stereotaxic space, using SPM99 software and the MNI/ICBM 152 template. We evaluated volume data for all structures both in native space and after spatial normalization, and used the normalized superimposed atlases to create a maximum probability map in stereotaxic space, which retains quantitative information regarding inter‐subject variability. Its potential applications range from the automatic labeling of new scans to the detection of anatomical abnormalities in patients. Further data can be extracted from the atlas for the detailed analysis of individual structures. Hum. Brain Mapping 19:224–247,2003. ©2003 Wiley‐Liss,Inc.