bluuebunny/crossref_metadata_2025 huggingface dataset:
Risky decision making in Huntington's disease
Authors: STOUT JULIE C. , RODAWALT WILLIAM C. , SIEMERS ERIC R.
Published: July 2002

In the clinical setting, Huntington's disease
is associated with problems in judgment and decision making,
however, the extent of these problems and their association
with clinical characteristics have not been assessed. Recently,
a laboratory-based simulated gambling task has been used
to quantify similar decision-making deficits in ventromedial
frontal lobe damaged participants. We hypothesized that
participants with Huntington's disease (HD) would
show deficits on this gambling task. For this study, 14
HD participants were asked to make 100 selections from
four decks of cards with varied payoffs in order to maximize
winnings of play money. They were compared to 22 participants
with Parkinson's disease (PD) and 33 healthy controls.
After an initial period in which participants had to learn
contingencies of the decks, the HD group made fewer advantageous
selections than the PD and control groups. In HD, the number
of advantageous selections in the gambling task was correlated
with measures of memory and conceptualization but not disinhibition.
Thus, people with HD may have had difficulties learning
or remembering win/loss contingencies of the decks, or
they may have failed to consistently take these into account
in their card selections. These findings are consistent
with current models of frontal-subcortical brain circuits
and behavior. (JINS, 2001, 7, 92–101.)
Effects of retroactive and proactive interference on word
list recall in schizophrenia
Authors: TORRES IVAN J. , FLASHMAN LAURA A. , O'LEARY DANIEL S. , ANDREASEN NANCY C.
Published: July 2002

Schizophrenia spectrum patients (N = 143) and
healthy controls (N = 160) were administered the
Rey Auditory Verbal Learning Test (RAVLT) and tests of
executive functioning to directly investigate the effects
of proactive interference (PI) and retroactive interference
(RI) on word list recall. It was hypothesized that by virtue
of the predicted preferential association between executive
functioning and RI (relative to PI), patients would demonstrate
increased susceptibility to RI in their ability to recall
word lists. Results indicated that patients show increased
susceptibility to RI relative to PI. Furthermore, this
difference appeared to be related to the frontally-mediated
central executive functions that were preferentially associated
with RI but not PI susceptibility. (JINS, 2001,
7, 481–490.)
The impact of HIV-related neuropsychological dysfunction
on driving behavior
Authors: MARCOTTE THOMAS D. , HEATON ROBERT K. , WOLFSON TANYA , TAYLOR MICHAEL J. , ALHASSOON OMAR , ARFAA KAIVON , GRANT IGOR ,   THE HNRC GROUP
Published: July 2002

HIV infection often results in neuropsychological
(NP) impairment. In order to assess the impact that HIV-related
NP deficits may have on automobile driving, we evaluated
68 HIV-seropositive drivers using an NP battery and two
PC-based driving simulations. Thirty-two participants were
classified as NP impaired; most (72%) evidenced only mild
impairment, and none met criteria for HIV-associated dementia.
After controlling for degree of immunosuppression and disease
stage, NP-impaired participants failed a previously validated
driving simulation at a much higher rate than cognitively
intact participants [OR = 5.3, 95% CI (1.7, 17.0),
p = .006]. Similarly, on a simulation of
city driving, NP impaired participants were more likely
to fail based upon the number of accidents [OR = 6.1,
95% CI (1.5, 24.6), p = .01]. Simulator performance
was predicted by functioning in a number of NP domains,
with NP tests accounting for 13–30% of the variance
on the simulations. Although it would be premature to extrapolate
these findings to impairment in on-the-road driving, they
do argue for greater attention to the impact that even
mild HIV-related NP deficits may have on driving skills.
(JINS, 1999, 5, 579–592.)
Water pollution abatement cost function: methodological issues and an application to small-scale factories in an industrial estate in India
Authors: GOLDAR BISHWANATH , MISRA SMITA , MUKHERJI BADAL
Published: July 2002

Formulation and estimation of a correctly specified abatement cost function would be central to policy formulation regarding imposing taxes or user-fees as well as of sharing social cost in the presence of environmental pollution. Often in research, the output of an abatement activity for water pollution appears to us not to have been clearly specified. This activity is very distinct from whatever is the actual product of the plant. We propose in this paper that the output is only and exclusively the reduction in the level of the pollutant in the outflow from the plant and illustrate this with primary data for small-scale factories in Nandesari Industrial Estate in Gujarat, India. The cost function estimates provide evidence of significant scale economies and high marginal abatement cost in wastewater treatment by small-scale factories.
Technical progress and pollution abatement: an economic view of selected technologies and practices
Authors: Anderson Dennis
Published: July 2002

The paper first presents evidence from the engineering literature on air and water pollution control, which shows that, when the pollution abatement technologies are in place, large reductions in pollution have been achieved at costs that are small relative to the costs of production. A simulation model is then developed to study the effects of technical progress on pollution abatement, and applied to particular cases in developing countries. The results are compared with the projections of an environmental Kuznets curve: they reproduce the latter if policies were not to be introduced until per capita incomes reached levels comparable to those of the industrial countries when they first introduced their policies; but show dramatically lower and earlier peaks if policies were to be introduced earlier. The conclusion is shown to apply more generally, and it is argued that developing countries can aspire to addressing their environmental problems at a much earlier phase of development than the industrial countries before them.
Resource depletion and economic sustainability in Malaysia
Authors: VINCENT JEFFREY R.
Published: July 2002

Countries richly endowed with natural resources have, on average, developed less rapidly than countries that are poor in natural resources. One possible explanation for this phenomenon is that the level of investment in reproducible capital has been insufficient to offset the depletion of natural capital. The empirical significance of this explanation can be investigated by analysing modified measures of net investment and net domestic product. Estimation of these measures involves calculating the economic depreciation of natural resources, a task that has been problematic in previous studies. Malaysia provides an ideal case for such empirical investigations, as it is one of the world's most resource-rich countries yet also has one of the world's fastest-growing economies, consists of three subnational regions that differ significantly in terms of economic structure, and has sufficient data for estimating conceptually correct measures of natural resource depreciation. Results of the analysis indicate that Malaysia has developed sustainably, despite substantial resource depletion. This is not the case in two of the regions, however, where trends in both net investment and net domestic product indicate that current consumption levels cannot be sustained. Nevertheless, the regional differences in sustainability might be consistent with optimal national use of the rents generated by exploitation of the country's natural resources.
Increasing the Attendance Rate for First Appointments at Child
and Family Psychiatry Clinics: An Opt-in System
Authors: Wiseman Malcolm , McBride Marie
Published: July 2002

Non-attendance for first outpatient appointments at Child Mental
Health
Clinics is a common problem affecting efficient use of resources, as well
as
staff morale. This study demonstrates that requiring families to confirm
that
they want an appointment, in order to receive one, significantly improves

the attendance rate for first appointments, compared to two other
commonly used procedures: a reminder letter before the appointment is
sent, and a standard appointment letter. Furthermore, this procedure did

not appear to reduce accessibility to the service.
On the history of if- and though-links with declarative complement clauses
Authors: López-Couso María José , Méndez-Naya Belén
Published: July 2002

This article examines the history of a construction type which has been almost completely disregarded in the extensive literature on complementation, namely declarative complement clauses introduced by if and though. Contrary to the standard view, which favours an adverbial analysis for these clauses, it is shown here that there are convincing arguments for considering certain if- and though-clauses as complements, though it is also admitted that their behaviour differs in some respects from standard cases of declarative complementation. The article also reveals the existence of a number of factors favouring the selection of the minor complementizers if and though over the major complement-clause links that and zero in Old, Middle, and Early Modern English. Evidence has primarily been drawn from the diachronic part of the Helsinki Corpus of English Texts.
The English get-passive in spoken discourse: description and implications for an interpersonal grammar
Authors: Carter Ronald , McCarthy Michael
Published: July 2002

Using a 1.5-million-word sample from the CANCODE spoken English corpus, we present a description of the get-passive in informal spoken British English. Previous studies of the get-passive are reviewed, and their focus on contextual and interpersonal meanings is noted. A number of related structures are then considered and the possibility of a passive gradient is discussed. The corpus sample contains 139 get-passives of the type X get + past participle (by Y) (e.g. He got killed), of which 124 occur in contexts interpreted as adversative or problematic from the speaker's viewpoint. Very few examples contain an explicit agent or adverbials. Main verb frequency is also considered. Where contexts are positive rather than adversative, newsworthiness or focus of some kind on the subject and/or events is still apparent. The corpus evidence is used to evaluate the terms upon which an interpersonal grammar of English might be developed, and a contrast is drawn between deterministic grammars and probabilistic ones, with probabilistic grammars offering the best potential for the understanding of interpersonal features.
Restore habitat or reduce mortality? Implications from a population viability analysis of the Iberian lynx
Authors: Ferreras Pablo , Gaona Pilar , Palomares Francisco , Delibes Miguel
Published: July 2002

Managers trying to preserve populations of endangered carnivores are often forced to choose between restoring habitat to allow larger breeding populations or reduce risks of mortality to increase survival rates. We modelled the viability of a metapopulation of the Iberian lynx (Lynx pardinus) under several scenarios (habitat restoration, anti‐poaching, reduction in road kills) in a real landscape to evaluate their relative effects. Increasing carrying capacity was highly effective when performed on the local populations that acted as sources but had no effect when carried out in the sinks. Realistic scenarios consisting of partial removal of the human‐related mortality (assuming additive effects of causes) predicted high risk of extinction. When combined, the effects of both management options are highly dependent on where they are carried out. If the sinks are the only targets of carrying capacity enlargement, a complete removal of human‐caused mortality is required, whereas increases in the carrying capacity of sources are always effective. The metapopulation risk of extinction decreases dramatically (from 45.5% to 2.1% in 100) if connectivity among source populations can be improved. According to our work, only a detailed knowledge of the spatial and demographic structure of the populations, combined with simulations of realistic situations, can help managers to select the a priori optimal strategy, which probably combines different management options.
Executive Turnovers in 2000
Authors: Kohno Masaru , Suga Atsuko
Published: July 2002

On April 5 2000, the Diet elected Yoshiro Mori as Japan's 55th prime minister. His predecessor, Keizo Obuchi, had suffered a stroke and became unable to carry out his official responsibility. Mori, who was the former Secretary General of the ruling Liberal Democratic Party (LDP), inherited the three party coalition between the LDP, the new Komei Party and the Conservative Party, and reappointed all of Obuchi's cabinet members. Yohei Kono was reposted as the Minister of Foreign Affairs; Hideo Usui as Justice; Kiichi Miyazawa as Finance; Hirofumi Nakasone as Education, Science and Technology; Yuya Niwa as Health and Welfare; Tokuichiro Tanazawa as Agriculture, Forestry and Fisheries; Takeshi Fukaya as International Trade and Industry; Toshihiro Nikai as Transport; Eita Yashiro as Posts and Telecommunications; Takamori Makino as Labor; Masaaki Nakayama as Construction; Kosuke Hori as Home Affairs, Mikio Aoki as Chief Cabinet Secretary; Kunihiro Tsuzuki as Management and Coordination; Tsutomu Kawara as Defense; Taichi Sakaiya as Economic Planning; Kayoko Shimizu as environment; and Sadakazu Tanigaki as Financial Reconstruction.
Foreword by the Director-General of the WTO
Authors: Moore Mike
Published: July 2002

Trade policy used to be a rather simple matter of defining conditions of access to
markets at the border. Little more was needed than rules defining non-discriminatory
tariff levels, circumscribing the use of quantitative trade restrictions, and protecting
the conditions of market access through the principle of national treatment. But the
very success of these simple rules in creating the conditions for successive bouts of
market-opening negotiations bred the complex and multi-faceted institution that is
the World Trade Organization of today. As tariffs tumbled, all manner of other
policies became crucial for continuing market integration. The rules had to follow
the reality. It is a brave person now who claims more than a passing familiarity with
each and every aspect of the WTO Agreements.

In this fascinating labyrinth of what passes for policy relating to trade, it is
unconvincing to argue that there is ever enough research and analysis. There will
always be more that needs to be explored and better understood. Every effort to
illuminate, to clarify, and to explain the trading system must surely be welcome. But
if we are to advance our understanding of what makes sense and what does not, and
contribute effectively to international economic cooperation, the quality and
integrity of analysis is vital. This has become more especially true in recent years as
dozens of developing countries facing formidable development challenges seek
progress through meaningful participation in the world trading system. One of the
great strengths of the WTO is its commitment to universality. If we are to give
meaning to this vision and foster confidence in the fairness of the system, we must
ensure its proper design on solid conceptual foundations.

I am proud to associate the WTO Secretariat with the birth of the World Trade
Review. The journal is committed to promoting high-quality policy analysis and
welcomes contributions from a wide range of disciplines and cross-section of
contributors. This is not an in-house journal devoted to selling pre-conceived ideas.
Its mission is to promote informed and honest debate and to deepen understanding.
The journal's editorial independence is central to these objectives. I wish the Editor
and the members of the Editorial Board of the World Trade Review well in this
important endeavour.
A Drosophila IκB kinase complex required for Relish cleavage and antibacterial immunity
Authors: Silverman Neal , Zhou Rui , Stöven Svenja , Pandey Niranjan , Hultmark Dan , Maniatis Tom
Published: July 2002

Here we report the identification of a Drosophila IκB kinase complex containing DmIKKβ and DmIKKγ, homologs of the human IKKβ and IKKγ proteins. We show that this complex is required for the signal-dependent cleavage of Relish, a member of the Rel family of transcriptional activator proteins, and for the activation of antibacterial immune response genes. In addition, we find that the activated DmIKK complex, as well as recombinant DmIKKβ, can phosphorylate Relish in vitro. Thus, we propose that theDrosophila IκB kinase complex functions, at least in part, by inducing the proteolytic cleavage of Relish. The N terminus of Relish then translocates to the nucleus and activates the transcription of antibacterial immune response genes. Remarkably, thisDrosophila IκB kinase complex is not required for the activation of the Rel proteins Dif and Dorsal through the Toll signaling pathway, which is essential for antifungal immunity and dorsoventral patterning during early development. Thus, a yet to be identified IκB kinase complex must be required for Rel protein activation via the Toll signaling pathway.
Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters
Authors: Schramm Laura , Pendergrast P. Shannon , Sun Yuling , Hernandez Nouria
Published: July 2002

Transcription initiation at RNA polymerase III promoters requires transcription factor IIIB (TFIIIB), an activity that binds to RNA polymerase III promoters, generally through protein–protein contacts with DNA binding factors, and directly recruits RNA polymerase III.Saccharomyces cerevisiae TFIIIB is a complex of three subunits, TBP, the TFIIB-related factor BRF, and the more loosely associated polypeptide β″. Although human homologs for two of the TFIIIB subunits, the TATA box–binding protein TBP and the TFIIB-related factor BRF, have been characterized, a human homolog of yeast B″ has not been described. Moreover, human BRF, unlike yeast BRF, is not universally required for RNA polymerase III transcription. In particular, it is not involved in transcription from the small nuclear RNA (snRNA)–type, TATA-containing, RNA polymerase III promoters. Here, we characterize two novel activities, a human homolog of yeast B″, which is required for transcription of both TATA-less and snRNA-type RNA polymerase III promoters, and a factor equally related to human BRF and TFIIB, designated BRFU, which is specifically required for transcription of snRNA-type RNA polymerase III promoters. Together, these results contribute to the definition of the basal RNA polymerase III transcription machinery and show that two types of TFIIIB activities, with specificities for different classes of RNA polymerase III promoters, have evolved in human cells.
Defective neurogenesis resulting from DNA ligase IV deficiency requires Atm
Authors: Lee Youngsoo , Barnes Deborah E. , Lindahl Tomas , McKinnon Peter J.
Published: July 2002

Ataxia telangiectasia results from mutations of ATM and is characterized by severe neurodegeneration and defective responses to DNA damage. Inactivation of certain DNA repair genes such as DNA ligase IV results in massive neuronal apoptosis and embryonic lethality in the mouse, indicating the occurrence of endogenously formed DNA double-strand breaks during nervous system development. Here we report that Atm is required for apoptosis in all areas of the DNA ligase IV-deficient developing nervous system. However, Atm deficiency failed to rescue deficits in immune differentiation in DNA ligase IV-null mice. These data indicate that ATM responds to endogenous DNA lesions and functions during development to eliminate neural cells that have incurred genomic damage. Therefore, ATM could be important for preventing accumulation of DNA-damaged cells in the nervous system that might eventually lead to the neurodegeneration observed in ataxia telangiectasia.
Continuous expression of Cbfa1 in nonhypertrophic chondrocytes uncovers its ability to induce hypertrophic chondrocyte differentiation and partially rescues Cbfa1-deficient mice
Authors: Takeda Shu , Bonnamy Jean-Pierre , Owen Michael J. , Ducy Patricia , Karsenty Gerard
Published: July 2002

Chondrocyte hypertrophy is a mandatory step during endochondral ossification. Cbfa1-deficient mice lack hypertrophic chondrocytes in some skeletal elements, indicating that Cbfa1 may control hypertrophic chondrocyte differentiation. To address this question we generated transgenic mice expressing Cbfa1 in nonhypertrophic chondrocytes (α1(II) Cbfa1). This continuous expression ofCbfa1 in nonhypertrophic chondrocytes induced chondrocyte hypertrophy and endochondral ossification in locations where it normally never occurs. To determine if this was caused by transdifferentiation of chondrocytes into osteoblasts or by a specific hypertrophic chondrocyte differentiation ability of Cbfa1, we used the α1(II) Cbfa1 transgene to restore Cbfa1 expression in mesenchymal condensations of the Cbfa1-deficient mice. The transgene restored chondrocyte hypertrophy and vascular invasion in the bones of the mutant mice but did not induce osteoblast differentiation. This rescue occurred cell-autonomously, as skeletal elements not expressing the transgene were not affected. Despite the absence of osteoblasts in the rescued animals there were multinucleated, TRAP-positive cells resorbing the hypertrophic cartilage matrix. These results identify Cbfa1 as a hypertrophic chondrocyte differentiation factor and provide a genetic argument for a common regulation of osteoblast and chondrocyte differentiation mediated by Cbfa1.
E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis
Authors: Müller Heiko , Bracken Adrian P. , Vernell Richard , Moroni M. Cristina , Christians Fred , Grassilli Emanuela , Prosperini Elena , Vigo Elena , Oliner Jonathan D. , Helin Kristian
Published: July 2002

The retinoblastoma protein (pRB) and its two relatives, p107 and p130, regulate development and cell proliferation in part by inhibiting the activity of E2F-regulated promoters. We have used high-density oligonucleotide arrays to identify genes in which expression changed in response to activation of E2F1, E2F2, and E2F3. We show that the E2Fs control the expression of several genes that are involved in cell proliferation. We also show that the E2Fs regulate a number of genes involved in apoptosis, differentiation, and development. These results provide possible genetic explanations to the variety of phenotypes observed as a consequence of a deregulated pRB/E2F pathway.
Tumorigenesis in mice carrying a truncating Brca1 mutation
Authors: Ludwig Thomas , Fisher Peter , Ganesan Shridar , Efstratiadis Argiris
Published: July 2002

We generated mouse mutants carrying in the Brca1 locus a modification (Brca1tr) that eliminates the C-terminal half of the protein product and obtained results indicating that, depending on genetic background, the missing BRCT and/or other domains are dispensable for survival, but essential for tumor suppression. Most of the apparently hypomorphic Brca1tr/tr mutants developed various tumors. Lymphomas were detected at all ages, whereas sarcomas and carcinomas, including breast cancer, appeared after a long latency. The mammary tumors showed striking variability in histopathological patterns suggesting stochastic engagement of tumorigenic pathways in their progression, to which theBrca1tr/tr mutation was apparently a late participant.
TSC1 and TSC2 tumor suppressors antagonize insulin signaling in cell growth
Authors: Gao Xinsheng , Pan Duojia
Published: July 2002

Tuberous sclerosis is a human disease caused by mutations in theTSC1 or the TSC2 tumor suppressor gene. Previous studies of a Drosophila TSC2 homolog suggested a role for the TSC genes in maintaining DNA content, with loss ofTSC2 leading to polyploidy and increased cell size. We have isolated mutations in the Drosophila homolog of theTSC1 gene. We show that TSC1 and TSC2 form a complex and function in a common pathway to control cellular growth. Unlike previous studies, our work shows that TSC1– orTSC2– cells are diploid. We find that, strikingly, the heterozygosity of TSC1 or TSC2 is sufficient to rescue the lethality of loss-of-function insulin receptor mutants. Further genetic analyses suggest that the TSC genes act in a parallel pathway that converges on the insulin pathway downstream fromAkt. Taken together, our studies identified the TSCtumor suppressors as novel negative regulators of insulin signaling.
Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans
Authors: Ketting René F. , Fischer Sylvia E.J. , Bernstein Emily , Sijen Titia , Hannon Gregory J. , Plasterk Ronald H.A.
Published: July 2002

Double-stranded RNAs can suppress expression of homologous genes through an evolutionarily conserved process named RNA interference (RNAi) or post-transcriptional gene silencing (PTGS). One mechanism underlying silencing is degradation of target mRNAs by an RNP complex, which contains ∼22 nt of siRNAs as guides to substrate selection. A bidentate nuclease called Dicer has been implicated as the protein responsible for siRNA production. Here we characterize theCaenorhabditis elegans ortholog of Dicer (K12H4.8;dcr-1) in vivo and in vitro. dcr-1 mutants show a defect in RNAi. Furthermore, a combination of phenotypic abnormalities and RNA analysis suggests a role for dcr-1 in a regulatory pathway comprised of small temporal RNA (let-7) and its target (e.g., lin-41).
Keratin 17 null mice exhibit age- and strain-dependent alopecia
Authors: McGowan Kevin M. , Tong Xuemei , Colucci-Guyon Emma , Langa Francina , Babinet Charles , Coulombe Pierre A.
Published: July 2002

Onset of type I keratin 17 (K17) synthesis marks the adoption of an appendageal fate within embryonic ectoderm, and its expression persists in specific cell types within mature hair, glands, and nail. We report that K17 null mice develop severe alopecia during the first week postbirth, correlating with hair fragility, alterations in follicular histology, and apoptosis in matrix cells. These alterations are incompletely penetrant and normalize starting with the first postnatal cycle. Absence of a hair phenotype correlates with a genetic strain-dependent compensation by related keratins, including K16. These findings reveal a crucial role for K17 in the structural integrity of the first hair produced and the survival of hair-producing cells. Given that identical inherited mutations in this gene can cause either pachyonychia congenita or steatocystoma multiplex, the features of this mouse model suggest that this clinical heterogeneity arises from a cell type-specific, genetically determined compensation by related keratins.
The Genomic Region Encompassing the Nephropathic Cystinosis Gene (CTNS): Complete Sequencing of a 200-kb Segment and Discovery of a Novel Gene within the Common Cystinosis-Causing Deletion
Authors: Touchman Jeffrey W. , Anikster Yair , Dietrich Nicole L. , Maduro Valerie V. Braden , McDowell Geraldine , Shotelersuk Vorasuk , Bouffard Gerard G. , Beckstrom-Sternberg Stephen M. , Gahl William A. , Green Eric D.
Published: July 2002

Nephropathic cystinosis is an autosomal recessive disorder caused by the defective transport of cystine out of lysosomes. Recently, the causative gene (CTNS) was identified and presumed to encode an integral membrane protein called cystinosin. Many of the disease-associated mutations inCTNSare deletions, including one >55 kb in size that represents the most common cystinosis allele encountered to date. In an effort to determine the precise genomic organization ofCTNSand to gain sequence-based insight about the DNA within and flanking cystinosis-associated deletions, we mapped and sequenced the region of human chromosome 17p13 encompassingCTNS. Specifically, a bacterial artificial chromosome (BAC)-based physical map spanningCTNSwas constructed by sequence-tagged site (STS)-content mapping. The resulting BAC contig provided the relative order of 43 STSs. Two overlapping BACs, which together contain all of theCTNSexons as well as extensive amounts of flanking DNA, were selected and subjected to shotgun sequencing. A total of 200,237 bp of contiguous, high-accuracy sequence was generated. Analysis of the resulting data revealed a number of interesting features about this genomic region, including the long-range organization ofCTNS, insight about the breakpoints and intervening DNA associated with the common cystinosis-causing deletion, and structural information about five genes neighboringCTNS(human ortholog of rat vanilloid receptor subtype 1 gene,CARKL, TIP-1, P2X5, andHUMINAE). In particular, sequence analysis detected the presence of a novel gene (CARKL) residing within the most common cystinosis-causing deletion. This gene encodes a previously unknown protein that is predicted to function as a carbohydrate kinase. Interestingly, bothCTNSandCARKLare absent in nearly half of all cystinosis patients (i.e., those homozygous for the common deletion).

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF168787andAF163573.]
Promoter Prediction on a Genomic Scale—TheAdhExperience
Authors: Ohler Uwe
Published: July 2002

We describe our statistical system for promoter recognition in genomic DNA with which we took part in the Genome Annotation Assessment Project (GASP1). We applied two versions of the system: the first uses a region-based approach toward transcription start site identification, namely, interpolated Markov chains; the second was a hybrid approach combining regions and signals within a stochastic segment model. We compare the results of both versions with each other and examine how well the application on a genomic scale compares with the results we previously obtained on smaller data sets.
Analyzing DNA Strand Compositional Asymmetry to Identify Candidate Replication Origins of Borrelia burgdorferi Linear and Circular Plasmids
Authors: Picardeau Mathieu , Lobry Jean R. , Hinnebusch B. Joseph
Published: July 2002

The Lyme disease agent Borrelia burgdorferi has a genome composed of a linear chromosome and a series of linear and circular plasmids. We previously mapped the oriC of the linear chromosome to the center of the molecule, where a pronounced switch in CG skew occurs. In this study, we analyzed B. burgdorferiplasmid sequences for AT and CG skew in an effort to similarly identify plasmid replication origins. Cumulative skew diagrams of the plasmids suggested that they, like the linear chromosome, replicate bidirectionally from an internal origin. The B. burgdorferilinear chromosome contains homologs to partitioning protein genessoj and spoOJ, which are closely linked tooriC at the minimum cumulative skew point of the 1-Mb molecule. A soj/parA homolog also maps to cumulative skew minima of the B. burgdorferi linear and circular plasmids, further suggesting that these regions contain the replication origin. The heterogeneity in these genes and in the nucleotide sequences of the putative origin regions could account for the mutual compatibility of the multiple DNA elements in B. burgdorferi.
Rapid Detection of Deletion, Insertion, and Substitution Mutations via Heteroduplex Analysis Using Capillary- and Microchip-Based Electrophoresis
Authors: Tian Huijun , Brody Lawrence C. , Landers James P.
Published: July 2002

In this report, we explore the potential of capillary and microchip electrophoresis for heteroduplex analysis– (HDA) based mutation detection. Fluorescent dye-labeled primers (6-FAM-tagged) were used to amplify the DNA fragments ranging from 130 to 400 bp. The effects of DNA fragment length, matrix additives, pH, and salt were evaluated for capillary electrophoresis– (CE) and/or microchip electrophoresis–based HDA, using six heterozygous mutations,185delAG, E1250X(3867GT),R1443G(4446CG),5382insC, 5677insAinBRCA1, and6174delTinBRCA2. For this system, the effective fragment size for CE-based HDA was found in the range of 200–300 bp, however, the effective range was 150–260 bp for microchip-based HDA. Sensitivity studies show CE-based HDA could detect a mutated DNA present at only 1%–10% of the total DNA. Discrimination between wild-type and deletion or insertion mutations in BRCA1 and BRCA2 with CE-based HDA could be achieved in <8 min, while the substitution mutations required 14 min of analysis time. For each mutation region, 15 samples were run to confirm the accuracy and reproducibility of the method. Using the method described, two previously reported mutations,E1038G(3232AG, missense) and4427 C/T(4427CT, polymorphism), were detected in the tested samples and confirmed by DNA sequencing. Translation of the CE-based methodology to the microchip format allowed the analysis time for each mutation to be decreased to 130 sec. Based on the results obtained with this model system, it is possible that CE-based HDA methodologies can be developed and used effectively in genetic testing. The fast separation time and automated operation afforded with CE instrumentation provide a powerful system for screening mutations that include small deletions, insertions, and point mutations. Translation to the microchip platform, especially to a multichannel microchip system, would allow for screening mutations with high throughput.
Effects of Worldwide Population Subdivision onALDH2Linkage Disequilibrium
Authors: Peterson Raymond J. , Goldman David , Long Jeffrey C.
Published: July 2002

The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium inALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations across five continents were estimated by maximum-likelihood from genotypes at six closely linkedALDH2nucleotide substitutions. Linkage disequilibrium was partitioned into three components: within populations, among populations within continents, and among continents. It was found that population subdivision among continents had a larger and more disparate effect on linkage disequilibrium than subdivision among local populations. Further, linkage disequilibrium did not increase with population divergence as predicted by a simple model. Rather, the patterns of linkage disequilibrium were complicated because of the interplay of a near absence of recombination, the linkage disequilibrium that existed prior to the divergence of modern humans, subsequent mutation, population subdivision, random genetic drift, and perhaps natural selection. These results suggest that simple models may not well predict patterns of linkage disequilibrium in human populations.
PACAP-38 Enhances Excitatory Synaptic Transmission in the Rat Hippocampal CA1 Region
Authors: Roberto Marisa , Brunelli Marcello
Published: July 2002

Specific receptors for pituitary adenylate cyclase-activating polypeptide (PACAP), a novel peptide with neuroregulatory and neurotrophic functions, have been identified recently in different brain regions, including the hippocampus. In this study, we examined the effects of PACAP-38 on the excitatory postsynaptic field potentials (fEPSPs) evoked at the Schaffer collateral-CA1 synapses. Brief bath application of PACAP-38 (0.05 nM) induced a long-lasting facilitation of the basal transmission. Enhancement of this response was occluded in part by previous high-frequency-induced long-term potentiation (LTP). PACAP-38 did not significantly alter the paired-pulse facilitation (PPF). PACAP-38 has been shown to have a presynaptic effect on the septohippocampal cholinergic terminals, which results in an increase in basal acetylcholine (ACh) release. To assess whether the PACAP-38 enhancement of CA1 synapses was related to the activation of the cholinergic system we examined the effect of this peptide in the presence of atropine, a muscarinic receptor antagonist. The enhancement of the fEPSPs by PACAP-38 was blocked by bath application of atropine. These results show that PACAP-38 induces facilitation of hippocampal synaptic transmission through activation of the cholinergic system via the muscarinic receptors.
A Systems Approach to the Cellular Analysis of Associative Learning in the Pond Snail Lymnaea
Authors: Benjamin Paul R. , Staras Kevin , Kemenes György
Published: July 2002

We show that appetitive and aversive conditioning can be analyzed at the cellular level in the well-described neural circuitries underlying rhythmic feeding and respiration in the pond snail, Lymnaea stagnalis. To relate electrical changes directly to behavior, the snails were first trained and the neural changes recorded at multiple sites in reduced preparations made from the same animals. Changes in neural activity following conditioning could be recorded at the level of motoneurons, central pattern generator interneurons and modulatory neurons. Of significant interest was recent work showing that neural correlates of long-term memory could be recorded in the feeding network following single-trial appetitive chemical conditioning. Available information on the synaptic connectivity and transmitter content of identified neurons within the Lymnaea circuits will allow further work on the synaptic and molecular mechanisms of learning and memory.
Developmental and Light-Regulated Expression of Individual Members of the Light-Harvesting Complex b Gene Family in Pinus palustris
Authors: Peer W. , Silverthorne J. , Peters J. L.
Published: July 2002

Angiosperms require light for multiple aspects of chloroplast development, including chlorophyll synthesis and induction of expression of the mRNAs encoding the major polypeptides of the light-harvesting complex of photosystem II (Lhcb genes). In contrast, many conifers, including pines, firs, and spruces, can accumulate chlorophyll and the light-harvesting chlorophyll a/b-binding proteins of photosystem II in complete darkness. To understand the factors responsible for the regulation of expression of individual Lhcb mRNAs in the pine Pinus palustris, we have prepared sequence-specific cDNA probes for each of three family members, Lhcb1*Pp1, Lhcb2*Pp1, and Lhcb2*Pp2, and have studied the expression of two of these, Lhcb1*Pp1 and Lhcb2*Pp2, in detail. The levels of expression of each sequence were disparate, and Lhcb1*Pp1-encoded transcripts were the most abundant in the light. Both Lhcb1*Pp1 and Lhcb2*Pp2 mRNAs were expressed in stems and cotyledons, but Lhcb1*Pp1 mRNA was present at about 10-fold lower levels in stems than in cotyledons, in contrast to Lhcb2*Pp2 mRNA, which was expressed at higher levels in stems than in cotyledons. Both Lhcb1*Pp1 and Lhcb2*Pp2 mRNAs were absent in embryos but were expressed during seedling development. The levels increased with age in both the light and the dark and in both cases were about 2-fold higher in the light than in the dark. Despite the expression of Lhcb1*Pp1 and Lhcb2*Pp2 mRNAs during development in darkness, the levels of both mRNAs increased in dark-grown seedlings given red light in the low fluence range within 2 h of treatment.
A Brassinosteroid-Insensitive Mutant in Arabidopsis thaliana Exhibits Multiple Defects in Growth and Development
Authors: Clouse S. D. , Langford M. , McMorris T. C.
Published: July 2002

Brassinosteroids are widely distributed plant compounds that modulate cell elongation and division, but little is known about the mechanism of action of these plant growth regulators. To investigate brassinosteroids as signals influencing plant growth and development, we identified a brassinosteroid-insensitive mutant in Arabidopsis thaliana (L.) Henyh. ecotype Columbia. The mutant, termed bri1, did not respond to brassinosteroids in hypocotyl elongation and primary root inhibition assays, but it did retain sensitivity to auxins, cytokinins, ethylene, abscisic acid, and gibberellins. The bri1 mutant showed multiple deficiencies in developmental pathways that could not be rescued by brassinosteroid treatment, including a severely dwarfed stature; dark green, thickened leaves; male sterility; reduced apical dominance; and de-etiolation of darkgrown seedlings. Genetic analysis suggests that the Bri1 phenotype is caused by a recessive mutation in a single gene with pleiotropic effects that maps 1.6 centimorgans from the cleaved, amplified, polymorphic sequence marker DHS1 on the bottom of chromosome IV. The multiple and dramatic effects of mutation of the BRI1 locus on development suggests that the BRI1 gene may play a critical role in brassinosteroid perception or signal transduction.
The Arabidopsis ACT7 Actin Gene Is Expressed in Rapidly Developing Tissues and Responds to Several External Stimuli
Authors: McDowell J. M. , An Yq. , Huang S. , McKinney E. C. , Meagher R. B.
Published: July 2002

ACT7 encodes one of the six distinct and ancient subclasses of actin protein in the complex Arabidopsis actin gene family. We determined the sequence and structure of the Arabidopsis thaliana ACT7 actin gene and investigated its tissue-specific expression and regulation. The ACT7 mRNA levels varied by 128-fold among several different tissues and organs. The highest levels of ACT7 mRNA were found in rapidly expanding vegetative organs, the lowest in pollen. A translational fusion with the 5[prime] end of ACT7 (1.9 kb) joined to the β-glucoronidase reporter gene was strongly and preferentially expressed in all young, developing vegetative tissues of transgenic Arabidopsis plants. ACT7 was the only Arabidopsis actin gene strongly expressed in the hypocotyl and seed coat. Although no β-glucoronidase expression was seen in developing ovules or immature seeds, strong expression was seen in dry seeds and immediately after imbibition in the entire seedling. ACT7 was the only Arabidopsis actin gene to respond strongly to auxin, other hormone treatments, light regime, and wounding, and may be the primary actin gene responding to external stimuli. The ACT7 promoter sequence contains a remarkable number of motifs with sequence similarity to putative phytohormone response elements.
Changes in the Composition of the Photosynthetic Apparatus in the Galactolipid-Deficient dgd1 Mutant of Arabidopsis thaliana
Authors: Hartel H. , Lokstein H. , Dormann P. , Grimm B. , Benning C.
Published: July 2002

The glycerolipid digalactosyl diacylglycerol (DGDG) is exclusively associated with photosynthetic membranes and thus may play a role in the proper assembly and maintenance of the photosynthetic apparatus. Here we employ a genetic approach based on the dgd1 mutant of Arabidopsis thaliana to investigate the function of DGDG in thylakoid membranes. The primary defect in the genetically well-characterized dgd1 mutant resulted in a 90% reduction of the DGDG content. The mutant showed a decreased photosystem II (PSII) to photosystem I ratio. In vivo room- and low-temperature (77 K) chlorophyll fluorescence measurements with thylakoid preparations are in agreement with a drastically altered excitation energy allocation to the reaction centers. Quantification of pigment-binding apoproteins and pigments supports an altered stoichiometry of individual pigment-protein complexes in the mutant. Most strikingly, an increase in the amount of peripheral light-harvesting complexes of PSII relative to the inner antenna complexes and the PSII reaction center/core complexes was observed. Regardless of the severe alterations in thylakoid organization, photosynthetic oxygen evolution was virtually not compromised in dgd1 mutant leaves.
Oxidative Damage in Pea Plants Exposed to Water Deficit or Paraquat1
Authors: Iturbe-Ormaetxe Iñaki , Escuredo Pedro R. , Arrese-Igor Cesar , Becana Manuel
Published: July 2002

The application of a moderate water deficit (water potential of −1.3 MPa) to pea (Pisum sativum L. cv Lincoln) leaves led to a 75% inhibition of photosynthesis and to increases in zeaxanthin, malondialdehyde, oxidized proteins, and mitochondrial, cytosolic, and chloroplastic superoxide dismutase activities. Severe water deficit (−1.9 MPa) almost completely inhibited photosynthesis, decreased chlorophylls, β-carotene, neoxanthin, and lutein, and caused further conversion of violaxanthin to zeaxanthin, suggesting damage to the photosynthetic apparatus. There were consistent decreases in antioxidants and pyridine nucleotides, and accumulation of catalytic Fe, malondialdehyde, and oxidized proteins. Paraquat (PQ) treatment led to similar major decreases in photosynthesis, water content, proteins, and most antioxidants, and induced the accumulation of zeaxanthin and damaged proteins. PQ decreased markedly ascorbate, NADPH, ascorbate peroxidase, and chloroplastic Fe-superoxide dismutase activity, and caused major increases in oxidized glutathione, NAD+, NADH, and catalytic Fe. It is concluded that, in cv Lincoln, the increase in catalytic Fe and the lowering of antioxidant protection may be involved in the oxidative damage caused by severe water deficit and PQ, but not necessarily in the incipient stress induced by moderate water deficit. Results also indicate that the tolerance to water deficit in terms of oxidative damage largely depends on the legume cultivar.
4-Coumarate:Coenzyme A Ligase in Hybrid Poplar1
Authors: Allina Sandra M. , Pri-Hadash Aviva , Theilmann David A. , Ellis Brian E. , Douglas Carl J.
Published: July 2002

The enzyme 4-coumarate:coenzyme A ligase (4CL) is important in providing activated thioester substrates for phenylpropanoid natural product biosynthesis. We tested different hybrid poplar (Populus trichocarpa × Populus deltoides) tissues for the presence of 4CL isoforms by fast-protein liquid chromatography and detected a minimum of three 4CL isoforms. These isoforms shared similar hydroxycinnamic acid substrate-utilization profiles and were all inactive against sinapic acid, but instability of the native forms precluded extensive further analysis. 4CL cDNA clones were isolated and grouped into two major classes, the predicted amino acid sequences of which were 86% identical. Genomic Southern blots showed that the cDNA classes represent two poplar 4CLgenes, and northern blots provided evidence for their differential expression. Recombinant enzymes corresponding to the two genes were expressed using a baculovirus system. The two recombinant proteins had substrate utilization profiles similar to each other and to the native poplar 4CL isoforms (4-coumaric acid > ferulic acid > caffeic acid; there was no conversion of sinapic acid), except that both had relatively high activity toward cinnamic acid. These results are discussed with respect to the role of 4CL in the partitioning of carbon in phenylpropanoid metabolism.