bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of pregnancy-associated glycoprotein 1 and 2 genes in in vivo, in vitro and parthenogenetically derived preimplantation pig embryos
Authors: Do Hyun-Jin , Kim Jae-Hwan , Abeydeera Lalantha R. , Han Yong-Mahn , Matteri Robert L. , Green Jonathan A. , Roberts R. Michael , Day Billy N. , Prather Randall S.
Published: July 2002

The objective of this study was to determine whether porcine PAG (poPAG) genes are expressed in embryos as they develop from the 1-cell stage to expanded blastocysts, and whether expression differed according to how embryos had been derived. Embryos at various preimplantation stages were assayed after in vivo fertilisation, after in vitro fertilisation of in vitro-matured oocytes, or following parthenogenetic activation of in vitro-matured oocytes. The presence of PAG transcripts was determined at the1-, 2-, and 4-cell, compact morula and blastocyst stages by reverse transcription-PCR procedures with PAG 1- and PAG 2-specific primers, followed by Southern blotting. The mRNAs for poPAG 1 and 2 were detected in in vitro-derived, in vivo-derived and parthenogenetically derived blastocyst stage embryos. In some replications poPAG 1 could be detected as early as the compact morula stage and poPAG 2 could be detected as early as the 4-cell stage. Our study revealed that poPAG 1 and 2 genes are expressed as early as the compact morula stage and 4-cell stage, respectively, in normal embryos and in parthenogenetically derived blastocysts. Thus it appears that the poPAGs are not maternally imprinted and they may be useful as potential candidates for markers of developmental competence.
Energy substrates and amino acids provided during in vitro maturation of bovine oocytes alter acquisition of developmental competence
Authors: Rose-Hellekant T.A. , Libersky-Williamson E.A. , Bavister B.D.
Published: July 2002

Energy substrates and amino acids were evaluated for supporting acquisition of developmental competence by bovine cumulus-oocyte complexes during in vitro maturation. The basic culture medium (Basic Medium-3) used for in vitro maturation of oocytes was modified to produce six media containing glucose or glutamine with lactate or pyruvate, or glucose + glutamine, or glucose + 11 amino acids; a seventh (control) medium was TCM199. All media contained polyvinyl alcohol, gonadotropins, epidermal growth factor and oestradiol. Following maturation, oocytes were incubated in medium TALP for fertilisation, then cumulus cells were removed and presumptive embryos cultured for 48 h in a chemically defined medium (HECM-6) followed by 120 h in medium TCM199 + bovine calf serum. Six substrate treatments yielded similar first cleavage responses (66-78%) at 72 h post-insemination; however, blastocyst development at 192 h varied significantly. Oocytes matured in medium with glucose + 11 amino acids gave the best blastocyst development: 21% of inseminated oocytes or 25% of 2-cell embryos. Cumulus expansion in HECM-6 required glucose with either glutamine, 11 amino acids or lactate, or glutamine + lactate. We conclude that (1) the type of energy substrate or nutrient supplied during in vitro maturation of oocytes profoundly affects subsequent developmental competence; (2) oocyte maturation in simple medium containing glucose with lactate or 11 amino acids or glutamine, or lactate + glutamine, can support development equally as well as the complex medium, TCM199; and (3) media supporting at least moderate cumulus expansion during oocyte maturation also support subsequent blastocyst development.
Functional interactions between sulphated polysaccharides and proacrosin:
implications in sperm binding and digestion of zona pellucida
Authors: Moreno R.
D. , Hoshi M. , Barros C.
Published: July 2002

Acrosin is a serine protease located within mammalian
acrosome as inactive proacrosin. Sulphated polymers bind to proacrosin and acrosin, to a domain
different from the active site. Upon binding, these polymers induce proacrosin activation and some of
them, such as fucoidan, inhibit sperm binding to the zona pellucida. In this work we have studied the
interaction of solubilised zona pellucida glycoproteins (ZPGs), heparin and ARIS (Acrosome Reaction
Inducing Substance of Starfish) with boar and human acrosin. We have found that ARIS, solubilised ZPGs
and fucoidan, but not heparin, inhibit the binding of the monoclonal antibody against human acrosin
C5F10 to boar or human proacrosin. These results suggest that fucoidan, solubilised ZPGs and ARIS bind
to a related domain on the proacrosin surface. Moreover, ARIS was able to induce human proacrosin
activation. On the other hand, neither ARIS nor heparin from porcine intestinal mucosa or bovine lung
induced hamster sperm acrosome reaction or sperm motility. Recent data showed that acrosin is involved
in dispersal of the acrosomal matrix after acrosome reaction. Thus, the control of the ZPG glycan
chains over proacrosin activation may regulate both sperm penetration rate and limited proteolysis of
zona pellucida proteins.
CONTEMPORARY BIOGRAPHERS OF NINETEENTH-CENTURY NOVELISTS
Authors: Karl Frederick R.
Published: July 2002

OF THE FIVE BIOGRAPHIES under scrutiny here, at least two have attempted to break with traditional biographical procedures. By traditional, I mean linear or chronological development, some elementary discussion of each work, an effort to detail all aspects of the life, the evasion of psychological elements that seem to defy explanation. Of the other three biographies, David Nokes’s Jane Austen: A Life purports to be more innovative than his study really is. He pursues Austen relentlessly as satirical and rebellious — picking up on her remark in one of her letters, “I am a wild beast.” But Nokes’s probe of her rebelliousness is not so new as he makes us believe it is, although he does edge Jane out of the “maiden aunt” posture. More on Nokes later, when he will be paired with Claire Tomalin’s very different Jane Austen: A Biography. Whatever else, both books indicate that Austen biography, despite the recent “definitive” study by Park Honan (1987), is still quite alive. Still, a corollary question remains whether we need two more Austen biographies when the material has already been so thoroughly defined.
The Sigüenza tornado: a case study based on convective ingredients concept and conceptual models
Authors: Martín F , R Riosalido  , de Esteban L
Published: July 2002

On 24 May 1993, part of the Iberian Peninsula was affected by convective activity concentrated on the eastern side of a low‐level thermal boundary which was orientated north–south. A series of storms evolved into a squall line striking at the province of Guadalajara (Central Spain). The southernmost cell of this mesoscale convective system generated a tornado that hit the city of Sigüenza between 1930 and 1940 UTC. This paper has two objectives. The first aim is to investigate the ingredients (buoyancy, wind shear, vertical distribution of moisture content, and synoptic and mesoscale lifting mechanisms) and the atmospheric agents (mid‐upper level trough, low level‐boundary, convergence zones, etc.) which favour the production of severe storms. The second one is to analyse information provided by operational remote‐sensing systems (satellite, radar and lightning) in order to test and evaluate some conceptual models of severe storms in an operational environment. For the first objective, the ingredient‐based methodology will be shown to be a valuable operational approach allowing forecasters to focus on the possibility of a severe event using the appropriate diagnostic or prognosis tools. For the second objective, special attention is given to the suitability of conceptual models associated with convective phenomena and the potential value of such models (lightning charge related to wind shear and radar‐based multicell conceptual models) for understanding the observed processes. From an operational viewpoint some problems may arise because of the technical characteristics of the equipment, particularly related to radars (e.g. scanning strategy, distance between radar and targets, and radar signal processing and displaying). Possible guidelines for using volumetric radar data (non Doppler) for deep convection monitoring are suggested for rugged and complex topographical regions. Copyright © 1997 Royal Meteorological Society
Scalable generation of texts using causal and temporal expansions of sentences
Authors: CHALI YLLIAS
Published: July 2002

This paper presents a exible bottom-up process to incrementally generate several versions of
the same text, building up the core text from its kernel version into other versions varying of
the levels of details. We devise a method for identifying the question/answer relations holding
between the propositions of a text, we give rules for characterizing the kernel version of a text,
and we provide a procedure, based on causal and temporal expansions of sentences, which
distinguishes semantically these levels of details according to their importance. This is based
on the assumption that we have a stock of information from the interpreter's knowledge base
available. The sentence expansion operation is formally defined according to three principles:
(1) the kernel principle ensures to obtain the gist information; (2) the expansion principle defines
an incremental augmentation of a text; and (3) the subsume principle defines an importance-based
order among the possible details of the information. The system developed allows users
to generate in a follow-up way their own text version which meets their expectations and
their demands expressed as questions about the text under consideration.
GROUP AND INDIVIDUAL TREATMENT OF COMPULSIVE HOARDING: A PILOT STUDY
Authors: Steketee Gail , Frost Randy O. , Wincze Jeff , Greene Kamala A.I. , Douglass Heidi
Published: July 2002

Treatment of compulsive hoarding has rarely been described in the literature, apart from standard treatments for obsessive compulsive disorder of which hoarding is thought to be a subset. This paper presents preliminary findings from seven patients treated with cognitive and behavioral interventions derived from Frost and Hartl's (1996) theoretical model of hoarding. Six clients attended 15 group treatment sessions over 20 weeks plus individual home treatment sessions and one client received 20 weekly-sessions of individual treatment only. After 20 weeks, treatment resulted in noticeable improvement in several hoarding symptoms for five of the seven patients, especially reduction in excessive acquisition of possessions, although problems with clutter persisted. Three of four clients who continued in treatment for approximately 1 year showed substantial further improvement, although none felt entirely recovered. Findings are discussed in light of the model of hoarding and possible modifications to treatment to enhance motivation and benefits.
Changes and Developments
Authors: Salkovskis Paul
Published: July 2002

There are a few more changes in this issue. Max Birchwood and Susan Robinson
have, for almost 10 years, done a magnificent job as book review editors. As
of this issue, they are stepping down. However, their association with the
journal will continue, as they join the Editorial Advisory Board. I and the
readers of this journal are grateful to Max and Susan for all the excellent
work they have put in over the years. There are parts of my bookshelf that
are attributable to their work, and I’m sure I’m not the only
one. Our thanks are also extended, of course, to Sobia Janjua, who so
competently supported them. The new book review editor is Allison Harvey,
and I very much look forward to working with her in her new role. Monika
Juszkiewicz has left the position of Editorial Assistant, and has been
succeeded by Carole Sherwood. Thanks to Monika and welcome to Carole.
Cognitive functioning after whiplash injury: A meta-analysis
Authors: KESSELS ROY P.C. , ALEMAN ANDRÉ , VERHAGEN WIM I.M. , VAN LUIJTELAAR EGIDIUS L.J.M.
Published: July 2002

Complaints on cognitive functioning are often reported
in patients suffering from whiplash syndrome, although
objective neuropsychological test results do not always
support these. In addition, radiological abnormalities
and anatomical lesions are found only in a minority of
these patients. This has led to a controversy about its
existence in the literature. In this systematic review,
the results of 22 neuropsychological studies on whiplash
were quantitatively analyzed, focusing on working memory,
attention, immediate and delayed recall, visuomotor tracking,
and cognitive flexibility. Our findings suggest that a
consistent overall pattern of cognitive dysfunction can
be demonstrated after whiplash injury through neuropsychological
testing, both compared to healthy and to asymptomatic controls.
Six months after the accident, improvement is found in
working memory, attention, immediate recall, and visuomotor
tracking. The results are discussed in the light of recent
findings on the effect of cerebral dysfunction, malingering,
pain-related factors, and the role of coping strategies
and posttraumatic stress on neuropsychological test performance.
(JINS, 2000, 6, 271–278.)
Neuropsychological Assessment Across the Life Span
Authors: Bobholz Julie A. , Hammeke Thomas A.
Published: July 2002

This volume is part of the series Human Brain
Function: Assessment and Rehabilitation and aims to
present information regarding how brain function is assessed
with neuropsychological instruments. In general, this text
is designed to cover assessment from the perspective of
both behavioral neurologists and neuropsychologists. The
book is divided into three sections: “Developmental
Considerations,” “Clinical Considerations,”
and “Specialized Assessment.”
Instantiation of semantic categories in sentence comprehension
by Alzheimer patients
Authors: NEBES ROBERT D. , HALLIGAN EDYTHE M.
Published: July 2002

This study examined whether Alzheimer patients
can make elaborative inferences based on the semantic context
provided by a sentence. More specifically, if presented
with the name of a category in a sentence do they, like
normals, infer (instantiate) the particular member of that
category most appropriate to the meaning of the sentence
(e.g., if a sentence mentions a container of juice, do
they infer it is a bottle). Patients were presented with
a sentence containing the name of a concrete category.
The sense of the sentence was consistent with a low-dominant
member of that category. Patients were then shown drawings
of four members of that category and asked to select the
one appropriate to the sentence. They were later asked
to name the drawings. If semantic information is degraded
in Alzheimer patients for those objects Alzheimer patients
cannot name (as has been claimed), then AD patients should
be unable to carry out the type of elaborative semantic
inference required to instantiate. Results showed that
Alzheimer patients were highly accurate at instantiating
even objects they could not name. This is consistent with
a relative preservation of semantic knowledge about concrete
objects in Alzheimer patients. (JINS, 1999, 5,
685–691.)
Intertemporal flexibility in a tradeable CO2 quota system
Authors: WESTSKOG HEGE
Published: July 2002

The paper compares the total costs of abating CO2 emissions in two different intertemporal trading systems. In addition, the paper gives an analysis of how abatement costs are distributed among different countries/regions. It is shown that the total cost of implementing a climate treaty is considerably reduced in a system where both banking and borrowing of quotas are allowed compared to a system where quotas only can be banked. The analysis also shows that the total cost of implementing a climate treaty can be reduced in a banking system by compensating the developing country parties for participating in the CO2 emission reductions such that their net costs of making emissions reductions after sale/purchase of quotas equal zero.
Trade and environment: policy linkages
Authors: COPELAND BRIAN R.
Published: July 2002

This paper develops a simple model to investigate linkages between trade and environmental policy. In the case of purely local pollution, trade liberalization without constraints on environmental policy induces a non-cooperative game between countries in pollution policy. Without any agreement on environmental policy, trade negotiations are unlikely to lead to a point on the Pareto frontier. When pollution is global, countries may be expected to disagree on linkages between trade agreements and environmental agreements. Countries importing pollution-intensive goods have an incentive to try to link trade agreements with environmental agreements, while countries exporting pollution-intensive goods have an incentive to try to obtain a binding commitment to free trade prior to negotiations over global pollution.
Reducing coal subsidies and trade barriers: their contribution to greenhouse gas abatement
Authors: ANDERSON KYM , McKIBBIN WARWICK J.
Published: July 2002

International negotiations for an agreement to reduce the emission of greenhouse gases have not produced cost-effective policies for reducing emissions, not least because they are unlikely to prevent ‘leakage’ through a re-location of carbon-intensive activities to poorer countries. An alternative or supplementary approach that is more likely to achieve at least some emission reductions, and at the same time generate national and global economic benefits rather than costs, involves lowering coal subsidies and trade barriers. Past coal policies have encouraged excessive production of coal in a number of industrial countries and excessive coal consumption in numerous developing and transition economies. This paper documents those distortions and outlines the circumstances under which their reform (currently under way in some countries) could both improve the economy and lower greenhouse gas emissions globally. It then quantifies the effects on economic activity as well as global carbon emissions, using the G-Cubed multi-country general equilibrium model of the world economy. Both the gains in economic efficiency and the reductions in carbon dioxide emissions that could result from such reforms are found to be substantial—a ‘no regrets’ outcome or win–win Pareto improvement for the economy and the environment.
Trade liberalization and the environment in Costa Rica
Authors: ABLER DAVID G. , RODRÍGUEZ ADRIÁN G. , SHORTLE JAMES S.
Published: July 2002

This study examines the environmental impacts of trade liberalization in Costa Rica. A CGE model is constructed which includes eight environmental indicators covering deforestation, pesticides, overfishing, hazardous wastes, inorganic wastes, organic wastes, greenhouse gases, and air pollution. Three trade liberalization scenarios are examined. Two sets of analyses are conducted for each scenario, one in which technologies do not change in response to trade liberalization and the other in which total factor productivity in each sector changes in response to changes in imports of machinery and equipment. To account for uncertainty regarding values of the model's parameters, a Monte Carlo experiment is conducted for each policy option. The impacts of trade liberalization on the environmental indicators are generally negative in sign but small or moderate in magnitude, both when technology is constant and when technology is allowed to vary.
An early case of algorithmic composition in Italy
Authors: GIOMI FRANCESCO
Published: July 2002

Pietro Grossi was the first pioneer of computer music in Italy. During his activities from 1961 to the 1980s he devoted much research to algorithmic composition. Grossi’s first experiments in this field are discussed, dealing particularly with three important phases of his work: initiating algorithmic composition at the S 2F M studio in Florence, writing digital programs at the CNUCE Institute in Pisa, and realising a musical algorithm by translating the curve designed by the mathematician Peano into a sonic form.
Sustained Release Methylphenidate
Authors: Ford Tamsin , Taylor Eric , Warner Rogers Jody
Published: July 2002

As sustained methylphenidate becomes available in the United Kingdom,
there is likely to be considerable demand related to the difficulties that
frequently arise with standard methylphenidate due to the need for midday
doses at school, as well as the pronounced ‘on/off’ therapeutic effects
sometimes seen with multiple doses. This article briefly discusses longer
acting stimulants, reviews the available literature, anticipates possible
problems in the use of slow release methylphenidate, and presents clinical
guidelines for its use.
Youth Justice Assessment Procedures
Authors: Curtis Sarah
Published: July 2002

This article analyses assessment procedures for young offenders aged 10
to 17 years who receive a police Final Warning or appear before Youth
Courts in England and Wales. Members of Youth Justice Teams (YOTs)
use detailed ‘Asset’ forms to collate information about the background,
education, life-style and personal characteristics of the young people. The
replies are scored to indicate the risk of further offending and the YOTs
make their recommendations for intervention. The author points out that
punishment has to be proportional to the crime but many young people
and their families require long-term help if they are to be diverted from
crime.
Using Personal Construct
Psychology with Pupils Who
Experience Emotional and
Behavioural Difficulties—A Case
Study
Authors: Clarke Steve
Published: July 2002

Personal construct psychology is presented and its application within a
school setting is described. Using case material derived from working with
an 11-year-old pupil displaying highly disruptive behaviour, the strengths
and limitations of this approach are illustrated. Personal construct
psychology can increase pupil and teacher understanding of behavioural
difficulties and lead directly to individualised strategies for successful
intervention.
Definite descriptions and cognitive status in English: why accommodation is unnecessary
Authors: Gundel Jeanette K. , Hedberg Nancy , Zacharski Ron
Published: July 2002

A commonly held view of English definite articles is that they signal that the referent of an NP is familiar to the addressee. However, it is well known that not all definite article phrases meet this familiarity requirement. To account for such nonfamiliar uses, Heim (1982) invokes the mechanism of ‘accommodation’, which enables an addressee to remedy a violation of the familiarity requirement by adding assumptions to the ‘common ground’. In this article we argue that the Givenness Hierarchy framework provides an insightful account of all uses of definite article phrases without requiring an appeal to accommodation. Such an account provides a unified treatment of definite article phrases, including demonstrative phrases and personal pronouns, while at the same time distinguishing among them in a principled way. This proposal is supported by results of a corpus-based examination of the use of definite articles and by an examination of cleft presuppositions.
INFORMATION, STABILIZATION, AND WELFARE: THE CASE OF SUNSPOTS
Authors: Chattopadhyay Subir
Published: July 2002

The stationary sunspot equilibria of a simple overlapping generations
economy with heterogeneous
agents are considered. These equilibria are known to be suboptimal. The focus
of the paper is on the efficacy,
based on welfare economic considerations and informational
requirements, of government policy in such an
environment. The main result is that
knowledge of the sunspot
equilibrium net trades, weak interval-type information on two
parameters, and
weak set-type information on the location of some optimal stationary
allocation
is sufficient to induce a competitive equilibrium that is a Pareto optimal
Pareto improvement over the
sunspot allocation, which has the further property of reaching
a Pareto optimal stationary allocation in finite time.
The results are interpreted as demonstrating that, in a simple model
with a sunspot environment,
policy is very effective and welfare economic considerations lead to
stabilization.
Pronunciation proficiency in the first and second languages of Korean–English bilinguals
Authors: Yeni-Komshian Grace H. , Flege James E. , Liu Serena
Published: July 2002

This study examined pronunciation proficiency in both the first (Korean) and second (English) languages of bilinguals. The participants were adult immigrants whose age of arrival in the USA ranged from 1–23 years. English and Korean sentences were rated by native listeners to obtain measures of pronunciation proficiency. English pronunciation of participants with ages of arrival of 1–5 years was close to monolinguals, heavier accents were noted as ages of arrival increased from 6 to 23 years. Korean pronunciation of participants with ages of arrival of 1–7 years was distinctly accented, while those with ages of arrival of 12–23 years were rated the same as monolinguals. Participants with ages of arrival of 1–9 years pronounced English better than Korean, whereas the reverse was true for ages of arrival of 12–23 years. Overall, the results were more consistent with the view that deviations from native pronunciation result from interactions between the languages of bilinguals rather than with the view of a maturationally defined critical period for language learning.
Subject realization in the syntactic development of a bilingual child
Authors: Juan-Garau Maria , Pérez-Vidal Carmen
Published: July 2002

The present article reports on the findings of a case study of bilingual first language acquisition in Catalan and English. It first presents a general overview of a child's syntactic development from the age of 1;3 to 4;2 and then focuses on the question of subject realization in the two contrasting languages he is acquiring simultaneously. In this case, Catalan is a null subject language in opposition to the overt subject properties of English. Such data allow us to provide evidence on a key issue in bilingual acquisition research: the question of language separation in the early stages of acquisition. The data available suggest the absence of any major influence of one language on the other. In other words, our subject seems to be acquiring word order patterns which are different in the two adult systems in a language-dependent manner from the beginning of his production in both languages.
Single mesodermal cells guide outgrowth of ectodermal tubular structures in Drosophila
Authors: Wolf Christian , Schuh Reinhard
Published: July 2002

The Drosophila tracheal system, a tubular network, is formed from isolated ectodermal metameres by guided branch outgrowth and branch fusion. Branch outgrowth is triggered by the localized and transient activity of Branchless (Bnl/dFGF). Here, we report the discovery of a mesodermal cell that links the leading cells of outgrowing main branches 2.5 hr before they fuse. This bridge-cell serves as an essential guidance post and needs Hunchback (Hb) activity to exert its function. The bridge-cell provides cues acting in concert with Bnl/dFGF signaling to mediate directed branch outgrowth that ultimately leads to position-specific branch fusion.
Context-dependent EKLF responsiveness defines the developmental specificity of the human ɛ-globin gene in erythroid cells of YAC transgenic mice
Authors: Tanimoto Keiji , Liu Qinghui , Grosveld Frank , Bungert Jörg , Engel James Douglas
Published: July 2002

We explored the mechanism of definitive-stage ɛ-globin transcriptional inactivity within a human β-globin YAC expressed in transgenic mice. We focused on the globin CAC and CAAT promoter motifs, as previous laboratory and clinical studies indicated a pivotal role for these elements in globin gene activation. A high-affinity CAC-binding site for the erythroid krüppel-like factor (EKLF) was placed in the ɛ-globin promoter at a position corresponding to that in the adult β-globin promoter, thereby simultaneously ablating a direct repeat (DR) element. This mutation led to EKLF-independent ɛ-globin transcription during definitive erythropoiesis. A second 4-bp substitution in the ɛ-globin CAAT sequence, which simultaneously disrupts a second DR element, further enhanced ectopic definitive erythroid activation of ɛ-globin transcription, which surprisingly became EKLF dependent. We finally examined factors in nuclear extracts prepared from embryonic or adult erythroid cells that bound these elements in vitro, and we identified a novel DR-binding protein (DRED) whose properties are consistent with those expected for a definitive-stage ɛ-globin repressor. We conclude that the suppression of ɛ-globin transcription during definitive erythropoiesis is mediated by the binding of a repressor that prevents EKLF from activating the ɛ-globin gene.
The retinoic acid-metabolizing enzyme, CYP26A1, is essential for normal hindbrain patterning, vertebral identity, and development of posterior structures
Authors: Abu-Abed Suzan , Dollé Pascal , Metzger Daniel , Beckett Barbara , Chambon Pierre , Petkovich Martin
Published: July 2002

The active derivative of vitamin A, retinoic acid (RA), is essential for normal embryonic development. The spatio-temporal distribution of embryonic RA results from regulated expression of RA-synthesizing retinaldehyde dehydrogenases and RA-metabolizing cytochrome P450s (CYP26). Excess RA administration or RA deficiency results in a complex spectrum of embryonic abnormalities. As a first step in understanding the developmental function of RA-metabolizing enzymes, we have disrupted the murine Cyp26A1 gene. We report thatCyp26A1-null mutants die during mid-late gestation and show a number of major morphogenetic defects. Spina bifida and truncation of the tail and lumbosacral region (including abnormalities of the kidneys, urogenital tract, and hindgut) are the most conspicuous defects, leading in extreme cases to a sirenomelia (“mermaid tail”) phenotype. Cyp26A1 mutants also show posterior transformations of cervical vertebrae and abnormal patterning of the rostral hindbrain, which appears to be partially posteriorly transformed. These defects correlate with two major sites of Cyp26A1 expression in the rostral neural plate and embryonic tail bud. Because all of theCyp26A1−/− abnormalities closely resemble RA teratogenic effects, we postulate that the key function of CYP26A1 is to maintain specific embryonic areas in a RA-depleted state, to protect them against the deleterious effect of ectopic RA signaling.
Requirement for math5 in the development of retinal ganglion cells
Authors: Wang Steven W. , Kim Byong Su , Ding Kan , Wang Huan , Sun Dantong , Johnson Randy L. , Klein William H. , Gan Lin
Published: July 2002

math5 is a murine orthologue of atonal, a bHLH proneural gene essential for the formation of photoreceptors and chordotonal organs in Drosophila. The expression ofmath5 coincides with the onset of retinal ganglion cell (RGC) differentiation. Targeted deletion of math5 blocks the initial differentiation of 80% of RGCs and results in an increase in differentiated amacrine cells. Furthermore, the absence ofmath5 abolishes the retinal expression of brn-3b and the formation of virtually all brn-3b-expressing RGCs. These results imply that math5 is a proneural gene essential for RGC differentiation and that math5 acts upstream to activatebrn-3b-dependent differentiation processes in RGCs.
Wnt antagonism initiates cardiogenesis in Xenopus laevis
Authors: Schneider Valerie A. , Mercola Mark
Published: July 2002

Heart induction in Xenopus occurs in paired regions of the dorsoanterior mesoderm in response to signals from the Spemann organizer and underlying dorsoanterior endoderm. These tissues together are sufficient to induce heart formation in noncardiogenic ventral marginal zone mesoderm. Similarly, in avians the underlying definitive endoderm induces cardiogenesis in precardiac mesoderm. Heart-inducing factors in amphibians are not known, and although certain BMPs and FGFs can mimic aspects of cardiogenesis in avians, neither can induce the full range of activities elicited by the inducing tissues. Here we report that the Wnt antagonists Dkk-1 and Crescent can induce heart formation in explants of ventral marginal zone mesoderm. Other Wnt antagonists, including the frizzled domain-containing proteins Frzb and Szl, lacked this activity. Unlike Wnt antagonism, inhibition of BMP signaling did not promote cardiogenesis. Ectopic expression of GSK3β, which inhibits β-catenin-mediated Wnt signaling, also induced cardiogenesis in ventral mesoderm. Analysis of Wnt proteins expressed during gastrulation revealed that Wnt3A and Wnt8, but not Wnt5A or Wnt11, inhibited endogenous heart induction. These results indicate that diffusion of Dkk-1 and Crescent from the organizer initiate cardiogenesis in adjacent mesoderm by establishing a zone of low Wnt3A and Wnt8 activity.
Brinker is a sequence-specific transcriptional repressor in theDrosophilaembryo
Authors: Zhang Hailan , Levine Michael , Ashe Hilary L.
Published: July 2002

A Dpp activity gradient specifies multiple thresholds of gene expression in the dorsal ectoderm of the early embryo. Some of these thresholds depend on a putative repressor, Brinker, which is expressed in the neurogenic ectoderm in response to the maternal Dorsal gradient and Dpp signaling. Here we show that Brinker is a sequence-specific transcriptional repressor. It binds the consensus sequence, TGGCGc/tc/t, and interacts with the Groucho corepressor through a conserved sequence motif, FKPY. An optimal Brinker binding site is contained within an 800-bp enhancer from thetolloidgene, which has been identified as a genetic target of the Brinker repressor. Atolloid-lacZtransgene containing point mutations in this site exhibits an expanded pattern of expression, suggesting that Brinker directly repressestolloidtranscription. We discuss other examples of transcriptional repressors constraining the activities of signaling pathways.
RAD51-independent break-induced replication to repair a broken chromosome depends on a distant enhancer site
Authors: Malkova Anna , Signon Laurence , Schaefer Christopher B. , Naylor Maria L. , Theis James F. , Newlon Carol S. , Haber James E.
Published: July 2002

Without the RAD51 strand exchange protein,Saccharomyces cerevisiae cannot repair a double-strand break (DSB) by gene conversion. However, cells can repair DSBs by recombination-dependent, break-induced replication (BIR).RAD51-independent BIR is initiated more than 13 kb from the DSB. Repair depends on a 200-bp sequence adjacent to ARS310, located ∼34 kb centromere-proximal to the DSB, but does not depend on the origin activity of ARS310. We conclude that the ability of a recombination-induced replication fork to copy >130 kb to the end of the chromosome depends on a special site that enhances assembly of a processive repair replication fork.
PDGF autocrine stimulation dedifferentiates cultured astrocytes and induces oligodendrogliomas and oligoastrocytomas from neural progenitors and astrocytes in vivo
Authors: Dai Chengkai , Celestino Joseph C. , Okada Yoshifumi , Louis David N. , Fuller Greory N. , Holland Eric C.
Published: July 2002

We present evidence that some low-grade oligodendrogliomas may be comprised of proliferating glial progenitor cells that are blocked in their ability to differentiate, whereas malignant gliomas have additionally acquired other mutations such as disruption of cell cycle arrest pathways by loss ofInk4a–Arf.We have modeled these effects in cell culture and in mice by generating autocrine stimulation of glia through the platelet-derived growth factor receptor (PDGFR). In cell culture, PDGF signaling induces proliferation of glial precursors and blocks their differentiation into oligodendrocytes and astrocytes. In addition, coexpression of PDGF and PDGF receptors has been demonstrated in human gliomas, implying that autocrine stimulation may be involved in glioma formation. In this study, using somatic cell type-specific gene transfer we investigated the functions of PDGF autocrine signaling in gliomagenesis by transferring the overexpression of PDGF-B into either nestin-expressing neural progenitors or glial fibrillary acidic protein (GFAP)-expressing astrocytes both in cell culture and in vivo. In cultured astrocytes, overexpression of PDGF-B caused significant increase in proliferation rate of both astrocytes and neural progenitors. Furthermore, PDGF gene transfer converted cultured astrocytes into cells with morphologic and gene expression characteristics of glial precursors. In vivo, gene transfer of PDGF to neural progenitors induced the formation of oligodendrogliomas in about 60% of mice by 12 wk of age; PDGF transfer to astrocytes induced the formation of either oligodendrogliomas or mixed oligoastrocytomas in about 40% of mice in the same time period. Loss ofInk4a–Arf, a mutation frequently found in high-grade human gliomas, resulted in shortened latency and enhanced malignancy of gliomas. The highest percentage of PDGF-induced malignant gliomas arose from ofInk4a–Arfnull progenitor cells. These data suggest that chronic autocrine PDGF signaling can promote a proliferating population of glial precursors and is potentially sufficient to induce gliomagenesis. Loss ofInk4a–Arfis not required for PDGF-induced glioma formation but promotes tumor progression toward a more malignant phenotype.
Congenic Mapping of the Type 1 Diabetes Locus,Idd3, to a 780-kb Region of Mouse Chromosome 3: Identification of a Candidate Segment of Ancestral DNA by Haplotype Mapping
Authors: Lyons Paul A. , Armitage Nicola , Argentina Fabio , Denny Paul , Hill Natasha J. , Lord Christopher J. , Wilusz Mary Beth , Peterson Laurence B. , Wicker Linda S. , Todd John A.
Published: July 2002

Type 1 diabetes in the nonobese diabetic (NOD) mouse arises as a consequence of T cell-mediated destruction of the insulin-producing β cells of the pancreas. Although little is known of the events that initiate and subsequently drive β-cell destruction it is clear that the entire process is under complex genetic control. At present 19 loci have been mapped that influence the development of diabetes either at the level of initiation of insulitis or at the level of progression from insulitis to overt diabetes, or both. Previously, we have mapped one of these loci,Idd3, to a 0.35-cM interval on proximal mouse chromosome 3. In the present study we have narrowed the map position of this locus to an interval of 0.15 cM by a combination of novel congenic strains and an ancestral haplotype analysis approach. We have constructed a physical contig in bacterial artificial chromosome (BAC) clones across the minimal interval. Restriction mapping of the BAC contig placed the maximum size of theIdd3interval at 780 kb between the markersD3Nds36andD3Nds76. To refine further theIdd3interval we developed a series of novel single nucleotide polymorphisms (SNPs) and carried out haplotype analysis on DNA from mouse strains known to carry eitherIdd3susceptibility or protective alleles. This haplotype analysis identified a 145-kb segment of ancestral DNA between the microsatellite markerD3Nds6and the SNP81.3. One haplotype of this ancestral segment of DNA is found in mouse strains carrying anIdd3susceptibility allele and another is found in mouse strains carrying anIdd3protective allelle. Within the 780-kb congenically defined interval this 145-kb segment represents the most likely location forIdd3. TheIl2gene, which encodes the cytokine interleukin 2 (IL2), maps to this interval and is a strong candidate forIdd3. To investigate whether sequence variation exists in the promoter region of theIl2gene, which might alter its expression, we sequenced the promoter region of theIl2gene from mouse strains carrying either anIdd3susceptibility or resistance allele. Two sequence variants were identified, neither of which fell in known regulatory elements within theIl2promoter. In agreement with this observation steady-stateIl2mRNA levels showed no variation between susceptible and resistant mouse strains. These data suggest that the profound protection from diabetes seen in congenic mice carrying anIdd3protective allele is unlikely to be due to differences in the level of expression of theIl2gene. Instead, all of the current data support our hypothesis thatIdd3corresponds to amino acid variation at the amino terminus ofIl2.

[Sequence data reported in this paper have been deposited in GenBank and assigned the following accession numbers: AF19594, AF19595, and AF19596.]
Tandem Repeats in Protein Coding Regions of Primate Genes
Authors: Borštnik Branko , Pumpernik Danilo
Published: July 2002

Tandem repeats in GenBank primate nucleotide sequences annotated as protein coding regions are analyzed. It is found that only trinucleotide repeats show repeat enrichment well above the threshold of statistical significance. The statistics are improved by a simultaneous search for repeats on both the amino acid and nucleotide levels. The results of the analyses of natural sequences are interpreted by comparing them with the results of the computer simulation of the model dedicated to protein coding regions. According to the simulation results, a limited set of trinucleotides, that is, cgg, ccg, cag, and gaa repeats coding for polyalanine, polyglycine, polyproline, polyglutamine, and polylysine are prone to proliferation. It is also found that within the repeat regions slippage is more frequent by a factor of 10 than point mutations, whereas the ratio of silent versus recognizable point mutations is approximately the same as elsewhere in coding regions. The trinucleotide repeats cover slightly more than 0.3% of the protein coding regions of genes.
Y-Chromosomal SNPs in Finno–Ugric-Speaking Populations Analyzed by Minisequencing on Microarrays
Authors: Raitio Mirja , Lindroos Katarina , Laukkanen Minna , Pastinen Tomi , Sistonen Pertti , Sajantila Antti , Syvänen Ann-Christine
Published: July 2002

An increasing number of single nucleotide polymorphisms (SNPs) on the Y chromosome are being identified. To utilize the full potential of the SNP markers in population genetic studies, new genotyping methods with high throughput are required. We describe a microarray system based on the minisequencing single nucleotide primer extension principle for multiplex genotyping of Y-chromosomal SNP markers. The system was applied for screening a panel of 25 Y-chromosomal SNPs in a unique collection of samples representing five Finno–Ugric populations. The specific minisequencing reaction provides 5-fold to infinite discrimination between the Y-chromosomal genotypes, and the microarray format of the system allows parallel and simultaneous analysis of large numbers of SNPs and samples. In addition to the SNP markers, five Y-chromosomal microsatellite loci were typed. Altogether 10,000 genotypes were generated to assess the genetic diversity in these population samples. Six of the 25 SNP markers (M9,Tat, SRY10831, M17, M12,92R7) were polymorphic in the analyzed populations, yielding six distinct SNP haplotypes. The microsatellite data were used to study the genetic structure of two major SNP haplotypes in the Finns and the Saami in more detail. We found that the most common haplotypes are shared between the Finns and the Saami, and that the SNP haplotypes show regional differences within the Finns and the Saami, which supports the hypothesis of two separate settlement waves to Finland.
cis Element/Transcription Factor Analysis (cis/TF): A Method for Discovering Transcription Factor/cis Element Relationships
Authors: Birnbaum Kenneth , Benfey Philip N. , Shasha Dennis E.
Published: July 2002

We report a simple new algorithm, cis/TF, that uses genomewide expression data and the full genomic sequence to match transcription factors to their binding sites. Most previous computational methods discovered binding sites by clustering genes having similar expression patterns and then identifying over-represented subsequences in the promoter regions of those genes. By contrast, cis/TF asserts that B is a likely binding site of a transcription factor T if the expression pattern of T is correlated to the composite expression patterns of all genes containing B, even when those genes are not mutually correlated. Thus, our method focuses on binding sites rather than genes. The algorithm has successfully identified experimentally-supported transcription factor binding relationships in tests on several data sets fromSaccharomyces cerevisiae.
A Proteomic View on Genome-Based Signal Peptide Predictions
Authors: Antelmann Haike , Tjalsma Harold , Voigt Birgit , Ohlmeier Steffen , Bron Sierd , van Dijl Jan Maarten , Hecker Michael
Published: July 2002

The availability of complete genome sequences has allowed the prediction of all exported proteins of the corresponding organisms with dedicated algorithms. Even though numerous studies report on genome-based predictions of signal peptides and cell retention signals, they lack a proteomic verification. For example, 180 secretory and 114 lipoprotein signal peptides were predicted recently for the Gram-positive eubacterium Bacillus subtilis. In the present studies, proteomic approaches were used to define the extracellular complement of the B. subtilis secretome. Using different growth conditions and a hyper-secreting mutant, ∼200 extracellular proteins were visualized by two-dimensional (2D) gel electrophoresis, of which 82 were identified by mass spectrometry. These include 41 proteins that have a potential signal peptide with a type I signal peptidase (SPase) cleavage site, and lack a retention signal. Strikingly, the remaining 41 proteins were predicted previously to be cell associated because of the apparent absence of a signal peptide (22), or the presence of specific cell retention signals in addition to an export signal (19). To test the importance of the five type I SPases and the unique lipoprotein-specific SPase of B. subtilis, the extracellular proteome of (multiple) SPase mutants was analyzed. Surprisingly, only the processing of the polytopic membrane protein YfnI was strongly inhibited in Spase I mutants, showing for the first time that a native eubacterial membrane protein is a genuine Spase I substrate. Furthermore, a mutation affecting lipoprotein modification and processing resulted in the shedding of at least 23 (lipo-)proteins into the medium. In conclusion, our observations show that genome-based predictions reflect the actual composition of the extracellular proteome for ∼50%. Major problems are currently encountered with the prediction of extracellular proteins lacking signal peptides (including cytoplasmic proteins) and lipoproteins.
Analysis of Flavanone 3-Hydroxylase in Arabidopsis Seedlings (Coordinate Regulation with Chalcone Synthase and Chalcone Isomerase)
Authors: Pelletier M. K. , Shirley B. W.
Published: July 2002

A genomic clone encoding flavanone 3-hydroxylase (F3H) was isolated from Arabidopsis thaliana. The deduced amino acid sequence is 72 to 94% identical to all previously reported F3H proteins. Low-stringency DNA blot analysis indicated that F3H is encoded by a single gene in Arabidopsis. The F3H locus was mapped to the bottom of chromosome 3 and therefore does not correspond to any of the 13 flavonoid-deficient transparent testa mutants for which a map position is known. Analysis of gene expression in etiolated seedlings exposed to white light and in two putative regulatory mutants, ttg and tt8, demonstrated that the Arabidopsis F3H gene is coordinately expressed with chalcone synthase and chalcone isomerase in seedlings, whereas dihydroflavonol reductase expression is controlled by distinct regulatory mechanisms. The F3H gene may represent a pivotal point in the regulation of flavonoid biosynthesis because its expression is coordinated with different subsets of genes in different plant species.