bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligonucleotide‐based microarray for DNA methylation analysis: Principles and applications
Authors: Shi Huidong , Maier Sabine , Nimmrich Inko , Yan Pearlly S. , Caldwell Charles W. , Olek Alexander , Huang Tim Hui‐Ming 
Published: December 2002

AbstractGene silencing via promoter CpG island hypermethylation offers tumor cells growth advantages. This epigenetic event is pharmacologically reversible, and uncovering a unique set of methylation‐silenced genes in tumor cells can bring a new avenue to cancer treatment. However, high‐throughput tools capable of surveying the methylation status of multiple gene promoters are needed for this discovery process. Herein we describe an oligonucleotide‐based microarray technique that is both versatile and sensitive in revealing hypermethylation in defined regions of the genome. DNA samples are bisulfite‐treated and PCR‐amplified to distinguish CpG dinucleotides that are methylated from those that are not. Fluorescently labeled PCR products are hybridized to arrayed oligonucleotides that can discriminate between methylated and unmethylated alleles in regions of interest. Using this technique, two clinical subtypes of non‐Hodgkin's lymphomas, mantle cell lymphoma, and grades I/II follicular lymphoma, were further separated based on the differential methylation profiles of several gene promoters. Work is underway in our laboratory to extend the interrogation power of this microarray system in multiple candidate genes. This novel tool, therefore, holds promise to monitor the outcome of various epigenetic therapies on cancer patients. © 2002 Wiley‐Liss, Inc.
Establishment of dependence relationships between genome replication and mitosis
Authors: Clarke Duncan J. 
Published: December 2002

AbstractAlthough budding yeast cell biology and genetics provided a powerful system to isolate S‐phase checkpoint mutants, initial studies relied on a defect not likely to be relevant in higher eukaryotes. The first mutants were isolated for their inability to restrain mitotic spindle elongation in S‐phase. Since most eukaryotes do not assemble spindles until prometaphase the validity of this approach might have been questioned. However, these early studies were designed with a highly valid assumption in mind; that checkpoints have a variety of targets, but comprise conserved kinase cascades that make up these signaling pathways. The task that lies ahead is to determine targets of the S‐phase checkpoint relevant to mammals. One step forward might be the realization that the budding yeast S‐phase checkpoint prevents loss of sister chromatid cohesion while DNA replication is ongoing. If this mechanism is conserved in mammals, it could prove vital for chromosome segregation fidelity. © 2002 Wiley‐Liss, Inc.
The 5′‐untranslated RNA of the human dhfr minor transcript alters transcription pre‐initiation complex assembly at the major (core) promoter
Authors: Blume Scott W. , Meng Zheng , Shrestha Kedar , Snyder Richard C. , Emanuel Peter D. 
Published: December 2002

AbstractThe human dhfr minor transcript is distinguished from the predominant dhfr mRNA by an ∼400 nucleotide extension of the 5′‐untranslated region, which corresponds to the major (core) promoter DNA (its template). Based on its unusual sequence composition, we hypothesized that the minor transcript 5′‐UTR might be capable of altering transcription pre‐initiation complex assembly at the core promoter, through direct interactions of the RNA with specific regulatory polypeptides or the promoter DNA itself. We found that the minor transcript 5′‐UTR selectively sequesters transcription factor Sp3, and to a lesser extent Sp1, preventing their binding to the dhfr core promoter. This allows a third putative transcriptional regulatory protein, which is relatively resistant to sequestration by the minor transcript RNA, the opportunity to bind the dhfr core promoter. The selective sequestration of Sp3 > Sp1 by the minor transcript 5′‐UTR involves an altered conformation of the RNA, and a structural domain of the protein distinct from that required for binding to DNA. As a consequence, the minor transcript 5′‐UTR inhibits transcription from the core promoter in vitro (in trans) in a concentration‐dependent manner. These results suggest that the dhfr minor transcript may function in vivo (in cis) to regulate the transcriptional activity of the major (core) promoter. © 2002 Wiley‐Liss, Inc.
Increased proteasome‐dependent degradation of estrogen receptor‐alpha by TGF‐β1 in breast cancer cell lines
Authors: Petrel Trevor A. , Brueggemeier Robert W. 
Published: December 2002

AbstractNormal mammary epithelial cells are rapidly induced to G1 arrest by the widely expressed cytokine, transforming growth factor beta (TGF‐β1). Studies in established breast cancer cell lines that express the estrogen receptor alpha (ERα) have demonstrated loss of this responsiveness. This inverse correlation suggests interpathway signaling important to cell growth and regulation. The adenocarcinoma breast cell line BT474, which was not growth arrested by TGF‐β1, was used as a model of estrogen‐inducible growth to explore interpathway crosstalk. Although BT474 cells were not growth‐arrested by TGF‐β1 as determined by flow cytometry analysis and 5′‐bromo‐3′‐deoxyuridine incorporation into DNA, estrogen receptor protein levels were attenuated by 100 pM TGF‐β1 after 6 h. This decrease in ERα reached 50% of untreated control levels by 24 h of treatment and was further supported by a 50% decrease in estrogen‐inducible DNA synthesis. Inspection of ERα transcripts suggested that this decrease was primarily the result of altered ERα protein stability or availability. Use of the proteasome inhibitor, MG132, abolished all effects on ERα by TGF‐β1. Collectively, this data supports a role for TGF‐β1 in regulating the growth of otherwise insensitive breast cancer cells through modulation of ERα stability. © 2002 Wiley‐Liss, Inc.
Proteomic analyses of arsenic‐induced cell transformation with SELDI‐TOF ProteinChip® technology
Authors: He Qing‐Yu , Yip Ta‐Tung , Li Muyao , Chiu Jen‐Fu 
Published: December 2002

AbstractIn this study, we demonstrated that low levels (1.5 μM) of arsenite induces B[a]P‐treated lung cell transformation. We then used a proteomic approach to identify protein expression by ProteinChips, which could potentially be important for transformation induced by this toxic metal. Most of the protein peaks in cell extracts of all samples, including the control, B[a]P‐treated, and B[a]P + As‐treated cells are identical. However, surface‐enhanced laser desorption/ionization time of flight (SELDI‐TOF) analysis with Cu‐ProteinChips and WCX‐ProteinChips revealed several dramatically different protein peaks that appeared in lung cells after being transformed by a treatment of 1.5 μM arsenite for 12 weeks. SAX2 ProteinChip also identified a prominent protein peak that was preferentially expressed in control cells. Interestingly, by using a SAX2 chip, we were able to detect several protein peaks that increased their expression in lung epithelial cells (LEC) treated with only B[a]P. Identification and characterization of these proteins may reveal the molecular basis of As‐induced cell transformation and provide insight into the mechanisms by which arsenic induces carcinogenesis. © 2002 Wiley‐Liss, Inc.
Copernican stem cells: Regulatory constellations in adult hippocampal neurogenesis
Authors: Fabel Klaus , Toda Hiroki , Fabel Konstanze , Palmer Theo 
Published: December 2002

AbstractIn the adult, neurogenesis occurs where constellations of signaling molecules are correctly orchestrated and where competent cells are present to interpret these signals. As the instruments used to observe adult neurogenesis become more sophisticated, the concept of a discrete competent “stem cell” has become less concrete. Neural progenitor cells once thought committed to a single lineage can be influenced to become multipotent and somatic tissues appear to yield cells capable of tremendous peripheral and central lineage potential. The variety of cell types that appear competent to generate neurons suggests that the “Hilios” of adult neurogenesis may not necessarily be a single cellular entity but rather the sum of signals that dictate, “Make a new neuron here.” These signals may not be limited to the recruitment of preexisting neural stem cells but may also, in some subtle way, reprogram local precursors to create “stem‐like cells,” where needed. © 2002 Wiley‐Liss, Inc.
An intranuclear frame for chromatin compartmentalization and higher‐order folding
Authors: Barboro Paola , D'Arrigo Cristina , Mormino Michele , Coradeghini Rosella , Parodi Silvio , Patrone Eligio , Balbi Cecilia 
Published: December 2002

AbstractRecent ultrastructural, immunoelectron, and confocal microscopy observations done in our laboratory [Barboro et al. [2002] Exp. Cell. Res. 279:202–218] have confirmed that lamins and the nuclear mitotic apparatus protein (NuMA) are localized inside the interphase nucleus in a polymerized form. This provided evidence of the existence of a RNA stabilized lamin/NuMA frame, consisting of a web of thin (∼3 and ∼5 nm) lamin filaments to which NuMA is anchored mainly in the form of discrete islands, which might correspond to the minilattices described by Harborth et al. [1999] (EMBO. J. 18:1689–1700). In this article we propose that this scaffold is involved in the compartmentalization of both chromatin and functional domains and further determines the higher‐order nuclear organization. This hypothesis is strongly supported by the scrutiny of different structural transitions which occur inside the nucleus, such as chromatin displacement and rearrangements, the collapse of the internal nuclear matrix after RNA digestion and the disruption of chromosome territories induced by RNase A and high salt treatment. All of these destructive events directly depend on the loss of the stabilizing effect exerted on the different levels of structural organization by the interaction of RNA with lamins and/or NuMA. Therefore, the integrity of nuclear RNA must be safeguarded as far as possible to isolate the matrix in the native form. This material will allow for the first time the unambiguous ultrastructural localization inside the INM of the components of the functional domains, so opening new avenues of investigation on the mechanisms of gene expression in eukaryotes. © 2003 Wiley‐Liss, Inc.
What are the characteristics of cycling cells in the adult central nervous system?
Authors: Goldman James E. 
Published: December 2002

AbstractMany regions of the adult central nervous system contain cycling cells. Such cells comprise a relatively small fraction of the total population of the CNS. Work over decades has attempted to determine the normal fates of these cells and their fates under pathological conditions. The recent interest in “stem” cells and “progenitors” in the adult CNS has sparked a much revived exploration into the nature of these cells and in the signals by which they may be induced to differentiate into mature neurons or glia. This population has not yet been fully characterized, although it has become clear that this is a heterogeneous group of cells, differing in morphology, antigen expression, migratory capacity, and potential fates. © 2002 Wiley‐Liss, Inc.
Paradoxical role of apoptosis in tumor progression
Authors: Gurova Katerina V. , Gudkov Andrei V. 
Published: December 2002

AbstractTumors frequently acquire resistance to apoptosis that is expected to contribute to malignant phenotype and reduce sensitivity to treatment. In fact, inactivation of p53 tumor suppressor gene resulting in suppression of apoptosis serves as a negative prognostic marker. Surprisingly, expression of a strong anti‐apoptotic protein Bcl‐2, another mechanism to avoid apoptosis, was found to be associated with a favorable prognosis. This paradoxical anti‐progressor function of Bcl‐2 has been explained in literature based on the negative effect of Bcl‐2 on cell proliferation. Here, by analyzing accumulated experimental and clinical data, we provide evidence supporting another hypothesis that defines apoptosis as an accelerator of tumor progression. The mechanism of anti‐progressor function of Bcl‐2 is based on creation of tumors that maintain control of genomic stability by eliminating selective advantages for the cells that acquire resistance to apoptosis through loss of p53. Thus, inhibition of apoptosis does not lead to loss of genomic stability and creates tumor environment that no longer supports further tumor progression and inhibitors of apoptosis can be considered as factors suppressing tumor progression. © 2002 Wiley‐Liss, Inc.
Microsatellite DNA library for Caiman latirostris
Authors: Zucoloto Rodrigo Barban , Verdade Luciano Martins , Coutinho Luiz Lehmann 
Published: December 2002

AbstractNew genetic markers were characterized for the broad‐snouted caiman (Caiman latirostris) by constructing libraries enriched for microsatellite DNA. Construction and characterization of these libraries are described in the present study. One microsatellite marker was developed from a (ACC‐TGG)nenriched microsatellite DNA library, and 12 microsatellite markers were developed from a (AC‐TG)nenriched microsatellite DNA library. These markers were tested in wild‐caught animals, and these tests resulted in ten new polymorphic microsatellites for C. latirostris. J. Exp. Zool. (Mol. Dev. Evol.) 294:346–351, 2002. © 2002 Wiley‐Liss, Inc.
The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications
Authors: Ray David Alfred , Densmore Llewellyn 
Published: December 2002

AbstractWe present the first comprehensive analysis of the crocodilian control region. We have analyzed sequences from all three families of Crocodylia (Crocodylidae, Gavialidae, Alligatoridae), incorporating all genera exceptPaleosuchusandMelanosuchus. Within the control region of other vertebrates, several sequence motifs and their order appear to be conserved. Herein, we compare aligned crocodilian D‐loop sequences to homologous sequences from other vertebrates ranging from fish to birds. Among other findings, we have discovered that while domain I tends to be shorter than the same region in mammals and birds, it contains sequences similar in structure to both the goose‐hairpin and termination associated sequences (TAS). Domain II is highly conservative with regard to size among the taxa examined and contains several of the conserved sequence boxes characterized in other vertebrates. Domain III contains several interesting sequence motifs including tandemly repeated sequences, a long poly‐A region in the Crocodylidae, and possible bidirection promoter sequences.J. Exp. Zool. (Mol. Dev. Evol.) 294:334–345, 2002. © 2002 Wiley‐Liss, Inc.
Generation of a sequence characterized amplified region probe for authentication of crocodilian species
Authors: Chung‐Fai Yau Forrest , Wong Ka‐Lok , Wang Jun , Pui‐Hay But Paul , Shaw Pang‐Chui 
Published: December 2002

AbstractA 209‐base pair (bp) crocodilian‐specific sequence characterized amplified region (SCAR) was identified from a 425‐bp randomly amplified polymorphic DNA (RAPD) fragment. The 209‐bp SCAR was produced from amplifications of DNA extracted from fresh and/or dry meat samples from at least three species of Crocodylus, Caiman crocodylus, and Alligator mississippiensis. No amplification was observed from DNA of other common animal species. The use of SCAR opens the way for quick authentication of crocodilian samples for conservation biology and trade regulation. J. Exp. Zool. (Mol. Dev. Evol.) 294:382–386, 2002. © 2002 Wiley‐Liss, Inc.
Microgeographic variation in Caiman latirostris
Authors: Verdade Luciano Martins , Zucoloto Rodrigo Barban , Coutinho Luiz Lehmann 
Published: December 2002

AbstractIn theory, geographic scale is related to genetic variation at the population level, whereas microgeographic scale may reveal intra‐population structure such as social groups and families. In the present work, both levels of genetic variation in the broad‐snouted caiman (Caiman latirostris) were evaluated in small wetlands associated with the Piracicaba River and some of its tributaries in the state of São Paulo, Brazil. Genetic variation was determined using microsatellite DNA markers originally developed for the American alligator (Alligator mississipiensis) and previously tested in pedigreed captive broad‐snouted caimans. Using these markers, we were able to detect variability among individuals from different sites, even those within a small geographic distance. Genetic results suggest that the groups sampled at each site are composed predominantly of related individuals. A possible combination of high mortality and low natality rates results in a low number of successfully dispersed individuals per generation. Future studies using a recently constructed Caiman latirostris microsatellite library (Zucoloto et al., 2002) might help us to understand metapopulation processes that may be occurring within this species. J. Exp. Zool. (Mol. Dev. Evol.) 294:387–396, 2002. © 2002 Wiley‐Liss, Inc.
Identification of purebredCrocodylus siamensisfor reintroduction in Vietnam
Authors: Fitzsimmons Nancy Nelson , Buchan Jason Craig , Lam Phan Viet , Polet Gert , Hung Ton That , Thang Nguyen Quoc , Gratten Jacob 
Published: December 2002

AbstractCrocodylus siamensis, the Siamese crocodile, is a critically endangered species of freshwater crocodile previously distributed throughout much of SE Asia. Recovery plans call for reintroductions to the wild using founder individuals currently in captivity, mostly in commercial crocodile farms. On many farmsC. siamensishas been intentionally hybridised with either Cuban crocodiles,C. rhombifer, or the estuarine crocodile,C. porosus, and hybrids may be difficult to distinguish morphologically. We report on the combined use of microsatellite and mtDNA genetic markers to determine the species status of potential founder individuals for reintroduction ofC. siamensis. Genetic markers were used to characterise 103 captive and wild‐caught individuals ofC. siamensis,C. rhombiferandC. porosusin Vietnam and to distinguish purebred versus hybrid individuals. Although the microsatellite loci used had some overlap of allele sizes among species, assignment tests allowed differentiation. Four hybrids were identified, two of which had not been recognised morphologically as hybrids, and one of these was thought to be aC. siamensissuitable for reintroduction. Ten of the identified purebredC. siamensiswere subsequently released into Cat Tien National Park in southern Vietnam.J. Exp. Zool. (Mol. Dev. Evol.) 294:373–381, 2002. © 2002 Wiley‐Liss, Inc.
Low mitochondrial DNA variation among American alligators and a novel non‐coding region in crocodilians
Authors: Glenn Travis C. , Staton Joseph L. , Vu Alex T. , Davis Lisa M. , Bremer Jaime R. Alvarado , Rhodes Walter E. , Brisbin I. Lehr , Sawyer Roger H. 
Published: December 2002

AbstractWe analyzed 1317–1823 base pairs (bp) of mitochondrial DNA sequence beginning in the 5' end of cytochrome b (cyt b) and ending in the central domain of the control region for 25 American alligators (Alligator mississippiensis) and compared these to a homologous sequence from a Chinese alligator (A. sinensis). Both species share a non‐coding spacer between cyt b and tRNAThr. Chinese alligator cyt b differs from that of the American alligator by 17.5% at the nucleotide level and 13.8% for inferred amino acids, which is consistent with their presumed ancient divergence. Only two cyt b haplotypes were detected among the 25 American alligators (693–1199 bp surveyed), with one haplotype shared among 24 individuals. One alligator from Mississippi differed from all other alligators by a single silent substitution. The control region contained only slightly more variation among the 25 American alligators, with two variable positions (624 bp surveyed), yielding three haplotypes with 22, two, and one individuals in each of these groups. Previous genetic studies examining allozymes and the proportion of variable microsatellite DNA loci also found low levels of genetic diversity in American alligators. However, in contrast with allozymes, microsatellites, and morphology, the mtDNA data shows no evidence of differentiation among populations from the extremes of the species range. These results suggest that American alligators underwent a severe population bottleneck in the late Pleistocene, resulting in nearly homogenous mtDNA among all American alligators today. J. Exp. Zool. (Mol. Dev. Evol.) 294:312–324, 2002. © 2002 Wiley‐Liss, Inc.
Genetic relationships of American alligator populations distributed across different ecological and geographic scales
Authors: Ryberg Wade A. , Fitzgerald Lee A. , Honeycutt Rodney L. , Cathey James C. 
Published: December 2002

AbstractAlthough much work has been conducted on coastal populations of the American alligator (Alligator mississippiensis), less is known about the population dynamics and genetic structure of populations of alligators confined to inland habitats. DNA microsatellite loci, derived from the American alligator, were used to investigate patterns of genetic variation within and between populations of alligators distributed at coastal and inland localities in Texas. These data were used to evaluate the genetic discreteness of different alligator stocks relative to their basic ecology at these sites. Observed mean heterozygosities across seven loci for both coastal and inland populations ranged from 0.50–0.61, with both inland and coastal populations revealing similar patterns of variation. Measures of Fst revealed significant population differentiation among all populations; however, analyses of molecular variance (AMOVAs) failed to demonstrate any apparent geographic pattern relative to the population differentiation indicated by Fst values. Each population contained unique alleles for at least one locus. Additionally, assignment tests based on the distribution of genotypes placed 76% of individuals to their source population. These genetic data suggest considerable subdivision among alligator populations, possibly influenced by demographic and life history differences as well as barriers to dispersal. These results have clear implications for management. Rather than managing alligators in Texas as a single panmictic population, translocation programs and harvest quotas should consider the ecological and genetic distinctiveness of local alligator populations. J. Exp. Zool. (Mol. Dev. Evol.) 294:325–333, 2002. © 2002 Wiley‐Liss, Inc.