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Molecular Markers (molecular + marker)
Kinds of Molecular Markers Terms modified by Molecular Markers Selected AbstractsUse of Green Fluorescent Protein-Conjugated ,-Actin as a Novel Molecular Marker for in Vitro Tumor Cell Chemotaxis AssayBIOTECHNOLOGY PROGRESS, Issue 6 2000Louis Hodgson To study the dynamics of actin cytoskeleton rearrangement in living cells, an eukaryotic expression vector expressing a ,-actin-GFP fusion protein was generated. The expression construct when transfected into NIH3T3 fibroblast, A2058 human melanoma and 293T human embryonic kidney carcinoma cell lines expressed ,-actin-GFP fusion protein, which colocalized with endogenous cellular actin as determined by histoimmunofluorescence staining. The ,-actin-GFP was also observed to be reorganized in response to treatments with the chemoattractant type IV collagen. Cells extended pseudopodial protrusions and altered the morphology of their cortical structure in response to type IV collagen stimulation. More importantly, ,-actin-GFP accumulated in areas undergoing these dynamic cytoskeleton changes, indicating that ,-actin-GFP could participate in actin polymerization. Although ectopic expression of ,-actin-GFP lead to minor side effects on cell proliferation, these studies suggest that this strategy provides an alternative to the invasive techniques currently used to study actin dynamics and permits real-time visualization of actin rearrangements in response to environmental cues. [source] Molecular marker-based pedigrees for animal conservation biologistsANIMAL CONSERVATION, Issue 1 2010O. R. Jones Abstract Pedigrees, depicting the genealogical relationships between individuals in a population, are of fundamental importance to several research areas including conservation biology. For example, they are useful for estimating inbreeding, heritability, selection, studying kin selection and for measuring gene flow between populations. Pedigrees constructed from direct observations of reproduction are usually unavailable for wild populations. Therefore, pedigrees for these populations are usually estimated using molecular marker data. Despite their obvious importance, and the fact that pedigrees are conceptually well understood, the methods, and limitations of marker-based pedigree inference are often less well understood. Here we introduce animal conservation biologists to molecular marker-based pedigrees. We briefly describe the history of pedigree inference research, before explaining the underlying theory and basic mechanics of pedigree construction using standard methods. We explain the assumptions and limitations that accompany many of these methods, before going on to explain methods that relax several of these assumptions. Finally, we look to future and discuss some recent exciting advances such as the use of single-nucleotide polymorphisms, inference of multigenerational pedigrees and incorporation of non-genetic data such as field observations into the calculations. We also provide some guidelines on efficient marker selection in order to maximize accuracy and power. Throughout we use examples from the field of animal conservation and refer readers to appropriate software where possible. It is our hope that this review will help animal conservation biologists to understand, choose, and use the methods and tools of this fast-moving field. [source] The Prestige oil spill.ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 9 2005Abstract In vitro biodegradation of the Prestige heavy fuel oil has been carried out using two microbial consortia obtained by enrichment in different substrates to simulate its environmental fate and potential utility for bioremediation. Different conditions, such as incubation time (i.e., 20 or 40 d), oil weathering, and addition of an oleophilic fertilizer (S200), were evaluated. Weathering slowed down the degradation of the fuel oil, probably because of the loss of lower and more labile components, but the addition of S200 enhanced significantly the extension of the biodegradation. n -Alkanes, alkylcyclohexanes, alkylbenzenes, and the two- to three-ring polycyclic aromatic hydrocarbons (PAHs) were degraded in 20 or 40 d of incubation of the original oil, whereas the biodegradation efficiency decreased for higher PAHs and with the increase of alkylation. Molecular markers were degraded according to the following sequence: Acyclic isoprenoids < diasteranes < C27 -steranes < ,,-steranes < homohopanes < monoaromatic steranes < triaromatic steranes. Isomeric selectivity was observed within the C1 - and C2 -phenanthrenes, dibenzothiophenes, pyrenes, and chrysenes, providing source and weathering indices for the characterization of the heavy oil spill. Acyclic isoprenoids, C27 -steranes, C1 - and C2 -naphthalenes, phenanthrenes, and dibenzothiophenes were degraded completely when S200 was used. The ratios of the C2 - and C3 -alkyl homologues of fluoranthene/pyrene and chrysene/benzo[a]anthracene are proposed as source ratios in moderately degraded oils. The 4-methylpyrene and 3-methylchrysene were refractory enough to serve as conserved internal markers in assessing the degradation of the aromatic fraction in a manner similar to that of hopane, as used for the aliphatic fraction. [source] Mining an Ostrinia nubilalis midgut expressed sequence tag (EST) library for candidate genes and single nucleotide polymorphisms (SNPs)INSECT MOLECULAR BIOLOGY, Issue 6 2008B. S. Coates Abstract Genes expressed in lepidopteran midgut tissues are involved in digestion and Bacillus thuringiensis (Bt) toxin resistance traits. Five hundred and thirty five unique transcripts were annotated from 1745 high quality O. nubilalis larval midgut expressed sequence tags (ESTs). Full-length cDNA sequence of 12 putative serine proteinase genes and 3 partial O. nubilalis aminopeptidase N protein genes, apn1, apn3, and apn4, were obtained, and genes may have roles in plant feeding and Bt toxin resistance traits of Ostrinia larvae. The EST library was not normalized and insert frequencies reflect transcript levels under the initial treatment conditions and redundancy of inserts from highly expressed transcripts allowed prediction of putative single nucleotide polymorphisms (SNPs). Ten di-, tri- or tetranucleotide repeat unit microsatellite loci were identified, and minisatellite repeats were observed within the C-termini of two encoded serine proteinases. Molecular markers showed polymorphism at 28 SNP loci and one microsatellite locus, and Mendelian inheritance indicated that markers were applicable to genome mapping applications. This O. nubilalis larval midgut EST collection is a resource for gene discovery, expression information, and allelic variation for use in genetic marker development. [source] Molecular markers of phase transition in locustsINSECT SCIENCE, Issue 1 2006ARNOLD DE LOOF Abstract The changes accompanying the transition from the gregarious to the solitary phase state in locusts are so drastic that for a long time these phases were considered as distinct species. It was Boris Uvarov who introduced the concept of polyphenism. Decades of research revealed that phase transition implies changes in morphometry, the color of the cuticle, behavior and several aspects of physiology. In particular, in the recent decade, quite a number of molecular studies have been undertaken to uncover phase-related differences. They resulted in novel insights into the role of corazonin, neuroparsins, some protease inhibitors, phenylacetonitrile and so on. The advent of EST-databases of locusts (e.g. Kang et al., 2004) is a most encouraging novel development in physiological and behavioral locust research. Yet, the answer to the most intriguing question, namely whether or not there is a primordial molecular inducer of phase transition, is probably not within reach in the very near future. [source] Molecular determinants of irinotecan efficacyINTERNATIONAL JOURNAL OF CANCER, Issue 10 2006Daniel Vallböhmer Abstract Molecular markers predicting the efficacy of CPT-11 based chemotherapies in patients with colorectal cancer (CRC) are unknown. Therefore, we investigated whether mRNA levels of drug targets (Topoisomerase I, TS), enzymes involved in 5-FU metabolism (DPD), in angiogenesis (EGFR, IL-8, VEGF) and in DNA-repair/drug detoxification (ERCC1, GST-P1) are associated with the clinical outcome of patients with CRC treated with first-line CPT-11 based chemotherapy. Thirty three patients with metastatic CRC were included in the study. Intratumoral gene expression levels were assessed from paraffin-embedded tissue samples, using laser capture microdissection and quantitative Real-Time PCR. Complete response was observed in 1 patient, partial response in 12 patients, stable disease in 13 patients and progressive disease in 6 patients. Response was inevaluable for 1 patient. Patients with complete response or partial response were classified as responders, while patients with stable disease or progressive disease were classified as nonresponders. High intratumoral mRNA levels of EGFR, ERCC1 and GSPT-P1 were each significantly associated with response to CPT-11 based chemotherapy. Recursive partitioning analysis showed that mRNA levels of EGFR and ERCC1 are primarily responsible for delineating responders from nonresponders. Also, the combination of high intratumoral gene expression levels of both EGFR and ERCC1 was significantly associated with progression-free survival. The mRNA levels of EGFR had a significant correlation with expression levels of ERCC1, GST-P1 and VEGF. This small retrospective study suggests that gene expression levels of EGFR, ERCC1 and GST-P1 may be useful in predicting the clinical outcome of patients with metastatic CRC treated with first-line CPT-11 based chemotherapy. © 2006 Wiley-Liss, Inc. [source] Molecular markers and determinants of prostate cancer metastasisJOURNAL OF CELLULAR PHYSIOLOGY, Issue 3 2001Rahul V. Gopalkrishnan Although intensely studied, the molecular and biochemical determinants of prostate cancer development and progression remain ill-defined. Moreover, current markers and methodologies cannot distinguish between a tumor that will remain indolent and not impinge on patient survival, versus a tumor with aggressive traits culminating in metastatic spread and death. Once prostate cancer is confirmed the most significant threat to a patient's survival and quality of life involves tumor metastasis. Radical surgery notwithstanding, prostate cancer accounts for 10% of all cancer-related deaths primarily arising through development of metastasis. Metastasis markers demonstrating an acceptable level of reliability are an obvious necessity if disproportionate and costly treatment is to be avoided and a reasonably accurate determination of clinical prognosis and measure of successful response to treatment is to be made. Therapeutic strategies that specifically inhibit metastatic spread are not presently possible and may not become available in the immediate future. This is because, while localized tumorigenesis has been relatively amenable to detection, analysis and treatment, metastasis remains a relatively undefined, complex and underexplored area of prostate cancer research. New findings in the field such subclasses of genes called metastasis suppressors and cancer progression suppressors, have opened up exciting avenues of investigation. We review current methodological approaches, model experimental systems and genes presently known or having potential involvement in human prostate cancer metastasis. © 2001 Wiley-Liss, Inc. [source] Use of Random Amplified Polymorphic DNA Analysis for Economically Important Food CropsJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 12 2007Halima Hassan Salem Abstract The objective of this review is to summarize numerous studies on the use of the random amplified polymorphic DNA (RAPD) technique on rice, corn, wheat, sorghum, barley, rye, and oats to examine its feasibility and validity for assessment of genetic variation, population genetics, mapping, linkage and marker assisted selection, phylogenetic analysis, and the detection of somaclonal variation. Also we discuss the advantages and limitations of RAPD. Molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The simplicity of the RAPD technique made it ideal for genetic mapping, plant and animal breeding programs, and DNA fingerprinting, with particular utility in the field of population genetics. [source] Identification and Molecular Characterization of ,Candidatus Phytoplasma mali' Isolates in North-western ItalyJOURNAL OF PHYTOPATHOLOGY, Issue 2 2010Paola Casati Abstract Apple proliferation (AP) is an important disease and is prevalent in several European countries. The causal agent of AP is ,Candidatus Phytoplasma mali' (,Ca. Phytoplasma mali'). In this work, isolates of ,Ca. Phytoplasma mali' were detected and characterized through polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analyses of 16S rRNA gene and non-ribosomal DNA fragment. The presence of three AP subtypes (AT-1, AT-2 and AP-15) was identified in 31 symptomatic apple trees and two samples each constituted by a pool of five insects, collected in north-western Italy, where AT-1 is a dominant subtype. Subsequent nucleotide sequence analysis of the PCR-amplified 1.8 kb (P1/P7) fragment, containing the 16S rDNA, the 16S,23S intergenic ribosomal region and the 5,-end of the 23S rDNA, revealed the presence of at least two phytoplasmal genetic lineages within the AT-1 subtype, designed AT-1a and AT-1b. Moreover, in silico single nucleotide polymorphism (SNP) analysis based on 16S rDNA sequence can differentiate AT-1 subtype from AT-2 and AP-15 subtypes. Our data showed a high degree of genetic diversity among ,Ca. Phytoplasma mali' population in north-western Italy and underlined the possible use of the 16S rDNA analysis for the identification and the geographical origin assignation of isolates of AP phytoplasma. Molecular markers on 16S rDNA, here identified, could be useful for studying the epidemiology of AP disease. [source] Molecular markers of prognosis in renal cell carcinoma: Insight into tumor biology helps define risk and provides targets for therapyJOURNAL OF SURGICAL ONCOLOGY, Issue 4 2006Christopher G. Wood MD No abstract is available for this article. [source] Fractional allelic imbalance could allow for the development of an equitable transplant selection policy for patients with hepatocellular carcinomaLIVER TRANSPLANTATION, Issue 4 2008Igor Dvorchik Liver transplantation (LT) in the presence of hepatocellular carcinoma (HCC) remains a controversial issue because the current staging systems are not sufficiently predictive of outcomes. Paraffin blocks from 183 patients that underwent LT in the presence of HCC were collected. Molecular analysis was carried out blindly on the native liver specimens in all cases with respect to recurrence outcomes. The fractional allelic imbalance (FAI) rate index was determined in each case and was used to compare the acquired mutational load between different tumors. The FAI was determined from the microdissected tissue site displaying the greatest amount of acquired allelic loss. FAI was found to be the strongest predictor of recurrence followed by vascular invasion and then by tumor number or hepatic lobar involvement. Based on these findings, 3 prognostic models were constructed for selection of candidates for LT in patients with concomitant HCC. Molecular markers of tumor progression are the strongest predictors of HCC recurrence currently available, surpassing all components of the tumor-node-metastasis classification system for staging of malignant tumors (TNM), including vascular invasion. Incorporation of these molecular markers of tumor progression could help resolve the ongoing conundrum of organ allocation for patients with HCC. Liver Transpl 2007. © 2007 AASLD. [source] Molecular markers and therapeutic targets in ductal carcinoma in situMICROSCOPY RESEARCH AND TECHNIQUE, Issue 1 2002Gary P. Boland Abstract Ductal carcinoma in situ (DCIS) of the breast is a premalignant condition which accounts for approximately 20% of all new breast cancers and up to 40% of neoplastic lesions detected by mammographic screening. Since recurrence is common after DCIS treated with breast conservation surgery, there is a need to determine molecular factors that predict recurrence. In parallel with this and with the finding that oestrogen receptor (ER) positive breast cancer can be prevented with anti-oestrogens, there have been recent advances in the understanding of the molecular biology of DCIS. Receptor coexpression in DCIS has been determined largely by immunohistochemistry. Animal models have provided evidence for the signalling pathways involved in the regulation and dysregulation of proliferation and apoptosis in both normal breast and in situ cancer. ER-negative DCIS has been shown to be hormone-independent. Blockade of the pathways involved in cell proliferation in ER-negative DCIS is possible and will be necessary to prevent ER-negative breast cancers if the goal of breast cancer chemoprevention is to be realistically achieved. Microsc. Res. Tech. 59:3,11, 2002. © 2002 Wiley-Liss, Inc. [source] Genome-enabled development of DNA markers for ecology, evolution and conservationMOLECULAR ECOLOGY, Issue 11 2010ROBERT C. THOMSON Abstract Molecular markers have become a fundamental piece of modern biology's toolkit. In the last decade, new genomic resources from model organisms and advances in DNA sequencing technology have altered the way that these tools are developed, alleviating the marker limitation that researchers previously faced and opening new areas of research for studies of non-model organisms. This availability of markers is directly responsible for advances in several areas of research, including fine-scaled estimation of population structure and demography, the inference of species phylogenies, and the examination of detailed selective pressures in non-model organisms. This review summarizes methods for the development of large numbers of DNA markers in non-model organisms, the challenges encountered when utilizing different methods, and new research applications resulting from these advances. [source] Diversification within glacial refugia: tempo and mode of evolution of the polytypic fish Barbus sclateriMOLECULAR ECOLOGY, Issue 15 2009HUGO F. GANTE Abstract A diversity of evolutionary processes can be responsible for generating and maintaining biodiversity. Molecular markers were used to investigate the influence of Plio-Pleistocene climatic oscillations on the evolutionary history of taxa restricted to the freshwaters of a classical glacial refugium. Population genetic, phylogenetic and phylogeographical methods allowed the inference of temporal dynamics of cladogenesis and processes shaping present-day genetic constitution of Barbus sclateri, a polytypic taxon found in several independent river drainages in southern Iberian Peninsula. Results from different analyses consistently indicate several range expansions, high levels of allopatric fragmentation, and admixture following secondary contacts throughout its evolutionary history. Using a Bayesian demographical coalescent model on mitochondrial DNA sequences calibrated with fossil evidence, all cladogenetic events within B. sclateri are inferred to have occurred during the Pleistocene and were probably driven by environmental factors. Our results suggest that glaciation cycles did not inhibit cladogenesis and probably interacted with regional geomorphology to promote diversification. We conclude that this polytypic taxon is a species complex that recently diversified in allopatry, and that Pleistocene glaciation,deglaciation cycles probably contributed to the generation of biological diversity in a classical glacial refugium with high endemicity. [source] Spatial population structure in a patchily distributed beetleMOLECULAR ECOLOGY, Issue 4 2001Tomas Roslin Abstract The dynamics and evolution of populations will critically depend on their spatial structure. Hence, a recent emphasis on one particular type of structure , the metapopulation concept of Levins , can only be justified by empirical assessment of spatial population structures in a wide range of organisms. This paper focuses on Aphodius fossor, a dung beetle specialized on cattle pastures. An agricultural database was used to locate nearly 50 000 local populations of A. fossor in Finland. Several independent methods were then used to quantify key processes in this vast population system. Allozyme markers and mitochondrial DNA (mtDNA) sequences were applied to examine genetic differentiation of local populations and to derive indirect estimates of gene flow. These estimates were compared to values expected on the basis of direct observations of dispersing individuals and assessments of local effective population size. Molecular markers revealed striking genetic homogeneity in A. fossor. Differentiation was only evident in mtDNA haplotype frequencies between the isolated Åland islands and the Finnish mainland. Thus, indirect estimates of gene flow agreed with direct observations that local effective population size in A. fossor is large (hundreds of individuals), and that in each generation, a substantial fraction (approximately one-fifth) of the individuals move between populations. Large local population size, extreme haplotype diversity and a high regional incidence of A. fossor all testify against recurrent population turnover. Taken together, these results provide strong evidence that the whole mainland population of A. fossor is better described as one large ,patchy population', with substantial movement between relatively persistent local populations, than as a classical metapopulation. [source] Polymorphic microsatellite markers for paternity assessment in southern calamari Sepioteuthis australis (Cephalopoda: Loliginidae)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003L. M. Van Camp Abstract Recent decades have seen the fast growth of cephalopod fisheries but their management is compromised by the critical gaps in our knowledge of cephalopod life histories. Molecular markers are invaluable tools for studying the evolutionary significance and management implications of variation in mating systems. We have developed seven polymorphic microsatellite loci for mating system analysis in the southern calamari Sepioteuthis australis Quoy & Gaimard 1833 using magnetic enrichment and colony hybridization techniques. Observed heterozygosities range from 32% to 100% and will have sufficient power to examine the relative success of alternate mating strategies in S. australis. [source] Standard and Swedish variant types of the hybrid alder Phytophthora attacking alder in Hungary,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 4 2003Zoltán Á Nagy Abstract A new Phytophthora disease of common alder (Alnus glutinosa) similar to that previously reported in several countries in Europe has been observed in Hungary. Based on these earlier studies, the alder Phytophthora was considered likely to be a hybrid between P cambivora and a P fragariae -like species: across Europe a range of new alder Phytophthora is spreading that comprise a range of heteroploid hybrids including a ,standard' hybrid type and several other hybrid types termed ,variants'. Phenotypic and molecular features of the pathogen in Hungary were characterised and compared with isolates from elsewhere. The morphologies of five isolates from one region (Hévíz) resembled the common, ,standard' type, whereas the three isolates from another region (Hanság) exhibited traits similar to those of one of the ,variant' types, ie the Swedish ,variant'. Molecular markers of these two groups of Hungarian isolates also represented a good fit to those of the standard type and the Swedish variant, respectively. Isozyme patterns and profiles of restriction fragments of the entire internal transcribed spacer (ITS) region or mitochondrial DNAs and of RAPD-PCR products did not differ within a group, but distinct polymorphisms were exhibited between the two groups of isolates. Southern analysis of random amplified polymorphic DNA (RAPD) revealed the homologous nature of co-migrating bands of P cambivora and the isolates of alder Phytophthora. Furthermore, restriction fragment profiles of the ITS region of ribosomal DNAs and the mtDNAs were consistent with reported biparental origin of alder Phytophthora. The hybrid status of these continuously evolving pathogens raises many issues and challenges concerning efficient control measures. © 2003 Society of Chemical Industry [source] Molecular markers of circulating melanoma cellsPIGMENT CELL & MELANOMA RESEARCH, Issue 2 2007Sandra Medic Summary Of all skin cancers, cutaneous malignant melanoma (CMM) is the most aggressive and the life expectancy of patients with lymphatic or systemic metastases is dramatically reduced. Understandably therefore, scientists and clinicians have focused on improving diagnostic and prognostic techniques. Of these, perhaps the most promising are multimarker real-time RT-PCR and microarray for detection of circulating CMM cells in peripheral blood. While the optimal set of markers is still to be identified that can accurately assess disease severity and progression at all clinical stages of the disease, recent progress has been dramatic. Here we provide an exhaustive review of recent studies in which a variety of markers are assessed. Moreover, the efficacy of the markers relative to clinical stage is discussed in light of experimental findings. From these studies, it is apparent that researchers are now much closer to defining a set of markers of circulating cells that can be utilized in routine diagnostic tests. [source] Molecular markers for Ve1 and Ve2 Verticillium resistance genes from Italian tomato germplasmPLANT BREEDING, Issue 6 2007N. Acciarri Abstract The so-called Rosa (= pink) tomatoes, which are typically grown in the Southern Italian area, are characterized by the pink colour of the fruit, due to the gene y, colourless fruit skin. In a preliminary survey, it was found that among these Rosa tomatoes there were some ,Rosa di Sorrento' local landraces showing resistance to Verticillium wilt (race 1). In tomato, resistance to race 1 of V. dahliae and V. albo-atrum is conferred by two strictly associated genes, Ve1 and Ve2, which independently confer resistance to the same pathogen. The development of two new markers for Ve1 and Ve2, based respectively on selective allele-specific PCR amplification and on a PCR amplification followed by enzymatic restriction, is reported. These two markers allow the identification of both allelic forms at the Ve loci and they are of potential interest for use in marker-assisted selection. Furthermore, ,Rosa di Sorrento'-resistant lines have the same resistance alleles as those found in the Ve -resistant cultivars. [source] Molecular markers linked to the Aegilops variabilis -derived root-knot nematode resistance gene Rkn-mn1 in wheatPLANT BREEDING, Issue 2 2000D. Barloy Abstract Aegilops variabilis no. 1 is the only known source of resistance to the root-knot nematode Meloidogyne naasi in wheat. Previous studies showed that a dominant gene, Rkn-mn1, was transferred to a wheat translocation line from the donor Ae. variabilis. Random amplified polymorphic DNA (RAPD) analysis was performed on the wheat cultivar ,Lutin', on Ae. variabilis, on a resistant disomic addition line and on a resistant translocation line. For genetic and molecular studies, 114-117 BC3F2 plants and F3 -derived families were tested. Five DNA and one isozyme marker were linked to Rkn-mn1. Three RAPD markers flanking the Rkn-mn1 locus were mapped at 0 cM (OpY16 -1065), 0.8 cM (OpB12 -1320) and 1.7 cM (OpN20 -1235), respectively. Since the Rkn-mn1 gene remained effective, its introduction into different wheat cultivars by marker-assisted selection is suggested. [source] Prognostic Significance of Oncogenic Markers in Ductal Carcinoma In Situ of the Breast: A Clinicopathologic StudyTHE BREAST JOURNAL, Issue 2 2009Sevilay Altintas MD Abstract:, Ductal carcinoma in situ (DCIS) is a heterogeneous malignant condition of the breast with an excellent prognosis. Until recently mastectomy was the standard treatment. As the results of the National Surgical Adjuvant Breast and Bowel Project-17 trial and the introduction of the Van Nuys Prognostic Index (VNPI) less radical therapies are used. Objectives are to identify clinicopathologic and biologic factors that may predict outcome. Cases of DCIS diagnosed in two Belgian University Centers were included. Paraffin-embedded material and Hematoxylin and Eosin stained slides of DCIS cases were reviewed and tumor size, margin width, nuclear grade, and comedo necrosis were assessed. Molecular markers (estrogen receptor, progesterone receptor, HER1-4, Ki67, and c-myc) were assayed immunohistochemically. Applied treatment strategies were correlated with the prospective use of the VNPI score. Kaplan,Meier survival plots were generated with log-rank significance and multiple regression analysis was carried out using Cox proportional hazards regression analysis; 159 patients were included with a median age of 54 years (range 29,78); 141 had DCIS and 18 DCIS with microinvasion. The median time of follow-up was 54 months (range 5,253). Twenty-three patients developed a recurrence (14.5%). The median time to recurrence was 46 months (range 5,253). Before the introduction of the VNPI, 37.5% of the DCIS patients showed a recurrence while thereafter 6.7% recurred (p < 0.005). Two recurrences occurred in the VNPI group I (7.1%); seven in the VNPI group II (8.5%) (median time to recurrence 66.3 months) and 14 in the VNPI group III (28.5%) (median time to recurrence 40.2 months) (disease-free survival [DFS]: p < 0.05). A Cox proportional hazards regression analysis indicated that tumor size, margin width, pathologic class, and age were independent predictors of recurrence, but none of the studied molecular markers showed this. Overexpression of HER4 in the presence of HER3 was found to be associated with a better DFS (p < 0.05). This study confirms the value of the VNPI score and questions the benefit of an aggressive approach in the low-risk DCIS lesions. Independent predictors for recurrence included size, margin width, pathologic class, and age, but none of the molecular markers were part of it. Overexpression of HER4 in the presence of HER3 was associated with a better DFS. [source] Phylogeny and phylogeography of squirrel monkeys (genus Saimiri) based on cytochrome b genetic analysisAMERICAN JOURNAL OF PRIMATOLOGY, Issue 3 2010Anne Lavergne Abstract Squirrel monkeys (genus Saimiri) are distributed over a wide area encompassing the Amazon Basin: French Guiana, Suriname, and Guyana, together with Western Panama and Western Costa Rica. The genus Saimiri includes a complex of species and subspecies displaying considerable morphological variation. Taxonomic and systematic studies have identified, in this genus, one to seven species comprising up to 16 subspecies. The phylogenetic relationships between these taxa are poorly understood. Molecular markers have yielded a consistent framework for the systematics of Central and South American Saimiri, identifying four distinct clades: S. oerstedii, S. sciureus, S. boliviensis, and S. ustus. Here, we reconsider the phylogenetic and biogeographic history of Saimiri on the basis of mitochondrial (mtDNA) sequence data, focusing mostly on individuals originating from the Amazon Basin. We studied 32 monkeys with well-defined geographic origins and inferred the phylogenetic relationships between them on the basis of full-length cytochrome b gene nucleotide sequences. The high level of gene diversity observed (0.966) is consistent with the high level of behavioral and morphological variation observed across the geographic range of the genus: 20 mtDNA haplotypes were identified with a maximum divergence of 4.81% between S. b. boliviensis and S. ustus. In addition to confirming the existence of the four clades previously identified on the basis of molecular characters, we suggest several new lineages, including S. s. macrodon, S. s. albigena, S. s. cassiquiarensis, and S. s. collinsi. We also propose new patterns of dispersion and diversification for the genus Saimiri, and discuss the contribution of certain rivers and forest refuges to its structuring. Am. J. Primatol. 72:242,253, 2010. © 2009 Wiley-Liss, Inc. [source] Molecular markers for assessing community diversity of coastal ciliatesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005MARY DOHERTY Biogeography of microbial eukaryotes is widely debated. While some claim that all microbial organisms have a cosmopolitan distribution, other data suggest evidence of endemism. To assess these hypotheses for the distribution of ciliates in the orders Choreotrichia and Oligotrichia, coastal community samples were taken from Long Island Sound. We are obtaining sequences of SSU rRNA, ITS rRNA, and mitochondrial genes to use as molecular markers for assessing gene flow across time and space. These data will serve as a basis for continued study of phylogeographic distribution of Choreotrichia and Oligotrichia. [source] DNA markers for estimation of inbreeding depression and heterosis in the guppy Poecilia reticulataAQUACULTURE RESEARCH, Issue 11 2003Takahito Shikano Abstract Molecular markers have significant potential for use in precise breeding programmes in aquaculture. This paper reviews the use of DNA markers to estimate inbreeding depression and heterosis in the guppy Poecilia reticulata. Full-sib matings revealed that inbreeding causes declines in survival and salinity tolerance, but not in undwarfism, growth and high water temperature tolerance, indicating the effects of inbreeding differ among fitness-related traits. Salinity tolerance was used to quantify the level of inbreeding depression and heterosis because the trait is strongly sensitive to inbreeding and shows a linear decrease with an increase in inbreeding coefficient. A positive correlation was observed between heterozygosity at microsatellite loci and salinity tolerance among 17 guppy populations. This indicates that heterozygosity estimated from microsatellites is a useful indicator for the estimation of inbreeding depression, suggesting that overall heterozygosity is important for fitness-related traits that show inbreeding depression. Use of DNA markers to estimate the amount of heterosis in various strain combinations was examined using diallele and reciprocal crosses among four domestic strains. The amount of heterosis differed among the strain combinations and correlated with Nei's genetic distance measured by microsatellites and also by dissimilarity using random amplified polymorphic DNA (RAPD) analysis. This indicates that microsatellite and RAPD markers are useful for estimating the amount of heterosis in various strain combinations, further suggesting that the amount of heterosis depends on the genetic differences between the strains. The present study showed that DNA markers are useful tools for estimating inbreeding depression and heterosis in guppy breeding. [source] Molecular markers and mortality in prostate cancerBJU INTERNATIONAL, Issue 6 2007John Concato OBJECTIVE To evaluate prognosis in prostate cancer by assessing the independent effect of selected molecular factors (e.g. markers of cell-cycle regulation), in addition to the effect of traditional clinical factors (e.g. anatomical stage, histological grade), in predicting long-term mortality among men newly diagnosed with prostate cancer. PATIENTS AND METHODS In a community-based population of 64 545 USA veterans aged ,,50 years and receiving ambulatory care during 1989,90 at nine Veterans Affairs (VA) medical centres in New England, 1274 had incident prostate cancer during 1991,95. We obtained the medical records and diagnostic tissue for these men, and then extracted demographic data and clinical information, and conducted immunohistochemical assays of molecular markers in biopsy tissue, as potential prognostic factors. In this interim analysis, data on 250 patients were analysed; the main outcome was overall mortality to 31 December 2003, providing 8,13 years of follow-up. RESULTS In 228 (91%) patients with available medical record and laboratory data, the median age was 72 years and the median prostate-specific antigen level was 10.4 ng/mL. In adjusted (multivariate) analyses that included traditional prognostic factors, bcl-2 staining (hazard ratio 2.14, 95% confidence interval 1.27,3.58, P = 0.004) and high microvessel density (1.76, 1.19,2.60; P = 0.005) had an independent effect on the outcome. CONCLUSIONS Bcl-2 and microvessel density are independent predictors of subsequent death among men with prostate cancer and might have a clinical role in assisting in deciding on treatment. [source] Molecular markers of outcome after radiotherapy in patients with prostate carcinomaCANCER, Issue 7 2003Ki-6, bcl-, bcl-x Abstract BACKGROUND Abnormal expression of key proteins of the apoptotic pathway has been associated with poor prognosis, although there have been few studies of these correlations in patients with prostate carcinoma who are treated with radiotherapy. The current study examined the association between expression levels of Ki-67, bcl-2, bax, and bcl-x in pretreatment biopsy specimens and patient outcome after definitive radiotherapy alone. METHODS Archival pretreatment prostate biopsy tumor tissue was retrieved from 106 patients with Stage T1,T3 prostate carcinoma who were treated at the University of Texas M. D. Anderson Cancer Center with external beam radiotherapy between 1987 and 1993. Expression levels of Ki-67 (MIB-1 staining; n = 106 patients), bcl-2 (n = 77 patients), bax (n = 70 patients), and bcl-x (both long and short splice variants; n = 72 patients) were determined by immunohistochemical staining. The Ki-67 labeling index (Ki67-LI) was available for all patients and was derived from the percentage of Ki-67 positive cells. Biochemical failure after radiotherapy was defined as three consecutive rises in prostate specific antigen level on follow-up. The median follow-up was 62 months. RESULTS High Ki67-LI (> 3.5%) expression was observed in 33% of patients, overexpression of bcl-2 was observed in 16% of patients, altered bax expression was observed in 23% of patients, and altered bcl-x expression was observed in 53% of patients. There was no correlation found between the biomarkers. Kaplan,Meier survival estimates of freedom from biochemical failure (bNED) and the log-rank test revealed significantly lower rates in association with high Ki67-LI, positive bcl-2, and altered bax staining. No correlation was observed between bcl-x staining and bNED. Cox proportional hazards multivariate analysis confirmed that bcl-2 and bax were independent of pretreatment PSA level, Gleason score, disease stage, and Ki67-LI in predicting bNED. CONCLUSIONS Abnormalities in the expression levels of bcl-2 and bax were associated with increased failure after patients were treated for prostate carcinoma with external beam radiotherapy. These biomarkers appeared to be useful in categorizing patient risk further, beyond Ki-67 staining and conventional clinical prognostic factors. Cancer 2003;97:1630,8. © 2003 American Cancer Society. DOI 10.1002/cncr.11230 [source] Molecular markers associated with lymph node metastasis in pancreatic ductal adenocarcinoma by genome-wide expression profilingCANCER SCIENCE, Issue 1 2010Seiko Hirono Lymph node metastasis (LNM) is the most important prognostic factor in patients undergoing surgical resection of pancreatic ductal adenocarcinoma (PDAC). In this study, we aimed to identify molecular markers associated with LNM in PDAC using genome-wide expression profiling. In this study, laser microdissection and genome-wide transcriptional profiling were used to identify genes that were differentially expressed between PDAC cells with and without LNM obtained from 20 patients with PDAC. Immunohistochemical staining was used to confirm the clinical significance of these markers in an additional validation set of 43 patients. In the results, microarray profiling identified 46 genes that were differently expressed between PDAC with and without LNM with certain significance. Four of these biomarkers were validated by immunohistochemical staining for association with LNM in PDAC in an additional validation set of patients. In 63 patients with PDAC, significant LNM predictors in PDAC elucidated from multivariate analysis were low expression of activating enhancer binding protein 2 (AP2,) (P = 0.012) and high expression of mucin 17 (MUC17) (P = 0.0192). Furthermore, multivariate analysis revealed that AP2, -low expression and MUC17 -high expression are independent prognostic factors for poor overall survival (P = 0.0012, 0.0001, respectively). In conclusion, AP2, and MUC17 were independent markers associated with LNM of PDAC. These two markers were also associated with survival in patients with resected PDAC. We demonstrate that AP2, and MUC17 may serve as potential prognostic molecular markers for LNM in patients with PDAC. (Cancer Sci 2009) [source] Diagnosis of Nonmelanoma Skin Cancer/Keratinocyte Carcinoma: A Review of Diagnostic Accuracy of Nonmelanoma Skin Cancer Diagnostic Tests and TechnologiesDERMATOLOGIC SURGERY, Issue 10 2007METTE MOGENSEN MD BACKGROUND Nonmelanoma skin cancer (NMSC) is the most prevalent cancer in the light-skinned population. Noninvasive treatment is increasingly used for NMSC patients with superficial lesions, making the development of noninvasive diagnostic technologies highly relevant. OBJECTIVE The scope of this review is to present data on the current state-of-the-art diagnostic methods for keratinocyte carcinoma: basal cell carcinoma, squamous cell carcinoma, and actinic keratosis. METHODS AND MATERIALS MEDLINE, BIOSIS, and EMBASE searches on NMSC and physical and clinical examination, biopsy, molecular marker, ultrasonography, Doppler, optical coherence tomography, dermoscopy, spectroscopy, fluorescence imaging, confocal microscopy, positron emission tomography, computed tomography, magnetic resonance imaging, terahertz imaging, electrical impedance and sensitivity, specificity, and diagnostic accuracy. RESULTS State-of-the-art diagnostic research has been limited in this field, but encouraging results from the reviewed diagnostic trials have suggested a high diagnostic accuracy for many of the technologies. Most of the studies, however, were pilot or small studies and the results would need to be validated in larger trials. CONCLUSIONS Some of these new imaging technologies have the capability of providing new, three-dimensional in vivo, in situ understanding of NMSC development over time. Some of the new technologies described here have the potential to make it from the bench to the clinic. [source] Analysis of Meox - 2 mutant mice reveals a novel postfusion-based cleft palateDEVELOPMENTAL DYNAMICS, Issue 2 2006Jiu-Zhen Jin Abstract Cleft palate represents a common human congential disease involving defects in the development of the secondary palate. Major steps in mammalian palatogenesis include vertical growth, elevation, and fusion of the palate shelves. Our current study with the homeobox gene Meox - 2 during mouse secondary palate development reveals a novel postfusion-based mechanism for cleft palate. Meox - 1 and Meox - 2 are two functionally related homeobox genes playing important roles in somitogenesis and limb muscle differentiation. We found that the expression of Meox - 2, not Meox - 1, marks the specification of early mouse palatal mesenchymal cells in the maxillary processes at embryonic day 11.5 (E11.5). From E12.5 to E15.5, the expression of Meox - 2 occupies only the posterior part of the palate, providing an early molecular marker for the anterior,posterior polarity in mouse secondary palate formation. A total of 35.3% of Meox - 2,/, (n = 17) and 25.5% of Meox - 2+/, (n = 55) mouse embryos display a cleft palate phenotype at E15.5, indicating that the reduction of Meox - 2 function is associated with susceptibility to cleft palate. Unlike previously reported clefts, none of the clefts found in Meox - 2 mutants contain any epithelial sheets in the medial edge areas, and detailed examination revealed that the clefts resulted from the breakdown of newly fused palates. This article is the first report of a gene required to maintain adherence of the palatal shelves after fusion. Developmental Dynamics 235:539,546, 2006. © 2005 Wiley-Liss, Inc. [source] ,-Methylacyl-CoA racemase (AMACR) in fine-needle aspiration specimens of prostate lesionsDIAGNOSTIC CYTOPATHOLOGY, Issue 11 2009Gordana Kai, M.D. Abstract The elevated expression of P504S gene and its product ,-methylacyl-CoA racemase (AMACR) can serve as a molecular marker for prostate cancer. The goal of this study is to investigate P504S/AMACR expression in fine-needle aspiration smears and correlate it with cytological diagnosis. Immunocytochemistry was performed in 35 patients with morphological diagnosis of prostate carcinoma (n = 16), atypia (n = 15), and benign hyperplasia (n = 4). Among 16 malignant cases there were two low-grade, eight intermediate, and six high-grade prostate carcinomas. Cytoplasmic positivity is analyzed qualitatively as predominantly diffuse or focal and quantitatively as <5%, 5,50%, and >50% of cells. Benign cases showed no P504S/AMACR expression. Positive staining was recorded in 75% of malignant cases, but in the majority of them it was weak and focal or diffuse and in a small amount of cells. The most intensive staining was seen in low-grade carcinomas and some atypical cases. This observation indicates a correlation between P504S/AMACR expression and differentiation of cells. P504S/AMACR staining might be of great value in cytodiagnosis of prostate lesions as well as an example of the characterization of cells at the molecular level using fresh tissue obtained by fine-needle aspiration. Diagn. Cytopathol. 2009. © 2009 Wiley-Liss, Inc. [source] |