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Maccoun Robert J RJ Goldman School of Public Policy, University of California at Berkeley, Berkeley, CA 94720-7320. maccoun@berkeley.edu - - 2014
I compare the collective behavior map proposed by Bentley et al. ("BOB" for short) with a similar "balance of pressures" (BOP) map proposed by MacCoun (2012). The BOB and BOP maps have important points of convergence, but also some differences. The comparison suggests that they are analogous to different map ...
Cirić Ljubomir L Faculty of Mathematics Engineering, Kraljice Marije 16, 11 000 Belgrade, - - 2014
We introduce the concept of triangular α c -admissible mappings (pair of mappings) with respect to η c nonself-mappings and establish the existence of PPF dependent fixed (coincidence) point theorems for contraction mappings involving triangular α c -admissible mappings (pair of mappings) with respect to η c nonself-mappings in Razumikhin ...
Ptaszek Leon M - - 2012
PURPOSE: Conventional electroanatomical mapping systems employ roving catheters with one or a small number of electrodes. Maps acquired using these systems usually contain a small number of points and take a long time to acquire. Use of a multielectrode catheter could facilitate rapid acquisition of higher-resolution maps through simultaneous collection ...
Taniguchi Fumiya - - 2012
A few linkage maps of tea have been constructed using pseudo-testcross theory based on dominant marker systems. However, dominant markers are not suitable as landmark markers across a wide range of materials. Therefore, we developed co-dominant SSR markers from genomic DNA and ESTs and constructed a reference map using these ...
Scott Richard T RT - - 2012
To demonstrate that a euploid embryo derived from an oocyte with reciprocal aneuploid polar bodies is capable of producing a chromosomally normal child. A case report of maternal MI error compensation where single nucleotide polymorphism (SNP) microarray based comprehensive chromosome screening (CCS) was performed on the 1st and 2nd polar ...
Loukovitis D - - 2012
Gilthead sea bream (Sparus aurata L.) is an important marine fish in Mediterranean aquaculture. Sex determination by age and/or body weight is a critical life-history trait, the genetic basis for which is largely unknown in this sequential hermaphrodite species. Herein, we performed a partial genome scan to map quantitative trait ...
Sciurano Roberta B - - 2012
Three xenarthrans species Chaetophractus villosus, Chaetophractus vellerosus, and Zaedyus pichiy have been used for the analysis of the structure, behavior, and immunochemical features of the XY body during pachytene. In all these species, the sex chromosomes form an XY body easily identifiable in thin sections by the special and regular ...
Wang S Z - - 2012
Body weight and abdominal fat traits in meat-type chickens are complex and economically important factors. Our objective was to identify quantitative trait loci (QTL) responsible for body weight and abdominal fat traits in broiler chickens. The Northeast Agricultural University Resource Population (NEAURP) is a cross between broiler sires and Baier ...
Blenda Anna - - 2012
A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be ...
Fujino Kenji - - 2011
In plant breeding with intensive selection, the haplotype patterns in the targeted chromosomal regions may become monogenic among local populations with the most desirable combination of loci. This study demonstrated that the chromosomal region surrounding qLTG3-1 was under selection during rice breeding programs in a local region of Japan, Hokkaido. ...
Okumura Akihisa - - 2011
There are only two reports on epileptic patients associated with microduplication of 2q. We found a de novo duplication of chromosome 2q24.2q24.3 in another infant with neonatal epilepsy. The patient had refractory focal seizures since the third day of life. Her seizures were refractory against phenobarbital and levetiracetam, but were ...
Pockwinse Shirwin M SM Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, - - 2011
The nuclear matrix bound transcription factor RUNX2 is a lineage-specific developmental regulator that is linked to cancer. We have previously shown that RUNX2 controls transcription of both RNA polymerase II genes and RNA polymerase I-dependent ribosomal RNA genes. RUNX2 is epigenetically retained through mitosis on both classes of target genes ...
Cole J B - - 2011
Limits to selection and Mendelian sampling (MS) terms can be calculated using haplotypes by summing the individual additive effects on each chromosome. Haplotypes were imputed for 43 382 single-nucleotide polymorphisms (SNP) in 1455 Brown Swiss, 40 351 Holstein and 4064 Jersey bulls and cows using the Fortran program findhap.f90, which combines population ...
Finan Kieran - - 2011
Four specific forces (H-bonds, van der Waals forces, hydrophobic and charge interactions) shape the structure of proteins, and many biologists assume they will determine the shape of all structures in the cell. However, as the mass and contour length of a human chromosome are ~7 orders of magnitude larger than ...
Chang Ti-Cheng - - 2011
The OFD1 (oral-facial-digital, type 1) gene is implicated in several developmental disorders in humans. The X-linked OFD1 (OFD1X) is conserved in Eutheria. Knowledge about the Y-linked paralog (OFD1Y) is limited. In this study, we identified an OFD1Y on the bovine Y chromosome, which is expressed differentially from the bovine OFD1X. ...
Heride Claire - - 2010
The organization of chromosomes is important for various biological processes and is involved in the formation of rearrangements often observed in cancer. In mammals, chromosomes are organized in territories that are radially positioned in the nucleus. However, it remains unclear whether chromosomes are organized relative to each other. Here, we ...
Naughton Catherine - - 2010
Using a genetic model, we present a high-resolution chromatin fiber analysis of transcriptionally active (Xa) and inactive (Xi) X chromosomes packaged into euchromatin and facultative heterochromatin. Our results show that gene promoters have an open chromatin structure that is enhanced upon transcriptional activation but the Xa and the Xi have ...
Botta Marco - - 2010
A prime goal in systems biology is the comprehensive use of existing high-throughput genomic datasets to gain a better understanding of chromatin organization and genome function. In this report, we use chromatin immunoprecipitation (ChIP) data that map protein-binding sites on the genome, and Hi-C data that map interactions between DNA ...
Ohta Shinya S Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, - - 2011
Mitotic chromosomes are the iconic structures into which the genome is packaged to ensure its accurate segregation during mitosis. Although they have appeared on countless journal cover illustrations, there remains no consensus on how the chromatin fiber is packaged during mitosis. In fact, work in recent years has both added ...
Pawlowski Wojciech P - - 2010
The past few years have brought renewed interest in understanding the dynamics of chromosomes in interphase cells as well as during cell division, particularly meiosis. This research has been fueled by new imaging methods, particularly three-dimensional, high-resolution, and live microscopy. Major contributors are also new genetic tools that allow elucidation ...
Wood Jason G JG Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, - - 2010
Chromatin structure affects the accessibility of DNA to transcription, repair, and replication. Changes in chromatin structure occur during development, but less is known about changes during aging. We examined the state of chromatin structure and its effect on gene expression during aging in Drosophila at the whole genome and cellular ...
van Steensel Bas - - 2010
The spatial organization of chromosomes inside the cell nucleus is still poorly understood. This organization is guided by intra- and interchromosomal contacts and by interactions of specific chromosomal loci with relatively fixed nuclear 'landmarks' such as the nuclear envelope and the nucleolus. Researchers have begun to use new molecular genome-wide ...
Gomez-Godinez Veronica V Beckman Laser Institute, Deparment of Developmental and Cell Biology, University of California Irvine, 1002 Health Sciences Road, Irvine, CA 92612, - - 2010
In this study the femtosecond near-IR and nanosecond green lasers are used to induce alterations in mitotic chromosomes. The subsequent double-strand break responses are studied. We show that both lasers are capable of creating comparable chromosomal alterations and that a phase paling observed within 1-2 s of laser exposure is ...
Hondele Maria - - 2010
Mitosis, nuclear envelope formation, and nucleocytoplasmic transport require chromosomes to identify themselves by enriching Ran-GTP around the chromatin fiber. In a recent Nature report, Makde et al. (2010) describe the structure of the Ran activator RCC1 anchored onto nucleosomes.
van Koningsbruggen Silvana S Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United - - 2010
The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene ...
Guffei Amanda - - 2010
Hodgkin's lymphoma is characterized by the presence of mono-nucleated Hodgkin cells and bi- to multi-nucleated Reed-Sternberg cells. We have recently shown telomere dysfunction and aberrant synchronous/asynchronous cell divisions during the transition of Hodgkin cells to Reed-Sternberg cells.1 To determine whether overall changes in nuclear architecture affect genomic instability during the ...
Sinclair Paul P Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, - - 2010
Interphase chromatin compaction well above the 30-nm fiber is well documented, but the structural motifs underlying this level of chromatin folding remain unknown. Taking a reductionist approach, we analyzed in mouse embryonic stem (ES) cells and ES-derived fibroblasts and erythroblasts the folding of 10-160-megabase pair engineered chromosome regions consisting of ...
Ikeda Kensuke - - 2010
The morphology of chromosomes (certain rod-shaped structures) is highly reproducible despite the high condensation of chromatin fibers (∼1 mm) into chromosomes (∼1 μm). However, the mechanism underlying the condensation of chromatin fibers into chromosomes is unclear. We assume that investigation of the internal structure of chromosomes will aid in elucidating ...
Grimaud Charlotte - - 2010
Does the three-dimensional (3D) conformation of interphase chromosomes merely reflect their function or does it actively contribute to gene regulation? The analysis of sex chromosomes that are subject to chromosome-wide dosage compensation processes promises new insight into this question. Chromosome conformations are dynamic and largely determined by association of distant ...
Sáez-Vásquez Julio - - 2010
Recent progress in understanding higher-order chromatin organization in the nucleus has been considerable. From single gene to chromosome territory, realistic biophysical models can now accurately predict some of the structural feature of cell nuclei. Despite growing evidence of a deterministic nuclear organization, the physiological consequence of spatial genome organization is ...
Misteli Tom - - 2010
Genomes are organized into complex higher-order structures by folding of the DNA into chromatin fibers, chromosome domains, and ultimately chromosomes. The higher-order organization of genomes is functionally important for gene regulation and control of gene expression programs. Defects in how chromatin is globally organized are relevant for physiological and pathological ...
Naumova Natalia N Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, - - 2010
Genomes exist in vivo as complex physical structures, and their functional output (i.e. the gene expression profile of a cell) is related to their spatial organization inside the nucleus as well as to local chromatin status. Chromatin modifications and chromosome conformation are distinct in different tissues and cell types, which ...
Rosa Angelo - - 2010
Fluorescence in-situ hybridization (FISH) and chromosome conformation capture (3C) are two powerful techniques for investigating the three-dimensional organization of the genome in interphase nuclei. The use of these techniques provides complementary information on average spatial distances (FISH) and contact probabilities (3C) for specific genomic sites. To infer the structure of ...
Delgado M - - 2010
Biologists have been fascinated for more than 2 centuries about how the nucleus in eukaryotes is organised. Certain of the component parts are well known, but the overall picture is blurred and often confusing. Small genome species have chromosomes in their interphase nuclei disposed in diffuse chromosome territories, without any ...
Laster Kyle - - 2010
The eukaryotic nucleus is functionally organized. Gene loci, for example, often reveal altered localization patterns according to their developmental regulation. Whole chromosomes also demonstrate non-random nuclear positions, correlated with inherent characteristics such as gene density or size. Given that hundreds to thousands of genes are coordinately regulated in any given ...
Castro-Hartmann Pablo - - 2010
In previous studies with partially denatured metaphase chromosomes, we detected platelike structures instead of the chromatin fibers currently considered in different structural models for chromosomes. Here we have observed that dilution of compact metaphase chromosomes with hyposmotic solutions can transform whole chromatids into extended plates formed by many layers. Since ...
Duan Zhijun - - 2010
Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or 'factories' ...
Chow Man H - - 2010
DNA can self-assemble in vitro into several liquid crystalline phases at high concentrations. The largest known genomes are encoded by the cholesteric liquid crystalline chromosomes (LCCs) of the dinoflagellates, a diverse group of protists related to the malarial parasites. Very little is known about how the liquid crystalline packaging strategy ...
O'Sullivan Justin M - - 2010
Biology is essentially the study of networks of interactions within or between organisms. The study of chromosomal interactions, while still in its infancy, is providing insights that enable us to study genome biology as a network of inter-linked systems and not simply as the isolated loci we were previously restricted ...
K?hler Alwin - - 2010
Nuclear pore complexes (NPCs) composed of approximately 30 individual nucleoporins form huge macromolecular assemblies in the nuclear envelope, through which bidirectional cargo movement between the nucleus and cytoplasm occurs. Beyond their transport function, NPCs can serve as docking sites for chromatin and thereby contribute to the organization of the overall ...
Woodcock Christopher L - - 2010
The primary role of the nucleus as an information storage, retrieval, and replication site requires the physical organization and compaction of meters of DNA. Although it has been clear for many years that nucleosomes constitute the first level of chromatin compaction, this contributes a relatively small fraction of the condensation ...
Drennan K J - - 2010
Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy. The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood. The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays ...
Illner Doris - - 2010
Extensive changes of higher order chromatin arrangements can be observed during prometaphase, terminal cell differentiation and cellular senescence. Experimental systems where major reorganization of nuclear architecture can be induced under defined conditions, may help to better understand the functional implications of such changes. Here, we report on profound chromatin reorganization ...
Schoenfelder Stefan S The Babraham Institute, Cambridge, - - 2010
Transcription in the eukaryotic nucleus has long been thought of as conforming to a model in which RNA polymerase complexes are recruited to and track along isolated templates. However, a more dynamic role for chromatin in transcriptional regulation is materializing: enhancer elements interact with promoters forming loops that often bridge ...
Iannuccelli E - - 2010
Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing ...
Therizols Pierre - - 2010
Physical interactions between distinct chromosomal genomic loci are important for genomic functions including recombination and gene expression, but the mechanisms by which these interactions occur remain obscure. Using telomeric association as a model system, we analyzed here the in vivo organization of chromosome ends of haploid yeast cells during interphase. ...
Joshi Ricky S - - 2010
How DNA helical tension is constrained along the linear chromosomes of eukaryotic cells is poorly understood. In this study, we induced the accumulation of DNA (+) helical tension in Saccharomyces cerevisiae cells and examined how DNA transcription was affected along yeast chromosomes. The results revealed that, whereas the overwinding of ...
Gall Joseph G JG Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA. - - 2010
One can manually isolate the giant oocyte nucleus or germinal vesicle (GV) of Xenopus from a living oocyte with nothing more complicated than jewelers' forceps and a dissecting microscope. Similarly, one can remove the nuclear envelope by hand and allow the lampbrush chromosomes and other nuclear organelles to spread on ...
Stojkovic Branislav - - 2010
In this paper, we study the problem of finding organization patterns of chromosomes inside the cell nucleus from microscopic nucleus images. Emerging evidence from cell biology research suggests that global chromosome organization has a vital role in fundamental cell processes related to gene expression and regulation. To understand how chromosome ...
Solovei Irina - - 2010
Fluorescence in situ hybridization on three-dimensionally preserved nuclei (3D-FISH), in combination with immunocytochemistry and 3D fluorescence microscopy, is a key tool to analyze the functional organization of the interphase nucleus. In the last decade, 3D-FISH on cultured cells has become a routine technique and is now widely used in nuclear ...
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