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3,377 full-text articles. Page 129 of 129.

High-Density Screening Reveals A Different Spectrum Of Genomic Aberrations In Chronic Lymphocytic Leukemia Patients With ‘Stereotyped’ Ighv3-21 And Ighv4-34 B-Cell Receptors, Millaray Marincevic, Nicola Cahill, Rebeqa Gunnarsson, Anders Isaksson, Mahmoud Mansouri, Hanna Göransson, Markus Rasmussen, Mattias Jansson, Fergus Ryan, Karin Karlsson, Hans-Olov Adami, Fred Davi, Jesper Jurlander, Gunnar Juliusson, Kostas Stamatopoulos, Richard Rosenquist 2010 Uppsala Universitet

High-Density Screening Reveals A Different Spectrum Of Genomic Aberrations In Chronic Lymphocytic Leukemia Patients With ‘Stereotyped’ Ighv3-21 And Ighv4-34 B-Cell Receptors, Millaray Marincevic, Nicola Cahill, Rebeqa Gunnarsson, Anders Isaksson, Mahmoud Mansouri, Hanna Göransson, Markus Rasmussen, Mattias Jansson, Fergus Ryan, Karin Karlsson, Hans-Olov Adami, Fred Davi, Jesper Jurlander, Gunnar Juliusson, Kostas Stamatopoulos, Richard Rosenquist

Articles

Background The existence of multiple subsets of chronic lymphocytic leukemia expressing ‘stereotyped’ Bcell receptors implies the involvement of antigen(s) in leukemogenesis. Studies also indicate that ‘stereotypy’ may influence the clinical course of patients with chronic lymphocytic leukemia, for example, in subsets with stereotyped IGHV3-21 and IGHV4-34 B-cell receptors; however, little is known regarding the genomic profile of patients in these subsets. Design and Methods We applied 250K single nucleotide polymorphism-arrays to study copy-number aberrations and copy-number neutral loss-of-heterozygosity in patients with stereotyped IGHV3-21 (subset #2, n=29), stereotyped IGHV4-34 (subset #4, n=17; subset #16, n=8) and non-subset ...


Predicting Success Of Oligomerized Pool Engineering (Open) For Zinc Finger Target Site Sequences, Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth J. Dahlborg, Matthew J. Goodwin, Fengli Fu, Daniel F. Voytas, J Keith Joung, Drena Dobbs 2010 Iowa State University

Predicting Success Of Oligomerized Pool Engineering (Open) For Zinc Finger Target Site Sequences, Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth J. Dahlborg, Matthew J. Goodwin, Fengli Fu, Daniel F. Voytas, J Keith Joung, Drena Dobbs

Genetics, Development and Cell Biology Publications

Background: Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN) is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs) designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable.

Results: Analysis of the base composition of experimentally ...


Zifit (Zinc Finger Targeter): An Updated Zinc Finger Engineering Tool, Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs 2010 Massachusetts General Hospital

Zifit (Zinc Finger Targeter): An Updated Zinc Finger Engineering Tool, Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs

Genetics, Development and Cell Biology Publications

ZiFiT (Zinc Finger Targeter) is a simple and intuitive web-based tool that provides an interface to identify potential binding sites for engineered zinc finger proteins (ZFPs) in user-supplied DNA sequences. In this updated version, ZiFiT identifies potential sites for ZFPs made by both the modular assembly and OPEN engineering methods. In addition, ZiFiT now integrates additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database (ZiFDB) of engineered ZFPs, and direct querying of NCBI BLAST servers for identifying potential off-target sites within a host genome. Taken together, these features facilitate design of ZFPs ...


Choosing A Genome Browser For A Model Organism Database: Surveying The Maize Community, Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence 2010 Iowa State University

Choosing A Genome Browser For A Model Organism Database: Surveying The Maize Community, Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence

Genetics, Development and Cell Biology Publications

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing ...


Potentials 'R'Us Web-Server For Protein Energy Estimations With Coarse-Grained Knowledge-Based Potentials, Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan 2010 Iowa State University

Potentials 'R'Us Web-Server For Protein Energy Estimations With Coarse-Grained Knowledge-Based Potentials, Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Background

Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.

Results

Our new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the ...


Food Consumption Trends And Drivers, John Kearney 2010 Technological University Dublin

Food Consumption Trends And Drivers, John Kearney

Articles

A picture of food consumption (availability) trends and projections to 2050, both globally and for different regions of the world along with the drivers largely responsible for these observed consumption trends are the subject of this review. Throughout the world, major shifts in dietary patterns are occurring, even in the consumption of basic staples towards more diversified diets. Accompanying these changes in food consumption at a global and regional level have been considerable health consequences. Populations in those countries undergoing rapid transition are experiencing nutritional transition. The diverse nature of this transition may be the result of differences in socio ...


Structural Interpretation Of Protein-Protein Interaction Network, Ataur R. Katebi, Andrzej Kloczkowski, Robert L. Jernigan 2010 Iowa State University

Structural Interpretation Of Protein-Protein Interaction Network, Ataur R. Katebi, Andrzej Kloczkowski, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Background

Currently a huge amount of protein-protein interaction data is available from high throughput experimental methods. In a large network of protein-protein interactions, groups of proteins can be identified as functional clusters having related functions where a single protein can occur in multiple clusters. However experimental methods are error-prone and thus the interactions in a functional cluster may include false positives or there may be unreported interactions. Therefore correctly identifying a functional cluster of proteins requires the knowledge of whether any two proteins in a cluster interact, whether an interaction can exclude other interactions, or how strong the affinity between ...


Polyphyly Of The Pikeminnows (Teleostei: Cyprinidae) Inferred Using Mitochondrial Dna Sequences, T. Heath Ogden 2009 Utah Valley University

Polyphyly Of The Pikeminnows (Teleostei: Cyprinidae) Inferred Using Mitochondrial Dna Sequences, T. Heath Ogden

T. Heath Ogden

The phylogenetic relationships of the Colorado pikeminnow Ptychocheilus lucius, northern pikeminnow P. oregonensis, Sacramento pikeminnow P. grandis, Umpqua pikeminnow P. umpquae, and hardhead Mylopharodon conocephalus were examined by using molecular data to investigate monophyly of the genus Ptychocheilus. Phylogenies generated using DNA sequence data from the cytochrome b and 16S ribosomal DNA genes of the mitochondrial genome reveal that Ptychocheilus is a polyphyletic genus and suggest that the taxonomy of the group is in need of further revision. These data yield insights into the evolution of the pikeminnows and help place the significant evolutionary events in context with the geological ...


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