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https://www.readbyqxmd.com/read/27933519/heterogeneous-stock-populations-for-analysis-of-complex-traits
#1
Leah C Solberg Woods, Richard Mott
Heterogeneous Stock (HS) populations allow for fine-resolution genetic mapping of a variety of complex traits. HS mice and rats were created from breeding together eight inbred strains, followed by maintaining the colony in a manner that minimizes inbreeding. After 50 or more generations of breeding, the resulting animals' chromosomes represent a genetic mosaic of the founders' haplotypes, with the average distance between recombination events in the centiMorgan range. This allows for genetic mapping to only a few Mb, a much smaller region than what can be identified using traditional F2 intercross or backcross mapping strategies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914091/toward-clinical-use-of-the-igg-specific-enzymes-ides-and-endos-against-antibody-mediated-diseases
#2
Mattias Collin, Lars Björck
The endoglycosidase EndoS and the protease IdeS from the human pathogen Streptococcus pyogenes are immunomodulating enzymes hydrolyzing human IgG. IdeS cleaves IgG in the lower hinge region, while EndoS hydrolyzes the conserved N-linked glycan in the Fc region. Both enzymes are remarkably specific for human IgG that after hydrolysis loses most of its effector functions, such as binding to leukocytes and complement activation, all contributing to bacterial evasion of adaptive immunity. However, taken out of their infectious context, we and others have shown that IdeS and EndoS can alleviate autoimmune disease in a number of animal models of antibody-mediated disorders...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#3
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914044/the-framework-of-computational-protein-design
#4
Ilan Samish
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein-protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910043/production-and-characterization-of-vectors-based-on-the-cardiotropic-aav-serotype-9
#5
Erik Kohlbrenner, Thomas Weber
Vectors based on adeno-associated virus serotype 9 (AAV9) efficiently transduce cardiomyocytes in both rodents and large animal models upon either systemic or regional vector delivery. In this chapter, we describe the most widely used production and purification method of AAV9. This production approach does not depend on the use of a helpervirus but instead on transient transfection of HEK293T cells with a plasmid containing the recombinant AAV genome and a second plasmid encoding the AAV9 capsid proteins, the AAV Rep proteins and the adenoviral helper functions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910015/chromosome-recognition
#6
Thomas S K Wan, Eleanor K C Hui, Margaret H L Ng
Chromosomal analysis of human cells serves to characterize aberrations of chromosome number and structure. Individual chromosome can be identified precisely by recognition of its morphological characteristics and staining patterns according to specific landmarks, regions, and bands as described in the ideogram. Since the quality of metaphases obtained from malignant cells is generally poor for karyotyping, a practical and accurate chromosome recognition training guide is mandatory for a trainee or newly employed cytogenetic technologist in a cancer cytogenetics laboratory...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27905691/is-volume-important-in-aneurysm-treatment-outcome
#7
Athanasios Katsargyris, Chris Klonaris, Eric L Verhoeven
Several studies have suggested that surgical procedures performed at high-volume centers may result in superior outcome. Technically more demanding procedures such as aortic aneurysm repair appear to demonstrate a stronger relationship with volume. The present chapter reviewed the literature using the MEDLINE database to identify studies investigating the effect of volume in aortic aneurysm repair outcomes. The great majority of studies identified shows an advantage for high-volume hospitals with regard to perioperative mortality of abdominal (AAA), thoracic (TAA) and thoracoabdominal (TAAA) aortic aneurysm repair...
December 1, 2016: Journal of Cardiovascular Surgery
https://www.readbyqxmd.com/read/27900609/dry-age-related-macular-degeneration-pharmacology
#8
Charles B Wright, Jayakrishna Ambati
Age-related macular degeneration (AMD), the most common form of irreversible blindness in the industrially developed world, can present years before a patient begins to lose vision. For most of these patients, AMD never progresses past its early stages to the advanced forms that are principally responsible for the vast majority of vision loss. Advanced AMD can manifest as either an advanced avascular form known as geographic atrophy (GA) marked by regional retinal pigment epithelium (RPE) cell death or as an advanced form known as neovascular AMD marked by the intrusion of fragile new blood vessels into the normally avascular retina...
November 30, 2016: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/27896725/finding-genes-in-genome-sequence
#9
Alice Carolyn McHardy, Andreas Kloetgen
Gene finding is the process of identifying genome sequence regions representing stretches of DNA that encode biologically active products, such as proteins or functional noncoding RNAs. As this is usually the first step in the analysis of any novel genomic sequence or resequenced sample of well-known organisms, it is a very important issue, as all downstream analyses depend on the results. This chapter describes the biological basis for gene finding, and the programs and computational approaches that are available for the automated identification of protein-coding genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896724/genomic-database-searching
#10
James R A Hutchins
The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895608/genetic-consideration-of-schizotypal-traits-a-review
#11
REVIEW
Emma E Walter, Francesca Fernandez, Mollie Snelling, Emma Barkus
Schizotypal traits are of interest and importance in their own right and also have theoretical and clinical associations with schizophrenia. These traits comprise attenuated psychotic symptoms, social withdrawal, reduced cognitive capacity, and affective dysregulation. The link between schizotypal traits and psychotic disorders has long since been debated. The status of knowledge at this point is such schizotypal traits are a risk for psychotic disorders, but in and of themselves only confer liability, with other risk factors needing to be present before a transition to psychosis occurs...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27886939/development-and-implementation-of-models-of-care-for-musculoskeletal-conditions-in-middle-income-and-low-income-asian-countries
#12
REVIEW
Keith K Lim, Madelynn Chan, Sandra Navarra, Syed Atiqul Haq, Chak Sing Lau
This chapter discusses the challenges faced in the development and implementation of musculoskeletal (MSK) Models of Care (MoCs) in middle-income and low-income countries in Asia and outlines the components of an effective MoC for MSK conditions. Case studies of four such countries (The Philippines, Malaysia, Bangladesh and Myanmar) are presented, and their unique implementation issues are discussed. The success experienced in one high-income country (Singapore) is also described as a comparison. The Community Oriented Program for Control of Rheumatic Diseases (COPCORD) project and the role of Asia Pacific League of Associations for Rheumatology (APLAR), a professional body supporting MoC initiatives in this region, are also discussed...
June 2016: Best Practice & Research. Clinical Rheumatology
https://www.readbyqxmd.com/read/27885600/method-for-the-successful-crystallization-of-the-ferric-uptake-regulator-from-campylobacter-jejuni
#13
Sabina Sarvan, Jean-François Couture
The Ferric Uptake Regulator (FUR) is a transcription factor (TF) regulating the expression of several genes to control iron levels in prokaryotes. Members of this family of TFs share a common structural scaffold that typically comprises two regions that include a DNA binding and dimerization domains. While this structural organization is conserved, FUR proteins employ different mechanisms to bind divergent DNA binding elements and regulate gene expression in the absence or presence of regulatory metals. These findings, combined with the observations that FUR proteins display different geometries in regard to the relative orientation of the DNA binding and dimerization domains, have highlighted an expanding repertoire of molecular mechanisms controlling the activity of this family of TFs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27859457/time-of-flight-mass-spectrometry-introduction-to-the-basics
#14
REVIEW
Ulrich Boesl
The intention of this tutorial is to introduce into the basic concepts of time-of-flight mass spectrometry, beginning with the most simple single-stage ion source with linear field-free drift region and continuing with two-stage ion sources combined with field-free drift regions and ion reflectors-the so-called reflectrons. Basic formulas are presented and discussed with the focus on understanding the physical relations of geometric and electric parameters, initial distribution of ionic parameters, ion flight times, and ion flight time incertitude...
January 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27854027/a-method-for-large-scale-screening-of-random-sequence-libraries-to-determine-the-function-of-unstructured-regions-from-essential-proteins
#15
Jean-François Millau, Benoit Guillemette, Luc Gaudreau
In this chapter we present a method allowing the screening of random sequences to discover essential aspects of unstructured protein regions in yeast. The approach can be applied to any protein with unstructured peptide sequences for which functions are difficult to decipher, for example the N-terminal tails of histones. The protocol first describes the building and preparation of a large library of random peptides in fusion with a protein of interest. Recent technical advances in oligonucleotide synthesis allow the construction of long random sequences up to 35 residues long...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27852022/-parietal-cortices-and-body-information
#16
Eiichi Naito, Kaoru Amemiya, Tomoyo Morita
Proprioceptive signals originating from skeletal muscles and joints contribute to the formation of both the human body schema and the body image. In this chapter, we introduce various types of bodily illusions that are elicited by proprioceptive inputs, and we discuss distinct functions implemented by different parietal cortices. First, we illustrate the primary importance of the motor network in the processing of proprioceptive (kinesthetic) signals originating from muscle spindles. Next, we argue that the right inferior parietal cortex, in concert with the inferior frontal cortex (both regions connected by the inferior branch of the superior longitudinal fasciculus-SLF III), may be involved in the conscious experience of body image...
November 2016: Brain and Nerve, Shinkei Kenkyū No Shinpo
https://www.readbyqxmd.com/read/27844432/probing-dna-dna-interactions-with-a-combination-of-quadruple-trap-optical-tweezers-and-microfluidics
#17
Ineke Brouwer, Graeme A King, Iddo Heller, Andreas S Biebricher, Erwin J G Peterman, Gijs J L Wuite
DNA metabolism and DNA compaction in vivo involve frequent interactions of remote DNA segments, mediated by proteins. In order to gain insight into such interactions, quadruple-trap optical tweezers have been developed. This technique provides an unprecedented degree of control through the ability to independently manipulate two DNA molecules in three dimensions. In this way, discrete regions of different DNA molecules can be brought into contact with one another, with a well-defined spatial configuration. At the same time, the tension and extension of the DNA molecules can be monitored...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27837534/elastic-liposomes-for-topical-and-transdermal-drug-delivery
#18
Heather A E Benson
Elastic liposomes have been developed and evaluated as novel topical and transdermal delivery systems. They share some similarities to conventional liposomes but their composition is designed to confer flexibility and elasticity in the lipid bilayer structure. Elastic liposomes are applied non-occluded to the skin and are reported to permeate through the stratum corneum lipid lamellar regions as a result of the hydration or osmotic force in the skin. They have been investigated as drug carriers for a range of small molecules, peptides, proteins, and vaccines, both in vitro and in vivo...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27832543/using-an-inducible-crispr-dcas9-krab-effector-system-to-dissect-transcriptional-regulation-in-human-embryonic-stem-cells
#19
Krishna Mohan Parsi, Erica Hennessy, Nicola Kearns, René Maehr
CRISPR-Cas9 effector systems have wide applications for the stem cell and regenerative medicine field. The ability to dissect the functional gene regulatory networks in pluripotency and potentially in differentiation intermediates of all three germ layers makes this a valuable tool for the stem cell community. Catalytically inactive Cas9 fused to transcriptional/chromatin effector domains allows for silencing or activation of a genomic region of interest. Here, we describe the application of an inducible, RNA-guided, nuclease-deficient (d) Cas9-KRAB system (adapted from Streptococcus pyogenes) to silence target gene expression in human embryonic stem cells, via KRAB repression at the promoter region...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27832542/unbiased-interrogation-of-3d-genome-topology-using-chromosome-conformation-capture-coupled-to-high-throughput-sequencing-4c-seq
#20
Rutger W W Brouwer, Mirjam C G N van den Hout, Wilfred F J van IJcken, Eric Soler, Ralph Stadhouders
The development and widespread implementation of chromosome conformation capture (3C) technology has allowed unprecedented new insight into how chromosomes are folded in three-dimensional (3D) space. 3C and its derivatives have contributed tremendously to the now widely accepted view that genome topology plays an important role in many major cellular processes, at a chromosome-wide scale, but certainly also at the level of individual genetic loci. A particularly popular application of 3C technology is to study transcriptional regulation, allowing researchers to draw maps of gene regulatory connections beyond the linear genome through addition of the third dimension...
2017: Methods in Molecular Biology
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