Shane C Burgess

PMID: 15782910;Abstract:

Dietary Lys needs for chicks were studied. A titration diet consisting of progressive amounts of dietary Lys from 0.95% up to 1.40% was fed to broiler chicks from 0 to 18 d of age. Optimal dietary Lys level was calculated using regression analysis. Body weight gain and feed conversion were maximized at Lys levels of 1.24% (1.10% digestible) and 1.27% (1.13% digestible) of diet, respectively. Blood samples were then collected from 2 groups: birds fed the lowest Lys level and birds fed dietary Lys nearest the determined requirement level (1.25% Lys). Plasma was analyzed for protein spectra via mass spectrometry and then classified by their functional characteristics. The number of proteins was similar between the 2 samples, but there was a tendency toward increased peptides for specific proteins in plasma from chicks fed adequate Lys levels. Furthermore, after these proteins were classified, more muscle-related proteins were found in plasma samples of birds fed Lys-adequate diets. It would appear that an individual dietary amino acid deficiency does not necessarily translate into decreasing protein synthesis proportionate to body weight, but rather significant changes may be occurring within the types of proteins undergoing anabolism. In conclusion, results herein illustrate the potential for using functional genomics in nutritionally related responses of poultry. ©2005 Poultry Science Association, Inc.

PMID: 21779156;PMCID: PMC3136433;Abstract:

Cell penetrating peptides (CPPs) are those peptides that can transverse cell membranes to enter cells. Once inside the cell, different CPPs can localize to different cellular components and perform different roles. Some generate pore-forming complexes resulting in the destruction of cells while others localize to various organelles. Use of machine learning methods to predict potential new CPPs will enable more rapid screening for applications such as drug delivery. We have investigated the influence of the composition of training datasets on the ability to classify peptides as cell penetrating using support vector machines (SVMs). We identified 111 known CPPs and 34 known non-penetrating peptides from the literature and commercial vendors and used several approaches to build training data sets for the classifiers. Features were calculated from the datasets using a set of basic biochemical properties combined with features from the literature determined to be relevant in the prediction of CPPs. Our results using different training datasets confirm the importance of a balanced training set with approximately equal number of positive and negative examples. The SVM based classifiers have greater classification accuracy than previously reported methods for the prediction of CPPs, and because they use primary biochemical properties of the peptides as features, these classifiers provide insight into the properties needed for cell-penetration. To confirm our SVM classifications, a subset of peptides classified as either penetrating or non-penetrating was selected for synthesis and experimental validation. Of the synthesized peptides predicted to be CPPs, 100% of these peptides were shown to be penetrating. © 2011 Sanders et al.

PMID: 17675869;Abstract:

The chicken genome is sequenced and this, together with microarray and other functional genomics technologies, makes post-genomic research possible in the chicken. At this time, however, such research is hindered by a lack of genomic structural and functional annotations. Bio-ontologies have been developed for different annotation requirements, as well as to facilitate data sharing and computational analysis, but these are not yet optimally utilized in the chicken. Here we discuss genomic annotation and bio-ontologies. We focus specifically on the Gene Ontology (GO), chicken GO annotations and how these can facilitate functional genomics in the chicken. The GO is the most developed and widely used bio-ontology. It is the de facto standard for functional annotation. Despite its critical importance in analyzing microarray and other functional genomics data, relatively few chicken gene products have any GO annotation. When these are available, the average quality of chicken gene products annotations (defined using evidence code weight and annotation depth) is much less than in mouse. Moreover, tools allowing chicken researchers to easily and rapidly use the GO are either lacking or hard to use. To address all of these problems we developed ChickGO and AgBase. Chicken GO annotations are provided by complementary work at MSU-AgBase and EBI-GOA. The GO tools pipeline at AgBase uses GO to derive functional and biological significance from microarray and other functional genomics data. Not only will improved genomic annotation and tools to use these annotations benefit the chicken research community but they will also facilitate research in other avian species and comparative genomics. Copyright © 2007 S. Karger AG.

PMID: 19130588;Abstract:

Dielectrophoretic manipulation of erythrocytes/red blood cells is investigated as a tool to identify blood type for medical diagnostic applications. Positive blood types of the ABO typing system (A+, B+, AB+ and O+) were tested and cell responses quantified. The dielectrophoretic response of each blood type was observed in a platinum electrode microdevice, delivering a field of 0.025Vpp/μm at 1 MHz. Responses were recorded via video microscopy for 120 s and erythrocyte positions were tabulated at 20-30 s intervals. Both vertical and horizontal motions of erythrocytes were quantified via image object recognition, object tracking in MATLAB, binning into appropriate electric field contoured regions (wedges) and statistical analysis. Cells of O+ type showed relatively attenuated response to the dielectrophoretic field and were distinguished with greater than 95% confidence from all the other three blood types. AB+ cell responses differed from A+ and B+ blood types likely because AB+ erythrocytes express both the A and B glycoforms on their membrane. This research suggests that dielectrophoresis of untreated erythrocytes beyond simple dilution depends on blood type and could be used in portable blood typing devices. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

PMID: 18539730;PMCID: PMC2493269;Abstract:

Oligotropha carboxidovorans OM5^T (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium with the capability to utilize carbon monoxide, carbon dioxide, and hydrogen. It is also capable of heterotrophic growth under appropriate environmental conditions. Here we report the annotated genome sequence of the circular chromosome of this organism. Copyright © 2008, American Society for Microbiology. All Rights Reserved.