Publications by authors named "Michael Keehan"

5 Publications

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Multiple QTL underlie milk phenotypes at the CSF2RB locus.

Genet Sel Evol 2019 Jan 24;51(1). Epub 2019 Jan 24.

Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand.

Background: Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously reported QTL located at the CSF2RB locus on chromosome 5, for several milk production phenotypes, to better understand its underlying genetic and molecular causes.

Results: Using a population of 29,350 taurine dairy cows, we conducted association analyses for milk yield and composition traits, and identified highly significant QTL for milk yield, milk fat concentration, and milk protein concentration. Strikingly, protein concentration and milk yield appear to show co-located yet genetically distinct QTL. To attempt to understand the molecular mechanisms that might be mediating these effects, gene expression data were used to investigate eQTL for 11 genes in the broader interval. This analysis highlighted genetic impacts on CSF2RB and NCF4 expression that share similar association signatures to those observed for lactation QTL, strongly implicating one or both of these genes as responsible for these effects. Using the same gene expression dataset representing 357 lactating cows, we also identified 38 novel RNA editing sites in the 3' UTR of CSF2RB transcripts. The extent to which two of these sites were edited also appears to be genetically co-regulated with lactation QTL, highlighting a further layer of regulatory complexity that involves the CSF2RB gene.

Conclusions: This locus presents a diversity of molecular and lactation QTL, likely representing multiple overlapping effects that, at a minimum, highlight the CSF2RB gene as having a causal role in these processes.
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http://dx.doi.org/10.1186/s12711-019-0446-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346582PMC
January 2019

DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content.

BMC Genomics 2017 Dec 15;18(1):968. Epub 2017 Dec 15.

Research and Development, Livestock Improvement Corporation, Ruakura Road, Newstead, Hamilton, New Zealand.

Background: Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS focussed on analysis of milk lactose traits.

Results: Using a discovery population of 12,000 taurine dairy cattle, we detail 27 QTL for lactose concentration and yield, and subsequently validate the effects of 26 of these loci in a distinct population of 18,000 cows. We next present data implicating causative genes and variants for these QTL. Fine mapping of these regions using imputed, whole genome sequence-resolution genotypes reveals protein-coding candidate causative variants affecting the ABCG2, DGAT1, STAT5B, KCNH4, NPFFR2 and RNF214 genes. Eleven of the remaining QTL appear to be driven by regulatory effects, suggested by the presence of co-locating, co-segregating eQTL discovered using mammary RNA sequence data from a population of 357 lactating cows. Pathway analysis of genes representing all lactose-associated loci shows significant enrichment of genes located in the endoplasmic reticulum, with functions related to ion channel activity mediated through the LRRC8C, P2RX4, KCNJ2 and ANKH genes. A number of the validated QTL are also found to be associated with additional milk volume, fat and protein phenotypes.

Conclusions: Overall, these findings highlight novel candidate genes and variants involved in milk lactose regulation, whose impacts on membrane transport mechanisms reinforce the key osmo-regulatory roles of lactose in milk.
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http://dx.doi.org/10.1186/s12864-017-4320-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731188PMC
December 2017

What controls open-pore and residual currents in the first sensing zone of alpha-hemolysin nanopore? Combined experimental and theoretical study.

Nanoscale 2016 Jun;8(22):11571-9

Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB T2N 2N4, Canada.

The electrophoretic transport of single-stranded DNA through biological nanopores such as alpha-hemolysin (αHL) is a promising and cost-effective technology with the potential to revolutionize genomics. The rational design of pores with the controlled polymer translocation rates and high contrast between different nucleotides could improve significantly nanopore sequencing applications. Here, we apply a combination of theoretical and experimental methods in an attempt to elucidate several selective modifications in the pore which were proposed to be central for the effective discrimination between purines and pyrimidines. Our nanopore test set includes the wild type αHL and six mutants (E111N/M113X/K147N) in which the cross-section and chemical functionality of the first constriction zone of the pore are modified. Electrophysiological recordings were combined with all-atom Molecular Dynamics simulations (MD) and a recently developed Brownian Dynamics (BROMOC) protocol to investigate residual ion currents and pore-DNA interactions for two homo-polymers e.g. poly(dA)40 or poly(dC)40 blocking the pore. The calculated residual currents and contrast in the poly(dA)40/poly(dC)40 blocked pore are in qualitative agreement with the experimental recordings. We showed that a simple structural metric allows rationalization of key elements in the emergent contrast between purines and pyrimidines in the modified αHL mutants. The shape of the pore and its capacity for hydrogen bonding to a translocated polynucleotide are two essential parameters for contrast optimization. To further probe the impact of these two factors in the ssDNA sensing, we eliminated the effect of the primary constriction using serine substitutions (i.e. E111S/M113S/T145S/K147S) and increased the hydrophobic volume of the central residue in the secondary constriction (L135I). This pore modification sharply increased the contrast between Adenine (A) and Cytosine (C).
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http://dx.doi.org/10.1039/c6nr00164eDOI Listing
June 2016

Monitoring the escape of DNA from a nanopore using an alternating current signal.

J Am Chem Soc 2010 Feb;132(6):1878-85

Electronic Bio Sciences, 5754 Pacific Center Boulevard, Suite 204, San Diego, California 92121, USA.

We present the use of an alternating current (AC) signal as a means to monitor the conductance of an alpha-hemolysin (alphaHL) pore as a DNA hairpin with a polydeoxyadenosine tail is driven into and released from the pore. Specifically, a 12 base pair DNA hairpin attached to a 50-nucleotide poly-A tail (HP-A(50)) is threaded into an alphaHL channel using a DC driving voltage. Once the HP-A(50) molecule is trapped within the alphaHL channel, the DC driving voltage is turned off and the conductance of the channel is monitored using an AC voltage. The escape time, defined as the time it takes the HP-A(50) molecule to transport out of the alphaHL channel, is then measured. This escape time has been monitored as a function of AC amplitude (20 to 250 mV(ac)), AC frequency (60-200 kHz), DC drive voltage (0 to 100 mV(dc)), and temperature (-10 to 20 degrees C), in order to determine their effect on the predominantly diffusive motion of the DNA through the nanopore. The applied AC voltage used to monitor the conductance of the nanopore has been found to play a significant role in the DNA/nanopore interaction. The experimental results are described by a one-dimensional asymmetric periodic potential model that includes the influence of the AC voltage. An activation enthalpy barrier of 1.74 x 10(-19) J and a periodic potential asymmetry parameter of 0.575 are obtained for the diffusion at zero electrical bias of a single nucleotide through alphaHL.
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http://dx.doi.org/10.1021/ja906951gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913974PMC
February 2010

Development of query strategies to identify a histologic lymphoma subtype in a large linked database system.

Cancer Inform 2007 May 4;3:149-58. Epub 2007 May 4.

Emory University School of Medicine, Winship Cancer Institute, Oncology Informatics, Atlanta, GA 30322, USA.

Background: Large linked databases (LLDB) represent a novel resource for cancer outcomes research. However, accurate means of identifying a patient population of interest within these LLDBs can be challenging. Our research group developed a fully integrated platform that provides a means of combining independent legacy databases into a single cancer-focused LLDB system. We compared the sensitivity and specificity of several SQL-based query strategies for identifying a histologic lymphoma subtype in this LLDB to determine the most accurate legacy data source for identifying a specific cancer patient population.

Methods: Query strategies were developed to identify patients with follicular lymphoma from a LLDB of cancer registry data, electronic medical records (EMR), laboratory, administrative, pharmacy, and other clinical data. Queries were performed using common diagnostic codes (ICD-9), cancer registry histology codes (ICD-O), and text searches of EMRs. We reviewed medical records and pathology reports to confirm each diagnosis and calculated the sensitivity and specificity for each query strategy.

Results: Together the queries identified 1538 potential cases of follicular lymphoma. Review of pathology and other medical reports confirmed 415 cases of follicular lymphoma, 300 pathology-verified and 115 verified from other medical reports. The query using ICD-O codes was highly specific (96%). Queries using text strings varied in sensitivity (range 7-92%) and specificity (range 86-99%). Queries using ICD-9 codes were both less sensitive (34-44%) and specific (35-87%).

Conclusions: Queries of linked-cancer databases that include cancer registry data should utilize ICD-O codes or employ structured free-text searches to identify patient populations with a precise histologic diagnosis.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675837PMC
May 2007