SNP model development for the prediction of eye colour in New Zealand.
AuthorsAllwood JS, Harbison S
JournalForensic Sci Int Genet
PubMed ID23597786
'The ability to predict externally visible characteristics (EVCs) from DNA has appeal for use in forensic science, particularly where a forensic database match is not made and an eye witness account is unavailable. This technology has yet to be implemented in casework in New Zealand. The broad cultural diversity and ... More
Differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population: a case study in an apple × Venturia inaequalis pathosystem.
AuthorsLê Van A, Caffier V, Lasserre-Zuber P, Chauveau A, Brunel D, Le Cam B, Durel CE
JournalNew Phytol
PubMed ID23278324
'Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. ... More
Amino-acid substitutions at the domain interface affect substrate and allosteric inhibitor binding in a-isopropylmalate synthase from Mycobacterium tuberculosis.
AuthorsHuisman FH, Squire CJ, Parker EJ
JournalBiochem Biophys Res Commun
PubMed ID23500460
'a-Isopropylmalate synthase (a-IPMS) is a multi-domain protein catalysing the condensation of a-ketoisovalerate (a-KIV) and acetyl coenzyme A (AcCoA) to form a-isopropylmalate. This reaction is the first committed step in the leucine biosynthetic pathway in bacteria and plants, and a-IPMS is allosterically regulated by this amino acid. Existing crystal structures of ... More
Amino acid sequence of the ligand-binding domain of the aryl hydrocarbon receptor 1 predicts sensitivity of wild birds to effects of dioxin-like compounds.
'The sensitivity of avian species to the toxic effects of dioxin-like compounds (DLCs) varies up to 1000-fold among species, and this variability has been associated with interspecies differences in aryl hydrocarbon receptor 1 ligand-binding domain (AHR1 LBD) sequence. We previously showed that LD(50) values, based on in ovo exposures to ... More
An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition.
AuthorsNuccio EE, Hodge A, Pett-Ridge J, Herman DJ, Weber PK, Firestone MK
JournalEnviron Microbiol
PubMed ID23360621
'Arbuscular mycorrhizal fungi (AMF) perform an important ecosystem service by improving plant nutrient capture from soil, yet little is known about how AMF influence soil microbial communities during nutrient uptake. We tested whether an AMF modifies the soil microbial community and nitrogen cycling during litter decomposition. A two-chamber microcosm system ... More
Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq.
AuthorsCui K, Zhao K
JournalMethods Mol Biol
PubMed ID22183607
'The precise location of nucleosomes in functional regulatory regions in chromatin is critical to the regulation of transcription. The nucleosome structure protects DNA from microccocal nuclease (MNase) digestion and leaves a footprint on DNA that indicates the position of nucleosomes. Short sequence reads (25-36 bp) from ends of mononucleosome-sized DNA ... More
Diverse and heritable lineage imprinting of early haematopoietic progenitors.
AuthorsNaik SH, Perié L, Swart E, Gerlach C, van Rooij N, de Boer RJ, Schumacher TN
JournalNature
PubMed ID23552896
'Haematopoietic stem cells (HSCs) and their subsequent progenitors produce blood cells, but the precise nature and kinetics of this production is a contentious issue. In one model, lymphoid and myeloid production branch after the lymphoid-primed multipotent progenitor (LMPP), with both branches subsequently producing dendritic cells. However, this model is based ... More
High-throughput multiplex sequencing of miRNA.
AuthorsVigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G
JournalCurr Protoc Hum Genet
PubMed ID22470142
'Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost ... More
454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber.
'The relative contribution of novel fibers such as polydextrose and soluble corn fiber (SCF) to the human gut microbiome and its association with host physiology has not been well studied. This study was conducted to test the impact of polydextrose and SCF on the composition of the human gut microbiota ... More
Genetic diversity of subgroup 1 ilarviruses from eastern Australia.
AuthorsSharman M, Thomas JE
JournalArch Virol
PubMed ID23474983
'This is the first report of the genetic diversity within ilarvirus subgroup 1 from eastern Australia. It supports the separation of tobacco streak virus (TSV) strains from parthenium (Parthenium hysterophorus) and crownbeard (Verbescina encelioides) based on serology and host specificity. It has confirmed one previously described strain of TSV as ... More
In vitro phenotyping of recombinant hepatitis B virus containing the polymerase/reverse transcriptase gene from clinical isolates.
AuthorsLiu Y, Kitrinos KM
Journal
PubMed ID23821268
'This chapter describes the procedures for the generation of recombinant hepatitis B virus (HBV) that contains the polymerase/reverse transcriptase (pol/RT) gene from clinical isolates. It also contains procedures for phenotypic testing of the recombinant HBV in HepG2 cells for susceptibility to nucleos(t)ide analogs. Amplification and cloning of the pol/RT gene ... More
Quantification of microRNA Expression with Next-Generation Sequencing.
AuthorsEminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG
Journal
PubMed ID23821442
'Rapid advancement of next-generation sequencing technologies has made it possible to study expression profiles of microRNAs (miRNAs) comprehensively and efficiently. Multiplexing miRNA libraries by barcoding can significantly reduce sequencing cost per sample without compromising library quality. This unit provides a step-by-step protocol for isolating miRNAs and constructing multiplexed miRNA libraries. ... More
Systemically administered gp100 encoding DNA vaccine for melanoma using water-in-oil-in-water multiple emulsion delivery systems.
AuthorsKalariya M, Amiji MM
Journal
PubMed ID23702000
'The purpose of this study was to develop a water-in-oil-in-water (W/O/W) multiple emulsions-based vaccine delivery system for plasmid DNA encoding the gp100 peptide antigen for melanoma immunotherapy. The gp100 encoding plasmid DNA was encapsulated in the inner-most aqueous phase of squalane oil containing W/O/W multiple emulsions using a two-step emulsification ... More
Ectopic expression of AtPAD4 broadens resistance of soybean to soybean cyst and root-knot nematodes.
The gene encoding PAD4 (PHYTOALEXIN-DEFICIENT4) is required in Arabidopsis for expression of several genes involved in the defense response to Pseudomonas syringae pv. maculicola. AtPAD4 (Arabidopsis thaliana PAD4) encodes a lipase-like protein that plays a regulatory role mediating salicylic acid signaling. ... More
Determination of the mode of action of enterolysin A, produced by Enterococcus faecalis B9510.
AuthorsKhan H, Flint SH, Yu PL
JournalJ Appl Microbiol
PubMed ID23639072
The current study aimed to visualize the damage caused by enterolysin A to the cells of sensitive strains and to find out cleavage site within the peptidoglycan moiety of bacterial cell walls. ... More
A case of Q fever prosthetic joint infection and description of an assay for detection of Coxiella burnetii.
AuthorsTande AJ, Cunningham SA, Raoult D, Sim FH, Berbari EF, Patel R
JournalJ Clin Microbiol
PubMed ID23077126
We present the first published case of Coxiella burnetii prosthetic joint infection. Diagnosis was established with PCR and culture of periprosthetic tissue and synovial fluid (and serology). A novel PCR assay is described herein. Q fever should be considered in patients with prosthetic joint infection without an identified pathogen. ... More
Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing.
AuthorsJohnson MD, Mueller M, Game L, Aitman TJ
JournalCurr Protoc Mol Biol
PubMed ID22870857
Unlike other methods to assess methylation, whole-genome shotgun bisulfite sequencing is used to generate quantitative genome-wide methylation profiles at single-nucleotide resolution. As described in this unit, this method allows for the quantitative measurement of methylation at each cytosine base by treatment of genomic DNA with sodium bisulfite followed by sequencing ... More
RNA purification and expression analysis using microarrays and RNA deep sequencing.
Transcriptome analysis or global gene expression profiling is a powerful tool for discovery as well as -understanding biological mechanisms in health and disease. We present in this chapter a description of methods used to isolate mRNA from cells and tissues that has been optimized for preservation of RNA quality using ... More
Identification of chemosensory receptor genes in Manduca sexta and knockdown by RNA interference.
AuthorsHowlett N, Dauber KL, Shukla A, Morton B, Glendinning JI, Brent E, Gleason C, Islam F, Izquierdo D, Sanghavi S, Afroz A, Aslam A, Barbaro M, Blutstein R, Borovka M, Desire B, Elikhis A, Fan Q, Hoffman K, Huang A, Keefe D, Lopatin S, Miller S, Patel P, Rizzini D, Robinson A, Rokins K, Turlik A, Mansfield JH
JournalBMC Genomics
PubMed ID22646846
Insects detect environmental chemicals via a large and rapidly evolving family of chemosensory receptor proteins. Although our understanding of the molecular genetic basis for Drosophila chemoreception has increased enormously in the last decade, similar understanding in other insects remains limited. The tobacco hornworm, Manduca sexta, has long been an important ... More
Discordance at D3S1358 locus involving SGM Plus™ and the European new generation multiplex kits.
AuthorsRaziel A, Oz C, Carmon AD, Ilsar R, Zamir A
JournalForensic Sci Int Genet
PubMed ID21474404
During the course of routine database sample analysis in the Israel Police DNA database, an off-ladder D3S1358 allele, calculated to be >22.1, extending into the adjacent vWA locus was observed using Applied Biosystems SGM Plus™ kit. To verify the size of this D3S1358 long allele and to ensure it was ... More
Performance comparison of benchtop high-throughput sequencing platforms.
Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying ... More
Molecular and genetic characteristics of small ruminant lentiviruses in Slovenia.
AuthorsKuhar U, Barlic-Maganja D, Zadnik T, Grom J
JournalActa Vet Hung
PubMed ID23439298
Small ruminant lentiviruses (SRLV) are spread throughout the world, including Slovenia, where the first evidence of caprine arthritis encephalitis virus (CAEV) infection was found in 1996. This study was conducted to investigate the molecular and genetic characteristics of SRLV infection in Slovenia in order to classify our strains in relation ... More
Rapid and highly specific screening for NPM1 mutations in acute myeloid leukemia.
AuthorsOppliger Leibundgut E, Porret NA, Bienz Muggli M, Baumgartner H, Dahlhaus M, Baerlocher GM
JournalAnn Hematol
PubMed ID23161387
NPM1 mutations, the most frequent molecular alterations in acute myeloid leukemia (AML), have become important for risk stratification and treatment decisions for patients with normal karyotype AML. Rapid screening for NPM1 mutations should be available shortly after diagnosis. Several methods for detecting NPM1 mutations have been described, most of which ... More
Light-emitting diode induced fluorescence (LED-IF) detection design for a pen-shaped cartridge based single capillary electrophoresis system.
AuthorsKerékgyártó M, Kerekes T, Tsai E, Amirkhanian VD, Guttman A
JournalElectrophoresis
PubMed ID22965722
CGE is a well-established separation technique for the analysis of biologically important molecules such as nucleic acids. The inherent high resolving power, rapid analysis times, excellent detection sensitivity, and quantification capabilities makes this method favorable compared to conventional manual polyacrylamide and agarose slab gel electrophoresis techniques. In this paper we ... More
Testing UK blood donors for exposure to human parvovirus 4 using a time-resolved fluorescence immunoassay to screen sera and Western blot to confirm reactive samples.
AuthorsMaple PA, Beard S, Parry RP, Brown KE
Journal
PubMed ID23721256
BACKGROUND: Human parvovirus 4 (ParV4), a newly described member of the family Parvoviridae, like B19V, has been found in pooled plasma preparations. The extent, and significance, of ParV4 exposure in UK blood donors remain to be determined and reliable detection of ParV4 immunoglobulin (Ig)G, using validated methods, is needed. STUDY ... More
Development of a universal RT-PCR for amplifying and sequencing the leader and capsid-coding region of foot-and-mouth disease virus.
Foot-and-mouth disease (FMD) is a highly infectious viral disease of cloven-hoofed animals with debilitating and devastating consequences for livestock industries throughout the world. Key antigenic determinants of the causative agent, FMD virus (FMDV), reside within the surface-exposed proteins of the viral capsid. Therefore, characterization of the sequence that encodes the ... More
Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake.
AuthorsMani V, Harris AJ, Keating AF, Weber TE, Dekkers JC, Gabler NK
JournalJ Anim Sci
PubMed ID23463550
Microbes and microbial components potentially impact the performance of pigs through immune stimulation and altered metabolism. These immune modulating factors can include endotoxin from gram negative bacterial outer membrane component, commonly referred to as lipopolysaccharide (LPS). In this study, our objective was to examine the relationship between intestinal barrier integrity, ... More
A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.
AuthorsBatty EM, Wong TH, Trebes A, Argoud K, Attar M, Buck D, Ip CL, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TE, Crook DW, Piazza P
Journal
PubMed ID23762474
To date, very large scale sequencing of many clinically important RNA viruses has been complicated by their high population molecular variation, which creates challenges for polymerase chain reaction and sequencing primer design. Many RNA viruses are also difficult or currently not possible to culture, severely limiting the amount and purity ... More
Electrofusion of mesenchymal stem cells and islet cells for diabetes therapy: a rat model.
AuthorsYanai G, Hayashi T, Zhi Q, Yang KC, Shirouzu Y, Shimabukuro T, Hiura A, Inoue K, Sumi S
Journal
PubMed ID23724055
Islet transplantation is a minimally invasive treatment for severe diabetes. However, it often requires multiple donors to accomplish insulin-independence and the long-term results are not yet satisfying. Therefore, novel ways to overcome these problems have been explored. Isolated islets are fragile and susceptible to pro-apoptotic factors and poorly proliferative. In ... More