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Find video protocols related to scientific articles indexed in Pubmed.
Enhanced Targeted Drug Delivery Through Controlled Release in a 3D Vascular Tree.
J Biomech Eng
PUBLISHED: 11-04-2014
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Controlled particle release and targeting is a technique using the particle release score map (PRSM) and transient particle release score map (TPRSM) via backtracking to determine the optimal drug injection locations to enhance the target efficiency (TE). The majority of work performed in this area has only focused on drug targeting within relatively simple geometries such as multiple bifurcations in a plane or limited level of bifurcations. This paper addresses this issue and investigates the possibility of target desired locations through an idealised but complex 3D vascular tree geometry under realistic hemodynamic conditions by imposing a Poiseuille velocity profile and a Womersley velocity profile derived from cine phase contrast MRI data for the steady and pulsatile simulations respectively. The shear thinning non-Newtonian behaviour of blood was accounted for by the Carreau-Yasuda model. Lagrangian particle tracking method was used to record the trajectories of individual drug particles. With the proposed optimal release scoring algorithm, it was found that there exist multiple optimal release locations under the steady flow condition while there exists one unique optimal release location under the pulsatile flow conditions. The initial in silico results appear promising, showing approximately 100% target efficiency in the steady simulations and on average 66% target efficiency in the pulsatile simulations, warranting further model improvement and experimental validation. Keywords: computational fluid dynamics, blood flow, drug targeting, nanoparticles, controlled release.
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Modeling the effect of adverse environmental conditions and clothing on temperature rise in a human body exposed to radiofrequency electromagnetic fields.
IEEE Trans Biomed Eng
PUBLISHED: 10-15-2014
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This study considers the computationally determined thermal profile of a fully clothed, finely discretised, heterogeneous human body model, subject to the maximum allowable reference level for a 1 GHz radio frequency electromagnetic field for a worker, and also subject to adverse environmental conditions, including high humidity and high ambient temperature. An initial observation is that while electromagnetic fields at the occupational safety limit will contribute an additional thermal load to the tissues and subsequently cause an elevated temperature, the magnitude of this effect is far outweighed by that due to the conditions including the ambient temperature, relative humidity, and the type of clothing worn. It is envisaged that the computational modeling approach outlined in this paper will be suitably modified in future studies to evaluate the thermal response of a body at elevated metabolic rates, and for different body shapes and sizes including children and pregnant women.
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Outbreak of type E foodborne botulism linked to traditionally prepared salted fish in Ontario, Canada.
Foodborne Pathog. Dis.
PUBLISHED: 09-04-2014
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Abstract On April 17, 2012, two adult females presented to the hospital with symptoms of botulism. Patient A displayed shortness of breath, increasing lethargy, ptosis, and fixed and dilated pupils, and was intubated after admission. Patient B presented with shortness of breath, vomiting, and stridor. Both patients consumed a meal consisting of a traditionally prepared salted fish, fesikh, on the evening of April 16 during a gathering to celebrate Sham el-Nessim, an Egyptian holiday marking the beginning of spring. Foodborne botulism was suspected based on symptoms and consumption of potentially hazardous food. Antitoxin was administered to both patients on April 18. Another attendee of the Sham el-Nessim gathering (patient C), who also consumed the implicated food, developed symptoms consistent with botulism on April 18. Clinical specimens from all three symptomatic attendees tested positive for either Clostridium botulinum or type E botulinum neurotoxin. Fesikh remaining from the shared meal contained both type E botulinum neurotoxin and C. botulinum type E organisms. Unsold fesikh shad and fesikh sardines tested positive for C. botulinum type E, while unsold fesikh mullet pieces in oil tested positive for both C. botulinum type E and type E botulinum neurotoxin. After consultation with public health investigators, all fesikh products were voluntarily withheld from sale by the manufacturer prior to laboratory confirmation of contamination. Additional illnesses were likely prevented by these precautionary holds, which underscores the importance of timely public health action based on epidemiological evidence available in advance of laboratory results. This is the first documented outbreak of foodborne botulism associated with fesikh to occur in Canada.
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Highly effective yet simple transmembrane anion transporters based upon ortho-phenylenediamine bis-ureas.
Chem. Commun. (Camb.)
PUBLISHED: 09-03-2014
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Simple, highly fluorinated receptors are shown to function as highly effective transmembrane anion antiporters with the most active transporters rivalling the transport efficacy of natural anion transporter prodigiosin for bicarbonate.
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Population-based passive tick surveillance and detection of expanding foci of blacklegged ticks Ixodes scapularis and the Lyme disease agent Borrelia burgdorferi in Ontario, Canada.
PLoS ONE
PUBLISHED: 08-29-2014
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We identified ticks submitted by the public from 2008 through 2012 in Ontario, Canada, and tested blacklegged ticks Ixodes scapularis for Borrelia burgdorferi and Anaplasma phagocytophilum. Among the 18 species of ticks identified, I. scapularis, Dermacentor variabilis, Ixodes cookei and Amblyomma americanum represented 98.1% of the 14,369 ticks submitted. Rates of blacklegged tick submission per 100,000 population were highest in Ontario's Eastern region; D. variabilis in Central West and Eastern regions; I. cookei in Eastern and South West regions; and A. americanum had a scattered distribution. Rates of blacklegged tick submission per 100,000 population were highest from children (0-9 years old) and older adults (55-74 years old). In two health units in the Eastern region (i.e., Leeds, Grenville & Lanark District and Kingston-Frontenac and Lennox & Addington), the rate of submission for engorged and B. burgdorferi-positive blacklegged ticks was 47× higher than the rest of Ontario. Rate of spread for blacklegged ticks was relatively faster and across a larger geographic area along the northern shore of Lake Ontario/St. Lawrence River, compared with slower spread from isolated populations along the northern shore of Lake Erie. The infection prevalence of B. burgdorferi in blacklegged ticks increased in Ontario over the study period from 8.4% in 2008 to 19.1% in 2012. The prevalence of B. burgdorferi-positive blacklegged ticks increased yearly during the surveillance period and, while increases were not uniform across all regions, increases were greatest in the Central West region, followed by Eastern and South West regions. The overall infection prevalence of A. phagocytophilum in blacklegged ticks was 0.3%. This study provides essential information on ticks of medical importance in Ontario, and identifies demographic and geographic areas for focused public education on the prevention of tick bites and tick-borne diseases.
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Numerical investigations of the haemodynamic changes associated with stent malapposition in an idealised coronary artery.
J Biomech
PUBLISHED: 08-02-2014
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The deployment of a coronary stent near complex lesions can sometimes lead to incomplete stent apposition (ISA), an undesirable side effect of coronary stent implantation. Three-dimensional computational fluid dynamics (CFD) calculations are performed on simplified stent models (with either square or circular cross-section struts) inside an idealised coronary artery to analyse the effect of different levels of ISA to the change in haemodynamics inside the artery. The clinical significance of ISA is reported using haemodynamic metrics like wall shear stress (WSS) and wall shear stress gradient (WSSG). A coronary stent with square cross-sectional strut shows different levels of reverse flow for malapposition distance (MD) between 0mm and 0.12 mm. Chaotic blood flow is usually observed at late diastole and early systole for MD=0mm and 0.12 mm but are suppressed for MD=0.06 mm. The struts with circular cross section delay the flow chaotic process as compared to square cross-sectional struts at the same MD and also reduce the level of fluctuations found in the flow field. However, further increase in MD can lead to chaotic flow not only at late diastole and early systole, but it also leads to chaotic flow at the end of systole. In all cases, WSS increases above the threshold value (0.5 Pa) as MD increases due to the diminishing reverse flow near the artery wall. Increasing MD also results in an elevated WSSG as flow becomes more chaotic, except for square struts at MD=0.06 mm.
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Anthrax lethal factor as an immune target in humans and transgenic mice and the impact of HLA polymorphism on CD4+ T cell immunity.
PLoS Pathog.
PUBLISHED: 05-01-2014
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Bacillus anthracis produces a binary toxin composed of protective antigen (PA) and one of two subunits, lethal factor (LF) or edema factor (EF). Most studies have concentrated on induction of toxin-specific antibodies as the correlate of protective immunity, in contrast to which understanding of cellular immunity to these toxins and its impact on infection is limited. We characterized CD4+ T cell immunity to LF in a panel of humanized HLA-DR and DQ transgenic mice and in naturally exposed patients. As the variation in antigen presentation governed by HLA polymorphism has a major impact on protective immunity to specific epitopes, we examined relative binding affinities of LF peptides to purified HLA class II molecules, identifying those regions likely to be of broad applicability to human immune studies through their ability to bind multiple alleles. Transgenics differing only in their expression of human HLA class II alleles showed a marked hierarchy of immunity to LF. Immunogenicity in HLA transgenics was primarily restricted to epitopes from domains II and IV of LF and promiscuous, dominant epitopes, common to all HLA types, were identified in domain II. The relevance of this model was further demonstrated by the fact that a number of the immunodominant epitopes identified in mice were recognized by T cells from humans previously infected with cutaneous anthrax and from vaccinated individuals. The ability of the identified epitopes to confer protective immunity was demonstrated by lethal anthrax challenge of HLA transgenic mice immunized with a peptide subunit vaccine comprising the immunodominant epitopes that we identified.
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Geometric dependence of the conductance drop in a nanopore due to a particle.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 04-04-2014
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We study the effect of a neutral particle on the ionic flow through a nanopore using a basic uniform field theory and the coupled Poisson-Nernst-Planck and Navier-Stokes (PNP-NS) equations. We consider hourglass and cylindrical pore profiles and examine how the difference in pore shape changes the position dependence of the current change due to the particle. Good quantitative agreement between both calculations is seen, though we find that the simple theory is unable to correctly capture the change in the access resistance of the pore if a particle is placed at the pore entrance. Finally, we examine the spatial variations in the solutions of the PNP-NS equations, finding that the electro-osmotic flow through the pore is completely disrupted for sufficiently large particles.
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Selective pathology fellowships: diverse, innovative, and valuable subspecialty training.
Arch. Pathol. Lab. Med.
PUBLISHED: 04-01-2014
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Although selective pathology fellowships have a long-standing history of developing trainees with advanced expertise in specific areas of pathology other than those of the American Board of Pathology-certified subspecialties, the widespread interest in this training continues to grow.
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Synthesis of 2'-O,4'-C-alkylene-bridged ribonucleosides and their evaluation as inhibitors of HCV NS5B polymerase.
Bioorg. Med. Chem. Lett.
PUBLISHED: 03-13-2014
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The synthesis of 2'-O,4'-C-methylene-bridged bicyclic guanine ribonucleosides bearing 2'-C-methyl or 5'-C-methyl modifications is described. Key to the successful installation of the methyl functionality in both cases was the use of a one-pot oxidation-Grignard procedure to avoid formation of the respective unreactive hydrates prior to alkylation. The 2'-C-methyl- and 5'-C-methyl-modified bicyclic guanosines were evaluated, along with the known uracil-, cytosine-, adenine-, guanine-LNA and guanine-ENA nucleosides, as potential antiviral agents and found to be inactive in the hepatitis C virus (HCV) cell-based replicon assay. Examination of the corresponding nucleoside triphosphates, however, against the purified HCV NS5B polymerase indicated that LNA-G and 2'-C-methyl-LNA-G are potent inhibitors of both 1b wild type and S282T mutant enzymes in vitro. Activity was further demonstrated for the LNA-G-triphosphate against HCV NS5B polymerase genotypes 1a, 2a, 3a and 4a. A phosphorylation by-pass prodrug strategy may be required to promote anti-HCV activity in the replicon assay.
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Imaging cardiac amyloidosis: a pilot study using ¹?F-florbetapir positron emission tomography.
Eur. J. Nucl. Med. Mol. Imaging
PUBLISHED: 02-03-2014
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Cardiac amyloidosis, a restrictive heart disease with high mortality and morbidity, is underdiagnosed due to limited targeted diagnostic imaging. The primary aim of this study was to evaluate the utility of (18)F-florbetapir for imaging cardiac amyloidosis.
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Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle.
BMC Genet.
PUBLISHED: 01-27-2014
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This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the effects of detected SNPs on carcass traits to avoid undesirable correlated effects on these economically important traits when selecting for feed efficiency; and (4) map the genes to biological mechanisms and pathways. A total number of 339 SNPs corresponding to 180 genes were tested for association with phenotypes using a single locus regression (SLRM) and genotypic model on 726 and 990 crossbred animals for feed efficiency and carcass traits, respectively.
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Abnormal partitioning of hexokinase 1 suggests disruption of a glutamate transport protein complex in schizophrenia.
Schizophr. Res.
PUBLISHED: 01-13-2014
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Excitatory amino acid transporter 2 (EAAT2) belongs to a family of Na(+) dependent glutamate transporters that maintain a low synaptic concentration of glutamate by removing glutamate from the synaptic cleft into astroglia and neurons. EAAT2 activity depends on Na(+) and K(+) gradients generated by Na(+)/K(+) ATPase and ATP. Hexokinase 1 (HK1), an initial enzyme of glycolysis, binds to mitochondrial outer membrane where it couples cytosolic glycolysis to mitochondrial oxidative phosphorylation, producing ATP utilized by the EAAT2/Na(+)/K(+) ATPase protein complex to facilitate glutamate reuptake. In this study, we hypothesized that the protein complex formed by EAAT2, Na(+)/K(+) ATPase and mitochondrial proteins in human postmortem prefrontal cortex may be disrupted, leading to abnormal glutamate transmission in schizophrenia. We first determined that EAAT2, Na(+)/K(+) ATPase, HK1 and aconitase were found in both EAAT2 and Na(+)/K(+) ATPase interactomes by immunoisolation and mass spectrometry in human postmortem prefrontal cortex. Next, we measured levels of glutamate transport complex proteins in subcellular fractions in the dorsolateral prefrontal cortex and found increases in the EAAT2B isoform of EAAT2 in a fraction containing extrasynaptic membranes and increased aconitase 1 in a mitochondrial fraction. Finally, an increased ratio of HK1 protein in the extrasynaptic membrane/mitochondrial fraction was found in subjects with schizophrenia, suggesting that HK1 protein is abnormally partitioned in this illness. Our findings indicate that the integrity of the glutamate transport protein complex may be disrupted, leading to decreased perisynaptic buffering and reuptake of glutamate, as well as impaired energy metabolism in schizophrenia.
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Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle.
BMC Genet.
PUBLISHED: 01-10-2014
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Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69-77 and 81-92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped.
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Genetic and Phenotypic Correlations between Performance Traits with Meat Quality and Carcass Characteristics in Commercial Crossbred Pigs.
PLoS ONE
PUBLISHED: 01-01-2014
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Genetic correlations between performance traits with meat quality and carcass traits were estimated on 6,408 commercial crossbred pigs with performance traits recorded in production systems with 2,100 of them having meat quality and carcass measurements. Significant fixed effects (company, sex and batch), covariates (birth weight, cold carcass weight, and age), random effects (additive, litter and maternal) were fitted in the statistical models. A series of pairwise bivariate analyses were implemented in ASREML to estimate heritability, phenotypic, and genetic correlations between performance traits (n?=?9) with meat quality (n?=?25) and carcass (n?=?19) traits. The animals had a pedigree compromised of 9,439 animals over 15 generations. Performance traits had low-to-moderate heritabilities (±SE), ranged from 0.07±0.13 to 0.45±0.07 for weaning weight, and ultrasound backfat depth, respectively. Genetic correlations between performance and carcass traits were moderate to high. The results indicate that: (a) selection for birth weight may increase drip loss, lightness of longissimus dorsi, and gluteus medius muscles but may reduce fat depth; (b) selection for nursery weight can be valuable for increasing both quantity and quality traits; (c) selection for increased daily gain may increase the carcass weight and most of the primal cuts. These findings suggest that deterioration of pork quality may have occurred over many generations through the selection for less backfat thickness, and feed efficiency, but selection for growth had no adverse effects on pork quality. Low-to-moderate heritabilities for performance traits indicate that they could be improved using traditional selection or genomic selection. The estimated genetic parameters for performance, carcass and meat quality traits may be incorporated into the breeding programs that emphasize product quality in these Canadian swine populations.
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Association between gene expression profiles and clinical outcome of pemetrexed-based treatment in patients with advanced non-squamous non-small cell lung cancer: exploratory results from a phase II study.
PLoS ONE
PUBLISHED: 01-01-2014
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We report exploratory gene-expression profiling data from a single-arm Phase-II-study in patients with non-squamous (ns)NSCLC treated with pemetrexed and cisplatin. Previously disclosed results indicated a significant association of low thymidylate-synthase (TS)-expression with longer progression-free and overall survival (PFS/OS).
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Sequence, structural and expression divergence of duplicate genes in the bovine genome.
PLoS ONE
PUBLISHED: 01-01-2014
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Gene duplication is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary innovation. In the present study, we performed the first comprehensive analysis of duplicate genes in the bovine genome. A total of 3131 putative duplicated gene pairs were identified, including 712 cattle-specific duplicate gene pairs unevenly distributed across the genome, which are significantly enriched for specific biological functions including immunity, growth, digestion, reproduction, embryonic development, inflammatory response, and defense response to bacterium. Around 97.1% (87.8%) of (cattle-specific) duplicate gene pairs were found to have distinct exon-intron structures. Analysis of gene expression by RNA-Seq and sequence divergence (synonymous or non-synonymous) revealed that expression divergence is correlated with sequence divergence, as has been previously observed in other species. This analysis also led to the identification of a subset of cattle-specific duplicate gene pairs exhibiting very high expression divergence. Interestingly, further investigation revealed a significant relationship between structural and expression divergence while controlling for the effect of synonymous sequence divergence. Together these results provide further insight into duplicate gene sequence and expression divergence in cattle, and their potential contributions to phenotypic divergence.
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Tumor-specific activation of an EGFR-targeting probody enhances therapeutic index.
Sci Transl Med
PUBLISHED: 10-18-2013
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Target-mediated toxicity constitutes a major limitation for the development of therapeutic antibodies. To redirect the activity of antibodies recognizing widely distributed targets to the site of disease, we have applied a prodrug strategy to create an epidermal growth factor receptor (EGFR)-directed Probody therapeutic-an antibody that remains masked against antigen binding until activated locally by proteases commonly active in the tumor microenvironment. In vitro, the masked Probody showed diminished antigen binding and cell-based activities, but when activated by appropriate proteases, it regained full activity compared to the parental anti-EGFR antibody cetuximab. In vivo, the Probody was largely inert in the systemic circulation of mice, but was activated within tumor tissue and showed antitumor efficacy that was similar to that of cetuximab. The Probody demonstrated markedly improved safety and increased half-life in nonhuman primates, enabling it to be dosed safely at much higher levels than cetuximab. In addition, we found that both Probody-responsive xenograft tumors and primary tumor samples from patients were capable of activating the Probody ex vivo. Probodies may therefore improve the safety profile of therapeutic antibodies without compromising efficacy of the parental antibody and may enable the wider use of empowered antibody formats such as antibody-drug conjugates and bispecifics.
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TCIA: An information resource to enable open science.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 10-11-2013
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Reusable, publicly available data is a pillar of open science. The Cancer Imaging Archive (TCIA) is an open image archive service supporting cancer research. TCIA collects, de-identifies, curates and manages rich collections of oncology image data. Image data sets have been contributed by 28 institutions and additional image collections are underway. Since June of 2011, more than 2,000 users have registered to search and access data from this freely available resource. TCIA encourages and supports cancer-related open science communities by hosting and managing the image archive, providing project wiki space and searchable metadata repositories. The success of TCIA is measured by the number of active research projects it enables (>40) and the number of scientific publications and presentations that are produced using data from TCIA collections (39).
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Genomic Resources Notes accepted 1 June 2013-31 July 2013.
Mol Ecol Resour
PUBLISHED: 09-25-2013
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This article documents the public availability of (i) raw transcriptome sequence data, assembled contigs and UniProt BLAST hits from common crossbill (Loxia curvirostra) and Plasmodium relictum (lineage SGS1) obtained from a controlled infection experiment; and (ii) raw transcriptome sequence data and 66 596 SNPs for the white-tailed deer (Odocoileus virginianus).
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Association analysis for feed efficiency traits in beef cattle using preserved haplotypes.
Genome
PUBLISHED: 09-05-2013
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This study reports a genome wide scan for chromosome regions and their haplotypes that significantly associated with average daily gain (ADG), dry matter intake (DMI), and residual feed intake (RFI) in beef cattle. The study used data from 597 Angus, 450 Charolais, and 616 crossbred beef cattle, and the Illumina Bovine SNP50 beadchip. Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups of animals. Such regions in the crossbreds were tested for association with ADG, DMI, and RFI. At false discovery rates of 5% and 10%, there were six and eight chromosome regions showing significant associations with the traits, respectively. At nominal significance levels (at least P < 0.05), 23 regions with a total number of 31 haplotypes were found significantly associated with at least one of the three traits. The proportion of phenotypic variance explained by these 23 regions varied depending on the trait; the highest proportion for ADG, DMI, and RFI was 13.50%, 9.92%, and 2.64%, respectively. Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple traits. Thirty-six quantitative trait loci for 16 production traits, from the current literature, covered fully or in part the 23 chromosome regions. The findings from this study might be an important contribution to the current knowledge of the beef cattle genome and to the effective identification of causative genes associated with important traits in cattle.
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Quantitative simultaneous 111In?99mTc SPECT-CT of osteomyelitis.
Med Phys
PUBLISHED: 08-10-2013
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A well-established approach for diagnostic imaging of osteomyelitis (OM), a bone infection, is simultaneous SPECT-CT of 99mTc sulfur colloid (SC) and 111In white blood cells (WBC). This method provides essentially perfect spatial registration of the tracers within anatomic sites of interest. Currently, diagnosis is based purely on a visual assessment-where relative discordance between 99mTc and 111In uptake in bone, i.e., high 111In and low 99mTc, suggests OM. To achieve more quantitative images, noise, scatter, and crosstalk between radionuclides must be addressed through reconstruction. Here the authors compare their Monte Carlo-based joint OSEM (MC-JOSEM) algorithm, which reconstructs both radionuclides simultaneously, to a more conventional triple-energy window-based reconstruction (TEW-OSEM), and to iterative reconstruction with no compensation for scatter (NC-OSEM).
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A crab with three eyes, two rostra, and a dorsal antenna-like structure.
Arthropod Struct Dev
PUBLISHED: 08-09-2013
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We describe a malformed specimen of the freshwater crab Amarinus lacustris from New Zealand. With three eyes in a horizontal row, two rostra, and a dorsal antenna-like structure, the pattern of malformation of this animal is unique and has not been described before. A careful inspection and description of external and internal structures, in particular the central nervous system, were carried out. These revealed, in addition to the external abnormalities, a retarded brain with a hypertrophied and backwards bent protocerebrum connected with all three eyes and putatively with the dorsal antenna-like structure. Based on these data, a variety of hypotheses about the causes for this kind of malformation are discussed. A scenario combining a conjoined twin (Duplicitas anterior) based on the duplication of the embryonic anterior head lobes and a regeneration event leading to the replacement of an eye by an antenna shows the best fit to the observed patterns.
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Congenital malignant melanoma: a case report with cytogenetic studies.
Am J Dermatopathol
PUBLISHED: 08-03-2013
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: Although rare, congenital malignant melanoma (CMM) should be considered in the differential diagnosis of congenital skin lesions. We report a case of CMM in a 4-month-old infant presenting with an enlarging scalp mass, initially thought to be a hemangioma. Incisional biopsy of the lesion showed a compound congenital nevus with atypical cells suggestive of a proliferative nodule versus malignancy on histopathology. Subsequent excisional biopsy revealed malignant melanoma, and further workup confirmed extensive disease with distant metastases. Cytogenetic analysis of both the tumor sites showed highly abnormal karyotypes including pseudotetraploidy, telomere associations, and evidence of gene amplification, all consistent with malignancy. Fluorescence in situ hybridization demonstrated amplification of the MYC gene, with no copy number changes in CDKN2A (INK4/ARF), PTEN, or Cyclin D1. Our report details the cytogenetic and molecular studies of CMM, which provide insight into the biologic behavior of the lesions and may confirm diagnosis when histopathology is not determinant.
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The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository.
J Digit Imaging
PUBLISHED: 07-26-2013
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The National Institutes of Health have placed significant emphasis on sharing of research data to support secondary research. Investigators have been encouraged to publish their clinical and imaging data as part of fulfilling their grant obligations. Realizing it was not sufficient to merely ask investigators to publish their collection of imaging and clinical data, the National Cancer Institute (NCI) created the open source National Biomedical Image Archive software package as a mechanism for centralized hosting of cancer related imaging. NCI has contracted with Washington University in Saint Louis to create The Cancer Imaging Archive (TCIA)-an open-source, open-access information resource to support research, development, and educational initiatives utilizing advanced medical imaging of cancer. In its first year of operation, TCIA accumulated 23 collections (3.3 million images). Operating and maintaining a high-availability image archive is a complex challenge involving varied archive-specific resources and driven by the needs of both image submitters and image consumers. Quality archives of any type (traditional library, PubMed, refereed journals) require management and customer service. This paper describes the management tasks and user support model for TCIA.
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DNA modifications repaired by base excision repair are epigenetic.
DNA Repair (Amst.)
PUBLISHED: 07-23-2013
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CREB controls ?25% of the mammalian transcriptome. Small changes in binding to its consensus (CRE) sequence are likely to be amplified many fold in initiating transcription. Here we show that DNA lesions repaired by the base excision repair (BER) pathway modulate CREB binding to CRE. We generated Kd values by electrophoretic mobility shift assays using purified human CREB and a 39-mer double-stranded oligonucleotide containing modified or wild-type CRE. CRE contains two guanine residues per strand, one in a CpG islet. Alterations in CRE resulted in positive or negative changes in Kd over two orders of magnitude depending on location and modification. Cytosine methylation or oxidation of both guanines greatly diminished binding; a G/U mispair in the CpG context enhanced binding. Intermediates in the BER pathway at one G residue or the other resulted in reduced binding, depending on the specific location, while there was no change in binding when the single G residue outside of the CpG islet was oxidized. CREB recruits other partners after dimers form on DNA. Only UpG increased DNA.CREB dimer formation. Since oxidation is ongoing and conversion of cytosine to uracil occurs spontaneously or at specific times during differentiation and development, we propose that BER substrates are epigenetic and modulate transcription factor recognition/binding.
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Validation of a previous-day recall measure of active and sedentary behaviors.
Med Sci Sports Exerc
PUBLISHED: 07-19-2013
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A previous-day recall (PDR) may be a less error-prone alternative to traditional questionnaire-based estimates of physical activity and sedentary behavior (e.g., past year), but the validity of the method is not established. We evaluated the validity of an interviewer administered PDR in adolescents (12-17 yr) and adults (18-71 yr).
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Genomic regions associated with fertility traits in male and female cattle: advances from microsatellites to high-density chips and beyond.
Anim. Reprod. Sci.
PUBLISHED: 07-03-2013
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A current challenge in genetic improvement of cattle is to identify genomic selection strategies that could work across breeds. Breed differences, scarcity of data, and lack of quantitative trait loci (QTL) validation contribute to this challenge. We conducted a review of the literature to identify QTL, markers, and candidate genes that are associated with fertility across breeds to arrive at an integrated view of bovine fertility genomics and to guide the direction of future studies. This review considers both male and female fertility traits as these are economically relevant for all breeds and production systems. Regions associated with fertility traits were found in each of the 30 bovine chromosomes, confirming the complexity of these polygenic traits. Across breeds, regions on chromosomes 1, 5, 14, and 16 were associated with female reproductive traits. The X chromosome was associated with male reproductive traits in both dairy and beef bulls. It has recently been proposed that a Y chromosome anomaly may be involved in infertility in cows. Knowledge of these QTL may assist discovery of causative mutations and has the potential to improve the accuracy of genomic selection, especially across breeds of cattle.
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Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity.
BMC Genomics
PUBLISHED: 06-18-2013
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Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo.
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Evaluation of imaging systems using the posterior variance of emission counts.
IEEE Trans Med Imaging
PUBLISHED: 06-03-2013
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We investigate an approach to evaluation of emission-tomography (ET) imaging systems used for region-of-interest (ROI) estimation tasks. In the evaluation we employ the concept of "emission counts" (EC), which are the number of events per voxel emitted during a scan. We use the reduction in posterior variance of ROI EC, compared to the prior ROI EC variance, as the metric of primary interest, which we call the "posterior variance reduction index" (PVRI). Systems that achieve a higher PVRI are considered superior to systems with lower PVRI. The approach is independent of the reconstruction method and is applicable to all photon-limited data types including list-mode data. We analyzed this approach using a model of 2-D tomography, and compared our results to the classical theory of tomographic sampling. We found that performance evaluations using the PVRI index were consistent with the classical theory. System evaluation based on EC posterior variance is an intuitively appealing and physically meaningful method that is useful for evaluation of system performance in ROI quantitation tasks.
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Genome-wide association analyses for carcass quality in crossbred beef cattle.
BMC Genet.
PUBLISHED: 05-16-2013
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Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. This paper presents a genome-wide association approach utilizing single nucleotide polymorphisms (SNP) in the Illumina BovineSNP50 BeadChip to seek genomic regions that potentially harbor genes or QTN underlying variation in carcass quality of beef cattle.This study used 747 genotyped animals, mainly crossbred, with phenotypes on twelve carcass quality traits, including hot carcass weight (HCW), back fat thickness (BF), Longissimus dorsi muscle area or ribeye area (REA), marbling scores (MRB), lean yield grade by Beef Improvement Federation formulae (BIFYLD), steak tenderness by Warner-Bratzler shear force 7-day post-mortem (LM7D) as well as body composition as determined by partial rib (IMPS 103) dissection presented as a percentage of total rib weight including body cavity fat (BDFR), lean (LNR), bone (BNR), intermuscular fat (INFR), subcutaneous fat (SQFR), and total fat (TLFR).
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Quantification of Myocardial Perfusion Reserve Using Dynamic SPECT Imaging in Humans: A Feasibility Study.
J. Nucl. Med.
PUBLISHED: 04-11-2013
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Myocardial perfusion imaging (MPI) is well established in the diagnosis and workup of patients with known or suspected coronary artery disease (CAD); however, it can underestimate the extent of obstructive CAD. Quantification of myocardial perfusion reserve with PET can assist in the diagnosis of multivessel CAD. We evaluated the feasibility of dynamic tomographic SPECT imaging and quantification of a retention index to describe global and regional myocardial perfusion reserve using a dedicated solid-state cardiac camera.
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Performance of a high-sensitivity dedicated cardiac SPECT scanner for striatal uptake quantification in the brain based on analysis of projection data.
Med Phys
PUBLISHED: 04-06-2013
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The authors have previously reported the advantages of high-sensitivity single-photon emission computed tomography (SPECT) systems for imaging structures located deep inside the brain. DaTscan (Isoflupane I-123) is a dopamine transporter (DaT) imaging agent that has shown potential for early detection of Parkinson disease (PD), as well as for monitoring progression of the disease. Realizing the full potential of DaTscan requires efficient estimation of striatal uptake from SPECT images. They have evaluated two SPECT systems, a conventional dual-head gamma camera with low-energy high-resolution collimators (conventional) and a dedicated high-sensitivity multidetector cardiac imaging system (dedicated) for imaging tasks related to PD.
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Understanding the impacts of allocation approaches during process-based life cycle assessment of water treatment chemicals.
Integr Environ Assess Manag
PUBLISHED: 03-20-2013
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Chemicals are an important component of advanced water treatment operations not only in terms of economics but also from an environmental standpoint. Tools such as life cycle assessment (LCA) are useful for estimating the environmental impacts of water treatment operations. At the same time, LCA analysts must manage several fundamental and as yet unresolved methodological challenges, one of which is the question of how best to "allocate" environmental burdens in multifunctional processes. Using water treatment chemicals as a case study example, this article aims to quantify the variability in greenhouse gas emissions estimates stemming from methodological choices made in respect of allocation during LCA. The chemicals investigated and reported here are those most important to coagulation and disinfection processes, and the outcomes are illustrated on the basis of treating 1000 ML of noncoagulated and nondisinfected water. Recent process and economic data for the production of these chemicals is used and methodological alternatives for solving the multifunctionality problem, including system expansion and mass, exergy, and economic allocation, are applied to data from chlor-alkali plants. In addition, Monte Carlo simulation is included to provide a comprehensive picture of the robustness of economic allocation results to changes in the market price of these industrial commodities. For disinfection, results demonstrate that chlorine gas has a lower global warming potential (GWP) than sodium hypochlorite regardless of the technique used to solve allocation issues. For coagulation, when mass or economic allocation is used to solve the multifunctionality problem in the chlor-alkali facility, ferric chloride was found to have a higher GWP than aluminum sulfate and a slightly lower burden where system expansion or exergy allocation are applied instead. Monte Carlo results demonstrate that when economic allocation is used, GWP results were relatively robust and resilient to the changes in commodity prices encountered during the study period, with standard deviations less than 6% for all chlor-alkali-produced chemicals reported here. Overall outcomes from the study demonstrate the potential variability in LCA results according to the allocation approach taken and emphasize the need for a consensus approach to water sector LCAs. Integr Environ Assess Manag 2013;X:000-000. © 2013 SETAC Integr Environ Assess Manag 2014;10:87-94. © 2013 SETAC.
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Analysis of biological networks and biological pathways associated with residual feed intake in beef cattle.
Anim. Sci. J.
PUBLISHED: 02-19-2013
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In this study, biological networks were reconstructed from genes and metabolites significantly associated with residual feed intake (RFI) in beef cattle. The networks were then used to identify biological pathways associated with RFI. RFI is a measure of feed efficiency, which is independent of body size and growth; therefore selection for RFI is expected to result in cattle that consume less feed without adverse effects on growth rate and mature size. Although several studies have identified genes associated with RFI, the mechanisms of the biological processes are not well understood. In this study, we utilised the results obtained from two association studies, one using 24 genes and one using plasma metabolites to reconstruct biological networks associated with RFI using IPA software (Igenuity Systems). The results pointed to biological processes such as lipid and steroid biosynthesis, protein and carbohydrate metabolism and regulation of gene expression through DNA transcription, protein stability and degradation. The major canonical pathways included signaling of growth hormone, Oncostatin M, insulin-like growth factor and AMP activated protein kinase, and cholesterol biosynthesis. This study provides information on potential biological mechanisms, and genes and metabolites involved in feed efficiency in beef cattle.
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Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle.
Mamm. Genome
PUBLISHED: 02-06-2013
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Hanwoo, Korean native cattle, is indigenous to the Korean peninsula. They have been used mainly as draft animals for about 5,000 years; however, in the last 30 years, their main role has been changed to meat production by selective breeding which has led to substantial increases in their productivity. Massively parallel sequencing technology has recently made possible the systematic identification of structural variations in cattle genomes. In particular, copy number variation (CNV) has been recognized as an important genetic variation complementary to single-nucleotide polymorphisms that can be used to account for variations of economically important traits in cattle. Here we report genome-wide copy number variation regions (CNVRs) in Hanwoo cattle obtained by comparing the whole genome sequence of Hanwoo with Black Angus and Holstein sequence datasets. We identified 1,173 and 963 putative CNVRs representing 16.7 and 7.8 Mbp from comparisons between Black Angus and Hanwoo and between Holstein and Hanwoo, respectively. The potential functional roles of the CNVRs were assessed by Gene Ontology enrichment analysis. The results showed that response to stimulus, immune system process, and cellular component organization were highly enriched in the genic-CNVRs that overlapped with annotated cattle genes. Of the 11 CNVRs that were selected for validation by quantitative real-time PCR, 9 exhibited the expected copy number differences. The results reported in this study show that genome-wide CNVs were detected successfully using massively parallel sequencing technology. The CNVs may be a valuable resource for further studies to correlate CNVs and economically important traits in cattle.
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Influence of sire breed on the interplay among rumen microbial populations inhabiting the rumen liquid of the progeny in beef cattle.
PLoS ONE
PUBLISHED: 02-04-2013
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This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB), fed high energy density (HE) and low energy density (LE) diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed-associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P<0.05). Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii) and M20 (Methanobrevibacter smithii), and bacterial phylotype B62 (Robinsoniella sp.) in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency.
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A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A.
Hum. Mol. Genet.
PUBLISHED: 01-30-2013
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Human genetic variation contributes to differences in susceptibility to HIV-1 infection. To search for novel host resistance factors, we performed a genome-wide association study (GWAS) in hemophilia patients highly exposed to potentially contaminated factor VIII infusions. Individuals with hemophilia A and a documented history of factor VIII infusions before the introduction of viral inactivation procedures (1979-1984) were recruited from 36 hemophilia treatment centers (HTCs), and their genome-wide genetic variants were compared with those from matched HIV-infected individuals. Homozygous carriers of known CCR5 resistance mutations were excluded. Single nucleotide polymorphisms (SNPs) and inferred copy number variants (CNVs) were tested using logistic regression. In addition, we performed a pathway enrichment analysis, a heritability analysis, and a search for epistatic interactions with CCR5 ?32 heterozygosity. A total of 560 HIV-uninfected cases were recruited: 36 (6.4%) were homozygous for CCR5 ?32 or m303. After quality control and SNP imputation, we tested 1 081 435 SNPs and 3686 CNVs for association with HIV-1 serostatus in 431 cases and 765 HIV-infected controls. No SNP or CNV reached genome-wide significance. The additional analyses did not reveal any strong genetic effect. Highly exposed, yet uninfected hemophiliacs form an ideal study group to investigate host resistance factors. Using a genome-wide approach, we did not detect any significant associations between SNPs and HIV-1 susceptibility, indicating that common genetic variants of major effect are unlikely to explain the observed resistance phenotype in this population.
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Whole genome identity-by-descent determination.
J Bioinform Comput Biol
PUBLISHED: 01-16-2013
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High-throughput single nucleotide polymorphism genotyping assays conveniently produce genotype data for genome-wide genetic linkage and association studies. For pedigree datasets, the unphased genotype data is used to infer the haplotypes for individuals, according to Mendelian inheritance rules. Linkage studies can then locate putative chromosomal regions based on the haplotype allele sharing among the pedigree members and their disease status. Most existing haplotyping programs require rather strict pedigree structures and return a single inferred solution for downstream analysis. In this research, we relax the pedigree structure to contain ungenotyped founders and present a cubic time whole genome haplotyping algorithm to minimize the number of zero-recombination haplotype blocks. With or without explicitly enumerating all the haplotyping solutions, the algorithm determines all distinct haplotype allele identity-by-descent (IBD) sharings among the pedigree members, in linear time in the total number of haplotyping solutions. Our algorithm is implemented as a computer program iBDD. Extensive simulation experiments using 2 sets of 16 pedigree structures from previous studies showed that, in general, there are trillions of haplotyping solutions, but only up to a few thousand distinct haplotype allele IBD sharings. iBDD is able to return all these sharings for downstream genome-wide linkage and association studies.
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Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle.
Appl. Environ. Microbiol.
PUBLISHED: 12-09-2011
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Limited knowledge of the structure and activities of the ruminal bacterial community prevents the understanding of the effect of population dynamics on functional bacterial groups and on host productivity. This study aimed to identify particular bacteria associated with host feed efficiency in steers with differing diets and residual feed intake (RFI) using culture-independent methods: PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis. PCR-DGGE profiles were generated from the ruminal fluid of 55 steers fed a low-energy-density diet and then switched to a high-energy-density diet. Bacterial profile comparisons by multivariate statistical analysis showed a trend only for RFI-related clusters on the high-energy diet. When steers (n = 19) belonging to the same RFI group under both diets were used to identify specific bacterial phylotypes related to feed efficiency traits, correlations were detected between dry matter intake, average daily gain, and copy numbers of the 16S rRNA gene of Succinivibrio sp. in low-RFI (efficient) steers, whereas correlations between Robinsoniella sp. and RFI (P < 0.05) were observed for high-RFI (inefficient) animals. Eubacterium sp. differed significantly (P < 0.05) between RFI groups that were only on the high-energy diet. Our work provides a comprehensive framework to understand how particular bacterial phylotypes contribute to differences in feed efficiency and ultimately influence host productivity, which may either depend on or be independent from diet factors.
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Joint optimization of collimator and reconstruction parameters in SPECT imaging for lesion quantification.
Phys Med Biol
PUBLISHED: 10-20-2011
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Obtaining the best possible task performance using reconstructed SPECT images requires optimization of both the collimator and reconstruction parameters. The goal of this study is to determine how to perform this optimization, namely whether the collimator parameters can be optimized solely from projection data, or whether reconstruction parameters should also be considered. In order to answer this question, and to determine the optimal collimation, a digital phantom representing a human torso with 16 mm diameter hot lesions (activity ratio 8:1) was generated and used to simulate clinical SPECT studies with parallel-hole collimation. Two approaches to optimizing the SPECT system were then compared in a lesion quantification task: sequential optimization, where collimation was optimized on projection data using the Cramer–Rao bound, and joint optimization, which simultaneously optimized collimator and reconstruction parameters. For every condition, quantification performance in reconstructed images was evaluated using the root-mean-squared-error of 400 estimates of lesion activity. Compared to the joint-optimization approach, the sequential-optimization approach favoured a poorer resolution collimator, which, under some conditions, resulted in sub-optimal estimation performance. This implies that inclusion of the reconstruction parameters in the optimization procedure is important in obtaining the best possible task performance; in this study, this was achieved with a collimator resolution similar to that of a general-purpose (LEGP) collimator. This collimator was found to outperform the more commonly used high-resolution (LEHR) collimator, in agreement with other task-based studies, using both quantification and detection tasks.
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Improved regional activity quantitation in nuclear medicine using a new approach to correct for tissue partial volume and spillover effects.
IEEE Trans Med Imaging
PUBLISHED: 09-29-2011
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We have developed a new method of compensating for effects of partial volume and spillover in dual-modality imaging. The approach requires segmentation of just a few tissue types within a small volume-of-interest (VOI) surrounding a lesion; the algorithm estimates simultaneously, from projection data, the activity concentration within each segmented tissue inside the VOI. Measured emission projections were fitted to the sum of resolution-blurred projections of each such tissue, scaled by its unknown activity concentration, plus a global background contribution obtained by reprojection through the reconstructed image volume outside the VOI. The method was evaluated using multiple-pinhole ?SPECT data simulated for the MOBY mouse phantom containing two spherical lung tumors and one liver tumor, as well as using multiple-bead phantom data acquired on ?SPECT and ?CT scanners. Each VOI in the simulation study was 4.8 mm (12 voxels) cubed and, depending on location, contained up to four tissues (tumor, liver, heart, lung) with different values of relative (99m)Tc concentration. All tumor activity estimates achieved bias after ? 15 ordered-subsets expectation maximization (OSEM) iterations (×10 subsets) , with better than 8% precision ( ? 25% greater than the Cramer-Rao lower bound). The projection-based fitting approach also outperformed three standardized uptake value (SUV)-like metrics, one of which was corrected for count spillover. In the bead phantom experiment, the mean ± standard deviation of the bias of VOI estimates of bead concentration were 0.9±9.5%, comparable to those of a perturbation geometric transfer matrix (pGTM) approach (-5.4±8.6%); however, VOI estimates were more stable with increasing iteration number than pGTM estimates, even in the presence of substantial axial misalignment between ?CT and ?SPECT image volumes.
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Short reads, circular genome: skimming solid sequence to construct the bighorn sheep mitochondrial genome.
J. Hered.
PUBLISHED: 09-26-2011
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As sequencing technology improves, an increasing number of projects aim to generate full genome sequence, even for nonmodel taxa. These projects may be feasibly conducted at lower read depths if the alignment can be aided by previously developed genomic resources from a closely related species. We investigated the feasibility of constructing a complete mitochondrial (mt) genome without preamplification or other targeting of the sequence. Here we present a full mt genome sequence (16,463 nucleotides) for the bighorn sheep (Ovis canadensis) generated though alignment of SOLiD short-read sequences to a reference genome. Average read depth was 1240, and each base was covered by at least 36 reads. We then conducted a phylogenomic analysis with 27 other bovid mitogenomes, which placed bighorn sheep firmly in the Ovis clade. These results show that it is possible to generate a complete mitogenome by skimming a low-coverage genomic sequencing library. This technique will become increasingly applicable as the number of taxa with some level of genome sequence rises.
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Screening of peptide libraries against protective antigen of Bacillus anthracis in a disposable microfluidic cartridge.
PLoS ONE
PUBLISHED: 09-01-2011
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Bacterial surface peptide display has gained popularity as a method of affinity reagent generation for a wide variety of applications ranging from drug discovery to pathogen detection. In order to isolate the bacterial clones that express peptides with high affinities to the target molecule, multiple rounds of manual magnetic activated cell sorting (MACS) followed by multiple rounds of fluorescence activated cell sorting (FACS) are conventionally used. Although such manual methods are effective, alternative means of library screening which improve the reproducibility, reduce the cost, reduce cross contamination, and minimize exposure to hazardous target materials are highly desired for practical application. Toward this end, we report the first semi-automated system demonstrating the potential for screening bacterially displayed peptides using disposable microfluidic cartridges. The Micro-Magnetic Separation platform (MMS) is capable of screening a bacterial library containing 3 × 10¹? members in 15 minutes and requires minimal operator training. Using this system, we report the isolation of twenty-four distinct peptide ligands that bind to the protective antigen (PA) of Bacilus anthracis in three rounds of selection. A consensus motif WXCFTC was found using the MMS and was also found in one of the PA binders isolated by the conventional MACS/FACS approach. We compared MMS and MACS rare cell recovery over cell populations ranging from 0.1% to 0.0000001% and found that both magnetic sorting methods could recover cells down to 0.0000001% initial cell population, with the MMS having overall lower standard deviation of cell recovery. We believe the MMS system offers a compelling approach towards highly efficient, semi-automated screening of molecular libraries that is at least equal to manual magnetic sorting methods and produced, for the first time, 15-mer peptide binders to PA protein that exhibit better affinity and specificity than peptides isolated using conventional MACS/FACS.
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MicroRNA regulation in mammalian adipogenesis.
Exp. Biol. Med. (Maywood)
PUBLISHED: 08-15-2011
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Adipogenesis, the complex development from preadipocytes or mesenchymal stem cells to mature adipocytes, is essential for fat formation and metabolism of adipose tissues in mammals. It has been reported to be regulated by hormones and various adipogenic transcription factors which are expressed as a transcriptional cascade promoting adipocyte differentiation, leading to the mature adipocyte phenotype. Recent findings indicate that microRNAs (miRNAs), a family of small RNA molecules of approximately 22 nucleotides in length, are involved in the regulatory network of many biological processes, including cell differentiation, through post-transcriptional regulation of transcription factors and/or other genes. In this review, we focus on the recent understanding of the roles of miRNAs in adipogenesis, including the most recent and relevant findings that support the role of several miRNAs as pro- or antiadipogenic factors regulating adipogenesis in mice, human and cattle to propose the future role of miRNA in adipogenesis of farm animal models.
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Genome-wide scan identifies loci associated with classical BSE occurrence.
PLoS ONE
PUBLISHED: 06-23-2011
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Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Sequence variations in the coding region of the prion gene (PRNP) have been associated with acquired transmissible spongiform encephalopathy (TSE) susceptibility in mammals; however, this is not the case in cattle. It has been hypothesized that genes, in addition to the prion gene, contribute to genetic susceptibility of acquired TSEs. Accordingly, genetic studies of classical BSE in cattle identified loci other than PRNP that are associated with disease incidence. The objective of this study was to utilize a genome-wide association study to test for genetic loci associated with classical BSE. The samples include 143 BSE affected (case) and 173 unaffected half sib (control) animals collected in the mid 1990s in Southern England. The data analysis identifies loci on two different chromosomes associated with BSE disease occurrence. Most notable is a single nucleotide polymorphism on chromosome 1 at 29.15 Mb that is associated with BSE disease (p = 3.09E-05). Additionally, a locus on chromosome 14, within a cluster of SNPs showed a trend toward significance (p = 5.24E-05). It is worth noting that in a human vCJD study markers on human chromosome 8, a region with shared synteny to the region identified on cattle chromosome 14, were associated with disease. Further, our candidate genes appear to have plausible biological relevance with the known etiology of TSE disease. One of the candidate genes is hypothetical gene LOC521010, similar to FK506 binding protein 2 located on chromosome 1 at 29.32 Mb. This gene encodes a protein that is a member of the immunophilin protein family and is involved in basic cellular processes including protein folding. The chromosomal regions identified in this study and candidate genes within these regions merit further investigation.
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Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle.
BMC Genomics
PUBLISHED: 06-16-2011
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Selection signatures delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle.
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Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery.
BMC Genomics
PUBLISHED: 05-24-2011
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One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or genomic regions with phenotypes. The completion of the bovine genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of the genetic variations present in cattle. Here we describe the whole-genome resequencing of two Bos taurus bulls from distinct breeds for the purpose of identifying and annotating novel forms of genetic variation in cattle.
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A synergistic approach to anion antiport.
Dalton Trans
PUBLISHED: 04-14-2011
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A synergistic approach to Cl(-)/HCO(3)(-) antiport has been demonstrated in POPC lipid bilayers using an ion selective electrode assay showing that, when using combinations of carriers each optimised for a particular component of the transport process, enhanced rates of transport are observed.
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Synthesis and preliminary evaluation of radiolabeled bis(zinc(II)-dipicolylamine) coordination complexes as cell death imaging agents.
Bioorg. Med. Chem.
PUBLISHED: 01-31-2011
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The aim of this study was the development of (??m)Tc labeled bis(zinc(II)-dipicolylamine) (Zn²?-DPA) coordination complexes, and the in vivo evaluation of their usefulness as radiotracers for the detection of cell death. DPA ligand 1 was labeled with (??m)Tc via the (??m)Tc-tricarbonyl core ([(??m)Tc(CO)?-1]³?) or via HYNIC ((??m)Tc-HYNIC-1) in good radiochemical yields. Highest in vitro stabilities were demonstrated for [(??m)Tc(CO)?-1]³?. A mouse model of hepatic apoptosis (anti-Fas mAb) was used to demonstrate binding to apoptotic cells. (??m)Tc-HYNIC-1 showed the best targeting of apoptotic hepatic tissue with a 2.2 times higher liver uptake in anti-Fas treated mice as compared to healthy animals. A rat model of ischemia-reperfusion injury was used to further explore the ability of the (??m)Tc-labeled Zn²?-DPA coordination complexes to target cell death. Selective accumulation could be detected for both tracers in the area at risk, correlating with histological proof of cell death. Area at risk to normal tissue uptake ratios were 3.82 for [(??m)Tc(CO)?-1]³? and 5.45 for (??m)Tc-HYNIC-1.
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Differences in HIV-specific T cell responses between HIV-exposed and -unexposed HIV-seronegative individuals.
J. Virol.
PUBLISHED: 01-26-2011
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HIV-1-specific T lymphocyte responses in individuals exposed to HIV-1 but who remain persistently seronegative (HESNs) have been reported in some but not all previous studies. This study was designed to resolve unequivocally the question of whether HESNs make HIV-1-specific T cell responses. We performed a blind investigation to measure HIV-1-specific T cell responses in both HIV-1-serodiscordant couples and HIV-1-unexposed seronegative controls (HUSNs). We found low-frequency HIV-1-specific T cells in both HESNs and HUSNs but show that the response rates were higher over time in the former (P = 0.01). Furthermore, the magnitudes of the HIV-1-specific T cell responses were significantly higher among responding HESNs than among HUSNs over time (P = 0.002). In both groups, responses were mediated by CD4 T cells. The responses were mapped to single peptides, which often corresponded to epitopes restricted by multiple HLA-DR types that have previously been detected in HIV-1-infected patients. HIV-1-specific T cell responses in HUSNs and some HESNs likely represent cross-reactivity to self or foreign non-HIV-1 antigens. The significantly greater T cell responses in HESNs, including in two who were homozygous for CCR5?32, demonstrates that HIV-1-specific T cell responses can be induced or augmented by exposure to HIV-1 without infection.
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Transcriptome analysis of the medulla tissue from cattle in response to bovine spongiform encephalopathy using digital gene expression tag profiling.
J. Toxicol. Environ. Health Part A
PUBLISHED: 01-11-2011
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Bovine spongiform encephalopathy (BSE) is a transmissible, fatal neurodegenerative disorder of cattle produced by prions. The use of excessive parallel sequencing for comparison of gene expression in bovine control and infected tissues may help to elucidate the molecular mechanisms associated with this disease. In this study, tag profiling Solexa sequencing was used for transcriptome analysis of bovine brain tissues. Replicate libraries were prepared from mRNA isolated from control and infected (challenged with 100 g of BSE-infected brain) medulla tissues 45 mo after infection. For each library, 5-6 million sequence reads were generated and approximately 67-70% of the reads were mapped against the Bovine Genome database to approximately 13,700-14,120 transcripts (each having at least one read). About 42-47% of the total reads mapped uniquely. Using the GeneSifter software package, 190 differentially expressed (DE) genes were identified (>2.0-fold change, p < .01): 73 upregulated and 117 downregulated. Seventy-nine DE genes had functions described in the Gene Ontology (GO) database and 16 DE genes were involved in 38 different pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Digital analysis expression by tag profiling may be a powerful approach to comprehensive transcriptome analysis to identify changes associated with disease progression, leading to a better understanding of the underlying mechanism of pathogenesis of BSE.
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Gene expression in the medulla following oral infection of cattle with bovine spongiform encephalopathy.
J. Toxicol. Environ. Health Part A
PUBLISHED: 01-11-2011
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The identification of variations in gene expression in response to bovine spongiform encephalopathy (BSE) may help to elucidate the mechanisms of neuropathology and prion replication and discover biomarkers for disease. In this study, genes that are differentially expressed in the caudal medulla tissues of animals infected with different doses of PrP(BSE) at 12 and 45 mo post infection were compared using array containing 24,000 oligonucleotide probes. Data analysis identified 966 differentially expressed (DE) genes between control and infected animals. Genes identified in at least two of four experiments (control versus 1-g infected animals at 12 and 45-mo; control versus 100-g infected animals at 12 and 45 mo) were considered to be the genes that may be associated with BSE disease. From the 176 DE genes associated with BSE, 84 had functions described in the Gene Ontology (GO) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 14 genes revealed that prion infection may cause dysfunction of several different networks, including extracellular matrix (ECM), cell adhesion, neuroactive ligand-receptor interaction, complement and coagulation cascades, MAPK signaling, neurodegenerative disorder, SNARE interactions in vesicular transport, and the transforming growth factor (TGF) beta signaling pathways. The identification of DE genes will contribute to a better understanding of the molecular mechanisms of neuropathology in bovine species. Additional studies on larger number of animals are in progress in our laboratory to investigate the roles of these DE genes in pathogenesis of BSE.
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Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome.
PLoS ONE
PUBLISHED: 01-06-2011
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The Antarctic krill Euphausia superba is a keystone species in the Antarctic food chain. Not only is it a significant grazer of phytoplankton, but it is also a major food item for charismatic megafauna such as whales and seals and an important Southern Ocean fisheries crop. Ecological data suggest that this species is being affected by climate change and this will have considerable consequences for the balance of the Southern Ocean ecosystem. Hence, understanding how this organism functions is a priority area and will provide fundamental data for life history studies, energy budget calculations and food web models.
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A report on a rare case of Klebsiella ozaenae causing atrophic rhinitis in the UK.
BMJ Case Rep
PUBLISHED: 01-01-2011
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Ozena is a chronic disease of the nasal cavity characterised by atrophy of the mucosa and bone caused by Klebsiella ozaenae. It is endemic to subtropical and temperate regions affecting the lower socio-economic group, usually the poor who live in unhygienic conditions. It is a rare disease in the UK. There is usually a delay in diagnosis due to unfamiliarity of the disease. A 25-year-old Nigerian migrant presented with nasal obstruction with purulent nasal discharge. Isolation of the bacterium was found from cultures of nasal discharge, crusting and tissue biopsies. She was treated successfully with ciprofloxacin. It is important to consider this rare condition in cases of nasal obstruction even in non-endemic areas especially with the advances of modern travel.
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A dual host approach to transmembrane transport of salts.
Chem. Commun. (Camb.)
PUBLISHED: 11-22-2010
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A dual host approach for M(+)/Cl(-) co-transport has been shown to be effective in lipid bilayers consisting of POPC using fluorescence-based transport assays.
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Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits.
Appl. Environ. Microbiol.
PUBLISHED: 08-13-2010
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The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.
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Tripodal transmembrane transporters for bicarbonate.
Chem. Commun. (Camb.)
PUBLISHED: 08-06-2010
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Easy-to-make tripodal tris-thiourea receptors based upon tris(2-aminoethyl)amine are capable of chloride/bicarbonate transport and as such represent a new class of bicarbonate transport agent.
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Robotic nephroureterectomy with partial duodenectomy for invasive ureteral tumor.
JSLS
PUBLISHED: 05-19-2010
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Robotic surgery is gaining acceptance in the management of diverse urological disorders. Any minimally invasive procedure carries a risk of open conversion either for complications or unexpected intraoperative findings, but the additional dexterity of robotic instrumentation may allow even complex situations to be managed laparoscopically. We report the case of an upper tract transitional cell carcinoma discovered at the time of robotic nephroureterectomy to be invading the duodenum that was successfully excised robotically.
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Recurrent hypoglycemia increases hypothalamic glucose phosphorylation activity in rats.
Metab. Clin. Exp.
PUBLISHED: 05-12-2010
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The mechanisms underpinning impaired defensive counterregulatory responses to hypoglycemia that develop in some people with diabetes who suffer recurrent episodes of hypoglycemia are unknown. Previous work examining whether this is a consequence of increased glucose delivery to the hypothalamus, postulated to be the major hypoglycemia-sensing region, has been inconclusive. Here, we hypothesized instead that increased hypothalamic glucose phosphorylation, the first committed intracellular step in glucose metabolism, might develop following exposure to hypoglycemia. We anticipated that this adaptation might tend to preserve glucose flux during hypoglycemia, thus reducing detection of a falling glucose. We first validated a model of recurrent hypoglycemia in chronically catheterized (right jugular vein) rats receiving daily injections of insulin. We confirmed that this model of recurrent insulin-induced hypoglycemia results in impaired counterregulation, with responses of the key counterregulatory hormone, epinephrine, being suppressed significantly and progressively from the first day to the fourth day of insulin-induced hypoglycemia. In another cohort, we investigated the changes in brain glucose phosphorylation activity over 4 days of recurrent insulin-induced hypoglycemia. In keeping with our hypothesis, we found that recurrent hypoglycemia markedly and significantly increased hypothalamic glucose phosphorylation activity in a day-dependent fashion, with day 4 values 2.8 ± 0.6-fold higher than day 1 (P < .05), whereas there was no change in glucose phosphorylation activity in brain stem and frontal cortex. These findings suggest that the hypothalamus may adapt to recurrent hypoglycemia by increasing glucose phosphorylation; and we speculate that this metabolic adaptation may contribute, at least partly, to hypoglycemia-induced counterregulatory failure.
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PRNP haplotype associated with classical BSE incidence in European Holstein cattle.
PLoS ONE
PUBLISHED: 05-05-2010
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Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease of cattle. The bovine prion gene (PRNP) contains regions of both high and low linkage disequilibrium (LD) that appear to be conserved across Bos taurus populations. The region of high LD, which spans the promoter and part of intron 2, contains polymorphic loci that have been associated with classical BSE status. However, the complex genetic architecture of PRNP has not been systematically tested for an association with classical BSE.
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Characterization of microRNA expression in bovine adipose tissues: a potential regulatory mechanism of subcutaneous adipose tissue development.
BMC Mol. Biol.
PUBLISHED: 04-27-2010
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MicroRNAs (miRNAs), a family of small non-coding RNA molecules, appear to regulate animal lipid metabolism and preadipocyte conversion to form lipid-assimilating adipocytes (i.e. adipogenesis). However, no miRNA to date has been reported to modulate adipogenesis and lipid deposition in beef cattle.
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An anthrax subunit vaccine candidate based on protective regions of Bacillus anthracis protective antigen and lethal factor.
Vaccine
PUBLISHED: 04-19-2010
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Studies have confirmed the key role of Bacillus anthracis protective antigen (PA) in the US and UK human anthrax vaccines. However, given the tripartite nature of the toxin, other components, including lethal factor (LF), are also likely to contribute to protection. We examined the antibody and T cell responses to PA and LF in human volunteers immunized with the UK anthrax vaccine (AVP). Individual LF domains were assessed for immunogenicity in mice when given alone or with PA. Based on the results obtained, a novel fusion protein comprising D1 of LF and the host cell-binding domain of PA (D4) was assessed for protective efficacy. Murine protection studies demonstrated that both full-length LF and D1 of LF conferred complete protection against a lethal intraperitoneal challenge with B. anthracis STI spores. Subsequent studies with the LFD1-PAD4 fusion protein showed a similar level of protection. LF is immunogenic in humans and is likely to contribute to the protection stimulated by AVP. A single vaccine comprising protective regions from LF and PA would simplify production and confer a broader spectrum of protection than that seen with PA alone.
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A 2cM genome-wide scan of European Holstein cattle affected by classical BSE.
BMC Genet.
PUBLISHED: 03-29-2010
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Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Polymorphisms that alter the prion protein of sheep or humans have been associated with variations in transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that non-synonymous mutations in the bovine prion gene (PRNP) are associated with classical BSE disease susceptibility. However, two bovine PRNP insertion/deletion polymorphisms, one within the promoter region and the other in intron 1, have been associated with susceptibility to classical BSE. These associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. To test for associations with BSE susceptibility, we conducted a genome wide scan using a panel of 3,072 single nucleotide polymorphism (SNP) markers on 814 animals representing cases and control Holstein cattle from the United Kingdom BSE epidemic.
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Brain glucosamine boosts protective glucoprivic feeding.
Endocrinology
PUBLISHED: 02-23-2010
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The risk of iatrogenic hypoglycemia is increased in diabetic patients who lose defensive glucoregulatory responses, including the important warning symptom of hunger. Protective hunger symptoms during hypoglycemia may be triggered by hypothalamic glucose-sensing neurons by monitoring changes downstream of glucose phosphorylation by the specialized glucose-sensing hexokinase, glucokinase (GK), during metabolism. Here we investigated the effects of intracerebroventricular (ICV) infusion of glucosamine (GSN), a GK inhibitor, on food intake at normoglycemia and protective feeding responses during glucoprivation and hypoglycemia in chronically catheterized rats. ICV infusion of either GSN or mannoheptulose, a structurally different GK inhibitor, dose-dependently stimulated feeding at normoglycemia. Consistent with an effect of GSN to inhibit competitively glucose metabolism, ICV coinfusion of d-glucose but not l-glucose abrogated the orexigenic effect of ICV GSN at normoglycemia. Importantly, ICV infusion of a low GSN dose (15 nmol/min) that was nonorexigenic at normoglycemia boosted feeding responses to glucoprivation in rats with impaired glucose counterregulation. ICV infusion of 15 nmol/min GSN also boosted feeding responses to threatened hypoglycemia in rats with defective glucose counterregulation. Altogether our findings suggest that GSN may be a potential therapeutic candidate for enhancing defensive hunger symptoms during hypoglycemia.
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DR with a DSLR: Digital Radiography with a Digital Single-Lens Reflex camera.
Proc Soc Photo Opt Instrum Eng
PUBLISHED: 02-15-2010
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An inexpensive, portable digital radiography (DR) detector system for use in remote regions has been built and evaluated. The system utilizes a large-format digital single-lens reflex (DSLR) camera to capture the image from a standard fluorescent screen. The large sensor area allows relatively small demagnification factors and hence minimizes the light loss. The system has been used for initial phantom tests in urban hospitals and Himalayan clinics in Nepal, and it has been evaluated in the laboratory at the University of Arizona by additional phantom studies. Typical phantom images are presented in this paper, and a simplified discussion of the detective quantum efficiency of the detector is given.
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Genomic instability after targeted irradiation of human lymphocytes: evidence for inter-individual differences under bystander conditions.
Mutat. Res.
PUBLISHED: 02-01-2010
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Environmental (222)radon exposure is a human health concern, and many studies demonstrate that very low doses of high LET alpha-particle irradiation initiate deleterious genetic consequences in both irradiated and non-irradiated bystander cells. One consequence, radiation-induced genomic instability (RIGI), is a hallmark of tumorigenesis and is often assessed by measuring delayed chromosomal aberrations. We utilised a technique that facilitates transient immobilization of primary lymphocytes for targeted microbeam irradiation and have reported that environmentally relevant doses, e.g. a single (3)He(2+) particle traversal to a single cell, are sufficient to induce RIGI. Herein we sought to determine differences in radiation response in lymphocytes isolated from five healthy male donors. Primary lymphocytes were irradiated with a single particle per cell nucleus. We found evidence for inter-individual variation in radiation response (RIGI, measured as delayed chromosome aberrations). Although this was not highly significant, it was possibly masked by high levels of intra-individual variation. While there are many studies showing a link between genetic predisposition and RIGI, there are few studies linking genetic background with bystander effects in normal human lymphocytes. In an attempt to investigate inter-individual variation in the induction of bystander effects, primary lymphocytes were irradiated with a single particle under conditions where fractions of the population were traversed. We showed a marked genotype-dependent bystander response in one donor after exposure to 15% of the population. The findings may also be regarded as a radiation-induced genotype-dependent bystander effect triggering an instability phenotype.
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Integrated surveys of neglected tropical diseases in southern Sudan: how much do they cost and can they be refined?
PLoS Negl Trop Dis
PUBLISHED: 01-15-2010
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Increasing emphasis on integrated control of neglected tropical diseases (NTDs) requires identification of co-endemic areas. Integrated surveys for lymphatic filariasis (LF), schistosomiasis and soil-transmitted helminth (STH) infection have been recommended for this purpose. Integrated survey designs inevitably involve balancing the costs of surveys against accuracy of classifying areas for treatment, so-called implementation units (IUs). This requires an understanding of the main cost drivers and of how operating procedures may affect both cost and accuracy of surveys. Here we report a detailed cost analysis of the first round of integrated NTD surveys in Southern Sudan.
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Substituted fused bicyclic pyrrolizinones as potent, orally bioavailable hNK1 antagonists.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-14-2010
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Previous work on human NK(1) (hNK(1)) antagonists in which the core of the structure is a 5,5-fused pyrrolizinone has been disclosed. The structural-activity-relationship studies on simple alpha- and beta-substituted compounds of this series provided several potent and bioavailable hNK(1) antagonists that displayed excellent brain penetration as observed by their good efficacy in the gerbil foot-tapping (GFT) model assay. Several of these compounds exhibited 100% inhibition of the foot-tapping response at 0.1 and 24h with ID(50)s of less than 1 mpk. One particular alpha-substituted compound (2b) had an excellent pharmacokinetic profile across preclinical species with reasonable in vivo functional activity and minimal ancillary activity.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.