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Consumers are often confused and reluctant to purchase products from fresh retail meat counters that exhibit significant color variations. This hesitation to purchase results in annual profit loss to the pork industry. Processes to minimize color variation remain a major focus of the industry and many meat science programs across the globe. Previously, we found inherent muscle characteristics contribute to variations in pork quality but these characteristics fail to explain the high frequency of two-toning and other pork quality defects routinely occurring in many hog processing facilities. Therefore, we hypothesized harvesting practices, such as scald alter color across muscles of the ham. Scald time was initially investigated using 32 carcasses subjected to either a 4 (n=16) or 8 (n=16) min scald time. Samples were collected before or after scalding and at 24 hrs. A 50% reduction in scald time resulted in (p < 0.0001) lighter muscle color (L*) early postmortem, although the 8 min scald treatment was lighter (p < 0.005) at 24 hrs. Although differences in pH (p < 0.0001) and color were noted, ultimate carcass temperature was not affected. To that end, we moved to validate our hypothesis in an industrial plant setting. Carcasses (n=200) were assigned treatments of 6.5 or 7.5 min scald times, and SM muscle samples were collected at 24 hrs. Surprisingly, the shorter scald time resulted in (p < 0.05) a lighter color, contradicting our first study. To explore this color issue further, we uncoupled scald from the dehairing process. To achieve this goal, carcasses (n=24) were assigned to either an 8 or 16 min time to dehair, with or without scalding. Protracted time to dehair resulted in higher ultimate pH (p < 0.005) and less color variation across the muscle (p < 0.05). Though a color gradient remained, the variation across the muscle was reduced by increasing time to dehair. These data show time to dehair affects pork quality development and suggest that delaying time t

A study of the development of the 'Dawn of Man' sequence in Stanley Kubrick and Arthur C. Clarke's 1968 film '2001: A Space Odyssey', and the ideas about human evolution, human nature, and man's future in space which lay behind it. Based principally on material in the Kubrick Archive at the University of the Arts, London.

A study of the development of the 'Dawn of Man' sequence in Stanley Kubrick and Arthur C. Clarke's 1968 film '2001: A Space Odyssey', and the ideas about human evolution, human nature, and man's future in space which lay behind it. Based principally on material in the Kubrick Archive at the University of the Arts, London.

A study of the development of the 'Dawn of Man' sequence in Stanley Kubrick and Arthur C. Clarke's 1968 film '2001: A Space Odyssey', and the ideas about human evolution, human nature, and man's future in space which lay behind it. Based principally on material in the Kubrick Archive at the University of the Arts, London.

A study of the development of the 'Dawn of Man' sequence in Stanley Kubrick and Arthur C. Clarke's 1968 film '2001: A Space Odyssey', and the ideas about human evolution, human nature, and man's future in space which lay behind it. Based principally on material in the Kubrick Archive at the University of the Arts, London.

Jeffrey Winfree, a career Army soldier,shares his experiences and insights from his time spent in Iraq during the Iraq War.

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (~1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome., Bill & Melinda Gates Foundation, Ellison Medical Foundation, Exxon Mobil Foundation, Fogarty International Center, National Institute of Allergy and Infectious Diseases (U.S.), Burroughs Wellcome Fund, David & Lucile Packard Foundation, National Science Foundation (U.S.). Graduate Research Fellowship Program

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (~1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome., Bill & Melinda Gates Foundation, Ellison Medical Foundation, Exxon Mobil Foundation, Fogarty International Center, National Institute of Allergy and Infectious Diseases (U.S.), Burroughs Wellcome Fund, David & Lucile Packard Foundation, National Science Foundation (U.S.). Graduate Research Fellowship Program

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.

Widespread antimalarial resistance has been a barrier to malaria elimination efforts in Sri Lanka. Analysis of genetic markers in historic parasites may uncover trends in the spread of resistance. We examined the frequency of Plasmodium falciparum chloroquine transporter (pfcrt; codons 72-76) haplotypes in Sri Lanka in 1996-1998 and 2004-2006 using a high-resolution melting assay. Among 59 samples from 1996 to 1998, we detected the SVMNT (86%), CVMNK (10%), and CVIET (2%) haplotypes, with a positive trend in SVMNT and a negative trend in CVMNK frequency (P = 0.004) over time. Among 24 samples from 2004 to 2006, we observed only the SVMNT haplotype. This finding indicates selection for the SVMNT haplotype over time and its possible fixation in the population.

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.

Widespread antimalarial resistance has been a barrier to malaria elimination efforts in Sri Lanka. Analysis of genetic markers in historic parasites may uncover trends in the spread of resistance. We examined the frequency of Plasmodium falciparum chloroquine transporter (pfcrt; codons 72-76) haplotypes in Sri Lanka in 1996-1998 and 2004-2006 using a high-resolution melting assay. Among 59 samples from 1996 to 1998, we detected the SVMNT (86%), CVMNK (10%), and CVIET (2%) haplotypes, with a positive trend in SVMNT and a negative trend in CVMNK frequency (P = 0.004) over time. Among 24 samples from 2004 to 2006, we observed only the SVMNT haplotype. This finding indicates selection for the SVMNT haplotype over time and its possible fixation in the population.

Widespread antimalarial resistance has been a barrier to malaria elimination efforts in Sri Lanka. Analysis of genetic markers in historic parasites may uncover trends in the spread of resistance. We examined the frequency of Plasmodium falciparum chloroquine transporter (pfcrt; codons 72-76) haplotypes in Sri Lanka in 1996-1998 and 2004-2006 using a high-resolution melting assay. Among 59 samples from 1996 to 1998, we detected the SVMNT (86%), CVMNK (10%), and CVIET (2%) haplotypes, with a positive trend in SVMNT and a negative trend in CVMNK frequency (P = 0.004) over time. Among 24 samples from 2004 to 2006, we observed only the SVMNT haplotype. This finding indicates selection for the SVMNT haplotype over time and its possible fixation in the population.

Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage. Methods A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%), for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome. Results Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing. Conclusion This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory., National Institutes of Health (U.S), Broad Institute of MIT and Harvard (SPARC funding), Ellison Medical Foundation, Burroughs Wellcome Fund, Bill & Melinda Gates Foundation, National Institute of Allergy and Infectious Diseases (U.S.) (NIAID). Microbial Sequencing Center, Fogarty International Center, Exxon Mobil Foundation, National Institutes of Health (U.S) (K23 grant K23AIO72033-01)

Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, inter-population differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits., National Institutes of Health (U.S.), Broad Institute of Harvard and MIT, Burroughs Wellcome Fund, Bill & Melinda Gates Foundation, National Institute of Allergy and Infectious Diseases (U.S.). Microbial Sequencing Center, Ellison Medical Foundation, Fogarty International Center, Exxon Mobil Foundation, National Center for Research Resources (U.S.) (Grant U54 RR020278)

Background: Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage. Methods: A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%), for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome. Results: Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing. Conclusion: This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory.