Grain Dryer Testing Facility

Our client, Dr. Maier, is a post-harvest engineer at Iowa State University. He presented our group with the problem that industry currently doesn’t have a third party facility that is able to test their grain dryers so this can lead to inconsistent results. There are tests being done on companies dryers, but it is by themselves and under their own procedure. The problem that arises from this is that each company is able to skew their data by their tests. Companies would like to be able to compare their dryers to other companies fairly to see the results. We have not found anyone who does such a procedure so this would be the first of its kind

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.Publisher PDFPeer reviewe

Grain Dryer Testing Facility

Our client, Dr. Maier, is a post-harvest engineer at Iowa State University. He presented our group with the problem that industry currently doesn’t have a third party facility that is able to test their grain dryers so this can lead to inconsistent results. There are tests being done on companies dryers, but it is by themselves and under their own procedure. The problem that arises from this is that each company is able to skew their data by their tests. Companies would like to be able to compare their dryers to other companies fairly to see the results. We have not found anyone who does such a procedure so this would be the first of its kind.</p

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations

Phylogenetic tree of mtDNA HVRI region and allele sharing matrix of mtDNA and autosomes.

<p>(<b>A</b>) The phylogenetic tree among human, chimpanzee, Bornean (red) and Sumatran (blue). The nodes shaded in cyan represent the grouping of the three Sumatran individuals that has the furthest distance to the rest clustering of the Sumatran group. The 10 re-sequenced individuals from our study are colored as red (Bornean) or blue (Sumatran). The corresponding geographic origins are shown on the right with the following annotation (SU: Sumatran; TU/SL: Tuanan or Sungai Lading; DV/K: Danum Valley or Kinabatangan; SA/GP: Sabangau or Gunung Palung; EK: East Kalimantan including Kutai national park or Sangatta; SAR/DS: Semongok Wildlife Rehabilitation Centre or Danau Sentarum). (<b>B</b>) The IBS allele sharing matrix among the 10 individuals from our study with the same group coloring scheme. The upper and lower triangular matrix represents the IBS sharing of all mtDNA variation loci (n = 1084) and autosomal variation loci (n = 11,866,619), respectively.</p

Genes under positive selection identified by SnIPRE.

*<p>and ** denote genes identified as putative positively selected on orang-utan and human lineage, respectively, in previous study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077175#pone.0077175-Locke1" target="_blank">[22]</a>.</p

Summary statistics of McDonald-Kreitman table entries for Bornean and Sumatran population using Human (hg19) as outgroup.

*<p>This is total aligned length.</p

SFS analysis.

<p>(<b>A</b>) SFS for all genomic SNPs (Genome), synonymous (S) or non-synonymous (NS) SNPs in Bornean (Red) and Sumatran (Blue) population. (<b>B</b>) Two-dimensional SFS (Bornean on Y axis and Sumatran on X axis). Top row: Spectra for different functional categories of SNPs. To make all the spectra directly comparable, the non-coding and synonymous spectra have been re-scaled to represent the same number of segregating SNPs as the non-synonymous spectrum. Bottom row: residuals between pairs of spectra. Bottom-left compares synonymous and non-coding spectra, and bottom-right compares non-synonymous and synonymous spectra. Red and blue entries indicate, respectively, that the first spectrum has greater or fewer SNPs in that entry than the second.</p

Distribution of the proportion SNPs within each of the PolyPhen categories based on PolyPhen-2 result.

<p>Error bars denote 95% confidence intervals on the proportion of SNPs in each category.</p