Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

[Image: see text] Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein level. This can advance our understanding of genome function, discovering novel genes and gene structure that have not yet been identified or validated. Because of the high-throughput shotgun nature of most proteomics experiments, it is essential to carefully control for false positives and prevent any potential misannotation. A number of statistical procedures to deal with this are in wide use in proteomics, calculating false discovery rate (FDR) and posterior error probability (PEP) values for groups and individual peptide spectrum matches (PSMs). These methods control for multiple testing and exploit decoy databases to estimate statistical significance. Here, we show that database choice has a major effect on these confidence estimates leading to significant differences in the number of PSMs reported. We note that standard target:decoy approaches using six-frame translations of nucleotide sequences, such as assembled transcriptome data, apparently underestimate the confidence assigned to the PSMs. The source of this error stems from the inflated and unusual nature of the six-frame database, where for every target sequence there exists five “incorrect” targets that are unlikely to code for protein. The attendant FDR and PEP estimates lead to fewer accepted PSMs at fixed thresholds, and we show that this effect is a product of the database and statistical modeling and not the search engine. A variety of approaches to limit database size and remove noncoding target sequences are examined and discussed in terms of the altered statistical estimates generated and PSMs reported. These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes, while still controlling for false positives

Spectroscopic And Computational Studies Of The Laser Photolysis Of Matrix Isolated 1,2-dibromoethanes: Formation And Fate Of The Bromoethyl Radicals

We report experimental and computational studies of the photolysis of atmospherically important 1,2-dibromoethanes (1,2-C(2)X(4)Br(2); X = H, F) in Ar matrixes at 5 K. Using the pulsed deposition method, we find that significant conformational relaxation occurs for 1,2-C(2)H(4)Br(2) (EDB; observed anti/gauche ratio =30:1) but not for 1,2-C(2)F(4)Br(2) (TFEDB; anti/gauche = 3:1), which is traced to a larger barrier to rotation about the C-C bond in the latter. Laser photolysis of matrix-isolated EDB at 220 nm reveals the growth of infrared bands assigned to the gauche conformer and C(2)H(4)-Br(2) charge transfer complex (both as major products), and the C(2)H(4)Br radical and C(2)H(3)Br-HBr complex as minor (trace) products. The presence of the C(2)H(4)-Br(2) complex is confirmed in the UV/visible spectrum, which shows an intense charge transfer band at 237 nm that grows in intensity upon annealing. In contrast to previous reports, our experimental and computational results do not support a bridged structure for the C(2)H(4)Br radical in either the gas phase or matrix environments. We also report on the laser photolysis of matrix-isolated TFEDB at 220 nm. Here, the dominant photoproducts are the anti and gauche conformers of the C(2)F(4)Br radical, the vibrational and electronic spectra of which are characterized here for the first time. The increase in yield of radical for TFEDB vs EDB is consistent with the stronger C-Br bond in the fluoro-substituted radical species. The photochemistry of the C(2)F(4)Br radical following excitation at 266 nm was investigated and found to lead C-Br bond cleavage and formation of C(2)F(4). The implications of this work for the atmospheric and condensed phase photochemistry of the alkyl halides is emphasized

Sonographic Findings of Pectoralis Major Tears With Surgical, Clinical, and Magnetic Resonance Imaging Correlation in 6 Patients

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135465/1/jum200524125.pd

Characterization of Iso -Cf2 I2 in Frequency and Ultrafast Time Domains

The photolysis of diiododifluoromethane (CF2 I2) in condensed phases was studied by a combination of matrix isolation and ultrafast time-resolved spectroscopy, in concert with ab initio calculations. Photolysis at wavelengths of 355 or 266 nm of CF2 I2:Ar samples (1:5000) held at ∼8 K yielded iso -CF2 I2 (F2 C-I-I), a metastable isomer of CF2 I2, characterized here for the first time. The infrared (IR) spectra of this isomer were recorded in matrix experiments, and the derived positions of the C-F stretching modes are in very good agreement with the predictions of high level ab initio calculations, which show that the iso -form is a minimum on the CF2 I2 ground state potential energy surface. The formation of this isomer following 350 nm excitation of CF2 I 2 in room temperature CCl4 solutions was monitored through its intense C-F stretching mode by means of ultrafast time-resolved IR absorption. Together, matrix isolation and ultrafast IR absorption experiments suggest that the formation of iso -CF2 I2 occurs via recombination of CF2 I radical and I atom. Ultrafast IR experiments detect a delayed rise of iso -CF2 I-I absorption, placing an upper limit of 400 fs for the C-I bond dissociation and primary geminate recombination processes. The product absorption spectrum recorded 1 ns after 350 nm excitation of CF2 I2 in solution is virtually identical to the visible absorption spectrum of i so -CF2 I2 trapped in matrix isolation experiments [with subtracted I2 (X) absorption]. The formation of this isomer in solution at room temperature has direct dynamic implications for the ultrafast production of molecular iodine from electronically excited CF 2 I2. © 2010 American Institute of Physics

Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region

Abstract Background The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa. Methods Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution. Results Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa. Conclusions Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes