The genome of Przewalski's horse (Equus ferus przewalskii).

The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild multiple conservation efforts convened to preserve the species, including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.

The genome of Przewalski's horse (Equus ferus przewalskii).

The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.

Comparison of linear model and artificial neural network using antler beam diameter and length of white-tailed deer (Odocoileus virginianus) dataset.

Evaluation of harvest data remains one of the most important sources of information in the development of strategies to manage regional populations of white-tailed deer. While descriptive statistics and simple linear models are utilized extensively, the use of artificial neural networks for this type of data analyses is unexplored. Linear model was compared to Artificial Neural Networks (ANN) models with Levenberg-Marquardt (L-M), Bayesian Regularization (BR) and Scaled Conjugate Gradient (SCG) learning algorithms, to evaluate the relative accuracy in predicting antler beam diameter and length using age and dressed body weight in white-tailed deer. Data utilized for this study were obtained from male animals harvested by hunters between 1977-2009 at the Berry College Wildlife Management Area. Metrics for evaluating model performance indicated that linear and ANN models resulted in close match and good agreement between predicted and observed values and thus good performance for all models. However, metrics values of Mean Absolute Error and Root Mean Squared Error for linear model and the ANN-BR model indicated smaller error and lower deviation relative to the mean values of antler beam diameter and length in comparison to other ANN models, demonstrating better agreement of the predicted and observed values of antler beam diameter and length. ANN-SCG model resulted in the highest error within the models. Overall, metrics for evaluating model performance from the ANN model with BR learning algorithm and linear model indicated better agreement of the predicted and observed values of antler beam diameter and length. Results of this study suggest the use of ANN generated results that are comparable to Linear Models of harvest data to aid in the development of strategies to manage white-tailed deer.

Sequencing artifacts in the type A influenza databases and attempts to correct them.

BACKGROUND: There are over 276 000 influenza gene sequences in public databases, with the quality of the sequences determined by the contributor. OBJECTIVE: As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate. METHODS: Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on sequences with additional nucleotides upstream or downstream of the highly conserved non-coding ends of the viral segments. RESULTS AND CONCLUSIONS: A total of 1081 sequences were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer sequence wasn't removed from the sequence; PCR product was cloned and plasmid sequence was included in the sequence; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide sequence were also commonly observed, but in many cases it was unclear if the sequence was correct or actually contained an error. A total of 215 sequences, or 22.8% of the suspect sequences, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional sequences with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of sequences submitted to public databases is needed to fully reap the benefits of these large data sets.

Modifications of human carboxylesterase for improved prodrug activation.

BACKGROUND: Carboxylesterases (CEs) are ubiquitous enzymes responsible for the hydrolysis of numerous clinically useful drugs. As ester moieties are frequently included in molecules to improve their water solubility and bioavailability, de facto they become substrates for CEs. OBJECTIVE: In this review, we describe the properties of human CEs with regard to their ability to activate anticancer prodrugs and demonstrate how structure-based design can be used to modulate substrate specificity and to increase efficiency of hydrolysis. METHODS: A specific example using CPT-11 and a human liver CE is discussed. However, these techniques can be applied to other enzymes and their associated prodrugs. RESULTS: Structure-guided mutagenesis of CEs can be employed to alter substrate specificity and generate novel enzymes that are efficacious at anticancer prodrug activation.

Characterization of chromodulin by X-ray absorption and electron paramagnetic resonance spectroscopies and magnetic susceptibility measurements.

The biologically active form of the essential trace element chromium is believed to be the oligopeptide chromodulin. Chromodulin binds four chromic ions before binding at or near the active site of activating insulin receptor and subsequently potentiating the tyrosine kinase activity of the receptor. Charge balance arguments and preliminary spectroscopic studies suggested that the chromic centers might be part of a multinuclear assembly. Using a combination of X-ray absorption and electron paramagnetic resonance spectroscopies and variable-temperature magnetic susceptibility measurements, we found that holochromodulin is shown to possess an antiferromagnetically coupled trinuclear assembly which probably weakly interacts with a fourth chromium center. The chromium centers possess octahedron coordination comprised of oxygen-based ligation, presumably derived primarily from oligopeptide-supplied carboxylate groups. X-ray absorption data cannot be reproduced with the presence of sulfur atom(s), indicating that the cysteine thiolate group does not coordinate to the chromium centers. Thus, chromodulin possesses a unique type of multinuclear assembly, distinct from those known in other bioinorganic systems.