The Chasm Between the Human and Chimpanzee Genomes: A Review of the Evolutionary Literature

Data has been extracted from secular literature that is contrary to the common claim that very few genetic differences exist between chimpanzees and humans. We found that significant reported differences exist in genomic similarity and gene regulation between chimpanzees and humans. The DNA sequence differences and genetic mechanisms reported in the literature support the conclusion that significant and unbridgeable genetic differences exist between humans and chimpanzees that defy evolutionary claims of a common ancestor

Understanding “Understanding” in Public Understanding of Science

This study examines the conflation of terms such as “knowledge” and “understanding” in peer-reviewed literature, and tests the hypothesis that little current research clearly distinguishes between importantly distinct epistemic states. Two sets of data are presented from papers published in the journal Public Understanding of Science. In the first set, the digital text analysis tool, Voyant, is used to analyze all papers published in 2014 for the use of epistemic success terms. In the second set of data, all papers published in Public Understanding of Science from 2010–2015 are systematically analyzed to identify instances in which epistemic states are empirically measured. The results indicate that epistemic success terms are inconsistently defined, and that measurement of understanding, in particular, is rarely achieved in public understanding of science studies. We suggest that more diligent attention to measuring understanding, as opposed to mere knowledge, will increase efficacy of scientific outreach and communication efforts

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity

Movements of House Sparrows Captured at an Experimental Grain Station in Fargo, North Dakota

From 2 August through 1 October 1993 we banded and leg flagged 362 house sparrows (126 adults, 236 juveniles) captured in a decoy trap at an experimental grain station on the campus of North Dakota State University, Fargo (NDSU). We documented sightings of leg-flagged birds between 3 August 1993 and 14 December 1994. Over this period, 56 (66%) of the total 76 observations of leg-flagged birds were on the NDSU campus; 21 (28%) of the 76 observations occurred between March and December 1994, a minimum of 5 months after the leg flags were attached and following the 1993-1994 winter. Of the 21 observations in 1994, 16 (76%) occurred on campus. The farthest sighting of a leg-flagged bird was 6.5 km (4 mi.) from the trap site. The data indicated that we captured and marked a localized population. A concerted effort based on trapping could reduce house sparrow damage on the small, experimental plots of cereal grains and sunflower grown at the station

A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants

Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and quantitative PCR to allow for a robust determination of the level of nearly any cellular RNA in the background of 5,500 different mutants. As an initial test of this approach, we sought to identify the full complement of factors that impact pre–mRNA splicing. Increasing lines of evidence suggest a relationship between pre–mRNA splicing and other cellular pathways including chromatin remodeling, transcription, and 3′ end processing, yet in many cases the specific proteins responsible for functionally connecting these pathways remain unclear. Moreover, it is unclear whether all pathways that are coupled to splicing have been identified. As expected, our approach sensitively detects pre–mRNA accumulation in the vast majority of strains containing mutations in known splicing factors. Remarkably, however, several additional candidates were found to cause increases in pre–mRNA levels similar to that seen for canonical splicing mutants, none of which had previously been implicated in the splicing pathway. Instead, several of these factors have been previously implicated to play roles in chromatin remodeling, 3′ end processing, and other novel categories. Further analysis of these factors using splicing-sensitive microarrays confirms that deletion of Bdf1, a factor that links transcription initiation and chromatin remodeling, leads to a global splicing defect, providing evidence for a novel connection between pre–mRNA splicing and this component of the SWR1 complex. By contrast, mutations in 3′ end processing factors such as Cft2 and Yth1 also result in pre–mRNA splicing defects, although only for a subset of transcripts, suggesting that spliceosome assembly in S. cerevisiae may more closely resemble mammalian models of exon-definition. More broadly, our work demonstrates the capacity of this approach to identify novel regulators of various cellular RNAs

Bundle gerbes and moduli spaces

In this paper, we construct the index bundle gerbe of a family of self-adjoint Dirac-type operators, refining a construction of Segal. In a special case, we construct a geometric bundle gerbe called the caloron bundle gerbe, which comes with a natural connection and curving, and show that it is isomorphic to the analytically constructed index bundle gerbe. We apply these constructions to certain moduli spaces associated to compact Riemann surfaces, constructing on these moduli spaces, natural bundle gerbes with connection and curving, whose 3-curvature represent Dixmier-Douady classes that are generators of the third de Rham cohomology groups of these moduli spaces.Comment: 19 pages. Latex2e, typos corrected, a reference adde

HAS AN INTEGRATED PEST MANAGEMENT APPROACH REDUCED BLACKBIRD DAMAGE TO SUNFLOWER?

Since the mid- 1970s many new and modified damage abatement methods have been used to reduce blackbird damage to ripening sunflower in the northern Great Plains. To assess the overall impact of these techniques, we analyzed the dynamic relationship between breeding blackbird densities and sunflower damage. Breeding density estimates were made at both the regional and county levels, whereas, sunflower damage estimates were made at the county level only. Periodic regional estimates of breeding densities between 1967 and 1998 for red-winged blackbirds (Agelaius phoeniceus), common grackles (Quiscalus quiscula), and yellow-headed blackbirds (Xanthocephalus xanthocephalus) showed no differences among years. To increase our ability to detect changes in breeding density, we started intensive county-level surveys in 1996. These surveys, in four counties in North Dakota and South Dakota, showed that blackbird densities were greater in 1998 and 1999 than during the previous two years. We surveyed sunflower damage in two of these counties from 1994 to 1998 and found no difference in damage (F= 1.8%) among years. In 1997 and 1998, with the two other counties added to the survey, we found that damage was similar between years, averaging 2.2%. Dollar loss per hectare was trending lower in three of the study counties that had a historical database for comparison. This supports the idea that \u27local\u27 breeding densities are not correlated with damage levels. We will continue to use annual estimates of breeding densities and sunflower damage to assess the effects of an evolving Integrated Pest Management program

Vascular Endothelial Growth Factor mRNA Isoforms 120 and 164 are Differentially Regulated Prior to Ovulation

Vascular Endothelial Growth Factor (VEGF) is produced by cells surrounding the egg in the follicle prior to ovulation. If VEGF is inhibited, ovulation does not occur. The VEGF gene can be spliced to produce different protein isoforms which have specific functions. Our objective was to determine if VEGF 120 and 164 mRNA isoforms are differentially regulated in the preovulatory follicle. From our studies, VEGF isoforms are differentially regulated during both CL regression and after a simulated LH surge. Differences observed in VEGF isoform regulation may allow for manipulation of ovulation in the beef cow