SOLUTIONS FOR IMPERILED BAT CONSERVATION: INTEGRATING ECOLOGY, TECHNOLOGY, AND THE PUBLIC

Bat populations have plummeted in Missouri since the introduction of white-nose syndrome (WNS) in 2012, presenting challenges in researching understudied species’ habitat ecology. Frequently incorporated survey techniques, such as mist netting and radio-telemetry, have become unreliable post-WNS. In response to address the challenge of studying rare species, we explored the alternative strategies of acoustic monitoring, acoustic lures, and human dimension surveys that may enhance surveys. Our goals from these objectives included comparing the methods to recommend better management decisions for imperiled bat species post-WNS. For Chapter I, we surveyed three imperiled bat species in southeastern Missouri, including the northern long-eared bat Myotis septentrionalis, little brown bat Myotis lucifugus, and tricolored bat Perimyotis subflavus using mist-netting and acoustic monitoring. We assessed the efficacy of modern acoustic monitoring activities to more traditional approaches of mist-netting and radio-telemetry. We never captured northern long-eared bats or little brown bats during our mist net surveys, but we did detect them acoustically. Chapter II evaluated the acoustic lures’ success in increasing detection success of mist net and acoustic detector surveys. We captured two tricolored bats when we used an acoustic lure and detected them acoustically during the two years of the study. Our capture success allowed us to identify the first tricolored bat maternity roost within a Missouri Department of Conservation (MDC) area in Carter County through radio-telemetry. We found our acoustic lure positively affected the acoustic activity of the endangered Indiana bat Myotis sodalis and big brown bat Eptesicus fuscus. We also assessed a human dimensions analysis to assess the level of public familiarity of bat species in Missouri, WNS awareness, perceived attitudes, and trust in the MDC. We found that respondents were less knowledgeable about WNS and bat natural history, despite their overall positive or neutral perception of bats. The public in our study trusted the MDC as a natural resource management agency. Both public trust and accurate knowledge of bat natural history and threats must be accounted for when suggesting forest management modifications to benefit our three imperiled target species

A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function.

BACKGROUND: Coronins belong to the superfamily of the eukaryotic-specific WD40-repeat proteins and play a role in several actin-dependent processes like cytokinesis, cell motility, phagocytosis, and vesicular trafficking. Two major types of coronins are known: First, the short coronins consisting of an N-terminal coronin domain, a unique region and a short coiled-coil region, and secondly the tandem coronins comprising two coronin domains. RESULTS: 723 coronin proteins from 358 species have been identified by analyzing the whole-genome assemblies of all available sequenced eukaryotes (March 2011). The organisms analyzed represent most eukaryotic kingdoms but also cover every taxon several times to provide a better statistical sampling. The phylogenetic tree of the coronin domains based on the Bayesian method is in accordance with the most recent grouping of the major kingdoms of the eukaryotes and also with the grouping of more recently separated branches. Based on this "holistic" approach the coronins group into four classes: class-1 (Type I) and class-2 (Type II) are metazoan/choanoflagellate specific classes, class-3 contains the tandem-coronins (Type III), and the new class-4 represents the coronins fused to villin (Type IV). Short coronins from non-metazoans are equally related to class-1 and class-2 coronins and thus remain unclassified. CONCLUSIONS: The coronin class distribution suggests that the last common eukaryotic ancestor possessed a single and a tandem-coronin, and most probably a class-4 coronin of which homologs have been identified in Excavata and Opisthokonts although most of these species subsequently lost the class-4 homolog. The most ancient short coronin already contained the trimerization motif in the coiled-coil domain

Habitat Ecology, Species Presense, and Public Perception of Three Declining Bat Species in Southeastern Missouri

The populations of three bat species, the Northern long-eared bat (Myotis septentrionalis), tricolored bat (Per­imyotis subflavus), and little brown bat (Myotis lucifugus), have declined in southeastern Missouri since the in­troduction of white-nose syndrome (WNS) in 2012. The current maternity habitat of the remaining populations in the counties of Shannon, Carter, and Reynolds are unknown. In order to provide protection and conservation for the species, it is critical that their maternity roosts be identified. To achieve these goals, we will incorporate bat survey tools such as acoustic surveys, acoustic lures, and mist netting within the three counties to determine spe­cies occupancy and roost locations. During our pilot season in 2018, we were unable to capture our target species but acoustically recorded likely P. subflavus echolocation calls. The next two summers of research will occur within the same counties but include a larger survey area. Beginning in 2019, we will assess the perceived attitudes of bats based on the results of a survey given to local citizens within the study areas to bolster bat conservation and education

Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

<p>Abstract</p> <p>Background</p> <p>Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3'- or 5'-end, intron retention, and mutually exclusive splicing. The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner.</p> <p>Results</p> <p>We have implemented an extension to the WebScipio software to search for mutually exclusive exons. Here, the search is based on the precondition that mutually exclusive exons encode regions of the same structural part of the protein product. This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. Mutually exclusive exons that are not homologous and not of about the same length will not be found. Using the new algorithm, mutually exclusive exons in several example genes, a dynein heavy chain, a muscle myosin heavy chain, and Dscam were correctly identified. In addition, the algorithm was applied to the whole <it>Drosophila melanogaster </it>X chromosome and the results were compared to the Flybase annotation and an <it>ab initio </it>prediction. Clusters of mutually exclusive exons might be subsequent to each other and might encode dozens of exons.</p> <p>Conclusions</p> <p>This is the first implementation of an automatic search for mutually exclusive exons in eukaryotes. Exons are predicted and reconstructed in the same run providing the complete gene structure for the protein query of interest. WebScipio offers high quality gene structure figures with the clusters of mutually exclusive exons colour-coded, and several analysis tools for further manual inspection. The genome scale analysis of all genes of the <it>Drosophila melanogaster </it>X chromosome showed that WebScipio is able to find all but two of the 28 annotated mutually exclusive spliced exons and predicts 39 new candidate exons. Thus, WebScipio should be able to identify mutually exclusive spliced exons in any query sequence from any species with a very high probability. WebScipio is freely available to academics at <url>http://www.webscipio.org</url>.</p

GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures

Background: All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results: GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol

LISA and LISA PathFinder, the endeavour to detect low frequency GWs

This is a review about LISA and its technology demonstrator, LISA PathFinder. We first describe the conceptual problems which need to be overcome in order to set up a working interferometric detector of low frequency Gravitational Waves (GW), then summarise the solutions to them as currently conceived by the LISA mission team. This will show that some of these solutions require new technological abilities which are still under development, and which need proper test before being fully implemented. LISA PathFinder (LPF) is the the testbed for such technologies. The final part of the paper will address the ideas and concepts behind the PathFinder as well as their impact on LISA.Comment: 25 pages, 21 figures, presented at the Spanish Relativity Meeting, Mallorca September 2006. Will be published in Journal of Physics: Conference Series, IOP. To be published in Journal of Physics: Conference Series, IO

Acceleration disturbances and requirements for ASTROD I

ASTRODynamical Space Test of Relativity using Optical Devices I (ASTROD I) mainly aims at testing relativistic gravity and measuring the solar-system parameters with high precision, by carrying out laser ranging between a spacecraft in a solar orbit and ground stations. In order to achieve these goals, the magnitude of the total acceleration disturbance of the proof mass has to be less than 10&#8722;13 m s&#8722;2 Hz&#8722;1/2 at 0.1 m Hz. In this paper, we give a preliminary overview of the sources and magnitude of acceleration disturbances that could arise in the ASTROD I proof mass. Based on the estimates of the acceleration disturbances and by assuming a simple controlloop model, we infer requirements for ASTROD I. Our estimates show that most of the requirements for ASTROD I can be relaxed in comparison with Laser Interferometer Space Antenna (LISA).Comment: 19 pages, two figures, accepted for publication by Class. Quantum Grav. (at press

diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data

<p>Abstract</p> <p>Background</p> <p>Nowadays, the sequencing of even the largest mammalian genomes has become a question of days with current next-generation sequencing methods. It comes as no surprise that dozens of genome assemblies are released per months now. Since the number of next-generation sequencing machines increases worldwide and new major sequencing plans are announced, a further increase in the speed of releasing genome assemblies is expected. Thus it becomes increasingly important to get an overview as well as detailed information about available sequenced genomes. The different sequencing and assembly methods have specific characteristics that need to be known to evaluate the various genome assemblies before performing subsequent analyses.</p> <p>Results</p> <p>diArk has been developed to provide fast and easy access to all sequenced eukaryotic genomes worldwide. Currently, diArk 2.0 contains information about more than 880 species and more than 2350 genome assembly files. Many meta-data like sequencing and read-assembly methods, sequencing coverage, GC-content, extended lists of alternatively used scientific names and common species names, and various kinds of statistics are provided. To intuitively approach the data the web interface makes extensive usage of modern web techniques. A number of search modules and result views facilitate finding and judging the data of interest. Subscribing to the RSS feed is the easiest way to stay up-to-date with the latest genome data.</p> <p>Conclusions</p> <p>diArk 2.0 is the most up-to-date database of sequenced eukaryotic genomes compared to databases like GOLD, NCBI Genome, NHGRI, and ISC. It is different in that only those projects are stored for which genome assembly data or considerable amounts of cDNA data are available. Projects in planning stage or in the process of being sequenced are not included. The user can easily search through the provided data and directly access the genome assembly files of the sequenced genome of interest. diArk 2.0 is available at <url>http://www.diark.org</url>.</p