The effect of toxic Microcystis aeruginosa on four different populations of Daphnia

Cyanobacteria reduce the fitness of many Daphnia species, and blooms in eutrophic lakes may place strong selective pressure upon these primary consumers. This study examines the ability of daphnids to resist the deleterious effects of toxic Microcystis and determine if this resistance is related to the trophic conditions of their native lakes. Three populations of Daphnia pulex/pulicaria were examined; D. pulicaria from eutrophic Klamath Lake in Oregon, D. pulex from eutrophic Old Durham Reservoir in New Hampshire, and D. pulicaria from oligotrophic Russell Pond in New Hampshire. D. carinata from meso-oligotrophic Lake Rotoaira in New Zealand was used as a known cyanobacteria-sensitive species. Ten-day old 5th-6th instar animals were exposed to a mixture of Microcystis aeruginosa and Chlorella vulgaris (25% and 100% M. aeruginosa). Body length, lipid index, reproductive index and clearance rate were assessed for each population after 120 hours of treatment. A feeding bioassay response quantifying the energetic (feeding rate) cost of post abdominal rejections was also determined for a gradient of M. aeruginosa concentrations from 0% to 100%. The four populations of Daphnia exhibited different rates of decline in overall fitness when exposed to Microcystis. Populations exposed to Microcystis exhibited reduced thoracic beat rate, lower lipid and reproductive indexes, and higher cost of post abdominal rejections in comparison to daphnids in the control Chlorella. Length was not a sensitive indicator of fitness level. D. pulex from eutrophic Klamath Lake had a mean clearance rate in 100% Microcystis that was three to four times higher than D. pulicaria from oligotrophic Russell Pond. In general, daphnids from oligotrophic lakes exhibited a more drastic decline in fitness than daphnids from eutrophic lakes. This suggests that taxonomically related populations of Daphnia have evolved a suite of adaptations to Microcystis depending upon their history of exposure

Formalization of the fundamental group in untyped set theory using auto2

We present a new framework for formalizing mathematics in untyped set theory using auto2. Using this framework, we formalize in Isabelle/FOL the entire chain of development from the axioms of set theory to the definition of the fundamental group for an arbitrary topological space. The auto2 prover is used as the sole automation tool, and enables succinct proof scripts throughout the project.Comment: 17 pages, accepted for ITP 201

Foundational nonuniform (co)datatypes for higher-order logic

Nonuniform (or “nested” or “heterogeneous”) datatypes are recursively defined types in which the type arguments vary recursively. They arise in the implementation of finger trees and other efficient functional data structures. We show how to reduce a large class of nonuniform datatypes and codatatypes to uniform types in higher-order logic. We programmed this reduction in the Isabelle/HOL proof assistant, thereby enriching its specification language. Moreover, we derive (co)recusion and (co)induction principles based on a weak variant of parametricity

PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE

Efficient Certified RAT Verification

Clausal proofs have become a popular approach to validate the results of SAT solvers. However, validating clausal proofs in the most widely supported format (DRAT) is expensive even in highly optimized implementations. We present a new format, called LRAT, which extends the DRAT format with hints that facilitate a simple and fast validation algorithm. Checking validity of LRAT proofs can be implemented using trusted systems such as the languages supported by theorem provers. We demonstrate this by implementing two certified LRAT checkers, one in Coq and one in ACL2

The Human Adenovirus Type 5 E4orf6/E1B55K E3 Ubiquitin Ligase Complex Enhances E1A Functional Activity

Human adenovirus (Ad) E1A proteins have long been known as the central regulators of virus infection as well as the major source of adenovirus oncogenic potential. Not only do they activate expression of other early viral genes, they make viral replication possible in terminally differentiated cells, at least in part, by binding to the retinoblastoma (Rb) tumor suppressor family of proteins to activate E2F transcription factors and thus viral and cellular DNA synthesis. We demonstrate in an accompanying article (F. Dallaire et al., mSphere 1:00014-15, 2016) that the human adenovirus E3 ubiquitin ligase complex formed by the E4orf6 and E1B55K proteins is able to mimic E1A activation of E2F transactivation factors. Acting alone in the absence of E1A, the Ad5 E4orf6 protein in complex with E1B55K was shown to bind E2F, disrupt E2F/Rb complexes, and induce hyperphosphorylation of Rb, leading to induction of viral and cellular DNA synthesis, as well as stimulation of early and late viral gene expression and production of viral progeny. While these activities were significantly lower than those exhibited by E1A, we report here that this ligase complex appeared to enhance E1A activity in two ways. First, the E4orf6/E1B55K complex was shown to stabilize E1A proteins, leading to higher levels in infected cells. Second, the complex was demonstrated to enhance the activation of E2F by E1A products. These findings indicated a new role of the E4orf6/E1B55K ligase complex in promoting adenovirus replication

Effect of Wood Particle Size on Fungal Growth in a Model Biomechanical Pulping Process

The pretreatment of aspen wood chips with white-rot fungus has been evaluated as a way of making biomechanical pulp. Our study addressed (1) whether wood particle size (chip size) affects the growth pattern of the attacking organism, and (2) whether the difference in particle size between chips and coarse pulp is related to the availability of wood polymers to the fungus. We qualitatively evaluated the growth of Phanerochaete chrysosporium BKM-F-1767 on aspen wood using standard industrial 6- and 19-mm chips and coarse refiner mechanical pulp. Scanning electron microscopy revealed a slight increase in the number of hyphae in the 19-mm chips compared to that in the 6-mm chips, but no major morphological differences in cellulose or lignin loss. Dense aerial hyphal growth occurred around the chips, but not around the coarse pulp. The fungus appeared to attack the coarse pulp from both outside and within the fiber wall. Hyphae within both the middle lamella and the cell lumina attacked the cell walls. The fungus eroded the chip cell walls and their constituents primarily from the wood cell lumen outward. After only 3 weeks of fungal treatment, both chips and coarse pulp showed marked localized cell-wall thinning and fragmentation as well as generalized swelling and relaxing of the normally rigid cell-wall structure. We conclude that particle size has only a minor effect on fungal growth on wood under conditions such as those likely to be used in a commercial biopulping process

Regulation of artisanal small scale gold mining (ASGM) in Ghana and Indonesia as currently implemented fails to adequately protect aquatic ecosystems

Artisanal small scale gold mining (ASGM) operations are largely unregulated, informal and transient. Rudimentary mining and processing techniques used in ASGM often result in degraded environmental, safety, health and social conditions. ASGM requires permanent sources of water, placing most operations close to natural water bodies. Until recently, the impact on these environments has been largely overlooked, with most studies focussing primarily on mercury contamination and health concerns. Based on Ghanaian and Indonesian experiences, regulation of ASGM is a good step toward improvement, but here we argue that regulation alone is insufficient to improve environmental performance, particularly when the impacts of ASGM on aquatic ecosystems are largely unknown

A formalized general theory of syntax with bindings

We present the formalization of a theory of syntax with bindings that has been developed and refined over the last decade to support several large formalization efforts. Terms are defined for an arbitrary number of constructors of varying numbers of inputs, quotiented to alpha-equivalence and sorted according to a binding signature. The theory includes a rich collection of properties of the standard operators on terms, such as substitution and freshness. It also includes induction and recursion principles and support for semantic interpretation, all tailored for smooth interaction with the bindings and the standard operators

Sharing HOL4 and HOL Light proof knowledge

New proof assistant developments often involve concepts similar to already formalized ones. When proving their properties, a human can often take inspiration from the existing formalized proofs available in other provers or libraries. In this paper we propose and evaluate a number of methods, which strengthen proof automation by learning from proof libraries of different provers. Certain conjectures can be proved directly from the dependencies induced by similar proofs in the other library. Even if exact correspondences are not found, learning-reasoning systems can make use of the association between proved theorems and their characteristics to predict the relevant premises. Such external help can be further combined with internal advice. We evaluate the proposed knowledge-sharing methods by reproving the HOL Light and HOL4 standard libraries. The learning-reasoning system HOL(y)Hammer, whose single best strategy could automatically find proofs for 30% of the HOL Light problems, can prove 40% with the knowledge from HOL4