OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes

G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings

Sympatric prey responses to lethal top-predator control: predator manipulation experiments

Introduction: Many prey species around the world are suffering declines due to a variety of interacting causes such as land use change, climate change, invasive species and novel disease. Recent studies on the ecological roles of top-predators have suggested that lethal top-predator control by humans (typically undertaken to protect livestock or managed game from predation) is an indirect additional cause of prey declines through trophic cascade effects. Such studies have prompted calls to prohibit lethal top-predator control with the expectation that doing so will result in widespread benefits for biodiversity at all trophic levels. However, applied experiments investigating in situ responses of prey populations to contemporary top-predator management practices are few and none have previously been conducted on the eclectic suite of native and exotic mammalian, reptilian, avian and amphibian predator and prey taxa we simultaneously assess. We conducted a series of landscape-scale, multi-year, manipulative experiments at nine sites spanning five ecosystem types across the Australian continental rangelands to investigate the responses of sympatric prey populations to contemporary poison-baiting programs intended to control top-predators (dingoes) for livestock protection. Results: Prey populations were almost always in similar or greater abundances in baited areas. Short-term prey responses to baiting were seldom apparent. Longer-term prey population trends fluctuated independently of baiting for every prey species at all sites, and divergence or convergence of prey population trends occurred rarely. Top-predator population trends fluctuated independently of baiting in all cases, and never did diverge or converge. Mesopredator population trends likewise fluctuated independently of baiting in almost all cases, but did diverge or converge in a few instances. Conclusions: These results demonstrate that Australian populations of prey fauna at lower trophic levels are typically unaffected by top-predator control because top-predator populations are not substantially affected by contemporary control practices, thus averting a trophic cascade. We conclude that alteration of current top-predator management practices is probably unnecessary for enhancing fauna recovery in the Australian rangelands. More generally, our results suggest that theoretical and observational studies advancing the idea that lethal control of top-predators induces trophic cascades may not be as universal as previously supposed

Energy Requirements for Quantum Data Compression and 1-1 Coding

By looking at quantum data compression in the second quantisation, we present a new model for the efficient generation and use of variable length codes. In this picture lossless data compression can be seen as the {\em minimum energy} required to faithfully represent or transmit classical information contained within a quantum state. In order to represent information we create quanta in some predefined modes (i.e. frequencies) prepared in one of two possible internal states (the information carrying degrees of freedom). Data compression is now seen as the selective annihilation of these quanta, the energy of whom is effectively dissipated into the environment. As any increase in the energy of the environment is intricately linked to any information loss and is subject to Landauer's erasure principle, we use this principle to distinguish lossless and lossy schemes and to suggest bounds on the efficiency of our lossless compression protocol. In line with the work of Bostr\"{o}m and Felbinger \cite{bostroem}, we also show that when using variable length codes the classical notions of prefix or uniquely decipherable codes are unnecessarily restrictive given the structure of quantum mechanics and that a 1-1 mapping is sufficient. In the absence of this restraint we translate existing classical results on 1-1 coding to the quantum domain to derive a new upper bound on the compression of quantum information. Finally we present a simple quantum circuit to implement our scheme.Comment: 10 pages, 5 figure

The (non)effects of lethal population control on the diet of Australian dingoes

Top-predators contribute to ecosystem resilience, yet individuals or populations are often subject to lethal control to protect livestock, managed game or humans from predation. Such management actions sometimes attract concern that lethal control might affect top-predator function in ways ultimately detrimental to biodiversity conservation. The primary function of a predator is predation, which is often investigated by assessing their diet. We therefore use data on prey remains found in 4,298 Australian dingo scats systematically collected from three arid sites over a four year period to experimentally assess the effects of repeated broad-scale poison-baiting programs on dingo diet. Indices of dingo dietary diversity and similarity were either identical or near-identical in baited and adjacent unbaited treatment areas in each case, demonstrating no control-induced change to dingo diets. Associated studies on dingoes' movement behaviour and interactions with sympatric mesopredators were similarly unaffected by poison-baiting. These results indicate that mid-sized top-predators with flexible and generalist diets (such as dingoes) may be resilient to ongoing and moderate levels of population control without substantial alteration of their diets and other related aspects of their ecological function

Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene predictions, repeats). However, creating genome browsers requires extensive computational skills; lack of the expertise required remains a major barrier for many biomedical researchers and educators.To address these challenges, the Genomics Education Partnership (GEP; https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Assembly Hubs and JBrowse genome browsers. G-OnRamp can also convert a JBrowse instance into an Apollo instance for collaborative genome annotations in research and educational settings. G-OnRamp enables researchers to easily visualize their experimental results, educators to create Course-based Undergraduate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomics research.Development of G-OnRamp was guided by extensive user feedback from in-person workshops. Sixty-five researchers and educators from over 40 institutions participated in these workshops, which produced over 20 genome browsers now available for research and education. For example, genome browsers for four parasitoid wasp species were used in a CURE engaging 142 students taught by 13 faculty members —producing a total of 192 gene models. G-OnRamp can be deployed on a personal computer or on cloud computing platforms, and the genome browsers produced can be transferred to the CyVerse Data Store for long-term access

Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle

Background: Purple acid phosphatases belong to the family of binuclear metallohydrolases and are involved in a multitude of biological functions, ranging from bacterial killing and bone metabolism in animals to phosphate uptake in plants. Due to its role in bone resorption purple acid phosphatase has evolved into a promising target for the development of anti-osteoporotic chemotherapeutics. The design of specific and potent inhibitors for this enzyme is aided by detailed knowledge of its reaction mechanism. However, despite considerable effort in the last 10 years various aspects of the basic molecular mechanism of action are still not fully understood

Insects for breakfast and whales for dinner: the diet and body condition of dingoes on Fraser Island (K’gari)

Top-predators play stabilising roles in island food webs, including Fraser Island, Australia. Subsidising generalist predators with human-sourced food could disrupt this balance, but has been proposed to improve the overall health of the island’s dingo (Canis lupus dingo) population, which is allegedly ‘starving’ or in ‘poor condition’. We assess this hypothesis by describing the diet and health of dingoes on Fraser Island from datasets collected between 2001 and 2015. Medium-sized mammals (such as bandicoots) and fish were the most common food items detected in dingo scat records. Stomach contents records revealed additional information on diet, such as the occurrence of human-sourced foods. Trail camera records highlighted dingo utilisation of stranded marine fauna, particularly turtles and whales. Mean adult body weights were higher than the national average, body condition scores and abundant-excessive fat reserves indicated a generally ideal-heavy physical condition, and parasite loads were low and comparable to other dingo populations. These data do not support hypotheses that Fraser Island dingoes have restricted diets or are in poor physical condition. Rather, they indicate that dingoes on Fraser Island are capable of exploiting a diverse array of food sources which contributes to the vast majority of dingoes being of good-excellent physical condition

Postoperative Considerations Based on Graft Type After Anterior Cruciate Ligament Reconstruction a Narrative Review

Background and Objective: Graft selection for anterior cruciate ligament reconstruction (ACLR) affects rehabilitation throughout the course of postoperative care. Methods: A search of PubMed and EBSCO was performed and abstracts independently reviewed by two authors. This search was also supplemented with additional evidence relevant to each phase of ACLR rehabilitation. Key Content and Findings: Direct implications of graft type on clinical decisions vary throughout treatment phases, transitioning from potential differences in acute postoperative pain management immediately after surgery to facilitating sufficient and appropriate lower extremity loading in subsequent weeks. Regardless of graft type, surgical limb weakness persists throughout the course of rehabilitation; however, harvest site selection for autografts contributes to disproportionate weakness of the harvested muscle group and the potential for surgical-induced tendinopathy. In later phases of rehabilitation, as athletes are transitioning into return to sport (RTS), treatment decisions and protocols are less affected by graft type but expectations for meeting clinical milestones and the time required to do so does differ between graft types. Conclusions: Targeted strengthening interventions to address muscle weakness following graft harvest in autografts should be continued throughout the rehabilitation process. Lingering deficits in quadriceps strength symmetry may also influence time to meet progression and RTS criteria following graft harvest from the extensor mechanism

Collapsing D-branes in one-parameter models and small/large radius duality

We finalize the study of collapsing D-branes in one-parameter models by completing the analysis of the associated hypergeometric hierarchy. This brings further evidence that the phenomenon of collapsing 6-branes at the mirror of the `conifold' point in IIA compactifications on one-parameter Calabi-Yau manifolds is generic. It also completes the reduction of the study of higher periods in one-parameter models to a few families which display characteristic behaviour. One of the models we consider displays an exotic form of small-large radius duality, which is a consequence of an ``accidental'' discrete symmetry of its moduli space. We discuss the implementation of this symmetry at the level of the associated type II string compactification and its action on D-brane states. We also argue that this model admits two special Lagrangian fibrations and that the symmetry can be understood as their exchange.Comment: 34 pages, 12 figure