Measuring spatial and temporal shifts in forest structure and composition in T high elevation beech forests in response to beech bark disease in Great Smoky Mountains National Park

Exotic forest pests and pathogens are among the most serious environmental threats to millions of hectares of forested land worldwide. Beech Bark Disease (BBD) is a non-native, pathogenic complex consisting of associations between scale insects and fungi. First confirmed in Great Smoky Mountains National Park (GRSM) in 1986, this complex has since threatened local high elevation beech forests, which are G-1 ranked (critically imperiled) forest communities where American beech (Fagus grandifolia Ehrh.) is a foundational tree species. In 1994, GRSM initiated the BBD Monitoring Protocol at 10 high elevation beech forest plots in the Park. The plots were sampled biennially from 1994 to 2012 and again in 2017 to investigate infestation patterns and host mortality. Permutational multivariate analysis of variance (PERMANOVA) and nonmetric multidimensional scaling (NMDS) techniques were used to investigate shifts in forest structure and composition over the 23-year study period. Species-specific changes were analyzed using repeated measures linear mixed-effects models (RMLMM). High elevation beech forest communities are changing through time with trajectories becoming more influenced by Acer and Betula species. Despite great variability in plot location, aspect, slope, and beginning species composition, time was a significant factor, explaining ~10% of the variation in relative basal area. Species-specific shifts were highly variable. While the overstory Fagus grandifolia basal area declined significantly over the 23-year study period, no significant change in total basal area was observed, indicating that the loss of these mature trees was compensated by co-occurring species. Understory sapling and woody seedling abundance of F. grandifolia increased relative to most other species in the study. The loss of the foundational species, F. grandifolia (the dominant tree species which defines high elevation beech forests), will have broad consequences for associated biota, ecosystem function, and potentially, the long-term persistence of high elevation beech forests in GRSM

Antibacterial activity of rationally designed antimicrobial peptides.

Many infectious diseases are still prevalent in the world’s populations since no effective treatments are available to eradicate them. e reasons may either be the antibiotic resistance towards the available therapeutic molecules or the slow rate of producing adequate therapeutic regimens to tackle the rapid growth of new infectious diseases, as well as the toxicity of current treatment regimens. Due to these reasons, there is a need to seek and develop novel therapeutic regimens to reduce the rapid scale of bacterial infections. Antimicrobial Peptides (AMPs) are components of the first line of defense for prokaryotes and eukaryotes and have a wide range of activities against Gram-negative and Gram-positive bacteria, fungi, cancer cells, and protozoa, as well as viruses. In this study, peptides which were initially identified for their HIV inhibitory activity were further screened for antibacterial activity through determination of their kinetics as well as their cytotoxicity. From the results obtained, the MICs of two AMPs (Molecule 3 and Molecule 7) were 12.5 μg/ml for K. pneumoniae (ATCC 700603) and 6.25 μg/ml for P. aeruginosa (ATCC 22108). e two AMPs killed these bacteria rapidly in vitro, preventing bacterial growth within few hours of treatment. Furthermore, the cytotoxic activity of these two peptides was significantly low, even at an AMP concentration of 100 μg/ml. ese results revealed that Molecule 3 and 7 have great potential as antibacterial drugs or could serve as lead compounds in the design of therapeutic regimens for the treatment of antibiotic-resistant bacteria

Collections Education: The Extended Specimen and Data Acumen

Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics

Mineralogy and chemistry of cobbles at Meridiani Planum, Mars, investigated by the Mars Exploration Rover Opportunity

Numerous loose rocks with dimensions of a few centimeters to tens of centimeters and with no obvious physical relationship to outcrop rocks have been observed along the traverse of the Mars Exploration Rover Opportunity. To date, about a dozen of these rocks have been analyzed with Opportunity’s contact instruments, providing information about elemental chemistry (Alpha Particle X‐ray Spectrometer), iron mineralogy and oxidation states (Mössbauer Spectrometer) and texture (Microscopic Imager). These “cobbles” appear to be impact related, and three distinct groups can be identified on the basis of chemistry and mineralogy. The first group comprises bright fragments of the sulfate‐rich bedrock that are compositionally and texturally indistinguishable from outcrop rocks. All other cobbles are dark and are divided into two groups, referred to as the “Barberton group” and the “Arkansas group,” after the first specimen of each that was encountered by Opportunity. Barberton group cobbles are interpreted as meteorites with an overall chemistry and mineralogy consistent with a mesosiderite silicate clast composition. Arkansas group cobbles appear to be related to Meridiani outcrop and contain an additional basaltic component. They have brecciated textures, pointing to an impact‐related origin during which local bedrock and basaltic material were mixed

Evaluating methods for the analysis of rare variants in sequence data

A number of rare variant statistical methods have been proposed for analysis of the impending wave of next-generation sequencing data. To date, there are few direct comparisons of these methods on real sequence data. Furthermore, there is a strong need for practical advice on the proper analytic strategies for rare variant analysis. We compare four recently proposed rare variant methods (combined multivariate and collapsing, weighted sum, proportion regression, and cumulative minor allele test) on simulated phenotype and next-generation sequencing data as part of Genetic Analysis Workshop 17. Overall, we find that all analyzed methods have serious practical limitations on identifying causal genes. Specifically, no method has more than a 5% true discovery rate (percentage of truly causal genes among all those identified as significantly associated with the phenotype). Further exploration shows that all methods suffer from inflated false-positive error rates (chance that a noncausal gene will be identified as associated with the phenotype) because of population stratification and gametic phase disequilibrium between noncausal SNPs and causal SNPs. Furthermore, observed true-positive rates (chance that a truly causal gene will be identified as significantly associated with the phenotype) for each of the four methods was very low (<19%). The combination of larger than anticipated false-positive rates, low true-positive rates, and only about 1% of all genes being causal yields poor discriminatory ability for all four methods. Gametic phase disequilibrium and population stratification are important areas for further research in the analysis of rare variant data

Small herbaria contribute unique biogeographic records to county, locality, and temporal scales

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales

Developing a re-configurable architecture for the remote operation of marine autonomous systems

In this experience report, we explain how we take advantage of microservices’ inherent modular nature to accomplish a highly adaptable software architecture that can deal with the trials and tribulations often occurring in marine research environments. We will show the National Oceanography Centre’s journey to develop a web system to remotely operate marine autonomous vehicles from anywhere in the world with an internet connection and how, due to new unforeseen requirements, we took the microservice pattern into a new direction to allow for standalone offline operations of Autonomous Underwater Vehicles (AUV) from research ships in some of the most challenging environments in the world

Evaluating methods for combining rare variant data in pathway-based tests of genetic association

Analyzing sets of genes in genome-wide association studies is a relatively new approach that aims to capitalize on biological knowledge about the interactions of genes in biological pathways. This approach, called pathway analysis or gene set analysis, has not yet been applied to the analysis of rare variants. Applying pathway analysis to rare variants offers two competing approaches. In the first approach rare variant statistics are used to generate p-values for each gene (e.g., combined multivariate collapsing [CMC] or weighted-sum [WS]) and the gene-level p-values are combined using standard pathway analysis methods (e.g., gene set enrichment analysis or Fisher’s combined probability method). In the second approach, rare variant methods (e.g., CMC and WS) are applied directly to sets of single-nucleotide polymorphisms (SNPs) representing all SNPs within genes in a pathway. In this paper we use simulated phenotype and real next-generation sequencing data from Genetic Analysis Workshop 17 to analyze sets of rare variants using these two competing approaches. The initial results suggest substantial differences in the methods, with Fisher’s combined probability method and the direct application of the WS method yielding the best power. Evidence suggests that the WS method works well in most situations, although Fisher’s method was more likely to be optimal when the number of causal SNPs in the set was low but the risk of the causal SNPs was high

Santorini, Another Meteorite on Mars and Third of a Kind

The Mars Exploration Rover (MER) Opportunity has been studying Meridiani Planum for five years. On sol 1634 of its mission, Opportunity left Victoria crater after investigating it for approximately 682 sols [1] and is now on a journey towards Endeavour, a 24 km diameter crater about 12 km southeast of Victoria. A priority along the way is the investigation of cobbles, which in the jargon of the MER science team denotes any loose rock fragment larger than a couple of centimeters. Cobbles investigated thus far are of diverse origin [2] and provide the only means to investigate material other than the ubiquitous sulfate-rich outcrop, basaltic sand or hematiterich spherules dubbed blueberries. Some of these cobbles are meteorites [3]. Meteorites on Mars are not just a curiosity that make Mars a more Earth-like planet. Metallic iron in meteorites, for example, may be used as a more sensitive tracer for volatile surface interactions compared to igneous minerals [4]. Between sols 1713 and 1749, including the period of Mars solar conjunction, Opportunity investigated a cobble informally named Santorini. Its chemical and mineralogical composition is very similar to Barberton and Santa Catarina, two cobbles that were identified as meteorites and which are probably related to each other [3]. Santorini was investigated with the rover s Panoramic Camera (Pancam), Microscopic Imager (MI), Alpha-Particle X-ray Spectrometer (APXS) and Moessbauer (MB) spectrometer. The miniature Thermal Emission Spectrometer (mini-TES) was not operational at the time. The Rock Abrasion Tool (RAT) could not be used to brush off potential dust coatings because of unfavorable geometry