A Scale-Explicit Framework for Conceptualizing the Environmental Impacts of Agricultural Land Use Changes

Demand for locally-produced food is growing in areas outside traditionally dominant agricultural regions due to concerns over food safety, quality, and sovereignty; rural livelihoods; and environmental integrity. Strategies for meeting this demand rely upon agricultural land use change, in various forms of either intensification or extensification (converting non-agricultural land, including native landforms, to agricultural use). The nature and extent of the impacts of these changes on non-food-provisioning ecosystem services are determined by a complex suite of scale-dependent interactions among farming practices, site-specific characteristics, and the ecosystem services under consideration. Ecosystem modeling strategies which honor such complexity are often impenetrable by non-experts, resulting in a prevalent conceptual gap between ecosystem sciences and the field of sustainable agriculture. Referencing heavily forested New England as an example, we present a conceptual framework designed to synthesize and convey understanding of the scale- and landscape-dependent nature of the relationship between agriculture and various ecosystem services. By accounting for the total impact of multiple disturbances across a landscape while considering the effects of scale, the framework is intended to stimulate and support the collaborative efforts of land managers, scientists, citizen stakeholders, and policy makers as they address the challenges of expanding local agriculture

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (<it>Acipenser fulvescens</it>) gonads.</p> <p>Results</p> <p>Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (~19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from > 50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type.</p> <p>Conclusion</p> <p>Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms.</p

A Submaximal Field Test of Aerobic Capacity does not Accurately Reflect VO2max in Career Firefighters

International Journal of Exercise Science 15(4): 221-230, 2022. Adequate aerobic capacity is crucial to maintaining firefighter safety. The purpose of this study was to compare predicted VO2max scores from a submaximal and maximal step test. Eighteen career male firefighters from a medium sized urban municipality completed both a submaximal Forestry step test and a maximal laboratory WFI step test. A lack of association (p = .017) and low level of agreement (p = .015) was determined between step test protocols producing a mean bias of ± 5.61 mL.kg-1/min-1 with most scores being overestimated. Use of the Forestry step test to predict true VO2max in firefighters should be used with caution when classifying firefighter fitness

A transient homotypic interaction model for the influenza A virus NS1 protein effector domain

Influenza A virus NS1 protein is a multifunctional virulence factor consisting of an RNA binding domain (RBD), a short linker, an effector domain (ED), and a C-terminal 'tail'. Although poorly understood, NS1 multimerization may autoregulate its actions. While RBD dimerization seems functionally conserved, two possible apo ED dimers have been proposed (helix-helix and strand-strand). Here, we analyze all available RBD, ED, and full-length NS1 structures, including four novel crystal structures obtained using EDs from divergent human and avian viruses, as well as two forms of a monomeric ED mutant. The data reveal the helix-helix interface as the only strictly conserved ED homodimeric contact. Furthermore, a mutant NS1 unable to form the helix-helix dimer is compromised in its ability to bind dsRNA efficiently, implying that ED multimerization influences RBD activity. Our bioinformatical work also suggests that the helix-helix interface is variable and transient, thereby allowing two ED monomers to twist relative to one another and possibly separate. In this regard, we found a mAb that recognizes NS1 via a residue completely buried within the ED helix-helix interface, and which may help highlight potential different conformational populations of NS1 (putatively termed 'helix-closed' and 'helix-open') in virus-infected cells. 'Helix-closed' conformations appear to enhance dsRNA binding, and 'helix-open' conformations allow otherwise inaccessible interactions with host factors. Our data support a new model of NS1 regulation in which the RBD remains dimeric throughout infection, while the ED switches between several quaternary states in order to expand its functional space. Such a concept may be applicable to other small multifunctional proteins

Collective modes of coupled phase oscillators with delayed coupling

We study the effects of delayed coupling on timing and pattern formation in spatially extended systems of dynamic oscillators. Starting from a discrete lattice of coupled oscillators, we derive a generic continuum theory for collective modes of long wavelength. We use this approach to study spatial phase profiles of cellular oscillators in the segmentation clock, a dynamic patterning system of vertebrate embryos. Collective wave patterns result from the interplay of coupling delays and moving boundary conditions. We show that the phase profiles of collective modes depend on coupling delays.Comment: 5 pages, 2 figure

Genome-wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis

Ash (Fraxinus spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest Agrilus planipennis (Coleoptera: Buprestidae; emerald ash borer), having negative impacts on both forest ecosystems and economic interests. The majority of trees succumb to attack by A. planipennis, but some trees have been found to be tolerant to infestation despite years of exposure. Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to A. planipennis attack, in order to identify single nucleotide polymorphism (SNP) patterns related to tolerance and health declines. de novo SNPs were called using SAMtools and, after filtering criteria were implemented, a set of 17,807 SNPs were generated. Principal component analysis (PCA) of SNPs aligned individual trees into clusters related to geography; however, five tolerant trees clustered together despite geographic location. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are potential candidates for the selection of host tolerance. Understanding the mechanisms of host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand A. planipennis infestation. This study was successful in using RAD-sequencing in order to identify SNPs that could contribute to tolerance of A. planipennis. This was a first step toward uncovering the genetic basis for host tolerance to A. planipennis. Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack

Dynamic compartmentalization of bacteria: accurate division in E. coli

Positioning of the midcell division plane within the bacterium E. coli is controlled by the min system of proteins: MinC, MinD and MinE. These proteins coherently oscillate from end to end of the bacterium. We present a reaction--diffusion model describing the diffusion of min proteins along the bacterium and their transfer between the cytoplasmic membrane and cytoplasm. Our model spontaneously generates protein oscillations in good agreement with experiments. We explore the oscillation stability, frequency and wavelength as a function of protein concentration and bacterial length.Comment: 4 pages, 4 figures, Latex2e, Revtex

Qualitative Analysis of String Cosmologies

A qualitative analysis is presented for spatially flat, isotropic and homogeneous cosmologies derived from the string effective action when the combined effects of a dilaton, modulus, two-form potential and central charge deficit are included. The latter has significant effects on the qualitative dynamics. The analysis is also directly applicable to the anisotropic Bianchi type I cosmology.Comment: 13 pages, 4 postscript figures, accepted to Physical Review