Comparison of Best Management Practice Adoption Between Virginia\u27s Chesapeake Bay Basin and Southern Rivers Watersheds

Producers in two regions of Virginia (Chesapeake Bay basin and Southern Rivers region) were surveyed to compare farming practices and agricultural best management practice (BMP) adoption. Objectives were to assess farming operations and determine the extent of cost-share and non-cost-share BMP implementation and gain insight into the impact of selected socioeconomic factors on the BMP adoption. Although farming characteristics and producer attitudes toward pollution and water quality were similar, BMP implementation differed between the two regions. Differences in BMP implementation may be due to a more focused, longer-term NPS pollution control educational effort in the Bay basin

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that occurs among all susceptible Z-forming regions at thermodynamic equilibrium in a superhelically stressed DNA of specified sequence. This method, which we call SIBZ, is similar to the SIDD algorithm that was previously developed to analyze superhelical duplex destabilization. A state of the system is determined by assigning to each base pair either the B- or the Z-conformation, accounting for the dinucleotide repeat unit of Z-DNA. The free energy of a state is comprised of the nucleation energy, the sequence-dependent B-Z transition energy, and the energy associated with the residual superhelicity remaining after the change of twist due to transition. Using this information, SIBZ calculates the equilibrium B-Z transition probability of each base pair in the sequence. This can be done at any physiologically reasonable level of negative superhelicity. We use SIBZ to analyze a variety of representative genomic DNA sequences. We show that the dominant Z-DNA forming regions in a sequence can compete in highly complex ways as the superhelicity level changes. Despite having no tunable parameters, the predictions of SIBZ agree precisely with experimental results, both for the onset of transition in plasmids containing introduced Z-forming sequences and for the locations of Z-forming regions in genomic sequences. We calculate the transition profiles of 5 kb regions taken from each of 12,841 mouse genes and centered on the transcription start site (TSS). We find a substantial increase in the frequency of Z-forming regions immediately upstream from the TSS. The approach developed here has the potential to illuminate the occurrence of Z-form regions in vivo, and the possible roles this transition may play in biological processes

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcribing. We apply our model to explore the correlation between stress-induced transitions and transcriptional activity in various organisms. In higher eukaryotes we find a strong enhancement of Z-forming regions immediately 5′ to their transcription start sites (TSS), and a depletion of strand separating sites in a broad region around the TSS. The opposite patterns occur around transcript end locations. We also show that susceptibility to each type of transition is different in eukaryotes and prokaryotes. By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downstream of the TSS is not preserved, suggesting it may be under selection pressure

EC02-179 Managing Livestock Manure to Protect Environmental Quality

This book covers the land application part of manure management. With increasing regulations, the livestock producer needs to understand the scientific principles that affect manure transformations and how to use these principles to manage the manure for maximum fertilizer value with minimal environmental impact. Improved land application of manure is one part of the solution, but we suggest that the producer evaluate the quantity of nutrients arriving on the farm as feed, animals, and fertilizer compared to the total that is exported. Achieving a nutrient balance will reduce potential environmental hazards often associated with animal agriculture

The UK Environmental Change Network datasets – integrated and co-located data for long-term environmental research (1993–2015)

Long-term datasets of integrated environmental variables, co-located together, are relatively rare. The UK Environmental Change Network (ECN) was launched in 1992 and provides the UK with its only long-term integrated environmental monitoring and research network for the assessment of the causes and consequences of environmental change. Measurements, covering a wide range of physical, chemical, and biological “driver” and “response” variables are made in close proximity at ECN terrestrial sites using protocols incorporating standard quality control procedures. This paper describes the datasets (there are 19 published ECN datasets) for these co-located measurements, containing over 20 years of data (1993–2015). The data and supporting documentation are freely available from the NERC Environmental Information Data Centre under the terms of the Open Government Licence (see paper for DOIs)

Salerno's model of DNA reanalysed: could solitons have biological significance?

We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/0

Ornithological expeditions to Sarawak, Malaysian Borneo, 2007-2017

Louisiana State University, the University of Kansas, and the Universiti Malaysia Sarawak undertook collaborative research on the evolution and ecology of Bornean birds starting in 2005. This collaboration included a series of expeditions from 2007–2017 to collect and study birds at \u3e30 sites in Sarawak, Malaysian Borneo. Here we provide information on the study-sites and summarize the main discoveries resulting from the collaboration

Impact of pollen on throughfall biochemistry in European temperate and boreal forests

Pollen is known to affect forest throughfall biochemistry, but underlying mechanisms are not fully understood. We used generalized additive mixed modelling to study the relationship between long-term series of measured throughfall fluxes in spring (April–June) at forest plots and corresponding airborne pollen concentrations (Seasonal Pollen Integral, SPIn) from nearby aerobiological monitoring stations. The forest plots were part of the intensive long term monitoring (Level II) network of the UNECE International Co-operative Programme on Assessment and Monitoring of Air Pollution Effects on Forests (ICP Forests) with dominant tree genera Fagus, Quercus, Pinus and Picea, and were distributed all across Europe. We also conducted a 7-day laboratory dissolution experiment with bud scales and flower stalks of European beech (Fagus sylvatica L.), pollen of beech, common oak (Quercus robur L.), silver birch (Betula pendula L.), Scots pine (Pinus sylvestris L.), Corsican pine (Pinus nigra Arnold ssp. laricio (Poiret) Maire), Norway spruce (Picea abies (L.) Karst.) and sterilized pollen of silver birch in a nitrate (NO3--N) solution (11.3 mg N L-1). Throughfall fluxes of potassium (K+), ammonium (NH4+-N), dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) showed a positive relationship with SPIn whereas NO3--N fluxes showed a negative relationship with SPIn. In years with massive seed production of beech and oak SPIn and throughfall fluxes of K+ and DOC were higher, but fluxes of NO3--N were lower. The experiment broadly confirmed the findings based on field data. Within two hours, pollen released large quantities of K+, phosphate, DOC and DON, and lesser amounts of sulphate, sodium and calcium. After 24-48 hours, NO3--N started to disappear, predominantly in the treatments with broadleaved pollen, while concentrations of nitrite and NH4+-N increased. At the end of the experiment, the inorganic nitrogen (DIN) was reduced, presumably because it was lost as gaseous nitric oxide (NO). There was no difference for sterilized pollen, indicating that the involvement of microbial activity was limited in above N transformations. Our results show that pollen dispersal might be an overlooked factor in forest nutrient cycling and might induce complex canopy N transformations, although the net-impact on N throughfall fluxes is rather lo

A Reference High-Pressure CO2\u3c/sub\u3e Adsorption Isotherm for Ammonium ZSM-5 Zeolite: Results of an Interlaboratory Study

© 2018, The Author(s). This paper reports the results of an international interlaboratory study led by the National Institute of Standards and Technology (NIST) on the measurement of high-pressure surface excess carbon dioxide adsorption isotherms on NIST Reference Material RM 8852 (ammonium ZSM-5 zeolite), at 293.15 K (20 °C) from 1 kPa up to 4.5 MPa. Eleven laboratories participated in this exercise and, for the first time, high-pressure adsorption reference data are reported using a reference material. An empirical reference equation nex=d(1+exp[(-ln(P)+a)/b])c, [nex-surface excess uptake (mmol/g), P-equilibrium pressure (MPa), a = −6.22, b = 1.97, c = 4.73, and d = 3.87] along with the 95% uncertainty interval (Uk = 2 = 0.075 mmol/g) were determined for the reference isotherm using a Bayesian, Markov Chain Monte Carlo method. Together, this zeolitic reference material and the associated adsorption data provide a means for laboratories to test and validate high-pressure adsorption equipment and measurements. Recommendations are provided for measuring reliable high-pressure adsorption isotherms using this material, including activation procedures, data processing methods to determine surface excess uptake, and the appropriate equation of state to be used