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The designability of orthogonal coiled coil (CC) dimers, which draw on well-established design rules, plays a pivotal role in fueling the development of CCs as synthetically versatile assembly-directing motifs for the fabrication of bionanomaterials. Here, we aim to expand the synthetic CC toolkit through establishing a “minimalistic” set of orthogonal,de novoCC peptides that comprise 3.5 heptads in length and a single buried Asn to prescribe dimer formation. The designed sequences display excellent partner fidelity, confirmed via circular dichroism (CD) spectroscopy, and are corroboratedin silicousing molecular dynamics (MD) simulation. Detailed analysis of the MD conformational data highlights the importance of interhelical E@g-N@ainteractions in coordinating an extensive 6-residue hydrogen bonding network that “locks” the interchain Asn-Asn’ contact in place. The enhanced stability imparted to the Asn-Asn’ bond elicits an increase in thermal stability of CCs up to ∼15°C and accounts for significant differences in stability within the collection of similarly designed orthogonal CC pairs. The presented work underlines the utility of MD simulation as a tool for constructingde novo, orthogonal CCs, and presents an alternative handle for modulating the stability of orthogonal CCs via tuning the number of interhelical E@g-N@acontacts. Expansion of CC design rules is a key ingredient for guiding the design and assembly of more complex, intricate CC-based architectures for tackling a variety of challenges within the fields of nanomedicine and bionanotechnology.

Length limits are often used in recreational fisheries management to prevent overharvest and manipulate fish size distributions. These regulations are ideally customized to meet water-specific stock dynamics and fishery objectives. However, in districts with numerous discrete waters, fisheries are commonly managed with a universal regional regulation. Evaluating alternative regional length limits requires consideration of management objectives that may not be important at the single-system level but that emerge as relevant at the regional scale, such as uniformity of regional harvest, diversity of average catch sizes, and opportunity to harvest. We developed a flexible tool for evaluating regional length limits. The tool joins the well-established Beverton–Holt yield-per-recruit model with elements of decision-support methods. The model quantifies regional management objectives as utility functions that are weighted and summed into a single value used to evaluate alternative length limits. The flexibility of the tool stems from its capacity to consider a mixture of stock parameters and associated uncertainty to evaluate multiple length limits, weighting an array of regional fishery objectives quantified by various performance metrics. This adjustability affords flexibility to consider a diversity of options that can stimulate innovation in setting regional length limits. We demonstrate the model by evaluating varying length limits on fishery objectives related to the management of hypothetical yellow perch ( Perca flavescens) populations and real black crappie ( Pomoxis nigromaculatus) populations.

Brush piles (i.e., trees and large woody debris) are often installed in reservoirs to supplement fish habitat. The retention and dimensional change of brush piles after installation is important information that can be used to maximize the effectiveness of this management action. We evaluated the retention and dimensional change of 70 eastern red cedar Juniperus virginiana and bald cypress Taxodium distichum brush piles in an embayment of a drawdown reservoir up to four annual cycles of submergence and exposure. We used satellite imagery to supplement our onsite measurements of retention. We also examined spatial patterns of brush pile retention and dimensional change. Brush piles were lost at 10% per year, and their volume was lost at 14% per year. We compared our rates of brush pile retention and dimensional change with those from a holdout data set of 50 brush piles. Estimates between data sets did not differ statistically. Spatial patterns of retention and dimensional change coincided with morphological features in our study area, suggesting that retention and dimensional change is influenced by variable physical forces (e.g., wave action and flow) at installation locations. Our estimates of brush pile retention and dimensional change can be used to generally sustain desirable brush densities. For example, to maintain a fixed total volume of brush in our study embayment, roughly 23% of the total brush volume installed would need to be replaced annually. Similar research in reservoirs managed for other purposes is needed, as length and cycle of inundation could lead to variable rates of retention and dimensional change. Additionally, advancements into computer-assisted detection and volume estimation could reduce the time and effort needed to monitor brush piles.

A multiweek standardized sampling regime during 2004–2016 in a 60-km reach of the Upper Missouri River assessed reproduction and catch rates for Sturgeon Chub Macrhybopsis gelida and Sicklefin Chub Macrhybopsis meeki. We sampled age-0 Macrhybopsis (primarily Sturgeon Chubs, but potentially including Sicklefin Chubs) all years to indicate successful reproduction, but noted an inverse correlation of catch per unit area (CPUA) with year. There was an inverse correlation for CPUA of age-1+ Sturgeon Chubs with year. There was no correlation for CPUA of age-1+ Sicklefin Chubs with year, but we noted a depression in CPUA during 2010 and 2012. The study reach includes restoration directives for federally endangered Pallid Sturgeon Scaphirhynchus albus, with 245,000 hatchery-origin Pallid Sturgeon (HOPS) stocked since 1998 to supplement the declining wild stock. Pallid Sturgeon longer than 350 mm fork length transition to piscivory and are known to prey on Sturgeon Chubs and Sicklefin Chubs. We examined the hypothesis that mass additions of HOPS to the existing predator community could have population-level effects on the two chub species. Population modeling for the stocked HOPS through time yielded estimates of nearly 1,300 piscivore-sized HOPS in 2004, an increase to 26,000 HOPS in 2012, and decreasing numbers through 2016 (14,500). A negative correlation between HOPS abundance and age-0 Macrhybopsis CPUA had the best support among other candidate variables (discharge, water temperature, catch rates of Sauger Sander canadensis). We found an inverse correlation for CPUA of age-1+ Sturgeon Chubs and estimated HOPS abundance, and there was also evidence of an inverse association between age-1+ Sicklefin Chub CPUA and HOPS in the study area. Results for a 60-km reach of the Upper Missouri River suggest declining CPUA for age-0 Macrhybopsis and Sturgeon Chubs during 2004–2016 and modest recovery of Sicklefin Chubs after 2012. Although causative factors driving CPUA changes through time are not known, correlative analyses suggest that large numbers of HOPS added to the Missouri River predator community potentially influence CPUA of Sturgeon Chubs and Sicklefin Chubs in the study area. Testing this hypothesis will require expanded quantification of chub populations and HOPS numbers through time.

We present a comprehensive classical molecular dynamics study of water nanodroplets under the influence of an externally applied electric field. Our simulations cover a wide range of droplet sizes ...

Approaches for white crappie, Pomoxis annularis sperm cryopreservation have led to interest in applying similar methods to black-stripe black crappie, Pomoxis nigromaculatus. Their rarity in wild populations makes them a preferred phenotype for hatchery use. Sperm cryopreservation procedures were compared between black-stripe black crappie and white crappie for sperm motility and egg fertilization rate. There was no difference in black-stripe black crappie sperm motility after thawing between 5% dimethyl sulfoxide (DMSO, 45% motility) and 10% methanol (50% motility). However, fertilization rates were higher (p < .001) for sperm cryoprotected with 5% DMSO (38 ± 8%) than 10% methanol (22 ± 7%). Hatchery use requires sperm-to-egg ratios and fertilizing potential of single doses (i.e., 0.5 ml straw). Using black-stripe black crappie sperm (2.5 × 108 sperm/ml; 5% DMSO), the highest fertilization (27%) was found using single straws with 785 eggs (0.25 ml); total sperm:egg ratio: 159,000:1; motile sperm:egg ratio: 71,700:1. Therefore, sperm of two Pomoxis species could be cryopreserved using 350 mOsmol/kg Hanks' balanced salt solution as an extender, 5% DMSO as a cryoprotectant, cooling at 40°C/min, and thawing for 8 s at 40°C to maintain sperm motility and fertility. Basic protocols can be generalized within a genus if variables such as sperm concentration, process timing, and sample volumes are controlled.

Representative indices of population abundance for at-risk species are necessary to inform conservation decision-making. Many madtoms (Noturusspp.) are considered imperiled; however, the efficacy of frequent monitoring efforts has been questioned due to their cryptic and nocturnal behaviors. We systematically evaluated a madtom monitoring tool by (1) evaluating the use of small (8 × 2 mm), surgically implanted 125 kHz passive integrated transponder (PIT) tags for frecklebelly madtomN. munitusand (2) assessing the effectiveness of a radio-frequency identification (RFID)-enhanced artificial cover unit to index madtom abundance. Surgically implanted PIT tags had no apparent influence on madtom survival between 45 and 110 mm total length, and all tags were retained throughout a 21 d laboratory study. In experimental mesocosms, the enhanced cover units confirmed occupancy during nearly all replicates (77.6%), even at extremely low densities (n = 2 madtoms). The enhanced cover units provided representative estimates of madtom relative abundance (p < 0.01), whereas catch per unit effort was not significantly associated with previously validated visual observations (p = 0.12). Although madtom density and the number detected using the enhanced cover units were correlated, the gear was potentially saturated at relatively high densities (~20 fish per mesocosm) when deploying a single unit. In most cases, occupancy was confirmed within 12 h, and nearly half of the individuals were detected within ~72 h. Small PIT tags and RFID-enhanced artificial cover units offer novel opportunities to efficiently describe the ecology and population dynamics of madtoms.

Two different methods, metagenetics and free-otolith identification, were used to identify prey in the stomach contents of 531 Gymnura lessae captured by trawling in Mobile Bay, Alabama 2016-2018. Both methods were found to produce analogous results and were therefore combined into a single complete dataset. All prey were teleosts; the families Sciaenidae and Engraulidae were the most important prey (prey specie index of relative importance 89.3% IPSRI ). Multivariate analyses indicated that the diet of G. lessae varied with sex and seasonality. Specifically, variability was probably due to morphologically larger females consuming larger teleost prey species compared with males, whereas seasonal variability was probably due to changes in the available prey community composition. The findings indicate that both metagenetics and free otolith identification, used independently or complementarily, offer robust means of characterising dietary habits for teleost-specialised species such as G. lessae, which may play an important role in the structure and maintenance of coastal food webs such as those in Mobile Bay.

In shallow reservoirs, seasonal water drawdowns expose littoral areas and over time produce barren mudflats. When flooded, mudflats provide homogeneous substrates, turbid water, and eroding shorelines of limited ecological value. We hypothesized that in mudflats structurally complex habitats are occupied by more fish, smaller fish of a larger range in sizes, more species, and fish assemblages that are different from those in simpler habitats. We tested these hypotheses over two consecutive years with fish collections made in sites with varying structural complexity. Results indicated that structural complexity harbors more fish in transects and enclosures. Structural complexity did not influence median length, but length range increased with structural complexity. Average species richness increased with structural complexity. Fish assemblage composition changed as structural complexity increased. The ability of cover to provide survival, growth, and carrying capacity benefits is fundamental to programs aimed at increasing structural complexity. Results suggest observed effects on fish assemblages can lead to such benefits. Considering mudflats are a major component of reservoirs, expand as reservoirs age, and there is a potential to exert meaningful change on fish assemblages of impounded rivers by managing mudflats, we suggest additional attention is needed to develop practical habitat restoration options.

Biological invasions often have contrasting consequences with reports of invasions decreasing diversity at small scales and facilitating diversity at large scales. Thus, previous literature has concluded that invasions have a fundamental spatial scale‐dependent relationship with diversity. Whether the scale‐dependent effects apply to vertebrate invaders is questionable because studies consistently report that vertebrate invasions produce different outcomes than plant or invertebrate invasions. Namely, vertebrate invasions generally have a larger effect size on species richness and vertebrate invaders commonly cause extinction, whereas extinctions are rare following invertebrate or plant invasions. In an agroecosystem invaded by a non‐native ungulate (i.e., feral swine, Sus scrofa), we monitored species richness of native vertebrates in forest fragments ranging across four orders of magnitude in area. We tested three predictions of the scale‐dependence hypothesis: (a) Vertebrate species richness would positively increase with area, (b) the species richness y‐intercept would be lower when invaded, and (c) the rate of native species accumulation with area would be steeper when invaded. Indeed, native vertebrate richness increased with area and the species richness was 26% lower than should be expected when the invasive ungulate was present. However, there was no evidence that the relationship was scale dependent. Our data indicate the scale‐dependent effect of biological invasions may not apply to vertebrate invasions.

Environmental management often requires making decisions despite system uncertainty. One such example is mudflat mediation in flood control reservoirs. Reservoir mudflats limit development of diverse fish assemblages due to the lack of structural habitat provided by plants. Seeding mudflats with agricultural plants may mimic floodplain wetlands once inundated and provide fish habitat and achieve habitat management objectives. However, planting success is uncertain because of unpredictable water level fluctuations that affect plant survival and growth. Decision support tools can account for uncertainty that influences decision outcomes and reduce the risk in reservoir mudflat planting decisions. We used Bayesian decision networks and sensitivity analyses to quantify uncertainty surrounding mudflat plantings as supplemental fish habitat in four northwest Mississippi reservoirs. When averaged across all uncertainty, planting was the optimal decision only in Enid Lake. Response profiles indicated planting decisions depended on elevation contours within Enid, Sardis, and Grenada reservoirs. No planting was optimal at all elevations for Arkabutla Lake. These results provide a quantified basis for establishing best management practices and identify key system states that influence decision outcomes. The process used in this study to evaluate planting decisions can be applied to any reservoir by modifying reservoir dependent inputs to evaluate planting decisions to provide supplemental fish habitat.

Miranda L, Bull L, Colvin M, Hubbard W, Pugh L. 2018. Segmentation of Mississippi’s natural and artificial lakes. Lake Reserv Manage. 34:376–391.Segmentations divide a diverse resource into groups,...

Animal space use is influenced by many factors and can affect individual survival and fitness. Under optimal foraging theory, individuals use landscapes to optimize high-quality resources while minimizing the amount of energy used to acquire them. The spatial resource variability hypothesis states that as patchiness of resources increases, individuals use larger areas to obtain the resources necessary to meet energetic requirements. Additionally, under the temporal resource variability hypothesis, seasonal variation in available resources can reduce distances moved while providing a variety of food sources. Our objective was to determine if seasonal home ranges of brown bears (Ursus arctos) were influenced by temporal availability and spatial distribution of resources and whether individual reproductive status, sex, or size (i.e., body mass) mediated space use. To test our hypotheses, we radio collared brown bears (n = 32 [9 male, 23 female]) in 2014–2016 and used 18 a priori selected linear models to evaluate seasonal utilization distributions (UD) in relation to our hypotheses. Our top-ranked model by AICc, supported the spatial resource variability hypothesis and included percentage of like adjacency (PLADJ) of all cover types (P 0.17 for males, solitary females, and females with dependent young), and body mass (kg; P = 0.66). Based on this model, for every percentage increase in PLADJ, UD area was predicted to increase 1.16 times for all sex and reproductive classes. Our results suggest that landscape heterogeneity influences brown bear space use; however, we found that bears used larger areas when landscape homogeneity increased, presumably to gain a diversity of food resources. Our results did not support the temporal resource variability hypothesis, suggesting that the spatial distribution of food was more important than seasonal availability in relation to brown bear home range size.

Behavioral differences within a population can allow use of a greater range of resources among individuals. The brown bear (Ursus arctos) is a generalist omnivore that occupies diverse habitats and displays considerable plasticity in food use. We evaluated whether brown bear foraging that resulted in deviations from a proposed optimal diet influenced body condition and, in turn, denning duration in Lake Clark National Park and Preserve, Alaska. To assess assimilated diet, we used sectioned guard hair samples (n = 23) collected in autumn to determine stable carbon and nitrogen isotope ratios. To index proportional contributions of meat and vegetation to assimilated diets, we compared the carbon (δ13C) and nitrogen (δ15N) values of hair samples with the values identified for major food categories. We then compared percentage body fat and body mass in relation to the proportion of assimilated meat in the diet using linear models. We also examined the influence of autumn percentage body fat and mass on denning duration. Percentage body fat was not influenced by the proportion of assimilated meat in the diet. Additionally, percentage body fat and body mass did not influence denning duration. However, body mass of bears assimilating proportionately more meat was greater than bears assimilating less meat. Our results provide support for previous findings that larger bears consume higher amounts of protein to maintain their body size and therefore forage further from the proposed optimal diet. Additionally, our results demonstrate that individuals can achieve similar biological outcomes (e.g., percentage body fat) despite variable foraging strategies, suggesting that individuals within generalist populations may confer an adaptive advantage through behavioral plasticity.

Length limits have been implemented by fisheries management agencies to achieve population density, size structure, and angler satisfaction objectives. By redirecting harvest towards or away from particular length- or age-groups, length limits rely on harvest by anglers to maintain a population at or near a desired state. The fish population changes that follow the implementation of harvest regulations may take several years to manifest, so long-term monitoring may be needed to adequately evaluate length limits. We used an innovative application of cluster analysis to facilitate evaluation of the effects of three consecutive length limits on a population of Largemouth Bass Micropterus salmoides over a 28-year period in Ross Barnett Reservoir, Mississippi. A 13–16-in protected slot length limit (10 years), followed by a 15-in minimum length limit (MLL; 11 years), followed by a 12-in MLL (7 years) failed to restructure the Largemouth Bass population due to what we suggest was the expansion of a volu...

After returning to spawning areas, adult Pacific salmon Oncorhynchus spp. often die without spawning successfully, which is commonly referred to as prespawn mortality. Prespawn mortality reduces reproductive success and can thereby hamper conservation, restoration, and reintroduction efforts. The primary source of information used to estimate prespawn mortality is collected through carcass surveys, but estimation can be difficult with these data due to imperfect detection and carcasses with unknown spawning status. To facilitate unbiased estimation of prespawn mortality and associated uncertainty, we developed a hidden-process mark–recovery model to estimate prespawn mortality rates from carcass survey data while accounting for imperfect detection and unknown spawning success. We then used the model to estimate prespawn mortality and identify potential associated factors for 3,352 adult spring Chinook Salmon O. tshawytscha that were transported above Foster Dam on the South Santiam River (Willamet...

A strain of atypical Aeromonas hydrophila (aAh) has caused issues within the channel catfish Ictalurus punctatus industry of the southeastern United States since 2009. These atypical pathotypes cause acute mortality events resulting in catastrophic losses, as opposed to more chronic mortality and lesions seen in typical infections of motile aeromonas septicemia (MAS). This study provides a basic framework for rapid field sampling negating the need for re-isolation or enrichment culture, thereby reducing the time between sampling and detection. Rapid and accurate quantitative PCR based methods for detection of aAh have been described and are important confirmative tools in research and diagnostic settings. These methods also have application in epidemiological surveys investigating the spread of disease and elucidating pathogen dynamics that may lead to outbreaks. To date, no field-based sampling technique for rapid aAh detection in resident pond populations has been explored. In this study, culture swabs taken from the gills and lower intestine of pond-raised catfish were assessed for their suitability as rapid field-based collection methods for downstream applications. Results showed the state of the pond has a significant effect on which swab location yields the highest proportion of PCR positive results. During an active outbreak, gill swabs identified more fish as aAh-positive; however, in apparently healthy populations, swabs taken from the lower intestine identified significantly more aAh-positive fish than gill swabs, despite no statistical difference in the concentration of aAh cell equivalents between swab sites. Naive prevalence estimates from the two swab types were compared to estimates provided by a hierarchical occupancy model. Prevalence estimates from gill swabs was 0.95% while vent swabs showed a prevalence of 2.2%; however, estimates based on the occupancy model were 6.6% and 9.8%, respectively. This multi-fold increase in prevalence estimates highlights the importance of accounting for imperfect detection in epidemiological studies and in assessing potential outbreak risk. Furthermore, occupancy models based on these data indicate resident fish can be aAh-positive carriers with no gross signs of infection, providing evidence aAh can reside in catfish ponds in the absence of disease. The presence of a carrier state indicates the pathogen may pose minimal risk to the host is compromised or a mechanical portal of entry into the blood stream is available. This provides an important direction for future research in understanding the mechanisms of aAh outbreaks in catfish aquaculture ponds.

A low-energy triggered switch that can generate mechanoresponse has great technological potential. A submolecular moiety, S-dibenzocyclooctadiene (DBCOD) that is composed of a flexible eight-membered ring connecting to a phenyl ring at each end, undergoes a conformational change from twist-boat to chair under a low-energy stimulus such as near infrared irradiation, resulting in thermal contraction of DBCOD-based polymer. Experimental evidence corroborated by theoretical calculations indicates that introducing molecular asymmetry can reduce crystallinity significantly and consequently facilitate the kinetics of the conformational change. It has been demonstrated that the negative thermal expansion (NTE) coefficient of a DBCOD-based polymer system can be adjusted in a range from -1140 to -2350 ppm K-1 . -2350 ppm K-1 is ≈10 times better than the value reported by the second best NTE system.

Effective reservoir fisheries management requires fish samples suitable for addressing objectives. These samples are typically attained with fish sampling gears using standardized protocols. Some standardized protocols for sampling reservoir fishes promote objective-based sampling, and many include a minimum number of gear deployments. This minimum number is often a function of reservoir surface area. However, reservoir size may not adequately predict the number of gear deployments needed to reach sample objectives. We used multiple linear regression to determine the relationships between the biological, chemical, and physical characteristics of reservoirs and the number of gear deployments needed to reach two sample objectives: (1) collecting 100 stock-length fish (N100), and (2) attaining relative SE of stock-length catch per effort (CPE) ≤25% (RSE25). These analyses were conducted using data from 34 Kansas reservoirs and six fish species. We used Akaike model averaging from a confidence model s...

To describe the life histories and demography of a fluvial population of Bull Trout Salvelinus confluentus, we PIT-tagged and radio-tagged Bull Trout captured in Mill Creek, a tributary of the Walla Walla River (Washington–Oregon), during 1998–2009. Adult abundance declined 63% during 2006–2010, driven primarily by a 10-fold reduction in subadult-to-adult returns. Larger subadults and fall–winter emigrants survived at higher rates, but they were a small proportion of the subadult migrants. The survival rates of larger, generally older adults were also more than 40% greater than those of smaller adults. Changes in abundance influenced other characteristics of the population. For example, adult upstream movement into spawning areas during 1999–2005 peaked in late July, whereas the smaller runs observed during 2006–2010 peaked in early September, and the relationship between fish size and migration timing shifted. Unlike many adfluvial populations, more than 90% of the adults in Mill Creek spawned an...

Molecular dynamics (MD) simulation is a powerful technique for sampling the conformational landscape of natively folded proteins (NFPs) and structurally dynamic intrinsically disordered proteins (IDPs). NFPs and IDPs can be viewed as nonlinear dynamical systems that exercise available degrees of freedom to explore their energetically-accessible conformation landscape. Dimensionality estimators have emerged as useful tools to characterize nonlinear dynamical systems in other domains, but their application to MD simulation has been limited due to thermal noise and a lack of ground-truth data. We develop a series of increasingly complex biopolymer models which exhibit a range of dynamics we seek to characterize in MD simulations (stochastic dynamics, helical structures, partially folded states, and correlated motions) and are of known dimensionality. We utilize the maximum-likelihood dimension (MLD) estimator to investigate the effects of thermal noise and noise-smoothing techniques on the estimates obtained from the polymer models and MD simulations of two NFPs and two IDPs. We find that under certain noise/smoothing conditions, the MLD over/under-estimates the true dimensionality of the models in a predictable manner, allowing us to relate differences between MLD estimates to differences between NFP and IDP motions for classification of biomolecular systems based on their dynamics.

Continuous harvest over an annual period is a common assumption of continuous biomass dynamics models (CBDMs); however fish are frequently harvested in a pulsed manner. We developed semi-discrete biomass dynamics models (SDBDMs) that allow discrete harvest events and evaluated differences between CBDMs and SDBDMs using an equilibrium yield analysis with varying levels of fishing mortality (F). Equilibrium fishery yields for CBDMs and SDBDMS were similar at low fishing mortalities and diverged as F approached and exceeded maximum sustained yield (FMSY). Discrete harvest resulted in lower equilibrium yields at high levels of F relative to continuous harvest. The effect of applying harvest continuously when it was in fact discrete was evaluated by fitting CBDMs and SDBDMs to time series data generated from a hypothetical fish stock undergoing discrete harvest and evaluating parameter estimates bias. Violating the assumption of continuous harvest resulted in biased parameter estimates for CBDM while SDBDM parameter estimates were unbiased. Biased parameter estimates resulted in biased biological reference points derived from CBDMs. Semi-discrete BDMs outperformed CBDMs and should be used when harvest is discrete, when the time and magnitude of harvest are known, and when F is greater than FMSY.