An evaluation of semi‐automated methods for collecting ecosystem‐level data in temperate marine systems

Historically, marine ecologists have lacked efficient tools that are capable of capturing detailed species distribution data over large areas. Emerging technologies such as high‐resolution imaging and associated machine‐learning image‐scoring software are providing new tools to map species over large areas in the ocean. Here, we combine a novel diver propulsion vehicle (DPV) imaging system with free‐to‐use machine‐learning software to semi‐automatically generate dense and widespread abundance records of a habitat‐forming algae over ~5,000 m² of temperate reef. We employ replicable spatial techniques to test the effectiveness of traditional diver‐based sampling, and better understand the distribution and spatial arrangement of one key algal species. We found that the effectiveness of a traditional survey depended on the level of spatial structuring, and generally 10–20 transects (50 × 1 m) were required to obtain reliable results. This represents 2–20 times greater replication than have been collected in previous studies. Furthermore, we demonstrate the usefulness of fine‐resolution distribution modeling for understanding patterns in canopy algae cover at multiple spatial scales, and discuss applications to other marine habitats. Our analyses demonstrate that semi‐automated methods of data gathering and processing provide more accurate results than traditional methods for describing habitat structure at seascape scales, and therefore represent vastly improved techniques for understanding and managing marine seascapes.     

9. The algal flora of the Primorsky Region, Russian Far East

A survey of the freshwater algal flora of the Primorsky Region, Russian Far East, is presented. During more than 70 years of investigations 1659 species (including varieties and forms 2276 taxa) belonging to 346 genera of different groups of algae have been recorded from this territory. The Primorsky Region is rich in habitats attractive to algae-rivers, lakes, reservoirs, and ponds. The details of the distribution of algae in different types of waterbodies have been examined. The algal flora of the region is comparable to the areas, and its taxonomical structure is typical for Eurasia. From this territory some new species and varieties have been described — Achnanthes chankensis, Cymbella ventricosa var. hankensis, Surirella alisoviana, and others. The flora includes some rare species — Fragilaria magocsyi, Perone dimorpha, and Heterothrix monochloron, and some endemics of Asia — Navicula scutelloides var. baicalensis, N. globulifera var. nipponica, Gomphonema sphaerophorum, and Surirella tientsinensis.     

Life history patterns of river invertebrates

The initiation of invertebrate distribution patterns in rivers occurs by choice of oviposition sites and is influenced by the evolved reproductive strategies of the individual species. Subsequent redistribution by migration or drifting establishes patterns which are then modified by environmental influences on growth and mortality. Continuity of life cycles is sustained by variations on a number of defined life history strategies combined with evolved behavioural responses.     

Electrical impedance of white spruce shoots in relation to pressure-volume analysis and free sugar content

Electrical impedance measurements made on white spruce, Picea glauca (Moench) Voss, stems were related to shoot free sugar contents and to osmotic, turgor and water potential. During seasonal dormancy induction, there were commensurate increases in free sugar contents, osmotic potential at full turgor and impedance which resulted in linear relationships among these variables. When measured over the course of laboratory drying, impedance increased curvilinearly with decreasing relative water content. There was a linear increase in impedance with decreasing water potential, with a break point coincident with the turgor loss point, possibly attributed to disruption to current flow through broken plasmodesmatal connections between adjacent cells. This technique offers a non-destructive method to measure tissue free sugar content, and therefore, short- and long-term shifts in parameters historically derived from pressure-volume analysis.     

Sensitivity of North American sturgeons and paddlefish to fishing mortality

Sturgeons and paddlefish exhibit unusual combinations of morphology, habits, and life history characteristics, which make them highly vulnerable to impacts from human activities, particularly fisheries. Five North American sturgeons (shortnose, Gulf, pallid, Alabama, and green sturgeon) are listed as endangered or threatened by management authorities. Managers have instituted fishery closures for the three other species of North American sturgeons (Atlantic, white, and shovelnose) and paddlefish because of low stock abundance at some point in this century. Reproductive potential in four species I examined (Atlantic, white, and shortnose sturgeon, and paddlefish) is more sensitive to fishing mortality than it is for three other intensively-fished coastal species in North America: striped bass, winter flounder, and bluefish. The sturgeons and paddlefish are generally longer-lived than the three other coastal species, and also have an older age at full maturity, lower maximum fecundity values, and older ages at which 50% of the lifetime egg production is realized with no fishing mortality.     

Range‐wide patterns of greater sage‐grouse persistence

Aim Greater sage‐grouse (Centrocercus urophasianus), a shrub‐steppe obligate species of western North America, currently occupies only half its historical range. Here we examine how broad‐scale, long‐term trends in landscape condition have affected range contraction. Location Sagebrush biome of the western USA. Methods Logistic regression was used to assess persistence and extirpation of greater sage‐grouse range based on landscape conditions measured by human population (density and population change), vegetation (percentage of sagebrush habitat), roads (density of and distance to roads), agriculture (cropland, farmland and cattle density), climate (number of severe and extreme droughts) and range periphery. Model predictions were used to identify areas where future extirpations can be expected, while also explaining possible causes of past extirpations. Results Greater sage‐grouse persistence and extirpation were significantly related to sagebrush habitat, cultivated cropland, human population density in 1950, prevalence of severe droughts and historical range periphery. Extirpation of sage‐grouse was most likely in areas having at least four persons per square kilometre in 1950, 25% cultivated cropland in 2002 or the presence of three or more severe droughts per decade. In contrast, persistence of sage‐grouse was expected when at least 30 km from historical range edge and in habitats containing at least 25% sagebrush cover within 30 km. Extirpation was most often explained (35%) by the combined effects of peripherality (within 30 km of range edge) and lack of sagebrush cover (less than 25% within 30 km). Based on patterns of prior extirpation and model predictions, we predict that 29% of remaining range may be at risk. Main Conclusions Spatial patterns in greater sage‐grouse range contraction can be explained by widely available landscape variables that describe patterns of remaining sagebrush habitat and loss due to cultivation, climatic trends, human population growth and peripherality of populations. However, future range loss may relate less to historical mechanisms and more to recent changes in land use and habitat condition, including energy developments and invasions by non‐native species such as cheatgrass (Bromus tectorum) and West Nile virus. In conjunction with local measures of population performance, landscape‐scale predictions of future range loss may be useful for prioritizing management and protection. Our results suggest that initial conservation efforts should focus on maintaining large expanses of sagebrush habitat, enhancing quality of existing habitats, and increasing habitat connectivity.     

Comparison of patient‐derived high and low phosphatidylserine‐exposing colorectal carcinoma cells in their interaction with anti‐cancer peptides

Current cancer treatment is frequently compromised by severe adverse effects on healthy cells and tissues as well as by the increasing burden of (multi‐)drug resistances. Some representatives of small, amphipathic peptides known as host defense peptides possess the potential to overcome these limitations and to evolve as future anti‐cancer therapeutics. Peptide NK‐2, derived from porcine NK‐lysin, was originally discovered due to its broad‐spectrum antimicrobial activities. Today, also potent anti‐cancer activity is proven and accompanied by low toxicity towards normal human cells. The molecular basis underlying this target selectivity remains rather elusive. Nevertheless, it is presumptive that preferential peptide interactions with surface factors non‐abundant on healthy human cells play a key role. Here, we investigated the cytotoxicity of peptide NK‐2 and structurally improved anti‐cancer variants thereof against two patient‐derived colorectal cancer cell lines, exposing high and low levels of phosphatidylserine on their cell surfaces, respectively. Concluding from a range of in vitro tests involving cellular as well as lipid vesicle‐based methods, it is proposed that the magnitude of the accessible membrane surface charge is not a primarily decisive factor for selective peptide interactions. Instead, it is suggested that the level of membrane surface‐exposed phosphatidylserine is of crucial importance for the activity of peptide NK‐2 and enhanced variants thereof in terms of their cancer cell selectivity, the overall efficacy, as well as the underlying mode of action and kinetics. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Functional tuning of the catalytic residue pKa in a de novo designed esterase

AlleyCatE is a de novo designed esterase that can be allosterically regulated by calcium ions. This artificial enzyme has been shown to hydrolyze p‐nitrophenyl acetate (pNPA) and 4‐nitrophenyl‐(2‐phenyl)‐propanoate (pNPP) with high catalytic efficiency. AlleyCatE was created by introducing a single‐histidine residue (His¹⁴⁴) into a hydrophobic pocket of calmodulin. In this work, we explore the determinants of catalytic properties of AlleyCatE. We obtained the pK_a value of the catalytic histidine using experimental measurements by NMR and pH rate profile and compared these values to those predicted from electrostatics pK_a calculations (from both empirical and continuum electrostatics calculations). Surprisingly, the pK_a value of the catalytic histidine inside the hydrophobic pocket of calmodulin is elevated as compared to the model compound pK_a value of this residue in water. We determined that a short‐range favorable interaction with Glu¹²⁷ contributes to the elevated pK_a of His¹⁴⁴. We have rationally modulated local electrostatic potential in AlleyCatE to decrease the pK_a of its active nucleophile, His¹⁴⁴, by 0.7 units. As a direct result of the decrease in the His¹⁴⁴ pK_a value, catalytic efficiency of the enzyme increased by 45% at pH 6. This work shows that a series of simple NMR experiments that can be performed using low field spectrometers, combined with straightforward computational analysis, provide rapid and accurate guidance to rationally improve catalytic efficiency of histidine‐promoted catalysis. Proteins 2017; 85:1656–1665. © 2017 Wiley Periodicals, Inc.     

Effects of nitrogen limitation on water relations of jack pine (Pinus banksiana Lamb.) seedlings

The water relations of shoots of young jack pine (Pinus banksiana Lamb.) seedlings were examined 6 and 15 weeks after the initiation of four different dynamic nitrogen (N) treatments using a pressure-volume analysis. The N treatments produced a wide range of needle N concentrations from 12 to 32 mg g^?1 dry mass and a 10-fold difference in total dry mass at 15 weeks. Osmotic potential at full turgor did not change over the range of needle N concentrations observed. Osmotic potential at turgor-loss point, however, declined as N concentrations decreased, indicating an increased ability of N-deficient jack pine plants to maintain turgor. The increase could be attributed largely to an increase in cell wall elasticity, suggesting that elasticity changes may be a common, significant adaptation of plants to environmental stresses. Dry mass per unit saturated water almost doubled as needle N level dropped from 32 to 12 mg g^?1 and was inversely correlated to the bulk modulus of elasticity. This suggests that cell wall elasticity is determined more by the nature of its cross-linking matrix than by the total amount of cell wall material present. Developmental change was evident in the response of some water relation variables to N limitation.     

Spatial clumping of food increases its monopolization and defense by convict cichlids, Cichlasoma nigrofasciatum

The hypothesis that resource monopolization and defense increaseas the spatial clumping of resources increases was tested usinggroups of three convict cichlids competing for 120 Daphnia magnaprey. Spatial clumping was manipulated by varying the distance(3, 20, or 40 cm) between three tubes through which the preyappeared. As predicted, monopolization of prey (percentage eatenby the dominant fish) and frequency of aggression (chases perminute) by dominant fish increased significantly as the distancebetween the tubes decreased. However, there was no evidenceof individual flexibility in the aggressiveness (percentageof conspecifics chased) of dominant fish across treatments.Differences among dominant fish in aggressiveness were positivelycorrelated with their ability to monopolize prey, but the strengthof the correlation decreased as the distance between the tubesincreased. Aggression appears to be a more effective mechanismof interference competition when resources are clumped thanwhen resources are dispersed.