Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating eutrophication management scenarios in the Baltic Sea using species distribution modelling

Summary 1. Eutrophication is severely affecting species distributions and ecosystem functioning in coastal areas. Targets for eutrophication reduction have been set in the Baltic Sea Action Plan (BSAP) using Secchi depth, a measure of water transparency, as the main status indicator. Despite the high economic costs involved, the potential effects of this political decision on key species and habitats have not been assessed. 2. In a case study including species central to coastal ecosystem functioning, we modelled the effects of changing Secchi depth on the distribution of bladderwrack Fucus vesiculosus and eelgrass Zostera marina vegetation as well as recruitment areas of the main predatory fish species, perch Perca fluviatilis and pikeperch Sander lucioperca. Specifically, we explored the effects of changing Secchi depth on species distributions under a set of scenarios based on the BSAP, using three fundamentally different modelling techniques: maximum entropy, generalized additive and random forest modelling. 3. Improved Secchi depth (reduced eutrophication) was predicted to cause a substantial increase in the distribution of bladderwrack, while the distribution of eelgrass remained largely unaffected. For the fish, a large increase in perch recruitment areas was predicted and a concurrent decrease in recruitment areas of pikeperch. These changes are likely to have effects on biodiversity and ecosystem services. 4. The three modelling methods exposed differences in the quantitative predictions for species with a weaker coupling to Secchi depth. Qualitatively, however, the results were consistent for all species. 5. Synthesis and applications. We show how ecological effects of environmental policies can be evaluated in an explicit spatial context using species distribution modelling. The modelspecific responses to changes in eutrophication status emphasize the importance of using ensemble modelling for exploring how species distributions may respond to alternative management regimes. A pronounced difference in response between species suggests that eutrophication mitigation will have consequences for ecosystem functioning, and thus ecosystem goods and services, by inducing changes in the simple food webs of the Baltic Sea. These model predictions form a basis for spatially explicit cost-benefit estimates under different scenarios, providing valuable information for both decision-makers and the wider society.
Microglial ectonucleotidases: Identification and functional roles

Microglial cells represent resident macrophages of the central nervous system where they resume a resting state of unknown physiological function. They are rapidly transformed into an activated state by acute pathological events affecting the nervous system. Activated microglia function in tissue repair and regeneration but may also enhance tissue damage. Cultured microglial cells express both P2Y and P2X receptors. Activation of the microglial P2X7 receptor can result in the release of cytokines or also mediate cytotoxicity in microglial cells. Microglial cells have developed mechanisms for controlling the surrounding concentrations of free extracellular ATP via a surface‐expressed ectonucleotidase chain. We analyzed the expression of the ectonucleotidases associated with resting microglia and microglia activated by two models of cerebral ischemia. Out of a plethora of enzymes with the potential to hydrolyze extracellular nucleotides, the major ectonucleotidases associated with microglia are NTPDase1, which hydrolyzes ATP and ADP, and ecto‐5′‐nucleotidase, which catalyzes the hydrolysis of AMP to adenosine. This is shown by enzyme histochemical analysis, immunocytochemistry, Northern hybridization, and the analysis of NTPDase1‐deficient mice. Our results suggest that a major function of resting microglia could be in the lowering of interstitial levels of ATP acting either via autocrine pathways or in the ATP‐involving signaling pathways between adjacent neurons and astrocytes. Enhanced activity of NTPDase1 may protect microglia, activated by various pathological settings, from overstimulation by ATP released from the injured tissue. The parallel increase in activity of ecto‐5′‐nucleotidase would facilitate the formation of the final hydrolysis product adenosine that exerts neuromodulatory and immunomodulatory actions and contributes to the protection of neurons. Drug Dev. Res. 53:208–217, 2001. © 2001 Wiley‐Liss, Inc.
Estimating Xanthoparmelia (Parmeliaceae) population density in subalpine communities in southern Utah, U.S.A. using two distance methods, with implications for assessing community composition

Abstract Lichens are often used to monitor air quality and ecosystem health, and to define ecological gradients. Quantitative methods for estimating lichen population density and community composition are essential to effectively assess species and community response to ecological and environmental change. In this study we used two distance methods (point-centered quarter and quartered-neighbor methods), along with a compound estimator (Diggle's) to remove bias from non-random spatial patterns, to estimate Xanthoparmelia population density at a generic level on the summit of a high elevation plateau in southern Utah, USA. The sampling was extended to assess species composition and diversity. Population densities and relative species abundance were evaluated between meadow areas, sites, cardinal directions, and general substrate classes. We found that Xanthoparmelia populations varied widely in density and community composition across a relatively homogeneous landscape. Microhabitat, meadow-wide, and plateau-wide factors significantly influenced density and community structure in Xanthoparmelia. Our data reemphasize the inherent variability found in lichen communities and the importance of effective sampling for accurate ecological and biomonitoring studies. The two distance methods implemented here, moderated by Diggle's population density estimator, provide an efficient alternative to cover methods for estimating density. This study also indicates that these methods provide an effective approach for estimating population density and community structure in conjunction with ecological and bio-monitoring studies of some types of terricolous and saxicolous lichen communities.
Below‐threshold mortality: implications for studies in evolution, ecology and demography

Evolutionary biologists, ecologists and experimental gerontologists have increasingly used estimates of age‐specific mortality as a critical component in studies of a range of important biological processes. However, the analysis of age‐specific mortality rates is plagued by specific statistical challenges caused by sampling error. Here we discuss the nature of this ‘demographic sampling error’, and the way in which it can bias our estimates of (1) rates of ageing, (2) age at onset of senescence, (3) costs of reproduction and (4) demographic tests of evolutionary models of ageing. We conducted simulations which suggest that using standard statistical techniques, we would need sample sizes on the order of tens of thousands in most experiments to effectively remove any bias due to sampling error. We argue that biologists should use much larger sample sizes than have previously been used. However, we also present simple maximum likelihood models that effectively remove biases due to demographic sampling error even at relatively small sample sizes.
Phospholipid Hydrolysate and Antistaling Amylase Effects on Retrogradation of Starch in Bread

Effects of phospholipid hydrolysate and antistaling amylase on starch retrogradation in bread and wheat flour were investigated by differential scanning calorimetry (DSC). Phospholipid hydrolysate containing more than 90% lysophospholipid was obtained using phospholipase A2 and was effective in forming amylose-lipid complexes. Both wheat flour and bread containing phospholipid hydrolysate were retrograded to a lesser degree when stored at room temperature. The retrogradation rate for bread with antistaling amylase was low. We postulated that antistaling amylase broke links in amylose and amylopectin, thereby promoting the formation of amylopectin-lipid complexes. The combined effect of phospholipid hydrolysate and antistaling amylase was greater than their individual effects.
Economics and the design of nature conservation policy: a case study of wild goose conservation in Scotland using choice experiments

This paper applies the ‘choice experiment’ method to investigate public preferences over the design of wild goose conservation policy in Scotland. We argue that this method can shed useful light on the design of conservation policy, allowing policy‐makers to take account of people's preferences, be they members of the general public (whose taxes often pay for conservation actions), local residents more directly affected by the policy, or visitors to wildlife areas. Preferences can be quantified in economic terms, so that the costs and benefits of different policy designs can be compared. In our study, we find that the general public, local residents and visitors have very different preferences for the conservation of geese. Whether geese are shot, the endangered status of geese, the spatial targeting of conservation and the size of the goose population all have impacts on the perceived benefits of conservation. In general, though, people are willing to pay for wild geese conservation.
Freeze-drying of lignin peroxidase: influence of lyoprotectants on enzyme activity and stability

The effect of different lyoprotectants (sucrose, dimethyl-succinate buffer (DMS), bovine serum albumin (BSA), mannitol and dextran, mw 60 kDa) on the stability of the enzyme lignin peroxidase (LiP, EC number: 1.11.1.-), both during the freeze-drying process and storage were investigated. The shelf stability tests were performed at 4 °C and 27 °C. Both DMS buffer and sucrose showed a good protective action: the former was particularly effective during the process, while the latter improved the stability during storage. In contrast, mannitol and dextran had negative effects, reducing the activity also in the lignin peroxidase solution. BSA was discarded because, in the range of compatible concentrations with LiP, it does not confer a consistent structure to the freeze-dried product. © 2002 Society of Chemical Industry
Electrophoretic Patterns of Soluble Proteins and Isoenzymes of Gaeumannomyces graminis

The wheat and oat take-all fungi show a close serological relationship with Gaeumannomyces graminis var. graminis isolated from kikuyu grass, supporting the conclusions of Walker, who recognized the three fungal groups as varieties of G. graminis based on morphological characters. Three techniques for studying proteins (disc and gradient gel electrophoresis and isoelectric focusing) were assessed as possible aids in identifying and classifying isolates of G. graminis. Protein patterns were affected by the age of the mycelium and the composition of the growth medium used. Patterns prepared by disc electrophoresis were helpful for identifying isolates of G. graminis, but not for separating the varieties. Gradient gel electrophoresis patterns were sufficient for distin- guishing the kikuyu grass isolate from take-all fungi isolated from wheat or oats, but the differences between the patterns of the wheat and oat take-all fungi were too slight to aid in identifying these varieties. Esterase and peroxidase isoenzyme patterns of the isolates from the three varieties were too variable to assist in identifying isolates of G. graminis at either the species or the variety level. Isoelectric focusing patterns of the proteins for each variety were useful for distinguishing the kikuyu grass isolate from the wheat and oat take-all fungi. The protein patterns illustrate a closer relationship between the wheat and oat take-all fungi than either has with the variety of G. graminis from kikuyu grass. None of the methods gave a convenient means of separating the wheat and oat take-all fungi.
Importance of Spatial and Temporal Dynamics in Species Regional Abundance and Distribution

Several recent models have been proposed to explain the pattern of species distribution within a region. Brown's niche-based model, Levins' stochastic immigration- extinction model, and Hanski's core-satellite hypothesis (a modification of Levins' model) differ in relative spatial scales, and degree of stochastic variation in species distribution over time. To test the predictions of these models, we analyzed the regional distribution and temporal dynamics of plant species across 19 sites in tallgrass prairie over an 8-yr period. Spatial patterns of species regional distribution were bimodal each year, a pattern in accord with the core-satellite hypothesis. In addition, temporal patterns of species distribution within a site were also bimodal. The dynamics of the core-satellite hypothesis are driven by patterns of immigration and extinction. Extinction was positively related to richness, however, in contrast to the theory of island biogeography, immigration was not related to species richness. In addition, the variances in the differences in species frequencies from one year to the next were greater than three times the mean, a condition necessary for bimodality in the core-satellite model, for 88 of 135 (65.1%) species. These results provide strong support in favor of the core-satellite hypothesis and imply that stochastic factors may be the primary determinant of plant species dynamics and plant community structure in grasslands at the scale of several kilometres. Evidence from prairie communities at much larger spatial scales supported the patterns predicted by Brown's niche-based model. Thus, these apparently competing models are, in fact, compatible when viewed at the appropriate spatial scale.
The genetic diversity of central and peripheral populations of ratlike hamster (Cricetulus triton)

The impact of habitat fragmentation and isolation on the genetic diversity of populations has attracted much attention in studies of meta-population and conservation biology. In this work, using the randomly amplified polymorphic DNA (RAPD) technique, we studied the genetic diversity of central, peripheral and peninsular populations of ratlike hamster, which were collected in five locations of the North China Plain and its surrounding areas, in 1999. The study revealed that, i) the genetic diversity of central population of Raoyang County>the sub-central populations of Gu’an County and Taikang County > the peripheral population of Shunyi District>the peninsular population of Mentougou District; ii) the genetic diversities of the five populations were positively correlated to the nearest distances to the peripheral line of population distribution; iii) there were significant differences of gene frequencies of some RAPD fragments among the five populations. More RAPD fragments disappeared in peripheral populations than in central or sub-central populations. The frequencies of two RAPD fragments were correlated to the latitude. This study clearly indicated that the variation of the genetic diversities of the five populations was caused by edge effect and fragmentation through the enhanced inbreeding and genetic drift, and thus supported the view that habitat fragmentation and related edge effect reduce the population genetic diversity.
Fish communities and habitat changes in the highly modified Goulburn Catchment, Victoria, Australia

Evidence for the decline in native fish communities in the lowland Goulburn Catchment has been based primarily on studies investigating changes to environmental conditions as a result of river regulation. The present study aggregates historical fisheries data to spatially compare native fish communities in different parts of the catchment. Multivariate analyses demonstrate that distinctly different community compositions are found in different parts of the catchment. Eildon Dam, a deep release reservoir, has drastically altered the hydrology and water quality of the upper Goulburn River, and ordination analyses show that this has created both physical and artificial barriers to movement of native fish into the main channel. Concurrently, fisheries data from the upper main channel show the community is highly divergent compared to the remaining catchment. Further downstream, Goulburn Weir creates a barrier to fish movement between Lake Nagambie and the lower Goulburn Catchment, and alters the natural hydrological regime. Similarity Percentage analyses demonstrate that these stressors have facilitated the establishment of alien species, which dominate fish abundance in the upper and lower main channels. The current study emphasises the need to explore alternatives for improving management strategies to rehabilitate fish communities throughout the Goulburn Catchment.
Long‐term exposure to dieldrin reduces γ‐aminobutyric acid type A and N‐methyl‐D‐aspartate receptor function in primary cultures of mouse cerebellar granule cells

The organochlorine pesticide dieldrin is a persistent organic pollutant that accumulates in the fatty tissue of living organisms. In mammals, it antagonizes the GABAA receptor, producing convulsions after acute exposure. Although accumulation in human brain has been reported, little is known about the effects of long‐term exposure to dieldrin in the nervous system. Homeostatic control of the balance between excitation and inhibition has been reported when neuronal activity is chronically altered. We hypothesized that noncytotoxic concentrations of dieldrin could decrease glutamatergic neurotransmission as a consequence of a prolonged reduction in GABAA receptor function. Long‐term exposure of primary cerebellar granule cell cultures to 3 μM dieldrin reduced the GABAA receptor function to 55% of control, as measured by the GABA‐induced 36Cl− uptake. This exposure produced a significant reduction (∼35%) of the NMDA‐induced increase in [Ca2+]i and of the [3H]MK‐801 binding, which was not accompanied by a reduction in the NMDA receptor subunit NR1, as determined by Western blot. Consistent with the decreased NMDA receptor function, dieldrin‐treated cultures were insensitive to an excitotoxic stimulus induced by exposure to high potassium. In summary, we report that the chronic reduction of GABAA receptor function induced by dieldrin decreases the number of functional NMDA receptors, which may be attributable to a mechanism of synaptic scaling. These effects could underlie neural mechanisms involved in cognitive impairment produced by low‐level exposure to dieldrin. © 2007 Wiley‐Liss, Inc.
Determinants of Binding Affinity and Specificity for the Interaction of TEM-1 and SME-1 β-Lactamase with β-Lactamase Inhibitory Protein*

The hydrolysis of β-lactam antibiotics by class A β-lactamases is a common cause of bacterial resistance to these agents. The β-lactamase inhibitory protein (BLIP) is able to bind and inhibit several class A β-lactamases, including TEM-1 β-lactamase and SME-1 β-lactamase. Although the TEM-1 and SME-1 enzymes share 33% amino acid sequence identity and a similar fold, they differ substantially in surface electrostatic properties and the conformation of a loop-helix region that BLIP binds. Alanine-scanning mutagenesis was performed to identify the residues on BLIP that contribute to its binding affinity for each of these enzymes. The results indicate that the sequence requirements for binding are similar for both enzymes with most of the binding free energy provided by two patches of aromatic residues on the surface of BLIP. Polar residues such as several serines in the interface do not make significant contributions to affinity for either enzyme. In addition, the specificity of binding is significantly altered by mutation of two charged residues, Glu73 and Lys74, that are buried in the structure of the TEM-1·BLIP complex as well as by residues located on two loops that insert into the active site pocket. Based on the results, a E73A/Y50A double mutant was constructed that exhibited a 220,000-fold change in binding specificity for the TEM-1 versus SME-1 enzymes.
Nutrient and energy content of freshwater fishes

The analyses of fresh total body homogenates of 2385 freshwater fishes from 17 species originating in natural waters and aquaculture facilities resulted in average values of 19.1–37.8% dry matter, 13.6–18.3% crude protein, 0.8–18.3% crude fat, 0.16–2.17% nitrogen-free extracts (NFE), 2.2–2.9% nitrogen and 0.39–1.02% phosphorus. The gross energy content ranged from 3.83 to 11.49 MJ/kg. With increasing fat content in the fishes, water content decreased and dry matter content increased. Through this interdependence, a significant correlation was found between dry matter and crude fat and energy content (r2=0.92–0.97). The values of crude protein, crude ash, NFE, nitrogen and phosphorus did not show any significant influence on dry matter content (r2=0.0005–0.46). Based on the significant correlation between dry matter and gross energy (gross energy [MJ/kg]=0.0253 dry matter [%]1.6783), the energy content of freshwater fishes can easily be estimated by the dry matter content in the total body.
DIGESTIBILITY AND RELATED NUTRITIONAL DATA FOR SEVEN NORTHERN DEER BROWSE SPECIES

Energy use and related data are presented for seven northern winter foods of white-tailed deer (Odocoileus virginianus). Hemlock (Tsuga canadensis), balsam fir (Abies balsamea), red maple (Acer rubrum), striped maple (A. pensylvanicum), mountain maple (A. spicatum), hobblebush (Viburnum alnifolium), and hazelnut (Corylus cornuta) were fed in mixed rations to captive deer. Species tested had gross energy digestibilities ranging from 30 (red maple) to 54 percent (hobblebush). The amount of digestible, metabolizable, and net energy in each of the three maple species evaluated was very sim- ilar. Metabolizable energy ranged from 24 percent (1.2 kcal/g) for striped maple to 46 percent (2.2 kcal/g) for hobblebush. The lowest net energy was observed for striped maple (5 percent or 0.2 kcal/g), the highest for hobblebush (37 percent or 1.8 kcal/g). Crude protein was digested poorly in hemlock, balsam, and red maple (-5, 11, and 1 percent digestible, respectively) as compared with an average value of 47 percent for the remaining 4 species. The digestibilities of fat, fiber, and nitrogen-free extract of the seven plant species are presented and discussed. An example of the calculation of browse require- ment during a northern winter period, based on these and related data, is presented. J. WILDL. MANAGE. 40(4):630-638
Choline metabolism in high-producing dairy cows: Metabolic and nutritional basis

Choline, the beta-hydroxyethyltrimethylammonium ion, is a strong base containing a trimethylated quaternary nitrogen. Choline occurs widely in biological materials as the compound itself, as acetylcholine and as various phospholipids. In feed ingredients and crude unprocessed fat sources, most choline is present as phosphatidylcholine (lecithin). Although soybean, soybean meal, rapeseed meal, fish meal and dried yeast are relatively rich sources of choline, the bioavailability of choline in these feedstuffs is only moderate. In dairy ruminants, choline is extensively degraded in the rumen. For this reason, dietary choline contributes insignificantly to the choline body pool, and methyl group metabolism is generally conservative with a relatively low rate of methyl catabolism and an elevated rate of de novo synthesis of methyl groups via the tetrahydrofolate system. Gluconeogenic precursors are the primary sources of the new methyl groups. Depending on energy balance and physiological state, such precursor.