nils-herrmann/clean_scirepeval huggingface dataset:
Molecular Mechanisms of Selenium Tolerance and Hyperaccumulation in Stanleya pinnata1[W][OA]
Venue: Plant Physiology

The molecular mechanisms responsible for selenium (Se) tolerance and hyperaccumulation were studied in the Se hyperaccumulator Stanleya pinnata (Brassicaceae) by comparing it with the related secondary Se accumulator Stanleya albescens using a combination of physiological, structural, genomic, and biochemical approaches. S. pinnata accumulated 3.6-fold more Se and was tolerant to 20 μm selenate, while S. albescens suffered reduced growth, chlorosis and necrosis, impaired photosynthesis, and high levels of reactive oxygen species. Levels of ascorbic acid, glutathione, total sulfur, and nonprotein thiols were higher in S. pinnata, suggesting that Se tolerance may in part be due to increased antioxidants and up-regulated sulfur assimilation. S. pinnata had higher selenocysteine methyltransferase protein levels and, judged from liquid chromatography-mass spectrometry, mainly accumulated the free amino acid methylselenocysteine, while S. albescens accumulated mainly the free amino acid selenocystathionine. S. albescens leaf x-ray absorption near-edge structure scans mainly detected a carbon-Se-carbon compound (presumably selenocystathionine) in addition to some selenocysteine and selenate. Thus, S. albescens may accumulate more toxic forms of Se in its leaves than S. pinnata. The species also showed different leaf Se sequestration patterns: while S. albescens showed a diffuse pattern, S. pinnata sequestered Se in localized epidermal cell clusters along leaf margins and tips, concentrated inside of epidermal cells. Transcript analyses of S. pinnata showed a constitutively higher expression of genes involved in sulfur assimilation, antioxidant activities, defense, and response to (methyl)jasmonic acid, salicylic acid, or ethylene. The levels of some of these hormones were constitutively elevated in S. pinnata compared with S. albescens, and leaf Se accumulation was slightly enhanced in both species when these hormones were supplied. Thus, defense-related phytohormones may play an important signaling role in the Se hyperaccumulation of S. pinnata, perhaps by constitutively up-regulating sulfur/Se assimilation followed by methylation of selenocysteine and the targeted sequestration of methylselenocysteine.
Hypoxia and Anoxia Tolerance in the Annual Killifish Austrofundulus limnaeus.
Venue: Integrative and Comparative Biology

Embryos of the annual killifish Austrofundulus limnaeus are routinely exposed to oxygen limitation during development and are extremely tolerant of anoxia. Importantly, tolerance of anoxia is not strictly associated with entrance into metabolic dormancy associated with diapause II, but rather any embryo will respond to anoxia by entering into a state of anoxia-induced quiescence. Hypoxia causes a reduction in the rate of development, reduced heart rates, and reduced capacities for metabolic enzyme activity in both aerobic and anaerobic pathways. Embryos of A. limnaeus begin life as oxyconformers, and transition into oxyregulators near the completion of embryonic development. As this transition occurs, extreme anoxia tolerance is lost. The rate of early development is independent of oxygen partial pressure, despite the fact that the embryos are oxyconformers. This suggests a contribution from anaerobic pathways to support early development. However, the specific pathways supporting this metabolism are unknown. The response of A. limnaeus embryos to hypoxia and anoxia is unique compared to other fishes and most other vertebrates, and thus future studies on this species may lend insight into novel mechanisms that support survival during prolonged oxygen limitation.
Cutin and Cutan Biopolymers: Their Role as Natural Sorbents
Venue: Soil Science Society of America Journal

The aliphatic biopolymers cutin and cutan are important precursors of soil organic matter. In this study, we examined the effects of these biopolymers' decomposition and transformation in the soil on their sorptive properties. The levels of cutin and cutan decreased by 35 and 30%, respectively, after 20 mo of incubation. Carbon-13 nuclear magnetic resonance and differential scanning calorimeter analyses suggested that the rigid (crystalline) polymethylene moieties of cutan decompose with time. This observation is in contrast to previous reports, which suggested that this alkyl-C moiety is resistant to biodegradation. Cutin, however, exhibited mainly decomposition of the mobile (amorphous) polymethylene moieties. Moreover, some of its degraded materials were transformed into humic materials. The phenanthrene sorption coefficient decreased by 80 and 37% with incubation time of the cutin and cutan samples, respectively. For 1-naphthol, the sorption capacity decreased by 90% due to cutin decomposition. With cutan, this parameter did not show any changes correlated with incubation time. Phenanthrene exhibited linear and reversible sorption isotherms. In contrast, pronounced desorption hysteresis was obtained for 1-naphthol with the 20-mo-incubated cutin sample and with all cutan samples. With all cutan samples, desorption hysteresis increased with decomposition. Our data suggest that the sorptive nature of both biopolymers was affected by soil decomposition. With degradation, the role of cutin as a natural sorbent decreases while cutan acts as a natural highly efficient sorbent for organic compounds in the soil.
The Bacterially Produced Metabolite Violacein Is Associated with Survival of Amphibians Infected with a Lethal Fungus
Venue: Applied and Environmental Microbiology

The disease chytridiomycosis, which is caused by the chytrid fungus Batrachochytrium dendrobatidis, is associated with recent declines in amphibian populations. Susceptibility to this disease varies among amphibian populations and species, and resistance appears to be attributable in part to the presence of antifungal microbial species associated with the skin of amphibians. The betaproteobacterium Janthinobacterium lividum has been isolated from the skins of several amphibian species and produces the antifungal metabolite violacein, which inhibits B. dendrobatidis. In this study, we added J. lividum to red-backed salamanders (Plethodon cinereus) to obtain an increased range of violacein concentrations on the skin. Adding J. lividum to the skin of the salamander increased the concentration of violacein on the skin, which was strongly associated with survival after experimental exposure to B. dendrobatidis. As expected from previous work, some individuals that did not receive J. lividum and were exposed to B. dendrobatidis survived. These individuals had concentrations of bacterially produced violacein on their skins that were predicted to kill B. dendrobatidis. Our study suggests that a threshold violacein concentration of about 18 μM on a salamander's skin prevents mortality and morbidity caused by B. dendrobatidis. In addition, we show that over one-half of individuals in nature support antifungal bacteria that produce violacein, which suggests that there is a mutualism between violacein-producing bacteria and P. cinereus and that adding J. lividum is effective for protecting individuals that lack violacein-producing skin bacteria.
Phase transitions of wax esters adjust buoyancy in diapausing Calanoides acutus
Venue: Limnology and Oceanography

We study the composition and biophysical properties of wax esters extracted from the Antarctic copepod, Calanoides acutus, to explore if these factors adjust buoyancy in diapausing copepods. Levels of wax ester in the copepods were correlated with depth, with deeper animals containing higher amounts. An unsaturation index was used to determine the proportions of polyunsaturated wax esters in the oil sac of the copepods. The proportion of polyunsaturated wax ester in copepods that had descended to depth was always close to 50% and attributable to high amounts of the diatom biomarker fatty acid 20:5(n-3) contained in these storage lipids. High-pressure differential scanning calorimetry indicated that wax esters with such high levels of unsaturation exhibited unusual properties, changing from a liquid to a solid phase at pressures and temperatures below 500 m in the ocean. The dense, solid wax esters reduce the overall buoyancy of the lipid-rich copepods at depth and help facilitate neutral buoyancy. The composition of wax esters is a key factor in buoyancy control in these organisms during diapause. Many calanoid copepods inhabiting high-latitude environments overwinter at great depths in the oceans in a state of diapause, a condition where metabolic processes are either arrested or greatly reduced (Dahms 1995). A fundamental requirement of successful overwintering is the acquisition of substantial lipid reserves during summer when microplankton and particularly diatom production is
Preparing for hibernation in ground squirrels: adrenal androgen production in summer linked to environmental severity in winter
Venue: Functional Ecology

1. At high latitudes, evolutionary adaptations focus on those that maximize survival, with hibernation being a major one used by many smaller mammals. Typically, mammalian hibernators overwinter in sites that are ≈0°C. However, in arctic regions, such sites do not exist, necessitating hibernation at sites well below 0°C. Lipid, the normal fuel of most hibernators, may not provide sufficient glucose needed by certain tissues to permit survival, with muscle breakdown being required. Critical to enhancing muscle stores are high concentrations of anabolic androgens prior to hibernation when the gonads are inactive. 
 
2. We compare and contrast androgen levels in arctic ground squirrels (AGS) (Urocitellus parryii Richardson) from the Yukon and Columbian ground squirrel (CGS) (U. columbianus Ord) from southern Alberta. 
 
3. In males, changes in testes mass over the active season were similar between AGS and CGS. In contrast, during the breeding and the nonbreeding, pre-hibernation periods, androgen levels in AGS were 6–10 and 20–25 times, respectively, those of CGS. From the breeding to the pre-hibernation periods, androgen levels declined 41% in AGS, but 86% in CGS. In females, androgen levels in AGS were high throughout the active season and, prior to hibernation, were 24 times those in CGS. 
 
4. In pre-hibernating AGS, we determined the source of these high androgen levels from two studies. First, using a hormonal challenge protocol to probe the hypothalamic-pituitary-adrenal axis, we found that androgen levels in both females and males decreased ≥10% in response to suppression by dexamethasone (an artificial glucocorticoid that inhibits ACTH release) and increased ≥18% in response to direct adrenal stimulation by adrenocorticorticotropic homone (ACTH). Second, by sequential hormonal injections in males of gonadotropin-releasing hormone (GnRH) and of ACTH coupled with gonadectomy (GDX), followed by adrenalectomy (ADX), we found that GnRH had no effect, whereas ACTH stimulated androgen levels by >40%, both before and after GDX. After ADX, levels fell by 80%. Thus, the adrenals, not the gonads, are the source of these androgens. 
 
5. We hypothesize that pre-hibernating AGS have evolved a solution seen in no other known mammal: exploiting the benefits of high adrenal androgen levels prior to hibernation to build muscle that is then catabolized overwinter. The unknown is how AGS have mitigated the costs of these high androgen levels.
The ecological engineering impact of a single tree species on the soil microbial community
Venue: Journal of Ecology

1. Ecosystem engineering by a single species can have a cascading effect on many ecosystem processes. While the impact of above-ground ecological engineers on soil chemical properties has been studied, few studies have assessed their impact on the soil microbial community, which is largely responsible for many ecosystem functions.

2. Utilizing a long-term experiment where birch was planted on heather moorland 20 years ago, the engineering impact of a single tree species (Betula pubescens) on the soil microbial community was assessed using phospholipid fatty acid (PLFA) analysis and fungal polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE). Changes in the soil microbial community were then related to soil chemical and physical variables and tree performance variables.

3. Under birch, total microbial biomass (total PLFA) declined, species richness increased and the ratio of fungal : bacterial PLFA declined. The fungal PLFA marker increased with increasing organic matter and depth of the LFH and O soil horizons, characteristics associated with moorland soils. Bacterial PLFAs increased with increasing birch canopy cover. The fungal community of the birch plots was different from that in the heather plots and changes in the fungal community composition were related to the size of the birch trees in the plots.

4. Changes in the soil microbial community were also related to changes in mineralizable N. Mineralizable N was correlated with both decreasing total soil microbial biomass and decreasing fungal : bacterial ratio.

5. The durability of the engineering effects of birch was studied in a second experiment. Plots were established in first-generation birch woodland that had developed on Calluna-dominated moorland. The plots were cleared of birch and planted with heather. After 20 years, there was no difference in the community composition of the PLFAs. In contrast, there were significant differences in the fungal community composition as judged by DGGE analysis, with the fungal community in the felled birch plots being similar to the heather moorland.

6. Synthesis. This work demonstrates that addition of a single tree species to heather moorland results in changes in below-ground soil microbial communities and in nutrient cycling.
Molecular basis of a novel adaptation to hypoxic-hypercapnia in a strictly fossorial mole
Venue: BMC Evolutionary Biology

BackgroundElevated blood O2 affinity enhances survival at low O2 pressures, and is perhaps the best known and most broadly accepted evolutionary adjustment of terrestrial vertebrates to environmental hypoxia. This phenotype arises by increasing the intrinsic O2 affinity of the hemoglobin (Hb) molecule, by decreasing the intracellular concentration of allosteric effectors (e.g., 2,3-diphosphoglycerate; DPG), or by suppressing the sensitivity of Hb to these physiological cofactors.ResultsHere we report that strictly fossorial eastern moles (Scalopus aquaticus) have evolved a low O2 affinity, DPG-insensitive Hb - contrary to expectations for a mammalian species that is adapted to the chronic hypoxia and hypercapnia of subterranean burrow systems. Molecular modelling indicates that this functional shift is principally attributable to a single charge altering amino acid substitution in the β-type δ-globin chain (δ136Gly→Glu) of this species that perturbs electrostatic interactions between the dimer subunits via formation of an intra-chain salt-bridge with δ82Lys. However, this replacement also abolishes key binding sites for the red blood cell effectors Cl-, lactate and DPG (the latter of which is virtually absent from the red cells of this species) at δ82Lys, thereby markedly reducing competition for carbamate formation (CO2 binding) at the δ-chain N-termini.ConclusionsWe propose this Hb phenotype illustrates a novel mechanism for adaptively elevating the CO2 carrying capacity of eastern mole blood during burst tunnelling activities associated with subterranean habitation.
Hypoxic survival strategies in two fishes: extreme anoxia tolerance in the North European crucian carp and natural hypoxic preconditioning in a coral-reef shark
Venue: The Journal of Experimental Biology

Especially in aquatic habitats, hypoxia can be an important evolutionary driving force resulting in both convergent and divergent physiological strategies for hypoxic survival. Examining adaptations to anoxic/hypoxic survival in hypoxia-tolerant animals may offer fresh ideas for the treatment of hypoxia-related diseases. Here, we summarise our present knowledge of two fishes that have evolved to survive hypoxia under very different circumstances. The crucian carp (Carassius carassius) is of particular interest because of its extreme anoxia tolerance. During the long North European winter, it survives for months in completely oxygen-deprived freshwater habitats. The crucian carp also tolerates a few days of anoxia at room temperature and, unlike anoxia-tolerant freshwater turtles, it is still physically active in anoxia. Moreover, the crucian carp does not appear to reduce neuronal ion permeability during anoxia and may primarily rely on more subtle neuromodulatory mechanisms for anoxic metabolic depression. The epaulette shark (Hemiscyllium ocellatum) is a tropical marine vertebrate. It lives on shallow reef platforms that repeatedly become cut off from the ocean during periods of low tides. During nocturnal low tides, the water [O2] can fall by 80% due to respiration of the coral and associated organisms. Since the tides become lower and lower over a period of a few days, the hypoxic exposure during subsequent low tides will become progressively longer and more severe. Thus, this shark is under a natural hypoxic preconditioning regimen. Interestingly, hypoxic preconditioning lowers its metabolic rate and its critical PO2. Moreover, repeated anoxia appears to stimulate metabolic depression in an adenosine-dependent way.
Thermoperception in the common vampire bat (Desmodus rotundus)
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

Summary1.The common vampire bat,Desmodus rotundus, is known to be capable of detecting temperature differences. In the experiments described here two animals were trained to give preference to the radiation emitted by a warm signal unit (the negative unit was left at room temperature). The distance between the decision line and the signal units was 8, 12 or 16 cm. Both animals responded to radiation as low as 0.5 × 10−4 W cm−2 . This sense for thermal radiation may aid these bats in localizing or selecting a suitable biting site.3.Histological studies of the bats' facial structures indicate that thermal stimuli are most probably perceived in the three pits surrounding the central nose leaf: the thin, hairless and glandless skin is underlaid with dense connective tissue. Thermography reveals that the surface temperature of the nasal region is up to 9 °C lower than that of the neighboring parts of the face .
The evolution of sweat glands
Venue: International Journal of Biometeorology

Mammals have two kinds of sweat glands, apocrine and eccrine, which provide for thermal cooling. In this paper we describe the distribution and characteristics of these glands in selected mammals, especially primates, and reject the suggested development of the eccrine gland from the apocrine gland during the Tertiary geological period. The evidence strongly suggests that the two glands, depending on the presence or absence of fur, have equal and similar functions among mammals; apocrine glands are not primitive. However, there is a unique and remarkable thermal eccrine system in humans; we suggest that this system evolved in concert with bipedalism and a smooth hairless skin.
Biodegradation of new quaternary ammonium compounds in treated wood by mould fungi
Venue: Wood Science and Technology

The degradation of seven potential wood preservatives based on imidazolium compounds (ICs) and quaternary ammonium compounds (QACs) with a modified anion structure by mould fungi was determined using soil-block method. Experiments were carried out on Scots pine (Pinus sylvestris L.) wood. Two-phase titration and high-performance liquid chromatography (HPLC) method were used to detect and quantify the degradation products. The performed soil-block tests showed that the ICs and QACs with alkoxymethyl substituents were leached from the experimental wood when in contact with moist soil and revealed their fungal detoxification by mould fungi, especially by Gliocladium roseum. The degree of biological decomposition of new compounds was higher than didecyldimethylammonium chloride and didecylmethylpoli(oxyethyl)ammonium propionate. The observations of the colonization by mould fungi were made using the scanning electron microscope (SEM). Decay of treated wood by mould fungi showed its tolerance to QACs.
Aerial roots of epiphytic orchids: the velamen radicum and its role in water and nutrient uptake
Venue: Oecologia

The velamen radicum, a spongy, usually multiple epidermis of the roots, which at maturity consists of dead cells, is frequently described as an important adaptation of epiphytic orchids. Yet, quantitative evidence for the alleged functions, e.g., efficient water and nutrient uptake, nutrient retention, reduction of water loss, mechanical protection, or the avoidance of overheating, is rare or missing. We tested the notion originally put forward by Went in 1940 that the velamen allows plants to capture and immobilize the first solutions arriving in a rainfall, which are the most heavily charged with nutrients. In a series of experiments, we examined whether all necessary functional characteristics are given for this scenario to be realistic under ecological conditions. First, we show that the velamen of a large number of orchid species takes up solutions within seconds, while evaporation from the velamen takes several hours. Charged ions are retained in the velamen probably due to positive and negative charges in the cell walls, while uncharged compounds are lost to the external medium. Finally, we demonstrate that nutrient uptake follows biphasic kinetics with a highly efficient, active transport system at low external concentrations. Thus, our results lend strong support to Went’s hypothesis: the velamen fulfills an important function in nutrient uptake in the epiphytic habitat. Most of the other functions outlined above still await similar experimental scrutiny.
Average nanorough skin surface of the pilot whale (Globicephalamelas, Delphinidae): considerations on the self-cleaning abilities based on nanoroughness
Venue: Marine Biology

In aquatic environments, the biofouling process is assumed to initiate from the conditioning layer of absorbed organic carbon residues on wetted surfaces. Microfouling organisms attach to this conditioning layer, building up a biofilm on which further biofouling proceeds. In dolphins, biofouling reduces hydrodynamic efficiency and may negatively affect health if not managed. In the present study we examined the skin surface of the pilot whale (Globicephalamelas). Employing cryo-scanning electron microscopic techniques combined with various sample preparations, the skin displayed an average nanorough surface characterized by a pattern of nanoridge-enclosed pores; the average pore size (approximately 0.20 µm2) was below the size of most marine biofouling organisms. Further, the implications of this type of surface to the self-cleaning abilities of the skin of pilot whales are discussed, based on reduced available space for biofouler attachment, the lack of any particular microniches as shelters for biofoulers, and the challenges of turbulent water flow and liquid–air interfaces during surfacing and jumping of the dolphin.