Miracle-dz/UniFAR-FTUs huggingface dataset:
N remineralization in planktonic protozoa

Ammonium excretion rates of two marine planktonic protozoa (an oligotrichous ciliate, Strombidium sulcatum, and an aplastidic flagellate, Pseudobodo sp.) both isolated from oligotrophic Mediterranean waters were quantified with heat-killed bacteria as the food source for the protozoans. Ammonium excretion rates ranged from 0.25 to 2 µg N mg DW−1 h−1 for the ciliate and from 2.8 to 8.5 for the phagotrophic flagellate. Maximum excretion rates took place during the early exponential growth phase, suggesting possible covariation of excretion rates with either protozoan body size or their growth rates or metabolic state. Comparison of these excretion and regeneration rates with those obtained in situ for oligotrophic waters (∼0–37 nmol liter−1 h−1) indicates that protozoa may account for >50% of the nutrient recycling in these waters.
On the reliability of enumeration for mark and recapture census of voles

Some studies of populations in small rodents rely on enumeration of individuals to provide an estimate of population size. A computer simulation of the capture–recapture process was used to examine the influence of five population parameters on the reliability of enumeration. Enumeration is shown to be insensitive to population size, survival between sampling intervals, and individual variation in the probability of capture. Enumeration is sensitive to the probability of capture; if the probability of capture for the average individual falls below 0.5, the enumeration technique provides a poor estimate of population size. Enumeration is also extremely sensitive to reduced probabilities of capture for unmarked animals. Data from capture–recapture studies of five species of Microtus were used in the computer simulation, and it was concluded for these five species that enumerated populations are at least 10–20% smaller than the actual populations.
The relationship between coverage and dry matter contribution of forage legumes in binary legume-grass mixtures.

An efficient and accurate detection of the contribution of legume dry matter (DM) in legume-grass mixtures is of great importance for a targeted management of legume-based swards. Legume coverage is a frequently used parameter to describe the dominance structure in vegetation because it is easily accessible. The present study investigates the relationships between legume coverage and different legume species and growth stages. A dataset was generated from a pot experiment that was conducted under controlled conditions across a wide range of legume species (Trifolium repens L., T. pratense L., Medicago sativa L.), proportions of legumes (0-800 g kg -1 ), and growth stages (tillering to heading). Multiple regression analysis revealed a positive relationship between legume contribution and coverage for the separate legume species (R 2 = 0.98-0.99), as well as for the combined dataset including all legumes (R 2 = 0.98). Total biomass was related to clover coverage in a complex manner, reducing legume contribution by up to 180 g kg -1 with an increase of total biomass from 300 to 1500 kg DM ha -1 . The validation of the models with mixed swards of grass and either white or red clover that were grown in the field showed good results (r 2 = 0.98).
Phylogenetics is not phylogenomics

Biology is undergoing a genomic revolution, driven by new sequencing technologies [. ] and the computational capacity necessary to analyze massive amounts of molecular data. This has led to the nascent field of phylogenomics—the use of genome-scale datasets to infer evolutionary relationships, test hypotheses concerning the selective regimes under which evolutionary changes have occurred, predict protein function, etc. [. ] Genomic data have been heralded as having great potential for the resolution of historically difficult problems in phylogenetics, by providing more character information to address these problems, by orders of magnitude, than singleor few-gene datasets.
Ecotypic differences and performance of the genetic resources of cocksfoot (Dactylis glomerata L.) in north-west Spain

Quantitative traits and allozymes were used in two experiments to clarify the ecotypic differentiation of natural cocksfoot (Dactylis glomerata) populations from north-west Spain. Thirty-nine populations belonging to the four main ecotypes in Galicia were cultivated in two field experiments. In the first experiment, there were significant differences between ecotypes for heading date, flag leaf length, growth habit and vigour. Coastal populations were the least infected by rust. In the second experiment, allozyme markers presumed to be diagnostic for ssp. glomerata vs. izcoi (TO1 1·00, TO1 1·03) were found in all populations studied (ten tetraploids and one diploid izcoi). This suggests that gene flow occurs between coastal and interior populations. Culm and panicle lengths of tetraploids (without application of fertilizer) were inside the izcoi range in 1997, but some plants from all populations exceeded it in 1998. It is concluded that ssp. izcoi also occurs on the coast. Populations with a high level of complementary seasonal growth were detected.
Native European eels as a potential biological control for invasive crayfish

SUMMARY 1. Invasive species may have strong negative impacts on ecosystems. Invasive crayfish are well known to cause ecological imbalances in freshwater systems and have become targets in eradication programmes. 2. The red swamp crayfish (Procambarus clarkii) is vulnerable to predation by several fish species. The European eel (Anguilla anguilla) appears to be a very good candidate given its benthic feeding activity and ability to recognise prey by odour. 3. Our study took place from 2009 to 2013 in a closed system in south-eastern France in which ponds were sampled twice a year by passive capture methods to evaluate trends in populations of potential prey. Eel population dynamics were assessed by means of a multistate capture–recapture model, and diet assessment was performed using stable isotope analysis in October 2010 and October 2012. 4. Our results show that the invasive crayfish was the most important prey in the eel diet, and every size-class of crayfish was preyed upon by the predator. 5. A high predator density, approaching carrying capacity for the European eel in this system, strongly affects P. clarkii populations, leading them to their collapse, but not eradication.
Intracellular Amyloid-β1–42, but Not Extracellular Soluble Amyloid-β Peptides, Induces Neuronal Apoptosis*

Alzheimer disease (AD), the most frequent cause of dementia, is characterized by an important neuronal loss. A typical histological hallmark of AD is the extracellular deposition of β-amyloid peptide (Aβ), which is produced by the cleavage of the amyloid precursor protein (APP). Most of the gene mutations that segregate with the inherited forms of AD result in increasing the ratio of Aβ42/Aβ40 production. Aβ42 also accumulates in neurons of AD patients. Altogether, these data strongly suggest that the neuronal production of Aβ42 is a critical event in AD, but the intraneuronal Aβ42 toxicity has never been demonstrated. Here, we report that the long term expression of human APP in rat cortical neurons induces apoptosis. Although APP processing leads to production of extracellular Aβ1–40 and soluble APP, these extracellular derivatives do not induce neuronal death. On the contrary, neurons undergo apoptosis as soon as they accumulate intracellular Aβ1–42 following the expression of full-length APP or a C-terminal deleted APP isoform. The inhibition of intraneuronal Aβ1–42 production by a functional γ-secretase inhibitor increases neuronal survival. Therefore, the accumulation of intraneuronal Aβ1–42 is the key event in the neurodegenerative process that we observed.
Recent advances of metal binding protein lactoferrin as an anti-microbial agent

Lactoferrin (Lf) is present in milk and gland secretions and serve as an antimicrobial function. Insufficient amounts of Lf in some secretions also appear to correlate with certain health problems. Protection against gastroenteritis is the most likely biologically relevant activity of lactoferrin. Multiple in vitro and animal studies have shown a protective effect of lactoferrin on infections with enteric microorganisms, including rotavirus, Giardia, Shigella, Salmonella and the diarrheagenic Escherichia coli. Lactoferrin has two major effects on enteric pathogens: it inhibits growth and it impairs function of surface expressed virulence factors thereby decreasing their ability to adhere or to invade mammalian cells. Lf also inhibits several species of fungi and certain parasites. This review covers the role of Lf in clearing the parasitic infections. The mechanism by which lactoferrin inhibits some parasites may be via stimulation of the process of phagocytosis, whereby immune cells engulf and digest foreign organisms. Trichomonas vaginalis is a protozoan responsible for the number one, non-viral sexually transmitted disease. In this review, we also discussed the role of Lf in cervical infections.
Competition, Disturbance, and Community Organization: The Provision and Subsequent Utilization of Space in a Rocky Intertidal Community

An understanding of community structure should be based on evidence that the growth and regulation of the component populations in the community are affected in a predictable manner by natural physical disturbances and by interactions with other species in the community. This study presents an experimental evaluation of the effects of such disturbances and competitive interactions on populations of sessile organisms in the rocky intertidal community, for which space can be demonstrated to be the most important limiting resource. This research was carried out at eight stations on the Washington coastline which have been ranked according to an exposure/desiccation gradient and subjected to comparable manipulation and observation. Physical variables such as wave exposure, battering by drift logs, and desiccation have important effects on the distribution and abundance of many of the sessile species in the community. In particular, wave exposure and desiccation have a major influence on the distribution patterns of all the algae and of the anemone Anthopleura elegantissima. The probability of damage from drift logs is very high in areas where logs have accumulated along the intertidal. Log damage and wave exposure have complementary effects in the provision of free space in a mussel bed, as wave shock enlarges a patch created by log damage by wrenching the mussels from the substratum at the periphery of the bare patch. Competition for primary space results in clear dominance hierarchies, in which barnacles are dominant over algae. Among the barnacles, Balanus cariosus is dominant over both B. glandula and Chthamalus dalli; B. glandula is dominant over C. dalli. The mussel Mytilus californianus requires secondary space (certain algae, barnacles, or byssal threads) for larval settlement, but is capable of growing over all other sessile species and potentially is the competitive dominant of space in the community.
Local variation in endoparasite infection of brushtail possums, Trichosurus vulpecula, along a forest margin transect, lower North Island, New Zealand

Abstract To assess fully the potential of parasites for biological control of Australian brushtail possums (Trichosurus vulpecula) introduced to New Zealand, factors affecting prevalence and intensity of infection need to be determined. The present study investigated local spatial variation in endoparasite infection in possums at sites along a 24 km forest margin transect, lower North Island, New Zealand, where most of the endoparasite species recorded from possums in New Zealand were present. Sampling sites varied little in the parasite species present in possums, or the prevalence and intensity of infection. Possum sex and age had much stronger effects on prevalence and intensity of infection than sampling site. Most site variation in prevalence and intensity of infection occurred among the Trichos‐trongylus spp. , for which possums are not the primary hosts, presumably reflecting variation in contact between possums and the primary hosts.
Rate of tube building and sediment particle size selection during tube construction by the tanaid crustacean,Leptochelia dubia

In estuaries, organic coatings play an important role in the aggregation of mineral particles. Particles acquire adhesive surfaces through the activities of bacteria and microalgae in the sediment and water column. Eventually, they may become incorporated into larger aggregates and structures, such as tubes, constructed by infaunal benthic animals. Where these structures are large enough, and the adhesive bonds between particles strong enough, individual particles may remain in place at bed shear stresses otherwise strong enough to cause sediment transport. This study examined the aggregation of particles during tube building by the ubiquitous tanaid crustaceanLeptochelia dubia. Particle size selection and rates of tube building were determined as functions of animal size, temperature, and the presence or absence of bacteria and microalgae. These data were used to model seasonal patterns of sediment binding by a population ofL. dubia in Yaquina Bay, Oregon, taking into account seasonal changes in sizes and abundance of animals. Rates of tube building (mass of sediment per day) increased with animal size, but temperature had no effect. The model indicated that the field population ofL. dubia bound sediment into tubes at a gross rate of 350 g m−2 d−1, averaged over a 2-yr period. Seasonally, gross rates of tube building were predicted to range from 70 g m−2 d−1 (during late winter-early spring) to 600 g m−2 d−1 (during autumn). When constructing tubes from sterile sediments, small animals selected silt-sized particles while large animals discriminated against these particles. The presence of microbes in sediments tended to reduce particle selectivity.
Abundance, biomass and production of mobile epibenthic fauna in Zostera marina (L.) meadows, western Sweden

Abstract Mobile epifauna was sampled quantitatively with a drop-trap in three Zostera marina (L.) meadows on the west coast of Sweden, 1980–82. Of 20 species recorded, 10 were crustaceans (mostly shrimps) and 10 fishes (gobies, pipe-fishes and sticklebacks). Crustaceans dominated in abundance and biomass throughout the season and in all areas. Total abundance and biomass varied between 20 and 160 ind. · m−2 and 1 and 12 g (ash-free dry weight, AFDW) · m−2. The shrimp Palaemon adspersus (Rathke) and the shore crab Carcinus maenas (L.) contributed 65 to 90% of the mean seasonal biomass in the three areas, and the dynamics of these two species are described in this paper. Production of the 6–8 dominant species during eight months (May–December) of investigation varied between 2.5 and 6.0 g AFDW · m−2. No relation was found between the biomass of fauna and standing stock of Zostera, but patches of Fucus vesiculosus in the Zostera were shown to play an important role for some species.
The distribution of calcium in the grass pollen tube

The distribution of calcium in the terminal regions of actively extending pollen tubes of two Gramineae, Zea mays and Pennisetum americanum, has been investigated by chlorotetracycline (CTC) fluorescence and by energy-dispersive X-ray analysis. Neither method reveals a concentration gradient declining from the tip towards the older parts of the tube comparable with that reported from the pollen tubes of Lilium longiflorum. The difference evidently arises from dissimilarities in pollen-tube growth physiology and the apical organization of the tube. Growth is achieved by the insertion of dictyosome-derived vesicles carrying wallprecursor materials at the tube tip. In L. longiflorum these are produced in a subapical zone of the tube, and a characteristic zonation of cytoplasmic organelles in the distal region develops during growth. In the grasses, large numbers of the wall precursor bodies (‘P-particles ’) are produced before pollen dispersal, and are stored in the grain; they are distributed throughout the tube during early growth, and the organelle zonation in the apex is less pronounced. CTC-induced fluorescence is strongly associated with mitochondria, membranes and P-particles, suggesting that the observed distribution of calcium may reflect mainly the distribution of the element held in organelles and membranes rather than mobile Ca2+ in the cytosol.
Deep-sea nematode biodiversity in the Mediterranean basin : testing for longitudinal, bathymetric and energetic gradients

The knowledge of the processes controlling the spatial distribution of species diversity is one of the main challenges of the present ecological research. Spatial patterns of benthic biodiversity in the deep sea are poorly known in comparison with other ecosystems and this limits our understanding of the mechanisms controlling the distribution and maintenance of high biodiversity in the largest ecosystems of our biosphere. Although the Mediterranean basin covers 7.5% of the global biodiversity. The high biogeographic complexity and the presence of steep ecological gradients contribute in making the Mediterranean a region of very high diversity. Here we report the results of an investigation on the patterns of nematode biodiversity in the deep-Mediterranean Sea, in relation with bathymetric, longitudinal and energetic gradients. Our results indicate that benthic biodiversity in the deep-Mediterranean decreases significantly with increasing depth. Moreover, at equally deep sites, nematode diversity decreased from the western to the eastern basin and longitudinal gradients were evident when comparing sites at 4000-m depth, with 3000-m depth. The analysis of the available energy (measured as labile organic matter content of the sediments) suggests that biodiversity patterns are not controlled by the amounts of food resources, but instead bio-availability is the key factor. A more detailed analysis revealed an extremely high deep-sea beta-diversity (turnover diversity), both among sites at different depths as well as at similar depths of different longitude or within the same basin. This new finding has not only important implications on the estimates of the overall regional diversity (gamma diversity), but also suggests the presence of high biogeographic complexity in the deep benthic domain of the Mediterranean Sea.
Antimutagenesis Studies: Where Have They Been and Where Are They Heading?

An anti-mutagen is any substance that reduces the rate of spontaneous mutations or counteracts or reverses the action of a mutagen, or any technique that protects cells against the effects of mutagens. Studies as early as the 1940s reported on substances that delayed detection of radiation-induced mutations, or reduced the appearance of mutations induced by chemicals such as acridine orange. However, a far more sophisticated range of anti-mutagens is now being identified. Mutagen scavengers act through absorption onto a larger molecule that is readily excreted. Good examples are provided by dietary fibre sources, such as wheat bran, or the planar molecule, chlorophyll and its stabilised derivative, chlorophyllin. Mutagens may be actively extruded from human cells through the action of one or more of a series of ATP-binding cassette (ABC) drug transporter proteins, including the multidrug resistance proteins (P-glycoproteins), multidrug resistance-associated proteins (MRP1-7) and the breast cancer resistance protein (BCRP). These proteins can affect the absorption, distribution and excretion of mutagens and carcinogens, as well as of their metabolites and conjugates. Even if the undesirable compound enters the cells, there are several mechanisms by which it may be prevented from interaction with DNA. Detoxification mechanisms are of increasing interest, especially those where transcription is regulated through the antioxidant response element (ARE), whose own transcription factor, Nrf2, is repressed under basal conditions. While much of the early literature on mutagenesis and carcinogenesis implicated exogenous chemicals, it is increasingly realised that unrepaired oxidative DNA lesions are important mutational precursors, and anti-oxidants represent an important class of anti-mutagens. It is also recognised that deficiency of certain micronutrients may lead to cell mutation, and that restoring nutrient balance is an important mechanism of anti-mutagenesis. An increasing number of studies focus on DNA repair and stress responses as novel mechanisms of anti-mutagenesis.
The human IgA-Fc α receptor interaction and its blockade by streptococcal IgA-binding proteins

IgA plays a key role in immune defence of the mucosal surfaces. IgA can trigger elimination mechanisms against pathogens through the interaction of its Fc region with FcαRs (receptors specific for the Fc region of IgA) present on neutrophils, macrophages, monocytes and eosinophils. The human FcαR (CD89) shares homology with receptors specific for the Fc region of IgG (FcαRs) and IgE (FcαRIs), but is a more distantly related member of the receptor family. CD89 interacts with residues lying at the interface of the two domains of IgA Fc, a site quite distinct from the homologous regions at the top of IgG and IgE Fc recognized by FcαR and FcαRI respectively. Certain pathogenic bacteria express surface proteins that bind to human IgA Fc. Experiments with domain-swap antibodies and mutant IgAs indicate that binding of three such proteins (Sir22 and Arp4 of Streptococcus pyogenes and β protein of group B streptococci) depend on sites in the Fc interdomain region of IgA, the binding region also used by CD89. Further, we have found that the streptococcal proteins can inhibit interaction of IgA with CD89, and have thereby identified a mechanism by which a bacterial IgA-binding protein may modulate IgA effector function.
The post-translational incorporation of arginine into a β-amyloid peptide increases the probability of α-helix formation

The β-amyloid peptide (βAP1-40) inhibited the in vitro post-translational incorporation of [14C]arginine at the N-terminus of brain soluble proteins and was labelled by the incorporation of [14C]arginine. Addition of arginine at the N-terminal position of βAP1-40 is predicted to increase the probability of an α-helix structure being formed on the first residues with a higher hydrophilic characteristic, increasing the possibility of these residues being exposed to the aqueous environment. Unmodified βAP1-40 has a low α-helix content and a higher probability of β-turn formation. Accumulation of βAP1-40 in Alzheimer's disease may therefore be due to a reduced arginylation reaction and consequently to a decrease in its normal degradation by the ubiquitin pathway.