Miracle-dz/UniFAR-FTUs huggingface dataset:
Predation risk from piscivorous fish influencing the diel use of macrophytes by planktivorous fish in experimental ponds

Abstract— This study investigated interactions between zooplanktivores (roach and perch) and piscivorcs (pike and large perch) in experimental ponds (16 m2) with open water habitat and three densities of natural macrophytes. Fish habitat selection was determined both day and night and was supported by daytime observations to study anti-predator behavioural patterns. Diel migration out from among macrophytes was seen in the absence of predators, particularly for roach, which changed from 13% of individuals being in open water during the day to 90% at night. The risk of predation from piscivores influenced the habitat selection of the zooplanktivores. Roach seemed to be the most vulnerable to predation from pike and selected the open water (90-92%) during daylight hours, but kept a 1-m distance from the macrophytes edge. The presence of pike thus reduced the use of macrophytes by roach, which in turn may improve macrophytes and the edge area as a refuge for zooplankton. Pike appeared to have less impact on the gross habitat selection of O+ perch, which were associated with the macrophytes (58–89%), though they were still vulnerable to predation. Adult perch, which was a generally less effective predator than pike, showed subdued behavior, concealing them selves in the macrophytes most of the time. No effect of the simultaneous presence of two predator species was found.
Interleukin-4 Induces Expression of the Integrin αvβ3 via Transactivation of the β3 Gene (*)

Osteoclastic bone resorption is dependent upon cell-matrix recognition. This process is mediated by the integrin αvβ3 whose expression is enhanced, in avian osteoclast precursors, by bone-seeking steroids. The purpose of this study was to determine if bone-modulating cytokines impact on αvβ3 expression by mouse marrow macrophages (BMMs), known to differentiate into osteoclasts. Of the cytokines tested. Interleukin-4 (IL-4) is most effective in increasing β3 mRNA levels by a mechanism involving transactivation of the β3 gene. Moreover, IL-4 augmented β3 mRNA is mirrored by plasma membrane appearance of αvβ3. As IL-4 induces β3 and not αv mRNA, the β3 chain appears to regulate surface expression of the heterodimer. The functional significance of IL-4-induced αvβ3 is underscored by the fact that, while attachment to fibronectin is unaltered, treatment of BMMs with the cytokine enhances αvβ3-mediated binding to vitronectin 5-fold. Expression of this heterodimer by BMMs driven along a non-osteoclastic lineage suggests αvβ3 may play a role in the inflammatory response of macrophages.
The Breeding Biology of the Stonechat and Whinchat

Analysis of Nest Record Cards reveals altitudinal and habitat differencesbetween these two species. The resident or partially migratory Stonechat has a longer breeding season (with a potential for rearing three broods) than the Whinchat which is a trans-Saharan migrant and arrives later. It is suggested that the greater productivity of the Stonechat might counterbalance a higher winter mortality.
The importance of sperm competition risk and nest appearance for male behavior and female choice in the sand goby, Pomatoschistus minutus

To test if an increased sperm competition risk affects male behavior and mating decisions of both sexes, we performed two experiments using the sand goby, Pomatoschistus minutus, a nest-building fish with exclusive paternal care. In our first experiment, a nest-holding male, with a confined female, was sequentially exposed to a vial with a sneaker male or an empty vial. While male courtship, nest building, displacement fanning, and time outside the nest were unaffected, individual males showed a higher mucus preparation effort inside the nest in the presence of a sneaker male than when alone. We found such mucus to contain sperm, thus clearly suggesting an importance in sperm competition. In our second experiment, a female was free to spawn with two different males, one of which was exposed to a confined sneaker male. Male mating success was not affected by the presence of a sneaker male. However, the volume of sand the male had put on his nest was positively associated with female spawning decision, while nest-opening width was not. In a partial correlation of five traits thought to attract females (nest-opening width, sand volume, male courtship display, displacement fanning, and male size), males that fanned well were found to also build large nests or display intensely, but not both. This indicates that rather than being jacks-of-all-trades, individual males focus on a subset of traits for attracting females. Copyright 2005.
Revision of the Octopus horridus species-group, including erection of a new subgenus and description of two member species from the Great Barrier Reef, Australia

The tropical Indo-West Pacific region contains a distinctive group of small to moderate-sized octopuses referred to in the past as the Octopus horridus species-group. Member species are found primarily on intertidal reef flats. They possess small bodies, long arms and complex skin sculpture and body patterns enabling excellent camouflage. When attacked, these octopuses are capable of autotomising their arms at the base: the writhing severed arm acting as a decoy to predators and aiding escape. Lost arms regenerate within 2–3 months. Attributes of this group of octopuses are described and the subgenus Abdopus, subgen. nov. is here coined to define this group. Historically, many members of this subgenus have been incorrectly identified as Octopus horridus, a distinct large-egg species known only from the Red Sea and the northwest Indian Ocean. Seven species are here recognised as belonging in Abdopus, subgen. nov. Two member species from Great Barrier Reef waters (Octopus aculeatus d’Orbigny, 1834 and Octopus capricornicus, sp. nov.) are described. A number of additional, as yet undescribed, species occur throughout the Indo-West Pacific region. Certain earlier works have linked other octopus genera and species with members of this subgenus on the grounds of long arms and arm autotomy. Significant differences occur in the morphologies of these taxa and the nature of the arm autotomy processes. It is proposed that these groups have evolved independently and that arm autotomy has arisen more than once amongst the octopuses. The restriction of the subgenus Abdopus to the tropical Indo-West Pacific region suggests relatively recent origins and radiation.
A molecular analysis of the evolutionary relationships in the Callitrichinae, with emphasis on the position of the dwarf marmoset

Schneider, H. , Bernardi, J. A. R. , da Cunha, D. B. , Tagliaro, C. H. , Vallinoto, M. , Ferrari, S. F. & Sampaio, I. (2011). A molecular analysis of the evolutionary relationships in the Callitrichinae, with emphasis on the position of the dwarf marmoset. —Zoologica Scripta, 41, 1–10.
Effects of seeding rates and seedbed preparations on the seedling establishment and yield of surface-sown pasture species.

An experiment was carried out ot determine the effects of seeding rates and seedbed preparations on the establishment and yield of surface-sown pasture species. Establishment of orchardgrass was significantly increased by the lowest seeding rate of 20 kg/ha as compared to 30 and 40 kg/ha, but no differences were found between the seeding rates of ladino clover. Both raking and burning significantly improved the establishment of pasture species in comparison with non-treatment. There was a significant difference between the raking and burning for the establishment of orchardgrass, but no significant difference was found between the two treatments for that of ladino clover. Increasing seeding rate of pasture species did not enhance the yield of surface-sown pasture, but both the raking and non-treatment significantly increased the yield of pasture species. The results suggest that both the raking and burning can improve the establishment but increasing seeding rate over 20 kg/ha and burning may not increase the yield.
Identification of a Novel Blocker of IκBα Kinase That Enhances Cellular Apoptosis and Inhibits Cellular Invasion through Suppression of NF-κB-Regulated Gene Products1

1′-Acetoxychavicol acetate (ACA), extracted from rhizomes of the commonly used ethno-medicinal plant Languas galanga, has been found to suppress chemical- and virus-induced tumor initiation and promotion through a poorly understood mechanism. Because several genes that regulate cellular proliferation, carcinogenesis, metastasis, and survival are regulated by activation of the transcription factor NF-κB, we postulated that ACA might mediate its activity through modulation of NF-κB activation. For this report, we investigated the effect of ACA on NF-κB and NF-κB-regulated gene expression activated by various carcinogens. We found that ACA suppressed NF-κB activation induced by a wide variety of inflammatory and carcinogenic agents, including TNF, IL-1β, PMA, LPS, H2O2, doxorubicin, and cigarette smoke condensate. Suppression was not cell type specific, because both inducible and constitutive NF-κB activations were blocked by ACA. ACA did not interfere with the binding of NF-κB to the DNA, but, rather, inhibited IκBα kinase activation, IκBα phosphorylation, IκBα degradation, p65 phosphorylation, and subsequent p65 nuclear translocation. ACA also inhibited NF-κB-dependent reporter gene expression activated by TNF, TNFR1, TNFR-associated death domain protein, TNFR-associated factor-2, and IκBα kinase, but not that activated by p65. Consequently, ACA suppressed the expression of TNF-induced NF-κB-regulated proliferative (e.g., cyclin D1 and c-Myc), antiapoptotic (survivin, inhibitor of apoptosis protein-1 (IAP1), IAP2, X-chromosome-linked IAP, Bcl-2, Bcl-xL, Bfl-1/A1, and FLIP), and metastatic (cyclooxygenase-2, ICAM-1, vascular endothelial growth factor, and matrix metalloprotease-9) gene products. ACA also enhanced the apoptosis induced by TNF and chemotherapeutic agents and suppressed invasion. Overall, our results indicate that ACA inhibits activation of NF-κB and NF-κB-regulated gene expression, which may explain the ability of ACA to enhance apoptosis and inhibit invasion.
Gelatin from cod skins as affected by chemical treatments

Concentrations of sodium hydroxide, sulfuric and citric acids used in processing gelatin from cod skins affected both yield and quality. The highest yield of gelatin was obtained when low concentrations [0.1–0.2% (w/v)] of sulfuric acid and sodium hydroxide were applied to the skins followed by treatment with 0.7% (w/v) citric acid. The effects on bloom value, viscosity, odor, clarity, color and pH of the gelatin varied. However, the use of 0.7% (w/v) citric acid in different combinations with sodium hydroxide and sulfuric acid usually gave best results. Freezedried gelatin had considerably higher bloom value than air-dried gelatin.
What size was Archaeopteryx

The size (mass) of Archaeopteryx, primarily the Berlin specimen, has been estimated in two ways. A new three-dimensional reconstruction suggests a mass of no more than 271 g. Application of allometric equations derived from both birds and mammals to various linear dimensions yields a range of estimates from 112 to 2269 g, but all the more plausible estimates lie in the range 220–330 g.
Morphological skin colour changes in teleosts

Morphological skin colour change in fish is often referred to in the sole context of background adaptation. It is becoming increasingly apparent that it is a broad phenomenon elicited by a variety of factors. To date, no review has attempted to integratethedifferenttypesofmorphologicalcolourchangesoccurringinteleosts,their ecological origins and the regulatory mechanisms involved, often restricting the view on the subject. First, the origin of skin colour is addressed in teleosts including chromatophore type and distribution, pigment biosynthetic pathways and their interactions to one-another. Second, the different types of morphological colour changes occurring in teleosts are categorized and a key distinction is made between proximate and ultimate morphological colour changes. These are defined respectively as the change of phenotype during an established life-stage in response to environmental interactions and during the transition between two developmental-stages phenotypically pre-adapted to their ancestral ecosystems. Nutrition and UV-light are primary factors of proximate morphological colour changes beyond the control of the organism. By contrast, background light conditions and social interactions are secondary proximate factors acting through the control of the organism. Highly diversifiedamongteleosts,ultimatemorphologicalskincolourchangesarepresentedin term of alterations in skin structure and pigment deposition during metamorphosis in different species. Finally, the physiological and endocrine mechanisms regulating both proximate and ultimate morphological colour changes are reviewed.
Phase II enzyme induction and anti-inflammatory effects of crude extracts and secondary fractions obtained from bran from five black glutinous rice cultivars

Summary Methanolic extracts of bran from black glutinous rice cultivars were screened for potential health benefits using cellular bioassays for quinone reductase (QR) induction in murine hepatoma cells and inhibition of NO production in lipopolysaccharide (LPS)-activated RAW 264.7 macrophages. Fractionation of the crude extract by semi-preparative HPLC afforded respective fractions enriched in phenolic acids, anthocyanins and proanthocyanidins. The relative potency of QR induction was phenolic acids > proanthocyanidins > anthocyanins, and the activity of the crude extract was conserved among the aggregate of these fractions. In contrast, all three fractions were more potent than the crude extract in terms of anti-inflammatory effect. This suggests synergism effects among anti-inflammatory agents through partial purification. Inhibition of macrophage NO production by binary mixtures of gallic acid or caffeic acid with the anthocyanin-rich fraction indicated potential synergism. These results warrant further efforts to identify the active agents and substantiate synergistic interactions through isobologram analysis.
Comparación de métodos de estimación de parámetros de crecimento del camarón blanco Litopenaeus schmitti en el occidente de Venezuela

Para el camaron blanco Litopenaeus schmitti se han reportado diferentes parametros de crecimiento en el occidente de Venezuela. Tales diferencias han sido atribuidas tanto a los distintos metodos como a las distintas bases de datos empleadas en la estimacion. Para evaluar esta explicacion se reanalizaron los parametros de crecimiento para la especie, utilizando dos bases de datos y dos metodos de ajuste: ELEFAN y una minimizacion de cuadrados. La primera base de datos consistio de frecuencias de longitudes de juveniles capturados en el Lago de Maracaibo en el periodo 1991-1993. La segunda consistio de frecuencias de longitudes de juveniles y adultos capturados en el Golfo de Venezuela y el Lago de Maracaibo durante el periodo 2001-2003. Para ajustar los parametros mediante ELEFAN se empleo el software FiSAT, en tanto que para el metodo de minimos cuadrados se usaron planillas de calculo. Los resultados mostraron que los tamanos registrados en las bases de datos tienen un mayor impacto que los metodos utilizados. Usando informacion de ambas bases de datos los resultados fueron similares entre metodos, pero diferentes cuando fueron comparados entre bases de datos, las cuales diferian en terminos de los intervalos de tamanos representados en cada una. Para Litopenaeus schmitti, en el occidente de Venezuela la base de datos con una mejor representatividad de tallas juveniles y adultas arrojo estimaciones mas confiables que el ajuste basado solo en juveniles.
IL-18 and IL-12 Signal Through the NF-κB Pathway to Induce NK-1R Expression on T Cells1

Substance P engages the T cell neurokinin 1 receptor (NK-1R) to enhance IFN-γ production. NK-1R on T cells is inducible. We studied mechanisms regulating T cell NK-1R expression. Murine splenocytes were cultured for 4 h with or without rIL-12 or rIL-18. Both IL-12 and IL-18 induced splenic T cells to express NK-1R transcripts. Induction was blocked by actinomycin D, but not cycloheximide, suggesting that protein synthesis was not required for initiation of NK-1R gene transcription. Inhibition of T cell NF-κB activation or NF-κB nuclear translocation also blocked NK-1R transcription. IL-12 and IL-18 strongly induce NK-1R mRNA expression in splenocytes from Stat4−/− mice, suggesting that the Stat4 pathway was not required for the induction of NK-1R transcription. Splenic T cells exposed to IL-12 or IL-18 in the presence of IL-10 expressed no NK-1R mRNA. However, TGFβ did not prevent NK-1R mRNA expression. Thus, IL-12 and IL-18 induce T cells to express NK-1R through NF-κB activation. IL-10, a regulator of the Th1 response, blocks this activation. These data further suggest that SP and NK-1R, which promote IFN-γ synthesis, are part of the Th1 pathway of immunity.
Characterization Of Genetic Variation In North African And Spanish Populations

High-density Single Nucleotide Polymorphism (SNP) scans of the human genome have been applied in many populations worldwide to investigate their genetic characteristics. However, populations in North Africa, an isolated subcontinental area between Sub-Sahara Africa and Europe, have not been examined. In the present study, seven North African populations and four neighboring Spanish populations are analyzed using a high-density SNP microarray. North African populations appear to form a clinal pattern of genetic differentiation between Sub-Saharan Africans and Europeans, being much more similar to Europeans than to Sub-Saharans. The genetic similarity between North African populations exhibits an east-west gradient pattern corresponding to their geographic locations. High and varying levels of autozygosity, as well as a potentially indigenous genetic component, are observed in North Africans. Noticeably, Tunisians turn out to be the North African population most distinct from Europeans and Sub-Saharans, and have the highest levels of autozygosity. Basques can be clearly distinguished from other Spanish populations, as being more similar to the Western Europeans, and also have the largest number of fixed ancestral and derived alleles among all the populations studied. The ancestral allele frequency distribution of Basques is most similar to that of East Asians, suggesting a small effective population size. All these results indicate that the Basque population is a genetic isolate distinct from the surrounding Spanish populations as well as from other Southern and Western European populations, although the magnitude of genetic differentiation is subtle.
Intercropping Annual Medic with Conventional Height and Semidwarf Barley Grown for Grain

Interseeding annual legumes with grain crops has been proposed as a cropping strategy to enhance ground cover, thereby reducing weed competition, suppressing soil erosion, and providing N for use by subsequent crops. The potential of annual medics (Medicago spp.) for intercropping in small-grain cropping systems has not been adequately assessed for the north-central United States. Our objective was to evaluate a spring barley (Hordeum Vulgare L.)-annual medic intercrop system for barley grain yield, fall biomass production, suppression of fall weeds, and quantity of N available for incorporation into the soil. Field experiments were conducted in four Minnesota environments (Becker, Morris, Rosemount, and St. Paul). Conventional height 'Robust' and semidwarf 'Royal' barley were intercropped with each of three medic species ['George' black medic (M. lupulina L.), 'Mogul' barrel medic (M. truncatula Gaertn.) and 'Santiago' burr medic (M. polymorpha L.)]. Intercropping with medics reduced barley yields by an average of 6% at Rosemount, 30% at St. Paul, and 76% at Becker, compared with monoculture barley fertilized with N. Medics increased yields by 9% at Morris. Intercropping with medic reduced fall weed mass by an average of 65% across environments, compared with the fertilized Royal monoculture. Nitrogen available for incorporation from the barley-medic intercrops ranged from 66 to 140 kg ha -1 over the environments, whereas N available for incorporation from fertilized barley monoculture ranged from 22 to 80 kg ha -1 . We conclude that the prospects for successfully intercropping with annual medic in a barley grain production system are mixed and depend in part on the medic species used and barley stature. A wider array of medic types should be evaluated for their suitability in intercropping with small grains.
Analysis of diversity of hepatitis C virus glycoproteins E1 and E2

Hepatitis C Virus (HCV) exists as a population of sequence variants that evolves during infection adapting to host pressures. The main targets for the immune response are the envelope glycoproteins E1 and E2, which also mediate viral cell entry. The first hypervariable region (HVR1) of E2, previously implicated in the outcome of acute infection, has been a focus of many studies. However more broadly neutralising antibodies tend to target epitopes outside this region, yet evolution of full length E1E2 heterodimer is poorly understood. The HCV transmission and window period as well as seroconversion are the evolutionary events shaping primary infection hence influencing outcome of acute infection. However, due to the asymptomatic character of the early phases of HCV infection, evolutionary data describing this interval is still lacking depth. Defining the genetic and phenotypic characteristics of HCV population of sequence variants that establish infection in a new host would aid vaccine and new therapy design. This study aimed to identify patterns of HCV envelope glycoprotein evolution upon transmission and during early phases of disease. We studied this in three settings: experimental transmission of immunocompromised mice by known inoculum; occurrence of horizontal transmission in a haemodialysis unit between hypothesised source and index case individuals; and unrelated cases of acutely infected HCV patients. The single genome amplification (SGA) approach was utilised, which allowed us to accurately assign linkage between substitutions and determine the frequency distribution of E1E2 variants in analysed viral populations. Data from the first experimental setting indicates that a selective sweep occurs upon HCV transmission, with selective amplification of envelope sequence variants that possess fitness advantage at entry level. Molecular determinants associated with this enhanced infectivity have also been identified. In further part of the project we confirmed a horizontal infection in haemodialysis unit with use of phylogenetic methods and suggested revision of current safety guidelines. Analysis of sequences from the last setting showed that indeed HVR1 might not be a good enough indicator of evolutionary events in the acute phase, as linked substitutions occur also outside this region. Seroconversion is associated with increasing population diversity indicating role of antibodies in driving HCV evolution, which is host specific.