Miracle-dz/UniFAR-FTUs huggingface dataset:
Further species of the opisthobranch genus Okenia (Nudibranchia: Goniodorididae) from the Indo-West Pacific

Five new species of the nudibranch genus Okenia Menke, 1830 (Goniodorididae) are described from Australian waters and the anatomy of another ten species from Australia and the Indo-West Pacific are described. Okenia purpurata sp. nov. and O. vena sp. nov. are reported from northern New South Wales where they feed on the bryozoan Amathia tortuosa Tenison Woods, 1880. Okenia mellita sp. nov. is reported from New South Wales, and a pair of species, O. hallucigenia sp. nov.and O. stellata sp. nov. are reported from various locations in northern Australia where they both feed on the bryozoan Pleurotoichus clathratus (Harmer, 1902). Okenia virginiae Gosliner, 2004 is reported for the first time from Australia as is the Atlantic species Okenia zoobotryon (Smallwood, 1910). Anatomical information for O. barnardi Baba, 1937, O. hiroi (Baba, 1938) and O. mija Burn, 1967 is provided for the first time, as is further information on O. plana Baba, 1960 and O. pilosa (Bouchet and Ortea, 1983) from Australia and Hong Kong. New observations on the bryozoan prey of various species is reported: O. mija feeding on Amathia wilsoni Kirkpatrick, 1888, O. zoobotryon on Zoobotryon verticillatum (delle Chiaje,1828), O. hiroi on an unnamed species of Integripelta Gordon, Mawatari & Kajihara, 2002, O. plana on Membranipora membranacea (Linnaeus, 1767), Jellyella tuberculata (Bosc, 1802) and Cryptosula pallasiana (Moll, 1803). Okenia japonica Baba, 1949 and O. purpureolineata Gosliner, 2004 are reported feeding on the same unidentified species of Amathia Lamouroux, 1812.
The Intestinal Mucosa of Coeliacs in Remission is Unable to Abolish the Agglutinating Activity of Gliadin Peptides on K562(S) Cells

The peptic-tryptic-cotazym digest of a wheat gliadin was fractionated into ten primary fractions. Subfraction 2R of fraction 9 is known to be toxic to patients with coeliac disease. Fraction 9 and subfraction 2R also agglutinate K562(S) cells, previously shown to be a good indication of toxicity to in vitro intestinal bioptic specimens from coeliac patients. Subfraction 2R was still able to agglutinate K562(S) cells after digestion by morphologically normal small intestinal mucosa of coeliacs in remission, but was inactivated after digestion by normal mucosa. These results are consistent with the hypothesis that there is a mucosal defect in handling gliadin peptides in coeliac patients, and suggest that there is either a primary (or secondary) enzyme deficiency, or some other mechanism, operating in the intestinal mucosa of coeliac patients in remission.
Genetic association and frequency distribution in segregating generations derived from pigeonpea crosses

Correlation and presence of genetic interactions was studied using F2 and F3 generations in three pigeonpea crosses for yield and its component traits. Most of the characters studied were positively skewed and were being governed by several genes indicating quantitative inheritance. Variance, skewness and kurtosis have also indicated that homozygosity has increased over the generation in pigeonpea crosses. Cross BRG 1 x ICP 8863 was found better than other two crosses (TTB 7 x ICP 8863 and TTB 7 x ICPL 87119) in providing high yielding segregants displaying parental diversity. Seed yield and other associated characters such as plant height and number of pods per plant had complementary gene action with other genes governing these characters. Yield increase is possible by following rigid selection for yield and its component characters. A shift in correlation coefficients between the generations was recorded which is likely to be attributed to difference in gene complementation of linkage blocks and an indication of unstable nature of breeding population.
A single molecule approach to investigate how AP1 transcriptional regulators find their target sites on DNA

Transcriptional regulator protein family members Activator Protein-1 (AP1) bind to their target site TGAC/GTCA during the normal cell cycle. Their over-expression is linked to the initiation of cancer. Regulating cFos and cJun interactions with AP1 binding sites is a potential cancer therapy strategy. How the proteins find their target sites and whether non-specific DNA binding occurs will be investigated. The Protein Fragment Complementation Assay (PCA) derived inhibitor FosW is also capable of interfering with its target cJun. To study these proteins, DNA tightropes were created where single strands of λ, pUC19, pUCap1 and target-free λ (TFλ) DNA were suspended above the surface of a glass coverslip on 5 μm high pedestals. Oblique Angle Fluorescence (OAF) microscopy was used to image Quantum dot (Qdot) conjugated proteins in vitro. The protein combinations cFos:cFos, cJun:cJun, cFos:cJun, FosW and FosW+cJun (Mason et al. 2006, Worrall and Mason 2011) were studied interacting with the different DNA substrates and within the AP1 family. 71 ± 3.1% cJun:cJun, 53 ± 6.1% cFos:cJun heterodimers diffused 3-Dimensionally and 1-Dimensionally along λ DNA, indicating this is a crucial part of their search mechanism. Surprisingly, cFos is capable of dimerising, a previously unseen observation. 45 ± 3.7% of these cFos:cFos homodimers also diffused 3-Dimensionally and 1-Dimensionally. Diffusion decreased when the proteins interacted with pUC19 and pUCap1 and cJun only showed 3 ± 1.5% movement on TFλ, an unexpected observation. The interaction between FosW and cJun:cJun indicated clear interference with cJun dimerization. 55 ± 11.0% FosW and 39 ± 11.0% FosW+cJun diffused 3-Dimensionally and 1-Dimensionally. This was observed to occur directly on DNA and clarifies the mechanism of competitive inhibition and partner exchange in the AP1 family. This insight may significantly impact our understanding on how these proteins regulate transcription and help define new mechanisms of inhibition.
In silico Analysis of Interactions between Nevirapine-related Compounds, HLA-B*14:02 and T-cell Receptor

A non-nucleoside reverse-transcriptase inhibitor nevirapine (NVP) used to treat HIV-1 infection can cause severe, life-threatening idiosyncratic drug toxicity (IDT). It is known that the IDT caused by NVP or its metabolites is associated with the HLA-B*14:02 haplotype. The molecular mechanism of the HLA -associated IDT, however, has not been disclosed. In this study, we have simulated the interaction modes between NVP-related compounds, HLA-B*14:02 , and a T-cell receptor in order to understand the molecular mechanism leading to the onset of IDT.
The clam Neilonella sulculata in San Jorge Gulf (Argentina, Southwest Atlantic): spatial distribution pattern and inverse relationship between size and density

ABSTRACT Neilonella sulculata is a dominant bivalve on muddy bottoms of the continental shelf and gulfs off Argentina (Southwest Atlantic). Two benthic surveys performed in 2007 and 2009 in San Jorge Gulf, a depositional area characterized by silt/clay sediments, gave us the opportunity to test whether the population of this clam displays a significant spatial structure and to analyse if there is an inverse relationship between size and density. Density, biomass and size–frequency distribution displayed significant spatial structure, being positively autocorrelated at the smallest spatial scales (c. 1.7–14/17 km). Biomass also showed spatial contagion at scales of 25–33 km. A substantial increase in density and biomass occurred between 2007 and 2009. Empty valves in the sediment showed that the maximum size attained by the species may exhibit considerable variation at relatively short temporal scales. Regardless of temporal changes in density and biomass, the spatial structure of these variables remained stable. In densely populated areas, shell size decreased with increasing density, suggesting a density-dependent control of growth. A clear north–south increase in density and biomass was detected, which might be related to a gradient in food availability caused by a thermohaline frontal system associated with wind-related upwelling.
Genetic evidence of the presence of Octopus mimus in the artisanal fisheries of octopus in Santa Elena Peninsula, Ecuador

Abstract: The geographic distribution of Octopus mimus Gould, 1852 is unclear, as most records are restricted to coastal localities of Peru and Chile, and some references have mentioned its presence off Central America. It is unknown whether this octopus is found off Ecuador as two previous unpublished records have suggested. The aim of the present study is to identify genetically the main octopus captured in a marine protected area known as Reserva de Produccion Faunistica Marino-Costera Puntilla de Santa Elena (REMACOPSE) off the Santa Elena peninsula, Ecuador. Samples collected from the local fishery were used to test the presence of this species based on the sequences of three mitochondrial markers and using a Bayesian approach. The phylogenetic analysis confirms that O. mimus inhabits the REMACOPSE. The results also indicate that the octopus specimens captured in the fishery from this marine protected area, are more closely related to O. mimus specimens from Central America than those from South America. The genetic identification of two groups of O. mimus could be associated with the different marine environmental conditions of the two biogeographic provinces. The finding in this study represents an important step for posterior research on the biology and fishery of octopus in Ecuador.
Molecular and Functional Characterization of Human P2X2 Receptors

P2X receptors are a family of ATP-gated ion channels. Four cDNAs with a high degree of homology to the rat P2X 2 receptor were isolated from human pituitary and pancreas RNA. Genomic sequence indicated that these cDNAs represent alternatively spliced messages. Northern analysis revealed high levels of human P2X 2 (hP2X 2 ) message in the pancreas, and splice variants could be detected in a variety of tissues. Two cDNAs encoded functional ion channels when expressed in Xenopus oocytes, a receptor structurally homologous to the prototype rat P2X 2 receptor (called hP2X 2a ) and a variant containing a deletion within its cytoplasmic C terminus (called hP2X 2b ). Pharmacologically, these functional human P2X 2 receptors were virtually indistinguishable, with the P2X receptor agonists ATP, 2-methylthio-ATP, 2′ and 3′- O -(4-benzoylbenzoyl)-ATP, and ATP5′- O -(3-thiotriphosphate) being approximately equipotent (EC 50 = 1 μM) in eliciting extracellular Ca 2+ influx. The P2 receptor agonists α,β-methylene ATP, adenosine, adenosine 5′- O -(2-thiodiphosphate), and UTP were inactive at concentrations up to 100 μM. Both hP2X 2a and hP2X 2b receptors were sensitive to the P2 receptor antagonist pyridoxal-5-phosphate-6-azophenyl-2′,4′-disulfonic acid (IC 50 = 3 μM). In contrast to the analogous rat P2X 2 and P2X 2b receptors, the desensitization rates of the hP2X 2a and hP2X 2b receptors were equivalent. Both functional forms of the human P2X 2 receptors formed heteromeric channels with the human P2X 3 receptor. These data demonstrate that the gene structure and mRNA heterogeneity of the P2X 2 receptor subtype are evolutionarily conserved between rat and human, but also suggest that alternative splicing serves a function other than regulating the desensitization rate of the human receptor.
An Overview of the Hazards and Management Strategies for Antibiotic Residue in Honey

Humans have kept bees for the production and harvest of honey since 4000 BC. In past societies, honey was of great importance, particularly for its medicinal purposes. Honey has the image of being a natural and healthy product. However, today honey is produced in an environment, polluted by different sources of contamination. The contamination sources can be environmental and apicultural ones. Antibiotics are found in honey largely because they are used in apiculture for treatment of bacterial diseases. Antibiotics such as oxytetracycline, erythromycin, lincomycin, monensin, streptomycin, and enrofloxacin are also reportedly used in beekeeping. The extensive use of antibiotics leads to an accumulation of residues in honey decreasing their quality and making their marketing more difficult. Antibiotic residues show a relatively long half-life and they may have direct toxic effects on consumer's e.g., allergic reactions in hypersensitive individuals and disorder of the haemopoietic system, or cause problems indirectly through induction of resistant strains of bacteria. The European Union (EU) regulates honey under the Council Directive 2001/110/EC, and the standard for antibiotics in food is listed in Regulation (EU) No. 37/2010.
The impact of cottage development on common loon reproductive success in central Ontario

In recent years, the increasing popularity of wilderness vacations has caused a sharp rise in recreational activity in many northern areas. In the Boundary Waters Canoe Area of Minnesota, for example, increased motorboat and canoe traffic appears to have a negative impact on the productivity of the Common Loon (Gavia immer); (Lucas 1967, Titus and Van Druff 1981). Lehtonen (1970) attributed a decline in the Arctic Loon (G. arctica) on Finnish lakes to increasing numbers of cottages and, in a 1-year study of 19 Alberta lakes, Vermeer (1973) found a significant, inverse correlation between the numbers of breeding Common Loons and the amount of human disturbance. Bundy (1979) and Andersson et al. (1980) also related that recreation appeared to have negative impacts on loons in Scotland and Sweden. The purpose of our study was to investigate the impact of cottage development on the reproductive success of Common Loons in central Ontario. The Muskoka and Haliburton districts of central Ontario (Fig. 1) are favorite resort locations. Summer cottages are built along lakeshores and boating, swimming, fishing or other similar activities are common and often very intense for short periods, e.g., holiday weekends. Since loons must nest near the shoreline of small islands and bog hummocks, and young loons spend their time prior to fledging entirely on the water, extensive water-oriented recreation may be detrimental to loon productivity.
Urban warming favours C4 plants in temperate European cities

Elucidating the mechanisms responsible for the structure of urban communities is a key aim of urban ecology, but one that is often confounded by the multitude of environmental changes that are caused by urbanization. We applied trait‐based techniques to identify the specific environmental drivers that shape urban plant assemblages and predict how these drivers will further impact biotas with increasing urbanization and global environmental change. Urbanized areas across temperate Europe have significantly higher abundance and richness of plants using the C4 photosynthetic pathway, relative to the total number and species richness of all plant records, than non‐urban areas. Urban warming, mediated by the contrasting physiological responses of C3 and C4 plants to warming, is the main driver of observed patterns of plant assemblage structure. This mirrors broadscale and historical distribution patterns of C3 and C4 plants. The increased relative abundance of C4 plants in cities demonstrated here may be indicative of more geographically widespread assemblage changes to be expected in temperate environments under continuing global climate change. Synthesis. Applying a combined trait‐based, ecoinformatic and remote‐sensing approach provides new insight into the landscape‐level consequences of urbanization. Specifically, we show that localized urban warming in cities across temperate Europe favours C4 plant species, which respond positively to increased temperatures. Urban plant assemblages are shaped by environmental warming and exhibit significant increases in C4 plant relative abundance compared to non‐urban assemblages.
Cellular selection and partial characterisation of gladiolus cell lines resistant to culture filtrate of Fusarium oxysporum

The pedicel explants of Gladiolus cv. Amsterdam were cultured on MS medium supplemented with NAA (10 mg/l) and kinetin (0.5mg/l) for callus initiation. For multiplication of callus MS medium supplemented with 2, 4 D (2mg/1) was used. Different concentrations of culture filtrate of Fusarium oxysporum f.sp. gladioli were added into the culture medium for selection of resistant cell lines. Upon incubation for six weeks, the resistant clones were selected at 10% concentration of culture filtrate. The selected clones were cultured on medium devoid of culture filtrate for 3 weeks and then characterised using biochemical parameters. Selected cell lines revealed a higher protein content, phenol content, total sugar and reducing sugar content compared to non-selected cell lines. In the non-selected cell lines higher activities of phenylalanine ammonia lyase and tyrosine ammonia lyase were found.
Contributions to the concepts of reproductive cycles and the systematics of the scalaris group of the lizard genus Sceloporus

The concept of parity type is proposed as a criterion of relation- ship among members of the Sceloporus aeneus-scalaris complex, with members of S. aeneus being regarded as viviparous and those of S. scalaris, as oviparous. The viviparous S. goidmani is regarded as a relative of S. aeneus , and S. a. subniger is not regarded as intermediate between S. scalaris and S. aeneus. The proposal by Davis and Smith that S. a. aeneus is oviparous and specifically distinct (as S. aeneus) from S. a. bicanthalis (as S. bicanthalis) is rejected. S. aeneus is hypothesized to have a biennial reproductive cycle. S. scalaris slevini auctorum is segregated into two subspecies: S. s. samcolemani subsp. nov. in the Sierra Oriental (northern end), and S. s. slevini sensu stricto in the Sierra Occidental (also northern end) of Mexico and of the adjacent United States. The systematics and phylogenetic history of the scalaris group of Sceloporus has long been viewed as enigmatic, beginning with the statement of the quandary by Smith (1939: 347-348) in explanation of the allocation of the northwestern member, slevini , to the species scalaris despite some contrary evidence. However, Smith and Pog- layen (1958: 13-15) allocated slevini to the species aeneus after another population exhibiting certain features of intermediacy be- tween the two polytypic species scalaris and aeneus was described (S. a. subniger) . Neither of the preceding accounts placed any overt emphasis upon parity types. Smith (1939: 332) made a passing comment that both oviparous and 4 'ovo viviparous" species occur in the group. Evi- dence now available makes it certain that members of the scalaris complex are oviparous, and we here postulate that members of the aeneus complex are viviparous (a broader term, more certainly ap- plicable than ovoviviparity, which has come to imply absence of placental structures, whereas "euviviparity" implies their presence; both conditions exist in viviparous reptiles and only by microscopic techniques can they be determined). Anderson (1962) has demon- strated that slevini is oviparous, and accordingly its allocation with the scalaris complex is correct. The most critical doubt cast upon this hypothesis is the proposi- tion by Davis and Smith (1953: 102) that S. a. aeneus is oviparous, whereas S. a. bicanthalis is incontrovertibly viviparous (Smith, 1939: 356, and personal data). On this basis these taxa were elevated to specific status ( S. aeneus , S. bicanthalis) . The data provided in Davis and Smith, however, strongly suggest that in S. a. aeneus viviparity does occur, but on a two-year cycle. Ten of 28 females collected from 25 July to 15 August "contained from 3 to 5 (average 4) large ova,
A roadmap for a quantitative ecosystem-based environmental impact assessment

A new roadmap for quantitative methodologies of Environmental Impact Assessment (EIA) is proposed, using an ecosystem-based approach. EIA recommendations are currently based on case-by-case rankings, distant from statistical methodologies, and based on ecological ideas that lack proof of generality or predictive capacities. These qualitative approaches ignore process dynamics, scales of variations and interdependencies and are unable to address societal demands to link socio-economic and ecological processes (e.g. population dynamics). We propose to re-focus EIA around the systemic formulation of interactions between organisms (organized in populations and communities) and their environments but inserted within a strict statistical framework. A systemic formulation allows scenarios to be built that simulate impacts on chosen receptors. To illustrate the approach, we design a minimum ecosystem model that demonstrates non-trivial effects and complex responses to environmental changes. We suggest further that an Ecosystem-Based EIA - in which the socio-economic system is an evolving driver of the ecological one - is more promising than a socio-economic-ecological system where all variables are treated as equal. This refocuses the debate on cause-and-effect, processes, identification of essential portable variables, and a potential for quantitative comparisons between projects, which is important in cumulative effects determinations.
Genomic footprints of selection under domestication in old world camelids. [W122]

In many parts of the Old World, domesticated camels (genus Camelus) are an essential resource, providing food, labor, commodities, and sport to millions of people. Of the three extant species, two have been domesticated (single-humped dromedaries, Camelus dromedarius, and two-humped Bactrian camels Camelus bactrianus) and one remains wild (two-humped wild Bactrian camels Camelus ferus). All three species possess a variety of adaptations to harsh desert conditions, including mechanisms to tolerate extreme temperatures, dehydration, and sandy terrain. Recent genomic studies of camels have identified patterns of selection consistent with the aforementioned adaptations in addition to quantifying genetic variation and examining demographic history. However, these studies are limited to analyses based upon a single genome from each species, thus biasing many inferences of selection and adaptation. Furthermore, draft genomes are extremely susceptible to errors in the estimated number of genes, thereby distorting conclusions of adaptation based upon orthologous genes between species. In this study, we take a population genomics approach to inferring both positive selection and demographic history of Old World camelids. By re-sequencing multiple genomes from all three species, our objectives were to i) identify genes or regions under selection within and between species related to domestication and/or adaptation, ii) examine the recent demographic history and genome ancestry, and iii) provide an extensive set of genomic resources for future studies of camels. (Texte integral)
Cytogenetic Studies in North American Minnows (Cyprinidae)

We have examined karyotypes from thirteen species of the North American cyprinid genus Notropis: N. chrysocephalus, N. fumeus, N. longirostris, N. lutrensis, N. oxyrhynchus, N. roseipinnis, N. sabinae, N. shumardi, N. signipinnis, N. texanus, N. umbratilis, N. venustus, and N. volucellus. All thirteen species have 2n=50 chromosomes. Estimated haploid arm numbers among the thirteen species ranged from 46-50; one-armed chromosomes (centromeres subterminal to terminal) comprised only a small portion of the karyotype of each species. Chromosomal evolution in Notropis, and in North American Cyprinidae, has been remarkably conservative. Almost all species karyotyped have 2n=50 chromosomes, and with one exception, cyprinid species with 50 chromosomes vary in estimated haploid chromosome arm number from only 46-50. In contrast, speciation in these fishes appears to have been rapid. Thus, the present data suggest that gross chromosomal rearrangement has played only a very minor role in the speciation and evolution of these fishes.