Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro. Cultures of Plants from the Rhamnaceae: Shoot Propagation and Anthraquinones Production

ABSTRACT This study was conducted to investigate the effect of physical and chemical features on metabolic production in plant cell culture. The best multiplication of Frangula alnus. Mill. shoots (8.84 ± 1.11) was obtained on woody plant medium (WPM) medium with indole-3-acetic acid (IAA) (0.1 mg l−1) and 6-benzylaminapurine (BAP) (1.0 mg l−1), but the highest metabolite production (1731 mg/100 g of total anthraquinone (AQ) aglycones) was in the shoots grown on the MS medium with addition of 1-naphthilaceneacetic (NAA) (0.1 mg l−1) and thidiazuron (TDZ) (0.1 mg l−1). The best multiplication of Frangula rupestris. (Scop.) Schur. shoots (6.20 ± 0.53) was obtained on MS medium supplemented with BAP (0.5 mg l−1). The highest metabolite production (451 mg/100 g of total anthraquinone aglycones) was in the shoots grown on medium with 2,4-D (0.1 mg l−1) and BAP (0.5 mg l−1). For the multiplication of Rhamnus catharticus. L. shoots, the best results (2.8 ± 0.7) were obtained on the medium with combination of 2,4-D (0.1 mg l−1) and kinetine (Kin) (1.0 mg l−1). The best synthesis of anthraquinones (AQs) (1205 mg/100 g of total AQ aglycones) was in the shoots, which were grown on MS medium supplemented with 2,4-D (0.1 mg l−1).
An annotated checklist of the orchids of Nepal

An annotated checklist comprised of 458 taxa of orchids known from Nepal is provided, including 104 genera, 437 species, 16 varieties, 3 subspecies and 2 forma and 18 endemic species. In Nepal, orchid species are distributed from 60–5200 m a.s. l. In the checklist, notes on altitudinal ranges, habit, habitat, global distribution, phenology, etc. are presented. Nepal, a small Himalayan country, lies between 26°12′ to 30°27′N and 80°04′E to 88°12′E covering an area of 147 181 km 2 . The diverse physiography, climate, edaphic factors, etc. within an altitude range of 60 – 8848 m a.s. l. has favored vegetation within six bioclimatic zones from tropical luxuriant forests in the south to the alpine scrub or barren high mountain in the north (Chaudhary 1998). The tropical zone is dominated by sal (Shorea robusta), tropical deciduous riverine and tropical evergreen forests. The sal forest is associated with Adina cardifolia, Albizia procera, Butea monosperma, Acacia catechu, Bombax ceiba, Dalbergia sisoo, Syzygium cumini, Terminalia bellirica, T. chebula, Zizyphus mauritiana, etc. In the subtropical zone, Schima–Castanopsis, pine and alder forest types are dominant. The temperate zone is represented by lower temperate mixed broad-leaved, temperate mixed evergreen and upper temperate mixed broad-leaved forests. The subalpine zone is characterized by silver fir (Abies spectabilis) and birch– Rhododendron forest. This zone also includes a pure forest belt of Betula utilis, in association with several species of Rhododendron, Junipererus, etc. In this region, tree trunks and branches are festooned with parasitic orchids, filaments of mosses and various lichens. The alpine zone covers areas above 4100 m a.s. l. and is associated with Juniperus, Rhododendron, Caragana–Lonicera and alpine meadows. In the nival zone, above 5000 m a.s. l. , some mosses and lichens are found up to 7400 m a.s. l. (Baniya et al. 2010) and they are known as the ‘Arctic or cold deserts. ’
λ-Cyhalothrin and cypermethrin induce stress in the freshwater muddy fish, Clarias batrachus

In order to understand the level of health risk posed by pyrethroid insecticides with strong soil-binding properties to freshwater fish, specifically living in muddy region of aquatic bodies, changes were examined in different biochemical stress markers in a freshwater muddy fish, Clarias batrachus, exposed to pyrethroid insecticides, cypermethrin and λ-cyhalothrin, in low sub-acute concentrations parts per million (ppm) for 96 hr. Data showed significant increase in levels of lipid peroxidation and in activities of lactate dehydrogenase, acid, and alkaline phosphatases along with marked decline in the specific activity of acetylcholinesterase in a concentration-dependent manner. The marked alterations in stress biomarkers indicate that pyrethroids induce significant stress in C. batrachus. This risk assessment study draws attention towards the potential health risk of freshwater muddy fish, which are continuously being exposed to the high concentrations of such insecticides accumulated as runoff in the muddy bottom of aquatic bodies.
MACROALGAL CANDIDATES FOR GENOMICS 1

Genomes from over 130 organisms have been either sequenced completely or are currently under investigation. These studies include a wide array of Bacteria, a smaller number of Archaea, model‐system eukaryotes, parasitic protists, and even several microalgae. However, no major effort is underway to acquire a complete nuclear genome sequence from a single macroalga or seaweed despite their crucial contribution to the biodiversity and energy economy of oceans and estuaries. Here we examine various macroalgae as potential candidates for a genome project. A set of criteria is presented, followed by a brief discussion of how well different candidates from the principal macroalgae groups, green, brown, and red algae, meet these criteria. Based on our analyses, we conclude that the red seaweed, Porphyra yezoensis Ueda, should be the leading candidate for a macroalgal genomics initiative. We realize, of course, that others in the phycological community might have a different opinion and that a broad consensus among algal researchers is required to make seaweed genomics a reality; thus the primary intention of this review is to initiate and encourage further discussion as to where the phycological community should focus its genomic efforts.
Oxidative modulation of transient potassium current by arachidonic acid in brain central neurons

Oxidative stress and dysfunction of potassium channels are believed to play a role in neuronal death in a number of CNS diseases (e.g. Alzheimer’s disease, epilepsy). The present study addresses selective neuronal vulnerability to oxidative stress by studying oxidative modulation of potassium channels in entorhinal cortex (EC) layer II stellate neurons (cell loss early in AD) and layer III pyramidal neurons (early damage in TLE), in comparison to hippocampal CA1 pyramidal neurons (late damage in TLE and AD). Using whole-cell patch-clamp, differential inhibition of transient IA and delayed rectifier K-currents IK(V) by arachidonic acid (AA) and H2O2 was demonstrated. Intracellular AA (1 pM) reduced IA in EC neurons significantly stronger than in CA1 neurons. AA affected the voltage dependence of steady-state inactivation as well. ETYA mimicked the effect of AA, excluding its metabolites as mediators of IA modulation. Neither AA nor ETYA reduced IK(V). In contrast, a non-lipid oxidizing agent, H2O2 reduced IA more effectively and robustly attenuated IK(V) in CA1, compared to EC neurons. AAmediated reduction of IA was blocked by free radical scavengers (glutathione, ascorbic acid, Trolox). Antioxidants did not simply inhibit AA and H2O2 effects. In particular, they even enhanced AA effects, suggesting more complex modulation of these currents in slices, compared to culture. Moreover, intracellular antioxidants, themselves, influenced maximal conductance and voltage-conductance characteristics of IA and IK(V). This should be considered in design of anti-oxidative therapies in AD and TLE. Heterologous expression of Kv1.4 and of Kv4.2 cDNA in HEK-293 cells formed functional channels and elicited A-type currents, which shared similar biophysical characteristics with native IA from the hippocampus. These currents were strongly decreased upon administration of 1pM AA, demonstrating that at least one of multiple sites for AA action is situated on the pore-forming alfa-subunit of the A-channel. In conclusion, beside contribution to cell damage, ROS may regulate physiological processes by acting on different signalling pathways. Since voltage-gated K-channels underlie many important cellular functions modulation of these channels by ROS would represent a mechanism for fine tuning of cellular processes.
Preliminary assessment of the environmental and selective effects of a captive breeding and rearing programme for endangered Atlantic salmon, Salmo salar

The selective and environmental effects of captivity on several fitness-correlated traits were assessed in smolts of endangered Atlantic salmon, Salmo salar L. , from the inner Bay of Fundy, produced via artificial spawning and released into the wild as juveniles. Smolts were sampled as they migrated downstream and identified through microsatellite-based parentage analysis as offspring of either wild-spawning adults or adults that were spawned in captivity. Overall, captive-origin smolts exhibited a significantly later run timing and smaller body size than wild smolts. Significant differences in run timing and body size were also found between captive-origin smolts that had experienced rearing environments that differed in duration of captivity and thermal regime. Significant differences in run timing, fork length and weight were found between first and second generation captive-origin smolts, although the expression of these differences depended on the rearing environment experienced, suggesting a possible genotype by environment effect. The ratio of effective-to-census number of breeders that produced the captive-origin smolts was higher than that of the wild-origin smolts due to successful captive breeding management practices. These results have direct implications for captive breeding and rearing programmes for salmonids and wider implications for understanding the rates of evolutionary and environmentally induced change that can occur in captivity.
Aspectos da biologia de Euplusia violacea (Blanchard) (Hymenoptera, Apidae, Euglossini)

Nests of orchid bee Euplusia violacea (Blanchard, 1840) colleted in trap-nests and in the wood of a construction in Vicosa, Minas Gerais (20o45'30"S, 42o52'05"W), Brazil, were studied under laboratory condictions. Some aspects of the biology of these bees were observed, such as sex-ratio, development time, Iongevity and others. Some aspects of the behavior of E. violada were also studied.
Molecular characterization and gene expression analysis of a metalloprotease from Pacific abalone Haliotis discus hannai

We isolated a metalloprotease (MP) homologue from an abalone muscle cDNA library. A 3284-kb full-length cDNA encoding a predicted polypeptide of 667 amino acids was sequenced. The abalone MP Haliotis discus hannai (HdMP) exhibited a domain structure typical of the peptidase M4 family, a 21-amino acid N-terminal hydrophobic signal sequence followed by a long propeptide sequence of 347 amino acids and the mature protease domain comprising 299 amino acids. The mature region contains features characteristic of a zinc protease, including a zinc-binding motif (HEXXH) and an active site. The protein showed 32–38% amino acid sequence identity with other known MP sequences and with a hypothetical protein from owl limpet. The mRNA transcript is expressed in almost all tissues, with high expression in the mantle and adductor muscle of healthy abalones, and is expressed constitutively during the early developmental stages after fertilization. Lipopolysaccharide or poly I:C stimulation induced the expression of the HdMP transcript in the digestive track and gills of abalones. Collectively, these results suggest that HdMP could play multiple roles in defense, the immune response, growth, and regulation of reproduction.
Fecundity and Brood Loss of Sand Shrimp, Crangon uritai (Decapoda: Crangonidae)

Abstract Fecundity and brood loss during incubation were investigated in the crangonid shrimp Crangon uritai. Changes in egg length, volume and dry weight were also studied. During embryonic development, egg length and egg volume increased by 43.5% and 69.3%, respectively, whereas egg dry weight decreased by 23.2%. Crangon uritai ovigerous females (5.61-14.11 mm CL) carried 412 to 13,824 eggs per brood, depending on their body size in both early and late stages of egg development. The reproductive output of C. uritai averaged 0.24, based on dry weight in early eggs. Brood loss through embryonic development was independent of female size and estimated to be a 5.56% loss in the number of eggs and an 8.44% loss in brood dry weight. Possible reasons for brood loss include the burrowing behavior of shrimp and increasing egg size, which results in reduced area for eggs to attach.
Expression and function of Kir7.1 in the Murine Central nervous system

Glia express a variety of ion channels, but the precise subtypes expressed by astrocytes and oligodendrocytes has not been fully elucidated. The Kir7.1 subtype of inwardly rectifying potassium channels (Kir) is highly expressed in retinal pigment epithelium and has been demonstrated in Purkinje neurons of the adult rat cerebellum and pyramidal neurons of the hippocampus, but it has not previously been identified in glia. Using quantitative real time PCR, an ion channel profile for the developing mouse optic nerve was constructed and Kir7.1 was identified as one of the major ion channels present. Immunostaining revealed widespread expression of Kir7.1 in glia and neurons in the mouse brain with the highest expression found in optic nerve oligodendrocytes. A major function of Kir is to maintain the membrane potential of glia in the face of large ionic shifts associated with normal neuronal function and pathology. Oligodendrocytes are particularly susceptible to ischemia so the role of Kir7.1 in maintaining oligodendrocyte integrity during oxygen and glucose deprivation (ODG) in the isolated intact mouse optic nerve was examined, using the Kir7.1 channel blocker VU590. Blockade of Kir7.1 resulted in increased cell death of optic nerve oligodendrocytes in normoxic conditions by activating caspase -dependent apoptotic pathways and significantly augmented cell death induced by OGD. Moreover, intracellular calcium fluctuations dependent on store operated calcium entry in optic nerve glia were identified as a potential mechanism for the cellular stress induced by Kir7.1 inhibition. The results presented within this thesis demonstrate functional expression of Kir7.1 in glial cells, and indicate they are important in maintaining oligodendrocytic integrity in both physiological and pathological conditions.
Evaluation of the Depensatory Fishing Hypothesis as an Explanation for Population Cycles in Fraser River Sockeye Salmon (Oncorhynchus nerka)

Causes of cyclic fluctuations in the abundance of Fraser River sockeye (Oncorhynchus nerka) have been the focus of considerable debate for much of this century. Most hypotheses to explain cyclic behaviour in Fraser River sockeye centre on identifying agents of depensatory mortality, and several recent papers argue that sockeye cycles are maintained primarily by depensatory fishing patterns. We assess the evidence for depensatory fishing as an explanation for these cycles. Using simulations, we demonstrate that empirical evidence for depensatory fishing is likely an artifact caused by bias in estimating stock composition of catches in mixed-stock fisheries. Moreover, recent trends in harvest rates among comigrating stocks with asynchronous cycles are inconsistent with the depensatory fishing hypothesis. It also seems very unlikely that aboriginal and early commercial fisheries were intensive enough to maintain cycles that persisted prior to 1860. Only during the unregulated, early commercial fishery prior .
Their Day in the Sun: molecular phylogenetics and origin of photosymbiosis in the ‘other’ group of photosymbiotic marine bivalves (Cardiidae: Fraginae)

The subfamily Fraginae (Cardiidae) is a morphologically diverse group of small-bodied marine clams inhabiting shallow seas worldwide. Like the exclusively photosymbiotic giant clams (Cardiidae: Tridacninae), some fragines are known to host zooxanthellae photosymbionts. However, surveys to widely determine photosymbiotic status and the lack of a comprehensive phylogeny have hindered attempts to track the evolution of photosymbiosis in the group. Worldwide sampling of all fragine genera and subgenera with phylogenetic reconstructions based on four gene regions [nuclear (28S) and mtDNA (16S, cytochrome oxidase I, cytochrome b)] does not support a monophyletic Fraginae. Sampled taxa form four restructured clades: (1) the ‘Fragum’ group, (2) the ‘Trigoniocardia’ and ‘Ctenocardia’ groups, (3) the ‘Parvicardium’ group and (4) the ‘Papillicardium’ group. Maximum likelihood analyses strongly support a clade of European cardiids uniting species from three subfamilies. Live examination of > 50% of species reveals that less than half of derived genera and subgenera host photosymbionts, supporting a single and relatively late origin of photosymbiosis in the Fraginae. The evolutionary implications for a small and little modified earliest diverging photosymbiotic lineage are discussed. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 448–465.
Group Effects and Computing Strategies for Models for Estimating Breeding Values

Abstract No criterion to define group effects in models for estimating breeding values is universally accepted. In this paper it is argued that models that assign group effects to classes of unidentified animals allow group effects and relationships between animals to be combined in a coherent manner. Such models are discussed together with computing strategies to fit them to large amounts of data. In particular, a computing strategy is presented to estimate genetic merits of bulls and cows using a best linear unbiased prediction model, which uses all relationships and all lactations.
Use of Plasma Amino Acid Concentration to Identify Limiting Amino Acids for Milk Production

Abstract The hypothesis that an essential amino acid will accumulate in blood plasma only when supplied in excess of requirement was the basis of an attempt to identify essential amino acids most likely limiting lactation. In a 5 X 5 Latin-square experiment, five lactating cows were fed a corn-based basal ration containing 9.0% crude protein. Casein treated with . 8% wt/wt formaldehyde to prevent protein breakdown by ruminal microorganisms was fed in five quantities to give diets containing 9.0 (basal), 11.2, 13.5, 15.7, and 18.0% crude protein (dry matter basis). Milk production and milk crude protein content for each of the five treatments were: 20.4kg and 2.98%; 22.1 and 3.04; 24.7 and 3.14; 26.8 and 3.17; and 25.7 and 3.15. This indicated that amino acid supply was inadequate at the two lowest but adequate at the two highest percents of dietary protein. Comparison of milk samples obtained at the lowest and highest protein feeding indicated that 82% of the increase in milk nitrogen content was accounted for as true protein (trichloroacetic acid-precipitable nitrogen). There was little evidence of change in the amino acid composition of milk protein with increased protein intake. Essential amino acid concentrations in jugular and mammary vein plasma for cows at all intakes of formaldehyde-treated casein indicated that methionine, valine, and lysine were the most likely limiting amino acids for milk production.
Does 900 MHZ GSM Mobile Phone Exposure Affect Rat Brain?

This study investigated the effects of cell phone exposure on the fatty acid composition in phospholipids, malondialdehyde concentration, p53 immune reactivity and histological structure of the rat brain. Sixteen Sprague-Dawley rats were divided into two groups of eight, sham and experimental (speech conditions). The rats were confined to Plexiglas cages, and cellular phone were placed 0.5 cm under the cages. For the experimental group, cellular phones were activated 20 minutes per day, 7 days a week, for 1 month. For the sham group, the cellular phones were placed beneath the cages with the phones turned off. The Whole Body Average SAR (rms) was 0.52 W/kg and 1 g averaged peak SAR (rms) 3.13 W/kg. The Mann-Whitney U-test was used for statistical comparisons of groups. Histological alteration and changes in brain phospholipid fatty acids composition were not observed in rat brains. Immunohistochemical staining of brain tissue shown that p53 immunoreactivity was not affected by cell phone exposure. Malondialdehyde concentration in exposed brains was significantly higher than sham (p < 0.05).
Determinants of demand for wood products in the US construction sector: an econometric analysis of a system of demand equations

A system of conditional demand equations for wood products in the US construction sector is derived from the relevant end-use cost functions by taking advantage of the duality between the production function and the cost functions. Seven different inputs, including five wood products, labor, and capital, and three different end uses (new housing construction, repair and remodeling, and nonresidential construction) are analyzed. A seemingly unrelated regression estimation procedure is employed using a detailed annual time series database that spans the period from 1950 to 2009. Results suggest large variability in own-price long-term demand elasticity among wood inputs and across end uses. Softwood lumber, for example, is highly inelastic for new housing construction, inelastic for repair and remodeling, and nearly unitary elastic for nonresidential construction. Softwood plywood, on the other hand, is elastic for new housing construction and highly inelastic for nonresidential construction. In addition, w.
Biochemical and genetic responses in cuticular mutants

The cuticle layer is essential for maintaining organ integrity and protecting plants against biotic and abiotic stresses present in their natural environment. Arabidopsis thaliana mutants with a defective cuticle layer may help to precisely determine which genes are actually taking part in the formation of the cuticle. The functions of some cuticular genes seem to be conserved between monocots and dicots as we could complement the Arabidopsis fiddlehead (fdh) mutant with the barley allele of the FDH gene. In addition to a defective cuticle, fdh, bodyguard (bdg), lacerata (lcr) and the novel htm Arabidopsis mutant show ectopic organ fusions and other developmental phenotypes. As the isolation of pure cutin from cuticular mutants is not doable, we analysed the cell wall bound lipid composition from leaves of the fdh and lcr mutants. As a consequence of fdh and lcr mutations, a significant increase in cutin monomer amount takes place. Even though FDH and LCR enzymes have very different functions, similar alterations in cell wall bound lipid composition were observed in their mutants. As it was observed in bdg earlier, we could also show that both fdh and lcr accumulated more wax. Even though each of these three mutants has its own particularities that, mutations in three genes coding for so different enzymes trigger similar phenotypical alterations was quite unexpected. This brought us to study the compensatory response to cuticular damage and to compare the transcriptome of mutants using microarrays. This analysis supports the idea that plants are able to compensate for cuticle defects specifically altering gene expression. We characterised the expression pattern of the recently cloned HTM gene using promoter and protein fusion reporter constructs. We found that the HTM gene is epidermis specific, and is particularly strongly expressed in petals and sepals. This goes well in hand with the phenotype of the htm mutant which is characterised by postgenital organ fusion within floral buds. The bound lipid analysis revealed that whereas htm deposits similar quantity of monomers on its outer cell wall, there is a shift in monomer proportions. The wax composition of this mutant was not found different from that of the wild type but a global decrease of 20% was observed. Thus it is more likely that HTM is indirectly involved in wax and cutin biosynthesis. We also characterised insertion lines in genes putatively involved in cutin biosynthesis, respectively encoding an aldehyde dehydrogenase, an epoxide hydrolase-like enzyme, and a member of the α/β hydrolase-fold super family.