Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression and regulation of human β‐defensin‐2 in osteoarthritic cartilage

Defensins are antibiotic peptides that are involved in host defence at epithelial and mesenchymal surfaces. Previous studies have shown the induction of human β‐defensin‐3 (HBD‐3) in osteoarthritic joints, suggesting that these molecules have functions in addition to their ability to kill microbes. The aim of this study was to investigate the production of a further human β‐defensin, named HBD‐2, in osteoarthritis (OA) and to determine its regulation by inflammatory cytokines. Healthy and osteoarthritic cartilage was assessed for HBD‐2 expression by RT‐PCR, immunohistochemistry, and ELISA. C28/I2 chondrocytes, primary chondrocytes, and cartilage explants were cultured for in vitro studies. After 24 h of stimulation with tumour necrosis factor‐α (TNF‐α), interleukin‐1 (IL‐1) or IL‐6, real‐time RT‐PCR and ELISA experiments were performed to evaluate the effect of these cytokines on the production of HBD‐2. In contrast to healthy cartilage, HBD‐2 expression was identified in most of the OA samples examined (eight of ten). Cytokines that are potentially involved in the pathogenesis of OA, namely TNF‐α, IL‐1, and IL‐6, were transcriptional inducers of HBD‐2 in cultured chondrocytes and cartilage explants in vitro, as measured by real‐time RT‐PCR and ELISA. These results illustrate the induction of HBD‐2 in osteoarthritic cartilage and suggest that it is a further factor in the pathogenesis of OA. However, further studies are required to elucidate the role played by HBD‐2 in osteoarthritic cartilage. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Spatio‐temporal co‐occurrence of cougars (Felis concolor), wolves (Canis lupus) and their prey during winter: a comparison of two analytical methods

Aims To examine the spatio‐temporal co‐occurrence of cougars (Felis concolor), wolves (Canis lupus), and their prey during winter using monthly (November–March) species–environment relationship models. In addition, to contrast predictions across two methods: logistic regression and Geographic Information System (GIS) image correlation.
Diet composition, rumen papillation and maintenance of carcass mass in female Norwegian reindeer (Rangifer tarandus tarandus) in winter

The uptake of volatile fatty acids (VFAs) from bacterial fermentation of forage in the rumen is enhanced by the presence of papillae which greatly increase the surface area of the mucosa of the rumen. The degree of papillation, expressed as the surface enlargement factor (SEF), seems to be closely related to the level of microbial activity and the rate of production of VFAs in the rumen. In several species of wild ruminants the SEF decreases markedly in winter, apparently in response to a decrease in the quality and availability of forage and also, presumably, in the level of ruminal microbial activity. Contrary to expectation, however, no reduction in the rate of production of VFAs in winter has been detected in semi-domesticated reindeer at natural pasture in northern Norway. We investigated the body mass, the composition and quality of the diet and the morphology of rumen papillae in adult female reindeer free-living at natural pasture. Animals were slaughtered in matched aged groups of nine on four occasions: in autumn (September) and winter (November, February and March). The composition and quality of the diet was determined by morphological and chemical analysis of plant fragments recovered from the rumen. The carcass mass of the animals did not differ significantly between collections. The animals ate vascular plants and lichens from 37 different genera. The composition of the diet varied little between months except for the inclusion of a substantial proportion (25.8% of fragments) of lichens in March. The mean density of rumen papillae increased from 55.6 papillae/cm2 in September to 75.7 papillae/cm2 in March (P < 0.001). All other parameters, including the length and perimeter of the papillae and the SEF of the rumen, were lower in March compared with September. However, the mean SEF increased from 8.8 in February to 10.6 in March (P < 0.05), indicating increased ruminal fermentation in late winter. We propose that the increase in the SEF in March might be associated with the increase in the proportion of lichens in the diet. Lichens are highly digestible in reindeer but do not score highly in conventional analyses of diet quality owing to the unusual chemical structure of the structural carbohydrates of which they are composed.
Phylogenetic Relationships within the Subfamily Sterculioideae (Malvaceae/Sterculiaceae-Sterculieae) Using the Chloroplast Gene ndhF

Abstract A parsimony analysis of ndhF nucleotide sequences representing 24 species and 13 genera of Sterculioideae strongly supports (100% bootstrap) the monophyly of the group. Within the Sterculioideae clade four major clades are recognized with good bootstrap support but relationships among them are not resolved. This analysis suggests the recognition of Argyrodendron as separate from Heritiera, supports Acropogon as separate from Sterculia, and Tarrietia as part of Heritiera. The current circumscriptions of Hildegardia and Firmiana are not supported. The use of fruit characters in the delimitation of genera within Sterculioideae may not be appropriate in some cases and other morphological characters need to be found.
Differential expression of the KLK2 and KLK3 genes in peripheral blood and tissues of patients with prostate cancer

We used the multiplex semi-quantitative reverse-transcriptase PCR (RT-PCR) to investigate kallikrein 2 and 3 (KLK2 and KLK3) mRNA levels in prostate tissue from 42 prostate cancer patients, 33 of whom were also assessed for peripheral blood KLK2 expression by qualitative semi-nested RT-PCR. We found that KLK2 was an important tissue biomarker for distinguishing between prostate cancer patients and those with benign prostatic hyperplasia, particularly when KLK2 expression was > 60% of that of the b2-microglobulin constitutive gene. Patients with an average relative expression value > 0.6 (cutoff value) had an eleven-fold higher chance of having prostate cancer. When one or two tissues samples were evaluated for KLK2 expression using the cutoff value the estimated chance of having prostate cancer was increased by seven times for one positive sample and 45 times for two positive samples. There was no significant correlation between KLK3 gene expression and prostate cancer diagnosis. Logistic regression for blood and tissue KLK2 expression successfully detected 92% of the prostate cancer cases. The detection of KLK2 in blood showed a sensitivity of 59% and a specificity of 82%. This study indicates that the KLK2 gene may be a useful molecular marker for the diagnosis of prostate cancer and that analysis of KLK2 expression in blood and tissues could provide a novel approach for the clinical investigation of this type of cancer.
Description and Molecular Characterization of Six New Species of Nassarius (Gastropoda, Nassariidae) from the Western Pacific Ocean

Abstract: Six new species of the genus Nassarius Duméril, 1805 are described, based on material collected from the Coral Triangle and the South Pacific. We combine traditional morphology-based descriptions with the molecular (Cytochrome c oxidase I - COI) signature of the new species. New species are: Nassarius ocellatus sp. nov. (Philippines to Vanuatu), Nassarius houbricki sp. nov. (Solomon Islands to Queensland and Tonga), Nassarius radians sp. nov. (Philippines to Vanuatu), Nassarius vanuatuensis sp. nov. (Vanuatu), Nassarius velvetosus sp. nov. (Western Australia to Fiji) and Nassarius martinezi sp. nov. (Solomon Islands to Tonga).
Intrinsic dynamics and stability properties of size-structured pelagic ecosystem models

Although pelagic ecosystem models, coupled with ocean circulation models, are being widely used to quantify fluxes of nutrients and carbon in the ocean at regional and basin scales, relatively little work has been done on understanding their intrinsic dynamics independently of physical forcing. In this study, the dynamics of three common formulations for the NPZD class of models (nutrient, phytoplankton, zooplankton and detritus) using two different types of predation functional response are analysed and compared. Our goal is to characterize the stability properties of this class of models with respect to variations in light and total nutrient concentrations. Despite important structural differences, the different model formulations all show asymptotic stable equilibria at low total nutrient concentrations and high to moderate light intensities, and limit cycle oscillations at low light intensities and high total nitrogen concentrations. Limit cycles are formed through a Hopf bifurcation as a phase lag develops between predator (Z i ) and prey (P i or Z i-1 ) due to a relatively sharp increase in the growth rate of the prey in relation to that of the predator. The use of variable preferences in the functional response provides a density-dependent mechanism that allows the system to self-regulate, increasing system stability considerably, but does not eliminate the instabilities completely. Instabilities occur at light and nutrient levels that correspond to those observed on the bottom of the euphotic zone near the nutricline, where the deep chlorophyll maximum is usually located. This suggests that the deep chlorophyll maximum might be dynamically unstable. This dynamic disequilibrium in species composition and the characteristically long transient times would allow species persistence in the presence of seasonal and mesoscale variations and provide a mechanism for species coexistence in the relatively homogeneous open ocean environment, thereby providing a potential solution for the 'paradox of plankton'. In the multi-species models, the higher diversity of species (wider range of values for the biological parameters) allows biological activity (photosynthesis, grazing and predation) to occur under a wider range of light and nutrient conditions, resulting in higher primary and secondary production and lower nutrient concentrations at light intensities equivalent to those in the upper part of the euphotic zone, than in the single-species model.
Antiglycation Activity of Otostegia persica (Burm.) Boiss

Diabetes mellitus is a common endocrine disorder characterized by hyperglycemia and long-term complications affecting the eyes, nerves, blood vessels, skin and kidneys. Increased glycation of proteins and accumulation of advanced glycation endproducts (AGEPs) have been implicated in the pathogenesis of diabetic complications. Glycation and AGEP formation are also accompanied by the formation of free radicals via autoxidation of glucose and glycated proteins. Compounds with combined antiglycation and antioxidant properties may offer therapeutic potential. Since the antioxidant activity of different extracts and fractions of aerial parts of Otostegia persica has been evaluated and this plant is used as an antidiabetic agent in Iranian traditional medicine, we evaluated the antiglycation activity of this species. Here, we report the isolation of known compound 3´, 7-dihydroxy-4´,6,8-trimethoxy-flavone for the antiglycation properties of this plant.
Antioxidant response of Chlamydomonas reinhardtii grown under different element regimes

Nutrient stress is one of the most favorable ways of increasing neutral lipid and high value‐added output production by microalgae. However, little is known about the level of the oxidative damage caused by nutrient stress for obtaining an optimal stress level for maximum production of specific molecules. In this study, the antioxidant response of Chlamydomonas reinhardtii grown under element deprivation (nitrogen, sulfur, phosphorus and magnesium) and supplementation (nitrogen and zinc) was investigated. All element regimes caused a decrease in growth, which was most pronounced under N deprivation. Element deprivation and Zn supplementation caused significant increases in H2O2 and lipid peroxidation levels of C. reinhardtii. Decrease in total chlorophyll level was followed by an increase of total carotenoid levels in C. reinhardtii under N and S deprivation while both increased under N supplementation. Confocal imaging of live cells revealed dramatic changes of cell shape and production of neutral lipid bodies accompanied by a decrease of chlorophyll clusters. Antioxidant capacity of cells decreased under N, S and P deprivation while it increased under N and Zn supplementation. Fluctuation of antioxidant enzyme activities in C. reinhardtii grown under different element regimes refers to different metabolic sources of reactive oxygen species production triggered by a specific element absence or overabundance.
A simple method for measuring the changing volume of small biological objects, illustrated by studies of suction feeding by fish larvae and of shrinkage due to histological fixation

A simple method has been devised to determine dynamic changes in volume of biological objects of a ‘smooth’ form. The method requires two perpendicular views (side and bottom). The method can be used also in static volume changes. Differential changes in length, width and height can be quantified. The volume of the object is approximated by a series of ellipses. The length of the axes of the ellipses is determined from the two views. Possible sources of error are discussed. The method is applied in a study of static volume changes of fish larvae due to fixation and in a study of the dynamic volume change of the mouth cavity of carp larvae, increasing their head volume 30% in 8 ms, when sucking prey.
Molecular Phylogenetic Study of Interspecific Variation in the Moss Isothecium (Brachytheciaceae)

Abstract Isothecium myosuroides is an abundant and taxonomically problematic moss that occurs in Europe and on the west and east coasts of North America. It has sometimes been split into two taxa, I. myosuroides on the east coast of North America and in Europe, and I. stoloniferum on the west coast of North America. Isothecium stoloniferum has four distinct morphological types known as the ordinary, julaceous, coarse, and pinnate morphs. The degree to which the morphotypes are genetically distinct versus ecologically determined has been debated as has the distinction between I. stoloniferum and I. myosuroides, resulting in conflicting taxonomic treatments. This study uses phylogenetic analyses of the trnL-trnF and trnG regions of the chloroplast genome to examine relationships among the two species and four morphotypes. Molecular phylogenetic analyses reveal that there is some genetic basis to the morphs of I. stoloniferum, and that I. stoloniferum is paraphyletic. Accessions of I. myosuroides form a trans-Atlantic monophyletic group. The remaining samples form two distinct groups that each include samples of two morphotypes within I. stoloniferum. Populations of julaceous and ordinary morphotypes form a monophyletic group. Populations of coarse and pinnate morphotypes form an unresolved polytomy at the base of the clade that includes accessions of I. myosuroides.
Characterization of waldmeister, a novel developmental mutant in Arabidopsis thaliana

A novel Arabidopsis thaliana (L.) Heynh. developmental mutant, waldmeister (warn), is described. This mutant was found in the progeny arising from an Ac-Ds tagging experiment, but does not appear to be tagged by an introduced transposon. This recessive nuclear mutation maps between GAPB and ap 1 on chromosome 1 and shows extreme morphological and physiological changes in both floral and vegetative tissues. Changes to the vegetative phenotype include altered leaf morphology, multiple rosettes, stem fasciation, retarded senescence and disturbed geotropic growth. Changes to the floral phenotype include delayed flowering, increased number of inflorescences, determinate inflorescences, altered number and morphology of floral organs, chimeric floral organs, and ectopic ovules, warn was crossed to a number of previously described floral mutants: apetela 2, apetela 3, pistillata, agamous, and leafy. The phenotype of the double mutant was in each case additive. In the case of agamous, however, the indeterminate repetitive floral structure of agamous was lacking, emphasizing the determinate inflorescence growth of warn. The extreme phenotype of the warn mutant is suggestive of a disturbance to a gene of global importance in the regulation of plant growth and development.
Long-term survival of cryopreserved sugarbeet pollen.

Hecker and coworkers demonstrated that sugarbeet (Beta vulgaris L.) pollen could be stored in liquid nitrogen vapor phase (-160°C) (LN) for 1 year and remain viable. We demonstrate that pollen, stored for 17 years in LN was able to pollinate sugarbeet and produce viable seed. two viability staining tests showed no significant differences between stored and fresh pollen, and differences in pollen tube germination were small. Long-term storage of pollen provides opportunities for uses in sugarbeet breeding and genetic resources preservation. In a heterozygous crop such as sugarbeet, collected pollen would be a way to pre serve superior, individual genotypes for use over long peri ods of time. In plant breeding, stored pollen could be used as a long term tester (individual genotype or population) or from an individual genotype as the parent in a recurrent backcrossing scheme for genetic analysis. Collection and storage of pollen could be a way to obtain a more represen tative sample of the genetic diversity in wild populations. With restrictions on the international transport of seed becoming increasingly stringent, pollen could be an alter nate way to distribute Beta germplasm. However routine use of Beta pollen collections requires a more complete understanding of physiological responses to LN storage.
Dietary arginine: metabolic, environmental, immunological and physiological interrelationships

Arginine is an essential amino acid for chickens due to the absence of a functional urea cycle in birds. Arginine plays critical roles in metabolic pathways associated with growth and immune-competence. Likewise, as a precursor of nitric oxide synthesis, arginine is important as the key vasodilator that opposes the onset of pulmonary hypertension in broiler (meat-type) chickens. Dietary arginine levels in commercial broiler diets meet NRC recommendations. However, this review shows that NRC recommendations may not be adequate to support maximal growth, support arginine-depleting immune responses, and prevent the onset of pulmonary hypertension in broilers reared under rigorous environmental conditions. Dietary composition is highly important and broiler performance may suffer when insufficient levels of arginine are included in the diet. Fortification of broiler diets with supplemental arginine may be necessary under such circumstances.
Effect of dietary energy level, addition of fat and physiological state on performance and energy balance of lactating and pregnant rabbit does

The effects of dietary energy level and added fat were studied by comparative slaughter on 60 primiparous rabbit does in different reproductive states. Nine does were slaughtered immediately after their first parturition (preliminary slaughter group) to estimate initial empty body composition. The 51 remaining does were divided into three groups and given diets differing in digestible energy (DE) content: M (11·28 MJ/kg dry matter (DM); H (12·16 MJ/kg DM); F (11·93 MJ/kg DM, obtained by the inclusion of 25 g/kg of animal fat). Thirty-six does (12 per group) were remated 3 to 4 days after parturition, after which 20 does were concurrently pregnant and lactating (LP) and gave birth a second time. At the second parturition these does were slaughtered with their new-born litters. The non-mated or non-pregnant lactating does (LN) were slaughtered at the same time. All litters from the first parturition were weaned at the 30th day of age. The diets influenced the DE intake (3·11 v. 3·31 and 3·36 MJ/day, P v. 180 v. 191 glday, P 0·05) (average of LP and LN does). The maternal diet significantly influenced the weight of the sucking litters (first parturition) at 20 days (2409 and 2454 v. 2629 g, P The LP does showed lower DE intake, milk yield (from 10 to 30 days) and litter weaning weights than LN does. Between the first and the second parturition, the LP does had a loss of empty body weight and a negative protein balance (-0·06 of the initial content), while the LN does had an increase in live weight and empty body weight and a positive protein balance (+0·11 of the initial content). Both LP and LN does had a negative energy balance (−0·24 v. −0·25, respectively; P
Spatial networks of fleshy-fruited trees drive the flow of avian seed dispersal through a landscape

Summary Seed dispersal by animals leads to plant genes, individuals and species flowing across the landscape, but this process has been seldom seen as the explicit result of structural or landscape connectivity. For two years, we studied avian seed dispersal of fleshy-fruited trees in a secondary forest of the northern Iberian Peninsula, considering the areas under the canopies of fruiting trees as hubs of seed deposition. Using graph-theory models, we set a spatially explicit network in a continuous landscape, with individual fruiting trees as nodes and expected frugivore movements as links between nodes. We calculated the contribution of each tree to network connectivity, finding strong inter-annual variability derived from tree properties (position, fruit crop and species). Trees contributing the most to connectivity accumulated larger seed clumps under their canopies, demonstrating agreement between a network structural connectivity and the functional connectivity of seed dispersal flow. This pattern, however, is accentuated when the large-scale distribution of fruiting crops closely matches that of individual trees, suggesting between-year variation in resource tracking by avian frugivores. Our findings reveal connectivity to be an emerging property of plant-disperser systems, operating at the scale of individual fruiting plants, but contingent on the yearly, large-scale templates of fruiting crops.
A marchi study of the distribution of the anterior commissure in the cat

Experimental studies of the anterior limb of the anterior commissure have dealt principally with the degeneration occurring in this commissure after removal of one of the olfactory bulbs. According to the investigations of Ram6n y Cajal ('01) and Probst ('01) brains treated by the Marchi method, following unilateral ablation of the anterior end of the olfactory bulb, revealed degenerated fibers crossing in the anterior commissure and ending in the opposite olfactory bulb. Cajal particularly emphasized that, in his experiments on rabbits and guinea pigs, only the olfactory bulbs were involved and that the olfactory lobes behind the bulbs were undamaged. Furthermore, on the basis of his Golgi studies, Cajal considered the interbulbar component of the anterior commissure as arising from the tufted cells in one olfactory bulb and terminating on the granule cells in the opposite olfactory bulb. On the other hand, Loewenthal (1897) and van Gehuchten ('04), also using the Marchi method, were not able to detect degeneration in the anterior commissure after destruction of the olfactory bulb, and it was only when their lesions included some of the olfactory lobe behind the olfactory bulb that these investigators were able to demonstrate dcgeiieratcd anterior commissure fibers ending in the opposite olfactory bulb. Other workers have obtained these same results (sce van Gehuchten, '04). Van Gehuchten concluded that these fibers mere not commissural fibers but