Miracle-dz/UniFAR-FTUs huggingface dataset:
Synaptic and dendritic mechanisms mediating direction-selective signaling in the retina

Understanding how information is integrated and processed in single neurons and small circuits is crucial for comprehending information processing in neural circuits, and will help elucidate the biophysical basis of cognition and cognitive dysfunction. The direction selective circuit of the retina has been an archetypical model for understanding how neural circuits process information in the brain since the direction selective ganglion cell (DSGC) was first discovered more than 40 years ago. Much progress has been made towards understanding how the direction selective circuits extracts information from moving stimuli on the retina and computes the direction of motion; however, several key questions have remained unanswered. While it had been shown that directional inhibitory inputs to the DSGC are crucial to forming directional responses, the mechanisms underlying the integration of synaptic inputs to produce directional spiking in the DSGC are unknown. Furthermore, the cell that mediates the crucial directional inhibition, the starburst amacrine cell (SBAC) has been identified, yet we do not have a complete understand how the SBAC generates this directional inhibitory signal. Using In-vitro patch-clamp recordings and two-photon calcium imaging, we show that DSGCs employ orthograde spikes originating in the dendrites to locally integrate excitatory and inhibitory synaptic inputs and signal the direction of motion, which enhances the directional selectivity of the circuit. This represents the first demonstration of how dendritic action potentials contribute to direction selectivity and more generally it is one of the first demonstrations of a
Hormone-induced changes in HeLa cell membrane architecture relate to changes in microbial adherence: Implications for treatment strategies

The female genital tract is susceptible to different microbial infections at different stages of the menstrual cycle. As microbial adherence is receptor-mediated, the effects of the menstrual cycle hormones, oestradiol and progesterone, on the receptor repertoire of HeLa S3 cells that facilitate the adherence of Staphylococcus aureus, Escherichia coli, Lactobacilluc casei and the potential pathogen, Candida albicans, were investigated. Treatment of HeLa S3 cells with progesterone (alone, or in combination with oestradiol mimicking the luteal phase of the menstrual cycle) significantly (p<0.05) promoted the adherence of all the tested microorganisms to the cells when compared with the effects of oestradiol (alone, or in combination with progesterone mimicking the follicular phase). C. albicans and L. casei bound preferentially to the protein fraction of progesterone-treated cells and to the lipid fraction of oestradiol-treated cells (p<0.05) while S. aureus bound to proteins of oestradiol-treated cells and lipids of progesterone-treated cells (p<0.05). E. coli adhered significantly (p<0.05) more to proteins of oestradiol-treated cells than progesterone-treated cells. Numerous hormonally influenced polypeptides and some lipids permitting the adherence of the tested microorganisms were identified by overlay experiments. Irrespective of hormone treatment, six polypeptides possessing saccharide residues with identical migratory properties bound both the potential pathogen, C. albicans and the potentially probiotic species, L. casei. The existence of a common target oligosaccharide on the cells, present irrespective of hormone environment, may indicate a rationale for the development of small oligosaccharide infection inhibitors. Alternatively, stringent selection of probiotic species with common binding patterns regardless of the hormonal milieu is suggested.
Studies on woloszynskioid dinoflagellates I: Woloszynskia coronata re-examined using light and electron microscopy and partial LSU rDNA sequences, with description of Tovellia gen. nov. and Jadwigia gen. nov. (Tovelliaceae fam. nov.)

K. Lindberg, Ø. Moestrup and N. Daugbjerg. 2005. Studies on woloszynskioid dinoflagellates I: Woloszynskia coronata re-examined using light and electron microscopy and partial LSU rDNA sequences, with description of Tovellia gen. nov. and Jadwigia gen. nov. (Tovelliaceae fam. nov.). Phycologia 44: 416–440. Sediment samples were collected from a small pond in southern Sweden. Several cysts from the samples germinated into clonal cultures, identified as Woloszynskia coronata (Wolosz.) R.H. Thompson 1951. They were compared with other species of Woloszynskia established in culture, using scanning electron microscopy, transmission electron microscopy, partial large subunit ribosomal DNA (LSU rDNA) and morphology of the resting cysts. Significant differences were found, and we conclude that the genus Woloszynskia as presently circumscribed is artificial, and comprises at least four genera. In this first paper we transfer W. coronata to a new genus; Tovellia gen. nov., type species: Tovellia coronata (Wolosz.) comb. nov. Previous studies on ultrastructure and DNA sequencing referring to Woloszynskia coronata are based on W. coronata var. glabra, which is raised to species level as Tovellia glabra sp. nov. Other species included in the new genus are Tovellia apiculata (basionym Woloszynskia apiculata Stosch) and Tovellia stoschii (basionym Woloszynskia stoschii R. Shyam & Sarma). Two identical cultures presently identified as Woloszynskia limnetica Bursa (from University of Washington Culture Collection, Seattle) and W. pseudopalustris (J. Schiller) Kiselev [from Culture Collection of Algae at the University of Cologne, Cologne] differ from Tovellia in LSU rDNA sequences and in cyst type and are transferred to Jadwigia gen. nov., as J. applanata sp. nov. The most striking feature of Tovellia and Jadwigia is the anatomy of the eyespot, which is extraplastidial, and composed of nonmembrane bound lipid globules. This type of eyespot is also present in Katodinium campylops (T.M. Harris) A.R. Loebl. , a species undoubtedly related to Tovellia, and in ‘Glenodinium sp. ’ sensu Kreimer 1999, and together they form a distinct family, Tovelliaceae fam. nov.
Plant Nutrition Requirements for an Installed Sedum-Vegetated Green Roof Module System: Effects of Fertilizer Rate and Type on Plant Growth and Leachate Nutrient Content

The objectives of this study were to compare fertilizer rates and types to identify an optimum rate to maintain green roof vegetative coverage and encourage plant growth (i.e., plant performance) while minimizing the amount and concentration of nutrients leached from a green roof module system. Sedum-vegetated modules with no added fertilizer (control) were compared with modules fertilized with 5, 7.5, 10, 15, 20, 30, and 60 g·m L2 nitrogen (N) of 16N-2.6P-10K POLYON Homogenous NPK plus Minors, 5-6 month controlled-release fertilizer (CRF), 5 g·m L2 N of a 2.9N-2.2P-2.3K fly-larvae processed chicken manure fertilizer (5-Sus), or 5 g·m L2 N of 4N-4P-4K Gaia Green All Purpose organic fertilizer (5-OR). The total amount and concentration of aluminum (Al), calcium (Ca), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), potassium (K), magnesium (Mg), sodium (Na), NH4 + , nickel (Ni), NO3 - , phosphorus (P), lead (Pb), sulfur (S), and zinc (Zn) in leachate as well as plant overall appearance, winter injury, vegetative coverage, shoot height, bloom duration, and leaf color of green roof modules were evaluated between July 2011 and Aug. 2012. A CRF fertilizer rate of 15 g·m L2 N maximized vegetative coverage and overall plant appearance while maintaining leachate quality within Ontario and Canadian guidelines for most of the measured elements. The amount of Zn in the CRF appeared to be higher than plant demand and the high amount and concentration of P in leachate was likely the result of release from the growing substrate. The 5-Sus fertilizer resulted in increased coverage the first spring and increased greenness soon after application compared with the same rate of CRF. Overall, 15 g·m L2 N of CRF was the best treatment based on vegetative coverage and plant growth in sedum-vegetated green roof modules.
Sugars Containing Galactose Occur in Honey

SummaryAnalysis of 87 honey samples for terminal galactose residues in the oligosaccharide fraction ('bound galactose') by a specific enzymic procedure showed that all samples contained this entity. The average value for 81 honeys was 3·1 mg (as galactose) per 100 g honey. Beet sugar products averaged ten-fold higher. Raffinose is the only commonly-occurring sugar responding to the conditions of the analysis. Whether the raffinose is a nectar constituent or arises from traces of honeydew is not clear; it is possible that both contribute.
RNA-seq: primary cells, cell lines and heat stress

Transcriptome analysis by RNA-seq has emerged as a high-throughput, cost-effective means to evaluate the expression pattern of genes in organisms. Unlike other methods, such as microarrays or quantitative PCR, RNA-seq is a target free method that permits analysis of essentially any RNA that can be amplified from a cell or tissue. At its most basic, RNA-seq can determine individual gene expression levels by counting the number of times a particular transcript was found in the sequence data. Transcript levels can be compared across multiple samples to identify differentially expressed genes and infer differences in biological states between the samples. We have used this approach to examine gene expression patterns in chicken and human cells, with particular interest in determining response to heat stress.
BLACK-TAILED, GUNNISON'S, AND UTAH PRAIRIE DOGS REPRODUCE SLOWLY

Abstract Long-term research with marked individuals shows that black-tailed, Gunnison's, and Utah prairie dogs (Sciuridae: Cynomys ludovicianus, C. gunnisoni, and C. parvidens) all reproduce slowly, despite claims of ranchers and early naturalists. Five factors are responsible for the slow reproduction. First, survivorship in the 1st year is <60% for all 3 species, and it remains low in later years. Second, even under optimal conditions, females of all 3 species produce only 1 litter/year. Third, the percentage of males that copulate as yearlings is only 6%, 24%, and 49% for black-tailed, Gunnison's, and Utah prairie dogs, respectively. The percentage of females that copulate as yearlings is only 35% for black-tailed prairie dogs, but it is 100% for both Gunnison's and Utah prairie dogs. Fourth, the probability of weaning a litter each year is only 43%, 82%, and 67% for female black-tailed, Gunnison's, and Utah prairie dogs, respectively. Fifth, for those females that wean offspring, mean litter size at 1st juvenile emergence from the nursery burrow is 3.08, 3.77, and 3.88 for black-tailed, Gunnison's, and Utah prairie dogs, respectively.
Genetic expression of heterosis for fruit yield and yield components in intraspecific hybrids of okra (Abelmoschus esculentus (L.) Moench).

Heterosis breeding is a potential method to achieve improvement in production and productivity of okra that otherwise cannot be achieved through existing traditional methods. A study of heterosis in 28 okra hybrids developed through 8 × 8 half diallel mating fashion involving the inbred lines ‘P-20’, ‘9801’, ‘VRO-4’, ‘Parbhani Kranti’, ‘P-8’, ‘Hisar Unnat’, ‘Tulsi-I’ and ‘SKBS-11’ was carried out at the Vegetable Experimental Farm of CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India, during the summer-rainy season of 2012 and 2013 (May to September). Heterosis over standard check was observed for the quantitative traits viz., days to flowering, days to first picking, first fruit producing node, nodes per plant, internodal length (cm), fruit length (cm), average fruit weight (g), plant height (cm), harvest duration (days), fruits per plant and fruit yield per plant (g). Among the traits, fruits per plant and fruit yield per plant exhibited maximum heterosis over the standard check “Hybrid Tulsi”. Heterosis for yield was generally accompanied by heterosis of yield components. On the basis of heterosis and mean performance, “VRO-4 × Hisar Unnat” was the best cross-combination followed by “Tusli-I × SKBS-11”, “P-20 × Tusli-I”, “VRO-4 × Parbhani Kranti” and “P-8 × Tulsi-I” for fruit yield per plant. These crosses also had high heterosis for most of the component traits. These hybrids offer high scope for the exploitation of heterosis. These cross-combinations can also be released as hybrids after further field testing.
An antibacterial assay of aqueous extract of garlic against anaerobic/microaerophilic and aerobic bacteria

Both the minimum inhibitory and minimum bactericidal concentration (expressed in terms of thiosulphinate concentration) of an aqueous extract of garlic was determined against nine species of bacteria. Helicobacter pylori proved to be extremely sensitive to garlic extract, whilst Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Escherichia coli, Pseudomonas aeruginosa, Salmonella typhimurium and Staphylococcus aureus all were moderately sensitive to the garlic extract treatment. Leuconostoc mesenteroides was used as a known resistant control to the action of garlic extracts. Both S. aureus and a methicillin-resistant strain of S. aureus were found to be equally inhibited by garlic.
Enzymes for the feed industry: past, present and future

The commercial application of enzymes as a feed additive has a history of less than 20 years. During this period, the feed enzyme industry came into existence and it has gone through several phases of development. The first phase was the use of enzymes to enhance nutrient digestibility, focusing primarily on removing the anti-nutritive effects of non-starch polysaccharides (NSP), such as arabinoxylans and β-glucans, from broiler diets based on viscous grains like wheat, rye, barley or triticale. During the early 1990s, the scope of enzyme application expanded to consider nutrients other than NSP and benefits other than digestibility enhancement. Phytase is a prime example, where not only was it used to increase the utilisation of phytate P, but also to alleviate environmental burdens by reducing P excretion in the excreta. The industry then started to advocate enzyme addition to poultry diets based on non-viscous grains, such as sorghum and corn. Although such a use is not uncommon in some parts of the world, the industry is still in search for highly efficacious enzymes for non-viscous cereal grains. The next phase is the application of enzymes to non-cereal grain components of the diet. These vegetable protein sources are often high in NSP, which are poorly characterised in regard to their molecular structures. Significant progress has been made on characterisation of the NSP in soybean, but the industry has not been able to produce commercially viable products that consistently improve the digestibility of vegetable proteins. The enzyme industry today is constantly searching for new areas of application. Some recent data demonstrate the role of glycanases (charbohydrate degrading enzymes) as an alternative to in-feed antibiotics. It is possible to produce enzymes tailored for (a) the generation of specific low molecular weight carbohydrates in vivo, which, in turn, produce specific health outcomes in birds; (b) de-activation of anti-nutrients other than NSP and phytate, and (c) degrading of non-conventional feed resources to yield ME. The development of enzyme technology needs to go hand in hand with better characterisation of substrate structures, the gut microflora, and the immune system.
Semidwarf Growth Habit in Clingstone Peach with Desirable Tree and Fruit Qualities

A single seedling exhibiting a semidwarf growth habit was found in an open- pollinated clingstone peach (Prunus persica (L.) Batsch) population. The growth habit was upright and open, with short, spur-like lateral branching. Tree size was about half that of its siblings as a result of shorter internodes. The total number of nodes on first-order branches was not significantly different from that on standard-sized trees. The semidwarf growth habit remained stable after vegetative propagation. Segregation in sexual progeny showed the trait to be highly heritable. The average planting density for new cling- stone peach orchards has increased from ≈275 trees/ha in 1983 to ≈500 trees/ha in 1989
Agronomic response of maize to limited levels of water under furrow irrigation in southern Spain

The yield response to limited irrigation is a major concern where water resources are limited. The objective of the work was to know the agronomic response of 12 maize hybrids cultivars under full and limited irrigation levels. Full irrigation consisted in 5 to 7 furrow irrigations events (90 mm) applying a total depth of 450-630 mm. In the limited irrigation treatment, three irrigations (90 mm) were applied, beginning 2-3 weeks before silking and ending 3-5 weeks after it. Results indicated a mean yield loss of 17% due to limited irrigation. The main effect of limited irrigation was a reduction of the ears per plant and 1,000 kernel weight. Maize yield decreased as season length was reduced. The main effect of season length reduction was a reduction of kernels per ear. Limited or regulated deficit irrigation is one way of maximizing productivity of total applied water (PAW); thus, the limited irrigation treatment reached a higher PAW value (2.66 kg m -3 ) than full irrigation (1.90 kg m -3 ). In both irrigation levels, PAW was higher as the growth cycle increased. It can be concluded that, in the conditions of Southern Spain, reduced irrigation provided larger yields when applied to long cycle cultivars (FAO 700-800), with increased PAW values. Additional key words: crop yield, FAO cycles, productivity of applied water. Resumen
Diatom-based Weighted-averaging Transfer Functions for Great Lakes Coastal Water Quality: Relationships to Watershed Characteristics

ABSTRACT In an effort to develop indicators for Great Lakes near-shore conditions, diatom-based transfer functions to infer water quality variables were developed from 155 samples collected from coastal Great Lakes wetlands, embayments and high-energy shoreline sites. Over 2,000 diatom taxa were identified, and 352 taxa were sufficiently abundant to include in transfer function development. Multivariate data exploration revealed strong responses of the diatom assemblages to stressor variables, including total phosphorus (TP). Spatial variables such as lake, latitude and longitude also had notable relationships with assemblage characteristics. A diatom inference transfer function for TP provided a robust reconstructive relationship (r2 = 0.67; RMSE = 0.28 log(μg/L); r2jackknife = 0.55; RMSEP = 0.33 log (μg/L)) that improved following the removal of 13 samples that had poor observed-inferred TP relationships (r2 = 0.75; RMSE = 0.22 log(μg/L); r2jackknife = 0.65; RMSEP = 0.26 log (μg/L)). Diatom-based transfer functions for other water quality variables, such as total nitrogen, chloride, and chlorophyll α also performed well. Measured and diatom-inferred water quality data were regressed against watershed characteristics (including gradients of agriculture, atmospheric deposition, and industrial facilities) to determine the relative strength of measured and diatom-inferred data to identify watershed stressor influences. With the exception of pH, diatom-inferred water quality variables were better predicted by watershed characteristics than were measured water quality variables. Because diatom communities are subject to the prevailing water quality in the Great Lakes coastal environment, it appears they can better integrate water quality information than snapshot measurements. These results strongly support the use of diatoms in Great Lakes coastal monitoring programs.
Variation in mutualisms : the spatio temporal mosaic of a pollinator assemblage

Variation in time (annual and seasonal) and space (between- and within-population) is examined for the pollinator assemblage of Lavandula latifolia (Labiatae), an insect-pollinated, summerflowering, evergreen shrub of Mediterranean woodlands in southeastern Spain. Lauandula latiflia is pollinated there by nearly 85 species of comparatively long-tongued Hymenoptera, Diptera and Lepidoptera. The diversity, composition and abundance of pollinators varied markedly between years. Lepidopteran taxa prevailed numerically in one year, hymenopterans in four years, and both groups had similar abundance in the remaining year. The vast majority of pollinators exhibited significant annual differences in average abundance. Only 35.7% of taxa were recorded in all of the six study years. The pollinator assemblage had marked seasonal dynamics. Important changes in species richness, abundance and composition took place over the flowering season of L. latiflia (nearly 3 months). Only 21.7y0 of insect taxa occurred throughout the flowering season. Lavandula latiflia populations at different distances from water courses differed broadly in the abundance and composition of pollinators. Hymenopterans dominated numerically at the water-distant sites, whereas lepidopterans prevailed in populations growing in the vicinity of streams. Only 40.7% of taxa were recorded at all of the four study populations. Within the same plant population, horizontal distances of the order of 25 m resulted in significant changes in pollinator composition. Variations at the four scales considered combine to produce, from the viewpoint of L. latifolia, a spatio-temporal mosaic of pollinators. As these differ broadly in frequency of pollen transfer, size of pollen loads deposited, and between-flower flight distance patterns, spatio-temporal variation will predictably result in inconsistent or contradictory selective pressures on the plant, thus hindering specialization in relation to particular pollinators.
Forensic genetic evidence of beak and feather disease virus infection in a Powerful Owl, Ninox strenua

Abstract Beak and feather disease virus (BFDV), which causes psittacine beak and feather disease (PBFD), is known to infect a wide range of bird species, with all members of the Psittaciformes recognised as being susceptible. Across the world, genetically distinct circovirus species cause feather disease akin to PBFD in the Australian Raven (Corvus coronoides), as well as a wide range of columbids, anatids and lariids. Until recently, BFDV was thought to be restricted to Psittaciformes, with a rich viral genetic diversity present in parrots and their allies throughout Australia. The possibility of rare spill-over infection of BFDV into non-psittacine birds has the potential to reveal insights into the disease ecology of PBFD and the ontology of BFDV. In this paper we report evidence of BFDV infection in a Powerful Owl (Ninox strenua), which had feather lesions characteristic of PBFD. Analysis of the BFDV genome associated with the infection revealed lorikeets, which are known prey items of Powerful Owls, to be a likely source.
The a ntimicrobial activity of proteins/peptides against antibiotic-resistant and -susceptible bacteria

CHAPTER 1. GENERAL INTRODUCTION I Thesis Organization 2 References Cited 2 CHAPTER 2. LITERATURE REVIEW 3 Need for Antibiotic Substitutes 3 Animal Antimicrobial Peptides 3 Plant Antimicrobial Peptides 22 Mechanism of Action of Antimicrobial Peptides 25 Toxicity of Antimicrobial Peptides 27 Bacterial Resistance to Antimicrobial Peptides 27 References Cited 29 CHAPTER 3. EVALUATION OF THE ANTIMCIROBIAL ACTIVITY OF NATURAL ANIMAL PROTEINS/PEPTIDES DM VITRO 41 Abstract 4