Miracle-dz/UniFAR-FTUs huggingface dataset:
Scale-dependent effects of density and habitat on foal survival

Identifying the most appropriate scale to study factors influencing life history is important to evolutionary ecology and wildlife management. For example, the scale at which density is assessed and explains variation in survival can affect how biologists observe and interpret population dynamics, which can influence plans for managing populations. Feral horses (Equus ferus caballus) contrast with most ungulates by exhibiting a mating system characterized by female-defense polygyny with persistent, non-territorial breeding groups (bands) and female-biased initial (natal) and subsequent (breeding) dispersal. We predicted that for horses, offspring movements coupled with female-biased breeding dispersal would increase the scale at which density best related to juvenile survival compared to species with greater female philopatry. From 2008 to 2013, we censused the population of feral horses on Sable Island, Canada. We annually computed individual-specific local densities for 442 foals (horses/km2 in radii of 2,000 m, 4,000 m, and 8,000 m fixed to a band’s centroid of movements) and whole-island (total) population density, group (band) size, and local access to surface freshwater, which affected movement patterns and selection of vegetation by females. The population of feral horses increased from 380 in 2008 to 559 in 2013. Overwinter survival of foals averaged 82.8%. Island-wide density was the most important predictor of foal mortality and was negatively associated with survival, with a lesser negative effect from local density. Increased access to surface freshwater (ponds) was an important predictor of foal survival but only at certain scales. Our study emphasizes the relevance of a multi-scale approach when analyzing the response of fitness components to changes in habitat and population processes, which may be influenced by the particular social organization of the species.
Isolation and characterisation of antioxidant components from oregano (Origanum heracleoticum)

Summary In this study, Origanum heracleoticum was examined as potential source of phenolic antioxidants. The components of the plant were extracted in a Soxhlet apparatus sequentially with solvents of increasing polarity, specifically with petroleum ether (P), diethyl ether (D) and ethanol (E); the ethanol extract was further fractionated to obtain a diethyl ether (ED) and an ethyl acetate (EEAc) fraction. The activity of the extracts to scavenge 2′2′-diphenyl-1-picrylhydrazyl followed the order ED > E> D > EEAc >> P. Moreover, the antioxidant activity in refined cottonseed oil at a concentration of 500 ppm was monitored through peroxide value measurements and revealed that ED resulted in the highest decrease in the rate of peroxide formation followed by D. Specific flavonoids and rosmarinic acid were detected as the main components of D, ED through HPLC–DAD and HPLC–MS/MS analyses.
Plant form, developmental plasticity, and survival following burial by volcanic tephra

The morphological responses of 28 shrub and 109 herbaceous species buried by 5–20 cm of tephra (volcanic aerial ejecta) from Mount St. Helens were examined after 1 year of burial. All shrub species produced adventitious roots in the tephra but the extent of roots varied greatly; three shrub species produced extensive rhizomes in the tephra. Most herbaceous species moved perennating buds into the tephra. Upward movement was accomplished in many ways, including upward growth of normally long rhizomes, accelerated elongation of normally short rhizomes, and development of perennating buds on aerial shoots that penetrated the tephra. Nineteen herbaceous species failed to move their perennating buds into the tephra; many of these are forest-dwelling members of the Liliaceae. Herbaceous plants representing a wide range of morphological types successfully penetrated tephra deeper than 12 cm; other species representing the same morphological types failed to penetrate deep deposits. A range of plasticity in several.
Bacterial community in the roots and rhizosphere of Hypericum silenoides Juss. 1804

Hypericum silenoides Juss. 1804 is an important medicinal plant used in Mexico, but the bacterial community associated with it is unknown. The bacterial communities in the rhizosphere and roots of H. silenoides were isolated and identified by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and ribosomal types were determined by amplified ribosomal rDNA restriction analysis (ARDRA) and 16S rRNA gene sequences. Sixty-six strains were obtained from roots of H. silenoides and 37 were isolated from the rhizosphere. ERIC fingerprinting distinguished 63 genetic patterns with 44 being unique and the remaining 19 containing 59 strains. Eighteen representative strains were distinguished with ARDRA analysis. 16S rRNA gene sequence analysis revealed that the bacteria isolated from the roots and rhizosphere of H. silenoides belonged to the genera Acinetobacter, Enterobacter, Pseudomonas, Sphingobium, Stenotrophomonas, Agrobacterium, Pantoea and Serratia. The largest number of isolates (30) belonged to the genus Agrobacterium. Richness and diversity of bacteria was higher on the roots than in the rhizosphere of H. silenoides.
In silico Structural Prediction of E6 and E7 Proteins of Human Papillomavirus Strains by Comparative Modeling

More than 200 different types of Human papillomavirus (HPV) are identified, 40 transmit extensively through sexual contacts affecting the genital tract. HPV strains have been etiologically linked to vaginal, vulvar, penile, anal, oral and cervical cancer (99.7%) as a result of mutations leading to cell transformations due to interference of E6 and E7 oncoproteins with p53 and pRB tumor suppressor genes respectively, besides other cellular proteins. As structures of E6 and E7 proteins are not available, the simultaneous structural analysis of E6 and E7 proteins of 50 different HPV strains was carried out in detail for prediction and validation, using bioinformatics tools. E6 and E7 proteins sequences were retrieved in FASTA format from NCBI and their structures predicted by comparative modeling using modeller9v6 software. Further, most of the HPV strains showed good stereochemistry results in most favored regions when subjected to PROCHECK analysis and subsequently each protein was validated using ProSA-web tool. The work carried out on comparing and exploring the structural variations in these oncogenic proteins might help in genome based drugs and vaccines designing, beyond their limitations.
Model selection and multimodel inference for standardizing catch rates of bycatch species: a case study of oceanic whitetip shark in the Hawaii-based longline fishery

One key issue for standardizing catch per unit effort (CPUE) of bycatch species is how to model observations of zero catch per fishing operation. Typically, the fraction of zero catches is high, and catch counts may be overdispersed. In this study, we develop a model selection and multimodel inference approach to standardize CPUE in a case study of oceanic whitetip shark (Carcharhinus longimanus) bycatch in the Hawaii-based pelagic longline fishery. Alternative hypotheses for shark catch per longline set were characterized by the variance to mean ratio of the count distribution. Zero-inflated and non-inflated Poisson, negative binomial, and delta-gamma models were fit to fishery observer data using stepwise variable selection. Alternative hypotheses were compared using multimodel inference. Results from the best-fitting zero-inflated negative binomial model showed that standardized CPUE of oceanic whitetip sharks decreased by about 90% during 1995–2010 because of increased zero catch sets and decreased CP.
Interactions between Plants and Epiphytic Bacteria Regarding Their Auxin Metabolism

Proofs of different kind are presented of the existence of highly active bacteria producing IAA from tryptophan on plant surfaces and in plant homogenates. Both homogenates and washing solutions of nonsterile pea plant parts are active in producing IAA from tryptophan. Activity is much enhanced by the addition of glucose or by preincubating the preparations; it is abolished by sterile filtration, by some bactericidic and bacteriostatic substances, by chloramphenicol, streptomycin, and albucid (penicillin being only partly effective). Preparations of sterile plants do not produce IAA from tryptophan within the detection limit of the Salkowski test. The bacteria are even present on seed surfaces, in the air, and in aceton or ammonium sulfate precipitations of homogenates. Main products of the bacterial tryptophan conversion, as demonstrated by paper chromatography, are indolepyruvic acid, indoleacetic acid, indolecarboxaldehyde, and indolecarboxylic acid. In presence of glucose indolepyruvic acid is by far dominating. Many hitherto known results about tryptophan conversion to IAA by higher plants are likely to be falsified by epiphytic bacteria.
The influence of maternal diet on offspring development and liver metabolism

Altering maternal nutrition affects fetal development and can have long-lasting effects on the offspring, potentially predisposing them to later metabolic disease. These effects can occur without affecting birth weight, although small for date offspring appear to be at increased risk. One mechanism linking changes in the maternal environment to an increased risk of later disease is enhanced exposure to glucocorticoids (GC). Tissue sensitivity to cortisol is regulated, in part, by the GC receptor (GR) and 11-beta-hydroxysteroid dehydrogenase (11βHSD) types 1 and 2. Several studies have shown the effects of maternal nutrient restriction on the programming of GC action in the offspring, however, dietary excess is far more characteristic of the diets consumed by contemporary pregnant women. The aim of this thesis was to provide a novel insight into the effects of moderate changes in the macronutrient ratio, within the maternal diet fed to pigs (whilst maintaining energy content), on offspring growth, development and liver metabolism until adolescence. Fat supplementation (Fat supplemented (FS): 9 %; Control (C): 2.5 %) from day 0 until 110 of gestation, reduced maternal glucose tolerance at term and decreased the survival rate of piglets after birth, possibly due to hypoglycaemia. In addition, supplementing the maternal diet with protein (Protein supplemented (PS): 16.3 %; C: 12.3 %) also increased the incidence of postnatal mortality, with surviving offspring demonstrating an up-regulation of mRNA transcripts involved in GC sensitivity i.e. GC receptor and 11βHSD-1, in the liver. Furthermore, this thesis demonstrated no negative effects of accelerated postnatal growth on low-birth weight piglets as others have suggested. In conclusion, this thesis has demonstrated a detrimental effect of fat and protein supplementation until day 110 of gestation on postnatal mortality. These findings could have profound consequences for the pig industry where reducing piglet mortality is of economic importance. In addition, an increased level of protein in the diet during gestation increases GC sensitivity in the offspring which may be indicative of excess GC exposure in utero. These types of adaptations could have significant implications in determining the programming effects of maternal diet on adult disease risk.
A new procedure for extraction and measurement of soluble sugars in ligneous plants

An original modification of an analytical procedure has been developed to obtain purified extracts for sugar measurement in different parts of ligneous plants by high-performance liquid chromatography. Extraction was performed at 4°C in the presence of water, methanol and chloroform. Only a representative part of the alcohol extract (methanol/water) was purified for analysis. An internal marker such as maltotriose, added during extraction, makes it possible to estimate possible sugar loss and to correct concentrations. Compared with a more standard method based on total soluble sugar extraction, this new method is more precise. The use of internal calibration standards shows good linear progression but does not guarantee good accuracy in the absence of a reference method or plant powder standard. It is a robust procedure which can tolerate experimental variations without affecting the results. The high recovery rate (90%) of maltotriose proves the quality of the procedure and makes it possible to correct sugar concentrations to acceptable limits. Une modification de procedure analytique est developpee dans cette etude pour obtenir des extraits purifies pour l'analyse des sucres dans differentes parties de plantes ligneuses par chromatographie HPLC. L'extraction est realise a 4°C en presence d'eau, de methanol et de chloroforme. Seule une partie de l'extrait alcoolique (methanol/eau) est purifiee pour l'analyse. Un marqueur interne comme le maltotriose, ajoute pendant l'extraction, permet d'evaluer la perte en sucre et de corriger les concentrations.
NADP+‐malate dehydrogenase in C3‐plants: Regulation and role of a light‐activated enzyme

The thioredoxin-dependent light/dark modulation system of the chloroplast is described as a prerequisite enabling the flexible control of fluxes through the various parts of the CO2-fixation pathway. Both the rapid turnover of the reduced thiol-containing form of the respective target enzyme, and the metabolite effect upon the reductive enzyme modulation, allow rapid adjustment of the amount of active species to the actual requirements. The structural basis of the regulation of chloroplast NADP+-malate dehydrogenase (EC 1.1.1.82) is described in more detail. The modulable plastid enzyme is characterized by two sequence extensions not present in any other known NADP+- and/or NAD+-specific malate dehydrogenase. The NADP+-malate dehydrogenase of C3-plants is part of the “malate valve”, which catalyzes the export of reducing equivalents in the form of malate from the chloroplast only when the NADPH to NADP+ ratio is high, thus poising the NADPH to ATP ratio required for optimal carbon reduction in the light. The mode of regulation of other light/dark modulated enzymes is discussed.
Systematics of two deep‐water species from the Indo‐West Pacific: Struvea gardineri A.Gepp & E.Gepp and Phyllodictyon orientale (A.Gepp & E.Gepp) Kraft & M.J.Wynne (Siphonocladales, Chlorophyta)

Two rare and ill-known subtidal species of stalked, net-forming green algae, Struvea gardineri A.Gepp & E.Gepp and Phyllodictyon orientale (A.Gepp & E.Gepp) Kraft & M.J.Wynne, are re-described on the basis of the examination of type material and recent collections from the Maldives, Seychelles, and Socotra Island in the tropical Indian Ocean. The taxonomic position of both species is re-appraised on the basis of morphological data (cell division, branching pattern, tenacular cells, crystalline cell inclusions, cell shape, and cell dimensions) and molecular phylogenetic evidence (partial large subunit nuclear ribosomal DNA sequences). On the basis of the occurrence of segregative cell division in young plants of S. gardineri, this species is returned to its original genus, Struvea. Cell division in P. orientale takes place exclusively by centripetal wall ingrowths, confirming its placement in the genus Phyllodictyon as currently defined. However, morphological observations and molecular phylogenetic studies indicate that the delineation of genera on the basis of modes of cell division is problematic, and that the genera Struvea and Phyllodictyon, as presently conceived, almost certainly do not represent natural groups. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 153, 115–132.
Genetic assessment for growth performance in diallel crosses of wild and cultured giant freshwater prawn, Macrobrachium rosenbergii

ABSTRACT We evaluated the growth performance of wild and cultured (four generations) strains of giant freshwater prawn (GFP) in 2 x 2 diallel crosses. From the four cross combinations, juveniles were produced using single pair mating. A total of 3,840 prawns (1,528 males and 2,312 females) were harvested after 15 weeks of grow-out in hapas. Additive genetic estimates of the crosses showed that wild stock had higher length (TL) and weight (BW) (12.17% and 22.33%), while the cultured stock had lower length and weight (−18.26% and −22.98%). Heterosis in the crossbred stock increased (TL:0.84 and BW:6.70%) with reduced carapace length (CL:1.34%) along with more than 5% increased additive genetic effect on body weight when compared with that of both purebred stocks. Genetic diversity data obtained for the wild, cultured, and crossbred stock using five microsatellite loci showed increased heterozygosity with decreased inbreeding in the crossbred stocks when compared with the cultured stock.
Growth, rumen development and meat quality in lambs of Blackhead Pleven breed, weaned at 25 and 70 days of age -

The objective of this study was to compare the growth rate, rumen development and some quality parameters of carcass and meat in lambs weaned at 25 and 70 days of age. The average live weight gain during experimental period was 268 g per day for suckling lambs and 233 g per day for lambs on dry feed. The difference of 13.1% in daily gain was not significant at P 0.05), compared to those weaned at 70 days of age. Therefore it is possible to obtain approximately the same growth in live weight and carcass in lambs weaned at 25 and 70 days of age. The lambs weaned at 25 kg live weight had higher weight of internal organs than the lambs weaned at 70 days, but the difference was significant (P<0.05) only for lung liver, small intestine, thick intestine and rumen. The length and thickness of rumen papillae were higher in lambs weaned at 25 days of age compared to the lambs weaned at 70 days of age (P<0.05). Significantly thicker was the rumen wall in the lambs weaned at 25 days of age compared to the weaned at 70 days (P<0.05).
Effect of age, body condition, pregnancy and lactation on circulating leptin concentrations in beef cattle

A series of experiments were conducted to evaluate the potential role of leptin in bovine reproduction. In Experiment 1, mean circulating leptin concentrations of postpartum cows were not affected by exogenous dexamethasone treatments. In Experiment 2, mean leptin concentrations were not correlated with female age or body weight but were positively correlated with body condition scores of beef cattle. Leptin concentrations were higher in 1 year old heifers (8.9 ng/ml) compared with 2 year old cows (6.0 ng/ml), but heifer leptin concentrations were not different than 4 to 6 year old cows (8.0 ng/ml) and cows ≥7 years of age (10.5 ng/ml). Mean leptin concentrations were negatively correlated with age in heifers and cows ≤2 years of age and positively correlated with age in cows >3 years of age. In Experiment 3, there were no differences in mean leptin concentrations for 56 days starting 14 days following AI among 2-year old and 3-year old cows pregnant to AI (1.2 ng/ml), the clean-up bulls (1.2 ng/ml) and nonpregnant females (2.2 ng/ml) after a 60-day breeding season. Plasma leptin concentrations were lower for lactating cows (1.0 ng/ml) compared with nonlactating cows (2.1 ng/ml). Female age did not affect circulating leptin concentrations. In Experiment 4, oviduct and uterine epithelial cells from mid-luteal phase females stained positive for the long form of the leptin receptor, and uterine biopsies revealed intense staining for the long form of the leptin receptor on the luminal side of the uterine endometrium. Bovine blastocysts stained positive for the long form of the leptin receptor in the trophoblast cells. In Experiment 5, addition of leptin to culture medium at 0, 100 and 1,000 ng/ml did not affect the percentage embryos developing to the blastocyst stage. Also, leptin did not affect the ratio of blastocysts:8- to 16-cell embryos among the 0 ng/ml treatment group, the 100 ng/ml treatment and the 1,000 ng/ml treatment groups. Results indicate that in the beef cow, the release of leptin and subsequent role(s) of leptin in reproductive processes are likely different than those that have been reported for mice, rats and humans.
EFFECT OF CULTURAL CONDITIONS ON ETHANOL PRODUCTION BY LOCALLY ISOLATED SACCHAROMYCES CEREVISIAE BIO-07

The present study describes the ethanol fermentation from sugarcane molasses by locally isolated yeast strain. Ten yeast strains were isolated from soil and cultured in 15% molassess medium. Saccharomyces cerevisiae Bio-07 gave maximum productivity (52.0g/L). Fermentation conditions were optimized for maximum production of ethanol. Maximum yield of ethanol (76.8 g/L) was obtained with 15% molasses concentration, 3% inoculum size, pH 4.5 and temperature 30 o C. Potassium Ferrocyanide (150ppm) was used to control the trace metals present in the molasses medium.
Effects on performance and behaviour of mixing 20-kg pigs fed individually

The effects of mixing on agonistic behaviour and performance were studied in 90 individually fed pigs, grouped at a mean live weight of 23 kg by one of the following three methods: (1) six unmixed littermates; (2) three pigs from each of two litters; and (3) one pig from each of six litters. Unmixed animals (treatment 1) did not fight and the mode of fighting differed between treatment 2 and 3. Mixing decreased daily weight gain in the period 23 to 100 kg for barrows, but not for gilts. For gilts, food conversion efficiency was negatively correlated with the number of received attacks in the observation period (80 min after mixing), and for the barrows to fighting injury scores.
Growth and Reproductive Phenology of Welwitschia Mirabilis Hook. F.

Reproductive phenology, reproductive traits and the pre emergent reproductive success (PERS) of Welwitschia mirabilis were studied in plants growing in the Botanical Garden of Portici. The leaves grow throughout the year and growth is positively correlated to temperature and day length; at flowering, the growth rate slows down. The plants have a reproductive cycle lasting 9-10 months; male plants form more branches and strobili than females, female strobili are larger than male ones. Both male and female plants produce cones that differ in the color of the covering bracts. Plants produce a lot of seeds, but most of them are empty; therefore the seed/ovule ratio is low. Filled and empty seeds are morphologically similar; filled seeds have high vitality that is maintained for several years. As probable causes of the low seed/ovule ratio, both pollination and embryo abortion are taken into account; our observations lead us to believe that the embryo abortion hypothesis is more accurate. However, since each plant may produce a discrete number of cones and filled seeds are highly viable, ultimately Welwitschia appears to be a rather efficient plant in terms of pre emergent repro- ductive success.