Miracle-dz/UniFAR-FTUs huggingface dataset:
SEXUAL AND SIZE-RELATED DIFFERENCES IN THE DIET OF THE SNAKE NATRIX MAURA FROM THE EBRO DELTA, SPAIN

The Ebro Delta is a wetland area partially covered by rice fields.The v iperine snake Natrix maura, is a common colubrid snake in this ecosystem. Males delayed feeding activity by one month, and foraged for a shorter time, compared to females. Diet consisted mainly of fish and frogs, although size-related and sexual d ifferences were found: immature snakes had a more d iverse diet than adults, and adult females ate more frogs than adult males. Males captured larger numbers of smaller fish than females. Like other water snakes, large viperine snakes avoid small prey. The b iomass ingested is higher in large females, providing supplementary resources for reproduction. These dietary d ifferences may be related to the ecological needs of each category of snakes and reflect the influence of the rice cycle on diet dynamics.
In vitro response of select regions of Azadirachta indica A. Juss (Meliaceae) as elucidated by biochemical and molecular variations

Micro-populations of neem from alkaline and neutral soils were grouped into high and low azadirachtin-A containing plants, respectively. The leaf explants from the seedlings of high azadirachtin-A containing seeds exhibited the best callus induction response on MS medium supplemented with NAA, whereas leaf explant of the seedlings from low azadirachtin-A seeds showed similar response on MS medium with Kn in addition to NAA. Calli from most of the explants showed root differentiation after 30 days, whereas the callus obtained from the leaf explants alone also redifferentiated into shoots. Callus biomass from leaf explants was increased by cold-treatment. Biochemical studies revealed detectable amounts of azadirachtin-A only in cotyledons of the seedlings from high azadirachtin-A containing seeds. Other secondary metabolites such as steroids and saponins were detected from calli of several explants from the seedlings of both high and low azadirachtin-A containing seeds. Genomic DNA amplification studies showed polymorphism not only between the two azadirachtin-A groups but also within that of DNA from the tender leaves, in vitro seedlings of high azadirachtin-A yielding seeds and calli of leaf explants.
HERITABILITY OF EGG PRODUCTION IN LAYING HENS UNDER CUMULATIVE, MULTITRAIT AND REPEATED MEASUREMENT ANIMAL MODELS

Six generations of three layer lines (13 770 recorded individuals of A22 line, 13 950 of A88, 9 351 of K66) were used to estimate genetic effects on egg production under cumulative, multitrait and repeatability models. Variance components were estimated by the AI-REML algorithm. The heritability of cumulative records ranged from 0.08 to 0.1. For the repeated measurements model the following genetic parameters were obtained: heritability 0.02–0.03, repeatability 0.04–0.38. The first two months of egg production were found to differ from the other periods: heritability was relatively high (h2 > 0.35) and low or negative correlations with the other periods were found. Heritability was low (h2 < 0.1) from the peak production until the end of recording and the consecutive periods were highly correlated. Further studies on monthly records are suggested.
Computational Methods for Prediction of Protein- Protein Interactions: PPI Prediction Methods

The key signaling pathways in cellular processes involve protein-protein interactions (PPIs). A perturbation in the balance of PPIs occurs in various pathophysiological processes. There are a large numbers of experimental methods for detection of PPIs. However, experimental PPI determination is time consuming, expensive, error prone and does not effectively cover transient interactions. Therefore, overlaying and integration of predictive methods with experimental results provides statistical robustness and biological significance to the PPI data. In this chapter, the authors describe PPIs in terms of types, importance, and biological consequences. This chapter also provides a comprehensive description on various computational approaches for PPI prediction. Prediction of PPI can be done through: 1) Genomic information based methods 2) Structure based methods 3) Network topology based methods: 4) Literature and data mining based methods 5) Machine learning methods. For ease of use and convenience, a summary of various databases and software for PPI prediction has been provided.
Solid‐Phase Synthesis of DNA and RNA 5′‐O‐Triphosphates Using cycloSal Chemistry

A chemical method for the synthesis of short strands of DNA and RNA 5′‐O‐triphosphates is described that makes use of the conventional coupling and oxidizing reagents that are readily available on standard DNA/RNA synthesizers. After automated solid‐phase synthesis of oligonucleotides and 5′‐O‐detritylation, a novel cycloSal‐phosphoramidite, 5‐chloro‐saligenyl‐N,N‐diisopropylphosphoramidite, was coupled to the 5′‐hydroxyl group and the product oxidized. The resulting support‐bonded 5′‐cycloSal‐oligonucleotide was reacted with pyrophosphate to yield 5′‐O‐triphosphorylated DNA/RNA oligonucleotides after cleavage from the support in high purity and excellent yields. The reaction sequence was adapted to be used completely on a standard automated oligonucleotide synthesizer. © 2016 by John Wiley & Sons, Inc.
Growth and carbon relations of mature Picea abies trees under 5 years of free‐air CO2 enrichment

Are mature forests carbon limited? To explore this question, we exposed ca. 110‐year‐old, 40‐m tall Picea abies trees to a 550‐ppm CO2 concentration in a mixed lowland forest in NW Switzerland. The site receives substantial soluble nitrogen (N) via atmospheric deposition, and thus, trees are unlikely N‐limited. We used a construction crane to operate the free‐air CO2 release system and for canopy access. Here, we summarize the major results for growth and carbon (C) fluxes. Tissue 13C signals confirmed the effectiveness of the CO2 enrichment system and permitted tracing the continuous flow of new C in trees. Tree responses were individually standardized by pre‐treatment signals. Over the five experimental years, needles retained their photosynthetic capacity and absorbed up to 37% more CO2 under elevated (E) compared to ambient (A) conditions. However, we did not detect an effect on stem radial growth, branch apical growth and needle litter production. Neither stem nor soil CO2 efflux was stimulated under elevated CO2. The rate at which fine roots filled soil ingrowth cores did not significantly differ between A‐ and E‐trees. Since trees showed no stomatal responses to elevated CO2, sap flow remained unresponsive, both in the long run as well as during short‐term CO2 on–off experiments. As a consequence, soil moisture remained unaffected. We trapped significantly more nitrate in the root sphere of E‐trees suggesting a CO2‐stimulated breakdown of soil organic matter, presumably induced by extra carbohydrate exudation (‘priming’). Synthesis. The lack of a single enhanced C sink to match the increased C uptake meant a missing C sink. Increased C transport to below‐ground sinks was indicated by C transfer to ectomycorrhiza and on to neighbouring trees and by increased C export to soil. We conclude that these tall Picea abies trees are not C limited at current CO2 concentrations and further atmospheric CO2 enrichment will have at most subtle effects on growth, despite enhanced N availability.
Evaluation of new lentiviral vector pseudotypes for gene transfer into hematopoietic cells

Lentiviral vectors and their ability to transfer gene into hematopoietic stem cells are currently evaluated for the cure of several single-gene diseases (eg : B-thalassemia, Adrenoleucodystrophy, SCID). Likewise, gene transfer into B and T lymphocytes is of major interest in gene therapy and immunotherapy. We engineered new lentiviral vectors pseudotyped by some chimeric (BaEV/TR) and mutant (BaEVRLess) glycoproteins from the baboon endogenous retrovirus. We demonstrated that these new vectors can transduce more efficiently resting and mild stimulated hematopoietic stem cells than obtained with lentivectors pseudotyped by the glycoprotein G from the vesicular stomatitis virus (VSV-G). It is the same with the recently developed lentiviral vectors pseudotyped by the H and F glycoprotein from measles virus (H/F-LVs). We also compared the ability of the H/F-LVs with the BaEV/TR and BaEVRLess lentiviral vector pseudotype to transfer genes into B and T lymphocytes and into the whole T lineage. From now on, we are able to propose adapted vectors for gene transfer at each stage of differentiation from CD34+ cells to thymocytes and mature T cells. This could allow us to propose some new clinical protocols in gene therapy with a co-transplantation of genetically modified stem cells and their differentiated T progenitors in order to reduce the aplasia stage induced by current transplantation protocols.
Aspergillose aviaire : développement d’un modèle d’aspergillose chez la dinde (Meleagris gallopavo) et évaluation de l’efficacité de l’énilconazole

Aspergillus fumigatus est un agent pathogene respiratoire majeur chez les oiseaux d’ornement comme de production. L’aspergillose qui peut etre responsable de mortalites importantes et de chutes de performances est difficile a traiter. Nous avons developpe un modele d’aspergillose aigue chez le dindonneau en inoculant differents lots d’oiseaux âges de moins d’une semaine via une aerosolisation intratracheale de doses croissantes de conidies (105 a 108/animal) en utilisant un MicroSprayer®. Le developpement de la masse fongique a ete evalue par qPCR, dosage du galactomannane (GM), culture fongique et evaluation histopathologique dans le but de comparer les resultats obtenus en fonction du nombre de conidies inoculees. Une mortalite significative a ete observee dans les 4 jours suivant l’inoculation uniquement pour l’inoculum le plus concentre. Les resultats des differents marqueurs du developpement du champignon (culture, qPCR et GM), sont tres bien correles avec la dose de l’inoculum administree. Les moyennes d’equivalents conidies/g de poumon obtenues par qPCR etaient 1,3 log10 plus importantes que les numerations obtenues par culture sur gelose. Ce nouveau modele incluant une combinaison inedite de biomarqueurs chez la dinde a ete utilise pour evaluer l’efficacite de l’enilconazole, seule molecule utilisee en elevage avicole pour lutter contre l’aspergillose
Characterization of Rhesus CMV as an in vivo model for cytomegalovirus inhibition of MHC I antigen presentation.

1 Chapter 1 Introduction I. Herpesviridae 2 II. Cytomegaloviruses 6 III. Rhesus cytomegalovirus 18 IV. Anti-viral immunity 23 V. Viral immune evasion 33 Chapter 2 RhCMV contains an additional inhibitor of MHC-I antigen presentation outside the US6-family of genes.
Properties of a lethal factor in stonefish Synanceia vorrucosa venom

Stonefish belonging to the genus Synanceia pos sess a pair of venom sacs in each dorsal, pelvic, or anal spine. Stings from the spines have caused severe poisoning and even a number of deaths in humans. Recently, the properties of le‚Pthal factors from S. horrida1) and S. trachynis2) have been ex tensively clarified. In this paper, we report some properties of a lethal factor in the venom of anoth er species, S. verrucosa. Specimens of S. verrucosa were captured on shal low reefs near Kuroshima Island, Okinawa Pre fecture, transported frozen to our laboratory, and stored at -20•Ž until used. Lethal activity was examined by intravenous injection of a test solution into ddY male mice; LD50 values were calculated according to the method of Litchfield and Wilcoxon.3) Hemolytic activity against rabbit erythrocytes was determined as reported previ ously;4) one hemolytic unit (HU) was defined as the amount of protein required to cause 50% hemo lysis. Capillary permeability-increasing activity was qualitatively assayed using Wistar male rats as described in a previous paper.5) Hyaluronidase activity was estimated by the method of Tolksdorf et al.6) and expressed in USP/NF units/mg. Protein was determined by the method of Lowry et al.7) Our previous study8) revealed that the S. verrucosa lethal factor is substantially insoluble in distilled water, but soluble in buffers with high ionic strength, and that it retains lethal activity even after it is precipitated in distilled water. These unique properties enabled us to purify the lethal factor as follows. About 0.1ml of the venom fluid was collected by a syringe from a pair of venom sacs in a dorsal spine and mixed well with 2ml of distilled water. The resulting suspension was re
Mutation of domain III and domain VI in L gene conserved domain of Nipah virus

Nipah virus (NiV) is the etiologic agent responsible for the respiratory illness and causes fatal encephalitis in human. NiV L protein subunit is thought to be responsible for the majority of enzymatic activities involved in viral transcription and replication. The L protein which is the viral RNA dependent RNA polymerase has high sequence homology among negative sense RNA viruses. In negative stranded RNA viruses, based on sequence alignment six conserved domain (domain I-IV) have been determined. Each domain is separated on variable regions that suggest the structure to consist concatenated functional domain. To directly address the roles of domains III and VI, site-directed mutations were constructed by the substitution of bases at sequences 2497, 2500, 5528 and 5532. Each mutated L gene can be used in future studies to test the ability for expression on in vitro translation.
Enterohaemorrhagic Escherichia coli colonisation of the human colonic epithelium and the innate immune response to infection

Enterohaemorrhagic Escherichia coli (EHEC) are of great public health importance, causing diarrhoea, haemorrhagic colitis and haemolytic uraemic syndrome. A wealth of evidence from cell line and animal studies has linked colonic pathogenesis with EHEC induction of mucosal attaching/effacing (A/E) lesions, which are characterised by intimate bacterial attachment to intestinal epithelial cells (IECs), microvillous effacement and actin polymerisation. However, the clinical relevance of A/E lesions has been called into question by the fact that adherent bacteria have not been located on colonic biopsies taken from EHEC-infected patients. In addition, in vitro organ culture (IVOC) of human intestinal biopsies with EHEC has not yielded signs of bacterial colonisation or A/E lesion formation. In this study, we have re-evaluated the colonic IVOC model and demonstrated for the first time that EHEC colonise the colonic epithelium ex vivo and induce A/E lesion formation. High levels of oxygen, as used in previous IVOC studies, were found to inhibit EHEC-IEC interactions. Adherence was dependent on expression of the bacterial adhesin intimin and the type III secretion system (T3SS). In contrast, EHEC adherence to the widely-used T84 colonic carcinoma cell line was associated with microvillous effacement but not actin polymerisation, and was not dependent on intimin or the T3SS, highlighting the importance of using physiologically relevant intestinal models when conducting EHEC research. EHEC pathogenesis has also been linked to induction of an inflammatory response in the colonic mucosa, characterised by recruitment of neutrophils to the epithelium. This process has been associated with expression of the neutrophil chemokine interleukin-8 (IL-8) by cultured IECs following exposure to EHEC flagellin. However, other aspects of the innate immune system, such as expression of antimicrobial peptides (AMPs), have been neglected. We have demonstrated that EHEC induces expression of the AMP human β-defensin-2 (hBD2) and IL-8 in human colonic IECs both in vitro and ex vivo. Induction was dependent on exposure of IECs to flagellin, and was mediated by mitogen activated protein kinase (MAPK) signalling. Furthermore, we present evidence that IL-8 is secreted apically in polarised T84 cells following apical stimulation, suggesting that this cytokine may be secreted into the lumen during infection. Put together, this PhD project has shed new light on EHEC-IEC interactions and has re-established the IVOC model as an important tool for future EHEC research.
Reaktionskinetische Untersuchungen der Hydratisierung von Acetylen zu Acetaldehyd an Molekularsieben, die mit katalytisch wirksamen Metall‐Ionen beladen sind

The kinetics of the catalytic hydration of acetylene to acetaldehyde in the gas-phase by incorporation of catalytic metal ions on molecular sieves has been studied in a differential reactor. The main product was acetaldehyde besides of small amounts of crotonaldehyde and acetic acid. The catalysts [cadmium(II)-, zinc(II)-, copper(II)- and silver(I)-13 X-molecular sieves] were deactivated at a rate proportional to the square of the hydration rate. The initial hydration rate calculated on the basis of this relation was first order in the acetylene concentration. Starting rate of hydration and rate of deactivation increase with increasing concentration of metal ions on the sieve. The temperature dependence of the rate follows the law of Arrhenius The activation energies of hydration and deactivation, respectively, were calculated. Pore diffusion is a limiting factor. The poison is homogeneously deposited on the catalyst and weakly adsorbed, as it is shown by the criterion of Wheeler. The rate of deactivation decreases with increasing water/acetylene ratio. The deactivation rate which is due to deposition of polymerised acetylene and/or acetaldehyde, is slow with zinc and cadmium catalysts, and more rapid with copper and silver catalysts.
Determinantes de la adopción de estándares en el subsector hortícola del Noroeste de México.

Vegetable production in the northwestern region of Mexico is an important economic activity; this is attributed to natural factors such as climate, soil quality, and proximity to the U.S. market. Clearly, the creation of competitive advantages gained by product differentiation, while maintaining quality, is extremely important and can be achieved through the application of standards. The adoption of standards is widespread; however, the role of institutions in these processes and their contribution to enhancing or inhibiting levels of implementation has not yet been quantified. The aim of this paper is to analyze the factors that most influence the execution of grades and standards in the horticultural industry in the northwest region of Mexico. Implementation levels were measured using a logit model that determined the effect of microenvironmental variables on them. The paper concludes that changes in production systems through the application of good agricultural practices and changes in organizations through training, monitoring, and support are what have helped companies that produce vegetables adopt and implement more standards.
Effect of two microbial phytases on the performance and nutrient retention on grower-finisher pigs fed barley-maize-soyabean meal-based diets

Two experiments were conducted to investigate the effects of the inclusion of Aspergillus oryzae (A. oryzae) and Peniophora lycii (P. lycii) phytase enzymes on nutrient retention, growth performance, carcass characteristics and bone parameters when offered to grower-finisher pigs (36 to 95 kg live weight). The experiment was a completely randomised design and the pigs were offered, individually, barley-maize-soyabean meal-based diets containing: adequate P and Ca (T1) (2.3 g available P/kg and 7.4 g Ca/kg), low P (T2) (1.3 g available P/kg and 5.3 g Ca/kg), low P + 500 units A. oryzae phytase/kg (T3), low P + 500 units P. lycii phytase/kg (T4), low P + 750 units P. lycii phytase/kg (T5) and low P + 1000 units P. lycii phytase / kg (T6). The pigs offered the low-P diet had a lower faecal-P excretion (P < 0.01) and P digestibility (P < 0.001) than the pigs offered the adequate-P diet. The inclusion of A. oryzae phytase in the low-P diet resulted in increases in the digestibility of ash (P < 0.05), P (P < 0.001) and Ca (P < 0.05). Supplementation of the low-P diet with P. lycii phytase resulted in a linear increase in the digestibility of N (P < 0.01), gross energy (P < 0.001), P (P < 0.001), Ca (P < 0.05) and Zn (P < 0.05). Feeding the unsupplemented low-P diet resulted in a decrease in daily gain (P < 0.01), feed intake (P < 0.05) and food conversion ratio (FCR) (P < 0.05) during the finisher period (60 to 95 kg) compared to the adequate-P diet. Supplementing the low-P diet with A. oryzae phytase increased daily gain (P < 0.001) and intake (P < 0.001) compared to the low-P diet. There was a quadratic response in feed intake (P < 0.01) and daily gain (P < 0.05) to increases in the P. lycii phytase concentration in the diet with no benefit from phytase inclusion above 500 units/kg. There was a linear improvement in carcass FCR (P < 0.05) and a linear increase in bone ash (P < 0.05), bone P (P < 0.01) and bone Ca (P < 0.01) and a linear decrease in lean yield (P < 0.05) in response to increased concentration of P. lycii phytase in the diet.
Genetically-based resistance of balsam fir (Pinaceae) to damage from the balsam twig aphid (Hemiptera: Aphididae)

Abstract We evaluated the effect of tree genotype on the resistance of balsam fir, Abies balsamea (Linnaeus) Miller (Pinaceae), to damage from the balsam twig aphid, Mindarus abietinus Koch (Hemiptera: Aphididae), by visually assessing aphid damage in clonal seed orchards located in New Brunswick and Nova Scotia, Canada, during four consecutive years. Estimates of clone mean heritability were moderate, suggesting that heritability of resistance is influenced by genetic factors. In New Brunswick, positive phenotypic and genetic correlations of clone-mean damage among years indicate that clones rank similarly each year. Our results suggest that selectively breeding for increased resistance could result in genetic gains.
Analysis of Seagrass Recovery in Experimental Excavations and Propeller Scar Disturbances in the Florida Keys National Marine Sanctuary

We investigated recovery of seagrasses in two types of mechanical sediment disturbances associated with motor vessel injuries: (1) artificial excavations where we removed all seagrasses in three size categories, 0.25 m2, 1.0 m2, and 2.25 m2; and (2) propeller scars of known age. We simulated mechanical sediment disturbance in the three excavation sizes in Thalassia testudinum, Syringodium filiforme, and Halodule wrightii meadows growing on soft, carbonate mud banks in the Florida Keys National Marine Sanctuary. After 700 days, results confirmed the long-standing paradigm that H. wrightii and S. filiforme recover significantly faster than T. testudinum. Results from the experimental excavations in monotypic seagrass meadows indicate that there were no significant differences in recovery rates between size categories for each of the species. In monotypic T testudinum, H. wrightii, and S. filiforme excavations, recovery was predicted to be 1.9, 1.5 and 10.5 years, respectively. Adjusted for a typical scar width of 0.45 m, recovery in propeller scars is estimated to be 9.5 years for T. testudinum, 1.7 years for H. wrightii, and 1.4 years for S. filiforme. In mixed species seagrass communities the subdominant, but pioneering and opportunistic species, H. wrightii or S. filiforme, sometimes colonized the artifical gaps as fast or faster than T testudinum, suggesting that physical disturbance from motor vessels can alter the relative abundance of seagrass species on a bank. For the 15 existing propeller scar injuries, the rate of recovery predicted for T. testudinum was faster than in the excavations, 6.9 years versus 9.5 years. These results suggest that injury recovery models and restoration strategies for vessel injuries should consider species composition of the injured site as well as the physical dimensions of the injury, including the excavation depth.