Miracle-dz/UniFAR-FTUs huggingface dataset:
Della protein function during differential growth processes in arabidopsis

The plant hormones gibberellins (GAs) regulate multiple processes of plant development, such as seed germination, photomorphogenesis, vegetative growth, and flower and fruit development. Most of this regulation occurs at the transcriptional level, through the activity of the DELLAs, which are nuclear-localized proteins subjected to GA-mediated proteolitic degradation. DELLAs do not bind DNA directly, but they have been shown to interact with DNA-binding transcription factors to regulate their targets. Moreover, DELLAs mobilizes distinct set of genes to trigger different GAs responses. In Arabidopsis, DELLAs are encoded by five genes, and genetic studies show that each DELLA displays specific, but also partially overlapping roles with respect to their paralogs. In this Thesis, we have addressed two issues: (1) the contribution of DELLA multiplication to the diversification of functions controlled by GAs; and (2) the identification of direct targets regulated by DELLAs in etiolated seedlings with special attention to those involved in differential growth processes. Using combinations of mutants and transgenic lines expressing two phylogenetically distant DELLA genes (RGA and RGL2), we have found that these two DELLA proteins can perform each other’s role as long as they are expressed under the reciprocal promoters, indicating that DELLA subfunctionalization relies mainly on their differential expression patterns. In agreement with this, none of these DELLA proteins displayed significant differences in their ability to interact with several bHLH transcription factors, again suggesting that the function of each DELLA protein probably depends on the set of transcription factors to which they are exposed, and their mutual interactions. To identify direct DELLA targets, we have performed transcriptomic analyses of darkgrown seedlings expressing an inducible version of gai-1, a stable, dominant allele of a DELLA gene. This approach rendered a list of over 150 genes differentially expressed between 30 and 240 min after induction of gai-1. Further in silico analysis of this set of targets has confirmed the functional interaction between DELLAs and bHLH transcription factors, but has also allowed the identification of additional transcription factor families putatively involved in transcriptional regulation by DELLAs. The presence of several auxin-related genes among the primary targets of DELLA proteins has allowed us to establish a new role for GAs in the modulation of hypocotyl gravitropism through the repression of IAA19/MASSUGU2 expression by DELLAs. Our results also suggest that this regulatory module fine tunes the auxin-driven gravitropic response, providing flexibility under competing tropic stimuli. Moreover, the repression of HOOKLESS1 and the auxin efflux carriers PIN3 and PIN7 by DELLAs, is proposed as the molecular mechanism to explain the already known physiological regulation of apical hook development by GAs.
Methane production from insect, worm and mushroom waste streams and combinations

In literature, the synergistic effect of several substrates on feedstocks for anaerobic digestion/methane production is described for several substrates. Champost from mushroom production, vermicompost from worm composting/vermiculture and BSF (black soldier fly) larvae frass from insect production were therefore tested for this report for their synergistic effect. It was found that insect frass had a very high biogas/methane production as a single substrate. Addition of the frass led to a concentration dependent biogas production in mixtures with ‘old’ digestate higher than was expected based on the results of the single substrates. Champost resulted in some biogas production but from vermicompost hardly any biogas could be produced. Also, no synergistic or concentration effects could be noted from the latter two.
In vitro caecal gas production and dry matter degradability of some browse leaves in presence of enzymes from anaerobic bacterium in NZW rabbits.

This work was conducted to assess the nutritive val ue of four browse leaves ( Acacia saligna, Atriplex halimus, Lucena leucocephala, and Eucalyptus camaldulensis ) grown in the northern region of Egypt using the c eacum content obtained directly after slaughtering of 12 New Zealand White rabbits. ZADO , enzymic preparation containing cellulases, xylanases, α-amylase and proteases from an anaerobic bacterium (patent No. 22155 of Egypt) was added at 0, 2 or 5 mg/ml of buffered cae cal content. In vitro caecal gas production after 24 h of incubations (IVGP24) and dry matter degradability (IVDMD) were determi ned. Crude protein content of browse leaves ranged from 105 g/kg DM ( A. halimus) to 221 g/kg DM ( L. leucocephala ). The highest ether extract (68 g/kg) was in L. leucocephala , while this species had the lowest neutral deterge nt fibre (NDF), acid detergent fibre (ADF), and acid detergent lignin content. E. camaldulensis had the highest NDF, ADF and lignin. Total extractable phenolics (TEP), saponins (SAP) and alk aloids (ALK) contents were low in L. leucocephala and high in A. halimus and E. camaldulensis . The IVGP24, and IVDMD varied (P<0.001) among leaves, with the highest (P<0.001) value in A. halimus, intermediate in A. saligna and E. camaldulensis, and the lowest (P<0.001) in L. leucocephala. When comparing all leaves species, addition of ZA DO improved (P<0.05) caecal IVGP 24, and DMD in all leaves without a significant difference (P>0.05) between the two ZADO ® levels (2 or 5 mg ZADO/ml). ZADO increased the rate of gas production during the fi rst 6 h of incubations. Our results suggest a positive effect of ZADO addition on browse leaves degradation in rabbits. ZADO could have a positive influence on the caecal microbial activity and nutr ient digestion, as well as the degradation of secon dary compounds of the browse leaves.
Vleesminnaars, vleesminderaars en vleesmijders : duurzame eiwitconsumptie in een carnivore eetcultuur

Deze studie behandelt de verduurzaming van onze vleesconsumptie vanuit een consumentenperspectief. Naast een historische schets van de Nederlandse eiwitpolitiek wordt ingegegaan op de huidige 'carnivore' eetcultuur, de rol van prijs en de veranderbaarheid van consumenten. Betrokken stakeholders spreken zich uit over de vermarkting van duurzame eiwitalternatieven. Consumenten zelf komen ook aan het woord over wat vlees voor hen betekent. Tot slot wordt aangegeven welke marktstrategieen en veranderingsroutes kunnen bijdragen aan de eiwittransitie.
Cold-induced photoinhibition and foliar pigment dynamics of Eucalyptus nitens seedlings during establishment

The effects of cold-induced photoinhibition on chlorophyll and carotenoid dynamics and xanthophyll cycling in Eucalyptus nitens (Deane and Maiden) Maiden were assessed between planting and 32 weeks after planting. The seedlings were fertilised or nutrient-deprived (non-fertilised) before planting and shaded or not shaded after planting. The experimental site was 700 m a.s. l. , which is considered marginal for establishment of E. nitens plantations in Tasmania due to low mean annual minimum temperatures. Low temperature–high light conditions caused a reduction in variable to maximal chlorophyll fluorescence ratio (F v /F m ), which was more pronounced in non-fertilised than in fertilised seedlings. Shadecloth shelters alleviated this depression. Except in shaded fertilised seedlings, F v /F m did not recover to the level before planting until after 20 weeks. Total chlorophyll content was initially reduced in shaded treatments but subsequently increased with increasing temperatures and F v /F m. Total xanthophyll content and xanthophylls per unit chlorophyll remained relatively constant in fertilised seedlings but decreased in non-fertilised seedlings within 2 weeks after planting. Total xanthophyll and xanthophylls per unit chlorophyll subsequently recovered in non-shaded, non-fertilised seedlings with increasing temperatures and F v /F m. Diurnal [yield and non-photochemical quenching (NPQ) and seasonal (F v /F m) variation in chlorophyll fluorescence parameters were not reflected in xanthophyll cycling during the period of most severe photoinhibition. This result may indicate that chlorophyll–xanthophylls protein complexes form in winter-acclimated E. nitens foliage as have been demonstrated to occur in Eucalyptus pauciflora Sieb. ex Spreng. (Gilmore and Ball 2000, Proceedings of the National Academy of Sciences USA 97, 11098–11101).
Optimization of phenolic compounds recovery and in vitro antioxidant activity of Algerian eggplant (Solanum melongena L.)

The optimum conditions for extraction of total phenolic contents (TPC) and maintaining the highest antioxidant activity from eggplant were determined. Extraction experiments were carried out by investigating the effects of the solvent nature (acetone, ethanol, methanol, or water), solvent concentration (30-90%), extraction temperature (30-100°C), extraction time (30-120 min), solid to solvent ratio (1/25-1/100 g/mL), and number of extractions (1, 2 and 3) on the recovery of phenolic compounds and antioxidant activity of the extracts. The TPC was assessed to determine the polyphenolic component while free radical scavenging activity (FRSA) and ferric-reducing power (FRP) were used to evaluate the antioxidant activity of eggplant extracts. All extraction parameters had significant effects (p<0.05) on the TPC extraction and the antioxidant activities. The best conditions were obtained using three extraction steps with aqueous acetone 70% (v/v) at 25°C for 60 min and with 1 g/50 mL solid to solvent ratio. The optimum extraction conditions exhibit the TPC concentrations of 794.94 mg GAE/100 g and antioxidant activities of 737.86 mg TE/g (FRSA) and 28.00 mg TE/g (FRP). The free radical scavenging and ferric-reducing potentials were found to be positively significantly correlated with phenolic content under the influence of all extraction parameters.
Differentiation of Flk-1 positive multipotent adult germline stem cells into endothelial cells in vitro and in vivo

Multipotent adult germline stem cells (maGSCs) offer a novel route to cell-based therapy without immune rejection and ethical limitations. The present study showed the generation and expansion of fetal liver kinase-1-positive (Flk-1+) cardiovascular progenitor cells from maGSCs as well as the differentiation of these cells into functional endothelial cells (ECs) in vitro and in vivo. First, we established a culture system that allows maGSC-derived Flk-1+ cells differentiating into functional ECs. These differentiated maGSC-ECs showed a typical endothelial morphology and gene expression patterns. In addition, they continued to proliferate and exhibit angiogenic potential both in vitro and in vivo. Second, we established a culture condition, under which cardiovascular progenitor cells proliferated rapidly and were maintained for at least 15 passages with freeze-thaw cycles. Under this culture condition, approximately 70% of cells retained Flk-1 expression and did not spontaneously differentiate into cardiovascular lineages. They were clonogenic and exhibited angiogenic potential in vitro. Furthermore, they were able to differentiate into all three cardiovascular lineages when cultured on OP9 cells. This is the first study showing that cardiovascular progenitor cells can be expanded and maintained in vitro for long periods. However, the impurity, i.e. the continued existence of pluripotent stem cells, within cultures of both maGSC-ECs and long-term cultured Flk-1+ cardiovascular progenitor cells still limits their usefulness in clinical applications. Thus, future work in this area will have to focus on the purification of both cell types.
Biology and production of the red-band trout (Salmo sp.) in four southeastern Oregon streams

approved: 1ac1 _14_. ' ' Dr. John Mclntyfe The red-band trout is native to many small, isolated streams in southeastern Oregon. A study of the red-band population of Three-. mile Creek and Reservoir was conducted from August 1973 to June 1975. Data were collected concerning population size, age composition, growth, biomass, recruitment, fecundity, and habitat. During the spring of 1975 similar data were collected for red-band populations in Home, Rattlesnake, and Buck creeks. The average trout 2 biomass in Threemile Creekwas 24. 2 g/m and average production was 17. 2 g/m /yr. The production rate of 17. 2 g/m /yris among the highest reported for salmonids in small streams and is probably in part due to the stable environment afforded by the springs which feed Threemile Creek. Biomass in the other study streams ranged from 2. 4 to more than 6. 7 g/m2 and production ranged from 1. 2 to more than 4. 2 g/m2/yr, not including production of age Q-I fish. Trout biomass in Threemile Reservoir was 84 kg/ha in September 1974, and annual production was 80 kg/ha. The presence of the reservoir has increased the total production of the Threemile system by at least 12 times. Most female trout in the streams and reservoir matured at age III. Egg production in the Threemile system was considerably greater than in the other study streams. Spawners from the reservoir contributed nearly five times as many eggs to Threemile Creek as did the stream-dwelling females during the spring of 1974. The egg contribution of reservoir fish was probably greater than that required to perpetuate the observed trout densities in the stream. However, the resulting high density of fry may insure adequate contribution of young trout to the reservoir. Reservoir trout could serve as an egg source for rehabilitation of native trout in southeastern Oregon streams, where desirable. During spring more than 250 reservoir trout averaging 39. 8 cm in length migrated irto Threernile Creek to spawn, and provided excellent opportunity for anglers. Terminal reservoirs might be considered as management tools for trout populations in small streams, providing larger trout than the stream would normally produce. Such reservoirs could serve as multiple purpose water storage facilities for irrigation, stock watering, and trout production. The status of the trout populations studied was relatively good in stream sections that had not been disturbed by man' s activities. Biology and Production of the Red-band Trout (Salmo sp.) in Four Southeastern Oregon Streams
Antibiotic Treatment Drives the Diversification of the Human Gut Resistome

Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.
The Effects of Trehalose on the Bioluminescence and Pigmentation of the Phase I Variant of Photorhabdus luminescens

Photorhabdus luminescens is a Gram-negative, bioluminescent, pigment producing enteric bacterium, which is pathogenic to insects and has the capability to undergo phase variation. The phase I variant of P. luminescens exists as a mutualistic symbiont where it plays a critical role in the life-cycle of the soil-dwelling nematode, Heterorhabditis bacteriophora. Both the bacterium and the nematode receive their nutritional requirements from the bioconversion of the insect host which is rich in many macromolecules such as the disaccharide, trehalose. Trehalose is a non-reducing disaccharide of glucose that is formed by an α-1,1-glycosidic bond and is associated with the physiology of many bacteria, insects and nematodes. Trehalose has been shown to be the most abundant storage sugar found within insect hemolymph (1%-2%). The physicochemical properties of trehalose allow this carbohydrate to act as a stress protectant where it has been implicated with thermal stress, dehydration, and osmotic protection of many microorganisms. Due to these properties, trehalose may allow culture stability of the phase I variant in vitro and in vivo. Traits of the phase I variant that were studied in this work include bioluminescence and the production of the red anthroquinone-derived pigment. The carbohydrates that were utilized in this study were glucose and trehalose; where shake flask cultures of the phase I variant were cultured at room temperature for up to six days in carbohydrate supplemented basal media with increasing carbohydrate concentrations of 0.1%, 0.5% and 1.0% (v/v). Relative luminosity, pigmentation and pH were graphed as a function of time, carbohydrate used, and carbohydrate concentration. Data obtained from this study suggests that the supplementation of 1.0% trehalose, when culturing the phase I variant of P. luminescens, can maintain bioluminosity and pigmentation over extended periods of time (five days) as compared to basal media and basal media supplemented with 1.0% glucose.
The role of repeat training in participants undertaking take home naloxone interventions.

Introduction and Aims: Training of consumers is seen as a necessary component of take home naloxone (THN) interventions, with demonstrated improvements in consumer knowledge, attitudes and self-efficacy. However, we query whether re-training is necessary component for individuals renewing naloxone supplies who have previously completed a THN intervention. Design and Methods: A secondary analysis of the Overdose Response and Take Home Naloxone (ORTHN) project, comparing participant characteristics, and changes in knowledge, attitudes and self-efficacy regarding overdose and response, following a brief THN intervention in participants who had previously undertaken THN interventions, compared to those with no prior THN interventions. Data was analysed for those completing both baseline (pre-ORTHN intervention) and follow up (3-months later). Results: Ninety-four participants completed both research interviews, of whom 29 (31%) had previously completed a THN intervention. There were few differences in baseline demographics or overdose histories between the two groups. Knowledge regarding overdose response and naloxone use indicated high baseline levels in both groups. Those with no prior THN training had lower rates of self-efficacy at baseline, and significantly improved following the ORTHN intervention, whereas those with prior THN training had higher baseline levels of self-efficacy, which was maintained following the intervention. Discussion and Conclusions: Individuals who have previously undertaken a THN intervention may not require repeat training when renewing naloxone supplies, increasing the efficiency of THN interventions.
Lactation Performance and Nutrient Deposition in Pups of the Harp Seal, Phoca groenlandica, on Ice Floes off Southeast Labrador

Harp seals (Phoca groenlandica) give birth on pack ice and nurse their pups for about 13 d. We hypothesized that lactating females would transfer milk and energy to pups at a high rate to compensate for the brevity of lactation. To test this hypothesis, the milk intake of five pups was measured over a 6-8-d period after administration of deuterium oxide; the initial age of pups was estimated to range from 0 to 5 d postpartum. Body water content of 17 pups was also measured by isotope dilution, and body composition of 12 pups was determined by chemical analysis. The proximate composition of harp seal milk (n = 21) was also assayed. Harp seal pups contained little fat (3%) at birth, but 61% of the increase in body mass (average 2.3 kg/d) was fat, with the result that fat accounted for 47% of body mass at weaning. Body water estimated by isotope dilution was not significantly different from that measured directly (n = 9 paired samples); water composed 72% of lean body mass. From birth to weaning, milk lipid increased from 36% to 57%, and milk water declined from 51% to 32%. Pup milk intake averaged 3.7 kg/d. Mass gain of pups was highly correlated with both milk intake and energy intake (r² > 0.98 for both). On average, pups consumed about 75 MJ/d, which is equivalent to a maternal energy yield of 1.9 MJ/(kg0.75 · d). This rate of energy output is higher than that measured in most other phocids. Daily energy output is inversely related to lactation duration in phocids: a polynomial regression relating energy output to lactation duration explained 99% of the interspecific variation.
Transendothelial Migratory Pathways of Vδ1+TCRγδ+ and Vδ2+TCRγδ+ T Lymphocytes from Healthy Donors and Multiple Sclerosis Patients: Involvement of Phosphatidylinositol 3 Kinase and Calcium Calmodulin-Dependent Kinase II1

We have previously reported that the Vδ2+TCRγδ+ T lymphocyte subset, expressing the NK receptor protein 1a (NKRP1a; CD161), is expanded in patients with relapsing-remitting multiple sclerosis and uses this molecule to migrate through endothelium. In this work, we show that Vδ1+ and Vδ2+ γδ T lymphocytes use distinct signal transduction pathways to accomplish this function. Indeed, we have found that Vδ1+ cells lack NKRP1a and selectively express the platelet endothelial cell adhesion molecule 1 (PECAM1; CD31), which drives transendothelial migration of this cell subset, at variance with Vδ2+ T cells, which are PECAM1 negative and use NKRP1a for transmigration. Interestingly, when Vδ2+ T cells were pretreated with two specific inhibitors of the calcium calmodulin-dependent kinase II KN62 and KN93, but not with the inactive compound KN92, the number of migrating cells and the rate of transmigration were significantly decreased. In turn, the phosphatidylinositol 3 kinase blockers wortmannin and LY294002 exerted a dose-dependent inhibition of Vδ1+ cell migration. Finally, NKRP1a and PECAM1 engagement led to activation of different signal transduction pathways: indeed, oligomerization of NKRP1a on Vδ2+ T cells activates calcium calmodulin-dependent kinase II, while occupancy of PECAM1 on Vδ1+ cells triggers the phosphatidylinositol 3 kinase-dependent Akt/protein kinase Bα activation. These findings suggest that subsets of γδ T lymphocytes may migrate to the site of lesion in multiple sclerosis using two different signaling pathways to extravasate.