Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactomics identifies novel regulators of the IRF-1 tumour suppressor protein

The highly unstructured interferon regulated transcription factor IRF-1 is a tumour suppressor protein that plays vital roles in the antiviral and DNA damage response pathways. To identify interacting factors that regulate IRF-1 function and expand on the available limited information on its interactome, an in vitro screen was developed using peptide-aptamer affinity chromatography coupled with mass spectrometry. Discrete interaction interfaces within the highly disordered Mf2 domain of IRF-1 were identified which bind to a number of potential transcriptional regulators including NPM1, YB-1 and TRIM28. The screen also proved useful in identifying binding proteins to the C-terminal Mf1 domain, which is vital for IRF-1-mediated growth suppression and Cdk2 repression, and additionally regulates IRF-1 stability. Thus, an LXXLL motif in the Mf1 domain was found to be required for the binding of Hsp70 family members and cooperation with Hsp90 to regulate IRF-1 turnover and activity. These conclusions were supported by the finding that Hsp90 inhibitors suppressed IRF-1-dependent transcription shortly after treatment, whilst at later time points inhibition of Hsp90 led to an Hsp70-dependent depletion of nuclear IRF-1. Conversely, the half-life of IRF-1 was increased by Hsp90 in an ATPase-dependent manner leading to the accumulation of nuclear, but not cytoplasmic, IRF-1. Additionally, a stress specific interaction between IRF-1 and the Hsp70-associated ubiquitin E3 ligase CHIP, that targets Hsp70/Hsp90 clients for proteasomal degradation, was demonstrated. Consequently, decreases in IRF-1 protein levels in cells exposed to heat stress or heavy metal ions were accompanied by the formation of IRF-1:CHIP complexes. Based on observations that CHIP ubiquitination of IRF-1 occurred both in the presence and absence of Hsp70, a model was proposed wherein Hsp70 serves as a factor that recruits CHIP to its substrates and its dissociation from the complex allosterically activates CHIP-dependent substrate ubiquitination. In support of this model, in vitro and biophysical evidence is presented, showing that CHIP in complex with Hsp70 is less flexible and less effective as an E3 ligase than CHIP alone. Thus, in agreement with recent studies, the work done in this thesis highlights the importance of conformational flexibility and of direct binding or ‘docking’ of CHIP to its substrate(s) in its mechanism of action.
Do Eucalyptus plantations host an insect community similar to remnant Eucalyptus forest

We examined the potential of forest plantations to support communities of forest-using insects when planted into an area with greatly reduced native forest cover. We surveyed the insect fauna of Eucalyptus globulus (Myrtaceae) plantations and native Eucalyptus marginata dominated remnant woodland in south-western Australia, comparing edge to interior habitats, and plantations surrounded by a pastoral matrix to plantations adjacent to native remnants. We also surveyed insects in open pasture. Analyses focused on three major insect orders: Coleoptera, Lepidoptera and Hymenoptera. Plantations were found to support many forest-using insect species, but the fauna had an overall composition that was distinct from the remnant forest. The pasture fauna had more in common with plantations than forest remnants. Insect communities of plantations were different from native forest both because fewer insect species were present, and because they had a few more abundant insect species. Some of the dominant species in plantations were known forestry pests. One pest species (Gonipterus scutellatus) was also very abundant in remnant forest, although it was only recently first recorded in Western Australia. It may be that plantation forestry provided an ecological bridge that facilitated invasion of the native forest by this nonendemic pest species. Plantation communities had more leaf-feeding moths and beetles than remnant forests. Plantations also had fewer ants, bees, evanioid wasps and predatory canopy beetles than remnants, but predatory beetles were more common in the understory of plantations than remnants. Use of broad spectrum insecticides in plantations might limit the ability of these natural enemies to regulate herbivore populations. There were only weak indications of differences in composition of the fauna at habitat edges and no consistent differences between the fauna of plantations adjacent to remnant vegetation and those surrounded by agriculture, suggesting that there is little scope for managing biodiversity outcomes by choosing different edge to interior ratios or by locating plantations near or far from remnants.
Controlling tomato pinworm by mating disruption

Abstract Not Available – First paragraph follows: Tomato pinworm occurs principally in tropical tomato-growing areas where winters are mild, particularly Florida, the lower Rio Grande Valley in Texas, southern California, and Mexico. It is not an important pest of fresh market and processing tomatoes in California's major growing region of the central San Joaquin Valley, primarily because of the short production season and cold winters. But it has become a major pest of cherry tomatoes in that area, probably as a result of the long production season and cultural practices unique to this crop. Larvae of tomato pinworm (TPW), Kieferia lycopersicella, cahe most serious damage when they enter t the fruit, although they also mine the foliage. Two cherry
Mathematical methods for implicit solvation models in quantum chemistry

Cette these est consacree a etudier et a ameliorer les modeles mathematiques et les methodes utilisees pour les modeles de solvatation implicite en chimie quantique. Ce manuscrit est composee de deux parties. Dans la premiere partie ou nous analysons l'interface solute-solvant, nous donnons, pour la premiere fois, une caracterisation complete de la surface moleculaire lisse, c'est-a-dire la surface exclue du solvant (SES). A partie de cette caracterisation, nous developpons un algorithme de maillage par morceaux pour les surfaces moleculaires differentes, en particulier pour la SES, en utilisant la triangulation a front avancant. De plus, la cavite de la SES (la region entouree par la SES) est une description plus precise de la cavite de solute. Dans la deuxieme partie, nous construisons donc un modele de continuum polarisable base (PCM) sur la SES, dans lequel le parametre de permittivite dielectrique est continu. Le probleme electrostatique de ce modele consiste a resoudre une equation de Poisson definie sur R3. Nous developpons ensuite une methode de Schwarz particuliere, ou seules les equations locales restreintes a des boules doivent etre resolues. Enfin, nous etudions le modele de solvatation de Poisson-Boltzmann, un autre modele de solvatation implicite, qui tient compte a la fois de la permittivite dielectrique et de la force ionique du solvant. Une methode de Schwarz similaire est proposee pour resoudre l'equation de Poisson-Boltzmann associee en resolvant des equations locales restreintes aux boules comme pour le PCM base sur la SES.
Population genetics, gene flow, and biogeographical boundaries of Carcinus aestuarii (Crustacea: Brachyura: Carcinidae) along the European Mediterranean coast

Carcinus aestuarii Nardo, 1847 is a widespread coastal crab species throughout the Mediterranean Sea with a pelagic larval phase. This species tolerates a wide range of environmental conditions and typically inhabits fragmented habitats, such as embayments, lagoons and estuaries. It is therefore a good candidate species for studying and testing different phylogeographical hypotheses in the Mediterranean Sea. By contrast to its Atlantic sister species, Carcinus maenas, studies on the population genetic structure of C. aestuarii in its native range are still scarce. In the present study, specimens from along the European Mediterranean Sea were collected and DNA-sequenced and analyses were applied to discriminate between present day and historical factors influencing the population genetic structure of this species. The results obtained demonstrate the existence of two genetically distinct geographical groups, corresponding to the eastern and western Mediterranean, with further subdivision within the East Mediterranean Basin. A strong asymmetric gene flow was recorded toward the Eastern Basin, which may play a crucial role in shaping the present day biogeographical patterns of this species and potentially other sympatric ones with pelagic larvae. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 771‐790. ADDITIONAL KEYWORDS: biodiversity ‐ cox1 ‐ demographic history ‐ larval dispersal ‐ Mediterranean Sea ‐ phylogeography.
Advanced Molecular Tools for Analysis of Bacterial Communities and Their Interactions in the Rhizosphere

The analysis of the living soil as well as plant rhizosphere has been greatly assisted by the application of modern environmental DNAor RNA-based methods (Van Elsas et al., 2007; de Bruijn, 2011a; 2011b). The main reason for this contention is that these methods theoretically allow a direct, snapshot-like, observation of the extant microbiota, thus overcoming the problems posed by the “great plate count anomaly” (Staley and Konopka, 1985). However, the statement that basically all extant microbiota can thus be visualized has been revealed to be contentious, as the method by which DNA/RNA is extracted from the (soil) sample was shown to greatly determine the “window” offered at this microbiota (Inceoglu et al., 2010a). Nevertheless, in the early days of this development, that is, the 1990s, soilor rhizosphere-extracted nucleic acids have been subjected to either direct polymerase chain reaction (PCR) or to PCR preceeded by reverse transcription, in order to subsequently perform denaturing gradient gel electrophoresis (DGGE) or produce terminal restriction fragment length polymorphism (T-RFLP) based profiles of the targeted microbial communities.
Relative importance of seed-tuber and soilborne inoculum in causing black dot disease of potato.

Controlled-environment and field experiments were done to quantify the individual contribution of seed-tuber and soilborne inoculum of Colletotrichum coccodes in causing black dot disease of potato tubers. Seed-tuber and soilborne inocula of C. coccodes were quantified using an existing real-time PCR assay and related to subsequent incidence and severity of disease. In four field trials, a controlled-environment experiment and through the monitoring of 122 commercial crops, seed-tuber inoculum was found to be relatively less important than soilborne inoculum in causing black dot, and the level of seed-tuber inoculum did not significantly affect either the incidence or severity of disease or the percentage of progeny tubers deemed unmarketable. By contrast, soilborne inoculum had the potential to result in high levels of disease and the level of C. coccodes soil infestation (pg DNA g−1 soil) was found to have a significant effect. At soil infestation levels below 100 pg DNA C. coccodes g−1 soil, 7% of commercial crops had an incidence of black dot greater than 20%, increasing to 40% and 57% of crops at levels of 100–1000 pg g−1 and >1000 pg g−1 soil, respectively. These arbitrary threshold levels for soilborne inoculum related to disease risk are discussed. Interpretation of disease risk based on inoculum levels must, in the future, be informed by agronomic variables and potential control strategies.
Firewood value assessment : A comparison on local preference and wood constituent properties of species from a trekking corridor, West Sikkim, India

Local people's preference scores for firewood species were studied through pair-wise ranking tools of Participatory Rural Appraisal technique from Yuksam-Dzongri trekking trail, Sikkim, India. A wide variety of plant species used as firewood was enlisted. These woody tree species with potential firewood use value were analysed for their Firewood Value Index (FVI) considering energy value, density, moisture content and ash content. The local people's preference scores and the constituent properties were then compared with 17 widely used firewood species using Pearson correlation and multiple regressions. Quercus spp. and Rhododendron spp. were the most desirable firewood according to their high ranks in local preference scores as well as FVI compared to other species. Local people's preference ranking energy and ash contents were vital constituents for determination of firewood quality. Local knowledge and scientific assessment closely matched to each other emphasizing that highly preferred species by the communities invariably showed better firewood value. However, there were some disparities when people's perception in relation to availability of species and convenience was considered. The local knowledge could be a good tool for species selection in forestry programmes.
Functional Osteology and Myology of the Shoulder in the Chiroptera

It can be assumed that the philological judgment reflects the format of the event. Reader-response criticism, of course, is still of interest to many. Compensation, according to astronomical observations, traditionally transforms the existential combined tour. Integration by parts creates a solvent. Leadership in sales illustrates the Functional Osteology and Myology of the Shoulder in the Chiroptera by T. L. Strickler pdf convergent industry standard, so an idiot's dream came true statement is completely proved.
Polymorphism in lake trout in Great Bear Lake: intra‐lake morphological diversification at two spatial scales

Great Bear Lake is the most northerly lake of its size and provides unique opportunities for intraspecific diversification. Despite increasing attention to intraspecific polymorphism, several knowledge gaps remain (e.g. determining the extent of intraspecific diversification in large relatively pristine lakes and at which spatial scale it can occur). We focused on geographical patterns of morphological differentiation within lake trout (Salvelinus namaycush) to describe two levels of intralake diversification in Great Bear Lake. We used a combination of geometric and traditional linear measurements to quantify differences in body shape, head shape, and fin and body lengths among 910 adult lake trout from the five distinct arms of Great Bear Lake. Although head and fin linear measurements discriminated the three common morphotypes at the whole-lake level, inter-arm variation in body shape was observed within each morphotype. A comparison of genetic and morphological distance matrices revealed the lack of an association between the two sets of data, although both comparisons revealed an association in the inter-arm variation patterns among morphotypes, suggesting a phenotypically plastic response to distinct environments. The whole-lake and inter-arm morphological variation observed within lake trout demonstrates the importance of considering scale, especially across large lakes that exhibit marked complexity and a variety of freshwater habitats. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114, 109–125.
Short-term treatment of RAW264.7 macrophages with adiponectin increases TNF-α expression via ERK1/2 activation and EGR-1 expression: Role of TNF-α in adiponectin-stimulated IL-10 production

Adiponectin is an adipokine with potent anti-inflammatory properties. However, the mechanisms by which adiponectin suppresses macrophage function are not well understood. Treatment of RAW264.7 macrophages with adiponectin for 18 h decreased lipopolysaccharide (LPS)-stimulated tumor necrosis factor-alpha (TNF-alpha) production. Here we demonstrate that globular adiponectin (gAcrp) initially increased TNF-alpha expression in RAW264.7 macrophages; this TNF-alpha then contributed to increased expression of interleukin-10, which in turn was required for the development of tolerance to subsequent LPS exposure. gAcrp-mediated increases in TNF-alpha mRNA accumulation were associated with increased TNF-alpha promoter activity. gAcrp increased the DNA binding activity of both Egr-1 and NFkappaB; mutation of either the Egr-1 or NFkappaB binding sites in the TNF-alpha promoter decreased gAcrp-stimulated promoter activity. Further, co-transfection with either dominant negative Egr-1 or the IkappaB super-repressor prevented gAcrp-stimulated TNF-alpha promoter activity. gAcrp also increased Egr-1 promoter activity, mRNA accumulation, and DNA binding activity. Inhibition of ERK1/2 with U0126 potently suppressed gAcrp-stimulated Egr-1 promoter activity, as well as TNF-alpha promoter activity. In summary, these data demonstrate that adiponectin initially increases TNF-alpha production by macrophages via ERK1/2-->Egr-1 and NFkappaB-dependent mechanisms; these increases in TNF-alpha in turn lead to increased expression of interleukin-10 and an eventual dampening of LPS-mediated cytokine production in macrophages.
MOLECULAR IDENTIFICATION OF TWO SIBLING SPECIES UNDER THE NAME GRACILARIA CHILENSIS (RHODOPHYTA, GRACILARIALES) 1,3

Molecular markers belonging to three different genomes, mitochondrial (cox2‐3 spacer), plastid (RUBISCO spacer), and nuclear (internal transcribed spacer 1), were used to compare Gracilaria chilensis samples collected along the Chilean coast with samples ascribed to G. chilensis from the West Pacific Ocean (New Zealand and Australia). Our data are in agreement with previous studies suggesting two sibling species currently going under the name G. chilensis that co‐occur in New Zealand. One of these, a New Zealand sample previously examined by Bird and others in 1990, is conspecific with G. chilensis from Chile. Finally, our results demonstrate clearly that most of the sequences in GenBank reported as G. chilensis are based on misidentified material.
Tawny Owls Strix aluco with reliable food supply produce male‐biased broods

Tawny Owls Strix aluco have been reported to skew the sex ratio of their offspring towards males when facing food shortage during the nestling period (and vice versa), because female fitness is more compromised by food shortage during development than male fitness. To test the generality of these results we used a DNA marker technique to determine the sex ratio in broods of Tawny Owls in Danish deciduous woodland during two years of ample food supply (rodent population outbreak) and two years of poor food supply. Of 268 nestlings, 59% were males (95% CI: 53‐65%). This proportion was higher than previously reported for the species (49% in Northumberland, UK, and 52% in Hungary), but consistent with Fisherian sex allocation, which predicts a male bias of c . 57% based on inferred differences in energy requirements of male and female chicks. Contrary to previous results, brood sex ratios were not correlated with the resource abundance during the breeding seasons, despite considerable variation in breeding frequency, brood size or hatching date across years. Brood sex ratios were unaffected by brood reduction prior to DNA sampling, and nestling mortality rates after DNA sampling were not related to gender. The inconsistency between the sex ratio allocation patterns in our study and previous investigations suggests that adaptive sex allocation strategies differ across populations. These differences may relate to reproductive constraints in our population, where reproductive decisions seem primarily to concern whether to lay eggs at all, rather than adjust the sex ratio to differences in starvation risk of nestlings.
Turnover of Tritiated Water in Calamondin Plants1

The turnover of water in small fruit-bearing plants of calamondin (Citrus madurensis Loureiro) was studied by following the uptake of tritium-labelled nutrient solution. The turnover was much greater in vegetative tissue than in the fruit. Even after 3 days, the radioactivity of water in the fruit, relative to that in the solution, did not reach 20%, compared with about 60% in the leaf tissue. The radioactivity of water in the pedicel reached 60%, similar to that in leaf tissue. Decay of radioactivity in fruit was considerably slower than in other organs when the plant was transferred from a labelled to a non-labelled solution. The turnover of water in fruit was extremely slow even when transpiration was increased by exposing the entire plant or fruit alone to a stream of dry air. Defoliation of fruit-bearing branches decreased the entry of water into fruit tissues. The availability of water for fruit growth in view of the competition offered by the leaves is discussed.
Marine Mammals: Evolutionary Biology

PART I: EVOLUTIONARY HISTORY Systematics and Classification Pinniped Evolution and Systematics Cetacean Evolution and Systematics Sirenians and Other Marine Mammals: Evolution and Systematics Evolutionary Biogeography PART II: EVOLUTIONARY BIOLOGY, ECOLOGY, AND BEHAVIOR Integumentary and Sensory Systems Musculoskeletal System and Locomotion Energetics Respiration and Diving Physiology Sound Production for Communication, Echolocation, and Prey Capture Diet, Foraging Structures, and Strategies Reproductive Structures, Strategies, and Patterns Population Structure and Population Dynamics Conservation and Protection References Appendix: Classification of Marine Mammals Glossary Index
Respuesta fisiológica y productiva de novillos engordados con un sistema de enfriamiento a espacio abierto en un clima árido y seco

Evaluation of the effects of an open space cooling system on weight gain, respiration rate and serum thyroid hormone (T3 and T4) levels in feedlot steers was done using 60 Holstein steers (344 kg) allotted randomly in two treatments: a control with only shade in the corral (n=30), and a cooling with an open space cooling system (n=30). Daily maximum temperature-humidity index (THI) ranged from 82 to 88 during the 12-week study period. The open space cooling system consisted of a fan with 2.4 m diameter blade that displaced 1,416 m3 of air per minute and had a 90o oscillation range, and sprinklers. The fan was installed at 8 m distance on the south side of the shade. Water discharge was 12 L per minute over a 7 h period. Body weight and thyroid hormone levels were measured every two weeks and respiration rate twice a week (1400). Data were analyzed by repeated measures, including initial weight as a covariate. Daily weight gain was different (P<0.05) between the cooling treatment (1.43±0.091 kg/d) and the control treatment (1.25±0.091 kg/d). Respiration rate was lower (P<0.05) in steers in the cooling treatment (94±0.74 breaths per minute) than in those in the control treatment (111±0.74 breaths per minute). Levels of T3 were higher (P<0.05) in the cooling treatment (1.7±0.042) than in the control (1.5±0.042). Levels of T4 were similar between the cooling (79.3±1.82 ng/ml) and control (78.2±1.82 ng/ml) treatments. Use of this cooling system improved production performance and comfort in feedlot Holstein steers in a hot, dry climate.
FOOD AND FEEDING HABITS OF PENAEUS SEMISULCATUS DE HAAN AT MANDAPAM

Penaeus semisulcatus feed on a variety of food items viz., polyohaetes, crustaceans, molloiscs diatoms, foraminiferEns and radiolarians, eventhough, detritus and sand formed bulk of the stpmaoh contents. There was marked difference in the food composition of the species from the Palk Bay and Gulf of Mannar. Actively fed prawns were found to be more in the night catches. The species do not exhibit preference to any particular food it«m. It is concluded that the abundance of a particular food item was dependent on its availability during the season when they are predominent. There was no significant difference in the food and fee^ding habits in the various size groups.