Miracle-dz/UniFAR-FTUs huggingface dataset:
Are Antioxidant Capacity and Oxidative Damage Related to Biological and Autecological Characteristics in Aquatic Insects

In this work, we study the oxidative state of nine taxa of aquatic insects [ Serratella ignita (Poda, 1761), Ephemera danica Muller, 1764 , Crocothemis erythraea (Brulle, 1832), Dinocras cephalotes (Curtis, 1827) , Perla bipunctata Pictet , 1833, Isoperla morenica Tierno de Figueroa & Luzon-Ortega, 2011, Notonecta maculata Fabricius, 1794, Gerris sp. , and Hydropsyche sp. ] in order to determine the relationships between this state and the biological and environmental characteristics of the species studied. The studied taxa are all in the same life cycle stage (nymph/larva), and many of them have different maximum life span potentials. We assess the antioxidant capacity through the determination of the trolox-equivalent antioxidant capacity, the ferric-reducing/antioxidant power and the activity of the antioxidant enzymes catalase, DT-diaphorase, glutathione peroxidase, glutathione reductase, glutathione transferase, superoxide dismutase and glucose-6-phosphate dehydrogenase. Furthermore, to determine the oxidative damage, we examine thiobarbituric acid reactive substances, free malondialdehyde, protein-bound malondialdehyde, total hydroperoxides, and protein hydroperoxides. In summary, we can consider that having predatory feeding habits, having a long-life cycle and living in permanent streams with cold, well-oxygenated waters are related to a proper oxidative state in the insects that we studied. On the other hand, non-exclusive predator species living in temporary streams with warm and poorly oxygenated waters with a short life cycle have a worse oxidative state. Thus, the oxidative state of each species could be defined by an interaction of biological and autecological factors, for which the relative importance is difficult to assess.
Investigation of Ophiostoma population infected elms in Poland

Dutch elm disease (DED) still occurs in Poland. Previous studies confirmed occurring O. ulmi and two subspecies of O. novo-ulmi: subsp. novo-ulmi and subsp. amerciana. In this study the population of Ophiostoma occurred in Poland was investigated. The disease incidence was investigated on elms growing in 39 locations. The pathogen’s mycelium was isolated from elm branches and twigs collected from 22 plots. The disease symptoms were noted in 5% to 35% trees. Fungi were identified based on the PCR amplification of the ITS 1/2 rDNA together with phylogenetic analysis of this region. Ophiostoma novo-ulmi was the only agent caused DED on Ulmus glabra, U. minor and U. laevis. There were no genetic diversity of O. novo-ulmi Polish population in analyzed ITS region. All kind of specific symptoms and disease intensity occurred independently on elm species and host age. Ulmus minor was infested most sever among the three elms species.
Privacy: a Machine Learning Perspective

Inside cover with acknowledgment of partners and partner logos 1-page executive summary with highlights from statistics. 3 main sections – each of these will have all of the graphs from the list of 16 that pertain to each respective section: Events Victims Fraudsters The format for each of these sections will more or less like a prettier version of the ITAP Template document I sent you. Basically each page will have 3+ graphs depending on design layout (however many fit) and then 2 text sections copy for: “Explanations”: A 1-2 sentence description of the graph “Insights” a 1-paragraph exposition on what the statistic indicates. Privacy: a Machine Learning Perspective
Vitamin or Salicylic acid treatments versus the adverse effects of copper stress on photosynthesis and some related activities of wheat seedlings.

The addition of 100 ppm of any of the vitamins; ascorbic acid (AsA) or thiamin (B1) as well salicylic acid (SA) to the hydroponic growth solution for one day of young wheat plants exerted protective effects against copper stress. Excessively copper supply (for 3 days) considerably retarded the rates of photosynthesis and some of the related activities of wheat seedlings; a serious effect was exhibited when copper was applied at relatively high levels. These negative alterations in net photosynthesis were generally associated with a reciprocal response in dark respiration. On the other side AsA, B1 or SA treatments were generally effective in alleviating partially or completely the inhibitory effects of copper stress on growth and net photosynthesis of the test seedlings. However, these treatments were associated with favorable effects on the biosynthesis of photosynthetic pigments. As regards the dark respiration, while in vitamin treated plants, it was mostly retarded, whatever the level of copper used and the type of vitamin applied, in salicylic acid treated plants, respiration was progressively stimulated.
Human Liver Fatty Acid Binding Protein cDNA and Amino Acid Sequence

Human liver fatty acid binding protein (L-FABP) cDNA clones were identified in a liver cDNA library. The two longest clones were completely sequenced. The nucleotide sequence predicts a protein of 127 amino acid residues. Identity of the clones was confirmed by limited amino acid sequence analysis of purified human L-FABP peptides and Edman degradation of radiola- beled
Effets des régimes hyperprotéiques et des métabolites bactériens dérivés des acides aminés sur la muqueuse du gros intestin

Resume : Les regimes hyperproteiques sont couramment consommes mais les consequences au niveau du gros intestin sont peu connues. L’objectif de la these etait d’etudier les effets des regimes hyperproteiques et des metabolites bacteriens derives des acides amines sur la muqueuse du gros intestinUne serie d’experimentations animales et in vitro a permis de montrer que deux metabolites bacteriens derives des acides amines (le sulfure d’hydrogene et le p-cresol) sont toxiques pour l’epithelium lorsqu’ils sont presents en concentration elevee. Les resultats obtenus lors d’une etude clinique montrent que la quantite et la qualite des proteines alimentaires n’ont pas d’effets marques sur la composition du microbiote fecal mais modifient les concentrations fecales et urinaires en metabolites bacteriens.Ces modifications de l’environnement luminal du gros intestin n’etaient pas associees a une augmentation de la cytotoxicite des eaux fecales in vitro. Neanmoins, dans la muqueuse rectale, l’augmentation de l’apport en proteines a regule l’expression de genes impliques dans le maintien de l’homeostasie et ces effets etaient distincts en fonction de la source de proteines utilisee. Toutefois, le niveau d’apport en proteines n’avait pas d’effet sur les parametres inflammatoires et histologiques dans la muqueuse. Ces resultats ont ete completes par une etude chez le rat montrant qu’un regime hyperproteique modifie le transcriptome dans les colonocytes mais n’a pas d’effets deleteres en termes d’integrite de l’ADN, de renouvellement de l’epithelium et de fonction barriere.
Characterization of ClC‐2 Chloride Channel/PKA Interaction in Mouse Heart

Background: A ClC‐2 encoded chloride inward rectifier channel (Cl.ir) has been identified in the heart of several species. Cl.ir may play a role in regulation of pacemaker activity of the heart. In this study, we studied the regulation of mouse cardiac ClC‐2 channels by protein kinase A (PKA) phosphorylation.
Simplicity is key: restoration protocols for nonregenerating forests degraded by overabundant herbivores

Global forests are being lost and degraded at an alarming rate; hence ecological restoration becomes an integral component ensuring future forest health. Beneficial effects of restoration will depend on scientifically based practices within an adaptive management framework. On the island of Newfoundland, moose (Alces alces) have become overabundant since their introduction in the early 1900s causing regeneration failure of the balsam fir (Abies balsamea) forest. Intensive selective browsing by moose on this foundation species within naturally insect‐generated gaps has created “spruce‐moose meadows. ” Experimental restoration to support Parks Canada Ecological Integrity targets was implemented in the boreal forest of Terra Nova National Park (Newfoundland, Canada), along a gradient of disturbance from closed canopy forest to large insect‐disturbed gaps. Seedling planting was carried out under various ground preparation treatments (field planting, aboveground suppression, and scarification). Seedling performance (survival, growth, and browsing occurrence) was monitored over 2 years and mixed‐effects models were constructed to determine seedling responses, which form the template of future forests. Results show minimally positive effects of the ground treatments along the gradient of disturbance, while environmental conditions and seedling individual traits explained the majority of seedling responses. Better growth, lower survival, and higher browsing intensity were observed with increasing forest disturbance, with taller seedlings at planting performing the best. Considering that no substantial biological benefits were detected following ground treatments, which are costly and time‐consuming to implement, active restoration in boreal forest can be implemented using standard forestry planting protocols, without any ground preparation, independently of the forest degradation state.
The last common ancestor of bilaterian animals pos- sessed at least 7 opsins

, Opsins, the primary proteins animals use to sense light, have un-dergone a dramatic expansion since they originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in the last common ancestor of all bilaterians and Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 15 animal phyla, including the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of nine opsin paralogs in the bilaterian ancestor and four opsin paralogs in the last common ancestor of cnidarians+bilaterians. Thus we have found a greater opsin diversity earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular
Expression and regulation of levansucrase in Pseudomonas syringae

Pseudomonas syringae pv. glycinea PG4180 is an opportunistic plant pathogen which causes bacterial blight disease of soybean (Glycine max). This organism can utilize sucrose, the most abundant plant sugar, with the help of enzyme levansucrase (Lsc). Sucrose is eventually cleaved into glucose, which is further metabolised by the cell, and fructosyl residues, which are polymerized by the same enzyme to form the exopolysaccharide levan. PG4180 has three genes for Lsc, of which two, lscB and lscC are expressed while lscA is not expressed. The first part of this study dealt with determining the presence of multiple lsc genes in P. syringae. Nucleotide sequence alignments between lscB/C and lscA helped identify a prophage associated promoter element present in the upstream of lscB/C ORF but not associated with lscA. We could, for the first time, express lscA in PG4180 under the lscB promoter. However, lscB could not be expressed under the lscA promoter indicating that lscA upstream region does not contain a promoter region. We speculate that lscA might be an ancestral Lsc variant in front of which an active promoter, possibly derived from a bacteriophage, got inserted leading to expression of lscB/C. The second part of this study dealt with identifying transcription factors involved in regulation of Lsc expression in P. syringae. The binding site for a hexose metabolism regulator, HexR, was identified in the promoter region of lscB. As compared to the wild-type, the hexR mutant had severely hampered growth characteristics in medium containing glucose or sucrose as sole source of carbon as well as in planta. DNA affinity chromatography was done to identify two H-NS-like regulatory proteins MvaT-MvaU binding to the promoter region of lscB. Protein-DNA binding assay and overexpression of MvaU in PG4180 suggested that these two proteins could act as repressors of lsc expression. The data suggest a co-regulation of genes involved in extra-cellular sugar acquisition with those involved in intra-cellular energy-providing metabolic pathways as well as virulence and biofilm expression in P. syringae.
Empirical Analysis of Energy Consumption of Acceleration-Based Wireless Sensor Nodes Used for Pipeline Monitoring

: Energy Consumption is one the major constraint in developing Wireless Sensor Network (WSN) applications. An application can take years to drain the battery of the sensor node or consume it in a matter of weeks. Consequently, many authors have proposed different techniques of analysing energy consumption in sensor nodes with preference to energy consumed in communicating information within the network. This paper presents the empirical analysis of energy consumption of acceleration-based sensor nodes used for pipeline monitoring. We considered energy dissipated in sensing, controlling and communicating data at different operating states. The Lifetime of the network and energy dissipated by the sensor nodes were estimated per unit bit and for active, idle listening and sleep mode for the accelerometer, microcontroller and transceiver units respectively. The graphs of energy consumed at different packet size and Node Voltage with Lifetime were analysed using Matlab Simulation.
A Gauge to Measure Mass Flow Rate of Sap in Stems and Trunks of Woody Plants

A stem flow gauge designed for herbaceous plants was adapted for measuring the absolute mass flow rate of sap in large stems and trunks of woody plants. The method uses a steady-state heat balance method in which a constant, known amount of heat is supplied to a stem segment. The axial and radial conductive heat fluxes away from the heated segment are measured, as well as the rise in sap temperature. The device can be operated by commonly available dataloggers and does not require calibration. In a greenhouse experiment with a small tree, the sap mass flow rate, as measured by the the gauge, agreed with the measured transpiration rate within 4% when both were integrated over 24-hr periods or longer. Short term comparisons (≤4hr) were less accurate, due to the changes in water content of the tree above the gauge, which cause a lag between transpiration rate and sap flow rate. The dynamic response of the tree and gauge system to sudden changes in sap flow was ≈20 min under midday conditions. Other than the insertion of temperature-sensing thermocouples 2 mm into the trunk, the gauge components are non-invasive and do not disturb the tree physically or physiologically to a significant extent.
Induction kinetics of the PhoQ-PhoP two-component system in Escherichia coli

Cells rely on signal transduction systems to sense and respond to changes in their enviroments. When a stimulus is present, the corresponding signal transduction system will activate and enact the appropriate biological response, often by modulating target gene expression. In many cases, the temporal dynamics of the activation of target gene expression in the presence of constant stimulus is complex, and often exhibits one or several pulses. How these complex temporal dynamics are regulated at the molecular level is unknown for many signal transduction systems. In this thesis, I discuss the molecular regulation of the temporal dynamics of PhoQ-PhoP induction in Escherichia coli. The PhoQ-PhoP pathway is a canonical two-component system that responds to low extracellular Mg'+, certain antimicrobial peptides, and potentially other unknown factors. Upon activation, the bifunctional histidine kinase PhoQ autophosphorylates and subsequently phosphotransfers to the response regulator PhoP, thereby activating it to increase transcription of PhoP target genes. Because PhoQ is bifunctional, PhoQ acts as a phosphatase on phosphorylated PhoP in the absence of stimulus, thereby keeping the system inactivated. When the PhoQ-PhoP system is strongly induced, PhoP target genes exhibit impulse kinetics, meaning gene expression increases to a maximal level and subsequently decreases to an eventual steady state. We discovered that this impulse response is caused by a negative feedback loop in which active PhoP transcribes mgrB, a gene encoding a small membrane protein that interacts directly with PhoQ to repress the output of the system. MgrB selectively inhibits the ability of PhoQ to phosphorylate PhoP, and permits PhoQ to act as a phosphatase on phosphorylated PhoP. This change in PhoQ activity causes a decrease in the level of active PhoP and the level of PhoP target genes. This thesis reveals how negative feedback loops and histidine kinase bifunctionality can drive the kinetics of two-component system induction in bacteria, and more generally explores how cells regulate changes in gene expression over time.
The roles of the Drosophila protein tribbles in oogenesis and insulin signaling pathway

In this dissertation, I examined the molecular mechanism of function of the Drosophila melanogaster protein Tribbles (Trbl) during oogenesis and larval development. Trbl is the founding member of an evolutionarily conserved family of kinase proteins that play diverse roles in cell signaling and energy homeostasis. In addition to the central Serine/Threonine kinase domain, members of the Tribbles gene family (Trib) shares C terminal mitogen activated protein kinase kinase MEK1 and E3 ubiquitin ligase COP1 binding motifs, the latter required for the degradation of target proteins via proteasome. During oogenesis, Trbl controls border cell (BC) cluster migration by mediating degradation of C/EBP transcription factor Slbo. I first investigated Trbl’s role during oogenesis using a Trbl specific antisera. Trbl localizes to the nucleus of main body follicle cells (MBFC) up to stage 10 of oogenesis. In the case of BC, Trbl expresses in a complementary pattern to Slbo expression. The Trbl level decreases gradually as the BC cluster delaminates from the epithelium and starts migrating when Slbo protein level increases. Moreover, Slbo was found to be essential but not sufficient to decrease the Trbl level required for BC migration. In a wing misexpression screen for Trbl interacting proteins, I identified the Serine/Threonine protein kinase Akt, a major mediator of insulin signaling. In recent years, mammalian Trib3 and Trib2 proteins have been implicated in the regulation of
PHOSPHORUS DEFICIENCY IMPAIRS SHOOT REGROWTH OF SUGARCANE VARIETIES

SUMMARY The shoot regrowth vigour of sugarcane varieties having contrasting phosphorus (P) efficiency was evaluated under varying soil P availability. The P-inefficient (IAC91–1099 and IACSP94–2101) and -efficient (IACSP94–2094 and IACSP95–5000) sugarcane varieties were grown under low (25 mg P kg−1 soil) or high (400 mg P kg−1 soil) P supply at planting. After 90 days (first cycle of growth), the shoots were harvested and regrowth was studied 70–75 days later by evaluating photosynthesis, leaf area formation, biomass production and P uptake. The shoot dry matter (DM) of sugarcane regrowth subjected to a low P supply was genotype-dependent, with the P-efficient varieties exhibiting greater values than the inefficient ones. This result was explained by the greater efficiency of IACSP94–2094 and IACSP95–5000 in acquiring P rather than P utilization efficiency for shoot biomass production. The root P stored during the first cycle of growth would represent only a minor fraction (< 20%) of the total P content in the shoots at the end of the regrowth period. Thus, we argue that the improved shoot P uptake of the P-efficient varieties was related to their ability to sustain P acquisition after harvesting rather than to the remobilization of root P reserves. Moreover, our data revealed that net CO2 assimilation per leaf area was not associated with differential performance among varieties under P deficiency, suggesting a more critical role of total leaf area in photosynthate supply for sugarcane regrowth. In conclusion, sugarcane regrowth is improved in P-efficient varieties under P deficiency conditions, a finding of practical relevance as such ability might benefit the productivity and the longevity of sugarcane ratoons in low P tropical soils.
BIOLOGICAL BASIS OF HOMOLOGY

A homolog is a part of the phenotype that is homologous to equivalent parts in other species. A biological homology concept is expected to explain three properties of homologs: 1) the conservation of those features that are used to define a homolog, 2) the individualization of the homolog with regard to the rest of the body, and 3) the uniqueness of homologs, i.e., their specificity for monophyletic groups. The main obstacle to describing a mechanistic basis for homology is the variability of the developmental pathways of undoubtedly homologous characters. However, not all aspects of the developmental pathway are of equal importance. The only organizational features of the developmental system that matter are those that have been historically acquired and cause developmental constraints on the further evolutionary modification of the characters. Two main factors contribute to historically acquired developmental constraints: generative rules of pattern formation and ontogenetic networks. In particular, hierarchical and cyclical inductive networks have the required properties to explain homology. How common such networks are is an open empirical question. The development and variation of pectoral fin hooks in blenniid fishes is presented as a model for the study of a simple ontogenetic network.
PROTEC łIA NATURAL Ă A LEMNULUI CU CIUPERCI ANTAGONICE NATURAL PROTECTION OF WOOD WITH ANTAGONISM FUNGI

Biological environments contain a certain number of microbial populations which, within a given ecological niche, display various relations ranging from symbiosis to parasitism. Researchers have been interested in these types of relations for around fifty years, especially in one very particular type of relationship: the antagonism exerted between individuals of the same microbial population. Today, the role played by biological agents, bringing into play inhibitive or destructive antibiotic substances, reveals a certain potential for their use in controlling microorganisms associated with such degradation processes. The work undertaken by HydroQuebec and CIRAD involved two types of experiment: 1) in Petri dishes to assess and characterize the antagonistic capacity of Trichoderma against white rot and brown rot fungi; 2) on pieces taken from untreated poles in order to study confrontation between the basidiomycete and the antagonistic strain in wood. This study investigated the antagonism of three ascomycetes of the genus Trichoderma against two white rot basidiomycetes, Pycnoporus sanguineus and Coriolus versicolor, and two brown rot basidiomycetes, Antrodia sp. and Coniophora puteana, through direct confrontation in Petri dishes and in the wood of HydroQuebec poles. The results obtained seemed to complete each other coherently. They revealed that the Trichoderma group of fungi was not aggressive to wood and the results obtained after direct confrontation in Petri dishes were confirmed in wood. By directly exposing the different basidiomycetes and antagonists to each other in Petri dishes, two by two, we effectively revealed an antagonism effect for a large majority of the pairs. However, there was substantial variability in reactions from one pair to the next.