Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Fatty Acids and their Derivatives on Aphid Resistance in Arabidopsis and Tomato

Fatty acid desaturases (FADs) are enzymes that act in the chloroplast or the endoplasmic reticulum (ER) to incorporate double bonds into the acyl chains of fatty acids, and recent evidence indicates that at least one of these enzymes, FAD7, also influences plant resistance to aphids. FAD7 is an enzyme in the chloroplast that is found throughout the plant kingdom and that desaturates 16and 18-carbon fatty acids (FAs) with two double bonds (dienoic acids) to generate FAs with three double bonds (trienoic acids). In tomato (Solanum lycopersicum) and the model plant Arabidopsis thaliana, mutants with impaired FAD7 function are more resistant to aphids than wild-type controls. Compared to wild-type plants, these mutants have increased 18-carbon FAs with one double bond (C18:1), higher 16and 18-carbon FAs with two double bonds (C16:2 and C18:2), and lower 16and 18-carbon FAs with three double bonds (C16:3 and C18:3). These changes in FA composition are most pronounced in galactolipids which are abundant in the chloroplast, but loss of function of FAD7 also has a modest effect on phospholipids from the endoplasmic reticulum (ER). In addition, loss of function of FAD7 also influences foliar profiles of C6 volatiles, a class of FA derivatives that have previously been reported to contribute to aphid resistance in potato and other plant species. The goal of this project was to investigate which of these changes in fatty acid metabolism contribute to aphid resistance in Arabidopsis and tomato mutants with impaired FAD7 activity. To this end, we compared aphid performance on a panel of mutant plant lines with variation in FA composition or C6 volatile production. Our results suggested that aphid resistance in plants with impaired FAD7 activity is independent of C6 volatile synthesis, because 1) the aphid-resistant fad7 mutant in Arabidopsis also carries a mutation in the hydroperoxide lyase (HPL) gene, which is required for C6 volatile synthesis; and 2) suppressing expression of HPL in a FAD7-impaired tomato line did not compromise aphid resistance in this line. Analysis of aphid resistance and FA profiles in a panel of Arabidopsis mutants with impairments in different FADs also indicated that aphid resistance was impacted by FAD activity in the ER as well as in the chloroplast. This suggested that C18 rather than C16 FAs plays a determining role in aphid resistance, since C16 FAs are exclusively synthesized in the chloroplast whereas C18 FAs are produced in both subcellular compartments. Furthermore, resistance appeared to be associated with high C18:2 levels, because mutant lines with high C18:2 displayed resistance to aphids, but other lines with low C18:2 were susceptible even if they had high C18:1 and low C18:3 levels. Potentially, C18:2 or its derivatives could contribute to defensive signaling or synthesis of defensive metabolites to combat aphid infestations. This study aids in identifying new sources of plant resistance to aphids, and advances our understanding of how FA metabolism modulates plant defenses
Protein Aggregation: A Review

Protein aggregation is arguably the most common and troubling manifestation of protein instability, encountered in almost all stage of protein drug development. Protein generally will tend to aggregate under variety of conditions. The extent of aggregation depends on many factors that can be classified as intrinsic (primary, secondary, tertiary or quaternary structure) and extrinsic (environment in which protein present or processed). These protein aggregate may exhibit less desirable characteristics like reduce or no biological activity. Although a variety of method has been used to inhibit protein aggregation, it involved structural (internal) and environmental (external) modifications.
In Silico Docking analysis of Mycobacterium tuberculosis potential targets AftB and EmbA with selected phytochemicals

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans, is a devastating infectious organism that kills approximately two million people annually. The current suite of antibiotics used to treat TB faces two main difficulties: (i) the emergence of multidrug-resistant (MDR) strains of M. tuberculosis, and (ii) the persistent state of the bacterium, which is less susceptible to antibiotics and causes very long antibiotic treatment regimes. It is a disease that cannot be cured through conventional remedies. Phytochemicals have played a vital role in the discovery of drugs against infectious diseases. In the current study, homology model of the targets were designed. Thirty three ligand molecules (basically secondary metabolites) which were commonly present in the plants were docked with the selected potential target of Mycobacterium tuberculosis, AftB and EmbA. The primary docking analysis was performed through iGemDock which is then validated through AutoDockVina docking software. The active sites were also predicted through the Ligand+ tool. Among all the phytochemicals palmarin had a significant inhibitory activity with both the receptors. Binding pocket for both the targets were predicted (AftB-THR 474, ASP 522, SER 524, PHE 525, LEU 526, ARG 585 and EmbA- PRO 918, ASN 924, ARG 926, VAL 1057) forming hydrogen bonds at a very low energy value, thus forming a stable complex. Palmarin had excellent conformations showing the flexible behaviour of the ligand. The total energy of the receptor and ligand complexes has also been calculated.
Detecting copper toxicity in sediments: from the subindividual level to the population level

Summary 1.Sediments accumulate chemicals that can be toxic to biota and often contribute to aquatic ecosystem decline. Measuring mortality in laboratory-bred organisms is a common way to assess sediment toxicity. However, mortality-based responses of resilient laboratory organisms may not reflect indigenous macroinvertebrate responses, which can be relatively more sensitive to sediment toxicants. A possible solution is to also measure responses at the sub-individual level. 2.Several organism responses to sediment copper toxicity were assessed in a field-based microcosm. Responses of laboratory-bred chironomids and snails deployed in microcosms were compared at sub-individual (metabolomic and gene expression), individual (survival and dry weight) and population (reproduction) levels, and contrasted to the abundance of colonizing macroinvertebrates in the microcosms. 3.Colonizing macroinvertebrate abundance showed a range of sensitivities based on EC50 (effect dose 50% change). Chironomidae made up 94.5% of the microcosm macroinvertebrates, with Paratanytarsus the most sensitive genus (EC50: 89 mg/kg copper) and Procladius the least sensitive (EC50: 681 mg/kg). 4.Survival of laboratory-bred organisms was the least sensitive response, comparable to decreased abundance of the least sensitive macroinvertebrate. Juvenile production in the snail, Potamopyrgus antipodarum, was the most sensitive population level response (EC50: 121 mg/kg), in contrast the snail Physella acuta was relatively more tolerant (EC50: 298 mg/kg). 5.Changes in sub-individual responses (gene expression and metabolite abundance) in laboratory-bred chironomid, Chironomus tepperi, were evident at 60 mg/kg. These changes likely reflect the direct effects of copper exposure and represent metal-specific responses. 6.Synthesis and applications. We showed that copper toxicity in sediments could be readily detected through changes in gene expression and metabolites in laboratory-bred chironomids exposed in field-based microcosms. These responses were more sensitive than mortality, and detected copper levels that caused microcosm chironomid populations to decline. These novel approaches will provide managers with new tools to better assess sediment toxicity. This article is protected by copyright. All rights reserved.
Phylogenetic distribution of regeneration and asexual reproduction in Annelida: regeneration is ancestral and fission evolves in regenerative clades

Regeneration, the ability to replace lost body structures, and agametic asexual reproduction, such as fission and budding, are post-embryonic developmental capabilities widely distributed yet highly variable across animals. Regeneration capabilities vary dramatically both within and across phyla, but the evolution of regeneration ability has rarely been reconstructed in an explicitly phylogenetic context. Agametic reproduction appears strongly associated with high regenerative abilities, and there are also extensive developmental similarities between these two processes, suggesting that the two are evolutionarily related. However, the directionality leading to this relationship remains unclear: while it has been proposed that regeneration precedes asexual reproduction, the reverse hypothesis has also been put forward. Here, we use phylogenetically explicit methods to reconstruct broad patterns of regeneration evolution and formally test these hypotheses about the evolution of fission in the phylum Annelida (segmented worms). We compiled from the literature a large dataset of information on anterior regeneration, posterior regeneration, and fission abilities for 401 species and mapped this information onto a phylogenetic tree based on recent molecular studies. We used Markovian maximum likelihood and Bayesian MCMC methods to evaluate different models for the evolution of regeneration and fission and to estimate the likelihood of each of these traits being present at each node of the tree. Our results strongly support anterior and posterior regeneration ability being present at the basal node of the annelid tree and being lost 18 and 5 times, respectively, but never regained. By contrast, the ability to fission is reconstructed as being absent at the basal node and being gained at least 19 times, with several possible losses. Models assuming independent evolution of regeneration and fission yield significantly lower likelihoods. Our findings suggest that anterior and posterior regeneration are ancestral for Annelida and are consistent with the hypothesis that regenerative ability is required to evolve fission.
Delivery of Targeted Nanoparticles Across the Blood-Brain Barrier Using a Detachable Targeting Ligand

Chronic diseases of the central nervous system are poorly treated due to the inability of most therapeutics to cross the blood-brain barrier. The blood-brain barrier is an anatomical and physiological barrier that severely restricts solute influx, including most drugs, from the blood to the brain. One promising method to overcome this obstacle is to use endogenous solute influx systems at the blood-brain barrier to transport drugs. Therapeutics designed to enter the brain through transcytosis by binding the transferrin receptor, however, are restricted within endothelial cells. The focus of this work was to develop a method to increase uptake of transferrin-containing nanoparticles into the brain by overcoming these restrictive processes. To accomplish this goal, nanoparticles were prepared with surface transferrin molecules bound through various liable chemical bonds. These nanoparticles were designed to shed the targeting molecule during transcytosis to allow increased accumulation of nanoparticles within the brain. Transferrin was added to the surface of nanoparticles through either redox or pH sensitive chemistry. First, nanoparticles with transferrin bound through disulfide bonds were prepared. These nanoparticles showed decreased avidity for the transferrin receptor after exposure to reducing agents and increased ability to enter the brain in vivo compared to those lacking the disulfide link. Next, transferrin was attached through a chemical bond that cleaves at mildly acidic pH. Nanoparticles containing a cleavable link between transferrin and gold nanoparticle cores were found to both cross an in vitro model of the blood-brain barrier and accumulate within the brain in significantly higher numbers than similar nanoparticles lacking the cleavable bond. Also, this increased accumulation was not seen when using this same strategy with an antibody to transferrin receptor, indicating that behavior of nanoparticles at the blood-brain barrier varies depending on what type of targeting ligand is used. Finally, polymeric nanoparticles loaded with dopamine and utilizing a superior acid-cleavable targeting chemistry were investigated as a potential treatment for Parkinson’s disease. These nanoparticles were capable of increasing dopamine quantities in the brains of healthy mice, highlighting the therapeutic potential of this design. Overall, this work describes a novel method to increase targeted nanoparticle accumulation in the brain.
Rôle de la sous-unité sigma de l'ARN polymérase bactérienne dans la tolérance aux antibiotiques

L’ARN polymerase (ARNP) est l'enzyme centrale d'expression des genes. Toutes les formes de vie possedent de l’ARNP. C’est un complexe proteique forme de plusieurs sous-unites responsables du processus de transcription qui aboutit a la synthese de l’ARN a partir d’une matrice ADN. Les procaryotes possedent un seul type d’ARNP responsable de la synthese de tous les ARNs de la cellule, alors que les eucaryotes possedent trois types d’ARNPs pour la synthese des differents types d’ARNs.L’ARNP est la cible d’un grand nombre de proteines et de petites molecules de regulation dont certains antibiotiques utilises en premiere ligne pour le traitement de diverses maladies infectieuses. La sous-unite sigma de l’ARN polymerase bacterienne est impliquee dans toutes les etapes de l'initiation de la transcription qui est le point crucial de l'expression des genes. Les sous-unites sigma activent par exemple les genes de virulence des bacteries pathogenes et sont impliquees dans la persistance qui est une forme de survie aux traitements antibiotiques.Ce projet a permis de determiner le role de la sous-unite sigma de l'ARN polymerase bacterienne dans la resistance a la lipiarmycine (Fidaxomicin). Nous avons utilise des approches biochimiques, biophysiques et genetiques pour l’etude de la dynamique des interactions ADN-proteine dans les complexes formes par l’ARN polymerase, l’antibiotique et de l’ADN des promoteurs.Les resultats de cette etude montrent que la sensibilite de l’ARNP depend fortement de la structure de la region 3.2 de sigma et que les regions 1.2 et 3.2 de la sous-unite sigma sont impliquees dans la formation du complexe d’initiation de la transcription. Les mutations au niveau de ces regions affectent allosteriquement l'action de la lipiarmycine en compromettant la formation du complexe ouvert. Ces resultats suggerent que la conformation et la mobilite de la region 3.2 dependent fortement de sa sequence. Ces travaux contribueront de maniere significative a la comprehension des bases moleculaires de la resistance aux antibiotiques; Les approches methodologiques developpees pendant ce projet pourront etre etendues a l'analyse d’autres antibiotiques ciblant l’ARNP bacterienne et a l’analyse des autres facteurs de transcription.
Fragilaria rinoi sp. nov. (Fragilariales, Fragilariophyceae) from periphytic river samples in Central Portugal

A new benthic freshwater diatom, Fragilaria rinoi Almeida & C.Delgado sp. nov., is described from river periphyton samples in Portugal. Fragilaria rinoi sp. nov. is illustrated and discussed based on populations collected from the Vouga, Mondego and Lis river basins in central Portugal and compared with the type material of Fragilaria vaucheriae (Kutz.) J.B. Petersen. The morphological features of the new diatom species are documented through light and scanning electron micrographs, including a comparative analysis with related species of the genus ( F. candidagilae Almeida, C.Delgado, Novais & S.Blanco, F. intermedia Grunow in Van Heurck, F. neointermedia Tuji & D.M.Williams, F. recapitellata Lange-Bert. & Metzeltin, F. perminuta (Grunow) Lange-Bert. , F. vaucheriae and F. microvaucheriae C.E. Wetzel & Ector). Fragilaria rinoi sp. nov. is characterized by solitary cells without spines, lanceolate valves with slightly rostrate apices, a narrow, linear axial area, and a large, unilateral central area. Fragilaria rinoi sp. nov. may be confused with F. microvaucheriae in terms of length, striae density and outline, although a morphometric analysis revealed that F. rinoi sp. nov. is significantly wider. Fragilaria rinoi sp. nov. is present in rivers with high dissolved oxygen concentrations, medium to high conductivity, neutral to slightly alkaline pH and high mean values of nitrates and ammonium.
Compatible and incompatible pathogen–plant interactions differentially affect plant volatile emissions and the attraction of parasitoid wasps

The effects of multiple insect attacks on herbivore-induced plant volatiles and carnivorous arthropods are increasingly studied. Phytopathogens also represent an important threat to plants, and plant defence strategies against pathogens and insects are strongly interconnected, yet the potential impact of pathogens on insect-induced volatiles has been largely overlooked, and degree of pathogenicity is rarely considered. We investigated how pathogen challenge, with virulent and avirulent strains of Xanthomonas campestris either alone or with simultaneous Pieris brassicae caterpillar herbivory, affected the volatile emissions of Brassica nigra plants. The impact of these volatiles on the foraging behaviour of Cotesia glomerata parasitoids wasps was then assessed. Pathogens themselves induced volatiles that were highly attractive to parasitoids, and enhanced the attractiveness of host-infested plant volatiles. Chemical analyses revealed that virulent and avirulent strains differentially induced plant volatiles, with primarily sesquiterpene, homoterpene and green leaf volatile compounds contributing to the differences. Strong similarities were found in the blends induced by the virulent strain and caterpillar herbivory. Challenge by either virulent or avirulent pathogens has a significant impact on plant chemistry and its interactions with other community members, demonstrating the importance of integrating pathogen- and insect-based research to broaden our knowledge of plant defences under conditions of increasing complexity.
A Case-Control Study to Determine the Prognostic Features of Salivary Epithelial Cells in Periodontitis

Periodontitis—a biofilm-induced immunoinflammatory pathology—often progresses gradually, exhibiting periodic bursts and resolution. Exfoliating oral epithelial cells act as reservoirs for key periodontal pathogens, facilitating reinfection or infection of new sites. Since saliva is a rich source of oral epithelial cells, we hypothesized that the microbial and functional profile of salivary epithelial cells (SECs) will reflect the in situ host response and disease severity. We used a case-control study design. Unstimulated whole saliva was collected from 20 chronic periodontitis patients and 20 healthy controls in accordance with the institutional review board. The isolated SECs were assessed for viability by trypan blue exclusion. Gram-stained SECs were analyzed by ImageJ, and Gram stain index (GSI) per SEC was calculated. Equal numbers of SECs from each sample were exposed to 2 periodontal pathogens—Porphyromonas gingivalis and Fusobacterium nucleatum—in biofilm or planktonic formulations at varying proportions. Cytokines in culture supernatants were assessed by ELISA (enzyme-linked immunosorbent assay). Additionally, soluble Toll-like receptor 2 (sTLR-2)—a pattern recognition receptor capable of binding microbial ligands associated with periodontitis—was measured in clarified saliva by ELISA. An increased number of SECs, a higher GSI/SEC, and a lower sTLR-2 were observed in periodontitis saliva as compared with healthy saliva. SECs from periodontitis saliva secreted higher amounts of interleukin 8 in response to P. gingivalis, and the presence of F. nucleatum dampened the response. Nonsurgical periodontal treatment improved clinical parameters, reduced the number of SECs, decreased GSI/SEC, and increased sTLR-2 in clarified saliva. In conclusion, our data suggest that SECs can provide a phenotypically distinct individualized resource for assessing epithelial response to pathogens in the course of periodontal disease. Furthermore, correlation between the sTLR-2 and GSI/SEC suggests that the expression profile of epithelial and soluble Toll-like receptor could provide an indirect measure of periodontal disease–associated dysbiosis. Knowledge Transfer Statement: The results of this study can be used for prognostic evaluation of chronic periodontitis in response to therapy and provide an opportunity for early identification of poor responders. A chip-based simple test incorporating the identified salivary epithelial cell characteristics can be developed and validated for future clinical applications, especially for monitoring patients with increased susceptibility for refractory and/or recurrent periodontitis.
Comparison between paper and electronic sleep diary

Abstract This study aimed to test the concurrent validity of an electronic version (to run on tablet) of a sleep diary derived from the core Consensus Sleep Diary compared with the traditional paper and pencil version. To this end, 15 healthy volunteers (6 males; mean age 37.20 ± 17.55 years) every morning, for at least 7 consecutive days, filled both paper and electronic sleep diary. Furthermore, sleep was objectively assessed through actigraphy. With reference to all sleep parameters examined, no significant differences were observed between paper and electronic sleep diary. As expected, paper and electronic sleep diary showed the same poor agreement with actigraphic estimates of sleep quantity and sleep quality. On the basis of the present data, we can conclude that electronic sleep diary performs like paper sleep diary. Bearing in mind that electronic sleep diary presents several benefits in comparison to the paper sleep diary (e.g. avoiding of the “parking lot syndrome”, in which patient retrospectively completes more days at the same time; reducing the time for data entry and scoring), we suggest that, if the present findings will be confirmed also in clinical populations, electronic sleep diary should replace paper sleep diary in both research and clinical settings.
The Role of clusterin in motor neuron disease and the molecular mechanism of its action

University of Wollongong Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorise you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: This work is copyright. Apart from any use permitted under the Copyright Act 1968, no part of this work may be reproduced by any process, nor may any other exclusive right be exercised, without the permission of the author. Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. A court may impose penalties and award damages in relation to offences and infringements relating to copyright material. Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.