Miracle-dz/UniFAR-FTUs huggingface dataset:
Modular Wear Facet Nomenclature for mammalian post-canine dentitions

Abstract Dental wear facets on the occlusal surface of premolars and molars are traces of their main function, the mastication and therefore reflect masticatory movements and also paramasticatory (i.e. non-dietary use of teeth) behavior. Here we present the Modular Wear Facet Nomenclature applicable to most mammalian dentitions. Topographic positions of wear facets in relation to the major cusps and crests of the teeth are used to designate the areas of the occlusal surface the facets occupy (e.g. their mesial, distal, lingual, or buccal position). Previous published systems for labeling wear facets have been inconsistent with each other. Therefore, we provide a synoptic review of the most widely-used terminologies, and introduce the alternative Modular Wear Facet Nomenclature. This nomenclature aims to overcome the difficulties caused by the existing inconsistent wear facet terminologies. Our new approach is applicable to dentitions where the occlusal morphology does not change significantly for most of the lifetime of the animal. In those dentitions, the primary occlusal surfaces are not significantly modified as wear facets become more extensive with wearing. This appears to be a common pattern in pre-tribosphenic, tribosphenic molars, and the teeth derived from tribosphenic precursors (e.g. bunodont molar morphologies). In teeth where the secondary occlusal surface is functionally intensely modified (i.e. high-crowned and evergrowing teeth with large areas of dentine exposed) any facet labeling system appears to be challenging, since the identification of individual facets is blurred and their spatial position may be indeterminable.
Genetic Interplay between Chloroplast Protein Import and Thylakoid Complex Assembly in Arabidopsis thaliana

II Acknowledgements III List of abbreviations used in this thesis VIII Chapter 1: General Introduction Chloroplast Protein Import and the Routing of Proteins to the Chloroplast Compartments . 1 1.1 Abstract . 2 1.2 Plastids: Form, functions, evolution . 3 1.2.1 Algae acquired chloroplasts through endosymbiosis . 3 1.2.2 Plastids are not always green . 4 1.2.3 Plastids fulfill a large variety of essential functions . 6 1.3 Protein import into chloroplasts . 11 1.3. 1 Targeting of proteins to the chloroplast requires a transit peptide . 11 1.3. 2 Most chloroplast proteins are targeted via the general import pathway . 13 1.3. 3 Toc159 and Toc34 are the primary receptors for transit peptide binding . 17 1.3. 4 Toc75 forms the preprotein channel in the outer envelope membrane . 19 1.3. 5 The existence of an intermembrane space complex is uncertain . 20 1.3. 6 Tic110 and Tic20/21 are candidates for the inner envelope protein channel . 22 1.3. 7 Tic110, Tic40 and Hsp93 form a motor complex at the stromal side of TIC . 25 1.3. 8 Transit peptides are removed and degraded after import . 29 1.4 Targeting of proteins to the thylakoids . 32 1.4. 1 Targeting to the thylakoid lumen occurs via the cpSec or cpTat pathway . 32 1.4. 2 Targeting to the thylakoid membranes occurs mostly via the cpSRP pathway 34 1.4. 3 ALB3 and ALB4 have distinct roles in Arabidopsis thylakoid biogenesis . 36 1.5 Aims. 39 1.6 Figures. 40 Chapter 2: Results I Characterisation of stic1 and stic2, Two Suppressors of the Protein Import Mutant tic40 . 42 2.1 Abstract . 43 2.2 Introduction . 44 2.3 Results . 49
Enzymatic browning of foods

The mechanism of enzymatic browning of foods which in most cases affects adversely the quality of foods is briefly described. Enzymatic browning is in most cases connected with the action of polyphenol oxidase (PPO), which in the presence of oxygen hydroxylates colorless monophenols to o-diphenols which are subsequently oxidized to colored o-quinones. Through a series of nonenzymatic reactions, o-quinones are often converted irreversibly to brown polymeric pigments. In order to prevent the deteriorating effect of enzymatic browning, various inhibitors are applied during processing and storage of foods. The inhibition of enzymatic browning generally proceeds via the following three mechanisms: 1. Direct inhibition of polyphenol oxidase, 2. Nonenzymatic reduction of o-quinones which are formed by enzymatic oxidation of o-phenols to the derivatives of o-diphenols, and 3. Chemical modification or removal of phenolic substrates of polyphenol oxidase. The most efficient multifunctional agents in control of enzymatic browning of foods are various sulfites. However, their use is in many cases limited by sanitary regulations. For this reason a very intensive research in the development of sulfite alternatives is underway. The best known alternative to sulfite in control of browning of foods is L-ascorbic acid and its cheaper stereoisomer D-ascorbic acid commercially known as erythorbic acid. The other well known substitute to sulfites is 4-hexylresorcinol, a part of EverFresh formulation. Very active inhibitors of enzymatic browning are various chelating agents, which either directly form complexes with PPO, or react with its substrates. Example of an inhibitor which reacts with the copper containing prosthetic group of PPO is b-cyclodextrin. Other inhibitors of enzymatic browning which are commercially used are: sulfhydryl containing amino acids, specially cysteine and reduced glutation, inorganic salts, like sodium and zinc chloride, and honey which inhibits the browning of white grapes. As part of our own work, the effect of erythorbic acid applied under pressure or vacuum to the discoloration of fruit and vegetables and the importance of proper selection of cultivar are briefly described in this review.
New trends in diagnosing and treating ovarian cancer using nanotechnology

Ovarian cancer stands as the fifth most prevalent cancer among women, causing more mortalities than any other disease of the female reproductive system. There are numerous histological subtypes of ovarian cancer, each of which has distinct clinical characteristics, risk factors, cell origins, molecular compositions, and therapeutic options. Typically, it is identified at a late stage, and there is no efficient screening method. Standard therapies for newly diagnosed cancer are cytoreductive surgery and platinum-based chemotherapy. The difficulties of traditional therapeutic procedures encourage researchers to search for other approaches, such as nanotechnology. Due to the unique characteristics of matter at the nanoscale, nanomedicine has emerged as a potent tool for creating novel drug carriers that are more effective and have fewer adverse effects than traditional treatments. Nanocarriers including liposomes, dendrimers, polymer nanoparticles, and polymer micelles have unique properties in surface chemistry, morphology, and mechanism of action that can distinguish between malignant and normal cells, paving the way for targeted drug delivery. In contrast to their non-functionalized counterparts, the development of functionalized nano-formulations with specific ligands permits selective targeting of ovarian cancers and ultimately increases the therapeutic potential. This review focuses on the application of various nanomaterials to the treatment and diagnosis of ovarian cancer, their advantages over conventional treatment methods, and the effective role of controlled drug delivery systems in the therapy of ovarian cancer.
Numerical taxonomy of eight Salvia L. species using anatomical properties

The anatomical characters of eight Salvia species of the Lamiaceae family have been investigated. The stem is regular or irregular quadrangular, with collenchymatous hypodermis, sclerenchyma group above vascular bundles with different number layers in species. Stems and petioles have glandular and eglandular hairs. Also, a cluster analysis was performed with nineteen anatomical characters. Based on our results, two main clusters separate two groups of species and the taxonomical results have been illustrated.
There is more to maerl than meets the eye: DNA barcoding reveals a new species in Britain, Lithothamnion erinaceum sp. nov. (Hapalidiales, Rhodophyta)

ABSTRACT Due to the high plasticity of coralline algae, identification based on morphology alone can be extremely difficult, so studies increasingly use a combination of morphology and genetics in species delimitation. A DNA barcoding study was carried out on maerl-forming coralline algae using the mitochondrial cytochrome oxidase 1 gene, CO1, and the plastid gene, psbA, on field specimens from Falmouth and Oban together with herbarium specimens from the Natural History Museum, UK, and the Smithsonian Institution, Washington, USA. Results revealed the presence in the north of Britain of a new species, Lithothamnion erinaceum Melbourne & J. Brodie, sp. nov., which was previously misidentified as Lithothamnion glaciale. The results also indicated that Lithothamnion lemoineae, which had earlier been recorded from Britain, was not present. One of the biggest concerns at present is how organisms will respond to climate change and ocean acidification, and it is imperative that investigations are put on a firm taxonomic basis. Our study has highlighted the importance of using molecular techniques to aid in the elucidation of cryptic diversity.
First Discovery of the Lichen-Feeding MothBacotia sakabei (Lepidoptera: Psychidae) from Korea

The family Psychidae is a small group consisting of 241 genera and 1,350 species in the world. The genus Bacotia , belonging to the family Psychidae, what was established by Tutt based on the type species, Fumea sepium Speyer and Speyer, 1846. In this study, we aimed to record lichen­feeding bagworms in Korea. The genus Bacotia Tutt is reported for the first time from Korea with one newly recorded species, Bacotia sakabei Seino, 1981. All available information, including the collecting localities, host plants, illustrations of adults and genitalia are presented. A DNA barcode for precise identification of the species is also described.
The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen Campylobacter jejuni

Worldwide, the food-born pathogen Campylobacter jejuni is the leading bacterial source of human gastroenteritis. C. jejuni produces a variety of diverse cell-surface carbohydrates that are essential for pathogenicity. A critical component of these oligo- and polysaccharides is the sugar N-acetylgalactosamine (GalNAc). The sole source of this sugar is the epimerization of UDP-N-acetylglucosamine (GlcNAc), a reaction catalyzed by the enzyme UDP-GlcNAc 4-epimerase (Gne). This enzyme is unique among known bacterial epimerases in that it also catalyzes the equivalent reaction with the non-N-acetylated sugars. Understanding how CjGne catalyzes these various interconversions is critical to designing novel inhibitors of this enzyme. Here, to further the mechanistic understanding we present a 2. 0Å structure of CjGne with its NAD+ co-factor bound. Based on novel features found in the structure we perform a variety of biochemical studies to probe the mechanism and compare these results to another bifunctional epimerase, human GalE. We further show that ebselen, previously identified for inhibition of HsGalE, is active against CjGne, suggesting a route for antibiotic development.
Protection de la levure Saccharomyces cerevisiae par un système biopolymérique multicouche : effet sur son activité métabolique en réponse aux conditions de l'environnement

Dans le but de proteger la levure Saccharomyces cerevisiae pendant la deshydratation, deux strategies ont ete envisagees pour ameliorer la survie cellulaire. D’une part, le renforcement de la resistance a l’oxydation (protection interne) a ete realise par l’enrichissement en glutathion intracellulaire de la levure. D’autre part, l’encapsulation par la methode couche-par-couche (layer-by-layer) en utilisant deux biopolymeres β-lactoglobuline et alginate a ete utilisee pour la protection externe de la levure. Un milieu adequat ainsi que des conditions favorables de culture permettant l’enrichissement en glutathion intracellulaire ont ete determines. La composition du milieu est riche en nutriments et precurseurs du glutathion se composant de 30 g/L de glucose, 30 g/L d’extrait de levure, 0,6 g/L de KH2PO4 et 0,6 g/L de cysteine. Le succes de l’encapsulation a ete confirme par differentes methodes d’analyse comme la zetametrie, la microscopie electronique et la spectroscopie infrarouge. Le depot des trois couches de β-lactoglobuline/alginate/β-lactoglobuline n’a pas affecte l’integrite membranaire et la croissance de la levure. De plus, la permeabilite membranaire n’a pas ete empechee par la presence de cette barriere biopolymerique. L’effet de l’enrichissement en glutathion et de l’encapsulation sur la resistance de la levure dans les conditions de deshydratation choisies a ete mesure par l’estimation de la survie, les modifications biochimiques et le metabolisme des cellules. Les resultats ont montre que la levure enrichie en glutathion presente une meilleure survie apres la deshydratation. De plus, la survie de la levure est amelioree par l’encapsulation, en particulier pendant la deshydratation a 45 °C. L’analyse des resultats d’infrarouge a releve un point commun dans la relation entre les proprietes biochimiques de la cellule et la survie cellulaire. Plus le groupement methyle (CH3) est important, plus la survie est importante. Le role du glutathion dans la protection de la levure a egalement ete mis en evidence pendant la deshydratation. Il semblerait que l’action du glutathion oxyde ait ete mise en place apres l’intervention du glutathion reduit. De plus, la protection interne par le glutathion a permis a la levure de resister au stress chimique alors que la protection externe par encapsulation renforce la resistance contre les stress physique ou mecanique. Les resultats de la these pourront etre utiles pour la recherche des nouvelles technologies de production et de protection des levures fragiles actives.
Accumulation and physiological response of cadmium in Hydrocharis dubia

Abstract The effects of increasing concentrations of cadmium (Cd) on the ultrastructure, Cd accumulation, nutrient elements contents, levels of chlorophyll pigments, hydrogen peroxide (H2O2), malondialdehyde (MDA), antioxidants, as well as the activities of antioxidant enzymes were investigated in the leaves of Hydrocharis dubia (Bl.) Backer. Cd exposure resulted in significant damage in chloroplasts and mitochondria, suggesting that Cd hastened the senescence of the tested plants. The accumulation of Cd was found to increase in a concentration dependent manner with a maximum of 1088 μg g−1 at 80 μM. The levels of Ca, P and Cu declined and the levels of Mg increased under all Cd concentrations, but K and Fe contents increased initially and decreased thereafter. Pigment content decreased with the rise of the Cd concentrations. H2O2 content enhanced gradually at all Cd concentrations. MDA content increased progressively up to 60 μM Cd, followed by a decline at higher concentration. The effect of Cd application on ascorbate (AsA) and reduced glutathione (GSH) contents was similar to that seen for H2O2 content. Peroxidase (POD) and catalase (CAT) activities first increased and then decreased, while superoxide dismutase (SOD) activity markedly decreased. Results suggest that Cd-induced oxidative damage in H. dubia is closely associated with the efficiency of its intrinsic antioxidant mechanisms, both the disorder of nutrient elements and the damage to the ultrastructure were indicative of general disarray in the cellular functions exerted by Cd.
First record in Japan of tortoise tick Amblyomma Geoemydae (Cantor 1847) (Acari: Ixodidae) parasitizing Pryer’s keelback snake Hebius Pryeri (Boulenger, 1887) (Reptile: Colubridae)

ABSTRACT Two larvae of tortoise tick Amblyomma geoemydae (Acari: Ixodidae) were collected from the fresh remains of a Pryer’s keelback snake Hebius pryeri (Boulenger, 1887), likely dead from accidental causes at the Kunigami-son in northern Okinawa Island, Okinawa Prefecture, Japan. This is the first such host record for A. geoemydae in Japan. Based on this finding, we have updated the available collection records of ticks found on Japanese snakes.
Targeting Introduced Species to Improve Plant Community Composition on USFWS-Managed Prairie Remnants

ABSTRACT: The quality of plant community composition on US Fish and Wildlife Service (USFWS) lands in North Dakota and South Dakota has declined over the past several decades—the abundance of native species has decreased while the abundance of introduced species has rapidly increased. Extensive efforts have been made to improve plant community composition on USFWS prairies; however, there was not a unified approach to this end in North Dakota and South Dakota until the advent of the Native Prairie Adaptive Management (NPAM) program. The NPAM program provides decision support for the selection of management actions to improve plant community composition of tallgrass and mixed-grass prairies in the Northern Great Plains. We evaluated plant community composition on USFWS native tallgrass and mixed-grass prairie remnants enrolled in the NPAM program in North Dakota and South Dakota to examine effects of management on plant community composition. Our analysis suggests that incorporating certain management actions can improve plant community characteristics on the agency's tallgrass and mixed-grass prairies. We documented increased native species richness and decreased Bromus inermis (smooth brome) relative cover at sites that had been burned two or more times during a four-year period. In contrast, smooth brome relative cover was higher at sites managed by the exclusion of fire and intermittent light grazing or rest. Smooth brome is extremely invasive in native prairie remnants throughout the Northern Great Plains. Thus, our results have marked implications for managers working to reduce the prevalence of smooth brome on public and private lands.
Techniques for the identification and differentiation of Cronobacter species

The Cronobacter genus currently consists of seven species: C. condimenti, C. dublinensis, C. malonaticus, C. muytjensii, C. sakazakii, C. turicensis, and C. universalis. The work presented here was undertaken to examine different methods for detection, identification, and characterization of the members of this genus. First, traditional cultural, biochemical, and molecular detection and identification methods were examined with regard to taxonomic changes that occurred within the genus in 2013. This work showed that these methods may not be sufficient for accurate and specific detection and identification of all Cronobacter spp. Next, the DNA sequence-based method of multilocus sequence typing (MLST) was used to identify and characterize a collection of Cronobacter strains and these results were used in a variety of applications. These sequences were used to identify a novel species, characterize outbreak strains, and resolve discrepancies in species identification. It was also shown that MLST does not necessarily correlate to observable phenotypes. This led to the final portion of work which used whole genome sequences to guide laboratory experiments and data analysis. First, the mutS-rpoS genomic region of Cronobacter spp. was examined. Though this region is highly variable in other related species, all seven Cronobacter spp. contained the same genes in this region, in the same order, indicating that these genes are not likely to be related differences in virulence observed between the species. Finally, production of cellulose as a component of the bacterial capsule was examined. An attempt was made to link colony morphologies on infant formula agar and Congo red agar to the genotypes as determined from whole genome sequence analysis. While some results could be explained by the differences identified in the cellulose gene cluster, it was not possible to predict the phenotype based only on these gene sequences. This is likely due to the presence of four additional components in the capsule of Cronobacter spp. Future work developing a capsular typing scheme and linking these capsular profiles to observable phenotypes is also discussed.
DNA-dependent protein synthesis exhibited by cancer shed particulates

Genetic heterogeneity in tumours is the bonafide hallmark applicable to all cancer types (Burrell et al, 2013). Furthermore, deregulated ribosome biogenesis and elevated protein biosynthesis have been consistently associated with multiple cancer types (Ruggero, 2012; Ruggero & Pandolfi, 2003). We observed that under cultivation conditions almost all cancer cell types actively shed significant amount of particulates as compared to non-malignant cell lines requiring frequent changing of cultivation media. We therefore asked if cancer cell shed particulates might still retain biological activity associated with protein biosynthesis. Here, we communicate our observations of DNA-dependent protein biosynthetic activity exhibited by the cell-free particulates shed by the cancer cell lines. Using pulsed isotope labelling approach we confirmed the cell-free protein translation activity exhibited by particulates shed by various cancer cell lines. Interestingly, the bioactivity was largely dependent on temperature, pH and on 3’-DNA elements. Our results demonstrate that cancer shed particulates are biologically active and may potentially drive expression of tissue non-specific promoters in distant organs.
First report of the brown shrimp Penaeus aztecus Ives, 1891 (Crustacea, Decapoda, Penaeidae) in the Tyrrhenian Sea

Two specimens of the penaeid shrimp Penaeus aztecus, a West Atlantic species, were collected off Castiglione della Pescaia, Tyrrhenian coast of Italy. The species identity was confirmed based on morphological characters and by sequencing 510 nucleotides of the mtDNA 16sRNA gene. This alien species has been previously recorded off Turkey, Greece and Montenegro.
Plant growth regulators on sweet sorghum: physiological and nutritional value analysis

Sweet sorghum has gained attention in tropical and subtropical regions because of its potential as a bioenergy crop. The present research was carried out to evaluate the physiological, biochemical and nutritional characteristics of sweet sorghum submitted to six plant growth regulators (thiamethoxam, biostimulant mixture, gibberellic acid, chlormequat chloride, ethephon, and trinexapac-ethyl). The compounds were applied via foliar spraying in order to increase the productive potential of plants and reduce the carbohydrates sink strength by inflorescences. The experiment was conducted in pots and the following variables were evaluated: plant height, inflorescence dry matter, soluble solids content, shoot dry matter, crude protein, ashes, neutral detergent fiber and in vitro digestibility. It were observed the action of trinexapac-ethyl and ethephon to reduce the inflorescence dry matter, chlormequat chloride to increase the shoot dry matter, and trinexapac-ethyl to improve ashes content and reduce the neutral detergent fiber contents. These results indicate that chlormequat chloride and trinexapac-ethyl are effective in restricting the plant growth and increasing sorghum nutritional quality.