Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of ISSR-PCR system and assessing genetic diversity amongst turf grass (Cynodon dactylon) mutants

Cynodon dactylon Pers. is highly valued warm season turf grass having global adaptability, robustness and resistance to trampling. In the present study, the ISSR protocol was standardized and quantities of template DNA, dNTPs, MgCl2, Taq DNA polymerase, primer concentration and annealing temperature for each primer were worked out. The reproducible amplifiable products were obtained in all PCR reactions. Analysis of molecular variance (AMOVA), Genetic diversity, Nei’s gene diversity, Shannon’s index, and Nei’s unbiased genetic distance, partition, within- and among-group, of all parameters was analyzed. Levels of genetic divergence between samples were calculated with the fixation index PhiPT. Statistics with AMOVA revealed 1 and 99 % variance among and within various mutants, respectively. Cluster analysis based on the Unweighted-Pair Group Method arithmetic Average (UPGMA), principal coordinate analysis (PCA) and Spatial correlation is a measured that looks at the relationship (genetic distance) amongst mutants. PCOA analysis of ISSR data showed that the first three factors comprised about 75.20% of total variance when the first, second and third axis comprised about 36.64, 23.96 and 14.63% of total variance, respectively. Variation within mutants was the maximum in DFR-C-448 followed by DFR-C-446(10.357). In DFR-C-448 unique number of bands to a single population was observed. Correlogram plot shows that there is significant positive genetic structure at distance class of mutants DFR-C-448.
Induced Responses to Herbivory

Plants face a daunting array of creatures which eat them, bore into them and use virtually every plant part for food or shelter. However, plants are far from defenceless under attack. Although they cannot flee their attackers, they can produce defences, such as thorns, and can actively alter their chemistry and physiology in response to damage. For instance, young potato leaves being eaten by potato beetles respond by producing chemicals which inhibit beetle digestive enzymes. Research on these induced responses to herbivory has proceeded since the 1980s, and this comprehensive evaluation and synthesis of a rapidly-developing field provides state-of-the-discipline reviews, and highlights areas of research which might be productive. This overview should appeal to a wide variety of theoretical and applied researchers in ecology, evolutionary biology, plant biology, entomology and agriculture.
The role of telomerase in brain during ageing and under dietary restriction

ii Declaration . iii Acknowledgements . iv List of figures . viii List of tables . x List of abbreviation . xi Chapter1 – Introduction . 1 1.1. Cellular senescence and organismal ageing . 1 1.2. Mitochondria . 3 1.2.1. Structure and function of mitochondria . 3 1.2.2. The role of mitochondria in senescence and ageing . 6 1.3. Dietary restriction and related signalling pathways . 9 1.3. 1. Dietary restriction . 9 1.3. 2. The role of mTOR pathway in DR response . 11 1.4. Structure and canonical function of telomerase . 14 1.4. 1. TERT and TERC complex . 14 1.4. 2. Canonical function of telomerase . 17 1.4. 3. Non-canonical functions of telomerase . 23 1.5. TERT in mitochondria . 25 1.5. 1. TERT shuttling and localisation . 25 1.5. 2. Functions of TERT protein in mitochondria . 28 1.6. Telomerase in mammalian brain and its role in neurodegenerative diseases . 31 1.7. Telomerase in mammalian liver . 34 1.8. Aims . 35 Chapter 2 Materials and methods . 36 2.1. Mice . 36 2.2. Genotyping . 36 2.3. Design of the dietary restriction experiments . 39 2.4. Rapamycin supplemented diet experiment in vivo . 39 2.5. ROS generation in female brain mitochondria.39 2.6. Mouse and human cell lines . 40
Uso de diferentes explantes e concentrações de benzilaminopurina na multiplicação in vitro de brotos de kielmeyera coriacea

Segmentos nodais e apicais de K. coriacea foram imergidos em meio basico de M.S. (Murashige/Skoog, 1962) com seis diferentes concentracoes de benzilaminopurina (BAP). Os segmentos nodais mostraram maior capacidade de producao de brotos (> 1,0 cm) que os apicais, sendo que a melhor percentagem de brotos foi conseguida com 0,5 mg/1 BAP. Ambos os segmentos sao sensiveis a niveis elevados de BAP, nao sendo eficazes para o crescimento e desenvolvimento dos explantes.
Studying Proteins Implicated in Cancer with a Computational Toolbox

Cancer formation is a complex, multi-step process that allows cells to grow abnormally and potentially invade and spread throughout the body. A single genetic or structural alteration of a single protein in a cellular physiological process is enough to stimulate cancer formation. In treating cancer, a ‘targeted therapy’ approach is becoming increasingly common, where we can develop drugs that specifically target these altered proteins implicated in cancer. Two proteins that are heavily involved in several human cancers are protein kinases and p53, which are the focus of this dissertation work. I chose to use molecular dynamics simulations and in silico virtual screening, two methods from the computational chemistry toolbox in studying protein kinases and p53. I demonstrate that performing molecular dynamics is worthwhile in conducting virtual screens against protein kinases, because it may result in that at least one conformation is more predictive than the crystal structure. I also reveal key insight into the transcriptional activation mechanism of p53, and show how this mechanism is altered as a result of the R175H cancer mutation.
Protein stabilization via hydrophilization

This paper experimentally verifies the idea presented earlier that the contact of nonpolar clusters located on the surface of protein molecules with water destabilizes proteins. It is demonstrated that protein stabilization can be achieved by artificial hydrophilization of the surface area of protein globules by chemical modification. Two experimental systems are studied for the verification of the hydrophilization approach. The surface tyrosine residues of trypsin are transformed to aminotyrosines using a two-step modification procedure: nitration by tetranitromethane followed by reduction with sodium dithionite. The modified enzyme is much more stable against irreversible thermoinactivation: the stabilizing effect increases with the number of aminotyrosine residues in trypsin and the modified enzyme can become even 100 times more stable than the native one. Alpha-chymotrypsin is covalently modified by treatment with anhydrides or chloroanhydrides of aromatic carboxylic acids. As a result, different numbers of additional carboxylic groups (up to five depending on the structure of the modifying reagent) are introduced into each Lys residue modified. Acylation of all available amino groups of alpha-chymotrypsin by cyclic anhydrides of pyromellitic and mellitic acids results in a substantial hydrophilization of the protein as estimated by partitioning in an aqueous Ficoll-400/Dextran-70 biphasic system. These modified enzyme preparations are extremely stable against irreversible thermal inactivation at elevated temperatures (65-98 degrees C); their thermostability is practically equal to the stability of proteolytic enzymes from extremely thermophilic bacteria, the most stable proteinases known to date.
Camanchaca,a new genus of Roccellaceae(Arthoniales,Loculoascomycetidae)from the Atacama Desert,North Chile,South America

: Camanchaca Follm. & Peine gen. nov. (aff. Fo/lmannie/la Peine & B. Wern.) is de scribed as new genus of Roccellaceae (Arthoniales). It is based on C. corallina Follm. & Peine sp. nov. from the rocky coast of the Atacama Desert, North Chile, where also a second species, C. ligula ta Peine & Follm. , occurs. Camanchaca is unique among the other genera of the family with regard to the following characters: perennial crustose thalli bearing fragile, polymorphic, fruticose pseudopodetia, irregularly interwoven cortical and reticular medullary hyphae, accumulation of con siderable amounts of psoromic acid, ascomata and conidiomata often united to synascornata and syn conidiomata, the first appearing as multiascal, pluricarpocentral, lecanorine discothecia of the Roc cella-type, the second being protrusive and corresponding to the acervular Lecanactis-type. The chorological, sociological, ecological and developmental attributes of the new taxa are outlined. Roc ce/la babingtonii Mont. , R. di.fficilis Darb. , R. dubia Darb. and R. montagnei Bel. should be deleted from the catalogue of Chilean lichens. However, with five endemic genera and 31 endemic species, the Atacama coastland holds its position as the primary diversity centre of the Roccellaceae s. str.
The Multiplicity of Heat Stress Transcription Factors Controlling the Complex Heat Stress Response of Plants

Heat stress proteins (Hsp) and heat stress transcription factors (Hsf) are structurally and functionally conserved elements of the eukaryotic heat stress response. However, compared to other organisms, plants have much more elaborate systems of chaperones and at least 21 transcription factors controlling their expression. I
Influence of environmental factors on seed germination and emergence of Chromolaena odorata in coconut plantations in Sri Lanka.

Chromolaena odorata L. King and Robinson (Asteraceae) is a prominent and dominant weed species in coconut plantations in Sri Lanka. This study reports laboratory and greenhouse studies conducted to determine the effects of several environmental factors on seed germination and seedling emergence of chromolaena seeds for means of developing control strategies. Seed germination was greatly reduced in solutions with osmotic potentials below -0.3MPa (13% at -0.4MPa and 5% at -0.6MPa). The highest germination was at 0 MPa, and germination was not observed at -0.9MPa. The optimum pH range for germination of chromolaena seed was between 5 and 7, although some seeds, germinated at pH levels of 4 and 8. Maximum chromolaena emergence occurred when seeding depth reached 4 cm. No seedlings emerged when seed was exposed to flooding for 13 days or more. The highest percentage (72%) of seed emerged from a depth of 1cm when not exposed to flood conditions. These results suggest that chromolaena seed is capable of germinating and surviving in a variety of climatic and edaphic conditions, and that flooding is not a viable management option for controlling this weed after emergence.
Etude de la composition et de l'assemblage du pore de translocation du système de sécrétion de type III chez Pseudomonas aeruginosa

Pseudomonas aeruginosa est un pathogene opportuniste responsable d'infections graves chez les individus immunodeprimes et chez les personnes atteintes de mucoviscidose. Cette pathogenicite repose sur de nombreux facteurs de virulence, dont l'un, le systeme de secretion de type III (SSTT) est present chez un grand nombre de bacteries pathogenes a Gram negatif. Ce systeme de secretion permet a la bacterie d'injecter des effecteurs cytotoxiques directement dans le cytoplasme de la cellule eucaryote cible. Chez P. aeruginosa, le SSTT est constitue d'un appareil de secretion, appele Psc (Pop secretion) permettant le passage des effecteurs a travers les membranes bacteriennes, et d'un translocon, code par l'operon pcrGVHpopBD, permettant l'injection des effecteurs cytotoxiques dans le cytosol de la cellule eucaryote. Nous avons montre dans le laboratoire que l'isolat clinique CHA de P. aeruginosa est capable d'echapper a l'activite bactericide des polymorphonucleaires neutrophiles humains (PMNs) et d'induire une mort rapide par oncose des phagocytes (Dacheux et al., 2000). Dans un premier volet, l'utilisation des hematies comme modele cellulaire m'a permis de montrer que cette oncose est precedee par la formation de pores, de taille estimee entre 28 et 35 A, dans la membrane cytoplasmique de ces cellules. Des experiences de mutagenese montrent que la formation de ces pores requiert les proteines PcrV, PopB et PopD. L'analyse par Western blot de membranes isolees d'hematies infectees par P. aeruginosa indiquent que les proteines PopB et PopD constituent le pore de translocation insere dans la membrane cytoplasmique des cellules eucaryotes. La proteine PcrV, qui n'est jamais retrouvee dans la fraction membranaire d'hematies infectees par P. aeruginosa, agit a la surface de la bacterie comme une « chaperonne extracellulaire » responsable de l'assemblage de PopB et PopD en un complexe hetero-oligomerique. Le second volet traite du mecanisme d'action des anticorps protecteurs anti-PcrV contre les infections a P. aeruginosa. Des experiences de fractionnement d'hematies infectees par P. aeruginosa en presence de ces anticorps protecteurs a permis d'etablir que ces derniers inhibent l'assemblage du pore de translocation du SSTT.
Peptide and Protein Neurotoxin Toolbox in Research on Nicotinic Acetylcholine Receptors

The chapter briefly covers the history of protein and peptide neurotoxins in research on nicotinic acetylcholine receptors (nAChR). It all started with a great help of α-bungarotoxin and other similar α-neurotoxins from snake venoms in isolation from the Torpedo ray electric organ of the muscle-type nAChR as a first individual membrane receptor. The next contribu‐ tion of α-neurotoxins was the discovery with their aid of the first neuronal nAChR in the brain now known as homooligomeric α7 nAChR. An overview of various α-neurotoxins (so-called three-finger toxins) is presented below showing the structural differences between them, as well as the benefits of their current application for identification and quantification of different nAChR subtypes at normal state and at various pathologies such as Alzheimer’s and Parkin‐ son’s diseases, psychiatric diseases and nicotine addiction. A special emphasis is placed on the work at our institute, starting with the first detection of nAChRs as targets for the so-called weak or “non-conventional” neurotoxins. Recently, in proteomic studies of snake venoms, novel structural types have been discovered, such as covalently connected dimeric α-cobra‐ toxin or, on the contrary azemiopsin, the first peptide from venoms which does not contain disulfide bonds but still blocks selectively the muscle-type nAChR.
Influence of Water Activity on Growth, Metabolic Activities and Survival of Yeasts and Molds.

The behavior of yeasts and molds as influenced by water activity (aw) is reviewed. Fungal spoilage of foods occurs more often than bacterial spoilage at aw 0.61-0.85 not because fungi grow faster at reduced aw but rather because the competitive effects of the vast majority of bacteria are absent. Higher aw is generally required for spore formation than for spore germination. The range of aw permitting germination of spores is greatest at an optimum temperature, but optimum availability of nutrients tends to broaden the range of aw and temperature at which germination and growth will occur. The minimum aw levels for growth of fungi are lower than those required for mycotoxin production. It is imperative that diluents and enumeration media with reduced aw be used to detect xerotolerant fungi in foods. Otherwise, vegetative cells and spores may be killed by osmotic shock or remain dormant when exposed to high aw associated with diluents and media routinely used for mycological analyses.
Development of Pichia pastoris as a ruminal escape vehicle

The yeast expression system Pichia pastoris was investigated as an encapsulation technology capable of serving as a rumen escape vehicle. Cellularly encapsulated protein is protected from the ruminal environment so long as the cell membrane, which surrounds and isolates the intracellular protein is physically intact. Intracellular expression of Green Fluorescent Protein (GFP) allows for the monitoring of cellular integrity as necessary for the protection of encapsulated protein from ruminal proteases. Upon cellular lysis GFP is exposed to extracellular proteases which result in both the proteolytic degradation of the protein-based GFP chromophore and its associated fluorescence. Visualization of rumen fluid under epifluorescent microscopy revealed a high level of background autofluorescence owing to the fluorescent plant particles, microbes, and fluorescent compounds therein. Visualization of GFP in rumen fluid can be optimized through GFP variant selection, filter set design, and light source selection based on bulb emission spectra. Incubation of intracellular GFP expressing P. pastoris in batch culture ruminal in vitro simulations demonstrated that 93%, 97%, and 25% of the P. pastoris inoculum maintained cellular integrity in clarified rumen fluid, bacterial fraction of rumen fluid, and whole rumen fluid, respectively, when incubated over 36 to 48 h. Continuous fermentation in vitro rumen simulations (Rusitec) demonstrated a P. pastoris escape rate of 19% when added daily to fully adapted Rusitec vessels having a dilution rate of 0.75 d"1. Abomasal in vitro simulations demonstrated that 84% of the P. pastoris inoculum was lysed within 12 h, as necessary for the release of encapsulated protein. P. pastoris may be an effective post-ruminal delivery vehicle, provided that similar results are obtained in vivo.
FCRLA is an intracellular FcR-related protein that binds IgM, IgG and IgA isotypes in B cells (45.11)

Fc-receptor-like A (FCRLA) is a novel member of the extended Fc receptor (FcR) family. Unlike the classical FcRs and Fc receptor-like (FCRL) molecules, which are typically transmembrane receptors with extracellular ligand binding domains, FCRLA has no predicted transmembrane domain or N-linked glycosylation sites and is positioned intracellularly. We show by confocal microscopy and biochemical assays that FCRLA is a soluble, resident ER protein; however, it lacks a characteristic KDEL retention sequence at its C-terminus. Using a series of deletion mutants, we found that its ER retention is most likely mediated by the amino terminal domain. We have also recently identified ER localized immunoglobulin as an FCRLA ligand. These results indicate that FCRLA is unique among the large FcR family in that can associate with multiple immunoglobulin isotypes, including IgM, IgG, and IgA. To better understand the role of this protein in human disease, B cell chronic lymphocytic leukemia (CLL) samples were assayed for FCRLA expression by flow cytometry. Interestingly, the receptor was more highly expressed by the indolent form of CLL, which is distinguished by somatically hypermutated heavy chain variable region genes, than by the aggressive high-risk form, which features more germline B cell receptor characteristics. These results indicate that FCRLA may thus be a useful diagnostic marker for CLL.
Determination of the Real Distance of Mandibular Third Molar to Inferior Alveolar Canal

Aims: To determine the real not radio graphical proximity of mandibular third molar tooth to the inferior dental canal (IDC) using panoramic radiograph. Materials and Methods: 144 mandibular third molars were evaluated by panoramic radiography. The teeth were grouped into erupted vs. un erupted further subdivided by tooth angulations. The real distance from the most inferior aspect of the mandibular third molar tooth to the superior border of the inferior alveolar canal (IAC) was calculated regarding to the reference object used. Descriptive statistics were performed as well as a t test was performed to compare erupted and unerupted teeth, and ANOVA was used to determine a significant difference where exists based upon tooth angulations. In addition, intra observer analysis was done to ensure the standardization of the radiologist interpretation. Results: The mean distance from erupted mandibular third molar teeth to the inferior alveolar canal was 0.23mm. This distance was significantly different from unerupted teeth (P = .000). The mean values for unerupted teeth were negative values which indicated that the apices of all teeth measured was below the superior border of the canal –1.26 mm and as follows: Mesioangular–1.32 mm, vertical – 1.34 mm and –1.04mm for horizontal impactions. Statistically there was no significant positional difference between the impaction groups (P = .835). In general there was a significant difference in third molar position between those age equal and less than 22 years old and those equal and over 23 years old. Conclusions: Unerupted mandibular third molar teeth (mostly vertical impaction) are closer to the inferior alveolar canal than erupted teeth and persons in general of an age equal or less than 23 years old have a closer lower third molar to mandibular canal than other ages and there is no significant relation between this age group and any of impaction types.
Alternative Respiratory Pathways in Higher Plants

Rapid developments in molecular and systems biology techniques have allowed researchers to unravel many new mechanisms through which plant cells switch over to alternative respiratory pathways. This book is a unique compendium of how and why higher plants evolved alternative respiratory metabolism. It offers a comprehensive review of current research in the biochemistry, physiology, classification and regulation of plant alternative respiratory pathways, from alternative oxidase diversity to functional marker development. The resource provides a broad range of perspectives on the applications of plant respiratory physiology, and suggests brand new areas of research. Other key features: written by an international team of reputed plant physiologists, known for their pioneering contributions to the knowledge of regular and alternative respiratory metabolism in higher plants includes step-by-step protocols for key molecular and imaging techniques advises on regulatory options for managing crop yields, food quality and environment for crop improvement and enhanced food security covers special pathways which are of key relevance in agriculture, particularly in plant post-harvest commodities Primarily for plant physiologists and plant biologists, this authoritative compendium will also be of great value to postdoctoral researchers working on plant respiration, as well as to graduate and postgraduate students and university staff in Plant Science. It is a useful resource for corporate and private firms involved in developing functional markers for breeding programs and controlling respiration for the prevention of post-harvest losses in fruit, vegetables, cut flowers and tubers.
Untersuchung zum Vorkommen und Verlauf von Epilepsie unbekannter Ursache bei der Katze

Background: The diagnosis of feline epilepsy of unknown cause (EUC) requires a thorough diagnostic evaluation, otherwise the prevalence of EUC could be overestimated. Hypothesis: Feline EUC is a clinically-defined disease entity, which differs from feline hippocampal necrosis (FHN) by the absence of magnetic resonance imaging (MRI) signal alteration of the hippocampus. The objectives of this study were (1) to evaluate the prevalence of EUC in a hospital population of cats by applying well-defined inclusion criteria, and (2) to describe the clinical course of EUC. Animals: Eighty-one cats with recurrent seizures. Methods: Retrospective study medical records were reviewed for cats presented for evaluation of recurrent seizures (2005 – 2010). Inclusion criteria were a defined diagnosis based on laboratory data, and either MRI or histopathology. Final outcome was confirmed by telephone interview with the owner. Magnetic resonance images were reviewed to evaluate hippocampal morphology and signal alterations. Results: Epilepsy of unknown cause was diagnosed in 22 % of cats with epilepsy. Physical, neurological and laboratory examinations, and either 1.5 T MRI and CSF analysis or post-mortem examination failed to identify an underlying cause. Cats with EUC had a higher survival rate (P < 0.05) and seizure remission occurred frequently (44.4%). Conclusion and clinical importance: A detailed clinical evaluation and diagnostic imaging with MRI is recommended in any cat with recurrent seizures. The prognosis of cats with normal MRI findings and a clinical diagnosis of EUC is good. Standardized imaging guidelines should be established to assess the hippocampus in cats.