Miracle-dz/UniFAR-FTUs huggingface dataset:
TOWARDS AN UNDERSTANDING OF PHARMACOLOGICALLY INDUCED INTRACELLULAR CHANGES IN NICOTINIC ACETYLCHOLINE RECEPTORS: A FLUORESCENCE MICROSCOPY APPROACH

OF DISSERTATION TOWARDS AN UNDERSTANDING OF PHARMACOLOGICALLY INDUCED INTRACELLULAR CHANGES IN NICOTINIC ACETYLCHOLINE RECEPTORS: A FLUORESCENCE MICROSCOPY APPROACH Upregulation of nicotinic acetylcholine receptors (nAChRs) is a well-documented response to chronic nicotine exposure. Nicotinic acetylcholine receptors are pentameric ligand-gated ion channels consisting of alpha (α2-10) and beta (β2-4) subunits. Nicotine, an agonist of nAChRs, alters trafficking and assembly of some subtypes of nAChRs, leading to an increase in expression of high sensitivity receptors on the plasma membrane. These physiological changes in nAChRs are believed to contribute to nicotine addiction, although the mechanism of these processes has not been resolved. Recently, many studies have converged on the idea that nicotine induces upregulation by an intracellular mechanism. In this dissertation, expression levels of nAChRs were quantified upon exposure to nicotine and its primary metabolite, cotinine. A pH sensitive variant of GFP, super ecliptic pHluorin (SEP), was integrated with a nAChR subunit to study expression and trafficking of nAChRs by differentiating intracellular and plasma membrane inserted receptors. In this work, cotinine is shown to increase the number of α4β2 nAChRs within a cell. Cotinine also affects trafficking of α4β2, evident by a redistribution of intracellular receptors and an increase in single vesicle insertion events on the plasma membrane. This work shows both nicotine and cotinine alter the overall assembly of α4β2 to favor the high sensitivity (α4)2(β2)3 version. Since cotinine and nicotine induce similar physiological changes in nAChRs, the metabolite potentially plays a role in the mechanism of nicotine addiction. Although an intracellular mechanism for upregulation has been supported, a shift in assembly to the high sensitivity (α4)2(β2)3 version exclusively in the endoplasmic reticulum has not previously been detected. In order to study organelle specific changes in stoichiometry, a novel method was developed to isolate single nAChRs in nanovesicles derived from native cell membranes. Separation of nanovesicles originating from the
Applying social network analysis to stakeholder analysis in Japan’s natural resource governance: two endangered species conservation activity cases

ABSTRACT Stakeholders with diverse interests, concerns, and needs regarding the use and management of natural resources are involved in their governance process. Because of their diversity, policy practitioners need to manage their conflicting interests and establish a conservation strategy that reflects those needs. Therefore, it is necessary to identify the relevant stakeholders who should be involved in decision making. This study sought to ascertain the relevant stakeholders in Japan’s natural resource governance by using a social network analysis. The conservation activities involved in protecting two endangered species, Cypripedium guttatum (Spotted Lady’s-Slipper) and Cypripedium macranthos var. rebunense (Rebun Lady’s-Slipper), were chosen as case studies. With the data obtained from surveys, social networks were analyzed using centrality, core-periphery, and factions. Then, the stakeholders were categorized into three classes (key, primary, and secondary stakeholders) according to their location in the networks. Because the Spotted Lady’s-Slipper case included stakeholders from a wide range of activity fields and all the key stakeholders in the decision-making arena, it enjoyed a preferable condition in terms of representativeness and inclusiveness of diverse stakeholders. However, in the Rebun Lady’s-Slipper case, the guards and several key stakeholders working on on-site activities were excluded. Consequently, the analysis identified key stakeholders, who should be included in the decision-making arena. The study demonstrated the usefulness of the methodology, which would assist policy practitioners by identifying relevant stakeholders who should be involved in decision making when organizing the arena in Japan’s natural resource governance.
Predator And Environmental Effects On The Polymorphic Egg Masses Of Spotted Salamanders (Ambystoma maculatum)

Polymorphisms may be maintained if selection intensity and gene flow vary across a species’geographic range. Jelly coats of amphibian eggs are under many different selective forces,such as predators and external environment interactions. Spotted salamanders (Ambystomamaculatum) have polymorphic egg masses that are either clear or opaque depending on the presence or absence of hydrophobic protein crystals in the outer egg layer. This study investigated how different predator communities and environmental parameters influence the distribution of the polymorphic egg masses in high and low elevations of North Carolina. I conducted surveys of A. maculatum clutches in breeding ponds and recorded numbers of clear and opaque egg masses, as well as the presence of predator and water chemistry in seven North Carolina counties. I found that egg masses at high elevation sites were predominately opaque (~82%), whereas egg masses at low elevation sites were predominately clear (~98%). Although water chemistry (pH, conductance) varied greatly between high and low elevation locations, water chemistry was correlated with egg polymorphism only in the mountains. At both elevations, locations with greater predator occupancy tended to have higher proportions of opaque egg masses. These results suggest the selective forces shaping the distribution of A. maculatum egg masses include both predator and physiochemical forces, but the additive effects of both stressors may drive the high ratios of opaque egg masses.
Efficient in vivo siRNA delivery by stabilized d -peptide-based lipid nanoparticles

RNA interference (RNAi) has shown great potential for clinical treatment of a variety of diseases. As an effective post-transcriptional regulation, RNAi induces degradation of specific target mRNA, leading to a decreased level of disease related gene product, which could be resistant to conventional small molecule therapeutics. Because of the relatively small size of short interfering RNA (siRNA) as well as it's robustness in the design of efficient 20–22 nucleotide sequences targeting any known gene, delivery of siRNA in vitro and in vivo has achieved tremendous success by the design and fabrication of various carrier materials including peptides, lipids, and polymers. While siRNA delivery efficiency of these materials proved to be appreciable, their tissue specificity, biocompatibility and cytotoxicity still need much improvement. We report a novel siRNA delivery material designed by optimization of our previously reported peptidomimetic based lipoplex. The novel lipoplex, which bears a D-amino acid based dipeptide head group, possesses an ideal balance of increased stability in a tissue environment, and enhanced efficiency of tissue specific delivery as well as minimized cytotoxicity. The novel lipoplex carrying siRNA efficiently targeted mouse liver, initiated RNAi and knocked down the apoB dose dependently, which is confirmed by both RT-qPCR and Western blotting. Moreover, the novel lipoplex does not induce any apparent cytotoxicity, as confirmed by the measurement of liver enzyme levels in serum.
Innate Immunity and Human Milk MicroRNAs Content: A New Perspective for Premature Newborns

Context: The premature newborns are prone to develop both early onset and late onset neonatal sepsis. The major causes of this phenomenon rely on the immaturity of the immune system, which has reduced capability to respond adequately to pathogens. EvidenceAcquisition: Titlesandabstractsof previouspaperswerescannedbeforereadingthefull-text, inordertoretrieveappro-priate information. The databases used for searching were PubMed, Cochrane, and Embase for articles published before 1st of July, 2016. Secondarysearchforarticlescitedinreferencelistswereidentiﬁedbytheprimarysearch. Thisreviewfocusedonneonatalsep-sis incidence and the associated immune response with regards to microRNAs of human milk as a new microelement that enables regulation of innate immunity functions. Results: Since human milk is a valuable source of microRNAs, a better understanding of its content will open a new therapeutic avenue for the clinical management of infectious diseases aﬀecting premature newborns. The variation in miRNAs quantity in hu-manmilkneedstobeconsidered. Mother’smilkcanhavediﬀerentamountsof miRNAsandtheidentiﬁcationof amicroMilkbatch richer of miRNAs can be a nutrition intervention method for modulating innate immunity in clinical management of premature newborns. Conclusions: Routine translation of the microMilk concept for neonatal intensive care unit (NICU), in the management of premature newborns could be a way of defending premature newborns and Very Low Birth Weight (VLBW) infants from both early and late sepsis.
Elucidation of the structure and function of the Mycosins, a family of essential subtilisin-like serine proteases of Mycobacterium tuberculosis

ii Opsomming . iii Acknowledgement . v List of Abbreviation . ix Chapter 1. General Introduction.1 1.1 General Introduction . 1 1.2 Reference . 2 Chapter 2. Type VII Secretion System in Mycobacteria.3 2.
Genetic differentiation and antioxidant activities of Bouea macrophylla Griffith in Nakhon Nayok province

Genetic differentiation and antioxidant activities in ethanolic extracts from leaves of Bouea macrophylla Griffith were determined. The result revealed genetic differentiation among sour ma-praang, ma-yong and sweet ma-praang of B. macrophylla Griffith ( φ PT =0.772, p -value=0.000). In addition, high genetic diversities were found in sour ma-praang and sweet ma-praang populations ( P : 51.4 and 57.1 %; He : 0.1900.035 and 0.2240.036, respectively), but low genetic diversity was found in ma-yong population ( P : 8.6 %; He : 0.0350.021). Total phenolic contents of sour ma-praang, ma-yong and sweet ma-praang were estimated as 680.51±89.81, 701.03±59.89 and 530.85±41.23 mg gallic acid/g extract, respectively. Free radical scavenging activities of sour ma-praang, ma-yong and sweet ma-praang were found (1/EC50= 4.17, 1.43 and 1.37, respectively) corresponding with metal-chelating activities (1/EC50=0.83, 0.65 and 0.17, respectively). Therefore, the obtained data may be applied to cultivation and utilization of their leaves as source of natural phenolics and antioxidants.
Isolation, Characterisation and Antagonistic Activity of Bacteria Symbionts Hardcoral Pavona sp. Isolated from Panjang Island, Jepara Against Infectious Multi-drug Resistant (MDR) Bacteria

Pavona sp. is highly spread over Indonesian waters including Panjang Island. Several studies showed that bacteria symbionts hardcoral were the big source of antibiotic product, but there was limited research of the bacteria symbionts with hardcoral Pavona sp. In this research bacteria symbionts from hardcoral Pavona sp. had been collected from Panjang Island, Jepara. Marine bacteria symbionts were isolated by serial dillution method, while antibacterial activity was performed by using overlay and agar block method. The total of 2 from 5 isolates were active to MDR bacteria such as Enterobacter aerogenes and Acinetobacter baumanii, the code were PHC 44/04 and PHC 44/05. Then both of them were identified by morphological and molecular DNA characterization using 16 S rRNA gene sequence. The result of 16 S rRNA identification shows PHC 44/04 has 99% similarities with Virgibacillus salarius strain sa-Vb 1, while PHC 44/05 shows 99% similarities with Pseudoalteromonas flavipulchra strain NCIMB 2033.
Pomological characteristics of autochthonous plum genotypes (prunus domestica) from Bosnia and Herzegovina

Plums represented a very significant economic factor in Bosnia in the twentieth century. Dominant in plum assortment is 'Pozegaca', but the appearance of the Plum pox caused a stagnation of plum production. The aim of this paper is to describe the basic pomological characteristics of fruit at six autochthonous plum genotypes: two types of 'Pozegaca' from locality Glavaticevo-Konjic, one type of 'Pozegaca' from locality Sovici-Jablanica, two types of 'Havaca' (from localities Doboj Istok and Gradacac) and one type of 'Sisaca' from locality Doboj Istok. Fruit weight of the genotypes ranged from 15.8 g in genotype 'Sisaca', up to 19.3 g in genotype 'Havaca'. Among the types of 'Pozegaca' there were no differences in terms of fruit weight. The biggest stone weight had 'Havaca' (1.21 g), and the lowest one had genotype 'Sisaca' (0.84 g). Due to this characteristic, there were differences among the types of 'Pozegaca'. Genotype ‘Pozegaca’, from locality Glavaticevo had the highest yield of fruit (95.3%), whereas the biggest genotype ‘Havaca’ had the lowest yield (93.67%). Among the types of ‘Pozegaca’, there were differences between localities in terms of the fruit yield.
The evolution of milk composition and lactation strategy of the Columbian ground squirrel, Urocitellus columbianus

ii Acknowledgments. iv List of Tables . ix List of Figures . x Introduction. 1 Literature Cited . 7 Chapter 1. The evolution of the nutrient composition of mammalian milks . 12 Abstract . 12 Introduction. 14 Methods. 21 Results. 26 Discussion. 29 Appendix 1. Milk composition of mammals at midlactation . 49 Appendix 2. Natural history, life history, and ecology of mammals whose milk composition has been described. 60 Literature Cited . 68 Chapter 2. Milk composition in a hibernating rodent; the Columbian ground squirrel, Urocitellus columbianus . 87 Abstract . 87. 87 Introduction. 88
Efficient Information Contents Flow Down from Memory to Predict the Identity of Faces

In the sciences of cognition, an influential idea is that the brain makes predictions about incoming sensory information to reduce inherent ambiguity. In the visual hierarchy, this implies that information content originating in memory–the identity of a face–propagates down to disambiguate incoming stimulus information. However, understanding this powerful prediction-for-recognition mechanism will remain elusive until we uncover the content of the information propagating down from memory. Here, we address this foundational limitation with a task ubiquitous to humans–familiar face identification. We developed a unique computer graphics platform that combines a generative model of random face identity information with the subjectivity of perception. In 14 individual participants, we reverse engineered the predicted information contents propagating down from memory to identify 4 familiar faces. In a follow-up validation, we used the predicted face information to synthesize the identity of new faces and confirmed the causal role of the predictions in face identification. We show these predictions comprise both local 3D surface patches, such as a particularly thin and pointy nose combined with a square chin and a prominent brow, or more global surface characteristics, such as a longer or broader face. Further analyses reveal that the predicted contents are efficient because they represent objective features that maximally distinguish each identity from a model norm. Our results reveal the contents that propagate down the visual hierarchy from memory, showing this coding scheme is efficient and compatible with norm-based coding, with implications for mechanistic accounts of brain and machine intelligence.
An alternative computing strategy for genomic prediction using a Bayesian mixture model

Chen, L. , Li, C. and Schenkel, F. 2015. An alternative computing strategy for genomic prediction using a Bayesian mixture model. Can. J. Anim. Sci. 95: 1-11. Bayesian methods for genomic prediction are commonly implemented via Markov chain Monte Carlo (MCMC) sampling schemes, which are computationally demanding in large-scale applications. An alternative computing algorithm, called right-hand side updating strategy (RHSU), was proposed by exploiting the sparsity feature of the marker effects in a Bayesian mixture model. The new algorithm was compared with the conventional Gauss-Seidel residual update (GSRU) algorithm by the number of floating point operations (FLOP) required in one round of MCMC sampling. The two algorithms were also compared in a Holstein data example with the training data size varying from 1000 to 10 000 and a marker density of 35 790 single nucleotide polymorphisms (SNP). Results showed that the proposed RHSU algorithm would outperform the traditional GSRU algorithm when the sample size exceeded a fraction of the number of the SNPs, which typically varied from 0.05 to 0.18 when the proportion of SNPs with no effect on the trait varied from 0.90 to 0.95. Results from the Holstein data example agreed very well with theoretical expectations. With adoption of a 50 k SNP panel and an increasing training data size, RHSU would be very useful if Bayesian methods are preferable for genomic prediction.
Unexpected paleopolyploid evolution in Stenopetalum - a genuswith the lowest chromosome numbers in the Brassicaceae

Stenopetalum harbors species with the lowest known chromosome number (n=4) in the Brassicaceae. Despite the extremly reduced chromosome complement, genome size of S. nutans (480 Mb) is three times larger than the Arabidopsis genome (157 Mb). In Stenopetalum nutans (n=4), comparative chromosome painting (CCP) using BAC contigs covering the top and bottom arm of two Arabidopsis chromosomes (At3 and At4) revealed two homeologous copies of both chromosome segments. The presence of multiple homeologous copies suggests that the Stenopetalum ancestor experienced a paleotetraploidy event followed by genome diploidization towards extremely reduced karyotypes.
Genetic determinants of phenotypic evolution in Saccharomyces yeast

Author(s): Roop, Jeremy Roop | Advisor(s): Brem, Rachel B; Taylor, John W | Abstract: Years of trait mapping studies have uncovered the genetic determinants underlying phenotypic evolution over both short and long timescales in a variety of organisms. A more general understanding of the mechanisms through which evolution produces phenotypic novelty, however, still remains out of reach. Many outstanding questions remain, among them how coding sequence divergence and gene expression divergence respectively contribute to trait evolution, as well as what role rare and large effect genetic variants play in the genetic networks underlying evolving phenotypes. Using Saccharomyces yeast as a genetically tractable model system in which to probe these questions, we identify and dissect several examples of trait divergence within and between yeast species. We first investigate an instance of intraspecific variation among yeasts isolated from a single population, finding that large effect rare variants at hypermutable loci are drivers of many common morphological and growth phenotypes. Next, in a comparison of both recently-diverged and long-diverged species, we investigate the role that gene expression variation plays in phenotypic evolution. We find evidence in multiple gene networks for complex and coherent regulatory evolution, and in one instance we succeed in identifying the loci that effect this change, as well as several phenotypic novelties they produce. Collectively, these investigations will contribute to the growing body of literature that describe the genetic mechanisms that underlie phenotypic change and seek, eventually, to achieve a greater understanding of basic evolutionary principles.
Pflp gene transformation in pomegranate (Punica granatum L.) resistance to bacterial blight disease (Xanthomonas axonopodis pv. punicae)

Pomegranate ( Punica granatum L.) is a woody perennial fruit crop grown in arid zones of India, the state of Maharashtra being considered as pomegranate basket contributes to 70 % of the total area followed by Karnataka and Andhra Pradesh. Protection of crops against bacterial disease is an important issue in agricultural production. Pomegranate production in India is severely hampered by the high incidence of bacterial blight disease caused by Xanthomonas axonopodis pv. punicae is air borne, the conventional ways and means of controlling this disease have failed. Evolving a resistant genotype using resistant variety through conventional breeding may be a way out but it is a time consuming process. Transgenic approach appears to be promising to minimize the losses caused by disease. In the present investigation efficient protocols were developed to get healthy and well-formed plants from juvenile and mature-origin explants of the pomegranate cv. ‘Bhagwa’ and transformants with PFLP gene. One of the strategies to lead plants become resistant against bacterial pathogens is employing a transgene, like plant ferredoxin-like protein (PFLP). Different treatment combinations of hormonal concentrations were taken for leaf, petal, nodes and cotyledonary explants to standardize an efficient in vitro regeneration protocol and find out the best treatment for faster regeneration. Agrobacterium tumefaciens carrying gene pCAMBIA construct with the constitutive CaMV35S promoter, PFLP gene, terminator and nptII selectable marker (Kanamycin resistance), was used for transformation of explants. Putative transformants were identified on selection medium containing kanamycin at different concentration. Integration of transgene and expression at various levels were confirmed using PCR. Out of 4 putative transformants analyzed, three plants showed amplification for PFLP gene specific primer. Key words In vitro , Pflp gene, transformation, bacterial blight disease, putative transformants, Agrobacterium tumefaciens
Characterization and potential applications of a recombinant antifreeze protein from an antarctic yeast Glaciozyma antarctica produced in Pichia pastoris

Ice recrystallization during thawing post-cryopreservation results in extensive cellular damage and ultimately leads to cell death and reduced cell viability. Antifreeze proteins (AFPs) are a group of proteins that allow organisms to survive in subzero environments. These proteins have thermal hysteresis and ice recrystallization inhibitory activities. In this present study, we demonstrated the efficiency of a recombinant antifreeze protein from the Antarctic yeast, Glaciozyma antarctica, as a recrystallization inhibitor (RI) of ice growth and assessed its application as a cryopreservative of the fungal cutinase enzyme against freeze-thaw cycles. Recombinant Afp1 from G. antarctica, a psychrophilic yeast, has been produced in a methylotrophic yeast, Pichia pastoris, system that results in the expression of a hyper-glycoprotein (~55 kDa). Recombinant Afp1 exhibits antifreeze functions: thermal hysteresis (TH) and recrystallization inhibition where the highest TH values recorded for ~0.5°C at 10 mg/mL. The cryoprotective effects of Afp1 on purified recombinant cutinase showed that Afp1 can retain enzymatic activity up to ~20% when subjected to several cycles of freeze thawing. These findings indicate that Afp1 might act as a cryoprotective agent and thus, has great potential in biotechnology applications.