Miracle-dz/UniFAR-FTUs huggingface dataset:
STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

Title of Document: STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3’ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES My Tra Le, Doctor of Philosophy, 2016 Directed By: Professor Anne E. Simon, Cell Biology and Molecular Genetics, and Professor T. Kwaku Dayie, Chemistry and Biochemistry Turnip crinkle virus (TCV) and Pea enation mosaic virus (PEMV) are two positive (+)-strand RNA viruses that are used to investigate the regulation of translation and replication due to their small size and simple genomes. Both viruses contain capindependent translation elements (CITEs) within their 3 ́ untranslated regions (UTRs) that fold into tRNA-shaped structures (TSS) according to nuclear magnetic resonance and small angle x-ray scattering analysis (TCV) and computational prediction (PEMV). Specifically, the TCV TSS can directly associate with ribosomes and participates in RNA-dependent RNA polymerase (RdRp) binding. The PEMV kissing-loop TSS (klTSS) can simultaneously bind to ribosomes and associate with the 5 ́ UTR of the viral genome. Mutational analysis and chemical structure probing methods provide great insight into the function and secondary structure of the two 3 ́ CITEs. However, lack of 3-D structural information has limited our understanding of their functional dynamics. Here, I report the folding dynamics for the TCV TSS using optical tweezers (OT), a single molecule technique. My study of the unfolding/folding pathways for the TCV TSS has provided an unexpected unfolding pathway, confirmed the presence of Ψ3 and hairpin elements, and suggested an interconnection between the hairpins and pseudoknots. In addition, this study has demonstrated the importance of the adjacent upstream adenylate-rich sequence for the formation of H4a/Ψ3 along with the contribution of magnesium to the stability of the TCV TSS. In my second project, I report on the structural analysis of the PEMV kl-TSS using NMR and SAXS. This study has re-confirmed the base-pair pattern for the PEMV kl-TSS and the proposed interaction of the PEMV kl-TSS with its interacting partner, hairpin 5H2. The molecular envelope of the kl-TSS built from SAXS analysis suggests the kl-TSS has two functional conformations, one of which has a different shape from the previously predicted tRNA-shaped form. Along with applying biophysical methods to study the structural folding dynamics of RNAs, I have also developed a technique that improves the production of large quantities of recombinant RNAs in vivo for NMR study. In this project, I report using the wild-type and mutant E.coli strains to produce cost-effective, site-specific labeled, recombinant RNAs. This technique was validated with four representative RNAs of different sizes and complexity to produce milligram amounts of RNAs. The benefit of using site-specific labeled RNAs made from E.coli was demonstrated with several NMR techniques. STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3 ́ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES
Production and characterization of monoclonal antibodies to barley ribulose 1,5-bisphosphate carboxylase/oxygenase

Purified barley (Hordeum vulgare) ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) was used for immunization of BALB/c mice in order to produce hybridomas secreting specific monoclonal antibodies. Stable hybridoma cell lines designated as Mab 2D11, Mab 2F4, Mab 2G2, Mab 2H5, Mab 3H9, Mab 4B9 were selected using an indirect enzyme linked immunosorbent assay (ELISA). According to their specificity these antibodies can be divided into two groups - Mab 2D11, Mab 2G2 and Mab 2H5 recognize overlapping enzyme epitopes in green leave extract from monocotyledonous - barley (H. vulgare), wheat (Triticum aestivum), maize (Zea mays) and dicotyledonous - pea (Pisum sativum), soybean (Glycine max)
Nutritional characteristics of ancient tuscan varieties of triticum aestivum L

Bread wheat ( Triticum aestivum L.) is an important cereal in human consumption. In recent years, there has been a growing interest in ancient wheat varieties. The latter represent an important source of germplasm, characterised by a broader genetic base and, therefore, a potential source of biodiversity. The objective of the study was to ascertain the optimal balance between the presence of secondary metabolites having beneficial effects on health and technological features that ensure successful baking quality. The experimental trial was performed in 2011-2012 on three organic farms located in three different areas within the province of Siena (Tuscany). In each location, an overall evaluation of the commercial, rheological and functional properties of five ancient Tuscan bread wheat varieties (Andriolo, Frassineto, Gentil rosso, Inallettabile 96, Verna) as compared with a commercial modern variety (Palesio) was carried out. The ancient varieties were compared both singularly (pure) and in combination (mixtures) of two varieties in equal proportion, respectively. Biometric and productive parameters were detected for each plot (32 plots in each farm). Macro- and trace elements, polyphenols, flavonoids and antioxidant activity (antiradical power, ARP) were similarly determined on representative whole grain samples. Rheological analysis was carried out on flour samples. The multivariate statistical analysis using principal components analysis was performed on all variables analysed. The results showed a significant environment effect on the different parameters measured and did not reveal significant improvements in the variables measured when varieties were cultivated in mixtures. However, the study did reveal various interesting trends that are warranting of further investigation. The most interesting effect from a nutritional and functional point of view is the relationship between ARP, rheological properties, protein content and gluten content. These connections permit the potential towards the improvement of ancient varieties.
Leucothoid and Maerid Amphipods (Crustacea) from deep regions of the North Atlantic

From amphipod collections from the deep Norwegian Sea, three species are here redescribed: Maera loveni (Bruzelius 1859) (Maeridae), Leucothoe aff. spini- carpa (Abildgaard, 1789) and L. uschakovi Gurjanova, 1951 (Leucothoidae). A key to all Atlantic and Mediter- ranean Leucothoe species (males only) is provided.
Genetic polymorphism of Indian tobacco types as revealed by amplified fragment length polymorphism

During the past five decades, a large number of tobacco varieties have been developed for different end uses in India through pure line selection from local land-races, mutation breeding and hybridization involving local selections and exotic introductions followed by pedigree selection. No systematic effort has been made to understand the existing diversity pattern in these varieties, which is crucial to define future breeding strategy in this important commercial crop. Amplified fragment length polymorphism (AFLP) analysis was used to determine genetic variation in 54 varieties of cultivated tobacco (Nicotiana tabacum and N. rustica) and three accessions of exotic germplasm. Nine oligonucleotide primer-pair combinations resolved a total of 967 AFLP fragments, of which 785 (81.2%) were polymorphic. The mean genetic distance among the 49 cultivars and three exotic accessions of N. tabacum was 15.35%; 22% among the five cultivars of rustica. Genetic polymorphism present among the cultivars of tobacco was low, as evidenced by the high degree of similarity in the AFLP profiles of different tobacco types. All the five cultivars of N. rustica can be readily identified using the primer pairs E-ACT/M-CAG and E-AAC/M-CTG. Two major clusters were formed on the basis of species and seven sub-clusters were formed on the basis of manufacturing quality traits in the cultivars of N. tabacum. Cultivated flue-cured varieties were clustered separately from other air cured types. Species-specific markers identified in this study would be useful in identification of the true hybrids and monitoring introgression of useful genes from the wild relatives. The markers found specific to the varieties can be used in correct identification of the carrier genotypes in trade and commerce.
Effects of varying growth irradiance and nitrogen sources on calcification and physiological performance of the coccolithophore Gephyrocapsa oceanica grown under nitrogen limitation

Gephyrocapsa oceanica is a widespread species of coccolithophore that has a significant impact on the global carbon cycle through photosynthesis and calcium carbonate precipitation. We investigated combined effects of light (50 μmol m−2 s−1, 190 μmol m−2 s−1, and 400 μmol m−2 s−1) and the nitrogen sources NO3− and NH4+ on its physiological performance under nitrogen‐limited conditions. The specific growth rate was highest at the mid‐range light level of 190 μmol m−2 s−1, where it was further accelerated by NH4+ relative to NO3− . There were no significant growth rate differences between NO3− ‐ and NH4+ ‐grown cells at the two light levels either above or below this optimum irradiance. Cellular particulate organic carbon (POC) and nitrogen (PON) content were not significantly affected by different light intensities and nitrogen sources. However, both the cellular particulate inorganic carbon (PIC) content and the PIC to POC ratio were greatly decreased by increased light levels, and were further decreased by NH4+ only at the highest light level. Non‐photochemical quenching (NPQ) increased with increasing light intensity, and was higher in NO3− rather than in NH4+ ‐grown cells at medium and high light intensities. Our results demonstrate that under low, relatively realistic oceanic nitrogen concentrations, increasing light intensity and the replacement of NO3− by NH4+ would have a significant negative effect on the calcification of the coccolithophore G. oceanica. If these findings are also applicable to other coccolithophore species, the future ocean carbon cycle may be greatly affected.
Fostering integration between biodiversity monitoring and modelling

Jo~ ao P. Honrado*, Henrique M. Pereira and Antoine Guisan InBIO Rede de Investigac ~ ao em Biodiversidade e Biologia Evolutiva/CIBIO Centro de Investigac ~ ao em Biodiversidade e Recursos Gen eticos, Universidade do Porto, Campus Agr ario de Vair~ ao, 4485-601 Vair~ ao, Portugal; Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edif ıcio FC4, 4169-007 Porto, Portugal; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany; Institute of Biology, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany; Department of Ecology & Evolution, University of Lausanne, 1015 Lausanne, Switzerland; and Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
IN VITRO COMPARATIVE STUDIES OF ADIPOCYTE STEM CELLS DERIVED FROM HUMAN ADIPOSE TISSUE AND AMNIOTIC FLUID CELLS

Mesenchymal stem cells (MSCs) represent an archetype of multipotent somatic stem cells that hold promise for application in regenerative medicine. The present study aimed to isolate MSCs from adipose tissue and amniotic fluid (hAFSCs) and re-differentiation into either adipose. Adult human adipose tissue (hATSCs) contains a population of mesenchymal stem cells, which can be harvested readily, safely, and in relative abundance by modern liposuction techniques. MSCs were separated from adipose tissue liposuction and amniotic fluid, cultured in dullbecus modified egal media (DMEM) for two weeks for proliferation of MSCs, which recollected and regrowing in specific media for differentiation of adipocyte cells (ACs). ACs were determined by staining with oil-red O and RT PCR assessments of adipocyte and adiponectin genes.Our findings revealed that the MSCs derived from amniotic fluid cells showed high capacity of differentiation into adipocytes comparing with that derived from adipose tissue. The ACs derived from hAFSCs were more prominent and characterized by reddish brown-droplets following staining with oil red O. Both types of adipocyte stem cells derived from either hATSCs or hAFSCs showed similar expression of molecular bands of adponectin and adipocyte gene. The authors concluded that adipocytes derived from MSCs of hAFSCs were markedly growing and expanded comparing with that hATSCs for application in regenerative medicine.
Culture of Megakaryocytes from Human Peripheral Blood Mononuclear Cells

1Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Centre (AMC), University of Amsterdam (UvA), Amsterdam, The Netherlands; 2Center for Human Genetics, KU Leuven, Leuven, Belgium; 3Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain *For correspondence: lgutierrezg@salud.madrid. org
Developmental features of Octopus macropus Risso, 1826 (Mollusca, Cephalopoda)

Octopus macropus Risso, 1826 est connu de la Mediterranee; l'espece est egalement signalee dans l'Atlantique. Son developpement embryonnaire est decrit brievement, mettant en relief les caracteres lies a l'existence d'une phase post-embryonnaire de type planctonique ou micronectonique. Celle-ci aboutit a l'adoption du mode de vie benthique, mais les conditions exactes de ce passage au mode adulte sont encore inconnues chez cette espece. La discussion replace les observations dans le contexte d'une difference, connue uniquement chez les Octopodidae, entre especes merobenthiques (caracterisees par une phase post-embryonnaire planctonique) et especes holobenthiques (caracterisees par une phase post-embryonnaire benthique).
Topically applied EGF and PDGFs affect positively the co-ordinate expression of EGF and PDGF receptor genes during acute cutaneous wound-healing process

Daily topical application of epidermal growth factor (EGF) and platelet-derived growth factors (PDGFs) individually resulted in approximately two- to threefold increase in EGF-R and α- and β-PDGF-R mRNA levels, and combinations of these growth factors produced a 2.5 to four-fold increase. Rapid attainment of maximum level of receptor mRNA on day one and its maintenance at comparatively higher level till day three appears to be essential for faster and better healing. PDGF-AA + EGF inhibited EGF-mediated increase in receptor mRNA levels when applied premixed or within 30 min following EGF application. The results are also suggestive of the possible role of PDGF-AA during later stages of wound healing.
Mitochondrial DNA phylogeography of Spodoptera exigua across a broad geographic area in China

The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae), is an important agriculture pest in China that causes serious economic losses in some of the main crop‐producing areas. To monitor and manage this pest effectively, it is necessary to investigate its phylogeographic patterns in China. In this study, we used a partial sequence of mitochondrial DNA Cytb gene consisting of 724 bps to investigate the genetic diversity of the beet armyworm. A total of 765 individuals from 47 populations across the main distribution range of the species were collected, and 112 haplotypes were identified. Moderate‐to‐high levels of genetic diversity (Hd = 0.672 ± 0.017, Pi = 0.00268 ± 0.00021) for the total populations were obtained. Phylogenetic and median‐joining network analyses indicated there was no distinct geographic distribution pattern among haplotypes. Overall, the study also revealed significant differentiation among some populations (P < 0.05). The FST values of Shenyang population (SY2012–SY 2014), as well as Baoding (BD), Taian (TA), Lucheng (LC), Zhengzhou (ZZ) and Wuhan (WH), were significantly different from those of the populations in most other locations. Hierarchical AMOVA showed there was no significantly genetic structure between populations located in seven geographic regions and four main bioclimatic zones. Finally, unimodal mismatch distribution combined with negative Tajima's D (D = −2.696, P < 0.001) and Fu's FS (FS = −207.228, P > 0.05) indicated recent population expansion of S. exigua at large spatial scales in China.
A Comparison of Five Irrigation Methods on Onions

Water use efficiencies of five irrigation methods on dry onions (Allium cepa L.) were compared in a two-year field study. The methods were: 1) graded furrows where water was measured into the upper end of the furrows and excess water was measured as it ran out the lower end; 2) level furrow where water was held in short, level furrows until infiltrated into the ground; 3) sprinkler; 4) trickle; and 5) trickle three times per week. Efficiency of water use (tonne per hectare per millimeter) was least with graded furrows and the same for the other four treatments in 1983, whereas there were no efficiency differences in 1984. Treatment differences in yield among onion grades occurred both years, but no differences in total yields among treatments for either year. The results do not justify the expense of conversion from existing furrow irrigation systems to pressurized systems for water savings on a uniform, heavy-textured soil where good-quality water is used.
Nutrient enrichment and flow regulation impair structure and function of a large river as revealed by aquatic hyphomycete species richness, biomass, and decomposition rates

Diversity, sporulation rates, and biomass of aquatic hyphomycetes (Kingdom Fungi) on leaf litter were examined to assess the effects of nutrient enrichment and flow regulation on the ecological integrity of the Saint John River, New Brunswick, Canada. Leaf decomposition rate was used as an indicator of ecological function, whereas fungal abundance and diversity were chosen as structural indicators. Leaf-litter bags of yellow birch (Betula alleghaniensis) were deployed at 8 sites, periodically retrieved, and analyzed during 2 consecutive years in unregulated and regulated reaches. The interaction between nutrient enrichment and flow regulation regime significantly affected leaf decomposition rate and fungal sporulation during summer and autumn and fungal diversity during autumn. Flow regulation regime was the primary driver for fungal diversity during summer. In contrast, nutrient enrichment significantly affected fungal biomass. In general, this large 7th-order river responded to flow regulation and nutrient enrichment in the same manner as smaller rivers. Both factors increased decomposition rates, but only nutrient enrichment increased fungal biomass, diversity, and sporulation. Within the regulated reach, leaves in constantly covered litter bags had faster decomposition rates and more aquatic hyphomycete species, spore release, and biomass than in intermittently covered litter bags. Nutrient enrichment, flow regulation, and their interactions decreased ecosystem integrity by altering diversity and biomass of aquatic hyphomycetes and their function in the Saint John River.
Phylogeny and divergence times of the Coluteoid clade with special reference to Colutea (Fabaceae) inferred from nrDNA ITS and two cpDNAs, matK and rpl32-trnL(UAG) sequences data

Abstract This study reconstructed the phylogeny of the Coluteoid clade using nrDNA ITS and plastid matK and rpl32-trnL(UAG) sequences data. The analyses resolve a well-supported Coluteoid clade, as sister to Astragalus s.str. + Oxytropis, nested within the larger, strongly supported Astragalean clade. The Coluteoid clade is now composed of 12 genera including Podlechiella, Swainsona, Carmichaelia, Clianthus, Montigena, Phyllolobium, Lessertia, Sutherlandia, Sphaerophysa, Smirnowia, Eremosparton and Colutea. Within this clade, Podlechiella is the first diverging lineage followed by successive subclades of Carmichaelia + Clianthus + Swainsona, Phyllolobium, Lessertia + Sutherlandia, Sphaerophysa + Smirnowia + Eremosparton, and Colutea. We assigned the formal tribal name to this clade and redefined the tribe Coluteae. A diagnostic key to the genera of the tribe is presented. Astragalus cysticalyx and A. sinicus have no relationship with the Coluteoid clade, instead, they are nested in Astragalus s. str. Resolution within Colutea is rather low, but several smaller subclades with low to high supports are found in the genus. None of the large sections in Colutea are monophyletic. Divergence time estimates revealed that the Coluteoid clade originated in the Early Miocene (20.4 Mya). Most of its members were diverged during the Late Miocene to Pliocene. Colutea and Podlechiella form the youngest lineages where the diversification occurred in the Pliocene-Pleistocene.
Molecular genetic map and QTL analysis of agronomic traits based on a Eragrostis tef x E. pilosa recombinant inbred population [Ethiopia]

Construction of genetic maps and identification of quantitative trait loci (QTL) are essential for initiating marker assisted selection (MAS). The purpose of this study was to construct a genetic linkage map and identify QTLs associated with yield and yield-related traits. One hundred twenty four F8 recombinant inbred lines (RILs) developed from an inter-specific cross between E. tef (DZ-01-2785) and E. pilosa (acc. 30-5), were evaluated in field trials at two locations, Debre Zeit and Melkassa, Ethiopia, in 2002 and 2003. The RILs were assayed for amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR), expressed sequence tag-simple sequence repeats (ESTSSR), and simple sequence repeats (SSR) markers. One hundred forty nine markers were mapped to 20 linkage groups. The distance between two marker loci ranged from 0.0 to 33.4 cM, with an average distance of 12.7 cM. A total of 34 QTLs were identified for yield and yield-related traits. The number of QTLs per trait ranged from one for seed weight to five for shoot biomass. The percentage of phenotypic variance explained by each QTL ranged from 12.4% to 63.9%. QTL analysis of means showed more QTLs detected across environments than at individual environments. The majority of QTLs were concentrated in four main clusters on LG2, LG3, LG4, and LG7, suggesting pleiotropic effects of genes. In this study, no QTLs were detected affecting total number of nodes, number of spikelets per main panicle, culm diameter of the second internode, and number of panicle branches. The QTLs identified were consistent over most environments, hence they may be useful for applied breeding programs in tef.
Identification and characterization of two faba bean (Vicia faba L.) WRKY transcription factors and their expression analysis during salt and drought stress

SUMMARY Drought and salinity are two major environmental factors limiting faba bean growth, leading to considerable reduction in their productivity. The WRKY gene family act as major transcription factors that might play an important role in abiotic stress tolerance. In the present study, two partial sequences sharing significant homology with known WRKY genes were isolated from faba bean by polymerase chain reaction (PCR) amplification using degenerate primers targeting the well-conserved WRKY domain. The isolated WRKY gene fragments were designated as VfWRKY1 and VfWRKY2 showing 62% similarity between them. Sequence and phylogenetic analyses revealed that VfWRKY1 and VfWRKY2 belong to WRKY group I and could be grouped with their orthologues from other plant species. The gene expression profile of VfWRKY1 and VfWRKY2 in faba bean showed that they are significantly accumulated in various plant organs. Further, quantitative real-time PCR analysis showed that both transcripts were responsive to drought and salt stress, and also they are genotype dependent, meaning that different faba bean cultivars respond in a different way to drought and salt challenge. The expression patterns obtained suggest the important roles of VfWRKY1 and VfWRKY2 in drought and salt stress response and tolerance. This knowledge might be helpful in the identification of drought-tolerant cultivars and provide potential candidate markers for faba bean breeding in order to develop osmotic-stress-tolerant cultivars.