Miracle-dz/UniFAR-FTUs huggingface dataset:
Intraspecific genetic variation in selected mosses of Scandinavian interglacial refugia suggests contrasting distribution history patterns

Three pleurocarpous mosses were studied to explore the haplotype diversity patterns in a Scandinavian system of interglacial refugia in which low-competitive species of calcareous or base-rich habitats occur. Hypnum bambergeri and H. vaucheri displayed little variation across Scandinavia. For the third species, Drepanocladus turgescens, an analysis of molecular variance showed that two S Scandinavian lowland regional populations were significantly different from each other and differed or almost differed (Gotland vs. Jamtland, according to pair-wise ΦPT) from the populations of the Scandinavian mountain range and Svalbard. Haplotype diversity displayed little variation among regional populations, and did not reflect the higher frequency of sexual reproduction in southern than in mountain populations. A coalescent-based analysis (LAMARC) indicated immigration into the population now found in the lowlands from that represented in the mountains. This is contrary to that found in Rhytidium rugosum in an earlier study and, together with the fact that sporophytes are produced almost exclusively in the lowlands, speaks against this direction of post-glacial migration. Therefore, if the LAMARC results reflect migration patterns, these most probably reflect events that occurred earlier. Taken together with the results on R. rugosum, this study emphasizes the fact that moss species having similar distribution patterns reached these distributions in partly different ways. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 295–310.
Global assessment of limitation to symbiotic nitrogen fixation by phosphorus availability in terrestrial ecosystems using a meta‐analysis approach

Symbiotic nitrogen fixation (SNF) is the main natural source of nitrogen (N) in terrestrial ecosystems worldwide. Previous studies have shown that fixation of N by plants can be limited by the availability of phosphorus (P) in soils. We used global meta‐analysis to investigate how P availability controls SNF. In experiments in which plants were grown in an artificial medium, severe P deficiencies in the nutritive solution ([PO4] < 5–42 μM) depressed SNF flux through both a direct decrease in the plant fixation rate (i.e., decreased N fixed per unit of plant biomass) and an indirect effect (i.e., through plant biomass). In most experiments with plants grown in soils, SNF was proportional to plant biomass and was consequently only indirectly limited by P. Some cases using unfertilized and weathered soils (ultisols or oxisols), where plants were particularly P stressed, were an exception with both direct and indirect P limitations. Our global analysis of the P‐SNF relationship indicated that P bioavailability commonly limited SNF flux. We conclude that the main driver of in situ P limitation is indirect via limitation of plant growth, except in certain cases where both indirect and direct constraints may play a role. These cases of severe P deficiency may be mainly found in weathered tropical soils of Africa and South America, probably in unfertilized croplands which are depleted in P due to repeated biomass harvests.
Movements and oceanographic associations of bigeye tuna (Thunnus obesus) in the Northwest Atlantic

To address the lack of fisheries-independent information for Atlantic bigeye tuna (Thunnus obesus), we released 21 adults (131 ± 12 cm curved fork length) between 2008 and 2010 in the Sargasso Sea and Northwest Atlantic. Data from nine tags (range: 1–292 days; mean: 89 days) revealed (i) pronounced north–south movements in pelagic waters between areas including Georges Bank, Mid- and South Atlantic Bight, Caribbean Sea, and Brazilian shelf, (ii) a lack of east–west exchange, and (iii) a high-use area in the Hatteras Plain, centered southwest of Bermuda. Bigeye tuna occupied water masses of 2.7–28.2 °C and depths of 0–1280 m, with deeper depths in the daytime (daily mean ± standard deviation: 196 ± 92 m) than at nighttime (45 ± 29 m). Even though bigeye tuna are assumed to forage on the deep scattered layer during the day, generalized additive mixed models did not identify the deep scattered layer as an important predictor of daytime swimming depth. Model results highlight the importance of geographic loca.
Extraction of Flavonoids and Quantification of Rutin from waste Tobacco Leaves

The potential of tobacco waste as a viable source of medicinally important flavonoids like rutin has been investigated. Three flavonoids, apigenin, quercetin and rutin, have been isolated from waste tobacco leaves, and their identities have been confirmed by UV-visible, 1 H-NMR and 13 C-NMR spectroscopy. By using analytical HPLC, the amount of rutin present in the tobacco leaves, before and after fermentation, and also in waste tobacco leaves, has been determined as 1.5, 0.5 and 0.6%, respectively.
Remarkable Bacterial Diversity in the Tidal Flat Sediment as Revealed by 16S rDNA Analysis

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.
Strong genetic cohesiveness between Italy and North Africa in four butterfly species

The sea acts as an effective dispersal barrier for most terrestrial animal species. Narrow sea straits, therefore, often represent areas where species are able to disperse from one land mass to another. In the Mediterranean Sea, the narrowest connecting points between North Africa and Europe are the Strait of Gibraltar and the Strait of Sicily. In the past, climatic oscillations caused changing sea levels and thus influenced the permeability of these sea straits. We analysed the genetic structure of four butterfly species that all occur on both sides of the Strait of Sicily. In all four species, we observed a lack of genetic differentiation between the populations of North Africa and those of Italy. Species distribution models support the strong cohesiveness in that they show a largely continuous glacial distribution over Italy and North Africa. The data obtained reveal that there was a large exchange of individuals between Italy and the eastern Maghreb during the last ice age. This might not only be the case for the species under investigation in the present study, but also might represent a more general pattern for mobile thermophilic western Palearctic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 818–830.
THE SHORT-TERM CONSERVATION OF THE SPECIES Gladiolus hybridus CULTIVAR OSCAR

The Gladiolus species are known to be on the 5 th place in the culture of decorative flowers. Still there are some inconveniences regarding their culture survival due to the fact that they are relatively easy attacked by biotic stressors. This research is focused on determining a strategy for the short-term conservation of in vitro cultivated Gladiolus hybridus varieties. For the initial step of this research we focused only on the conservation of the Gladiolus hybridus Oscar variety. Explants isolated from the species mentioned above were cultured in vitro on two types of culture media and under two types of environmental condition. The results obtained were encouraging showing us the possibility of the short-term conservation for this particular Gladiolus hybridus variety.
Role of microRNAs in renal fibrosis

This thesis examines the role of microRNAs in renal fibrosis. MicroRNAs constitute a large family of approximately 22-nucleotide-long non-coding RNAs, that in animal cells regulate gene expression posttranscriptionally. At the start of the project, microRNAs were emerging as potentially important factors in various physiological and pathological processes however, there was very little known about their expression and function in the kidney, in particular in tubulointerstitial fibrosis. In this thesis, global microRNA expression has been analysed in vitro in proximal tubular epithelial cells, and in vivo in formalin-fixed, paraffin-embedded kidney biopsy samples from patients with diabetic nephropathy. Among microRNAs altered by profibrotic stimuli, the greatest difference has been found in expression ofmiR-192, which is downregulated in severe diabetic nephropathy. Further examination of miR-192 in kidney biopsy samples has revealed that its expression correlates well with renal function and inversely correlates with fibrosis. A possible function of miR-192 has been then studied in vitro in proximal tubular epithelial cells. It has been found that treatment of the cells with the profibrotic cytokine TGF-β1 downregulates miR-192. Moreover, manipulation of miR-192 expression has shown that miR-192 is involved in E-cadherin regulation. The mechanism of that regulation has been investigated, pointing to two transcriptional repressors of E-cadherin, ZEB1 and ZEB2, as direct targets of miR-192. The presented data suggest that, in the kidney, miR-192 may prevent epithelial-to-mesenchymal transition, known to contribute to renal fibrosis. In parallel, global microRNA downregulation in proximal tubular epithelial cells has been attempted. However, knockdown of Dicer or TRBP, proteins involved in microRNA processing, has not been sufficient to induce changes in microRNA expression. The possible explanations have been discussed. Finally, microRNA role in direct regulation of TGF-β1 synthesis has been investigated. In particular, human microRNAs similar to viral hsv-miR-LAT, reported to directly target TGF-β1 mRNA, have been tested.
Metapopulation dynamics in an aphid‐parasitoid system

Metapopulation theory makes a number of predictions concerning the effects of dispersal on the persistence of predator‐prey or host‐parasitoid systems. While the stabilising effects of dispersal have been shown in a number of laboratory studies, evidence from field studies remains scarce due to a lack of suitable model systems. I describe a host‐parasitoid system that shows a classical metapopulation structure with frequent extinctions and colonisations consisting of the aphidiid Lysiphlebus hirticornis and the aphid Metopeurum fuscoviride. Both the parasitoid and the aphid are specialists on their respective hosts. I followed the dynamics of host and parasitoid on individually marked tansy (Tanacetum vulgare) plants, the host of M. fuscoviride. Dynamics of host and parasitoid populations were characterized by frequent extinctions and colonisations. Mean longevity of aphid colonies was only 3.1 weeks. Parasitism by L. hirticornis was a main cause of extinction for the aphid as rates of parasitism often reached 100%, in particular towards the end of the field season. Patchiness in this system occurs at two spatial scales. Aphid colonies form on single tansy ramets = shoots but movements of aphid individuals among ramets within a particular tansy genet are frequent. Because aphids can persist on a genet for a large numer of generations, it is argued that local populations form on genets rather than ramets. The number of host and parasitoid extinctions described in this study exceeds the number of extinctions usually observed in field studies of host‐parasitoid metapopulations. It is suggested that aphid‐parasitoid systems such as the one studied in this paper may be good models to test the predictions of metapopulation theory.
Effects of long-term salinity on growth and performance of two pistachio (Pistacia L.) rootstocks.

Salinization is one of the most important problems that restrict cultivation of crops in arid and semi-arid regions; Pistachio (Pistacia vera L.) is one of the most important trees that grown in these restricts. In this greenhouse study, the effects of salinity on growth of 2 pistachio rootstocks 'Badami' and 'Ghazvini' evaluated. Seedlings of these cultivars were grown in 25×30cm plastic bags containing 4.5kg soil. Salinity was imposed, by adding salt (NaCl) to the pots at 6 leaf stage (about 1 month after planting) to obtain concentration of 0, 800, 1600, and 3200 mg NaCl kg-1 soil. Plants irrigated with 7 days intervals. Ninety days after salt treatment, pistachio seedlings were harvested and length of shoots and roots, number of leaves, relative water content, plant biomass, chlorophyll content, photosynthesis rate, reducing sugar concentration, and proline content of leaves were measured. Salinity decreased shoots and roots growth, number of leaves per plant, plant biomass, net photosynthesis rate, and chlorophyll content in comparison with the control. These parameters had higher value in the 'Ghazvini' rootstock than in the 'Badami' rootstock. The concentrations of reducing sugars in the leaves of the both rootstock improved with increasing salinity concentration up to 3200. Free proline content in the leaves of pistachio cultivars also increased with the increased salnity level. Proline content and reducing sugars in 'Ghazvini' rootstock was much higher than 'Badami'. Data obtained in present study emphasised that 'Ghazvini' rootstock is more tolerant to salinity than 'Badami'.
Regulation and Programming of Antibody Effector Function through IgG Glycosylation

Antibodies are the defining characteristic of the humoral immune response. Their functions are diverse, including direct neutralization of pathogens and recruitment of other immune molecules or cells. While most successful vaccines induce protective neutralizing antibody responses, effective vaccine-elicited neutralizing antibodies against some pathogens, including HIV, HCV, malaria, and TB, remain elusive. Thus, researchers have begun to focus on how vaccines can elicit strong non-neutralizing antibody functions, including recruitment of innate immune factors for antibody-dependent cellular cytotoxicity, complement deposition, and antibody-dependent phagocytosis. The antibody’s constant region (Fc) mediates most effector functions through isotype and subclass selection or alteration of the structure of the Fc-attached N-glycan, which controls function with exquisite specificity. Glycan modifications are naturally induced during inflammatory conditions such as autoimmune disease and natural infection however, the specific signals that regulate Fc-glycosylation remain unknown. This dissertation sought to understand how antibody glycosylation is regulated and how it can be programmed through vaccination. To do this, we first developed a technique to analyze antibody glycan structures both of bulk Fc and antigenspecific antibodies. Using this technique, we observed significant modulation of antibody glycans during viral infection as well as in vaccine-elicited antibodies. To
Observações citológicas em Coffea: XI - Métodos de tratamento pela colchicina

Colchicine treated seeds of Coffea canephora (2n = 22), C. Dewevrei (2n = 22) and C. arabica (2n=44) produced plants with doubled chromosome numbers (2n = 44 in the first two and 2n = 88 in the last mentioned species)! The strength of the solutions varied from 0,15 to 0,60% ; the treatment was given when the seeds were already germinating. The immersion of seeds in the solution even for many days did not affect the embryo. Colchicine in lanolin (0,10 to 0,60%) did not produce doubling of chromosomes when applied to buds of the same three species. A new method has been devised for the treatment of sterile plants. This is the case of the triploid (2n = 33) hybrids between Coffea arabica and C. canephora and of the di-haploid (2n = 22) form of Coffea arabica known as the monosperma variety : both are highly sterile producing only a few round seeds whose embryos are of varied chromosome numbers. The method is the following : twigs of the plants are taken to the laboratory where they are placed in individual vials containing a solution of colchicine ; after having absorbed a certain amount of the liquid, they are grafted. In the case of Coffee the strength of the solution was of 0,25 and 0,50%. Through this method, 66 - chromosome branches have been obtained on these grafts by treating original triploid (2n=33) tissue. Many 44 - chromosome branches were also obtained from a di-haploid (2n=22) variety. In the first case the sterility was almost entirely eliminated ; in the second case a complete change from sterility to fertility has occurred. This method is also applicable to other plants, when the treatment of seeds is not possible and grafting is an usual means of propagation.
Impact of two Williopsis yeast strains on the volatile composition of mango wine

Summary The aim of the research was to study the volatile composition of mango wine fermented with two Williopsis yeast strains: Williopsis saturnus var. mrakii NCYC500 and W. staurnus var. suaveolens NCYC2586. Thirty terpenoids, twenty-six esters, ten alcohols, nine acids, seven aldehydes and ketones, two ethers, two phenols and one sulphur compound were identified in the mango wine fermented with strain NCYC500, while twenty-seven terpenoids, thirty esters, eleven alcohols, eight acids, eight aldehydes and ketones, three ethers, two phenols, one sulphur compound and one furan were detected in the mango wine fermented with the strain NCYC2586. The kinetic changes, final concentrations and odour activity values of major volatiles were compared between the two Williopsis yeast strains and also with other yeast reported in the literature. The results showed that Williopsis yeast strains NCYC500 and NCYC2586 were high producers of acetic acid and acetate esters, but low producers of medium- to long-chain fatty acids and their corresponding ethyl esters. Unlike mango wine fermented with Saccharomyces cerevisiae, most terpenoids derived from mango juice were retained in the resultant mango wine fermented with the two Williopsis yeast strains, suggesting the mango wine could retain the aromatic hints of fresh mango.
The Protein Tyrosine Phosphatase SHP2 as a Mediator of Differential Cellular Sensitivity to EGFR Kinase Inhibitors

SRC homology 2 domain-containing phosphatase 2 (SHP2) is a ubiquitously expressed cytosolic protein tyrosine phosphatase. Downstream of epidermal growth factor receptor (EGFR) and other receptors, SHP2 is activated by binding to phosphotyrosine-containing receptors and adapter proteins, is required for complete extracellular regulated kinase 1/2 (ERK) pathway activity, which promotes cellular proliferation and survival, and regulates other signaling processes. In this thesis, we explored the signaling functions of SHP2 in lung and brain cancer cell systems with or without clinically relevant mutations that render EGFR constitutively active and developed computational models of EGFR-mediated SHP2 activation. In non-small cell lung cancer cells, SHP2 promoted ERK-dependent resistance to EGFR inhibition, but in cells with EGFR kinase-activating mutations this SHP2 functional role was impaired through sequestration of biochemically active SHP2 with internalization-impaired EGFR mutants. In glioblastoma multiforme cells, SHP2 simultaneously promoted ERK activity and antagonized STAT3 phosphorylation such that SHP2 drove proliferation while also promoting sensitivity to EGFR and c-MET co-inhibition. These SHP2 functions were perturbed by sufficiently high expression of the EGFR variant III mutant. Furthermore, SHP2 was found to regulate EGFRvIII and c-MET phosphorylation and control hypoxia-inducible factor expression in a way that may regulate tumorigenesis. We next developed computational models and associated quantitative experimental data sets to gain quantitative understanding of the regulation of protein complexes containing SHP2 and GRB2-associated binder 1 (GAB1), the primary phosphorylated adapter with which SHP2 associates following EGFR activation. Our analysis revealed that in some cell settings EGFR activity is amplified by intermediary SRC family kinases (SFKs) which drive GAB1 phosphorylation and enable GAB1-SHP2 complexes to persist in the cytosol distal from EGFR. A reaction-diffusion model further predicted that EGFR-initiated GAB1-SHP2 complexes persist over the entire cell length scale, which could permit membrane-localized EGFR to regulate signaling events through SHP2 at subcellular locations where EGFR itself is not present. Overall, these results motivate the continued search for specific SHP2 inhibitors, while providing a contextual basis for predicting when such interventions may be particularly effective, and establish a quantitative framework for understanding EGFR's ability to activate SHP2 and how this might be perturbed in different pathological contexts. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemical and Biomolecular Engineering First Advisor Matthew J. Lazzara This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1279
The effects of herbivory and competition on the invasive alien plant Senecio inaequidens (Asteraceae)

Abstract. Senecio inaequidens DC. (Asteraceae) is an invasive alien plant introduced to Europe from South Africa in around 1896. It contains pyrrolizidine alkaloids that are toxic to livestock and humans. S. inaequidens would therefore be an economic and ecological problem if it became established and abundant in natural or farmed grassland ecosystems.
Enrichment and characterization of MTBE-degrading cultures under iron and sulfate reducing conditions

The aim of this study was to enrich cultures capable of anaerobic methyl tert-butyl ether (MTBE) biodegradation and to determine their compositions using biomolecular tools. MTBE biodegradation as the sole carbon source was observed under Fe(III) and SO42– reducing conditions and with both electron acceptors present together. The estimated MTBE biodegradation rates ranged from 3.80 to 9.20 mg·L–1·d–1 when Fe(III) was the sole electron acceptor, from 1.46 to 1.70 mg·L–1·d–1 when Fe(III) and SO42– were present together, and from 1.13 to 1.71 mg·L–1·d–1 when SO42– was the sole electron acceptor. Five to eight members were identified in the three consortia, and their characteristics were congruent with the electron acceptor conditions. A clone 99% similar to a recently described MTBE degrader, Ochrobactrum cytisi, was detected in both cultures containing Fe(III). Other 16S rRNA gene sequences detected were highly similar at the species or genus level to additional known MTBE degraders, including Pseudomonas s.