Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the Mechanism for the Selective Induction of Apoptosis in Transformed Cells by CAV Apoptin: a Dissertation

Most existing chemotherapeutics lack adequate specificity for transformed cells and therefore have high rates of collateral damage to normal tissue. Moreover, such therapies often depend on p53 to induce cell death and are ineffective on the large number of human cancers that have lost p53 function. The discovery of novel p53independent cancer therapies is therefore of significant interest. The Chicken Anemia Virus protein Apoptin selectively induces apoptosis in transformed cells in a p53independent manner while leaving normal primary cells unaffected. This selectivity is thought to be largely due to cell type-specific localization: in primary cells Apoptin is cytoplasmic, whereas in transformed cells the protein localizes to the nucleus. The basis for this cell type-specific localization remains to be determined. In this study, Apoptin is revealed to be a nucleo-cytoplasmic shuttling protein whose localization is mediated by an N-terminal nuclear export signal (NES) and a C-terminal nuclear localization signal (NLS). Both signals are required for cell type-specific localization, as Apoptin fragments containing either the NES or NLS fail to localize differently between transformed and primary cells. Significantly, cell type-specific localization can be rescued in trans by coexpression of the two separate fragments, which are able to interact through an Apoptin multimerization domain. Interestingly, this multimerization domain overlaps with the NES suggesting that these two activities may be functionally coupled in cytoplasmic retention in primary cell types. Factors present in transformed cells induce localization of
Potential for Utilization of Algal Biomass for Components of the Diet in CELSS

Techniques which eliminate or reduce the undesirable cell components of algae and enhance the potential nutritional and organoleptic acceptability of algae products are studied. The cell walls, nucleic acids, and pigments and lipids of the green algae Scenedesmus obiliquus need to be removed. The procedures for determining the composition of proteins, pigments and lipids, and moisture and ash are described. Chemical, enzymatic, and physical methods of removing the cell wall to make the algae digestable are analyzed; a homogenization technique is utilized. The problems encountered if algae nucleic acids are ingested directly are discussed; the reduction of DNA and RNA by applying extracellular DNase and RNase to the nucleic acids is examined. The color and flavor of the algae are enhanced with the extraction of pigments and lipids from the algae protein concentration.
Avian Malaria Parasites and other Haemosporidia

When studying the effects of parasites on natural populations, the avian haematozoa fulfills many of the specifications of an ideal model. Featuring a multitude of tables and illustrations, Avian Malaria Parasites and Other Haemosporidia summarizes more than a century of research on bird haemosporidians. For a long time, bird blood parasites served as important models in studying human diseases. Although now largely replaced, a wealth of data and research remain. With chapters addressing life cycles and morphology, pathogenicity, ultrastructure, geographical distribution, and illustrated keys to all known species of the parasites, this book is a masterful assessment of the biology of bird haemosporidian parasites.
Methods and devices for comprehensive molecular analysis of single cells

Typical analytical methods for evaluating the protein and gene expression of cells rely on the molecular analysis of analytes from a large number of cells. These methods, however, do not reveal insight into the heterogeneous nature of cells and instead only provide average results of the bulk population. Moreover, these methods are insensitive to low copy number proteins or mRNA that may in fact play a significant role in a cell's phenotypic state. The ability to discern the true distributions of protein and gene expression in a cell population will give rise to the effective identification of unique subpopulations. This allows for a deeper understanding of disease progression, molecular pathways, and cellular differentiation by revealing previously undetectable states of cells. Therefore, it is essential that technologies capable of isolating and comprehensively analyzing many single cells in parallel be developed. In this dissertation, I present new methods and technologies for integrating the capture and isolation of single cells with comprehensive, quantitative on-chip molecular analysis within a single microfluidic platform. I first present the design, development, and function of polymethyldisiloxane (PDMS) microfluidic devices capable of trapping and fully isolating many single cells along a series of compartments. Additionally, I discuss various methods for trapping (dielectrophoretic or hydrodynamic) and lysing (electric-field or chemical) of the cells directly in individual, nanoliter-sized compartments. Subsequently, I present methods for the fabrication, assembly, and application of high-density antibody- conjugated microbead arrays for single-cell proteome analysis. I then discuss how such arrays can be integrated directly into the PDMS devices using a protective patterning scheme to overcome current challenges in producing patterned, modified surfaces in PDMS devices. I also present methods we have developed which could enable analysis of single-cell gene expression by directly sequencing the mRNA transcripts captured from each single cell on the device. Finally, I present my work on electric field-directed assembly of enzyme-nanoparticle layers for biosensor applications. Together, these methods and devices constitute key advancements towards the development of a technology capable of fully integrating single-cell capture and comprehensive molecular analysis
Ca2+/calmodulin‐dependent protein kinase II isoenzymes γ and δ are both present in H+/K+‐ATPase‐containing rabbit gastric tubulovesicles

Ca 2+ /calmodulin-dependent protein kinase II is thought to participate in M3 muscarinic receptor-mediated acid secretion in gastric parietal cells. During acid secretion tubulovesicles carrying H + /K + -ATPase fuse with the apical membrane. We localized Ca 2+ /calmodulin-dependent protein kinase II from highly purified rabbit gastric tubulovesicles using Ca 2+ /calmodulin-dependent protein kinase II isoform-specific antibodies, in vitro phosphorylation and pharmacological inhibition of Ca 2+ /calmodulin-dependent protein kinase II activity by the potent Ca 2+ /calmodulin-dependent protein kinase II inhibitor KN-62. The presence of Ca 2+ /calmodulindependent protein kinase II in tubulovesicles was shown by immunoblot detection of both Ca 2+ / calmodulin-dependent protein kinase II-g (54 kDa) and Ca 2+ /calmodulin-dependent protein kinase II-d (56.5 kDa). The immunoprecipitated Ca 2+ /calmodulin-dependent protein kinase II from tubulovesicles showed Ca 2+ /calmodulin-dependent protein kinase activity by phosphorylating autocamtide-II, a specific synthetic Ca 2+ /calmodulin-dependent protein kinase II substrate. KN-62 inhibited the in vitro autophosphorylation of tubulovesicle-associated Ca 2+ /calmodulin-dependent protein kinase II (IC50 =1 1 n m). During the search for potential Ca 2+ /calmodulin-dependent protein kinase II substrates we identified different proteins associated with tubulovesicles, such as synaptophysin and b-tubulin immunoreactivity, which were identified using specific antibodies. These targets are known to participate in intracellular membrane traffic. Ca 2+ /
RFC 2413: Dublin core metadata for resource discovery

The Dublin Core Metadata Workshop Series began in 1995 with an invitational workshop which brought together librarians, digital library researchers, content experts, and text-markup experts to promote better discovery standards for electronic resources. The Dublin Core is a 15-element set of descriptors that has emerged from this effort in interdisciplinary and international consensus building. This is the first of a set of Informational RFCs describing the Dublin Core. Its purpose is to introduce the Dublin Core and to describe the consensus reached on the semantics of each of the 15 elements.
Evolution and domestication of rice

This chapter intends to explore some implications of rice evolution from the viewpoints of genetics and ecology. Core issues are (1) what genetic changes are associated with differentiation among and within species of cultivated rice and their wild relatives and (2) what factors are responsible for the domestication process. First, genetic diversity among and within AA genome species is summarized. Second, four directions of differentiation within the Asian AA genome gene pool are clarified: differentiation from wild to cultivated type (domestication), ecotype differentiation from perennials to annuals in wild races, geographical variation in wild races, and indica-japonica differentiation in cultivars. Third, the genetic basis of the domestication syndrome is discussed. Our recent study demonstrated that mapped genomic locations of quantitative trait loci (QTLs) tended to cluster, reflecting the domestication syndrome as well as the indica-japonica syndrome. This phenomenon was explained by “multifactorial linkages. ”Domestication might be a process driven by conscious and unconscious selection of adaptive gene blocks distributed over the genome. In the past decade, a wealth of data provided by molecular markers, together with phenotypic, ecological, and archaeological data, significantly increased our evolutionary understanding of the genus Oryza. The target species dealt with in this chapter are diploid AA genome species—cultivated rice and its wild relatives. Several important problems such as the genetic basis of reproductive isolation are not included, but some new information obtained from our recent studies is discussed.
Dry matter accumulation and forage quality characteristics of different soybean genotypes

Three different soybean [Glycine max (L.) Merr. ] cultivars (A-3127, Derry, and Yemsoy) were evaluated for dry matter (DM) yield, plant components, and crop growth rate (CGR) at different row spacings and harvesting stages in 3 locations with Mediterranean-type climate in a split-split plot design with 3 replications in 2009 and 2010. In addition, crude protein (CP), crude protein yield (CPY), acid detergent fiber (ADF), neutral detergent fiber (NDF), total digestible nutrients (TDN), and relative feed value (RFV) of harvested forage soybeans were determined at the Bursa (Turkey) location. Increased row spacings significantly reduced DM yield at all locations. Combined over other main effects, the 25-cm row spacing produced 35% more DM yield than the 75-cm row spacing. Row spacings greatly affected DM yield at the R5 and particularly the R7 stage, but this effect was minimal at the R1 stage. The forage-type cultivar Derry produced significantly higher DM yield in all locations, particularly at the R5 and R7 stages. The constituent components of DM were similar at different row spacings of soybean cultivars. In general, the CGR decreased from 25-cm row spacing to 75-cm row spacing in all locations, and the CGR of the cultivars varied significantly according to harvest period, row spacing, and location. Derry had a significantly higher CGR than the other cultivars in the Antalya and Bursa locations. Quality characteristics of soybean forage were not significantly affected by row spacing and showed little effect by cultivar. Harvest stage significantly affected CP, ADF, NDF, TDN, and RFV concentrations of soybean forage. It was concluded that in Mediterranean environments forage-type soybeans (i.e. Derry) can be seeded in narrow rows (25 cm) at high plant population (100 kg ha-1) and offer the most DM yield when harvested at later R stages (e.g., R7) rather than at the early reproductive stage.
On Trimmed Data Effect in Parameter Estimation of Some Population Growth Models

Logistic model, Gompertz model, Richard model, Weibull model and Morgan-Mercer-Flodin model are commonly used to describe growth model of a population. In this paper, we study the effect of trimmed data on parameter estimation results of those models. We use chicken weight data cited from literature. Parameter values of the models from the complete data and the trimmed data are compared. Then, the sensitivity index of all parameters is evaluated. We found that that sensitivity order of the models from the highest sensitivity was the Morgan-Mercer-Flodin, Weibull, Richards, logistic and Gompertz growth model. For practical applications, Gompertz model and Richards are recommended in order to modelling growth of a population.
The Level of Anxiety among Jordanian EFL Undergraduates in Oral Communication Performance

The main aim of this study is to investigate the level of anxiety of Jordanian English as a foreign language (EFL) undergraduates in oral communication performance in Jerash University, Jordan. This study is significant in determining student’s level of anxiety and find solutions for reducing their anxiety. The sample of the study consists of 351 students and five lecturers. A 33-item questionnaire adopted from Horwitz et al. (1986) was used to investigate student’s level of anxiety. 35 students and five lecturers sat for interviews. SPSS 22 was used in this study to analyse the quantitative data while NVivo 10 was used for analysing the qualitative data. The findings revealed that 60.7 per cent of the respondents showed that they experience anxiety while speaking in English. Qualitative findings from respondents suggest having collaboration between parents, lecturers and students, departure from current teacher-centered approaches, providing stress-free and congenial exercise of public speaking and debates. Future researchers are encouraged to add another research instrument when conducting studies investigating foreign language anxiety such as include students’ journals to get more accurate findings.
Laboratory Protocols for Conditional Gene Targeting

Section 1: The Cre-loxP recombination system and gene targeting in ES cells 1. Gene targeting strategies 2. Cre-loxP recombination system 3. Gene targeting vectors - consideration and use of loxP 4. Nonselectablae modifications and removal of selection marker genes 5. Large deletions 6. Gene replacement 7. Targeted integrations 9. Conditional gene modification 10. LoxP-containing transgenes 11. Conditional gene targeting Section 2: Working with ES cells 12. ES cell transfection overview 13. Embryonic feeder cells 14. ES cells - handling and use 15. ES cell culture and transfection 16. ES clone picking 17. Identification of homologous recombinants 18. Freezing ES clones 19. Thawing ES clones 20. Genomic DNA preparation 21. Cre-mediated neomycin deletion in ES cells 22. Generation of mice - preparation 23. Mouse breeding for ES cell injection or aggregation 24. Injection needles and holders 25. Blastocyst preparation/injection 26. Embryo aggregation 27. Blastocyst transfer Appendices References Selected references for further reading
Fistularia commersonii (Teleostea: Fistulariidae): walking through the Lessepsian paradox of mitochondrial DNA

Abstract The Mediterranean Lessepsian migrations excite the interest of biologists who are devoted to inferring the effects of selection on the genetic structure of immigrants. The bluespotted cornetfish Fistularia commersonii is an Indo-Pacific species that was first recorded in the Levantine cost of Mediterranean, and within a few years, it rapidly expanded throughout the entire basin. Studies on its genetic variability, performed via mitochondrial sequencing of the Mediterranean specimens, suggest that a limited number of mitochondrial lineages passed through the Suez Canal. However, nuclear markers provide a scenario, with a high genetic variability among the Mediterranean F. commersonii migrants, along with the occurrence of haplotype sharing between the Mediterranean and the Red Sea. The aim of this study was to enlarge the number of Mediterranean sites in order to evaluate if the rapid expansion and different patterns of spread of F. commersonii in the basin could have led to a genetic structuring. The analysis was carried out by sequencing mitochondrial D-loop I in individuals from Sardinia, Sicily, Tunisia, Lampedusa, Libya and Lebanon. Sequences available from previous studies were included in the data set, allowing us to obtain a data set that likely represents the entire distribution range of the species. Results suggest the possible occurrence of two mitochondrial lineages involved in the Mediterranean invasion of F. commersonii, a bottleneck may have caused a loss in the genetic variation, leading to the fixation of specific lineages as an adaptive response to the new environmental conditions.
In Vitro Alterations of a Putative Phospholipid Translocase, Atp10c , and Its Role in Glucose Metabolism

Atp10c is a putative phospholipid “flippase” that encodes for a type 4 P-type ATPase. Based on previous research, we hypothesize that ATP10C due to its flippase nature plays a role in DIO and T2D as Atp10c heterozygous mice display this phenotype. For our investigation, we characterized Atp10c/ATP10C in order to gleam information about its biological role and/or function. In order to do this, an ATP10C-GFP plasmid construct was commercially obtained and transfected into HEK293T cells. Results showed a band at the expected molecular weight, about 165 kD. Next, immunolocalization by fluorescence confocal microscopy was employed, and we were able to show that the ATP10C-GFP fusion protein localized to the plasma membrane of HEK293T cells; also we see some co-localization of ATP10C with GLUT4 (about 81%). Finally, the expression of Atp10c in two mice models, one DIO and the other genetic (ob/ob) was measured. Results from these experiments revealed a high expression in all the tissues tested. The expression of Atp10c was highest in fat for the ob/ob mice (2.94 fold). For the DIO mice, the expression of Atp10c was higher in the skeletal muscle (3.78 fold). All the results presented strengthen Atp10c’s role in glucose and lipid metabolism.
Producción de pigmentos por callos de Mammillaria candida Scheidweiler (cactaceae)

Con el fin de obtener colorantes naturales a partir de cactaceas sin afectar las poblaciones naturales, se establecieron cultivos de callos de Mammillaria candida altamente pigmentados. Los callos se cultivaron en el medio de Murashige y Skoog con 3 mg L-----1 de acido 2, 4-diclorofenoxiacetico, acido naftalenacetico o acido clorofenoxiacetico, solos o en combinacion con 0.1 mg L-----1 de cinetina, cinetin ribosido o benciladenina. Aproximadamente 80% de los callos se pigmento en medios con auxinas y 50% en medios con auxinas y citocininas. La coloracion del tejido aumento cuatro veces en medios con 50 y 100 g L-----1 de glucosa o sacarosa (estres abiotico) y con extractos de hongos (estres biotico). El analisis espectrofotometrico mostro que el pigmento corresponde a una betaxantina modificada.
The 5′‐flanking region of the rat GABAA receptor α2‐subunit gene (Gabra2)

The GABAA receptor α2‐subunit gene (Gabra2) has a specific spatial and temporal pattern of expression in rat brain. As a first step towards understanding the molecular mechanism underlying this regulation, we have investigated the structural properties of the 5′‐ flanking region of the rat Gabra2 gene. We identified six α2 transcript isoforms, each of which differs only in the 5′‐untranslated region (UTR). Alignment of cDNA and genomic DNA sequences revealed that six 5′‐UTRs are generated from three alternative first exons by alternative splicing using internal and terminal 5′‐splice donor sites present in these exons. Promoter regions containing multiple transcription initiation sites were identified in the 5′ proximity of each first exon. Two of these promoters lack TATA and CCAAT sequences. Finally, we have shown that differential activation of alternative promoters is used for the expression of the α2 mRNA isoforms during brain development, and that the diversity at the 5′‐end of these transcripts affects GABAA receptor expression. Taken together, these results suggest that the expression of the Gabra2 gene can be influenced at both the transcriptional and post‐transcriptional levels.
Sexual maturity and sexual dimorphism in a population of the rocket-frog Colostethus aff. fraterdanieli (Anura: Dendrobatidae) on the northeastern Cordillera Central of Colombia

El tamano minimo de madurez sexual y el dimorfismo sexual son importantes caracteristicas de historia de vida, utiles para estudiar y comprender la dinamica poblacional de cualquier especie. En este estudio, determinamos el tamano minimo de madurez sexual y la existencia de dimorfismo sexual en una poblacion de la ranita cohete, Colostethus aff. fraterdanieli, a traves de datos morfologicos y morfometricos y de observaciones macro y microscopicas de las gonadas. Las hembras alcanzan la madurez sexual a los 17,90 ± 0,1 mm de longitud rostro cloaca (SVL), mientras que los machos alcanzan la madurez sexual sobre los 16,13 ± 0,06 mm (SVL). Las hembras difirieron de los machos en tamano, forma y coloracion de la garganta. Los machos fueron mas pequenos que las hembras y tuvieron una marcada y oscura coloracion gular que algunas veces se extiende hasta el pecho, mientras que las hembras carecen de esta caracteristica, con una garganta inmaculada o debilmente manchada. En este estudio, describimos algunos aspectos importantes de la ecologia reproductiva de una poblacion de C. aff. fraterdanieli utiles como linea base para otros estudios mas especializados.
Characterization of Quercus Species Distributed in Jordan Using Molecular Markers

Genetic diversity among 25 natural populations of three different species of Quercus in Jordan at molecular levels using Random Amplified Polymorphic DNA (RAPD) primers was assessed. Significant molecular variations among and within 25 Quercus populations were estimated. Twenty-seven polymorphic markers and 5917 scored bands were generated using six RAPD primers. Based on RAPD data, the populations were grouped together in the same cluster according to species regardless to local of collections. This study has emphasized the ability of the molecular markers in the determining the genetic diversity among and within the populations of Quercus and the resulted high genetic variability could be utilized in implications of improving conservation, restoration, and reforestation strategies of Quercus in Jordan.
Additional copies of virG from pTiBo542 provide a super-transformation ability to Agrobacterium tumefaciens in citrus

Abstract Agrobacterium tumefaciens strain A281 carrying pTiBo542 was described as able to induce large and early-appearing tumours on a wider range of plants than other Agrobacterium strains. Here we show a strict correlation between the supervirulence of A281 and super-transformation ability of its disarmed derivative EHA105/p35SGUSINT. This strain produced much higher transformation than the disarmed derivative of the common strain C58, called C58(pMP90)/p35SGUSINT. Transformation frequency increased from six to 22-fold, depending on the citrus genotype. This increase permitted to regenerate for the first time, whole transgenic plants from lemon, alemow and Cleopatra mandarin. Since the chromosomal background from C58 as well as the T-DNA from p35SGUSINT are identical for both bacterial strains, the super-transformation ability of EHA105/p35SGUSINT in citrus may be attributed to the vir region of pTiBo542. In addition, introduction of extra copies of virG from pTiBo542 into either EHA105/p35SGUSINT or C58(pMP90)/p35SGUSINT further increased transformation, demonstrating the importance of vir induction, and mainly virG activation, in the super-transformation ability of this Ti plasmid in citrus.