Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome mapping of Eucalyptus globulus

This thesis covers the construction of genetic linkage maps of two Eucalyptus globulus parental trees (chapter 2), the detection of quantitative trait loci (QTL) carried out using these linkage maps (chapter 3) and a genetic analysis of rooting ability of micropropagated cuttings from two E. globulus families (chapter 4). Genetic linkage maps of two parent trees were constructed using 326 RAPD and 21 microsatellite markers. At a LOD score threshold of 4.9 for grouping and 3.0 for marker ordering, the male parent had 13 linkage groups consisting of 101 framework markers and the female parent had 11 linkage groups with 97 framework markers. Even though both parents originated from the same provenance it was found that polymorphic RAPD markers were readily detectable. Linkages between microsatellites previously reported for E. grandis/E. urophylla were conserved in the E. globulus cross. Segregation distortion of markers was found to be more prevalent than expected by chance. The linkage maps were used to detect QTLs based on 155 progeny grown in field trials. Twelve traits were included in the QTL analysis. These included: wood density (Pilodyn penetration), extent of early flowering (bud abundance), and growth (height at years one and two, stem diameter at years two, three, four and six, and relative incremental growth between years one and two, two and four, and four and six). Using interval mapping a total of eight QTL with LOD score peaks over 2.0 were detected, corresponding to seven map intervals. QTL detected included: two for cumulative growth; two for wood density; one for early flowering and three for relative incremental growth. Since the 155 progeny trees were grown at seven trial sites, an analysis of marker by site interaction was carried out with more marker by site interactions being found than expected by chance. Markers with significant QTL effects were examined for interaction with site with both of the cumulative growth QTL found to have significant site interaction. QTL stability with age was also analysed for these QTL, and both growth QTL were found to have a detectable association with the first measurements of height and diameter. A study of the rooting ability of cuttings grown in tissue culture from two families of E. globulus was undertaken with the aim of detecting QTLs for this trait. The two families were found to have significantly different rooting abilities indicating that genetic variation for the trait was present. Estimates of variance components relating to genetic and environmental effects indicated that within both families the variance due to genetic effects was small compared to the environmental variance with clonal repeatabilities of 0.17 and 0.14 for the two families. These estimates were used in power calculations based on t-tests of single markers under some simple assumptions. However even under optimistic circumstances the power for QTL detection was found to be too low to warrant the time and expense of genotyping required for QTL analysis.
Investigations of tetraspanin functions using large extracellular loops

This thesis describes our characterization of a specific tetraspanin domain: the large extracellular loop (LEL). Tetraspanins are involved in cellular migration, adhesion, and metastasis, sperm-egg fusion, and viral infectivity. The large extracellular loop domain is the major extracellular domain of tetraspanins and the binding of a monoclonal antibody against the tetraspanin CD9 serves to inhibit fertilization, consistent with the CD9-null mouse model. The first area of focus in this thesis is the characterization of the murine CD9-LEL domain. We present a methodology to express and purify the mCD9-LEL to homogeneity. Biophysical characterization of the mCD9-LEL protein reveals that it is an autonomously folding, a-helical dimer. Mutagenesis over much of the mCD9-LEL protein reveals that it is composed of two subdomains: a dimerization subdomain and a variable subdomain proposed to mediate heterotypic interactions. These results suggest both a means for exploring endogenous tetraspanins functions and a mechanism by which tetraspanins may oligomerize. Surprisingly, we were not able to detect oligomerization of the intact CD9 molecule, in discordance with our biophysical data on the mCD9-LEL. In the latter part of this thesis, we expand our methodology to purify and characterize three different tetraspanins-LELs, the hCD9-LEL, the hCD63-LEL, and the hCD8 1-LEL. These tetraspanins-LELs all exhibit similar characteristics to the mCD9-LEL, consistent with a published crystal structure of the hCD81-LEL. Lastly, we demonstrate the ability of our tetraspanin-LEL proteins to bind integrins, to inhibit sperm-egg fusion, and to inhibit hepatitis C viral infectivity. Taken as a whole, these studies present novel, biophysically validated tetraspanins-LELs that lend insight into endogenous tetraspanins functions. Thesis Co-Supervisor: Peter S. Kim Title: Professor of Biology Thesis Co-Supervisor: Richard 0. Hynes Title: Professor of Biology
Yield response to nitrogen fertilization and harvest timing on a mature Miscanthus x giganteus stand

The U.S. demand for renewable fuels has increased due to the concerns about the availability of nonrenewable fuels in the future and the impacts these fuels have on the environment. It is likely that Miscanthus x giganteus will be an important renewable energy crop in the U.S. due to great biomass production and low input requirements. This research focuses on the effects of nitrogen fertilization rates and harvest timings on yields and quality of a four-year-old crop of M. x giganteus. Research plots in Champaign, IL were harvested at five dates from August through March 2009, 2010, and 2011, and received five rates of nitrogen fertilizer (from 0 to 224 kg ha) to determine biomass yields and quality over three growing seasons. From this study, we concluded that M. x giganteus production increased with nitrogen applications up to 112 kg ha, and that harvesting following senescence is optimal for long-term biomass yield, increases carbon content and reduces nitrogen, moisture, and ash content in the harvested biomass. These results lay a foundation as agronomic researchers to develop best management practices for the emerging feedstock industry.
A combined morphological and molecular phylogenetic analysis of Parthenocissus (Vitaceae) and taxonomic implications

Parthenocissus (the Virginia creeper genus, Vitaceae) consists of 13 species and shows a disjunct distribution between Asia and North America. We investigated the inflorescence structure, calyx morphology, appendages on the inner side of petals, leaf epidermis, pollen and seed characters throughout the genus. A combined phylogenetic analysis with 27 morphological and 4137 molecular characters was conducted and the result was largely congruent with that of the previous molecular work, but with higher resolution. The combined analysis identified two clades corresponding to the Asian and North American taxa. Parthenocissus feddei was resolved as closely related to the clade containing P. cuspidifera, P. heterophylla and P. semicordata. The four species share synapomorphies of having conspicuously raised veinlets, an obscurely five- (to eight-) lobed calyx, appendages on the inner side of petals covering the entire length of anthers and foveolate pollen exine ornamentation. Within the Old World clade, the pentafoliolate species were weakly supported as more closely related to species with both simple and trifoliolate leaves. Furthermore, the ancestral states of tendril apices, inflorescence structure, appendages on the inner side of petals and exine ornamentation of pollen grains were reconstructed on the molecular strict consensus tree. The appendages on the inner side of petals and exine ornamentation of pollen grains were suggested to be important characters in the taxonomy of Parthenocissus, especially for species with trifoliolate leaves. Finally, the previous classifications of Parthenocissus were evaluated within the phylogenetic framework. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, ••, ••–••.
Nutritional value of carrot juice as affected by different blanching media.

Effects of different blanching media on the yield and nutritional value of carrot juice was investigated in this study. Each blanching medium showed different effect on the yield and nutritional value of carrot juice. Maximum amount of carrot juice (76.0%) was obtained on blanching carrots in 0.5 % acetic acid solution containing 1.0% CaCl2. However, 66.0% juice was obtained from unblanched carrots. Highest amount of protein (1.34%) minerals (2.50%) and soluble sugars (5.46%) were found in carrot juice, which was obtained after blanching carrots in acetic acid solution containing 1.0% CaCl2. Similarly, this blanching media also showed highest amount of carotene (195 mg 100 g) and vitamin C (8.0 mg 100 g) contents in carrot juice. However, 0.88% protein, 1.26% minerals and 4.81% soluble sugars along with carotene (175 mg 100 g) and vitamin C (44.0 mg 100 g) contents were present in juice from un-blanched carrots.
A study of ontogenetic level of language development and gender differences affecting language use in Acehnese language

There have been numerous studies analysing gender differences in language use. Most of them predominantly adopted static or hierarchical approach with obsolete understanding of gender differences. Concurrently with the high demand of socio-cultural aspects inclusion in language development studies, the research of gender in language use has also driven to the same direction with mixed talk and the use of dynamic approach as an alternative for more inclusive socio-cultural spectrum. Two student university classes were observed and their classroom conversations in mixed gender were meticulously selected for detailed analysis via N-VIVO. The study shows that social dimensions such as power, status, economy, and identity seem to be influential to Acehnese language users in mixed talks. Yet, some mixed talks are more likely to be affected by individual ontogenetic language development; the dominance of talk is relatively fading and mutual-respect is bold. Therefore, the advocacy for the dynamic approach to conducting further research in this domain is decisively important. It is also crucial for more thorough and deep analysis on the genetic language development of speakers such as their social backgrounds and study or learning experiences. This paper draws merely a minor part of a larger research project conducted in Aceh and is expected to be a trigger for future studies.
Community Food Security of the Southeastern Appalachian Region of Ohio

Community food security (CFS) is “a situation in which all community residents obtain a safe, culturally acceptable, nutritionally adequate diet through a sustainable food system that maximizes self‐reliance and social justice (Hamm, 2003),” without resorting to emergency food sources (Gottlieb, 1996). There is a paucity of data available on the CFS of regions in the United States (U.S.), including Appalachian Ohio. In order to better understand U.S. communities, their resources, and their needs, CFS must be explored. Therefore, this study was conducted to explore the CFS of the Southeastern region of Appalachian Ohio using the methods of Lopez and Tchumtchoua (2005). Thirty‐eight indicators of CFS were measured in the largest areas of census (cities, towns, townships) in the study region and included general community characteristics (population density, percent of female households), community food resources (participation in Federal food assistance programs, number of supermarkets and convenience stores per capita), community resource accessibility (income, available transportation), and community food production (farmland usage, community supported agriculture). These data were obtained from U.S. Bureau of Census, State of Ohio, and Ohio county governments. Descriptive and inferential statistics were tabulated using the Statistical Program for the Social Sciences (Chicago, IL). Prior to this study, no research had been conducted in this region regarding CFS. This study will promote a better understanding of CFS in Appalachian Ohio and fill a gap in the CFS literature.
Study on Comparison of Growth Performance, Feed Efficiency and Carcass Characteristics for Holstein and F1(Holstein ♀ x Hanwoo ♂) Steers and Heifers

S. W. Kang*, Y. K. Oh*, K. H. Kim*, C. W. Choi* and Y. S. Son**National Livestock Research Institute, R.D. A. *,College of Life & Environmental Sciences, Korea University**ABSTRACTPresent study was conducted to investigate the optimal feeding levels for producing the high qualitymeat on the basis of the information deriving from the comparison of the growth performance and carcasscharacteristics among breeds(Holstein vs F1, Holstein ♀×Hanwoo ), sex♂ (steer vs heifer) and interactionbetween breed and sex. Thirty two animals on 4 treatments(i.e. eight head each) were used for 540 daysfrom seven to 24 months of age.The results obtained are summarized as follows; the range of average daily gains was 0.733 to 1.018,0.994 to 1.255, 0.947 to 1.259 and 0.736 to 0.824kg for the growing, the early-fattening, the mid-fattening and the finishing periods, respectively. The range of average daily gains for the entire period was0.882 to 1.061kg. The gains were higher for Holstein(7.3%) and the steers(10.5%) than F1 and theheifers, respectively. Concentrates and total digestible nutrients intakes per kg gain were higher for Holsteinand the heifers than F1 and the steers, respectively. These findings may indicate that feed utilization ishigher for Holstein than F1, and higher for the steers than the heifers.In carcass characteristics, back fat thickness was thicker for Holstein than F1, and rib-eye area wassmaller for Holstein than F1. The rib-eye area per kg carcass weight was larger for F1 and the heifersthan Holstein and the steers, respectively. Meat color was better for Holstein than F1, but the sexdistinction did not show any differences. In physicochemical properties of longissimus dorsi, shear force,cooking loss, water holding capacity and the panel test scores of juiciness, tenderness and flavor for F1and the heifers were better than those for Holstein and the steers, respectively.According to the above results, we may conclude that F1 and heifers rather than Holstein and steers arerecommended for high quality meat production. In steers and heifers of Holstein and F1, the optimalfeeding levels may be 1.9% of apparent body weight for concentrates and 25% of concentrates intake forrice straw. (Keywords : Holstein, F1, Steers, Heifers, Growth, Carcass Characteristics)Corresponding author:S. W. Kang, National Livestock Research Institute, R. D. A. , Omokchun-dong, Kwonsun-gu, Suwon-Si, Kyeongki-do, 441-350, Korea. Tel:031-290-1641, Fax:031-290-1660,E-mail:swkang@rda.go. kr.
Effect of Nitrogen and phosphorus nutrition at different physiological stages of soybean on yield and grain quality in Uttarakhand hills

An experiment on soybean cv. PK-416 to evaluate the effect of nitrogen fertilizer management strategies at different stages of soybean with P on grain yield, oil and protein content of soybean, in a split plot design with the three replications was conducted at Pantnagar during Kharif, 2000 and 2001. The main plot treatments were 40 kg P2O5/ha, 60 kg P2O5/ha, 80 kg P2O5/ha as basal and sub-plot treatments were 20 kg N/ha as basal, 20 kg N/ha as basal + 20 kg N/ha at 60 DAS as top dressing, 20 kg N/ha as basal + 20 kg N/ha at 60 DAS + 20 kg N/ha at 75 DAS as top dressing, 40 kg N/ha as basal + 40 kg N/ha at 60 DAS at top dressing, 40 kg N/ha as basal + 40 kg N/ha at 60 DAS + 20 kg N/ha at 75 DAS as top dressing. The grain yield of soybean was significantly higher with 40 kg N/ha as basal + 40 kg N/ha at 60 DAS + 20 kg N/ha at 75 DAS along with 80 kg P2Os/ha and resulted in 43.2 and 45.2 per cent increase over 20 kg N/ha as basal along with 40 kg P2O5/ha during 2000 and 2001, respectively. The oil content was maximum with 40 kg N/ha basal + 40 kg N/ha at 60 DAS with an increase of 8.99% in oil content over control. The protein content was maximum with 40 kg N/ha basal + 40 kg N/ha at 60 DAS + 20 kg N/ha at 75 DAS resulted 24.39% increase in protein content of grain over control. Thus, it can be concluded that soybean seed yield and quality can be increased with application of nitrogen at the seed filling stage.
Genetic variability, heritability, genetic advance, correlation and path analysis in Okra.

AB STRACT : A field ex per i ment was con ducted with twenty di verse ge no types of Okra (Pusa Makhamali, VRO-6, VRO-5, Se lec tion-10, IIVR-10, HRB-10, IIVR-11, Perkins Long Green,VRO-4, HRB-9-2, Parbhani Kranti, RS-410, Punjab-7, DOV-91-4, D-1-87-1, EMS-8-1,Bhindi Vaphy, 315, and BO-2) in ran dom ized block de sign with three rep li ca tions. Ana lysed data re vealed that among all the ge no types, Pusa Makhamali, Perkins Long Green, Parbhani Kranti, VRO-6, VRO-5 and Se lec tion-10 gave prom is ing re sults.
Limits and constraints: A comment on premises and methods in recent studies of particle capture mechanisms in bivalves

The moving seascape of research into bivalve suspensionfeeding mechanisms presents challenges which suffice to redirect many curious biologists toward less choppy waters. The anatomical complexity of the various pallial organs alone leave many potential workers bewildered. The range of techniques employed is also rather spectacular, from clearance studies to endoscopy, flow cytometry, confocal microscopy, new histochemical techniques, and ciliary mapping, each with different constraints and generating different types of information. The scales involved simultaneously span the molecular and the organismic. And then there is the unfortunate tendency of the handful of workers in this field to form rigid schools of thought, periodically circling the wagons and shooting in all directions (e.g., Jørgensen 1996). The paper by my colleagues Ward et al. (1998a) entitled ‘‘A new explanation of particle capture in suspension-feeding bivalve molluscs,’’ derives its ‘‘new explanation’’ of particle capture exclusively from video endoscopic observations. Many of the basic ideas were presented in Ward (1996), although the present paper concentrates somewhat more on the roles of the laterofrontal cilia/cirri. I would like to point out some questionable preliminary suppositions and generalizations, limitations of the methodology which limit depth of analysis, and indicate the most useful areas of contribution of endoscopy.
High‐Throughput Identification of Combinatorial Ligands for DNA Delivery in Cell Culture

Finding the optimal combinations of ligands for tissue‐specific delivery is tedious even if only a few well‐established compounds are tested. The cargo affects the receptor‐ligand interaction, especially when it is charged like DNA. The ligand should therefore be evaluated together with its cargo. Several viruses have been shown to interact with more than one receptor, for efficient internalization. We here present a DNA oligonucleotide‐based method for inexpensive and rapid screening of biotin labeled ligands for combinatorial effects on cellular binding and uptake. The oligonucleotide complex was designed as a 44 bp double‐stranded DNA oligonucleotide with one central streptavidin molecule and a second streptavidin at the terminus. The use of a highly advanced robotic platform ensured stringent processing and execution of the experiments. The oligonucleotides were fluorescently labeled and used for detection and analysis of cell‐bound, internalized and intra‐cellular compartmentalized constructs by an a.
The scale of illegal meat importation from Africa to Europe via Paris

Concerns have been raised about the illegal import of bushmeat from Africa into Europe, particularly regarding the health risks posed to people and livestock. The role of international trade in driving unsustainable hunting in source countries is unknown, but generally assumed to be limited. Here, we present the first systematic study of the scale and nature of this international trade. We estimate that around five tonnes of bushmeat per week is smuggled in personal baggage through Paris Roissy‐Charles de Gaulle airport. Bushmeat is not only imported for personal consumption but is part of a lucrative organized trade, with high prices indicating luxury status. A wide range of species is carried, many of which are CITES‐listed. Based on these findings, we suggest ways in which customs, airlines, and airport authorities could reduce imports, focussing on raising awareness of regulations, and improving surveillance and deterrence, particularly where CITES‐listed species are concerned.
Walking Ability, Participation, and Quality of Life in Children with Spastic Diplegic Cerebral Palsy: A Path Analysis Study

Objectives This study aims to design a conceptual model for the effect of various factors on walking ability, participation, and quality of life in children with spastic diplegic cerebral palsy (SDCP) and test it based on field data using path analysis. Materials & Methods This cross-sectional study was performed on 181 children with SDCP. The following were used to measure each of the variables: the Modified Ashworth Scale, the Micro Manual Muscle Tester, the Timed Up and Go Test (TUG), the Boyd and Graham test, the goniometer, weight and height, the Gross Motor Function Classification System, the Life Habits Questionnaire, and cerebral palsy Quality of Life Questionnaire for Children. The structural model was tested in Amos 17. Results All paths of the proposed model were significant (P <0.05). Among evaluated variables, muscle strength (B = -0.466), balance (B = 0.326), and spasticity (B = 0.143) affected walking ability. Moreover, as an intermediate factor, walking ability affected the subjects’ participation (B = -0.819) and quality of life (B = -0.183). Conclusion Muscle strength, balance, and spasticity are the most influential factors in the walking ability of children with SDCP. Furthermore, walking ability and participation are two critical factors in promoting the quality of life of these children.
In vitro propagation of a medicinal plant - mango ginger (Curcuma amada Roxb.).

This paper describes efficient in vitro propagation protocol of Curcuma amada Roxb. , an important aromatic zingiberaceous plant in the countries of Indian subcontinent, using rhizome explants. Rhizome tip explants showed better response than rhizome bud explants in terms of shoot proliferation and hence excised rhizome tip explants were inoculated aseptically on Murashige and Skoog’s (MS) medium supplemented with different 6Benzyl adenine (BA) or 6-furfurylamino purine (Kn) concentrations (0.0, 2.0, 4.0, 6.0, 8.0, 10.0 µM) alone or in combinations with α- Naphthalene acetic acid (NAA) and Indole-3-butyric acid (IBA) (1.0, 1.5, 2.0 µM). Optimum proliferation was obtained on MS medium having 8.0 µM BA + 1.0 µM NAA. Shoot proliferation was maximal (99.8%) with 10.6 ± 0.26 shoots per explant after 6 weeks of culture. The successfully proliferated shoots with an average height of 38 cm were transferred to rooting medium augmented with NAA and IBA at four different concentrations (2.0, 4.0, 6.0, 8.0 µM) and 4.0 µM IBA was found to be best for in vitro adventitious rooting. Rooted plantlets were then transferred to plastic cups containing autoclaved garden soil and compost (1:1), gradually acclimatized and finally transferred to the field condition with 80% survival rate.