Miracle-dz/UniFAR-FTUs huggingface dataset:
Simple rules for the coexistence and competitive dominance of plants mediated by mycorrhizal fungi

Mycorrhizal fungi have been demonstrated to be important in the makeup of plant communities. Likely, their most important role is in altering mineral nutrition of plants, which, in turn, is thought to be among the most important determinants of plant competitive ability. Using mathematical models we examine what role these fungi can play in determining the competitive outcome between two plants in competition for one mineral resource. Depending on different relationships between the benefit accrued to the plant and the fungi, the presence of mycorrhizal fungi can (i) have no impact on which plant wins in competition, (ii) change the order of competitive dominance or (iii) enable coexistence when compared with the system in the absence of mycorrhizal fungi. Furthermore, environmental conditions, such as light and nutrient levels, can determine if coexistence is possible. We describe the necessary biological trade-offs for coexistence and experimental tests for these trade-offs.
Genetic diversity and genetic similarities between Iranian rose species

Summary Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified alleles in all species, even if they were from different sections within the genus. An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main Groups. The data showed no support for any distinction between R. canina and R. iberica, as all the accessions were placed in one Group, and accessions of these two species were more closely-related to each other within a Province than to accessions of the same species in other Provinces. Accessions of sect. Pimpinellifoliae were combined with plants from sect. Rosa and Cinnamomeae in two different Groups. Genetically, R. persica clustered distinctly from all others, with few alleles shared with the other taxa. We discuss the use of SSR markers for phylogenetic analysis when these markers are amplified in all species of a genus.
An SSR from the leucine-rich repeat region of the rose Rdr1 gene family is a useful resistance gene analogue marker for roses and other Rosaceae

With 1 figure and 1 table Abstract We developed the Rd1LRR microsatellite marker from a highly conserved part of the LRR region of nine completely sequenced Rdr1 paralogues of a black spot-resistant Rosa multiflora genotype. The black spot resistance gene Rdr1 belongs to the class of nucleotide-binding site and leucine-rich repeat (NBS-LRR)-encoding genes. The occurrence of a distinct (CT)n repeat in each Rdr1 paralogue allowed us to fingerprint rose genotypes for the diversity within the Rdr1 gene family. PCR analysis with Rd1LRR in 34 rose cultivars resulted in 52 distinct bands corresponding to a minimum of 52 different NBS-LRR encoding resistance gene analogue genes. In addition, 31 wild rose species and 34 accessions of R. arvensis were analysed with this marker. The high diversity for the number and allelic composition of Rd1LRR banding patterns even within individuals of R. arvensis indicated that the Rdr1 locus is highly diverse. The Rd1LRR may be used in future mapping projects for tests of cosegregation of new resistance specificities to the Rdr1 gene cluster. Furthermore, this marker is a useful tool for the identification of distinct Rdr1 genes in cloning experiments.
Peptides and Protein Phosphorylation

cAMP-Dependent Protein Kinase: Mechanism for ATP: Protein Phosphotransfer. The Inhibitor Protein of the cAMP-Dependent Protein Kinase. The SRC Family of Protein-Tyrosine Kinases. Myosin Light Chain Kinases. Use of Synthetic Peptides to Study Substrate Specificity of Protein Phosphatases. Type-2 Casein Kinases: General Properties and Substrate Specificity. Substrate Specificity of Cyclic AMP-Dependent Protein Kinase. Unique Specificity Determinants for an S6/H4 Kinase and Protein Kinase C: Phosphorylation of Synthetic Peptides Derived from the Smooth Muscle Myosin Light Chain. Substrate Specificity of the Cyclic GMP-Dependent Protein Kinase. Protein-Tyrosine Kinases. Antibodies Against Synthetic Phosphorylation Site Peptides. Modern Methods of O-Phosphoserine- and O-Phosphotyrosine-Containing Peptide Synthesis.
Spreadsheet Exercises in Ecology and Evolution

PART I: SPREADSHEETS AND STATISTICS - Mathematical Functions and Graphs - Spreadsheet Functions and Macros - Statistical Distributions - Hypothesis Testing: Alpha, Beta, and Power - PART II: ECOLOGY - Geometric and Exponential Population Models - Logistic Population Growth - Interspecific Competition - Predator-Prey Dynamics (Lotka-Volterra) - Island Biogeography - Life Tables and Survivorship Curves - Reproductive Value: Matrix Approach - Reproductive Value: Life Table Approach - Demographic Stochasticity - Key Factor Analysis - Age-Structured Matrix Models (Leslie) - Stage-Structured Matrix Models - Sensitivity and Elasticity Analysis - Metapopulation Dynamics - Source-Sink Dynamics - Niche Breadth and Resource Partitioning - Population Estimation - Survival Analysis - Habitat Selection - Optimal Foraging Models - Range Expansion - Succession - PART III: EVOLUTION - Hardy-Weinberg - Multi-Locus Hardy-Weinberg - Measures of Genetic Diversity - Natural Selection and Fitness - Adaptation - Gene Flow and Population Structure - Life History Evolution - Heritability - Quantitative Genetics - Sexual Selection - Evolutionarily Stable Strategies - Parental Care and Mating Systems - Inbreeding and Outbreeding - Genetic Drift - Effective Population Size
Leaf rust resistance in spring barley cultivars and breeding lines

A total of 67 barley cultivars and breeding lines were tested for leaf rust resistance were tested with eight differential isolates. These isolates originated from IHAR Radzikow collection and were chosen according to their virulence spectra. Among 67 cultivars and breeding lines 41 (61%) showed resistance reaction after inoculation with at least one isolate of leaf rust. In 29 cultivars and breeding lines (43.2%) the presence of specific resistance alleles was postulated. For most tested cultivars and breeding lines (56.8%) it was impossible to postulate the presence of the specific resistance alleles. Twenty six (38.8%) cultivars and breeding lines showed susceptible reaction after inoculation with all isolates used. Four cultivars and breeding lines (NAD 2298, Granal, Barke, BKH 4300) were composed of lines carrying different genes for resistance. Four different resistance alleles (Rph3, Rph7, Rph9 and Rph12) were detected alone or in combinations. Among tested cultivars and breeding lines, twenty had one gene for resistance and 8 had combination of different genes for resistance. The most common resistance allele was Rph12 (19 cultivars and breeding lines). Alleles Rph9 and Rph3 were postulated in 4 cultivars and breeding lines. Allele Rph7 was postulated to be present in only one cultivar Hanka. Different strategies for control of barley leaf rust using resistance genes were discussed.
Optimal reinsurance and investment strategies for an insurer and a reinsurer under Hestons SV model: HARA utility and Legendre transform

The present paper investigates an optimal reinsurance-investment problem with Hyperbolic Absolute Risk Aversion (HARA) utility. The paper is distinguished from other literature by taking into account the interests of both an insurer and a reinsurer. The insurer is allowed to purchase reinsurance from the reinsurer. Both the insurer and the reinsurer are assumed to invest in one risk-free asset and one risky asset whose price follows Heston's SV model. Our aim is to seek optimal investment-reinsurance strategies to maximize the expected HARA utility of the insurer's and the reinsurer's terminal wealth. In the utility theory, HARA utility consists of power utility, exponential utility and logarithmic utility as special cases. In addition, HARA utility is seldom studied in the optimal investment and reinsurance problem due to its sophisticated expression. In this paper, we choose HARA utility as the risky preference of the insurer. Due to the complexity of the structure of the solution to the original Hamilton-Jacobi-Bellman (HJB) equation, we use Legendre transform to change the original non-linear HJB equation into its linear dual one, whose solution is easy to conjecture in the case of HARA utility. By calculations and deductions, we obtain the closed-form solutions of optimal investment-reinsurance strategies. Moreover, some special cases are also discussed in detail. Finally, some numerical examples are presented to illustrate the impacts of our model parameters (e.g., interest and volatility) on the optimal reinsurance-investment strategies.
A red water caused by Mesodinium rubrum on the coast of Santa Catarina, southern Brazil

is an obligate phototroph due to the presence of a cryptomonad as an endosymbiot (Hibberd, 1977). Although the strong symbiosis between the ciliate and its host assures an autotrophic function, in general it is not commonly included as a phytoplankter. On the other hand, studies of the overall phytoplankton assemblage have shown that
The shoot apical meristem

Preface: the shoot apex: what it is and what it does 1. A source of cells: the apical cell 2. A source of cells: the meristem 3. Growth rates within the shoot apex 4. Cell cycles 5. The subcellular and biochemical structure of the meristem 6. The mechanism of primordium initiation 7. Positioning the primordia 8. Partitioning the apex: the size of the apical meristem and the primordia 9. The transition to flowering 10. The new floral meristem Index.
Cis-acting elements and a conformational switch involved in replication of a positive-strand RNA virus

Title of dissertation: CIS-ACTING ELEMENTS AND A CONFORMATIONAL SWITCH INVOLVED IN REPLICATION OF A POSITIVE-STRAND RNA VIRUS Jiuchun Zhang, Doctor of Philosophy, 2006 Dissertation directed by: Professor Anne E. Simon Department of Cell Biology and Molecular Genetics Replication of positive (+)-strand RNA virus genomes is a fundamental process in a virus’s life cycle. Turnip crinkle virus (TCV) and an associated satellite RNA (satC) share 151 nt of 3' terminal sequence, which are predicted to fold into four phylogenetically-inferred hairpins (from the 3’ end: Pr hairpin, H5, H4b and H4a). Pr hairpin is part of the core promoter (Pr) required for satC (Song and Simon, 1995) and TCV (Sun and Simon, in press) negative (-)-strand synthesis. To identify other regulatory cis-acting elements throughout satC, individual deletions of six other predicted hairpins (H5, H4b, H4a, M1H, H6, and H2) were performed. The results show that these deletions significantly reduce accumulation of (+)-strand monomers and differentially affect accumulation of (+)-strand dimers and (-)-strands in Arabidopsis protoplasts. Results from in vivo genetic selection and mutational analyses of satC H5 indicate that robust satC accumulation in vivo requires specific sequences in the large symmetrical internal loop (LSL) and a stable stem and specific base pairs in the lower stem. The upper stem-loop has considerable plasticity. Moreover, H5 may be involved in accumulation of both strands. Mutational analyses also suggest that the LSL and/or the 3’ terminus may have other functions in addition to forming a pseudoknot (Ψ1), which is required for replication. An RNA conformational switch from a pre-active structure to an active structure appears required to regulate initiation of satC (-)-strand synthesis (Zhang et al., 2006). Results from mutational analyses suggest that H4a and H4b function as a unit and Ψ2, formed between H4b and sequence flanking the 3' side of H5 and whose disruption reduces satC accumulation in vivo, stabilizes the pre-active satC structure. In addition, an upstream element (DR) may help to promote the switch. Step-wise conversion of satC and TCV 3' terminal homologous sequences into the counterpart's sequence revealed the importance of having the cognate Pr. The satC Pr is a substantially better promoter than the TCV Pr when assayed in vitro. These results suggest that the TCV Pr requires upstream elements for full functionality and that evolution of satC generated a Pr that functions more efficiently by itself. CIS-ACTING ELEMENTS AND A CONFORMATIONAL SWITCH INVOLVED IN REPLICATION OF A POSITIVE-STRAND RNA VIRUS
Convenient Assay of O 2 - Generated on Potato Tuber Tissue Slices Treated with Fungal Elicitor by Electron Spin Resonance - No Secondary Oxidative Burst Induction by H 2 O 2 Treatment

Since the discovery of generation of in plant, many evidence for the oxidative burst (OXB) has been accumulated in various combinations of plant and pathogen or elicitor systems. generating system responsible for the OXB was coupled with oxidation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) in microsomal fraction isolated from sliced aged potato tuber slices which were treated by hyphal wall components elicitor from Phytophthora infestans (HWC). We developed new assay method for quantitative measurement of oxygen radical by using electron spin resonance (ESR) analysis during elicitor­induced OXB on the surface of plant tissues. The ESR analysis using an trapper, Tiron (1,2-dihydroxy-3,5­benzenedisulfonic acid), provided a convenient assay for detecting only during elicitor-induced OXB producing various active oxygen species (AOS) on plant tissue surface. Tiron was oxidized to Tiron semiquinon radical by . Quantity of the radical signal was measured by specific spectra on ESR spectroscopy. The level of was high in from surface of potato tuber tissue treated with hyphal cell wall elicitor (HWC) from Phytophthora infestans. There was no secondary OXB induction by treatment in plant.
Lactate induces tumour necrosis factor‐α, interleukin‐6 and interleukin‐1β release in microglial‐ and astroglial‐enriched primary cultures

Hyperammonaemia has deleterious effects on the CNS in patients with liver dysfunction. Cellular mechanisms underlying the effects of hyperammonaemia are largely unknown, although astrocytes have been the main target of interest. This study investigated how treatment with NH4Cl and lactate, which increase in the brain as a consequence of hyperammonaemia, affects cells in primary rat cultures enriched in either astrocytes or microglia. Morphological changes were studied over time using light microscopy. Release of the proinflammatory cytokines tumour necrosis factor‐α (TNF‐α), interleukin (IL)‐6 and IL‐1β was measured using ELISA. NH4Cl was found to induce vacuole formation in both culture systems. Lactate treatment altered astrocytic appearance, resulting in increased space between individual cells. Microglia adopted a round morphology with either NH4Cl or lactate treatment. Lactate, but not NH4Cl, induced release of TNF‐α and IL‐6 in both astroglial‐ and microglial‐enriched cultures, while IL‐1β was released only in microglial cultures. Cytokine release was higher in the microglial‐ than in the astroglial‐enriched cultures. Additionally, the astroglial‐enriched cultures containing approximately 10% microglial cells released more cytokines than cultures containing about 5% microglial cells. Taken together, our data suggest that most TNF‐α, IL‐6 and IL‐1β release comes from microglia. Thus, microglia could play an important role in the pathological process of hyperammonaemia.
A New Species Of Mictyris (Decapoda, Brachyura, Mictyridae) From The Ryukyu Islands, Japan

The Asian soldier crab Mictyris brevidactylus Stimpson, 1858, was re-examined genetically and morphologically from specimens collected across its range. It was found to consist of two cryptic sister species, with crabs from the Ryukyu Islands representing a new species, M. guinotae. Mictyris guinotae is smaller at maturity than M. brevidactylus, has plain blue colouring without red banding on the legs, and has a differently shaped apex of its male first gonopod. The two species also differ genetically, with 16S rRNA and COI showing a mean divergence (K2P distance) of 1.08% and 4.39%, respectively, representing 2.0 and 3.5 times more divergence than present intraspecifically. Results provide further evidence that some elements of the marine fauna of the Ryukyu Islands have had a separate evolutionary history from continental Asia as well as Taiwan.
Genetic Diversity and Conservation of South-East Asian Cattle: From Indian Zebu to Indonesian Banteng, and then to the Cambodian Kouprey

Since 15 years, DNA analysis has allowed a reconstruction of the origin of most domestic species (Bruford et al., 2003). For instance, analysis of mitochondrial DNA established a taurine maternal origin of all zebu populations outside Asia. Indonesian cattle breeds are supposed to be derived from zebu as well as banteng (Rollingson, 1994), species that in contrast to taurine cattle and zebu are not fully interfertile (Lenstra and Bradley, 1999). However, this mixed species origin is not supported by breeding records, while there are only sporadic molecular data (Namikawa et al., 1981; Kikkawa et al., 1995, 2003; Nijman et al., 2003; Verkaar et al., 2003 ).
Atomic force microscopy study on the mechanics of influenza viruses and liposomes

Physics exists wherever there is matter: measures such as energy, mass, temperature, speed, dimension and stiffness are all examples of the physical properties. Such quantities are important characterizations for biological organisms: they are changing all the time during the life cycle. For a bio-mechanist, stiffness is an important measure to understand biological design. Because biological building blocks can be as small as 1 nm (protein/DNA/lipid), special techniques are required to study their stiffness. Both atomic force microscopy (AFM) and optical tweezers can be used to actively deform the objects at pN-nN forces and measure the deformation on nanometer length scales. In this thesis AFM is applied to study the mechanics of influenza viruses, liposomes and living cells. The genome of viruses is packed by a protein shell and in some cases an additional lipid envelope. This composite shell has conflicting roles: it has to protect the viral genome, but it should also allow unpacking during the viral infection to release the genome. Influenza virus is the softest virus ever found, but at the same time a very persistent virus causing yearly pandemics. A better understanding of the mechanical properties of influenza virus may help us to understand why this virus is so successful. The mechanical properties of influenza viruses were measured by AFM and compared with the liposomes made of the viral lipid. We have found that, the influenza virus mechanics are dominated by its lipid envelope (~70%). In chapter 2 we proved that instead of using a rigid protein capsid, the lipid envelope is sufficient to protect the influenza viral genome. In chapter 3, we further looked into the function of the M1 protein shell during viral infection. An intermediate unpacking step was discovered by measuring the influenza viral stiffness at pH 7, 6, 5.5, and 5, conditions that mimic the acidifying environments on the viral infection pathway. The intermediate step was further proven to be essential for successful infection. We propose that the influenza virus has evolved to tightly synchronize the different steps of its unpacking with pH changes in its biological environment while traveling through the cell. By carrying out the aforementioned investigations, I have increased our understanding of how the influenza virus protects itself and how the virus structure disassembles in multiple steps during infection. The methods described in this thesis are innovative and will also be useful for the mechanical characterization of other samples. The results are also important from a virological point of view, since they indicate that enveloped viruses taken up by endocytosis may have to undergo a gradual acidification in order to reach infectivity.
Cytohistological Studies During Cotton Somatic Embryogenesis With Brassinosteroid Application

The histology and chromosome alterations of somatic embryo initiation and development in cotton ( Gossypium hirsutum L. cv. Coker) was examined during in vitro exogenous brassinosteroid (BR) application. Calli developed from hypocotyl explants were subjected to 0.5 μM BR. After 10 weeks of calli cultures with somatic embryos at different developmental stages were fixed for histological examinations. The histological examination showed that two types of embryogenic cells induced; epidermal or subepidermal. The embryogenic mass and somatic embryos were mostly derived from several morphologically competent cells from subepidermal cases; however single progenitor cells for epidermal situations. Chromosome behaviour of the cells surrounding embryogenic cells showed abnormal divisions and higher level of polyploidy on BR treated calli when compared to control group.
High throughput micropatterning of interspersed cell arrays using capillary assembly

A novel technology is reported to immobilize different types of particles or cells on a surface at predefined positions with a micrometric precision. The process uses capillary assembly on arrays of crescent-shaped structures with different orientations. Sequential assemblies in different substrate orientations with different types of particles allow for the creation of imbricated and multiplexed arrays. In this work up to four different types of particles were deterministically localized on a surface. Using this process, antibody coated microparticles were assembled on substrates and used as capture patterns for the creation of complex cell networks. This new technology may have numerous applications in biology, e.g. for fast cell imaging, cell–cell interactions studies, or construction of cell arrays.
Knowledge Management (KM) Model of Scientific Work by The Faculty of Information and Communication Technology: Case Study East Timor Institute of Business (IOB)

East Timor Institute of Business (IOB) is one of the Private Institute in Timor Leste. In order to support the teaching and learning activities and support and assist in the implementation of learning in Higher Education in the Faculty of Information Technology needs to make a system that can support knowledge sharing. This study aims to design Model Knowledge Management (KM) Student Scientific Work on the Faculty of Information Technology and Communications and Communications. The Framework for KM in Higher Education Institution is used as a method of designing Model Knowledge Management (KM) in the Faculty of Information and Communication Technology as a form of learning for students to share knowledge and strive to develop their skills and knowledge. Knowledge Management Model (KM) is designed to help students searching information about the existing Scientific Work in the Faculty of Information and Communication Technology. The results of the research can be represented in the Knowledge Management model (KM) model stage of knowledge resources in the Faculty of Information and Communication Technology.