Miracle-dz/UniFAR-FTUs huggingface dataset:
Seed Germination and Seedling Emergence of Jointed Goatgrass (Aegilops cylindrica)

Germination of jointed goatgrass (Aegilops cylindrica Host.) seed in nitrate nitrogen (NO− 3-N), gibberellic acid (GA3), or distilled water was studied in the laboratory, and depth of emergence of seedlings from soil was studied in the greenhouse and laboratory. After 14 days in germination chambers in distilled water, no difference in percent germination of 1-yr-old or freshly harvested seed existed between 10, 15, or 20 C. Jointed goatgrass seed germinated at temperatures ranging from 10 to 35 C and responded to temperature more than to NO− 3-N. Seedlings did not emerge from below 5 cm in greenhouse and 6 cm in laboratory studies even though germination occurred. Jointed goatgrass has the seed germination and seedling emergence characteristics to develop into a severe annual grass weed in winter wheat (Triticum aestivum L.)-producing regions, particularly where reduced-tillage practices are utilized.
Screening of Biocontrol Agents Against Rhizoctonia solani Causing Web Blight Disease of Groundnut (Arachis hypogaea L.)

Soil borne plant pathogenic fungi cause heavy crop losses all over the world. With variable climate from region to region, most of the crops grown in India are susceptible to diseases caused by soil borne fungal pathogens. Among tropical, subtropical land crops groundnut (Arachis hypogaea L.) is an important annual oil seed crop, which provides vegetable oil as human food and oil cake meal as animal poultry feed. A large number of diseases attack groundnut in India (Ganesan and Sekar, 2004a). Fungi cause majorities and several of them are yield reducers in certain region and seasons (Bowyer, 1999). Among the soil borne fungal diseases of groundnut, Web blight, caused by Rhizoctonia solani is the most common disease (Dubey, 2000). Majority of work done on plant disease biocontrol relate to soil borne diseases using either bacteria or fungal antagonists (Montealegre et al., 2003; Askar and Rashad, 2010; Pandya and Saraf, 2010). Among bacteria, Pseudomonas and Bacillus spp. are widely used. However, the use of antagonistic fungi, especially Trichoderma and Gliocladium spp. has been more extensive than their bacterial counterparts (Harman, 2000; Ganesan, 2004; Harman, 2006; Neha and Dawande, 2010). Bacteria isolated from the rhizosphere and belonging to a wide variety of genera have the potential to suppress diseases caused by a diversity of soil borne plant pathogens. But the information available on the antagonistic effect of rhizobacteria against R. solani is very scanty. Rhizoctonia solani Kuhn (teleomorph: Thanatephorus cucumeris (A.B. Frank) Donk is a widespread and an ecologically diverse soil-borne fungus, causing different types of diseases in many plant species. It causes root rot, stem rot, fruit and seed decay, damping-off, foliar blight, stem canker and crown rot in various crops (Guleria et al., 2007). Understanding the mechanism of action is important because it gives much useful information in determining the maintenance, enhancement and implementation of biological control. Biological control agents interact with phytopathogens directly or indirectly to reduce the population of pathogens or reduction in the ability of the pathogens to cause disease. In general, mechanisms implicated in antagonism towards the biological control of phytopathogenic fungi includes, A) Direct mechanism: parasitism, antibiosis, competition for nutrients or space, production of enzymes and inactivation of pathogen enzymes. B) Indirect mechanism: tolerance to stress through enhanced root and plant
Values, Migrant Parents, Leadership, and the Public Good

This reflective essay posits an examination on how migrant experiences and educational development shape identity and inform their core values. Under-standing the formal academic socialization experi-ences of migrants can serve to inform a commitment to the public good through exposure to academic readings, research and service that shape knowledge, values and perspective. This socialization trajectory grounded in knowledge and experience has enlight-ened the author’s perspective to improve access, guidance, opportunity, mentoring and engagement to migrant students. The leadership challenge is to master the art of “barn raising” as we share finite institutional resources.
Framing Wikileaks In The Networked Fourth Estate

WikiLeaks’ rise to prominence in 2010, with its release of classified U.S. government and military documents, polarised opinion worldwide; some viewed it as a cyber-terrorist group, others saw it as journalism’s saviour. This paper situates WikiLeaks within the framework of Yochai Benkler’s networked public sphere. In the age of the Internet and networked communications, the role of information gathering, investigation and analysis regarding the powerful has extended beyond the boundaries of traditional news organisations and professional journalists in what Benkler theorises as the networked fourth estate. Benkler contends the emergent forms of the networked fourth estate are increasingly vulnerable to attacks from institutional media fearful of the decentralisation they represent. Placing WikiLeaks within the context of the networked fourth estate, the paper analyses WikiLeaks’ depiction in two major political journals of record by identifying the construction and use of media frames in the editorial pages of _The New York Times_ and _The Washington Post_. As a technologically novel, politically reformist and internationally networked media entity, WikiLeaks can be considered as a form of alternative networked media that challenges hegemonic media and political power. The paper found the elite mainstream media news framing of WikiLeaks as transgressive and irresponsible, delegitimised the organisation’s value to public sphere discourse and reasserted the mainstream media’s central importance in the democratic public sphere. Dismissing the informational value of the disclosures denied WikiLeaks’ capacity to exercise any political counterpower that might have meaningful consequences for policy or the mainstream networked public sphere.
Marine ornamental molluscs

The molluscs recorded from the world range from 80,000 to 1,00,000, out of which 50,000 are gastropods, 15,000 bivalves, 500 polyplacophora, 400 cephalopods, 130 aplacophora and 5 monoplacophora. There are 31,463 marine, 8,765 fresh water and 24,503 land molluscs reported from different parts of the world. Humans have valued marine mollusc shells since prehistoric times
Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia

Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter), so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa.
The development of genetic resistance to Plum pox virus in transgenic Nicotiana benthamiana and Prunus domestica.

Plum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. It is the causal agent of the most devastating viral disease on many stone-fruit spp. The viral disease, known as Sharka in Europe, was recently found in the United States and Canada. Genetic resistance is considered the most effective means to control PPV, but despite over 60 years of extensive screening for germplasm resistant to PPV, few resistant resources have been identified. Here we report engineering genetic resistance against PPV through the hairpin-mediated RNA silencing (RNAi) approach. Two highly conserved regions of the PPV genome corresponding to portions of viral RNA coding for P1 and CP, respectively, were cloned into a plant transformation vector under the control of the double Cauliflower mosaic virus 35S promoter as inverted repeats spanned by an intron from the peach endo polygalacturonase genomic DNA. These two constructs (pAWp1 and pAWcp) were initially tested in Nicotiana benthamiana. Over 50 transgenic lines transformed with pAWp1, pAWcp and an empty plasmid pAWck (as a control) were generated. The transgenic N. benthamiana plants were mechanically inoculated with PPV. ELISA and RT-PCR analysis revealed that 49.1% of pAWp1-derived lines and 41.2% of pAWcp-derived lines were PPV-negative and 100% of control lines (transformed with pAWck) showed PPV-positive. The pAWp1 plasmid was used to transform plum (Prunus domestica L.). Transgenic plum plants were challenged with PPV by chip-bud inoculation. PPV was detected in all the pAWck-derived plum lines but was not detectable in 50% of pAWp1-derived transgenic lines. Two species of PPV-specific small interfering RNAs, a hallmark of posttranscriptional gene silencing (PTGS), were present in the resistant plum lines, suggesting PTGS is responsible for resistance. The PPV-resistant transgenic plum generated in this study may provide an alternative resistant source for the control of PPV.
Methods in Microarray Normalization

A Comprehensive Analysis of the Effect of Microarray Data Preprocessing Methods on Differentially Expressed Transcript Selection M. Ray, J. Freudenberg, and W. Zhang Differentiation Detection in Microarray Normalization L.M. Li and C. Cheng Preprocessing and Normalization for Affymetrix GeneChip Expression Microarrays B. Bolstad Spatial Detrending and Normalization Methods for Two-Channel DNA and Protein Microarray Data A. Laurentiu Tarca, S. Draghici, R. Romero, and M. Tainsky A Survey of cDNA Microarray Normalization and a Comparison by k-NN Classification W. Wu and E.P. Xing Technical Variation in Modeling the Joint Expression of Several Genes W. Liggett Biological Interpretation for Microarray Normalization Selection P. Stafford and Y. Tak Methodology of Functional Analysis for Omics Data Normalization A. Perlina, T. Nikolskaya, and Y. Nikolsky Exon Array Analysis for the Detection of Alternative Splicing P. Gardina and Y. Turpaz Normalization of Array CGH Data B. Curry, J. Ghosh, and C. Troup SNP Array-Based Analysis for Detection of Chromosomal Aberrations and Copy Number Variations B. Bolstad, S. Ghosh, and Y. Turpaz Index
Successive legumes tested in a greenhouse crop rotation experiment modify the inoculum potential of soils naturally infested by Aphanomyces euteiches

The consequence of 10 successive monocultural cycles involving different legume species/cultivars on the inoculum potential (IP) of soils naturally infested by Aphanomyces euteiches was investigated under greenhouse conditions. The results showed that the IP of a soil naturally infested by A.euteiches can be significantly modified not only by the non-host or host status of crop species but also by the level of resistance of the cultivar. Susceptible species/cultivars (pea, lentil and susceptible cultivars of vetch and faba bean) are very favourable to pathogen multiplication, and continuous cultivation of each of these increased the IP values of a soil with a moderate initial IP (from 1 center dot 9 to 3 center dot 5 after 10 cycles). Conversely, non-host species and resistant cultivars of vetch or faba bean contributed to reducing the IP values of soils irrespective of the initial IP (from 1 center dot 9 to 0 center dot 5 and from 4 to 2, respectively, after 10 cycles). Aphanomyces root rot severity values on the resistant legume species/cultivars were not affected by the successive cultural cycles. This study, which showed that the IP of A.euteiches in soil can be reduced by planting appropriate legume species and cultivars in greenhouse conditions, will be useful for defining better crop successions for legumes.
The molecular regulation of Hox gene RNA processing during Drosophila embryonic development

The Hox genes encode a family of developmental regulators that are essential for the normal patterning of the animal body axis. Their correct expression is controlled by a number of mechanisms including RNA processing, a molecular system that allows the formation of alternative mRNAs from a single gene. Previous work in the Alonso Lab has demonstrated that RNA processing of the Drosophila Hox gene Ultrabithorax (Ubx) by means of alternative splicing and alternative polyadenylation plays an important role during Drosophila development, but the mechanisms underlying these regulatory processes are not well understood. In this project we found that the Drosophila neural RNA binding protein ELAV has an important role in the control of both Ubx alternative splicing and polyadenylation during embryonic development. Furthermore, by conducting a series of in vitro experiments we demonstrate that ELAV is able to interact with two specific RNA elements located within Ubx intronic sequences and mutation of such elements abolishes the interaction. We also establish that embryos carrying a loss of function mutation in the elav gene produce lower levels of Ubx mRNA and protein suggesting a role of ELAV on Hox gene expression. Finally we investigated the roles that other Drosophila factors including RNA binding proteins, chromatin regulators and splicing regulatory proteins may have on Ubx RNA processing and found several potential regulators. All in all our work contributes to the understanding of the molecular basis of Hox RNA processing control during Drosophila development.
Amylases, alpha and beta

This article describes a number of methods for the assay of amylase. The purification procedure for human salivary alpha-Amylase, the properties of human salivary alpha-Amaylase is described. The purification procedure of sweet potato beta-Amylase and the properties of sweet potato beta-Amylase are also described.
Binary interaction along the RGB: The Barium Star perspective

Abstract Barium (Ba) stars form via mass-transfer in binary systems, and can subsequently interact with their white dwarf companion in a second stage of binary interaction. We used observations of main-sequence Ba systems as input for our evolutionary models, and try to reproduce the orbits of the Ba giants. We show that to explain short and sometimes eccentric orbits, additional interaction mechanisms are needed along the RGB.
Lateral Gene Transfer in Operons and Its Effects on Neighbouring Genes

Prokaryotes evolve, in part, by lateral gene transfer (LGT) . This transfer of genetic material is likely important in the evolution of operons, a group of genes that are transcribed as a single mRNA. Genes that are transferred may then be integr ated into genomes by homologous recombination. In this thesis, it was proposed tha t homologous recombination is the mechanism of integration of laterally transferred ge nes into operons. To investigate this proposal, a phylogenetic tree of Bacillus was inferred u sing DNA sequence alignments. LGT was inferred using a parsimony algorithm, and ope rons were inferred using OperonDB. Homologous recombination breakpoints were ident fi d by permutation tests, GENECONV and maximum chi square algorithm. The results indicate that there is evidence for integration of functionally annotated genes into opero ns by homologous recombination. There are several laterally transferred genes that have rec ombination breakpoints before the start codon or after the stop codon of the genes. It was also pr oposed in this thesis that LGT causes an increase in the rate of evolution of genes that are n eighbours of laterally transferred genes. To investigate this proposal, genes that are n eighbours of laterally transferred genes in Bacillus were identified. These genes were classified as upstream or downstream genes to the LGT event. Genes that are not neighbours of later ally transferred genes were also identified as a control. Selection and the rate of evolut ion was studied using maximum likelihood models implemented in CodeML of PAML. Genes under positive selection were inferred using likelihood ratio tests. The results indicat e that only a few neighbouring genes were under positive selection, and the rate of evoluti on of the neighbouring genes was slightly higher than that of the non-neighbouring genes . The high rates of evolution of the neighbouring genes are likely due to relaxed selection o n the neighbouring genes.
CHANGES IN PHYSICAL PROPERTIES OF CHITOSAN FILMS AT SUBZERO TEMPERATURES

The influence of frozen storage conditions (temperature and relative humidity) on water vapor permeability coefficients (WVPC), mechanical properties, color, transparency, thickness and moisture content of chitosan films were evaluated after 20 and 40 days of storage. Chitosan films (2% w/v) were prepared by casting using 25% glycerol (v/g chitosan) as plasticizer and 0.2% Tween 80 (v/v) as emulsifier. The films were stored in freezers at -20°C and 82% relative humidity or at -50°C and 62% relative humidity. WVPC values decreased gradually from 2.4 to 1.5x10 -5 g·cm -1 ·day -1 ·kPa -1 for the films stored at -20°C, however, WVPC of the films at -50°C declined from 8.2 to 4.1×10 -5 g·cm -1 ·day -1 ·kPa -1 in about 34 days then increased to 18.5×10 -5 g·cm -1 ·day -1 ·kPa -1 . Tensile strength decreased after 20 days and then increased sharply after 40 days. Elongation (50.3-23.2%) decreased with storage time. No significant differences occurred between tensile strength and elongation values of the films stored at -20° and -50°C during the same test period (P<0.05). Elastic modulus evolution was similar to the changes observed in tensile strength change. The films became more yellowish as the temperature decreased and storage time increased. There were no differences in the color between films kept at -20° and -50°C (P<0.05). The transparency of the films kept at -50°C was about six times greater than that of the control and films kept at -20°C up to 40 days.
Generation of reactive oxygen species and activation of NF‐κB by non‐Aβ component of Alzheimer's disease amyloid

Non‐amyloid beta (Aβ) component of Alzheimer's disease (AD) amyloid (NAC) coexists with Aβ protein in senile plaques. After exposure to NAC fibrils, cortical neurons of rat brain primary culture became apoptotic, while astrocytes were activated with extension of their processes. NAC fibrils decreased the activity of reducing 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) in cortical neurons more markedly (IC50 = 5.6 µm) than in astrocytes (IC50≈ 50 µm). The neuron‐specific toxicity of NAC fibrils was indicated also by an increased release of lactate dehydrogenase from the cells. Neuronal apoptosis was suppressed by pre‐treatment with the antioxidants, propyl gallate (PG) and N‐t‐butyl‐phenylnitrone (BPN), or overexpression of human Bcl‐2. Exposure to NAC fibrils enhanced generation of reactive oxygen species (ROS) in neurons and less efficiently in astrocytes, as demonstrated by oxidation of 2′,7′‐dichlorofluorescin. The site of ROS generation was shown to be mitochondria by oxidation of chloromethyl‐tetramethyl rosamine. Exposure to NAC fibrils increased also the nuclear translocation of nuclear factor kappa B (NF‐κB) and enhanced its DNA‐binding activity, which was inhibited by PG and BPN more efficiently in neurons than in astrocytes. These results suggest that NAC fibrils increase mitochondrial ROS generation and activate NF‐κB, thereby causing a differential change in gene expression between neurons and astrocytes in the AD brain.
Extending a dynamic mathematical model of metabolism in Trypanosoma brucei

There is an urgent need for new chemotherapies against human African trypanosomiasis (HAT), caused by the protozoan parasite Trypanosoma brucei. It is anticipated that the parasites’ divergent biochemistry will enable development of novel therapies. To study the behaviour of a complex network as metabolism, one can employ mathematical models. In this thesis, metabolism of bloodstream form T. brucei was investigated. Cellular metabolism consists as a complex system connecting enzymes with metabolites, and to study such a network one can construct mathematical models that describe the connections within the biological system. A previously published, and well-curated model of glycolysis in bloodstream form T. brucei (Bakker BM, et al. (1997) J Biol Chem 272:3207 15), was extended here with the pentose phosphate pathway (PPP), the second major pathway in glucose metabolism in most life forms. Several hypotheses were derived during the model building process and these were tested experimentally. It became apparent that the glycosomal bound-phosphate balance is essential for the parasite. Extension of the glycolytic model with the PPP introduced the risk of a so-called ’phosphate leak’, where bound-phosphates are depleted in the glycosome. Two hypotheses were investigated in silico, while one hypothesis could also be tested experimentally; (i) a glycosomal ATP:ADP antiporter was proposed, but in silico analysis indicated that the activity of such an antiporter requires tight regulation. (ii) A glycosomal ribokinase was investigated both in silico and experimentally. Genetic mutants indicated that ribokinase is essential to bloodstream form T. brucei, albeit at low levels. Additional analysis of the generated models indicated that ablation of 6-phosphogluconate dehydrogenase (6PGDH) in T. brucei is lethal by a different mechanism as seen in other organisms. Overall, extension of the glycolytic model with the PPP demonstrated the fragility of the model regarding the bound-phosphate balance and indicated that future analysis on glycosomal metabolism should be focused on this. Important in the use of mathematical models of metabolism is that the underlying stoichiometry of the model reflects (albeit with simplification) the in vivo system. It is therefore paramount to know what enzyme activities are present in the organism of interest. In this thesis a metabolomics approach was used to elucidate the function of three T. brucei genes. These genes were putatively annotated as arginase (ARG), N-acetylornithine deacetylase (NAO) and nicotinamidase (NAM). The results suggested that ARG has catalytic activity as tryptophan monooxygenase (EC 1.3.12.3), while substrate promiscuity was indicated for NAO and NAM. The work presented in this thesis has provided us with new insights on trypanosomal metabolism. The extended model now allows us to research a larger part of T. brucei metabolism with mathematical modelling, and will thereby aid in the identification and further investigation of (proposed) drug targets.