Miracle-dz/UniFAR-FTUs huggingface dataset:
FUNCTIONAL GENOMICS OF PANTOEA STEWARTII SUBSP. STEWARTII AND PARTIAL GENOME SEQUENCE OF THE MAIZE STOLBUR PHYTOPLASMA SOLANI, TWO INSECT-TRANSMITTED BACTERIAL PATHOGENS OF MAIZE

ii Acknowledgments. v Vita. vii List of tables . xi List of figures. xiii List of abbreviations. xv Chapters: 1. Literature review. 1 1.1. Preface. 2 1.2. Introduction. 3 1.2.1. Stewart‟s wilt disease of maize. 3 1.2.2. General background. 3 1.2.3. Geographic distribution of Pnss. 4 1.2.4. Symptoms of Stewart‟s wilt. 4 1.2.5. Host range. 5 1.2.6. Pnss taxonomy, nomenclature and cell properties. 6 1.2. 7. Disease cycle and epidemiology. 7 1.2. 8. Pathogenesis mechanisms of maize infection by Pnss. 9 1.2. 9. Diagnosis and control. 11 1.3. Interactions of Pnss with its insect vector. 12 1.4. Biology of phytoplasmas. 13 1.4.1. General background. 13 1.4.2. Typical symptoms induced by phytoplasmas. 15 1.4. 3. Classification and taxonomy of phytoplasmas. 16 1.4. 4. Molecular and genetic studies of phytoplasmas. 17 1.5. Interactions of phytoplasmas with their insect vectors. 19 1.6. The MR disease. 21 1.6. 1. Historical background. 21 1.6. 2. Disease cycle and epidemiology of MR. 22 1.6. 3. Preliminary studies that indicate the two insect species carry different isolates of stolbur phytoplasma. 23 x 1.7. Rationale and significance. 24 1.8. Research objectives. 26 2. Molecular and cellular interactions of Pantoea stewartii subsp. stewartii with its insect vector Chaetocnema pulicaria. 30 2.1. Abstract. 31 2.2. Introduction. 33 2.3. Materials and methods. 35 2.4. Results. 43 2.5. Discussion. 50 2.6. Acknowledgements. 53 3. Mining the maize redness stolbur phytoplasma genome sequence for strain-specific sequences. 65 3.1. Abstract. 66 3.2. Introduction. 67 3.3. Materials and methods. 70 3.4. Results. 78 3.5. Discussion. 83 3.6. Acknowledgements. 89 4. General conclusion and discussion. 116 4.1. Overall conclusion. 117 4.2. Overall discussion and future studies. 119 List of references. 122
Relationship quality affects fission decisions 1 in wild spider monkeys ( Ateles geoffroyi ) 2

LJMU has developed LJMU Research Online for users to access the research output of the University more effectively. Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Users may download and/or print one copy of any article(s) in LJMU Research Online to facilitate their private study or for non-commercial research. You may not engage in further distribution of the material or use it for any profit-making activities or any commercial gain.
The role of the AP-1 adaptor complex in trafficking between the trans-Golgi Network and endosomal system

iv LIST OF TABLES.vi LIST OF FIGURES.vii LIST OF ABBREVIATIONS.viii CHAPTER I: INTRODUCTION.1 CHAPTER II: MATERIALS AND METHODS.20 CHAPTER III: THE TRAFFICKING ITINERARY OF A(F→A)-ALP INCLUDES THE EE.30 CHAPTER IV: AP-1 IS NOT REQUIRED FOR ANTEROGRADE TRAFFICKING OF A(F→A)-ALP, RATHER IT DELAYS ITS DELIVERY TO THE PVC.45 CHAPTER V: AP-1 BINDS TO THE 2-11 REGION OF Ste13p AND SLOWS ITS PROGRESSION TO THE PVC.58 CHAPTER VI: CLATHRIN AND ADAPTOR PROTEINS ACCUMULATE ON MEMBRANES IN inp53Δ MUTANTS.71 CHAPTER VII: SUMMARY.81 REFERENCES.90 VITA.100
Regeneration Potential of Ascocentrum ampullaceum (Roxb.) Schlter throughInflorescence culture

Regeneration Potential of Ascocentrum ampullaceum (Roxb.) Schlter through Inflorescence culture The paper deals with the in vitro regeneration response of immature inflorescence segments (buds, nodes and internodes) of Ascocentrum ampullaceum explants. The nutrient medium used played a key role in induction and multiplication of callus, protocorm like bodies and shoot. Inflorescence buds cultured in V&W medium supplemented with 15% coconut milk and 2% sucrose produced highest (80%) protocorm like bodies formation without any growth regulator. Inflorescence node culture in MKC medium supplemented with only 15% CM, and 15% CM and 1.0 mg l-1 NAA produced highest callus (70%) and plbs (50%) formation, respectively. Incorporation of 15% CM in all the media proved best for formation of callus and plbs. Our results suggest that Ascocentrum ampullaceum, which regenerates poorly in nature, can be micropropagated using inflorescence based explants.
Toleration of Lucilia cuprina (Diptera: Calliphoridae) Eggs to Agitation Within Insect Saline

Microorganisms have an ability to attach themselves to surfaces, where they then multiply and form a protective biofilm, which protects the microorganisms from outside influences, including chemicals for sanitation. This makes the cleaning of fly eggs for maggot therapy difficult. The purpose of this study was to test the toleration of Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae)eggs for agitation, which is used to degrade biofilms. Lucilia cuprina eggs were washed with insect saline and treated by undergoing five minutes of agitation. It was found that there was a significant difference between the control group, which did not undergo any agitation, and the treatment group, which did. This knowledge is useful for further testing of the extent to which agitation impacts survivability of the eggs and the debridement of the biofilm.
Parental Risk-Taking at Natural Northern Bobwhite Nests

Parental risk-taking at the nest is critical to examining the trade-offs between current and future reproduction. Using Northern Bobwhites (Colinus virginianus) at camera-monitored nests in the natural environment, we examined how parental and offspring characteristics, predator community, and predator type affected flush distance of incubating birds to approaching predators. During 1999–2006, we monitored 118 predation interactions at nests at two pairs of study sites in southern Georgia and northern Florida, USA where mesomammalian predators were experimentally reduced or not reduced. The results showed that incubating parent birds allowed closer approaches by predators that typically only consumed eggs (e.g. Nine-banded Armadillos Dasypus novemcinctus, Virginia Opossums Didelphis virginiana, and snakes) than by predators that could harm the adults (including Bobcats Lynx rufus and Raccoons Procyon lotor) prior to flushing from the nest. Our data did not support the hypotheses that parent-offspring characteristics and predator community affect parental risk-taking at the nest. Our findings suggest that parent birds incorporate information about predator identity over parental and offspring characteristics or predator community into anti-predator decisions at the nest in systems with high predation risk.
Morphological variation among populations of Hemigrammus coeruleus (Characiformes: Characidae) in a Negro River tributary, Brazilian Amazon

We explored patterns of phenotypic variation in Hemigrammus coeruleus from the Unini River basin, a blackwater river in the Brazilian Amazon. Geometric morphometrics was used to evaluate variation in body shape among populations from four tributaries (UN2-UN5). We found no evidence for sexual dimorphism in body size and shape. However, morphological differences among populations were detected as the analyses recovered significant groups corresponding to each sub-basin, with some overlap among them. The populations from UN2, UN3 and UN5 had more elongate bodies than fish from UN4. The most morphologically divergent population belonged to UN4, the tributary with the most divergent environmental conditions and the only one with seasonally-muddy waters. The morphological variation found among these populations is likely due to phenotypic plasticity or local adaptation, arising as a product of divergent ecological selection pressures among sub-basins. This work constitutes one of the first to employ a population-level geometric morphometric approach to assess phenotypic variation in Amazonian fishes. This method was able to distinguish subtle differences in body morphology, and its use with additional species can bring novel perspectives on the evaluation of general patterns of phenotypic differentiation in the Amazon.
Metal Binding and Response of Helicobacter pylori HypB and Escherichia coli YjiA

The biosynthesis of [NiFe]-hydrogenase and urease in Helicobacter pylori requires several accessory proteins for proper assembly of the nickel-containing active sites. Critical to the maturation of both enzymes in H. pylori is the GTPase HypB. In this work, the metal-binding properties of H. pylori HypB (HpHypB) were investigated and a link between metal binding and the other biochemical properties of HpHypB was established. HpHypB binds stoichiometric nickel or zinc with nanomolar affinities, in partially overlapping sites located between two major GTPase motifs. Upon metal binding, the GTP hydrolysis activity and oligomeric properties of the protein are modulated. Furthermore, the stoichiometry and affinity of the nickel is altered when HpHypB is bound to nucleotide, a change not observed for zinc. Mutagenesis of the metal ligands suggest that a conserved cysteine is responsible for transducing the metal-bound state to altered GTPase activity and a conserved histidine is a required nickel ligand only in the nucleotide-bound state. Together, these results suggest that the metal-binding and GTP hydrolysis properties of HpHypB are intimately linked and may comprise a mechanism through which the [NiFe]-hydrogenase and urease maturation pathways can discriminate between Ni(II) and Zn(II). Characterization of the Escherichia coli GTPase YjiA, a member of the same GTPase family as HpHypB, demonstrated that YjiA can bind Ni(II), Zn(II), or Co(II) at a site in a similar iii location as in HpHypB. Metal binding also regulates the GTPase activity and oligomerization of YjiA. This finding suggests that metal-responsive GTPase activity may be a trait of this family of GTPases. Together, this work describes a unique link between the metal-binding and biochemical properties of the G3E GTPases and provides insight into the role of HpHypB in [NiFe]-hydrogenase and urease maturation.
The odd one out: Arabidopsis reticulon20 has a role in lipid biosynthesis

The family of reticulon proteins has been shown to be involved in a variety of functions in eukaryotic cells including tubulation of the endoplasmic reticulum (ER), formation of cell plates and primary plasmodesmata. Reticulons are integral ER membrane proteins characterised by a reticulon homology domain comprising four transmembrane domains which results in the reticulons sitting in the membrane in a W-topology. Here we report on a subgroup of reticulons with an extended N-terminal domain and in particular on arabidopsis reticulon 20. We show that reticulon 20 is located in a unique punctate pattern on the ER membrane. Its closest homologue reticulon 19 labels the whole ER. We show that mutants in RTN20 or RTN19, respectively, display a significant change in sterol composition in the roots indicating a role in lipid biosynthesis or regulation. A third homologue in this family - 3BETAHSD/D1- is localised to ER exit sites resulting in an intriguing location difference for the three proteins.
Heterogeneity and Decision-Making in Cellular Signaling Networks

Signaling networks are the means by which cells adapt to their environment. Over the last decade, cellular decision-making has been shown to exist in the midst of substantial heterogeneity, even among isogenic cells. The presence of such variability is generally assumed to be an obstacle that cells overcome in order to precisely resolve information about their environment. In this work, we investigated the effects of two specific types of intracellular heterogeneity on signal transduction in cells. The first is the presence of substantial compositional heterogeneity in the sets of macromolecular complexes used for signal transduction, which we observe in a model of the yeast pheromone signaling system. In spite of this, the model is able to reliably reproduce experimentally observed dynamical and dose-response trends. We then contrasted this model with one that employs a hierarchically assembled, stable signaling complex and found that the two signaling paradigms can exhibit distinctive behaviors. These differences can be attributed in part to the role of the scaffold protein in signal complex assembly, which is required for signal transduction in the pheromone network. We found that features such as signal amplification and crosstalk prevention vary depending on how the assembly of scaffold-based signaling species occurs. Our results clearly show that a dynamical understanding of signal transduction must take place in the context of compositional heterogeneity. The second form of heterogeneity we consider, biochemical noise, occurs at a more fundamental level. We examined how variability in the response to signal impacts the ability of cells to make reliable decisions by quantifying signal transduction using concepts from information theory. Our results revealed the existence of a fundamental trade-off: increased noise in individual
The Role of Divalent Metals in DNA Replication During Periods of Oxidative Stress

2 Introduction . 3 Materials and Methods . 6 Results. 9 Discussion . 13 Tables . 16 Figures . 17 Acknowledgements. 24 References . 25
Population-specific imputation of gene expression improves prediction of pharmacogenomic traits for African Americans

Genome-wide association studies (GWAS) are useful for discovering genotype-phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power, and allows the effects of both protein coding variation as well as variation in expression to be combined into “gene level” effects. Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein coding regions. Here, we introduce a method that improves the predicted dose by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression—on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic (PK) and pharmacodynamic (PD) pathways of warfarin within training and validation sets comprising both European and African-descent individuals. We build gene-tissue signatures associated with warfarin dose, and identify a signature of eleven gene-tissue pairs that significantly augment the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Our results demonstrate that imputed expression can improve dose prediction, in a population-specific manner.
Characterisation and structural studies of a superoxide dismutase and OmpA-like proteins from Borrelia burgdorferi sensu lato

Lyme borreliosis is the most common tick-borne, human infection across the Northern hemisphere. The agent responsible, Borrelia burgdorferi sensu lato (s.l.) covers a family of Spirochaetes with unique characteristics which are shared by both Gram-negative and Grampositive bacteria. The outer membrane (OM) is rich in lipoproteins but contains a relatively low density of integral membrane proteins (OMPs), of these OMPs very few have been identified and even fewer are well characterised. The OmpA-like transmembrane domain defined by the Pfam family PF01389 is a 8-stranded membrane spanning β-barrel and is well conserved among Gram-negative bacteria but to date remains unknown in Spirochaetes. Building from previous computational work which had sought to identify possible OMPs from B. burgdorferi s.l. four OmpA-like proteins, BAPKO_0422 (Borrelia afzelii), BB_0562, BB_0406 (B. burgdorferi) and BG0408 (Borrelia garinii) have been identified and structurally characterised. The four proteins are encoded by chromosomal genes and highly conserved between Borrelia species and may be of diagnostic or therapeutic value. Structural characterisation by both circular dichroism and small angle X-ray scattering suggests these four proteins adopt a compact globular structure rich in β-strand (~40%) with Ab initio molecular envelopes resembling a cylindrical peanut shape with dimensions of ~25x45 A consistent with an 8-stranded β-barrel. The present work demonstrates that BAPKO_0422 can bind human factor H (hfH) and some evidence for a further interaction between the BAPKO_0422 protein and heparin. The interaction with hfH may contribute to the spirochaete’s immune evasion mechanisms by the inhibition of the complement response. The zoonotic life-cycle of Borrelia and challenges by the host’s immune system causes an ever changing environment which often leads to fluctuations of O2 exposure. Although B. burgdorferi s.l. have a distinct lack of metabolic systems including peroxidases and catalase enzymes the Spirochaetes genome does encode a single superoxide dismutase gene (sodA - bb_0157). Previously assigned as a Fe-SOD there has been some debate whether this protein requires iron or manganese as a co-factor. The present work demonstrates that the B. burgdorferi enzyme SodA requires manganese for activity and does not display cambialistic behaviour. Structural and proteomic characterisation suggests the B. burgdorferi SodA enzyme shares significant sequence similarity to a superoxide dismutase from Thermus thermophilus.
Helping cells jump to conclusions.

Many cellular processes rely on the ability of cells to sense and respond to chemical information in their immediate surroundings. Cells can achieve this by binding chemical signals (ligand) to specific receptor proteins, that convert the chemical information into intracellular signals to which the cells can respond. Furthermore, different concentrations of ligand may be distinguished by the fraction of bound to unbound receptor. Although this is generally only possible for concentrations that do not saturate the receptors, it was recently shown that cells’ ability to distinguish between ligand concentrations could in theory be expanded into the saturating range, by the utilization of pre-equilibrium information resulting from the ligand–receptor binding kinetics. This mechanism was termed pre-equilibrium sensing and signaling (PrESS). Here, the possibility to biologically implement this idea as a simple, controllable genetic circuit is investigated. Via computational modeling and experiments it is shown that repression-based sensing, aided by slow influx of ligand, generates pre-equilibrium dynamics that may enable cells to distinguish between different saturating concentrations of ligand. Potential improvements are also discussed.
Cis-2,4,5-triphenyl-imidazolines and their use in the treatment of tumors

The present invention, symbols are as defined herein, and the MDM2 protein inhibiting the interaction of p53- like peptide, to provide a salt and an ester compound and a pharmaceutically acceptable of the formula (I) and formula (II) with a moderate activity: [Formula I] MDM2, p53, anti-tumor agent
Identification of Insect-Plant Pollination Networks for a Midwest Installation: Fort McCoy, WI

Abstract : Pollinating insects and pollinator dependent plants are critical components of functioning ecosystems yet, for many U.S. Department of Defense (DoD) installations, the identities and relationships between pollinators and plants are unknown. This study demonstrated methods for compiling and analyzing readily available information for insect pollinators and pollination dependent plants for a single installation, Fort McCoy, WI. Although installation documents identified a total of 1470 insect species and 972 plant species were identified on the installation, this work focused on species of conservation concern (nine pollinator insect species and three pollinator-associated plant species). Published information on insect pollinators and pollination dependent plants was then used to conduct a basic plant-pollinator network analyses using free analytical network software (software package R), which revealed that all the plant species of conservation concern are pollinated by several insect pollinator species. However, many pollinator insect species of conservation concern were associated with a limited number of host plant species. The results of this work suggest that analyses that rely on publicly available information provide a useful starting point in determining basic, binary plant-pollinator relationships. Field-collected data, e.g., frequency of pollinator-plant interactions, would be required for a more detailed, robust network analysis.
Analytical Validation of Relative Average Telomere Length Measurement in a Clinical Laboratory Environment.

BACKGROUND Average telomere length in whole blood has become a biomarker of aging, disease, and mortality risk across a broad range of clinical conditions. The most common method of telomere length measurement for large patient sample sets is based on quantitative PCR (qPCR). For laboratory-developed tests to be performed on clinical samples, they must undergo a rigorous analytical validation, currently regulated under CLIA. METHODS Whole blood samples from 40 donors were used in the analytical validation of methods for relative average telomere length (rATL) measurement. Three technical replicate DNA samples were extracted from each whole blood sample and placed in three independent wells on a sample plate. Each of these sample plates was assayed 12 times during the validation process. The study was conducted over a 20-day period, once in the morning and once in the evening, using 3 different operators. RESULTS Our process of rATL measurement beginning with DNA extraction followed by qPCR-based assay resulted in repeatability and reproducibility CV of <5% and amplification efficiencies near 100%. The validated assay was used to establish a reference interval derived from 2 cohorts of individuals: (a) San Francisco Bay area (n = 504) and (b) a US cross-sectional, demographic population (n = 357). CONCLUSIONS We present advances in the establishment of a highly reproducible analytically validated process for determining rATLs in a CLIA laboratory environment.
Survey of huanglongbing associated with ‘Candidatus Liberibacter’ species in Spain: analyses of citrus plants and Trioza erytreae

The disease huanglongbing (HLB), caused by the phloem-limited and psyllid-vectored ‘ Candidatus Liberibacter’ spp. , is threatening the Mediterranean citrus industry. The African psyllid ( Trioza erytreae ) vector of the pathogen was detected in Madeira (Portugal) in 1994 and in the Canary Islands (Spain) in 2002, and its arrival in 2014 in northwest Spain and Portugal along the Atlantic coast instigated a biological alert, and a contingency management plan was developed. Extensive surveys were conducted in Canary Islands from 2009 to 2015 and in the northwest mainland Spain (Galicia) since the first detection of T. erytreae . Symptoms of the psyllid were observed in most sweet orange orchards of five islands in Canary Islands (93% of the inspected plots). In northwest mainland Spain, 65% of the inspected plots up to 2016 showed T. erytreae symptoms. During the surveys, ten leaves/tree from trees showing suspicious symptoms and from symptomless trees, as well as adult psyllids, were collected and analysed by real-time PCR using a universal ‘ Ca . Liberibacter’ spp. kit, according to the EPPO standard. Suspected samples from other surveyed Spanish regions free of the vector were also analysed. The few samples that were positive in the screening test were tested by species-specific real-time PCR protocols, and they did not show amplification. These data confirm that the Spanish citrus industry is currently free of the ‘ Ca . Liberibacter’ spp. , but strict measures to prevent the introduction of this pathogen are required as the presence of T. erytreae increases the risk of its dissemination.
Antimicrobial Peptide Daptomycin and its Inhibition by Pulmonary Surfactant: Biophysical Studies using Model Membrane Systems

iv ACKNOWLEDGEMENTS . vi DEDICATION . viii TABLE OF CONTENTS . ix LIST OF FIGURES . xv LIST OF TABLES . xviii LIST OF ABBREVIATIONS . xix LIST OF SYMBOLS . xxii