Miracle-dz/UniFAR-FTUs huggingface dataset:
Imperata yellow mottle virus: An Emerging Threat to Maize, Sorghum and Pearl Millet in Burkina Faso

Imperata yellow mottle caused by Imperata yellow mottle virus (IYMV) of the genus Sobemovirus was first characterized on Imperata cylindrical and Zea mays in Burkina Faso. The disease has been reported in several localities of the country but its ecology and epidemiology are poorly known. In particular, only I. cylindrical and maize have been reported within IYMV host range. The aim of this study was to investigate the experimental host range of the virus. Mechanical inoculation of a mixture of four IYMV isolates to 18 plant species, including four crops (maize, rice, sorghum and pearl millet) and 14 wild grasses showed clear mottle symptoms in maize, sorghum and pearl millet and two wild grass species (Setaria verticillata and Rottboellia exaltata). Symptom development was confirmed by Enzyme-linked immunosorbent assay and reverse transcription–polymerase chain reaction (RT-PCR). Infection of crop species by IYMV depended on cultivars tested. Therefore, proportions of positive cultivars were 16/36 in maize, 4/10 in sorghum and 4/9 in pearl millet, respectively. Studies on virus-host interactions using individual virus isolates showed two pathogenic patterns. Three out of the four isolates tested infected all plant species and cultivars. In contrast, the fourth IYMV isolate could infect only one maize cultivar. These results expand the previously known host range of IYMV from two to five species, indicating a narrow host range. Among the new characterized host species, sorghum and pearl millet are important cereal crops. Therefore, Imperata yellow motte disease is a potential threat for the cereal crop production and its ecology and epidemiology should be thoroughly investigated.
Diet of small mammals in Atlantic Forest fragments in southeastern Brazil

Diet of six species of small mammals (five marsupials and one rodent) was studied through analysing a total of 163 fecal samples obtained from live-trapping in Atlantic Forest fragments at Poco das Antas, Brazil, 1995-1999. For the marsupial Micoureus demerarae the most frequent food itens were arthropods from the orders Coleoptera and Hymenoptera, pupae and larvae of Diptera and Lepidoptera, and seeds of plants from secondary vegetation; freshwater crustaceans were also recorded. Caluromys philander also consumed mostly Coleoptera, Hymenoptera and seeds from secondary plants, but seeds were less diverse, more frequent and more abundant than for M. demerarae. Patterns recorded for the remaining marsupials included the importance of termites for Metachirus nudicaudatus, presence of a vertebrate (rodent) only for Philander frenata, and a diverse diet for Didelphis aurita despite a small sample size. The diet of the sixth species, Akodon cursor, included mostly insects and arachnids with seeds in lower frequency.
Assessment of the prevalence of pathogenic bacteria in street vended ready-to-eat meats in Windhoek, Namibia

i Table of contents.iii List of tables.viii List of figures.ix Abbreviations.x Acknowledgements.xiii Dedication.xv Declaration.xvi CHAPTER 1: INTRODUCTION.1 1.1 Orientation of the study.1 1.2 Statement of the problem.3 1.3 Objectives of the study.4 1.3. 1 Specific objectives.4 1.4 Research questions.4 1.5 Significance of the study.5 1.6 Limitation of the study . 5
Increased appendicularian zooplankton alter carbon cycling under warmer more acidified ocean conditions

Anthropogenic atmospheric loading of CO2 raises concerns about combined effects of increasing ocean temperature and acidification, on biological processes. In particular, the response of appendicularian zooplankton to climate change may have significant ecosystem implications as they can alter biogeochemical cycling compared to classical copepod dominated food webs. However, the response of appendicularians to multiple climate drivers and effect on carbon cycling are still not well understood. Here, we investigated how gelatinous zooplankton (appendicularians) affect carbon cycling of marine food webs under conditions predicted by future climate scenarios. Appendicularians performed well in warmer conditions and benefited from low pH levels, which in turn altered the direction of carbon flow. Increased appendicularians removed particles from the water column that might otherwise nourish copepods by increasing carbon transport to depth from continuous discarding of filtration houses and fecal pellets. This helps to remove CO2 from the atmosphere, and may also have fisheries implications.
Quantifying Stress in Marine Mammals: Measuring Biologically Active Cortisol in Cetaceans and Pinnipeds

Abstract : This research will improve our ability to measure stress in marine mammals. Stress hormones (glucocorticoids either cortisol or corticosterone) are easily measured in blood and are an important measure of stress. However, a large proportion of glucocorticoids are bound by a protein in blood (corticosteroid binding globulin, CBG) and do not have immediate biological effects. Immediate biological effects are best estimated by measuring free glucocorticoid levels (i.e. that hormone not bound by CBG). This project will improve the capacity of marine mammal researchers to measure free glucocorticoid levels.
Faecal Culture and IS900 PCR Assay for the Detection of Mycobacterium avium subsp. paratuberculosis in Bovine Faecal Samples

Mycobacterium avium subsp. paratuberculosis is a pathogen that causes johne’s disease in animals and is implicated in Crohn’s disease in humans. Culture of Mycobacterium avium subsp. paratuberculosis (MAP) from faeces has been considered the gold standard for the diagnosis of paratuberculosis for many years. However, direct faecal polymerase chain reaction (PCR) is becoming more widely used, demonstrating similar sensitivity and specificity to culture. In the present study, faecal culture and IS900 Polymerase chain reaction (PCR) assay of faecal samples was done on 200 clinically suspected cases of Johne’s disease in dairy cattle. One isolates appeared only on the mycobactin J supplemented media at 8–16 weeks post-inoculation. A total of 7 faecal samples out of 200 samples were detected positive by IS900 PCR assay for Mycobacterium avium subsp. paratuberculosis (MAP) yielding an expected product of size 229 bp. The sensitivity of the IS900 PCR was assessed by making ten fold serial dilutions of the known concentration (5 ng/μl) of the standard genomic DNA of MAP. The detection limit of the IS900 PCR was upto5 pg/μl.
Levan and levansucrases: Polymer, enzyme, micro-organisms and biomedical applications

Abstract Nowadays, levan synthesis and its biocatalysis is a step claiming attention due to its promising uses in biomedical field. Levansucrase, as the enzyme responsible of levan biocatalysis is studied in this work concerning sequence homology, signal peptide, metal binding, etc. More than 650 different levansucrase sequences were studied and many interesting results were obtained such as phylogenetic trees and conserved residues that could be essential for biocatalysis machinery. Moreover, a review of levan applications in biomedicine and health field was made. It is showed the advances in applications such as a film agent, a carrier for drug delivery systems, an anti-inflammatory compound or its potential use for functional food as prebiotic.
Endophytic Bacillus spp. from Wild Solanaceae and Their AntifungalPotential against Fusarium oxysporum f. sp. lycopersici Elucidated UsingWhole Cells, Filtrate Cultures and Organic Extracts

Six isolates of culturable bacteria, isolated from stems of wild Solanaceae species (Datura metel, Solanum nigrum, S. elaeagnifolium, and Nicotiana glauca), were assessed for their antifungal activity against F. oxysporum f. sp. lycopersici (FOL), the causal agent of the tomato Fusarium wilt. Blast analysis of 16S rDNA sequencing genes homology showed that the isolates belonged to the genus Bacillus (Bacillus cereus str. S42, B. tequilensis str. SV39, B. subtilis str. SV41, B. methylotrophicus str. SV44, B. amyloliquefaciens subsp. plantarum str. SV65, and B. mojavensis str. SV104). The mycelium growth of FOL was significantly reduced by 36 to 46% by diffusible metabolites and by 18 to 21% by volatile compounds. Cell-free cultures were found to be mostly active when issued from 4 days-old cultures where FOL growth inhibition significantly varied from 31.1 to 59.5%. Active metabolites present in the cell-free cultures were extracted with n-butanol and chloroform. Both organic extracts exhibited antifungal potential towards FOL higher than that induced by the two commercial products i.e. Bavistin® (50%, chemical fungicide) and Bactospeine® (16000UI/mg, biopesticide). This study clearly indicates that endophytic Bacillus spp. from wild Solanaceae species can be used as natural sources of bioactive metabolites towards FOL. Wild Solanaceae are frequent in Tunisia and were not explored as potent sources of candidate antagonistic bacteria. In view of the endogenous progress of the pathogen via the vascular tissues, the use of endophytic bacteria can suppress tomato Fusarium wilt disease.
Sixteen New Records of Ascomycetes from Crop Field Soil in Korea

The present study reports 16 species of Ascomycota that were previously unknown in Korea, namely Acremonium cellulolyticus (KNU14-25), Acremonium zonatum (KNU14-15), Chaetomium madrasense (KNU14-9), Cladosporium silenes (KNU 14-18-1), Humicolopsis cephalosporioides (KNU15-3), Leptosphaerulina chartarum (KNU14-16), Paecilomyces marquandii (KNU14- 8), Paecilomyces tenuis (KNU14-18-2), Paraphaeosphaeria sporulosa (KNU15-2), Penicillium rubidurum (KNU14-12), Pochonia suchlasporia (KNU15-6), Sporothrix inflata (KNU15-8), Thielavia hyrcaniae (KNU15-1), Thielavia terricola (KNU14-23-1), Xylogone sphaerospora (KNU15-7), and Zopfiella longicaudata (KNU15-5). These fungal species were isolated from soil samples collected from various regions of Korea and identified based on their morphological characteristics and rDNA internal transcribed spacer sequence data. Full descriptions and illustrations for each species are provided.
The effect of elevated Temperature on Larval Development of Acropora palmata

Acropora palmata thrived in the Caribbean and Florida but has suffered a great reduction in numbers over the past few decades. Temperature is the most prominent factor leading to coral decline. This experiment focuses on the effects of changes in temperature on A. palmata embryonic development. Larval development was observed via microscopic pictures. Pictures were taken of n=901 larval samples collected in August of 2008 and 2009. Ratios of larvae belonging to 7 developmental stages were recorded. High temperature (30oC and 29oC) accelerated the larval development as larvae entered later developmental stages at an earlier time point. Low temperature (25oC and 27oC) resulted in slowed larval development rate and delayed metamorphosis for settlement. Samples from different parentage also showed different patterns in development. Among them, batch 2 and individual cross x by 88 had the greatest fertilization rates and greatest larval surface areas. The strong effect of temperature on A. palmata larval development likely influences the dispersal, settlement and survival of the larvae.
Epigenetic Regulation of Tumor Cell Phenotype

The Transforming Growth Factor-β (TGFβ)/SMAD signaling pathway can function as either a tumor suppressor or metastasis promoter during tumor progression. In normal epithelial cells and early stages of epithelial tumorigenesis TGFβ functions as a tumor suppressor to decrease cell proliferation or induce apoptosis. However, during malignant progression tumor cells no longer respond to the anti-proliferative effects of TGFβ, but instead undergo an epithelial-to-mesenchymal transition (EMT) whereby cells acquire a migratory and invasive phenotype which promotes tumor metastasis. Resolution of the dichotomy in TGFβ function and a further understanding of its tumor suppressor and metastasis promoting functions may uncover new strategies for the treatment of epithelial cancers. Previous studies have demonstrated an important role of the TGFβ-Inducible Early Gene-1 (TIEG1)/Kruppel-like Factor-10 (KLF10) as a central regulator of TGFβ/SMAD signaling and the anti-proliferative functions of TGFβ. In this study we examined the role of KLF10 in controlling the TGFβ-induced EMT and show that depletion of KLF10 results in a more pronounced induction of EMT. Moreover, chromatin immunoprecipitation (ChIP) and chromatin immunoprecipitation- sequencing (ChIP-seq) analysis shows that KLF10 directly binds to GC-rich sequences in the promoter region of the EMT-promoting transcription factor SLUG/SNAI2 to repress its transcription. Consistent with these findings, an analysis of KLF10 in lung cancer revealed that KLF10 levels are decreased in lung cancer vs. normal samples. Furthermore, in vivo study revealed a significantly increased tumor incidence and tumor size in Klf10-/- mice compared to the wild type mice. Additional ChIP studies showed that KLF10 recruits HDAC1 to the SNAI2 promoter and is required for the removal of activating histone acetylation marks. These findings reveal a previously unknown function of KLF10 in suppressing TGFβ-induced EMT and Abstract x represent a significant advancement in the understanding the molecular dichotomy of TGFβ function during tumor progression. In a more global approach, we have utilized a dual LSD1/HDAC inhibitor 4SC-202 to study the effect on tumor cell phenotype. We have shown that combined inhibition of LSD1 and HDACs significantly block the TGFβ-induced EMT. Immunohistochemical staining of LSD1 in pancreatic cancer samples revealed that LSD1 is highly expressed in a subset of tumors. Consistent with this finding, in our xenograft study we have shown that 4SC-202 significantly decreases the tumor size. Together these findings revealed the potential role of small molecule inhibitors against epigenetic modifiers in targeted anticancer therapy.
DEVELOPMENT OF FUNCTIONAL PROTEOMICS APPROACHES FOR STUDYING RETROGRADE TRANSPORT

Retrograde trafficking allows for proteins transport from the plasma membrane to the endoplasmic reticulum, via the Golgi apparatus, bypassing the degrading environment of lysosomes. Previous studies have shown that retrograde transport is crucial for cellular functions such as signaling, ion homeostasis, and the establishment of wnt morphogen gradients. Furthermore, retrograde transport plays an essential role in cellular uptake of pathogenic factors like protein toxins and virus proteins. However, the current list of cargo proteins is limited, and it is likely that many cellular functions of retrograde transport still remain to be discovered. Clearly, a strong need exists for further characterization of this transport route. In this study, four different proteomics approaches have been developed aiming to identify membrane proteins taking retrograde transport route: SNAP-tag, sulfation, FKBP, and streptavidin. Amongst these, the SNAP-tag approach turned out to be the most efficient strategy to identify cargo candidates of the retrograde route. This strategy is based on the covalent modification of the plasma membrane proteome with a benzylguanine (BG) derivative. Only BG-tagged plasma membrane proteins that are then transported via the retrograde route can covalently couple to a TGN-localized SNAP-tag fusion protein. The approach was validated step-by-step using a well studied retrograde cargo protein, Shiga toxin B-subunit (STxB). We could show that STxB can be captured and identified by the SNAP-tag approach. Furthermore, coupled with LC-MS, new protein candidates of the retrograde route have been identified. The other three approaches have guided our choice towards the most efficient proteomics strategy, by bringing up experimental opportunities and threats in the fields of organic chemistry and cell biology. Altogether, this thesis work has allowed to develop a novel proteomics strategy that could be applied to identify new cargo candidates of the retrograde route. We have pioneered a dynamic proteomics approach that complements traditional proteomics. Moreover, the concept of using chemical tools to study retrograde transport can also be applied to other endocytic pathways.
Herbarium genomics: skimming and plastomics from archival specimens

Abstract Using massive parallel sequencing, which has become known as second-generation sequencing, some of the classic roadblocks to using herbarium DNA have been overcome. For instance, no longer is the degraded nature of most herbarium DNA preventing sequencing (because of blocking effective amplification). Instead, several kilobases of genomic sequence can be obtained on a routine basis, especially from high-copy number compartments such as plastomes (chloroplast genomes). With approaches such as genomic skimming a fair coverage of repetitive genome compartments (such as plastomes) can be obtained, enabling fast assembly of associated sequences. Although assembly of complete 150+ kilobase herbarium plastomes based on skimming still needs more investment, the generation of large contigs spanning several kilo bases is straightforward. It presents an important and cost-effective boost to using herbarium DNA-sequences in phylogenetic studies at species-level and beyond. At the same time, although herbarium DNA appears to bear the signature of ancient DNA, the accuracy of the herbarium DNA sequences obtained appears to be surprisingly high, as post-mortem miscoding lesion damage in most herbarium DNA is found to be negligible.
Titanium Dioxide Nanoparticles Improve Growth and Enhance Tolerance of Broad Bean Plants under Saline Soil Conditions

Soil salinity is established as one of the major environmental problems, decreasing crop productivity worldwide, thereby threatening sustainable agriculture. In the present study, we evaluated the effects of titanium dioxide nanoparticles (nTiO2) for ameliorating soil salinity in broad bean, an important leguminous crop. As nTiO2 is known to have pro‐oxidant and antioxidant properties, the effects of three different nTiO2 concentrations (0·01%, 0·02% and 0·03%) were compared with respect to plant growth and stress responses. The 0·01% nTiO2 application significantly increased shoot length, leaf area and root dry weight of plants under normal conditions. These growth‐promoting effects were simultaneous with increased levels of chlorophyll b, soluble sugars and proline and enhanced activities of antioxidant enzymes. Under saline soil conditions, although proline level and enzymatic antioxidant activities were increased, plant growth significantly reduced. The 0·01% nTiO2 supplementation significantly increased the activities of enzymatic antioxidants and levels of soluble sugars, amino acids and proline in salt‐affected plants versus plants subjected to salinity alone. Thus, the increased antioxidant enzyme activities contributed to the observed reduction in hydrogen peroxide and malondialdehyde contents, while enhanced levels of proline and other metabolites contributed to osmoprotection, collectively resulting in significant plant growth improvement under salinity. Furthermore, nTiO2‐mediated positive effects were concentration dependent with 0·01% nTiO2 being the most effective, whereas 0·02% showed an intermediate response and 0·03% was almost ineffective under both control and saline soil conditions. Our findings provide a foundation for nTiO2 application in improving growth of plants cultivated on naturally contaminated saline soils. Copyright © 2017 John Wiley & Sons, Ltd.
Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models

Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene transfer and gene duplication. Among these, deep coalescence is usually quantified as the number of extra linages and has been studied as the principal source of discordance among gene trees, while the other processes that could contribute to gene tree discordance have not been fully explored. This is an important issue for hybridization because interspecific gene flow is well documented and widespread across many plant and animal groups. Here, we propose a new way to detect gene flow when ILS is present that evaluates the likelihood of different models with various levels of gene flow, by comparing the expected gene tree discordance, using the number of extra lineages. This approach consists of proposing a model, simulating a set of gene trees to infer a distribution of expected extra lineages given the model, and calculating a likelihood function by comparing the fit of the real gene trees to the simulated distribution. To count extra lineages, the gene tree is first reconciled within the species tree, and for a given species tree branch the number of gene lineages minus one is counted. We develop a set of r functions to parallelize software to allow simulations, and to compare hypotheses via a likelihood ratio test to evaluate the presence of gene flow when ILS is present, in a fast and simple way. Our results show high accuracy under very challenging scenarios of high impact of ILS and low gene flow levels, even using a modest dataset of 5–10 loci and 5–10 individuals per species. We present a powerful and fast method to detect hybridization in the presence of ILS. We discuss its advantage with large dataset (such as genomic scale), and also identifies possible issues that should be explored with more complex models in future studies.
Sheddable armour: identification of osteoderms in the integument of Geckolepis maculata (Gekkota)

Abstract Osteoderms are bony deposits that form within the dermal layer of skin in vertebrates. Within geckos, osteoderms are uncommon, only described in Gekko gecko and the genus Tarentola. A previous report of osteoderms in the Afro-Malagasy gekkonid genus Geckolepis has been questioned due to the extreme skin fragility and regional integumentary loss within the group. We re-evaluated the integument anatomy of Geckolepis maculata using µCT scanning, histology, and clearing and staining to verify the presence or absence of osteoderms and, if present, to characterise and compare their morphology to the osteoderms of Gekko gecko and Tarentola, as well as osteoderm diversity within squamates. Osteoderms were confirmed present in Geckolepis maculata; however, these osteoderms are compound, imbricating, squamous elements that are morphologically similar to the dermal ossifications observed in scincids and gerrhosaurids, while G. gecko and Tarentola possess plate-like and granular osteoderms. Our results suggest that osteoderms have independently evolved at least three times within the Gekkota and that epidermal anatomy may be a better predictor of osteoderm morphology than ancestral history. Further research is required to investigate the regenerative capability of Geckolepis osteoderms following skin autotomy.
Antioxidative Enzyme Responses against Fusarium wilt (Fusarium oxysporum f. sp. ciceris) in Chickpea Genotypes

Three wilt resistant chickpea genotypes activity profile of in wilt antioxidative enzymes pre and post three wilt susceptible checks. of antioxidative enzyme profile normal and wilt activity of three antioxidative . , APX guaiacol superoxide Vikas at post infection resistant susceptible group of genotypes from 2.07 to 2.38 µmoles ascorbate oxidized mg -1 protein min -1 with mean percent increase of 97.94%. Though APX activity increased at post infection stage in wilt sick soil in the wilt resistant genotypes percent increase was from 33.03 to 57.64 with a mean percent increase of 40.4%. Same trend was recorded in GPX and SOD activity.