Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic analysis of two Ukrainian isolates of Wheat streak mosaic virus

The study of molecular characteristics and, in particular, the nucleotide (nt) and amino acid (aa) sequences of the viral genomes, is necessary to know the changes in their geographical range, phylogenetic relationships, viruses’ evolution, and their emergence as new epidemics. Aim. Phylogenetic analysis of the coat protein ( CP ) gene sequences of two new Ukrainian isolates of Wheat streak mosaic virus : Ukraine-Mal-18 and Ukraine-Ep-18. Results. The nucleotide sequences of 676 nt region of the CP gene of two Ukrainian WSMV isolates were compared with the sequences of 72 WSMV isolates/strains from GenBank. The phylogenetic analysis showed that the Ukrainian WSMV isolates cluster with the clade B or WSMV-ΔE isolates (originating from Europe and Asia) and have a typical for this clade triplet deletion at the position 8412-8414 nt in the CP gene. The isolate Ukraine-Mal-18 has the highest level of the sequence identity (93.5 %-95.9 % nt and 93.6-95.0 % aa) with the clade B isolates. The Ukraine-Ep-18 isolate shares 89.2 %-91.4 % (nt) and 88.6-87.1 % (аа) identity with the clade B isolates. Additionally, both Ukrainian WSMV isolates have a number of unique aa substitutions in the central CP gene domain. Conclusions. Ukrainian WSMV isolates belong to the clade B. But Ukraine-Mal-18 and Ukraine-Ep-18 have some differences from other members of the clade: i) a higher divergence compared to other B isolates (the Ukraine-Mal-18 has 12 aa substitutions, the Ukraine-Ep-18 has 25 aa substitutions, where as the other clade B isolates have no more than 2 aa substitutions); ii) have aa substitution identical with the B1 non-crop isolates of this virus, many aa substitutions are in the same motifs as the substitutions of B1 grass WSMV isolates.
Phenolic composition and in vitro antioxidant capacity of South African plums (Prunus salicina Lindl.)

62 INTRODUCTION 63 MATERIALS AND METHODS 64 Chemicals 64 Sample preparation 65 High-performance liquid chromatography with diode-array and fluorescence detection (HPLC-DAD-FLD) 67 HPLC method validation 68 Liquid chromatography-mass spectrometry (HPLC-DAD-MS) 69 On-line antioxidant analysis 70 RESULTS AND DISCUSSION 70 HPLC method development 70 Identification of phenolic compounds using HPLC-DAD-MS 71 HPLC method validation 79 On-line antioxidant analysis 83 CONCLUSIONS 92 REFERENCES 93 CHAPTER 4: FRUIT ATTRIBUTES, PHENOLIC COMPOSITION AND ANTIOXIDANT CAPACITY OF SOUTH AFRICAN PLUMS: COMPARISON OF CULTIVARS AND SELECTIONS AND THE ROLE OF SEASON AND A COMMERCIAL COLD STORAGE AND RIPENING REGIME ABSTRACT 100 INTRODUCTION 101 MATERIALS AND METHODS 102 Chemicals 102 Analysis of whole fruit 102 Sample collection 102 Colour analysis 103 Stellenbosch University http://scholar.sun.ac.za100 INTRODUCTION 101 MATERIALS AND METHODS 102 Chemicals 102 Analysis of whole fruit 102 Sample collection 102 Colour analysis 103 Stellenbosch University http://scholar.sun.ac.za
Estudio de capas delgadas de InAlN para su posible utilización en celdas solares de alta eficiencia

En esta tesis de doctorado se estudiaron las propiedades quimicas, fisicas, estructurales, morfologicas, opticas y electricas de la aleacion semiconductora InAlN, con posibles aplicaciones en celdas solares. Se usaron estrategias para obtener la aleacion semiconductora a un costo menor a los metodos actuales usados en materiales fotovoltaicos comerciales. Para esto se logro obtener el material tanto por magnetron Sputering RF como por Sputtering DC; mediante el uso de un unico blanco de InAl, y a temperatura ambiente. Asi mismo, se logro sintetizar peliculas amorfas, policristalinas, y altamente cristalinas; lo cual permite alto grado de versatilidad en la metodologia propuesta. Para realizar el estudio sistematico de las propiedades del material, se variaron principalmente tres parametros en las capas de InAlN: La fraccion molar x de InN en la aleacion InxAl1-xN, el espesor, y por ultimo el tipo de sustrato sobre el cual se depositan las capas. Como aspectos interesantes se destacan varios asuntos: El primero es la obtencion de band-gaps (Eg) adecuados para emplear el material InAlN en la capa absorbente y la capa ventana de celdas solares. En segundo lugar, valores de coeficientes opticos de absorcion por encima de los asociados a materiales fotovoltaicos convencionales, lo cual permitiria usar espesores de la capa activa menores a los actuales. En tercer lugar, se reporta por primera vez la posibilidad de variar el Eg variando el espesor de la pelicula. Por ultimo, se construyo un dispositivo basico de celda solar heterounion tipo InAlN-n/Si-p, y asi confirmar que la aleacion InxAl1-xN tiene potencial su uso en celdas solares.
Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake

Environmental DNA offers great potential as a biodiversity monitoring tool. Previous work has demonstrated that eDNA metabarcoding provides reliable information for lake fish monitoring, but important questions remain about temporal and spatial repeatability, which is critical for understanding the ecology of eDNA and developing effective sampling strategies. Here, we carried out comprehensive spatial sampling of England’s largest lake, Windermere, during summer and winter to 1) examine repeatability of the method, 2) compare eDNA results with contemporary gill-net survey data, 3) test the hypothesis of greater spatial structure of eDNA in summer compared to winter due to differences in water mixing between seasons, and 4) compare the effectiveness of shore and offshore sampling for species detection. We find broad consistency between results from three sampling events in terms of species detection and abundance, with eDNA detecting more species than established methods and being significantly correlated to rank abundance determined by long-term data. As predicted, spatial structure was much greater in the summer, reflecting less mixing of eDNA than in the winter. For example Arctic charr, a deep-water species, was only detected in deep, mid-lake samples in the summer, while littoral or benthic species such as minnow and stickleback were more frequently detected in shore samples. By contrast in winter, the eDNA of these species was more uniformly distributed. This has important implications for design of sampling campaigns, for example, deep-water species could be missed and littoral/benthic species overrepresented by focusing exclusively on shoreline samples collected in the summer.
Selected body temperature, metabolic rate and activity pattern of the Australian fossorial skink, Saiphos equalis

Fossorial and nocturnal lizards have limited opportunities to thermoregulate because they do not have access to basking opportunities, which has implications for their thermal physiology and metabolism. We measured substrate temperatures (Ts) in the field, and selected body temperatures (Tb) and metabolic rates in the laboratory, in fossorial skinks, Saiphos equalis, to quantify basic aspects of their thermal and metabolic physiology. Saiphos equalis selects relatively cool temperatures over a broad range (approximately 17–24 oC), suggesting that it does not thermoregulate precisely. Individuals of S. equalis are active more often at night than during the day. Rate of oxygen consumption was measured at 2 °C intervals from 10–30 °C in adult lizards. Metabolic rate increased as a function of temperature but there was no significant difference in VO2 over the preferred temperature range. Like many other fossorial lizards, S. equalis is nocturnal and selects relatively low body temperatures compared to heliothermic lizard species.
Nutrient sufficiency levels for haskap (Lonicera caerulea L.) using the boundary-line approach

Abstract: Adequate supply of plant nutrients is crucial for haskap plant growth and increased productivity. A study was carried out to determine the variability in haskap (Lonicera caerulea L. cv. Indigo Gem) plant characteristics in relation to soil and leaf tissue nutrient status. A total of 19 composite soil samples and corresponding plant leaf tissue samples were collected in 2016 from 12 locations in Nova Scotia. Plant parameters measured include growth rate, leaf size, leaf chlorophyll content, and visual observations. A boundary-line approach was used to determine nutrient sufficiency ranges in leaf tissues of 2.23%–2.96% for N, 0.22%–0.28% for P, 0.84%–1.32% for K, 1.63%–2.10% for Ca, and 0.14%–0.50% for Mg. Principal component and correlation analysis suggested a possible antagonistic interaction between leaf K and Mg. Negative associations were observed most frequently between Ca and Mg and other nutrients, especially K. Plant parameters such as bush volume, leaf size, and growth rate were closely related to soil and leaf K. Deficiencies in leaf tissue K and P were identified as potentially important factors limiting growth. Therefore, there is a need to adjust or balance the application of these nutrients. In conclusion, the sufficiency ranges derived can be used as a guiding principle in diagnosing the nutritional status of haskap cv. Indigo Gem on representative farms in Nova Scotia.
The observed decline of Western Toads (Anaxyrus boreas) over several decades at a novel winter breeding site

The Western Toad (Anaxyrus boreas) population of the Atlin Warm Springs in northwestern British Columbia has persisted since at least 1924. An extraordinary feature of the population has been winter breeding in late February to early March, while nearby cold-water populations breed in late-May. Metamorphosis of tadpoles, enhanced by the warm water, occurs as early as late-March. In 2008, Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) was documented in toadlets at the warm springs. Until 2005, as many as eight egg clutches and 25 breeding adults had been observed at the warm springs, after which the population declined. In 2017, novel spring breeding occurred in a cooler pond in the spring complex. Future observations will help determine whether the population is recovering and whether breeding phenology and habitat use have changed.
Molecular Genetic Analysis of RB1 gene among Sudanese children with Retinoblastoma

BACKGROUND Retinoblastoma (RB), the commonest early childhood intraocular tumor, is most often related to mutations in the RB1 gene with an incidence of 3% of all pediatric tumors. It has good prognosis if diagnosed early but it is life-threatening when diagnosed late. OBJECTIVE To study the Molecular Genetic Analysis of Retinoblastoma (RB) in Sudanese families. METHODS Thirty one (n=31) clinically and histopathologically diagnosed cases of RB attending Makkah Eye Complex (MEC) Orbit clinic (Khartoum, Sudan) were included in this Molecular Genetic RB Analysis. Fresh blood samples extracted from seven RB patients and 15 close families for DNA extraction and PCR were sent for Genetic Sequencing and In silico approach for “Exon 18 mutations” which is one of the highly mutated exons worldwide. RESULTS The majority of patients (41.9%) were below five years old. Females were 58.1%, males were 41.9%. Leukocoria was the commonest sign at presentation (41.9%). RB Unilaterality were in (77.4%) while Bilaterality in 19.4%. Both eyes were equally affected 50% each. The age at diagnosis time ranged from 0.02 to five years. Consanguinity of parents was very high (85.7%), the 1st degree cousins were less (28.6%) while the 2nd degree was high (57.1%). The patients’ ethnic background and geographical area were from seven different tribes; all belong to the Western Sudan. The molecular genetic study showed that exon 18 was free of mutation among the seven patients + their three relatives. The Functional Analysis and (SNPs) prediction study of exon 18 from NCBI data base showed that the various computational approaches used (SIFT, PolyPhen-2, I-mutant and Project hope) identified 16 reported mutations worldwide, three of which (rs137853292, rs375645171 and rs772068738) are major nsSNPs (non-synonymous) which might contribute to native RB1 protein malfunction and ultimately causing carcinoma. CONCLUSION RB mainly affected children under five years and both sexes are equally affected. Unilaterality was predominant. Consanguinity plays a role in inheritance and the majority of patients were from Western Sudan. The most commonly detected deleterious mutations worldwide in exon 18 were not found in the Sudanese studies samples. Further screening for the highly reported mutations in exons 8, 10 and 14 or Next Generation Sequencing (NGS) are recommended. In silico tools are useful in studying the functional analysis of SNPs.
The Great Lakes Region is a melting pot for vicariant red fox (Vulpes vulpes) populations

During the Pleistocene, red fox (Vulpes vulpes) populations in North America were isolated in glacial refugia and diverged into 3 major lineages: the Nearctic-Eastern subclade of eastern Canada, the Nearctic-Mountain subclade of the western mountains, and the Holarctic clade of Alaska. Following glacial retreats, these genetically distinct populations of foxes expanded into newly available habitat. Along with subsequent translocation from fur farms, these expansions have resulted in red foxes now occupying most of the continent. The origin of foxes that colonized the Great Lakes Region, however, remains unknown. Furthermore, it is unclear whether contemporary populations inhabiting this region are the result of natural range expansion or if foxes released from fur farms colonized the landscape in the 1900s. To determine the origin of red foxes in the Great Lakes Region, we collected genetic samples from 3 groups: 1) contemporary wild foxes, 2) historical wild foxes collected before fur farming, and 3) fur-farmed foxes from a contemporary fur farm. We constructed a network of mtDNA haplotypes to identify phylogeographic relationships between the 3 sample groups, and examined genetic signatures of fur-farmed foxes via the androgen receptor gene (AR) associated with tame phenotypes. Historical wild foxes demonstrated natural colonization from all 3 major North American lineages, which converged within the Great Lakes Region, and contemporary wild foxes maintained the historically high genetic diversity. Most contemporary wild foxes also matched haplotypes of fur-farmed foxes; however, AR was not useful in distinguishing fur-farm origins in samples of contemporary wild foxes. Our results show that geographically disparate populations naturally merged in the Great Lakes Region before fur-farmed foxes were introduced. Due to the historically high genetic diversity in the Great Lakes Region, any introductions from fur farms likely contributed to, but did not create, the genetic structure observed in this region.
Honey Bees Species Differentiation using Geometric Morphometric on Wing Venations

Wings are the most interesting part for morphometric study in any species of insect, including honey bees. The geometric morphometric is a strong analytical method to identify the species of insect, therefore we used wing venations to explore the wing variations among five honey bee species in Indonesia, i.e. A. mellifera, A. cerana, A. dorsata, A. andreniformis, and A. koschevnikovi. We used Thin Plate Splin (TPS) software to conduct the landmark digitation on wing venation and geometric morphometric analysis based on the 19 anatomically points of venation through tpsdig2 and tpsRelw software to describe the variations of wing venations. Our result of Relative Warp ordination plot showed variations of wing venation of five honey bee species, particularly on the five points. Grid deformations show the difference patterns among the five species of honey bees as well. Moreover, based on phylogenetic tree by using Neighbour Joining approach, the morphometric geometric wings venation is also able to separate the species of honey bees; thus, a possibility method to differentiate the honey bee species in Indonesia.
Genetics, genomics and breeding of groundnut (Arachis hypogaea L.)

Abstract Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker‐assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
Effects of selected processing treatments on antigenicity of banana prawn (Fenneropenaeus merguiensis) tropomyosin

Different processing techniques were assessed to attenuate the antigenicity of banana prawn tropomyosin (Fenneropenaeus merguiensis). Frying and boiling at different temperatures, acid treatment using different acids and storage at 20 °C up to 3 months were investigated. Untreated prawn sample was used as a control. Frying significantly increased antigenicity (6–8 times) in temperature-dependent manner, whereas the trend was fundamentally reversed with boiling. Boiling at 121 °C resulted in the lowest antigenicity (12.99 mg mL ) among all heat-treated samples, yet higher than the control (5.06 mg mL ). Freezing had initially very minor impact, although prolonged storage at 20 °C increased antigenicity slightly (2.29 mg mL ) compared with control. Antigenicity was impacted the most by a reduction in pH independent on the type of acid as both acetic and HCl acids significantly reduced antigenicity of tropomyosin by ~90% compared with control. This could be considered as a new approach to processing that may potentially reduce tropomyosin-derived antigenicity in prawns and prawn products. This study also confirmed the actual molecular weight of banana prawn tropomyosin was 37 kDa implementing a new methodology using unstained gel.
A Break from the Past or Business as Usual? EU-ACP Relations at a Crossroad

Recent scholarly literature on the EU’s development policy has argued that the Union is using its provision of development cooperation to advance its geo-strategic interests. This paper investigates whether there has been an equivalent rupture with the EU’s core normative commitment, namely to conduct a human rights-based approach to development. Contrary to the hypothesis of change, I find that continuity characterises the EU’s mandate for a new partnership with the Africa, Caribbean and Pacific group of states. In fact, the EU’s commitment to a rights-based approach to development shaped the EU’s negotiating directives for a post-Cotonou agreement. In particular, the EU sought to make sure that human rights commitments in the self-standing EPA trade agreements were not lost, as these relied on references to the Cotonou-acquis. However, drawing on a concept of justice as impartiality, I also find that there are ambiguities to the EU’s rights-based approach. I find that national executives’ delegated authority to initiate and conduct dispute settlement on violations of the Cotonou-acquis comes at the cost of promoting individuals’ and civil society’s right to autonomy. Arguably, the EU’s political conditionality policy prioritises support to duty-bearers (states) to uphold their obligations over the empowerment of rights-holders (individuals) to claim their rights.
Molecular analysis of circadian photosensitivity and diapause in the jewel wasp Nasonia vitripennis

Cycling environmental conditions that vary with latitude have led to the evolution of intricate timing mechanisms. Nasonia vitripennis, a small parasitic wasp (Hymenoptera), is known to have strong light-driven seasonal response in the form of diapause (insect type of hibernation) signalled by short days of upcoming winter, as well as circadian rhythms in behaviours such as locomotor activity. Circadian rhythms are governed by a biological “clock”, whose molecular composition differs between species. Whether this clock also regulates seasonal rhythms is debated, as the regulation of the “seasonal timer” is poorly known. Because Nasonia is missing the clock protein CRYPTOCHROME1, a “light-sensor” for the clock synchronisation in Drosophila, CRYPTOCHROME2 was hypothesised as possible light-sensor in Nasonia. Despite being a core clock component, various in vivo and in vitro experiments did not confirm CRYPTOCHROME2 as a light-sensor in Nasonia. The molecular basis of the seasonal response was studied in a set of genetically variable N. vitripennis lines from a single latitudinal location. Lines varied in the proportion of diapausing broods, under short day conditions, indicating variation in the regulation of the seasonal clock, possibly involving other regulatory pathways. This study has provided insight in the molecular regulation of the Nasonia clock and its light synchronisation, information that is important . for understanding how organisms adapt to a cycling environment.
The lipid phosphatase-like protein PLPPR1 increases cell adhesion by modulating RhoA/Rac1 activity

Phospholipid Phosphatase-Related Protein Type 1 (PLPPR1) is a member of a family of lipid phosphatase related proteins, integral membrane proteins characterized by six transmembrane domains. PLPPR1 is enriched in the brain and recent data indicate potential pleiotropic functions in several different contexts. An inherent ability of PLPPR1 is to induce membrane protrusions, and we have previously reported that members within this family may act in concert. However, the mechanism by which PLPPR1 produces these actions is not yet understood. Here, we report that exogenous expression of PLPPR1 reduces cell motility and increases cell adhesion to the ECM substrate by altering cytoskeletal dynamics and modulating RhoA and Rac1 activity through association with RhoGDI. This signaling also allows overexpression of PLPPR1 to overcome the inhibitory activity of CSPGs and LPA on neurites. Together, these results establish a novel signaling pathway for the PLPPR1 protein. SUMMARY PLPPR1 increases cell adhesion and decreases cell motility by modulating RhoA and Rac1 activation through its association with RhoGDI.