Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of genetic diversity of the Kenyan yam (Dioscorea spp.) using microsatellite markers

Yam landraces in Kenya have not been fully characterized both at morphological and molecular level. Application of molecular markers can overcome this bottleneck. 187 accessions comprising of 166 yam landraces and 21 Yam DNA samples from IITA, Nigeria were extracted from leaf samples grown at Muguga and genotyped at BeCA. DNA was extracted using CTAB method. Twelve (12) primer pairs were used for genotyping and PCR products detected on ABI-3730 capillary system. Data was analyzed for genetic diversity, ordination and analysis of molecular variance with GenAIEx software. A total of 131 alleles were amplified with a minimum of two alleles and a maximum of 13 alleles per primer with a minimum allele size of 64 bp and a maximum of 368 bp. Accessions from Eastern province had the highest number of unique alleles. Shannon’s information index (I) was 0.1444 for West African samples and 0.2366 for Central province. Accession dispersion revealed four clusters with no distinct geographical pattern. Dense clustering of accessions was an indication of genetic relatedness. Analysis of molecular variance revealed that most variation of 88% (P<0.010) was found within populations or provinces. The simple sequence repeats (SSR) markers were polymorphic and were able to discriminate local yam landraces. Key words: Genetic diversity, microsatellite, yam, Kenya.
Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis originome

Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs) that constitute the originome. A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have determined the originome and chromatin landscape of Arabidopsis thaliana at two stages of postembryonic development. ORIs associate with multiple chromatin signatures including TSS but also regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin whereas at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the originome of an organism at the postembryo stage that should allow us to study ORI biology in response to development, environment and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.
POTENTIAL COMPLEMENTATION OF POTATO VIRUS X MOVEMENT WITH GRAPEVINE RUPESTRIS STEM PITTING-ASSOCIATED VIRUS TRIPLE GENE BLOCK PROTEINS

POTENTIAL COMPLEMENTATION OF POTATO VIRUS X MOVEMENT WITH GRAPEVINE RUPESTRIS STEM PITTINGASSOCIATED VIRUS TRIPLE GENE BLOCK PROTEINS Krin Mann Advisor: University of Guelph, 2011 Dr. Baozhong Meng Committee: Dr. Peter Krell Dr. George van der Merwe A movement protein Potato virus X (PVX) chimera virus (PVX.GFP(CH3)) bearing the grapevine virus Grapevine rupestris stem pitting-associated virus (GRSPaV) triple gene block proteins (TGB) (denoted P1, P2 and P3) instead of the PVX TGB was delivered into N. benthamiana and other related species by agro-inoculation. This movement protein PVX chimera virus was found to be unable to support the local and systemic movement of PVX in cis. Local and systemic movement of this PVX chimera virus was restored in trans by the dianthovirus Red clover necrotic mosaic virus (RCNMV) movement protein and by a PVX TGB rescue virus that replaced the GRSPaV TGB with the PVX TGB (PVX.GFP(Rescue)). However, a PVX TGB hybrid chimera virus (PVX.GFP(HY2)) containing PVX P1 and the GRSPaV TGB had limited cell-to-cell, but not systemic, movement.
Mesovoid shallow substratum as a biodiversity hotspot for conservation priorities: analysis of oribatid mite (Acari: Oribatida) fauna

The mesovoid shallow substratum (MSS) is a unique habitat that shelters and serves as a microrefuge for epigean, endogean and hypogean invertebrate species. Understanding the MSS community′s spatio-temporal structure and species diversity patterns in relation to the environmental parameters plays a crucial role in conservation. In this study we investigated: i) the diversity and community structure of oribatid mites from edaphic habitat, superficial MSS (i.e., the upper layer of MSS) and deep MSS (i.e., lower layer of MSS) in an alpine region of Southern Carpathians, Romania, and ii) the relationships between the oribatid mite communities and the environmental variables, such as temperature and humidity. The composition and the structure of oribatid communities differed along the three habitats indicating possible habitat specialization. The structure of the oribatid community was influenced by temperature and humidity. The rich and mixed oribatid communities in the MSS and the oribatid communities\' response to surface and subsurface environmental variables suggest that the MSS may offer a micro-refuge for edaphic species when the conditions in the surface habitats become too harsh. Thus, we suggest that MSS should be prioritized for conservation because it may be the key component in maintaining biodiversity.
GPRIN1 modulates neuronal signal transduction and affects mouse-learning behavior

In the adult and developing brain, G protein-regulated inducer of neurite outgrowth 1 (GPRIN1) is a downstream effector for Gαo/i/z proteins that promotes neurite outgrowth. However, so far, the physiological role of GPRIN1 in brain health has not been reported. We generated a viable GPRIN1 whole-body knockout mouse to assess its physiological role in synaptic function both ex vivo and in vivo. In adult neurons, GPRIN1 is highly localized to the plasma membrane and synapses where it regulates neuronal signal transduction and Ca2+ homeostasis. Our results reveal that GPRIN1 might be a novel protein involved in agonist-stimulated cytoskeletal reorganization, which is crucial for early neuronal network development and in functionally mature neurons. Finally, we show that loss of GPRIN1 leads to a learning deficit in vivo and sensitizes neurons to stress, suggesting a modulatory role in brain health and disease.
Impact of Adding Chia Seeds (Salvia hispanica) on the Quality Properties of Camel Burger “Camburger” during Cold Storage

Although fat is an important component in meat products, the demand for low fat meat products formulated with healthier lipid sources has greatly increased since high fat intake, especially saturated fats, is associated with obesity, cardiovascular and chronic diseases (AHA, 1996). Since fat contributes texture and flavor to meat products, reducing fat content in formulation may alter product quality; products with less fat content is firmer, more rubbery, less juicy, darker in color and more costly (Keeton, 1994). In order to conquer these problems, fat replacers are candidates to improve the texture and sensorial properties of low-fat meat products. Incorporation of some ingredients into foods such as flax seed and chia seed, as well as in oils rich in unsaturated fatty acids could be used as fat replacer.
Marked differences in seed dormancy in two populations of the Mediterranean shrub, Cistus albidus L.

Background: Population structure and dynamics in natural ecosystems can be affected by seed viability and dormancy. However, how the endogenous contents of phytohormones and vitamin E in seeds relative to the environment affect viability and dormancy is not yet fully understood. Aims: We studied seed viability and germination capacity in two populations of the Mediterranean shrub, Cistus albidus, exposed to contrasting environmental conditions. Methods: We measured seed viability and germination capacity and endogenous contents of abscisic acid (ABA), gibberellins and vitamin E in seeds collected from two populations, in two environmentally contrasting environments in north-eastern Spain. Results: Plants growing in the natural site produced seeds with lower germination percentage but similar viability, indicating higher seed dormancy. Enhanced seed dormancy was paralleled with higher contents of ABA and lower contents of gibberellins (GAs). Contents of tocopherols and tocotrienols were higher in seeds of the natural population. Tocopherol contents in seeds correlated positively with the ratio living:total aerial biomass. Conclusions: Two Mediterranean populations of C. albidus growing in two sites with contrasting environmental conditions showed marked differences in seed dormancy and germination, which may be explained, at least in part, by differences in seed hormonal contents.
Incubation Routine of Saunders's Tern Sternula Saundersi in a Harsh Environment

Saunders's Tern (Sternula saundersi) is a small ground-nesting seabird which breeds in the coasts and islands of Africa and Asia bordering the northern Indian Ocean. Despite having a wide distribution, little information is available on the breeding biology of this species. This study was carried out on Farasan Islands, Saudi Arabia, to document some aspects of the breeding biology of this species using a small trail camera. Such camera systems can reveal the incubation routine of this species in such a harsh environment. The midday ground temperature in March may reach up to 50 °C, while the midnight ground temperature may only reach 20 °C, thus leaving the eggs unattended even for few minutes, especially during the hottest and coldest parts of the day, may cause nest failure. This huge variation in ground temperatures between day and night gave us an excellent opportunity to test the behavioural mechanism used by the parents for maintaining the optimal egg temperature so as to protect their eggs. We found that nest attendance increases when the temperatures deviated from the optimal egg temperature, and nests were incubated for more than 90% of the time during the hottest and coldest parts of the day to prevent eggs from harmful temperatures.
Vegetation and soil seed bank in a 23-year grazing exclusion chronosequence in a Mediterranean dry grassland

Abstract Long-term grazing shaped plant diversity in dry Mediterranean grasslands. Abandonment of grazing affects plant diversity especially in the northern Mediterranean. Considerable efforts are, therefore, under way for grassland conservation and restoration. Yet, we do not know at which temporal scales impacts of grazing abandonment appear and in particular how soil seed banks evolve after longer grazing abandonment. Here, we provide detailed data from one of the very few long-term experiments available. These experiments provide data for up to 23 years (1982–2005) of grazing exclusion built in 1982, 1989, 2000 and 2001. Grazing exclusion decreased species richness, modified vegetation structure and changed soil parameters. Decline in species richness appears in communities that experienced 16 and 23 years of grazing exclusion. Only four to nine plant species of this Mediterranean grassland built persistent soil seed banks appearing after grazing exclusion, compared to 40–50 species in the established vegetation of grazed plots. Hence, similarity between vegetation and soil seed bank decreased with time of grazing exclusion. Even 23 years after abandonment, no woody plants colonised the experiments. We conclude that vegetation will recover fast from grazing abandonment in the short-term. Nevertheless, longer abandonment will impact diversity due to reduced soil seed banks.
Achene micromorphology of 26 Crepis L. (Asteraceae) taxa from Turkey with notes on its systematic and ecological significance

Abstract In this study, achene surface sculpturing and pappus ultrastructure of 26 Crepis taxa from Turkey were investigated using scanning electron microscopy (SEM). The achene microcharacters in the studied taxa were described here for the first time. Considerable differences in the shape of the epidermal cells and the ornamentation type of the outer cell wall have been found at interspecific levels. The differences in the achene surface sculpturing are also associated with achene dimorphism and habitat in some taxa. There are remarkable differences in the shape of the epidermal cells on the ribs of the achene among some clades within Crepis. The pappus ultrastructure is similar in all the taxa and is composed of spiky cells. Statistically significant difference has been found in the diameter of the pappus bristles among the taxa. It is concluded that achene micromorphology is useful for delimitation of the Crepis taxa. The microsculpture patterns on the ribs of the achene can also be used as a marker among major phylogenetic lineages as well as between closely related species. Additionally, the achene surface sculpturing could play an important role in the colonization of new habitats as well as in the adaptation to higher altitudes.
Cercariae (Digenea: Strigeidae, Diplostomidae) in Biomphalaria straminea (Planorbidae) from a rice field in Northeastern Argentina

The rice fields can provide habitats for many species of aquatic invertebrates, as insects, molluscs, crustaceans; and vertebrates, as fish, amphibians, reptiles and birds, which may act as hosts in the life cycles of digenean parasites. In this context, the goal of the present study was to describe the cercariae found in Biomphalaria straminea from a rice field in Northeastern Argentina. This freshwater snail inhabits a wide variety of environments, favoring shallow, temporary and standing or slow-flowing freshwater bodies. For this study, snails were collected from the cultivated parcels and irrigated channels during the flooding periods (from the time of sowing to soon after harvesting of the rice) between December 2010 and May 2011 and December 2011 and April 2012, in a rice field from Corrientes province, one of the main rice producers of Argentina. A total of 5 510 snails were examined of which 26 were infected with three different larval trematodes belonging to Strigeidae, Furcocercaria V (0.40 %) and Furcocercaria XX (0.04 %), and Diplostomidae, Furcocercaria XIX (0.04 %). Furcocercaria XX and Furcocercaria XIX were present in one rice cultivation cycle, while Furcocercaria V was present in both rice cultivation cycles. The prevalence of the different furcocercariae was somewhat higher in the second rice cultivation cycle. The cercariae described are new records for Argentina that added to 53 cercariae previously reported for Biomphalaria spp. in different aquatic environments of country. The study of the digenean larval in rice fields is important because contribute to the knowledge of the biodiversity of these environments.
CGG Repeat RNAs Regulate Granule Translation

CGG repeats in the 5’UTR of Fragile X Mental Retardation 1 (FMR1) RNA mediate RNA localization and translation in granules. Large expansions of CGG repeats (> 200 repeats) in FMR1, referred to as full mutations, are associated with fragile X syndrome (FXS). Smaller expansions (55-200 repeats), referred to as premutations, are associated with fragile X tremor ataxia syndrome (FXTAS) and fragile X primary ovarian insufficiency (FXPOI). TMPyP4 is a porphyrin ring compound that destabilizes CGG repeat RNA secondary structure. Here we show that exogenous CGG repeat RNA by itself, lacking the FMRP ORF, microinjected into hippocampal neurons is localized in RNA granules and inhibits translation of ARC RNA, which is localized in the same granules. TMPyP4 rescues translation of ARC RNA in granules. We also show that in human premutation fibroblasts with endogenous CGG repeat expansions in the FMR1 gene, translation of ARC RNA is inhibited and calcium homeostasis is disrupted and both phenotypes are rescued by TMPyP4. Inhibition of granule RNA translation by expanded CGG repeats and rescue of granule RNA translation by TMPy4, represent potential pathogenic mechanism and therapeutic strategy, respectively, for FXTAS and FXPOI.
CUT FLOWER PRODUCTION OF LILY BULBS GROWN IN DIFFERENT SITES IN ARGENTINA - A COMPARATIVE APPROACH

Fil: Facchinetti, Cecilia. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Bahia Blanca. Centro de Recursos Naturales Renovables de la Zona Semiarida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiarida; Argentina
Saccharomyces cerevisiae histone Chaperones FACT and Spt6 modulate Pol II and histone occupancy genome-wide

Histone chaperones, chromatin remodelers, and histone modifying complexes play a critical role in alleviating the nucleosomal barrier. Here, we have examined the role of two highly conserved yeast (Saccharomyces cerevisiae) histone chaperones, FACT and Spt6, in regulating transcription and histone occupancy. We show that the H3 tail contributes to the recruitment of FACT to coding sequences in a manner dependent on acetylation. We found that deleting a H3 HAT Gcn5 or mutating lysines on the H3 tail impairs FACT recruitment at ADH1 and ARG1 genes. However, deleting the H4 tail or mutating the H4 lysines failed to dampen FACT occupancy in coding regions. Additionally, we show that FACT-depletion greatly reduces Pol II occupancy in the 5’ ends genome-wide. By contrast, Spt6-depletion led to reduction in Pol II occupancy towards the 3’ end, in a manner dependent on the gene-length. Severe transcription and histone eviction defects were also observed in a strain that was impaired for Spt6 recruitment (spt6Δ202) and depleted of FACT. Importantly, the severity of the defect strongly correlated with WT Pol II occupancies at these genes, indicating critical roles of Spt6 and Spt16 in promoting high-level transcription. Collectively, our study shows cooperation, as well as redundancy between chaperones, FACT and Spt6, in regulating transcription and chromatin in coding regions of transcribed genes.
Production and persistence of bacterial and labile organic matter at the hypoxic water–sediment interface of the St. Lawrence Estuary

Amino acid (AA) l‐ and d‐enantiomers were quantified in whole seawater samples from the Lower St. Lawrence Estuary (LSLE) and the Gulf of St. Lawrence (GSL). The bottom waters of the LSLE display a recent decrease in dissolved O2 concentrations. Concentrations of AA, including bacterial d‐enantiomers of AA (d‐AA), generally decreased with depth, but sharply increased in the nepheloid layer of the LSLE (not in GSL) with values slightly exceeding those measured in surface waters. The organic matter (OM) in this nepheloid layer was also enriched in AA and d‐AA. Although the particles of the nepheloid layer contributed to less than 13% of total organic carbon (TOC) their contributions to total AA and AA concentration increase were estimated to be almost as important as the dissolved phase. Estimates indicated that bacterial OM represented 67.1–79.4% of TOC in the nepheloid layer of the LSLE, but 18.5–56.9% in the other analyzed waters. All the diagenetic indicators confirmed that the OM just above the sediment in the LSLE was on average less altered than in the rest of the water column or in the GSL. This study suggests that bacteria recycle relatively altered OM into biomass and bacterial dissolved OM near the water–sediment interface in the LSLE. The presence of heterogeneous OM and hypoxic conditions likely reduce OM degradation rate and thus allow for the accumulation of labile OM. Unfavorable conditions for OM degradation might be present in many areas and represent a negative feedback limiting O2 consumption and CO2 production.
PLANTS VISITED BY Apis mellifera L. (HYMENOPTERA: APIDAE) IN RECÔNCAVO BAIANO, STATE OF BAHIA, BRAZIL

The objective of this study was to identify the plants visited by Apis mellifera L. (Hymenoptera: Apidae) in the region of Reconcavo Baiano, State of Bahia, Brazil. Flowering plants were assessed in a radius of 1.500 m around the apiaries visited. A total of 240 species belonging to 171 genera and 50 families were recorded. The family Leguminosae had the highest species richness (22%), followed by Asteraceae (14%) and Malvaceae (7%) of all plant species visited by Apis mellifera . The highest percentage of plants collected had herbaceous growth habit (44%), followed by woody plants (26%) and shrubs (18%). Lianas, vines and palm trees were significantly less represented. It was found that 65% of species had actinomorphic flowers and 33% had zygomorphic flowers. The genera that showed higher diversity were Sida with nine species, Croton with six species, Senna with five species, while Chamaecrista , Eucalyptus, Eupatorium, Ocimum, Passiflora and Vernonia were represented by four species each. The flora of apicultural interest in the region of Reconcavo Baiano has a wide range of species with varying growth habits.
Maternal oxidative stress and reproduction: Testing the constraint, cost and shielding hypotheses in a wild mammal

Oxidative stress has been proposed as a central causal mechanism underlying the life‐history trade‐off between current and future reproduction and survival in wild animals. While mixed evidence suggests that maternal oxidative stress may act both as a constraint and a cost to reproduction, some studies have reported a lack of association between reproduction and maternal oxidative stress. The oxidative shielding hypothesis offers an alternative explanation, suggesting that mothers may pre‐emptively mitigate the oxidative costs of reproduction by increasing antioxidant defences prior to reproduction. We tested the oxidative constraint, cost and shielding hypotheses using a longitudinal field study of oxidative stress levels in a species that breeds using daily energy income, the Columbian ground squirrel (Urocitellus columbianus). Elevated maternal oxidative damage prior to reproduction was associated with higher maternal investment in litter mass at birth, but not at weaning. Breeding females increased their antioxidant capacity and decreased their oxidative damage from birth to lactation, compared to non‐breeding females measured at the same time periods. However, lower maternal oxidative stress during lactation was not associated with higher offspring survival or mass growth over this period. Our results provide little evidence for maternal oxidative stress acting as a constraint on, or cost to, reproduction in Columbian ground squirrels, but partially support the idea that oxidative shielding occurred to buffer potential oxidative costs of reproduction.