Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Temporal Cladoceran Community Responses to Environmental Change and Anthropogenic Impacts in Southwestern Québec

ABSTRACT A high-resolution sediment record from Lac Brûlé, southwestern Québec, was studied to determine the effects of long-term climate change and anthropogenic impacts on cladoceran assemblages of the late Holocene. Temporal shifts in cladoceran communities were closely associated with known century-scale climatic episodes, namely the Medieval Warm Period (750–1250 CE), the Little Ice Age (1450–1850 CE) and the twentieth-century warming. Forward selection indicated the importance of catchment variables and aquatic primary production in governing cladoceran communities. This suggests that higher trophic levels in Lac Brûlé were responsive to changes in the physical and chemical properties of the lake, perhaps as an indirect consequence of climatic change. The exploitation of the Wallingford-Back Mine in the immediate watershed of Lac Brûlé from 1924 to 1972 CE also had notable impacts on cladoceran assemblages. To strengthen interpretations of the Lac Brûlé record, relationships between cladoceran assemblages and limnological variables were studied in surface samples from 31 lakes from the surrounding region. This spatial analysis identified nutrients (phosphorus and nitrogen) and pH as the most influential variables driving changes in present-day cladoceran communities. However, the performance of cladocera-based inference models was insufficient to quantitatively reconstruct variables in the down-core analysis of Lac Brûlé.
Chemical characterisation of low molecular weight phenolic compounds from the forage legume sainfoin ( Onobrychis viciifolia )

Bioactive compounds of sainfoin ( Onobrychis viciifolia ) are assumed to be responsible for its multiple benefits. A wide range of phenolic compounds were investigated for the first time in sainfoin. Among these were eight new acylated flavonols which comprised either feruloylated or sinapoylated derivatives of 3-O-di- and 3-O-triglycosides of kaempferol or quercetin. A high performance liquid chromatography method was optimized to investigate complex phenolic mixtures and was validated for the analysis of an sainfoin extract.
Effects of glucose and acetate infusion on milk protein yield and related gene expression in muscle and mammary glands of lactating dairy cows

EFFECTS OF GLUCOSE AND ACETATE INFUSION ON MILK PROTEIN YIELD AND RELATED GENE EXPRESSION IN MUSCLE AND MAMMARY GLANDS OF LACTATING DAIRY COWS Boning Li Advisor: University of Guelph, 2017 Professor John P. Cant The objective of this study was to explore hypotheses of the mechanism by which NEL stimulates MPY in cows and to determine if glucogenic and lipogenic substrates stimulate MPY by similar mechanisms. Five rumen-fistulated Holstein cows were randomly assigned to a 5 x 5 Latin square design. Treatments were CTL, LoG, HiG, LoA and HiA. Glucose infusion for 5 to 7 d tended to increase milk and protein yields and increased lactose yield. Milk yield, protein yield and lactose yield decreased during acetate infusion. Glucose infusion affected expression of mammary genes related to cell proliferation, differentiation and protein accretion capacity while supplement acetate affected expression of milk protein genes, and those related to protein accretion capacity and cell differentiation.
The Osteology of the Giant Snake Gigantophis garstini from the Upper Eocene of North Africa and Its Bearing on the Phylogenetic Relationships and Biogeography of Madtsoiidae

ABSTRACT Madtsoiidae is a speciose family of extinct snakes that achieved a wide Gondwanan and trans-Tethyan distribution by the Late Cretaceous, surviving until the late Pleistocene. Gigantophis garstini, the first and largest described madtsoiid, was recovered from the upper Eocene of Fayum, Egypt. The 20 vertebrae that constitute the syntype have only received brief description, hindering the referral of specimens to this taxon and our understanding of madtsoiid interrelationships in general. A detailed redescription of the syntype material demonstrates the validity of Gigantophis, based on two autapomorphies (including a strongly depressed neural canal in posterior trunk vertebrae) and a unique combination of characters. Referred material from the lower Paleocene of Pakistan differs significantly, and we restrict Gigantophis to the middle—late Eocene of North Africa. Using a model of morphological variation in extant snakes, we estimate that Gigantophis was 6.9 ±0.3 m long. A phylogenetic analysis using the largest sample of putative madtsoiids (20 operational taxonomic units) and a revised and augmented matrix (148 characters) places Gigantophis as sister taxon to the latest Cretaceous Indian snake Madtsoia pisdurensis. Whereas our topology might suggest that a dispersal route was present between India and North Africa in the latest Cretaceous—early Paleogene, an evaluation of putative dispersal routes leads us to conclude that the paleobiogeography of Madtsoiidae is best explained by a poorly sampled, earlier widespread distribution in Africa, Indo-Madagascar, and South America. In contrast, latest Cretaceous madtsoiid occurrences in Europe might be explicable by trans-Tethyan dispersal from Africa across the Apulian Route.
Isolation and Structure Determination of New Antibacterial Peptide Curacomycin Based on Genome Mining

A new antibacterial cyclic peptide, named curacomycin (1), and its analogue dechlorocuracomycin (2) were isolated from Streptomyces curacoi (NBRC 12761T) and Streptomyces noursei (NBRC 15452T), respectively, by using genome mining. The chemical structures of these two peptides were determined by using a combination of MS (ESI) and NMR spectroscopy. The structure of compound 1 was determined to be a cyclic peptide that consisted of six amino acids, including: valine (Val), leucine (Leu), isoleucine (Ile), ornithine (Orn), β-hydroxyasparagine (OHAsn), and 5-chlorotryptophan (ClTrp). The NMR data of compound 2 were very similar to that of compound 1, which indicated that the structure of compound 2 was a dechlorinated analogue of compound 1. A comparison of the antimicrobial activities of these two peptides indicated that the presence of chlorine in compound 1 was critical for its antimicrobial activity. The proposed biosynthetic gene clusters for compounds 1 and 2 were found in the genome data of S. curacoi and S. noursei, respectively. The functions of the biosynthetic genes were considered by comparison of the two gene clusters.
Overyielding in young tree plantations is driven by local complementarity and selection effects related to shade tolerance

Overyielding in mixed‐species forests has been demonstrated in a vast body of literature, and the focus of functional biodiversity research is now shifting towards a mechanistic understanding of these observations. We explored diversity–productivity relationships at two sites of a large‐scale tree diversity experiment, with harsh (Ged) and benign (Zed) environmental conditions for plantation establishment. Additive partitioning methodologies were adopted to detect phenomenological patterns in the productivity data, and the trait structure of mixed communities was used to advance insights into compositional effects. After 6 years of plantation development, biomass productivity was significantly higher in mixtures compared to the monocultures of component species. We observed that processes operated through direct tree–tree interactions, as the diversity signal disappeared where trees in mixed stands were surrounded by conspecific neighbours only. This result is particularly relevant for mixed‐species plantation systems, as trees are commonly planted in monospecific patches to simplify management. Partitioning unveiled strong selection effects at both plantation sites. However, at the harsh Ged‐site this was caused by competitive dominance of species with fast young growth, whereas at the benign Zed‐site, species with slow young growth improved their performances but not at the expense of others (i.e. trait‐dependent complementarity). Species tolerance to shading is an influential trait for predicting biodiversity effects, with community‐weighted means in shade tolerance mediating dominance effects (Ged) and functional diversity in shade tolerance mediating (trait‐dependent) complementarity effects (Zed). Synthesis. This study highlights that biodiversity effects in young tree plantations could be explained by the functional composition of mixed communities, with a key role for species levels of shade tolerance. As contrasting results between plantation sites were observed, future research should target the context‐dependency of diversity–productivity relationships.
Occurrence of puffer fishes (Tetraodontidae) in the eastern Mediterranean, Egyptian coast - filling in the gap.

The occurrence of puffer fish species along the Egyptian Mediterranean coast was evaluated using samples obtained from the commercial fishing operations during 2012 – 2015. Six species were identified: Lagocephalus sceleratus (Gmelin, 1789), Lagocephalus suezensis Clark and Gohar, 1953, Lagocephalus guentheri Miranda Ribeiro, 1915, Lagocephalus lagocephalus (Linnaeus, 1758), Torquigener flavimaculosus Hardy & Randall, 1983 and Sphoeroides pachygaster (Müller & Troschel, 1848). Of these, L. guentheri, L. suezensis, S. pachygaster and T. flavimaculosus were recorded for first time in the Egyptian Mediterranean waters. Pufferfishes were captured from sandy, rocky and muddy-bottom habitats from shallow waters to more than 150 m deep. The presence of different tropical puffer fish species in the Egyptian Mediterranean waters reflects the ongoing Lessepsian migration and expansion of its distributions, particularly for L. sceleratus which was the common distributed one along the coast. This study filled in a major the gap in records of species’ distributions and is further evidence of the changing of biodiversity in the Mediterranean Sea, which may affect the ecosystem and the commercial fisheries. The results emphasize the need for a continuous, directed, monitoring and management plan for the detection and abundance monitoring of alien species.
Local and regional drivers of the African coffee white stem borer (Monochamus leuconotus) in Uganda

The African coffee white stem borer (CWSB) Monochamus leuconotus is a destructive pest of Arabica coffee in Africa. Documentation on outbreaks, spatiotemporal development and the relationship with different environmental conditions and coffee production system is limited. To underpin effective control measures, we studied aspects of local and regional pest drivers in Eastern Uganda. At the local scale, we (i) characterized the temporal development of CWSB and explored associations with environmental and shade‐related indicators. During two growing seasons and on 84 coffee plots, we recorded CWSB incidence/infestation and microclimate on an altitudinal gradient and different shading systems. The bimodal rainfall, altitude and shade affected CWSB development through their effect on minimum temperature. At the landscape level, we (ii) analyzed the spatial pattern of CWSB. Data on CWSB were collected on 180 plots. Pest incidence showed a spatial arrangement varying by districts. A possible relationship with human movement and the landscape context contributing to pest spread is suggested. CWSB control measures should be synchronized with the bimodal rainfall patterns and an emphasis should be given to identifying and limiting pathways of pest spread from highly infested to new areas.
(Peer Review) Structural Characteristics of Chitin and Chitosan Isolated from the Biomass of Cultivated Rotifer, Brachionus rotundiformis.

We characterized the molecular structure of chitin and chitosan isolated from the biomass of cultivated rotifer (B. rotundiformis). Chitin and chitosan are potential biomaterials for biotechnological industries due to their structural and functional characteristics. Zooplankton seems to be a better source of chitin, associated with the very low degree of calcification and sclerotization of the cuticles. Cultivation of local strain rotifer from North Sulawesi waters has been successfully conducted in a very simple medium with raw fish input without aeration in fiber tanks. This mass production technology has enabled to harvest 45-48 million individuals with estimated 5 to 48 g rotifer biomass in each production cycle. From this rotifer biomass, 4.6% chitin was extracted and 52.7% chitosan could be derived by deacetylation of chitin. Structural characteristics of the rotifer chitin and chitosan were discussed on the basis of the X-ray and infrared analysis data. X-ray analysis was done using X-Ray Defraction (XRD) with CuK radiation at a voltage of 40 kV and 30 m A. X-ray diffraction diagram of chitin indicated the molecular form at three strongest peaks, 8.1, 9.2 and 19 2θ, differed from that of chitosan at peaks, 9.6, 19.5 and 21.1. Christalinity of chitosan (47.06%), was higher than that of chitin (33.94%). Molecular structure of chitin, C18H26N2O10, where the hydroxyl group on the second carbon replaced by acetyl amide, was shown by the infrared spectra. In the infrared spectra, the rotifer chitin indicated the amide II band at 1558.48 cm, a typical one for marine chitin. A marked difference was observed for the amide I bands, at 1651.07 cm. Chitosan showed no amide band, but hydroxyl and amino bands at the ranged spectra up to 3500 cm. The yields of chitin isolated from rotifer biomass and its deacetylated products (chitosan) were relatively small and as a polymer of N-acetyl D-glucosamine, both molecules showed difference in specific functional groups. Chitin is composed of 2-acetamido-2-deoxy-D-glucose, while chitosan composed primarily of glucosamine, 2-amino-2-deoxy-D-glucose. Some treatments are necessary to confirm the molecular conformation and deacetylation behavior. Chitosan could be more accessible for structural modifications to develop biocompatible materials for pharmaceutical purposes.
Synergistic effect of spinosad with selected botanical powders as biorational insecticides against adults of Tribolium castaneum Herbst, 1797 (Coleoptera: Tenebrionidae)

The synergistic effect of spinosad with three botanical (Aframomum melegueta, Eugenia aromatica and Piper guineense) powders as biorational insecticides against Tribolium castaneum Herbst (Coleoptera: Tenebrionidae) infesting melon (Citrullus lanatus) seeds was investigated. Treatments included sole application of each botanical powder (50 g/kg of melon seed), sole application of spinosad (SASp) (1.0 g/kg), mixture of spinosad (0.5 g/kg) + botanical powders (25 g/kg) and an untreated control. Data were collected on tenebronid mortality rate (%) (PM) and melon seed weight loss rate in % (PWL). Phytochemical analysis of the botanicals was also carried out. At 3-14 days after treatment (DAT), PM observed in melon seeds treated with SASp (90.00-100.00%) was not significantly (p>0.05) different from PM observed in melon seeds treated with spinosad + E. aromatica powder (86.67-100.00%) and spinosad + P. guineense powder (85.00-100.00%). PWL observed in melon seeds treated with spinosad + botanical powders (1.17-1.40%) was not significantly different from PWL observed in seeds treated with SASp (0.42%), but it was significantly lower than PWL (3.28%) observed in melon seeds treated with sole application of A. melegueta powder. P. guineense powder had the highest contents of alkaloids (868.33 mg/100 g), tannins (550.00 mg/100 g), phenolics (53.57 GAE/g), and steroids (740.00 mg/100 g). E. aromatica powder had the highest contents of flavonoids (1466.67 mg/100 g), terpenoids (1276.00 mg/100 g) and cardiac glycosides (7.33 mg/100 g), while A. melegueta powder had the highest content of saponins (376.67 mg/100 g). The combination of spinosad with P. guineense powder or E. aromatica powder performed better than the combination with A. melegueta powder and is therefore recommended as a biorational approach for the control of T. castaneum.
Effect of biofertilizers and micronutrients on growth, leaf yield and quality of coriander (Coriandrum sativum L.) cv. Sadhana

A field experiment was conducted during rabi 2015-16 at Research Farm, College of Horticulture, Dr.Y. S.R. Horticultural University, Anantharajupeta (Andhra Pradesh), India, to study the effect of different biofertilizers and micronutrients on growth, leaf yield and quality of coriander (Coriandrum sativum L.) cv. Sadhana. The experiment was conducted in a factorial randomized block design with biofertilizers and micronutrients. The biofertilizer treatments were seed inoculation with Azospirillum, Phosphate Solubilising Bacteria (PSB), Azospirillum + Phosphate Solubilising Bacteria (PSB) and control (without any biofertilizer), while the micronutrient treatments comprised of foliar sprays of Zinc sulphate, Copper sulphate, Ferrous sulphate each at @ 0.5% and control (without any micronutrient). The sixteen treatment combinations were replicated thrice. Among the treatments, seed inoculation with Azospirillum + PSB+ foliar spray of zinc sulphate @ 0.5% recorded maximum plant height, number of primary branches, leaf area, fresh leaf yield per plant, leaf yield per plot, leaf yield per hectare, dry matter production, protein content, ascorbic acid content and moisture content. While, the lowest days to germination and leaf chlorophyll contents were recorded with the seed inoculation of Azospirillum + PSB + foliar spray of ferrous sulphate @ 0.5%.
Intercropping patterns and different farming systems affect the yield and yield components of safflower and bitter vetch

ABSTRACT This factorial field experiment was done based on a randomized complete block design in Urmia University, Iran, in 2013 and was repeated in 2014. Treatments included two farming systems (high input and organic) and different intercropping patterns that alternated bitter vetch (Vicia ervilia L.) and safflower (Carthamus tinctorius L.) with row ratios of 2:2, 3:2, 4:2 and 5:2. Sole cropping of bitter vetch and safflower was used as the control. In both years, the 2:2 intercropping pattern had biomass yield advantages compared to sole cropping and the other intercropping ratios, based on greater land equivalent ratio values. Safflower had higher relative crowding coefﬁcients, competitive ratio (CR) and aggressivity (A) values than bitter vetch. High-input farming was more effective than the organic system in both years. Safflower was the superior competitor when grown with bitter vetch, and its productivity dominated the total biomass yields. Thus, intercropping of safflower with bitter vetch has the potential to improve performance with high land-use efficiency.
Do stem cells transfected with CXCR4 enhance bone formation in osteoporosis

Osteoporosis affects bone mass and bone micro-architecture, reducing mechanical strength. SDF-1 and its ligand CXCR4 play significant roles in the migration and engraftment of mesenchymal stem cells (MSCs). The aim of this study was to investigate the effects of CXCR4 transfected MSCs on bone formation in osteopenic rats. The hypothesis was that MSCs genetically modified to over-express CXCR4, would enhance migration of stem cells from osteopenic rats and when injected intravenously in ovariectomised (OVX) rats, would improve bone formation. MSCs were harvested from femora of young, OVX and adult control rats. The differentiation, CXCR4 expression, in vitro migration and phenotypic characteristics of the cells were compared. Although the phenotypic characteristics of cells from all groups of rats were the same, their differentiation capability, CXCR4 expression and migration was significantly different. MSCs were genetically modified to over-express CXCR4 and in vitro migration investigated. It was found that although young MSCs had the highest migration capability (2x more than their uninfected counterparts, p=0.006), the OVX MSCs when transfected with CXCR4 had the most significant migration from their un-transfected counterpart cells(5x more, p=0.025). Additionally, differentiating MSCs to osteoblasts reduced their CXCR4 expression as well as their migration towards SDF1. The CXCR4 transfected MSCs were administered intravenously in OVX rats. Fluorescent labelled cells were tracked after 1 week and were located in the blood vessels of the femur. 11-weeks post-injection, OVX rats injected with young-CXCR4 MSCs had significantly higher BMD(694.0±80.1mg/cm3) (p<0.05) in comparison to rats injected with saline. Rats injected with OVX-CXCR4 MSCs(645.4±79.3mg/ccm) had a higher BMD in comparison to those injected with OVX MSCs(631.4±69.5mg/ccm) and saline(563.4±82.9mg/ccm). The L4 vertebral stiffness was also higher in rats treated with young-CXCR4 MSCs in comparison to those treated with saline. CXCR4 genetically modified MSCs from young and OVX patients may help in boosting bone formation in osteoporosis.
Fourier Landscape Pattern Indices for Predicting South Carolina Watershed Fecal Coliform

Abstract Extending the Landscape Pattern Metric (LPM) model analysis in Smith et al. (2001) into a LPM decision model, decadal scale prediction of fecal coliform compromised South Carolina watersheds is developed. The model’s parameter variability identifies the greatest contributors to a compromised watershed’s prediction. The complete set of model parameters include Land Cover Land Use (LCLU) & slope, along stream proportion, Fourier Metric of Fragmentation (FMF), Fourier Metric of Proportion (FMP), and Least Squares Fourier Transform Fractal Dimension (LsFT). The 1992 National Land Cover Data (NLCD) Land Cover Land Use (LCLU) within fecal coliform compromised watersheds is used to train the model parameters, and the 2001 NLCD LCLU is used to test the LPM model. The most significant model parameters are along stream bare rock LsFT, FMF between urban/recreational grasses and evergreen forests, and FMF between deciduous forests and high density residential areas. These metrics contribute significantly more than the best proportion descriptor: proportion of urban/recreational grasses. In training, the proposed model correctly identified 92 % of the compromised watersheds; while the Smith et al. (2001) model 94 % of the compromised watersheds were correctly identified. This study reveals the ability of Fourier metrics to interpret ecological processes, and the need for more appropriate landscape level models.