Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of extensive positive selection acting on cherry (Prunus avium L.) resistance gene analogs (RGAs)

The cherry tree (Prunus avium L.), is an important tree species which is intensively plagued by many phytopathogenic fungal species. Resistance gene analogs (RGAs) are the largest class of resistance (R) genes and are pivotal components at breeding projects, serving as useful functional markers linked to R genes. In order to assess the evolutionary pressures acting upon P. avium RGAs candidates, their 173 homologues that have previously been deposited in GenBank were mined. Their proteins were clustered according to their blast(p) similarities in 12 MCL (Markov Cluster Algorithm) tribes, resulting in unique and well supported paralogous gene groups (PGGs). The extent to which these genes exhibit evidence of adaptive, positive selective pressures, which are causing excessive fixation of non-synonymous mutations, was determined using a series of maximum likelihood analyses using the PAML package. The results postulate existence of robust evidence of positive selection, acting in almost all of the clustered PGGs across their phylogenies. Furthermore, analyses revealed that the majority of the positively selected amino acid residues sites are localized widely across these RGAs sequences. We speculate that the clustered distribution of these RGAs might also be pronounced of high birth and death genes rates with diversifying episodes acting on their NB-ARC domains, putatively affecting their ligandbinding specificities. Such evolutionary insights shed light on how these NBS-encoding RGAs in P. avium are being evolved, assigning them as the foremost surveillance mechanism against rapidly evolving fungal pathogens, and providing breeders with effective tools for fast-tracking the development of varieties with more durable resistance.
Phytoremediation of petroleum-contaminated soils in the tropics: Pre-selection of plant species from eastern Venezuela

Phytoremediation, i.e. the use of plants to recover contaminated soils, is a non-destructive and cost-effective in situ technology. In the case of oil contamination, it is based on the stimulation of petroleum hydrocarbon-degrading microorganisms in the rhizosphere. Investigations about this technology in the tropics are scarce. Before starting time and cost-intensive greenhouse studies, a pre-selection of suitable native plants is indicated. In our work we present an approach to effectively pre-select species for the development and application of phytoremediation of petroleum-contaminated soils. In the eastern savannahs of Venezuela, plant species found on contaminated sites and therefore obviously tolerant of oil pollution were assessed regarding characteristics considered beneficial for their use in phytoremediation, like ease of propagation and favorable root system characteristics. Fifty-seven native or naturalized species, comprising 18 legumes, 19 grasses, 3 sedges and 17 other herbaceous species were found to occur on contaminated sites. Almost forty percent were found on more than one site. The legumes proved to be the easiest group to propagate, whereas most of the wild grasses and the other herbaceous species could not be propagated successfully. The most favorable root system, i.e. deep-reaching, widely branched roots creating an extended rhizosphere, was found in some grasses and sedges. Legumes had, in general, less ramified but deeper reaching roots. The species selected for further research are some wild legumes and cultivated pasture grasses that are widely used in the tropics. Additionally, some native wild grasses and one sedge were included. The study should serve as a basis for further investigations on phytoremediation in the tropics.
Diurnal fluctuations in CO2 and dissolved oxygen concentrations do not provide a refuge from hypoxia and acidification for early-life-stage bivalves

This study assessed the effects of constant and diurnally fluctuating acidification and hypoxia on the survival, growth, and development of larval stages of 3 bivalves indigenous to the east coast of North America: bay scallops Argopecten irradians, hard clams Mercenaria mercenaria, and eastern oysters Crassostrea virginica. Bivalves were exposed to ideal (pH = ~7.9, dissolved oxygen [DO] = ~7 mg l−1), acidified (pH = ~7.2, DO = ~7 mg l−1), hypoxic (pH = ~7.9, DO = ~2 mg l−1), and acidified and hypoxic (pH = ~7.2, DO = ~2 mg l−1) conditions, as well as treatments that fluctuated between ideal conditions by day and acidified, hypoxic, or acidified and hypoxic conditions by night. Continuously acidified conditions reduced survival of larvae of all 3 species, slowed growth of larval bay scallops and eastern oysters, and delayed the development of bay scallop larvae. Continuously hypoxic conditions reduced the survival, growth, and development of larval bay scallops and slowed the development of larval hard clams. Simultaneous exposure to continuously low pH and DO yielded more negative effects than each factor independently. Diurnal exposure to low pH and/or low DO rarely altered, and never fully mitigated, the negative effects of hypoxia and/or acidification despite significantly higher mean pH and DO levels. This suggests that pH and DO fluctuations were too intense, and/or the durations of normoxic and normcapnic conditions were not long enough for bivalve larvae to overcome the physiological stress of hypoxia and acidification. Therefore, the diurnal fluctuations of pH and DO in this study did not provide a temporal refuge from hypoxia and acidification for North Atlantic bivalve larvae, suggesting that such fluctuations in an ecosystem setting can be a significant threat to these larvae. Periods of higher DO and pH within diurnal fluctuations do not provide a temporal refuge from hypoxia and acidification for larvae of bivalves such as the adult bay scallop Argopecten irradians shown here. Such fluctuations can represent a significant environmental threat at the ecosystem level. Photo: Stephanie Talmage-Forsberg OPEN ACCESS © The authors 2016. Open Access under Creative Commons by Attribution Licence. Use, distribution and reproduction are un restricted. Authors and original publication must be credited. Publisher: Inter-Research · www.int-res.com
The Effect of Environmental Conditions on the Development of Pea Seeds

The effects of environmental conditions on pea seeds developing in pods were investigated by 'growing the plants under controlled conditions in the Earhart Plant Research Laboratory. In one experiment plants were kept under a variety of conditions throughout their period of growth and of seed-pod development. In two experiments plants were grown under standard conditions until they flowered and were then transferred to a series of different environments. The environmental conditions investigated included photoperiod, light intensity, and day and night temperatures. Samples of seeds were taken at different times after flowering and seed growth was recorded by fresh weight and dry weight measurements. 'The samples were analysed for total sugar, reducing sugar, starch, total nitrogen, and protein nitrogen. The most striking results were the effects of night and day tem-peratures on the growth and composition of the seeds, particularly on the sugar content. At low temperatures, the conversion of sugar to starch was much delayed and sugar continued to increase in concentration during growth; at higher tem-peratures the sugar entering the seeds was rapidly converted to starch; thus the carbohydrate composition of seeds grown at different temperatures was markedly different. Protein synthesis was also delayed at lower temperatures. Water uptake and rate of drying out of the seeds were also affected. The possible implications and interrelations of these observations are discussed.
The Microbiology of Phane, an Edible Caterpillar of the Emperor Moth, Imbrasia belina.

The larvae of Imbrasia belina (Westwood) are cooked and sun dried to make a product known as phane, which is consumed as a delicacy. A study was conducted to determine the sanitary quality of phane and the kinds of microorganisms associated with it. It also looked into the potential for the existence of health risk associated with its consumption. Laboratory- and field-processed phane and that from open markets were subjected to microbiological analyses. The total microbial population for the larvae was in the range of 3 × 105 to 2 × 107 CFU/g. Species belonging to seven genera of bacteria and five genera of fungi were isolated from the larvae. About 50% of the identified bacteria were gram-positive, yet their combined population was much lower than that of the gram-negative bacteria. Cooking (89 to 93°C) under both sets of conditions (laboratory and field) reduced the microbial population to less than 9 × 103 CFU/g. The survivors were mostly sporeformers. Laboratory-processed phane was contaminated during drying, but none of the isolates were coliforms and the population increment was marginal. Field-processed phane, on the other hand, had a population of 4 × 104 to 1 ×108 CFU/g after 24 h of drying. The high moisture content of phane (55%) and a high degree of contamination from the soil and air appeared to have contributed to the increased population. Aspergilli including A. flavus and phycomycetes were frequently isolated from the samples. Coliforms were present in 30% and 50% of the phane processed in the field and in market phane, respectively. Escherichia coli and Klebsiella pneumoniae were found in 33% and 21%, respectively, of samples acquired from the market. The presence of K. pneumoniae . E. coli , a toxin-producing sporeformer ( Bacillus cereus ), and mycotoxin-producing fungi ( A. flavus , Penicillium sp., and Fusarium sp.) all point to the possible existence of health risks associated with its consumption.
Sugars and acids of raspberries, blackberries and other brambles

Ripe berries of six cultivars of raspberries, three of blackberries and one each of boysenberry and loganberry were analysed for sugars and acids in three crop years. It the invertase activity of bramble berries was inactivated shortly after picking to prevent transformations of sugars, then distinct contrasted differences of concentrations of sugars were found for raspberries and for blackberries. Boysenberries were close to blackberries in the sugar and acid profiles whereas loganberries had a blackberry-like sugar profile and a raspberry-like acid profile.
The Occurrence of Mesocarpic Stone Cells in the Fruit of Cultivated Highbush Blueberry

Stone cells of highbush blueberry (Vaccinium corymbosum L.) were distributed primarily toward the periphery of the fruit; they apparently differentiated from ground parenchyma shortly after anthesis. Secondary cell wall material continued to be accreted through harvest, with lamellations about 1μm in width. The lignified walls were heavily pitted, with pits contiguous with those of adjacent stone cells. The number of stone cells may be correlated positively to the length of the growth season for each cultivar.
Screening of Some Basidiomycetes for Bio-polymers and Biomass Production in Submerged Cultivation

Twenty-one species of edible and non-edible basidiomycetes were screened for bio-polymers and biomass production in submerged cultivation. All the basidiomycetes produced bio-polymers and there was variation in quantities of bio-polymers produced by the strains at different incubation times. The bio-polymers production ranged within 44 - 9,177 mg/l, 63 - 14,525 mg/l and 69 - 6,367 mg/l at days 2, 7 and 14, respectively. Coriolus versicolor produced the highest yield at day 7. The biomass production at days 2, 7 and 14 ranged within 0.12 - 0.23g dry w/l, 0.13 - 0.25g dry w/l and 0.13 - 0.30g dry w/l in which C. versicolor also had the highest yield. The highest biomass production was recorded on day 14.
Effect of Peat : Vermiculite Mixes Containing Trichoderma harzianum on Increased Growth Response of Radish

The effects of peat: vermiculite mixes on increased growth response of radish (Raphanus sativus L. ‘Early Scarlet Globe’) induced by Trichoderma harzianum Rifai (isolate T-12) were investigated. Canadian sphagnum peat and vermiculite were mixed in various ratios to form 0-100% peat mixes. Four levels of T-12 amendment were added to these mixes—0%, 2%, 5%, and 10% (v/v) or 0%, 0.1%, 1%, and 10%. In general, increasing levels of T-12 amendment induced linear increases in radish dry weights after 4 and 5 weeks. Greatest increases were seen in mixes containing 20% peat or 80% peat. The smallest increases were observed when T. harzianum was added to 0% peat or 100% peat mixes. There was no effect on the population densities of T-12 after it was introduced into the mixes. No Pythium spp. or root disease were detected in the mixes, suggesting that T. harzianum, a biological control agent, can increase plant growth independent of any detectable root pathogens.
Trypanosoma cruzi and Trypanosoma rangeli co-infection patterns in insect vectors vary across habitat types in a fragmented forest landscape

NICOLE L. GOTTDENKER*, LUIS F. CHAVES, JOSE E. CALZADA, JENNIFER K. PETERSON, ANAMARIA SANTAMARÍA, VANESSA PINEDA and AZAEL SALDAÑA Department of Veterinary Pathology, University of Georgia College of Veterinary Medicine, 501 DW Brooks Drive, Athens, Georgia 30602, USA 2 Institute of Tropical Medicine (NEKKEN), Nagasaki University, 852-8523, Sakamoto 1-12-4, Nagasaki, Japan Department of Parasitology, Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City, Panamá Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NG 08544-2016, USA
Ecology shapes metabolic and life history scalings in termites

1. Metabolic rate (B) is a fundamental property of organisms, and scales with body mass (M) as B = αMβ. There has been much debate on whether scaling parameters should be viewed as constants or variables. However, there is increasing evidence that ecological differentiation can affect both α and β.
A test of a single disk for estimation of harwood bole and branch nutrient concentrations

Etude concue pour determiner la valeur d'un procede d'echantillonnage (un seul disque par arbre) pour l'estimation des concentrations des elements mineraux dans les troncs et les branches de feuillus de peuplements mixtes etablis en terrain bas. Cette etude s'inscrit dans un projet plus vaste de constitution d'une base de donnees relatives a la biomasse, aux elements mineraux et a l'energie pour ce type de forets du sud des Etats Unis. La methode permet egalement d'etudier l'impact des procedes de recolte totale sur l'exportation d'elements mineraux
Heritability of Ease of Hazelnut Pellicle Removal

Hazelnut kernels from which the pellicle can be removed easily by dry heat are highly desirable for the international kernel market. Cultivars vary from no to complete pellicle removal after heating. Nut samples of 951 seedlings representing 62 parental combinations were roasted at 130°C for 13.5 min, rubbed, and scored for degree of pellicle removal. Narrow sense heritability, estimated by regression of progeny means on midparent values, was 48% (±10%). This moderately high heritability estimate indicates that selection of easy-to-blanch seedlings should result in rapid progress.
Influence of antioxidants addition on the oxidative stability of a mixture of sunflower and corn oils.

Oxidative stability is an important parameter in evaluation the quality of oils and fats, as it gives a good estimation of their susceptibility to oxidative deterioration. It is generally accepted that natural antioxidants are more potent, more efficient and safer than synthetic antioxidants. The aim of this study was to investigate the oxidative stability of sunflower oil, corn germ oil, and mixtures there of (50:50), and the effect of addition of rosemary extract (StabilEnhance ® OSR and OxyLess ® CS of 0.1% and 0.3%), and propyl gallate (0.01%) on the extension oxidative stability of the oil mixture (50:50). A determination of oxidation stability of oils and their combination, and the effect of antioxidants (rosemary extract and propyl gallate) was conducted by a test of rapid oxidation of oil (Schaal oven and Rancimat test). The result of oil oxidation was expressed by the induction period (IP), a protective factor (PF) and by antioxidant activity of antioxidants (AA). The stability of a mixture of oil is proportional to the induction period. From these results it can be concluded that an addition of corn germ oil (50%) in sunflower oil led to changes in the oxidation stability of oil blends expressed within the induction period. The addition of corn germ oil in sunflower oil prolongs the stability of blends of oil degradation by oxidation. The natural antioxidant rosemary extract OxyLess®CS significantly increases the oxidative stability of a mixture of sunflower and corn oils compared to StabilEnhance®OSR and propyl gallate.
Riverine influence determines nearshore heterogeneity of nutrient (C, N, P) content and stoichiometry in the KwaZulu-Natal Bight, South Africa

Riverine influences on nearshore oceanic habitats often have detrimental consequences leading to algal blooms and hypoxia. In oligo- to mesotrophic systems, however, nutrient delivery via rivers may stimulate production and even be a vital source of nutrients, as may nutrient supplements from upwelling. We investigated the nutrient content (C, N, P) and stoichiometry of sediment, and several pelagic, benthopelagic and benthic species in the KwaZulu-Natal (KZN) Bight, a narrow shelf area on the south-east coast of South Africa, bordering the Agulhas Current. Three suggested nutrient sources to the bight are the Thukela River in the central region of the bight, upwelling in the northern part and a semi-permanent eddy (Durban Eddy) in the southern part. Elemental content of the various groups studied showed significantly higher values for most groups at the site near the Thukela River. C:P and N:P were highest in the southern part of the bight, and lowest near the Thukela Mouth or at Richards Bay in the north, indicating the latter were the P-richer sites. Sediment organic matter showed lowest elemental content, as expected, and zooplankton stoichiometry was highest compared to all other biotic groups. Environmental heterogeneity played a greater role in organismal C, N and P content and stoichiometry compared to phylogeny, with the exception of the differences in C:P and N:P of zooplankton. From this bight-wide study, the higher elemental content and lower ratios at the Thukela Mouth site supported previous findings of the importance of coastal nutrient sources to the bight ecosystem. Reductions in river flow for water use in the catchment areas may therefore have negative consequences for the productivity of the entire ecosystem.
Develoumental Changes in the Properties of Potato (Solanum tuberosum L.) Starches

Yoshimi SUGIM0T0, * 1 Yasuyo YAMASHITA, * 1 Ikumi HORI, * 1 Kazuhiro ABE*2,3 and Hidetsugu FUWA*4 * 1 Department of Food and Nutrition , School of Human Environmental Sciences, Mukogawa Women's University (6-46, Ikebiraki, Nishinomiya 663, Japan) * 2 Osaka Prefecture Agriculture Research Institute (Shakudo, Habikino 583, Japan) *3 Present address: University of Osaka Prefecture College of Agriculture (4-804, Mozuumemachi, Sakai 591, Japan) *4 Department of Food Science and Technology, Faculty of Engineering, Fukuyama University (Sanzo, Higashimura, Fukuyama 729-02, Japan)
Comparative Effects of Graded Levels of Moringa Leaf Meal on Haematological and Serum Biochemical Profile of Broiler Chickens

This study was carried out to determine the effects of Moringa oleifera leaf meal on the haematological and serum biochemical profile of broiler chickens. Fresh Moringa leaves (FML) were shade – dried for four (04) days and milled into meal. A total of two hundred (200) unsexed broiler chickens (Anak strain) with a mean body weight of 49.16 g/bird ± 0.09 were allotted to five (05) treatments at forty (40) birds per each in a completely randomized design experiment. Each treatment group was further divided into five (05) replicates. Moringa oleifera leaf meal (MOLM) was incorporated into the broiler starter and finisher diets at 0%, 5%, 10% 15% and 20% levels respectively. The chemical composition of the MOLM showed higher values of crude protein, crude fibre, calcium, iron, tannin, phytic acid, saponin and oxalate contents than FML. The haematological profile in birds fed 5% and 15% MOLM showed higher (P volume than those fed 20% MOLM. The haemoglobin values were similar (P>0.05) between birds fed 5%, 10% and 15% MOLM - based diets, but reduced significantly (P<0.05) in birds fed 20% MOLM. The white blood cell count was significantly (P<0.05) higher in birds fed 15% MOLM, while the lowest was obtained in those fed with 20% MOLM. The serum biochemical indices in birds fed 20% MOLM showed significant reductions (P<0.05) in albumin, total protein, uric acid, aspartate amino transferase and alanine amino transferase contents. The creatinine content was significantly (P<0.05) higher in birds fed 20% MOLM -based diet. The present study concluded that MOLM can be incorporated into broiler diets at 15% level without adverse effects on the haematological and serum biochemical indices of the broiler chickens.
Control of Rush Skeletonweed (Chondrilla juncea) with Herbicides

A range of herbicide treatments was evaluated for long-term control of rush skeletonweed, a perennial weed of crops and pastures in North and South America, the Mediterranean region, central Europe, and Australia. Clopyralid (75 to 300 g ai/ha) and clopyralid mixtures with 2,4-D, MCPA, or dicamba were effective, resulting in survival rates of 0 to 4% for the most successful treatments applied for three consecutive seasons. Metsulfuron (9 g ai/ha) and 2,4-D (850 g ai/ha) significantly reduced survival when applied at high rates for three years. Barley yield in the season following control was increased by up to 195 to 199% of yield from untreated plots. Evidence was found for differences in herbicide susceptibility between narrowleaf and broadleaf forms of rush skeletonweed.