Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting Selection Signals In Plasmodium falciparum Using Identity-By-Descent Analysis

Detection of selection signals using genomic data is vital for tracking drug resistance loci in microorganisms that cause disease, such as malaria, and monitoring of such loci is crucial for disease control efforts. Here we present a novel method of detecting relatively recent selection using identity-by-descent approaches suitable for multiclonal, recombining microorganisms. Application of this new method to a large whole genome sequencing study of Plasmodium falciparum identifies many well-known signatures such as crt and k13, associated with chloroquine resistance and artemisinin resistance respectively, and through relatedness networks shows how these signatures are distributed in Southeast Asia, Africa and Oceania. Using these networks, we confirmed an independent origin of chloroquine resistance in Papua New Guinea and the spread of multiple artemisinin resistance mutations in Southeast Asia. We also found two novel signals of selection not yet investigated in detail.
Acumulation Properties and Foliar Limb Effects of Tetracycline and Metabolites in Lactuca Sativa L., Eruca Sativa L. and Spinacia Oleracea L.

The main goal of this study is to study the tetracycline and metabolites (TCS) accumulation properties in three vegetable plants leafs (lettuce, arugula and spinach). Residues of TCS, used in veterinary and human medicine, end up in crops due to the agricultural farmlands where manure application is used. The studied vegetables were grown hydroponically in greenhouses, using controlled nutrient solution containing 21.00 μgL TCS (quantity from the literature). Mature plants leafs were chemically characterized (water and cations), TCS measured using ELISA screening method (enzyme-linked immunosorbent assay) and foliar limb in terms of anatomical structure studied. Tetracycline was accumulated in the studied vegetables plants leafs in low concentrations (10-15 μgkg-1), the accumulation rate depending on the plant characteristics. Normal aspect of foliar limb structure was highlighted in leaves of the studied plants, so the TCS accumulation does not lead to leaf structure alterations.
Size and Morphology of Sella Turcica in Malay populations: A 3D CT Study

The purpose of this study was to analyse the linear and area dimensions and morphological shape of sella turcica to determine if differences exist due to gender or age and compared with available global data. A total of 183 (113 men and 70 women) Malay subjects who had their computed tomography (CT) scan at the Radiology Department, Hospital University Sains Malaysia (HUSM) for ordinary diagnosis not related to craniofacial deformities. The selected age groups were divided into four groups as children (0-6 years), preadolescents (7-12 years), adolescents (13-20 years) and adults (21-35 years). The images were processed using Mimics V17.0 software. Conventional measurements included three different heights of the sella turcica (anterior, posterior, median), its length, diameter, area and width, measured in relation to the Frankfort reference line (FH). Morphometric methods were used to assess shape. No significant differences in size of the sella were found except at sella height anterior between genders. When age was evaluated, significant differences were found among all age groups. The study found that sella turcica presented with a three different shapes: in a U shape (57.9 %), in a J shape (24.5 %) and shallow (17.5 %). Sella shape and dimensions reported in the current study can be used for discovering Pathological enlargement of the pituitary fossa and may also be helpful in providing reference data in the assessment of racial, gender and age specific variation in Malay population.
The ecology and phylogeny of the mediterranean nausithoidae (Cnidaria, Scyphozoa)

- Coronates occur in all oceans from coastal to abyssal waters. In the Mediterranean, three of the six local nausithoid species inhabit marine caves. They have a reduced pelagic life stage in common, which presumably offers them advantages in cave or shallow water habitats, though the mechanisms differ. Within that small number of species, apogamy, parthenogenesis, hermaphrodity and brood care are encountered. In this study, knowledge of habitat and ecology of the Mediterranean Nausithoidae is compiled and the relationships of the species are investigated through a combined approach of morphological and molecular character analysis. Three clades are evidenced. These results are corroborated by studies of the life cycles and observations on the behaviour.
Response of Snap Beans to Tillage and Cover Crop Combinations

Field experiments were conducted on a Norfolk loamy sand (fine-loamy, siliceous, thermic Typic Paleudult) from 1983 through 1985 to determine the effects of tillage method, cover crop, and N fertilization on inorganic soil N and yield, yield components, and N content of snap bean (Phaseolus vulgaris L.). Hairy vetch (Vicia villosa Roth), hairy vetch plus wheat (Triticum aestivum L.), Austrian winter pea (Pisum sativum ssp. arvense L. Poir), Austrian winter pea plus wheat, wheat, crimson clover (Trifolium incarnatum L.) and no cover were the cover crop treatments. Inorganic N concentrations generally were greater in soil with cover crop treatments containing legumes than in soil with no cover and wheat treatments. The use of Austrian winter pea, hairy vetch, and crimson clover as cover crops without supplemental N resulted in snap bean yields comparable to those obtained when 90 kg·ha−1 additional N was supplied. Supplemental N decreased the amount of dry matter partitioned into pods. Inorganic N profiles in the soil indicated that conventional tillage (CT) practices resulted in greater mineralization of N fixed by the legume cover crops than no-tillage (NT) practices. However, snap bean yields for NT were comparable to or greater than those obtained with CT, suggesting that N released from legume residues provided sufficient supplemental N for optimum growth and yield.
Proteomic Profiling of Ewing Sarcoma Reveals a Role for TRAF6 inProliferation and Ribonucleoproteins/RNA Processing

Notwithstanding advances over the last decade in the comprehension of the molecular biology of Ewing sarcoma (ES), we still lack an understanding of critical issues, especially those regarding its genesis. In particular, little effort has been devoted to characterization of the proteic component of the mechanisms and pathways deployed by the activation of the fusion protein resulting from chromosomal translocation. We decided to investigate the proteic alterations of an ES cell line bearing a representative fusion protein. The combination of RNA interference of EWSFLI1 in the ES cell line TC-71, a proteomic analysis by 2-D electrophoresis and subsequent mass-spectrometry identification, and a global overrepresentation study detected changes in more than 500 spots. Forty-three proteins were identified as being significantly differentially abundant. As expected, we found and validated changes in proteins linked to nucleotide processing, transcription regulation, ribonucleoproteins, helicases, cell-cycle control and proliferation, and metabolic processes. Additionally, TNF receptor-associated factor 6 was revealed as a hub node. Our strategy showed the potential to reveal the protein interplay associated with the known functions of the fusion protein: binding to DNA and RNA in order to act as aberrant transcription factors or potent repressors, or by altering RNA processing.
Genetic Basis of Some Yield Related Traits in Wheat (Triticum aestivum L.) Under Drought Conditions

This study was performed to determine the combining ability of seven lines for hybrid production. Line × tester analysis was used to estimate the combining ability and gene action for yield related traits. Twelve F 1 hybrids and their seven parents were evaluated in drought conditions for yield and yield related traits in a replicated trial during the year 2013-14. Among lines, 41IBWSN1143 that showed best GCA for yield and two of its component traits (FT and 100GW) and among testers, the genotype SEHER-2006 that had positive GCA effects for grain yield and most of its components, were pointed as the best female and male general combiners respectively. In case of hybrids, 27SAWSN3002 × SEHER-2006, 41IBWSN1142 × ASS-11, 41IBWSN1143 × 41IBWSN1149, 41IBWSN1134 × 41IBWSN1149 and 41IBWSN1134 × ASS-11 performed better for almost all traits (PH, FT, SL, S/S, GW/S, 100GW and Y/P). GCA and SCA variances revealed predominantly non-additive gene action for all three important yield traits (FT, SL and Y/P), While rest of the traits (PH, S/S, G/S, GW/S and 100 GW) showed additive type of gene action. These superior parental genotypes could be included as promising parents in future research for successful wheat hybridization and hybrids can be further exploited in future generations for the improvement of morphological traits which confer resistance to water deficit stress with stable grain yields.
Cloning and Sequence Analysis of the Gene Encoding Endopolygalacturonases in the Cotton Black Spot Disease Fungus Alternaria macrospora

The fungus Alternaria macrospora is the causal pathogen of cotton black spot disease in cotton seedlings from the cotyledon period to the seedling stages, causing black spots on leaves and their damping off. Endopolygalacturonases (endoPGs) play major roles in pathogen penetration into plants at the initial phase of invasion. In this phase, the pectic polysaccharides in the plant primary cell walls used as potential barriers against pathogens are digested. The present study aimed to clone and characterize the endoPG-encoding gene ampg-1 in Alternaria macrospora . A 1241 bp open reading frame of ampg-1 was cloned. The nucleotide and its deduced peptide sequence alignment showed that it shared quite high identities with two other Alternaria fungi, i.e. Alternaria alternata and Alternaria citri . The analysis of the predicted amino acid sequence of ampg-1 revealed that the endopolygalacturonase in Alternaria macrospora had four PbH1 domains, which was less than those of five other species. Phytopathogenesis was implicated in the quantity of the PbH1 domains. Therefore, the cotton black spot disease prolonged the latency.
Molecular Detection of Theileria and Babesia in a Diversity of Stomoxyini Flies (Diptera: Muscidae) from Khao Yai National Park, Thailand

Blood protozoan species of the genera Theileria and Babesia are known to infect both domestic and wild animals. This study was carried out to detect Theileria and Babesia DNA in Stomoxyini flies collected in Khao Yai National Park, Thailand. A total of 110 Stomoxyini flies including 6 species, Stomoxys calcitrans, Stomoxys indicus, Stomoxys pullus, Stomoxys uruma, Haematobosca sanguinolenta and Haematostoma austeni, were examined by amplification against the 18S rRNA gene of the Theileria/Babesia species and then the PCR products were sequenced for species identification by comparison with published sequences from the GenBank database. Ten (9.1%) out of 110 samples were positive against the 18S rRNA gene of the Theileria/Babesia species. For sequence analysis, 7 samples (6.4%) were identified as Theileria sp. and showed high identity (99%) with Theileria sp. (JQ751279) and T. cervi (HQ184406 and HQ184411), while 3 samples (2.7%) were identified as Babesia canis vogeli and showed 100% identity with reported sequences of B. canis vogeli (AB083374 and HM590440). Phylogenetic relationships among the sequenced samples showed that the Theileria sp. appeared in the same group as T. cervi, while B. canis vogeli appeared in a distinct group. This study is the first report on a variety of Stomoxyini flies infected with the Theileria and Babesia species in Thailand conducted using molecular identification techniques.
DNA barcoding of fiddler crabs Uca annulipes and U. perplexa (Arthropoda, Ocypodidae) from the southwest coast of India

DNA barcoding of fiddler crabs Uca annulipes and U. perplexa from the mangrove ecosystems of the southwest coast of India has been carried out. The sequencing of mitochondrial CO1 gene confirmed the identification of the species. The record of the specimen U. perplexa from the eastern Arabian Sea shows the continuous distribution of the species from African coast to the Bay of Bengal.
Age of maturation and behavioral tactics in male yellow ground squirrel Spermophilus fulvus during mating season

Life-history theory predicts that in hibernators age of maturation is related positively to body size and negatively to the duration of active season aboveground. Yellow souslik is a large-sized ground squirrel with long hibernation, which suggests late maturation. We used four-year field observations of marked individuals to determine the age of maturation in males through analysis of age-dependent variation in body size, mass, androgen status, timing of spring emergence, ranging patterns and social behavior during the mating season. Yearling males were smaller, lighter, had lower level of fecal testosterone, emerged later and had smaller home ranges than older males. Social activity and the number of females encountered did not differ between age classes. After the second hibernation none of the studied parameters varied with age. Cluster analysis revealed two behavioral tactics: "active" males (adults only) emerged earlier, ranged more widely, initiated more contacts, encountered more females and were heavier than "passive" males (both yearling and adult). Thus, males of S. fulvus reached adult size and matured after two hibernations, which is relatively fast for such a big species with short active period. Indirect evidence for copulations and high variation among yearlings in all parameters suggest that some of them might successfully compete with adults. Active tactic of wandering and searching for females is energetically costly, and probably only adult males in good physical condition can afford it, whereas passive tactic of residing is energy saving and good for adults in poor condition and for yearlings that are continuing to grow (Current Zoology 60 (6): 700-711, 2014).
Location of breeding warrens as indicators of habitat use by maras (Dolichotis patagonum) in Península Valdés, Argentina

Abstract We characterized the habitat use by maras (Dolichotis patagonum) on a microhabitat scale in the area surrounding the warren, assessing the conditioning effect of the warren over space use and exploitation of other resources. We evaluated the relationships between the probability and intensity of use, habitat configuration and distance to the warren, counting feces along transects departing from each warren. Our results showed that the location of breeding warrens was positively associated with the habitat use by maras on a microhabitat scale. The core area of the annual activity of maras was concentrated around the warren and there was no evidence of alternative areas of activity. According to the fitted models, maras used microhabitats with a high proportion of bare soil and close to infrastructure elements. The spatial autocorrelation components indicated that intensively used patches are small and disperse. The patterns of habitat use observed in this study suggest that maras use multipurpose areas including the breeding site and resources needed throughout the year. These patterns suggest that warrens are good all year-round indicators of mara habitat use and spatial ecology.
On the nature of the coastal lagoon winkles attributed to Littorina tenebrosa and Littorina saxatilis

Le nom de Littorina tenebrosa (Montagu) a ete utilise dans le passe pour (au moins) deux especes differentes: sensu Muus (1967) pour l'espece lagunaire, forme petite, fragile, peu spiralee, visant en permanence submergee accrochee a des macrophytes dans des lagunes cotieres non soumises a maree et sensu Forbes & Hanley (1853) et al. pour une forme grande, intertidale, d'eau saumâtre et de cote abritee avec une large spirale, forme qui apparait communement dans les langues bien qu'habituellement seulement sur le substrat. L'usage de Forbes & Hanley parait etre la forme de l'auteur d'origine et dans cet usage Littorina tenebrosa est generalement admis comme synonyme de la forme a l'habitat abrite de Littorina saxatilis
Structures of photosynthetic membrane complexes

Photosynthesis is essential to all life on Earth. It is the biological process that captures energy of sunlight and converts it into chemical compounds usable by any living organism. The processes occurring within photosynthesis can be divided into the light-dependent reactions and the light-independent reactions. In my PhD thesis several integral membrane protein complexes were investigated that catalyze the light dependent reactions. Primarily the photosystem I and II that are taking part in the conversion of light energy into the chemical energy. Photosystems function and exist in all green plants and some lower organisms such as cyanobacteria. For some prokaryotes the primary complex responsible for light conversion is smaller and named a reaction center. Antenna complexes are essential for light absorption and energy transfer to photosystems and reaction centers. There is a substantial variation in antenna’s composition and size between groups of organisms. The association of photosystems and reaction centers into higher complexes is another issue. Unlike the monomeric reaction centers in green and purple bacteria, PSI forms trimeric complexes in most cyanobacteria. Recently, in some species a tetrameric PSI complex was observed. However, in plants/algae, PSI is monomeric. In contrast, PSII in cyanobacteria and plants is monomeric or dimeric, but never forms trimers or tetramers. Our researches described in these thesis goes through the variety of living species, placing different positions on the evolutionary scale. These thesis focused primarily on a fundamental research but some of the findings can boost the applied scientific research such as clean energy obtainment.
Characterization of Chirped volume bragg grating (CVBG)

If the pulse exhibits very short duration for example few cycle pulses below 5fs with high power, the intensity may reach 10 w cm2 . This tremendous amount of energy is more than enough to study non linear process for example high harmonic generation [1]. As a result of that fact, the compression of high power laser pulses becomes a vital process to produce high harmonic generation according to the three step model [2]. The temporal form of ultrashort laser pulse is shown in figure 1
Vitamin E: An Essential Nutrient for Horses?

Vitamin E is an essential nutrient for horses beneficial to combat the multitude of effects of free radical production that can damage membranes and components of cells. As such, Vitamin E appears to be most beneficial to young rapidly growing foals, pregnant and lactating mares, stallions, and especially, equine athletes. Natural and synthetic-sources of vitamin E, unlike other vitamins, have different structures. The natural sources are preferentially transported to and retained in tissues at higher levels than synthetic source vitamin E. Although not as stable as the acetate ester, micellized natural tocopherol, is utilized better than natural vitamin E-acetate.
First Report of Gray Mold Disease of Sponge Gourd ( Luffa cylindrica ) Caused by Botrytis cinerea in Korea

cal vegetable belongs to the family Cucurbitaceae. Luffa gourds are grown primarily for their fibrous tissue skeleton, which is commonly used as scrubbers, cleaning pads or bath sponges, but green immature fruits were cooked as vegetable and eaten as squash or substituted for cucumber in salads (Oboh and Aluyor, 2009). Botrytis cinerea (teleomorph Botryo­ tinia fuckeliana) is an air borne, ubiquitous filamentous fungal pathogen and may cause gray mold on a variety of dicotyledonous plants, including many vegetables, fruits, ornamental flowers, and greenhouse plants (Elad, 1997; Jarvis, 1977). The pathogen is a necrotroph, inducing host cell death resulting in serious damage to plant tissues culminating in rot of the plant (Govrin and Levine, 2000; Staats et al., 2005). Botrytis infections are favored by a cool weather, rainy spring season and summer temperatures of approximately 15C (60F). Gray mold can be particularly damaging when rainy and/or damp weather occurs over several days. Since 2014, gray mold of sponge gourd caused by B. cinerea has been found at different locations in Korea. The aim of the present study was to identify the causal agent associated with gray mold observed on sponge gourd in Korea, based on culture characteristics, molecular phylogenetics, and pathogenicity.
Minimum Longevity and Growth of the Invasive Green Anole, Anolis carolinensis, in Chichi-jima of the Ogasawara Islands, Japan

Abstract: We studied the longevity and growth pattern of the wild populations of invasive green anoles (Anolis carolinensis) in Chichi-jima Island, Japan. We estimated specimen age using skeletochronology and counted the number of lines of arrested growth (LAGs) on thin cross sections of femur bones. We observed from zero to five of LAGs for both male and female specimens. This indicated that the green anoles can survive at least five years in Chichi-jima Island. Body size increased with the number of LAGs, but the growth rate decreased when individuals had two LAGs. Our results suggest that the wild anoles might expend more energy for reproduction rather than for growth at this stage.
Growth responses of hydroponic green fodder system and Fusarium oxysporum to external supply of mycolytic enzymes applied on seaweed bagasse as carrier

High humidity, nutritional and environmental conditions involved in hydroponic green fodder (HGF) production increases fungal contamination risk. Chemical fungicides application is limited because of their toxicity to animals. An alternative biotechnological option is the use of mycolytic enzymes such as chitinase and laminarinase. The goal of the present study was to immobilize chitinase and laminarinase on seaweed bagasse as a carrier in order to increase their action time in HGF system, and compare the effect of those enzymes onFusarium oxysporum viability and HGF growth. Chitinase and laminarinase immobilization on seaweed bagasse was carried out at 4°C and stirred at 250 rpm. Immobilization was assayed at different incubation times (60, 90, 120, and 180 min). Enzymes immobilization kinetics was monitored from protein quantity balance. Enzymatic activity of chitinase and laminarinase were evaluated. Higher immobilization (65 and 84% for chitinase and laminarinase, respectively) was obtained at 120 min of incubation time. Wheat grains in HGF systems under different treatments were inoculated with F. oxysporum at 2×104spores/ (g of seed). Kinetics of growth measured by height of green shoots, as well as wet mass, dry mass of HGF, and fungal viability after 10 days of germination were evaluated. The higher antifungal effect was observed with immobilized enzymes. It was demonstrated that applied treatments did not affect negatively the fodder growth. Moreover, the bagasse presence can improve HGF height. The obtained results demonstrated that seaweed bagasse may be effectively applied as carrier for biologically active substances in HGF system. Key words: Antifungal effect, chitinase, laminarinase, seaweed bagasse.