Miracle-dz/UniFAR-FTUs huggingface dataset:
Resolving evolutionary relationships in closely related nonmodel organisms: a case study using chromosomally distinct members of a black fly species complex

Coalescent‐based analyses have been recommended for species delimitation and tree reconstruction. Yet, despite recent advances in molecular methods, acquiring sufficient genetic data often precludes coalescent‐based analyses in nonmodel organisms. We show that these methods are accessible to questions in nonmodel systems. Specifically, we use coalescent‐based analyses to investigate evolutionary independence and relationships among chromosomally distinct members (sibling species) of a black fly (Diptera: Simuliidae) species complex. Our dataset consists of nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) markers – the former developed using the black fly transcriptome and available genomes from model relatives. We show that individual gene trees exhibit considerable discordance among one another and reveal little about potential species limits. Consistent species tree topologies are obtained from analyses of nuDNA, both with and without the inclusion of mtDNA data. Nodes on the tree receive robust support with the addition of mtDNA. Coalescent‐based species validation approaches recognize all sibling species. However, unlike species tree analyses, the addition of mtDNA data does not improve or alter the results. Thus, analyses of nuDNA alone can validate sibling species. Contrary to these results, population genetic patterns of neutral diversity, within‐locus recombination, and linkage disequilibrium suggest that sibling species represent a single species with high levels of nucleotide polymorphism, large effective population sizes, and extensive gene flow. Demographic patterns inferred from neutrality tests integrate seemingly disparate results by showing signatures of gene flow among structured populations that are expanding in size. Thus, admixture associated with geographic range expansions may be assimilating sibling species into a single genetic lineage.
Bioactive compounds, antioxidant activity and minerals of Caju (Anacardium humile St. Hill) during the ripening

The present study aimed to determine the content of minerals, bioactive compounds and the antioxidant activity of ‘Cajuí’ ( Anacardium humille St. Hill) during the ripening. The fruits were collected in three maturity stages. The content of the minerals, total phenolics, proanthocyanidin and carotenoids contents as well as the antioxidant activity, ABTS (2,2-azinobis-3-ethylben-zothiazoline-6-sulphonic acid), DPPH (2,2-diphenyl-1-picrylhydrazyl) and FRAP (ferric reducing antioxidant power) were determined, with results expressed on Trolox equivalent antioxidant capacity (TEAC). The Student’s t-test was employed to analyse the data, based on a significance level of p < 0.05. The total phenolic contents were determined as 1424.33 ± 28.62, 991.16 ± 21.52 and 867.08 ± 28.56 mg GAE.100 g -1 for the immature, semi-mature and mature stages, respectively. Regarding the carotenoid content, 18.05 ± 1.01 was obtained for the immature stage, 8.62 ± 0.96 was obtained for the semi-mature stage, and 8.32 ± 0.97 mg-β-carotene.100 g -1 was obtained for the mature stage. Regarding the antioxidant activity; it was particularly relevant for the fruits in the immature stage in the three methods used: DPPH (30399.63 ± 27.06 µM TEAC.100g -1 ), ABTS (40860.62 ± 9.32 µM TEAC 100 g -1 ) and FRAP (6118.22 ± 83.04 µM TEAC.100 g -1 ). The ‘cajuí’ exhibited high antioxidant activity and content of bioactive compounds, especially for the immature stage. Among the minerals, ‘cajuí’ showed high levels of K (potassium), P (phosphorus), and Mg (magnesium). Thus, the cajuí presents itself as a good source of antioxidant compounds which can be exploited by the food industry as an ingredient for the development of a food with functional properties and the pharmaceutical industry, as phytochemical.
Red Snapper Distribution on Natural Habitats and Artificial Structures in the Northern Gulf of Mexico

AbstractIn 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, patchy “hot spots” at a variety of depths along the Alabama coast and the west Florida shelf. Red Snapper biomass and fecundity estimates were higher for the northwestern GOM than for the northeastern GOM, as the latter area contained mostly smaller, younger individuals. The existence of similar surveys on petroleum platforms and artificial reefs also e.
Characterization of Pilot Scale Processed Canadian Organic Cranberry (Vaccinium macrocarpon) and Blueberry (Vaccinium angustifolium) Juice Pressing Residues and Phenolic-Enriched Extractives

ABSTRACT This work examined the processing yields, physico-chemical characteristics, and bioactive properties of Canadian organic cranberry and blueberry pomace and phenolic-enriched extractives. The ethanol extracts from each berry contained three to four times the soluble solids and sugar contents compared to the pomace. The lipid content of organic cranberry pomace (4.44%), cranberry ethanol extractives (3.86%), and blueberry ethanol extractives (4.44%) were significantly lower than the lipid content of the organic blueberry pomace (5.42%). The organic blueberry pomace showed higher protein content (8.41%) than organic cranberry pomace (5.76%); however, both organic cranberry and blueberry ethanol extracts showed similarly low protein contents. Significant differences were observed in the mineral and elemental contents of both pomaces and their extractives. Total phenolics, tartaric esters, flavonols, anthocyanins, and antioxidant activities were increased by two to three times in both organic cranberry and blueberry ethanol extracts compared to their respective pomaces. The major anthocyanins detected in organic blueberry pomace and ethanol extracts were peonidin 3-glucoside, malvidin 3-galactoside, malvidin 3-glucoside, and cyanidin 3-arabinoside. Peonidin 3-galactoside, cyanidin 3-galactoside, cyanidin 3-arabinoside, and peonidin 3-arabinside were the major anthocyanins in the organic cranberry and ethanol extacts. Results indicated that cranberry and blueberry pomace could be used to develop bioactives with antioxidant activity for potential health benefit and/or bioenergy production.
Preparation, characterization, and enhanced antimicrobial activity: quercetin-loaded PLGA nanoparticles against foodborne pathogens

The use of quercetin as a bioflavonoid is becoming increasingly common in food industries even though poor water solubility, instability, absorption, and permeability have limited its application. The oil-in-water single-emulsion solvent evaporation method to synthesize highly stable and soluble quercetin-encapsulated nanoparticles (NPs), in which the reaction yield, particle size, and polydispersity of the NPs are varied greatly within the process parameters of the synthesis method, has been optimized. NPs with different initial quercetin amounts were used to determine how the quercetin amount affected nanoparticle properties and antimicrobial eficiency. Listeria monocytogenes, Salmonella typhimurium, Escherichia coli, and Staphylococcus aureus were chosen as model bacteria due to their being foodborne pathogens. The results of antimicrobial activity evaluated by three different methods showed that the antimicrobial activity of both quercetin NPs and free quercetin was effective on gram-positive strains (L. monocytogenes and S. aureus). Additionally, it was detected that Q31 NPs have more effective antimicrobial activity than other synthesized quercetin nanoparticles depending on the amount of substance and release. Furthermore, on the basis of assessing the antibacterial effects by scanning electron microscopy, it was detected that bacteria cells lost their integrity and became pale with the release of cytoplasm and decomposed after treatment with Q31 NPs.
Short‐term changes in the structure of termite assemblages associated with slash‐and‐burn agriculture in Côte d'Ivoire

Termites are major decomposers in tropical regions and play critical roles in many soil‐related processes. Studies conducted in Asia and the Neotropics suggest that habitat modification can strongly affect termite assemblages, but data on termite communities from forests in Africa, especially West Africa, are scarce. Here, we measured the short‐term impact of slash‐and‐burn agriculture on termite assemblages in an agricultural region of central Côte d'Ivoire. We assessed termite diversity and relative abundance in four habitat types: secondary forest, cleared forest, burned forest, and crop fields. The secondary forest had higher species richness compared with the other habitats, but all habitat types had similar assemblage structures. Fungus‐growing termites were the most abundant feeding group in all habitats. Soil feeders were most abundant in secondary forest, intermediately abundant in cleared and burned forests, and almost entirely absent in crop fields. Wood‐feeding species showed clear responses to burning; their abundances decreased after fire. We conclude that slash‐and‐burn agriculture does not appear to severely erode the diversity of termite assemblages. This could be due to the dominance of ecologically versatile fungus growers or to the relatively long time between clearing and burning. However, forest clearing negatively affects soil feeders, with the Apicotermitinae most affected by canopy loss.
Genomewide analysis of road-block termination

Transcription of DNA into RNA intermediates constitutes the first step in gene expression. During the last decade, several studies showed that about 80-90% of the genome is transcribed, and that transcription can initiate almost anywhere. This process—known as pervasive transcription—represents a serious threat to proper gene expression as it has the potential to interfere with not only other transcription events, but any DNA-based process. Selective transcription termination is therefore a mechanism of paramount importance for genome transcriptome stability and correct regulation of gene expression. Here we describe road-block termination, a novel termination mechanism for RNA polymerase II that functions to limit pervasive transcription and buffer the consequences of readthrough transcription at canonical terminators in S.cerevisiae. We show that several transcription factors can elicit this termination and that a number of unexpected genomic loci are associated with it. Additionally, we explore the possibility that road-block termination might contribute to specification of replication origins.
Cryptorchidism in Mammals: A Review

Cryptorchidism is seen more often in horses, cats, dogs, and pigs and rare in ruminant. It is believed to result from heredity, an autosomal recessive mode of inheritance or a dominant gene with the incomplete penetrance. Ruling out castration as well as conducting physical examinations can easily diagnose cryptorchidism. It can be controlled by complete castration or culling of the affected animal and where appropriate, the animal be used as food animal other than for breeding purposes.
Antimicrobial susceptibility pattern of Neisseria gonorrhoeae isolated from fertile and infertile women

Purpose: To study the prevalence of Neisseria gonorrhoeae in the high vaginal swab samples of fertile and infertile women who were referred to Infertility and Sterility Hospitals, Tehran, Iran as well as investigate their antibiotic resistance pattern. Methods: Three hundred and twenty high vaginal swabs were taken from fertile and infertile women. The samples were cultured and those that were N. gonorrhoeae -positive subjected to the disk diffusion susceptibility test. Results: Prevalence of N. gonorrhoeae in fertile and infertile women were 5.26 and 16.92 %, respectively. All isolates harbored orf1 gene. Patients in the age bracket > 40 years were at high risk. N. gonorrhoeae strains showed high level resistance against ampicillin (87.5 %), ciprofloxacin (75 %), tetracycline (71.87 %) and penicillin (68.75 %). Conclusion: The possible role of resistant N. gonorrhoeae as pathogens causing female infertility constitutes an important finding of the study. The high levels of bacterial resistance against ampicillin, ciprofloxacin, tetracycline, penicillin and spectinomycin, should be taken into account in developing any new guidelines in the management of the infection. Keywords: Neisseria gonorrhoeae , Female infertility Drug Resistance, Ciprofloxacin, Tetracycline, Spectinomycin
Biochemical and nutritional characterizations of date palm fruits (Phoenix dactylifera L.).

The date (Phoenix dactylifera L.), a high-energy fruit, is regarded as a popular food commodity for thousands of years in Egypt, the Arabian Gulf peninsula and its neighboring region. The aim of present study is to characterize the biochemical and nutritional values of constituents of the Egyptian date fruits. Date palm fruits contain a variety of B-complex vitamins B1, B2, Nicotinic acid and vitamin A. the date palm extracts contains 13.80 % moisture and 86.50 % total solid. Ash and Crud fibers contents were 2.13 and 5.20 respectively. Protein, carbohydrates and lipids contents were 3.00%, 73.00% and 2.90 % respectively. The low level of lipids content 2.90% compared with its content of sugars means that, the date palm is save to heart and blood patients because its containing a very low level of fatty acids and cholesterol. HPLC analysis of sugars content showed that, the carbohydrate content consists of a large amount of glucose, fructose and sucrose, The protein pattern on SDS-PAGE showed that, most of proteins in the date palm are a high molecular weight proteins between 80 and 135 KD and contained a minimum levels of the LMW proteins less than 55 KD. Date Palm contained high concentration of Aspartic acid, Proline, Glycine, Histidine, Valine, Leucine and Arginine, but low concentration of Threonine, Serine, Methionine, Isoleucine, Tyrosine, Phenylalanine and Lysine and very low concentration of Alanine. The date palm fruits provide unique functional and nutritional values. Numerous health benefits beyond its nutritional value have been associated with consuming date palm fruits to enrich nutrition values of different kinds of food.
On-farm seed loss does not differ between windrowed and direct-harvested canola

Haile, T. A. , Gulden, R. H. and Shirtliffe, S. J. 2014. On-farm seed loss does not differ between windrowed and direct-harvested canola. Can. J. Plant Sci. 94: 785-789. Seed loss in canola (Brassica napus) leads to considerable loss of revenue and dispersal of seeds into the soil seedbank. The resulting volunteer canola can create weed problems in subsequent crops and result in further yield loss. The objective of this study was to quantify and compare canola seed loss and seedbank addition from windrowing and direct-harvesting operations on commercial farms in western Canada. A total of 16 direct-harvested and 19 windrowed canola fields were surveyed in central and southern Saskatchewan during 2010, 2011 and 2012. Shattered seeds from these fields were sampled within 3 wk after harvest of the crop using a vacuum cleaner. There were no differences in seed yield, loss or seedbank addition of canola between windrowing and direct-harvesting operations. There was a difference in 1000-seed weight between the harvest methods and seeds of the direct-harvested canola were larger in size. This may suggest that direct-harvesting can be considered as a viable option to harvest canola in western Canada.
Molecular cloning, expression and characterization of bile salt hydrolase from Lactobacillus rhamnosus E9 strain

ABSTRACT Bile salt hydrolase (BSH) enzyme, commonly found in probiotic bacteria of gut origin, catalyzes the hydrolysis of glycine and/or taurine-conjugated bile salts allowing for colonization of the bacteria in the gut and contributing to a decrease in levels of cholesterol. However an excessive deconjugation of tauro-conjugated bile salts and production of secondary bile acid can have harmful side-effects. The aim of this study was to characterize the activity of BSH enzymes from Lactobacillus rhamnosus E9, a popular probiotic strain. The bsh gene was cloned, expressed, purified and characterized in Escherichia coli BLR(DE3) strain. The hydrolysis activities and substrate specificities of the recombinant BSH (rBSH) enzyme were examined using six different bile acids. Nucleotide sequence analysis results indicated that the bsh of E9 contained an open reading frame (ORF) of 1014 and nucleotides encoding a 338-amino acid protein with a molecular weight of 37 kDa. Five catalytically important amino acids and the amino acid motifs located around the active site were highly conserved. The rBSH showed a slight preference towards glycine-conjugated to tauro-conjugated bile salts. This confirms that it is a safe strain for probiotics and its preference for glycine-conjugated bile salts should be further investigated.
Efficacy of Different Grain Protectants on the Effect of Fecundity, Adult Emergence and Weight Loss of Cigarette Beetle (Lasioderma serricorne Fabricius) Infestation in Cured Turmeric Rhizomes (Curcuma longa Linnaeus)

Turmeric is a rhizomatous herbaceous perennial plant belonging to the ginger family (Zingiberaceae), botanically known as Curcuma longa Linnaeus, originated from Tropical south Asia (India). It is one of the oldest spices and an important spice bowl of India which had been used since ages. The world production of turmeric stands at around 8, 00,000 tons in which India hold a share of approximately 75 to 80 per cent. India consumes around 80 per cent of its own production. In India the total area under cultivation is 184.4 thousand hectares with production of 830.40 thousand metric tonnes and productivity of 4.50 MT Ha -1 . Among all the states, Telangana state stands first in area with 43.50 thousand hectares and production of 216.30 thousand metric tonnes while International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 4 (2017) pp. 963-971 Journal homepage: http://www.ijcmas. com
Major Histocompatibility Complex-Associated Resistance to Infectious Diseases: The Case of Bovine Leukemia Virus Infection

The major histocompatibility complex (MHC) is a polymorphic gene cluster of about 150 genes, present in all vertebrates. Many of these genes contribute to immunity. Particularly, MHC‐encoded class I and class II molecules, which are typically highly polymorphic and polygenic, are central in defining the specificity of the adaptive immune response. Among the diversity of genes associated with disease resistance, MHC genes are particularly interesting as they are associated with resistance and susceptibility to a wide range of diseases, some of which produce important economic losses in livestock. Enzootic bovine leukosis is an infectious disease caused by the retrovirus bovine leuke‐ mia virus (BLV), with an important economic impact, mainly in dairy herds. In this chap‐ ter, MHC‐associated genetic resistance to BLV is revised. Certain alleles of the bovine MHC (BoLA) class II locus have been found strongly associated with resistance to viral dissemination. Genetic selection of resistant animals emerges as a natural strategy for the control of infectious diseases, especially when there is no other alternative of control or prevention, as vaccines. Founded on this knowledge, a BLV control program based on selection of genetically resistant cattle was designed. The proof of concept indicates that this strategy is feasible to implement in dairy herds.
Phytochemical Analysis and Antibacterial activity of Methanolicextract of Clinacanthus nutans Leaf

Clinacanthus nutans is a medicinal herb found in South East Asia. It has been traditionally used for skin infections. Hence, this study aimed to investigate the antibacterial effect of C. nutans against selected bacteria. C. nutans leaf was extracted with methanol. The dried methanolic extract was qualitatively screened for the presence of phytochemicals and quantitatively analysed for total phenols and total flavonoids. The strains of Propionibacterium acnes (ATCC 11827), Staphylococcus aureus (ATCC 29213), Staphylococcus epidermidis (ATCC 12228), Bacillus cereus (ATCC 10876) and Escherichia coli (ATCC 25922) were selected for the study. The antibacterial effect was tested by microbroth dilution method in a 96-well microtiter plate and minimum inhibitory concentrations (MIC) were determined. The yield of methanolic extract of C. nutans leaves was 15.29 %w/w. Total phenolic content was 1.77±0.008 mg gallic acid equivalent/g. Total flavonoid content was 0.04±0.001 mg quercetin equivalent/g. Phytochemical screening revealed the presence of saponins, phenolics, flavonoids, diterpenes and phytosterols. The C. nutans extract exhibited antibacterial effect against Propionibacterium acnes (MIC > 12.5 mg/ml), Staphylococcus aureus (MIC 12.5 mg/ml), Staphylococcus epidermidis (MIC > 12.5 mg/ml), Bacillus cereus (MIC > 12.5 mg/ml) and Escherichia coli (MIC 12.5 mg/ml). Our study indicated that C. nutans possess significant antibacterial effect against S. aureus and E. coli. Further studies are required to identify the antibacterial compounds.
Environmental heterogeneity effects on predator and parasitoid insects vary across spatial scales and seasons: a multi‐taxon approach

As predator and parasitoid insects depend on multiple resources for adult feeding and reproduction, environmental heterogeneity (EH) is expected to be a key driver of their species diversity. In temperate regions, the benefits of EH are expected to vary across spatial scales and seasons, depending on species life‐history traits and temporal fluctuations in resources. We tested the importance of EH at multiple spatial scales on diversity and abundance of predator and parasitoid insects, and whether its effects changed across seasons. Insect sampling was carried out in highly fragmented landscapes in a Mediterranean region (Tuscany, Central Italy). We selected 18 semi‐natural patches, embedded in an intensive agricultural matrix. For each patch, EH was measured at three spatial scales (micro, patch, and landscape). Five groups of predator and parasitoid insects were sampled 16 times with pan traps between March and November, 2012. EH at the landscape scale positively influenced the diversity of predator and parasitoid insects, while the effects at smaller spatial scales were less evident. The strength and the direction of EH˗diversity relationship changed between groups and across seasons, indicating that the mechanisms by which EH affects predators and parasitoids are various and complex. Conservation strategies aimed at maximising the diversity of predators and parasitoids should focus more on increasing EH at the landscape scale than at the local scale.