Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling the effects of temperature change on the dynamics of tsetse flies and trypanosomiasis disease transmission

Modelling the effects of temperature change on the population dynamics of tsetse flies and trypanosomiasis transmission Zinhle Emily Mthombothi Department of Mathematical Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Thesis: MSc. (Mathematics) March 2018 Global temperatures have increased over recent decades. This is expected to have an impact on vector-borne diseases, raising questions such as: Will the increased temperature result in changing disease prevalence? How will vector populations be affected in terms of their density and distribution? It has been suggested that African trypanosomiasis, a zoonotic disease transmitted by tsetse flies, will exhibit increased incidence, and expand its geographical range, due to increasing temperatures. This project uses mathematical modelling to assess the impact of temperature change on tsetse fly population dynamics. Understanding these impacts could help us understand how trypanosomiasis transmission dynamics will be affected by global warming. We develop a temperaturedependent ordinary differential equations (ODE) model to model the growth in the numbers of pupal and adult tsetse. We fit the model to data on the number of tsetse flies (Glossina pallidipes Austen) on Antelope Island, Zimbabwe, between 5 February 1980 and 29 December 1981, estimated using mark recapture. The findings from this project concur with previous studies suggesting that temperature is the most important ii Stellenbosch University https://scholar.sun.ac.za
Tolerance of potentially diazotrophic bacteria to adverse environmental conditions and plant growth-promotion in sugarcane

ABSTRACT Sugarcane is one of the crops responsible for the high consumption of fertilizers in Brazil. To minimize this demand a sustainable alternative is to increase the studies to evaluate the beneficial effects of the relationship between plants/microorganisms, mainly plant growth-promoting bacteria. The objectives of this study were: a) to evaluate potentially diazotrophic bacteria isolates from sugarcane in adverse environmental conditions; b) inoculate these bacteria in sugarcane to evaluate their ability in plant growth-promotion. The study was carried in the Northeast of Brazil. Bacterial genera Burkholderia sp. , Pantoea sp. , Stenotrophomonas sp. and Enterobacter sp. were evaluated in different culture medium and later the bacterial isolates were inoculated in sugarcane evaluating the plant growth-promotion. Stenotrophomonas sp. and Pantoea sp. were tolerant to salinity and to different sources of carbon in acid medium and too tolerated high concentrations of pesticides and produced quorum sensing molecules (QS), but did not increase the dry matter production of sugarcane. Burkholderia sp. and Enterobacter sp. were more sensitive to salinity and pest control, but were more effective in plant growth-promotion. The tolerance of the bacteria to the adverse environmental conditions interfered negatively in the ability to plant growth-promotion.
Isolation of Natural Compounds from Syzygium densiflorum Fruits and Exploring its Chemical Property, Therapeutic Role in Diabetic Management

Syzygium densiflorum Wall. ex Wight & Arn (Myrtaceae) has been traditionally used by the local tribes of the Nilgiris, Tamil Nadu, India, for the treatment of diabetes. This study aimed to isolate the major phytoconstituents from the S. densiflorum fruits and to perform computational studies for chemical reactivity and biological activity of the isolated compound. Two different compounds were isolated from ethanolic extract of S. densiflorum fruits and purified using HPLC. The structures of the compounds were elucidated on the basis of their 1H NMR, 13C NMR, 1H-1H COSY, HMBC, HRESIMS, and FT-IR data. Further, the chemical reactivity of the compounds was analyzed by density functional theory calculations and its therapeutic role in diabetic management was examined by comparing the structure of isolated compounds with previously reported bioactive compounds. Of the two compounds ((6,6 & 1-kestopentaose (1) and 6-(hydroxymethyl)-3-[3,4,5- trihydroxy- 6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyoxane-2,4,5-triol)(2)). β-glucosidase, β-galactosidase, α-glucosidase and β-amylase inhibition activity of the compounds were predicted by structure activity relationship. Structure-activity relationship analysis was performed to predict the therapeutic role of isolated compounds. These computational studies may be performed to minimize the efforts to determine the therapeutic role of natural compounds.
Impacts of silencing CD105 and Ki67 gene expression on the biological behavior of ovarian cancer OVCAR3 cells

Objective: To investigate the effect of silencing CD105 and Ki67 gene expression on OVCAR3 cell line in ovarian cancer. Methods: According to cell transfection results, OVCAR3 cells were divided into CD105-siRNA, Ki67-siRNA, CD105-siRNA + Ki67-siRNA, negative control (NC1 and NC2) and control (non-transfection) groups. The effect of silencing CD105, Ki67 and their combined gene on proliferation, migration, invasion and apoptosis of human ovarian cancer cells can be studied and analyzed with MTT assay, wound-healing assay, Transwell chamber and ﬂow cytometry. Results: Compared with their respective negative control and liposome control groups, proliferation, migration and invasion abilities of OVCAR3 cells were decreased obviously in CD105-siRNA, Ki67-siRNA and CD105-siRNA + Ki67-siRNA groups after gene silencing. Whereas, the most signiﬁcant change was detected in CD105-siRNA + Ki67-siRNA group along with obviously increased apoptosis rate of cancer cells, and the differences were of statistical signiﬁcance ( p < .01, p < .05). Conclusions: Expression vectors of CD105-siRNA and Ki67-siRNA can inhibit the proliferation of OVCAR3 cells, reduce their abilities of migration and invasion, and induce apoptosis of tumor cells. The effect of combined gene silence will be more signiﬁcant.
Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 7: suitability of taxonomic units notified to EFSA until September 2017

Abstract The qualified presumption of safety (QPS) concept was developed to provide a harmonised generic pre‐evaluation to support safety risk assessments of biological agents performed by EFSA's scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, considered to be ‘qualifications’ which should be assessed at the strain level by the EFSA's scientific Panels. No new information was found that would change the previously recommended QPS taxonomic units and their qualifications. The BIOHAZ Panel confirms that the QPS approach can be extended to a genetically modified production strain if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Between April and September 2017, the QPS notification list was updated with 46 applications for market authorisation. From these, 14 biological agents already had QPS status and 16 were not included as they are filamentous fungi or enterococci. One notification of Streptomyces K‐61 (notified as former S. griseoviridis) and four of Escherichia coli were not considered for the assessment as they belong to taxonomic units that were excluded from further evaluations within the current QPS mandate. Eight notifications of Bacillus thuringiensis and one of an oomycete are pending the reception of the complete application. Two taxonomic units were evaluated: Kitasatospora paracochleata, which had not been evaluated before, and Komagataella phaffii, previously notified as Pichia pastoris included due to a change in the taxonomic identity. Kitasatospora paracochleata cannot be granted QPS status due to lack of information on its biology and to its possible production of toxic secondary metabolites. The species Komagataella phaffii can be recommended for the QPS list when used for enzyme production.
In vitro Antiproliferative and Antidermatophyte Activities of Essential Oils from Three Moroccan Medicinal Plants

Abstract The main of this study is to evaluate the anticancer and anti-dermatophyte activities of Mentha pulegium, Rosmarinus officinalis and Lavandula stoechas essential oils. The cytotoxic effect was carried out on cancer cell lines Vero, L20B and RD using MTT colorimetric assay. The anti-dermatophyte activity was tested on Trichophyton violaceum, Trichophyton tonsurans and Trichophyton mentagrophytes using direct contact method. Essential oils of three aromatic species are rich in bioactive compounds such oxygenated and no-oxygenated monoterpenes. Lavandula stoechas essential oil showed interesting anticancer activity against RD (IC50 =19.03±28.05% (v/v)) and L20B (IC50 =33.84±1.72% (v/v)). Moreover, M. pulegium essential oil had an important cytotoxic effect against Vero cell line (IC50 =60.21±1.9% (v/v)). The best pharmacological selectivity indexes were obtained with L. stoechas essential oil on RD (11.098) and L20B (6.241) cell lines. The essential oil of R. officinalis showed remarkable anti-dermatophyte effects than L. stoechas and P. pulegium. The IC50 values of R. Officinalis essential oil against T. mentagrophytes, T. violaecum and T. tonsurans were respectively 0.53, 0.60 and 0.64% (v/v). The findings of these results showed that essential oils of L. stoechas and M. pulegium are a good source for anticancer drug discovery and the essential oil of R. officinalis is a promising source as anti-dermatophyte agents. Whereas, further studies investigating the pharmacological properties on other type of cancer cell lines and fungal species are necessary. Moreover, investigations regarding the mechanism of action of these oils and their major compounds are also necessary.
Fractionation of canola meal using sieving technology

Abstract: The present study explored the potential for the production of canola meal (CM) fractions of different chemical and nutritive composition. Three meals from conventional black- and yellow-seeded Brassica napus and Brassica juncea canola were subjected to sieving. The use of sieves from 250 to 600 µm resulted in the production of fractions fine 1, fine 2, medium, and coarse. When compared with the parent meals, the content of total dietary fiber of fractions fine 1 and 2 decreased from 300 to 214 and 267 g kg−1 for conventional CM, 270 to 216 and 234 g kg−1 for B. napus yellow, and 255 to 153 and 187 g kg−1 for B. juncea meal. Crude protein increased from 368 to 420 and 396 g kg−1 for conventional CM, 410 to 436 and 430 g kg−1 for yellow CM, and 423 to 479 and 468 g kg−1 for B. juncea meal. The effects of three parent meals and their respective fractions fine 1 and 2 were evaluated in a growth performance experiment with broiler chickens. There was no significant effect of CM diets on growth performance indicating that CM and its low-fiber fractions could effectively replace soybean meal in diets for young poultry.
Performance of different shapes of traps in capturing Bactrocera spp. (Diptera: Tephritidae) in peach and pear orchards

The role of different shapes of methyl eugenol based traps in peach and pear were studied at PunjabAgricultural University, Ludhiana, India against major fruit fly species i.e. Bactrocera zonata (Saunders) and Bactrocera dorsalis (Hendel). In this experiment, cylindrical traps, spherical traps, triangular traps and PAU fruit fly traps were used. The results revealed that triangular traps (71.58 males) had captured significantly more population followed by cylindrical traps (38.86 males), PAU fruit fly traps (29.61 males) and spherical traps (21.30 males) in peach; whereas in pear, the number of fruit fly males captured/trap/week were significantly high in triangular traps (127.92 males) as compared to PAU fruit fly traps (55.30 males), cylindrical traps (51.08 males) and spherical traps (42.44 males). The mean percentage of fruit fly damage was also lowest in triangular traps in peach (4.33%) and in pear (6.72%) respectively. However, cost: benefit ratio was quite low in triangular traps in both peach (1:30.86) and pear (1:20.93).
Impact of KNO3 Primed Seeds on the Performance of Late Sown Sesame (Sesamum indicum L.)

In the present piece of work the effects of seed priming with KNO 3 on late sown sesame crop ( Sesamum indicum ) var. T-4 (V 1 ), T-12 (V 2 ) and Shekhar (V 3 ) in respect of germination, physiomorphological, biochemical and yield parameters were observed. The treatments comprised of KNO 3 [10 mM (T 1 ), 15 mM (T 2 )] and distilled water (DW) primed sets (T 0 ). The results showed that the KNO 3 treatment promoted germination percentage, root and shoot length, fresh and dry weights of seedling, catalase, peroxidase and proline content as well as yield attributes like number of capsules plant -1 , number of seeds capsule -1 , test weight (1000 seed weight in g) and yield plant -1 (g). After 80 h, the highest germination percentage was recorded in 15 mM KNO 3 (T 2 ) primed seeds of Sesamum indicum var. T-4, T-12 and Shekhar. The average of root length, shoot length, fresh weight, and dry weight was recorded highest in treatment T 2 in comparison to distilled water primed seeds (control) at 25 DAS in all varieties i.e., T-4, T-12 and Shekhar respectively. Yield attributes like number of capsules plant -1 , number of seeds capsule -1 , test weight and yield plant -1 were also highest in treatment T 2 in all varieties V 1 , V 2 and V 3 respectively. Variety V 1 and treatment T 2 recorded the highest values of catalase, peroxidase and proline content followed by variety V 3 and V 2 and treatment T 1 and T 0 at 45 DAS respectively. It had been found that seed priming with KNO 3 ameliorate the effect of late sowing.
Controlling insulin resistance through modulation of interplay between mediators of cellular senescence: A mathematical study

Obesity, metabolic syndrome and premature ageing form a hugely researched and discussed area of interest these days. In the pathology of this cluster of conditions, adipose tissue is gaining attention as a major playground for interplay between metabolic stress, inflammation and accelerated ageing, and not merely being an energy storage tank. Drastic elevation in the levels of reactive oxygen species, due to lipid overload and excessive lipolysis, causes genotoxic damage such as shortening of telomeres (an indicator of accelerated cell ageing), increased mRNA and protein expression for p53, p21, TNF–α, IL-6 (interleukin 6), impaired insulin mediated glucose uptake, and decreased TERT mRNA expression. The increase of p53 in adipocytes is deleterious, since elevated p53 results in pre-mature ageing of fat tissues which secrete pro-inflammatory cytokines thereby contributing to insulin resistance. But inhibition of p53 as a therapeutic target, as suggested by many previous studies, could result in developing high risks of cancer. The association between hyperlipidemic/hyperglycaemic stress, premature growth arrest and insulin resistance, thus, forms an interesting premise for searching targets and designing interventions for therapy of metabolic syndrome, type 2 diabetes mellitus etc. We developed a mathematical study involving a 5D ODE model, which revealed crucial parametric conditions governing p53 dynamics in the case of metabolic stress-induced cellular senescence, and shed light on potential strategies to reduce pro-inflammatory cytokine levels which exacerbate insulin resistance through premature cellular ageing. Highlights p53 oscillations signify DNA repair, and persistent stress causes prolonged surge in p53 levels inducing cellular senescence. p53-induced cellular senescence promotes inflammation and enhances progression of insulin resistance. Regulation of Mdmx and Akt can be a strategy to rejuvenate ageing cells through management of IL-6 dynamics.
Marker based assessment of genetic diversity in aethiopicum and melongena species of genus Solanum.

The genetic diversity among 14 genotypes of Solanum melongena and Solanum aethiopicum was assessed using 40 polymorphic markers of SSR, ISSR and RAPD. Twelve RAPD markers with polymorphism percentage of 63.0 to 100.0 amplified 7.75 loci per marker with a total of 93 polymorphic bands. Sixteen polymorphic ISSR markers revealed 73 polymorphic loci with 4.56 polymorphic loci per marker and polymorphism percentage of 43.0 to 100.0 whereas 12 SSR markers amplified 43 polymorphic alleles with average polymorphic alleles per marker of 3.58. Forty markers of RAPD, ISSR and SSR detected a total of 57 unique/novel alleles with aethiopicum whereas 19 unique/novel alleles were generated in different genotypes of melongena. Each marker system individually as well as altogether exhibited least similarity coefficients of 0.24 to 0.29 between aethiopicum and melongena species of Solanum whereas higher order of similarity was observed within melongena group. Dendrograms generated using marker data of RAPD, ISSR, SSR and RAPD+ISSR+SSR separated aethiopicum and melongena in two divergent groups. We did not observe exactly similar pattern of grouping of different genotypes of melongena group in more homogenous cluster when different marker systems were compared. The Mantel test between the two Jaccard’s similarity matrices indicated high correspondence between RAPD and ISSR, RAPD and SSR, and ISSR and SSR based similarity matrices. Distribution of genotypes from different regions did not show clear clustering pattern when three marker systems were compared. Three dimensional plots of genotypes based on principal component analysis indicate close correspondence with UPGMA clustering approach.
Abundance of Bacteria, Fungi, and Sclerotinia homoeocarpa in the Thatch and Soil of Golf Courses

Thatch management in turfgrass has been recommended as part of integrated pest management; however, there is limited understanding of the microbial community in thatch. Previous studies on the turfgrass phytobiome mostly focused on the soil; however, culture-based studies have suggested that the thatch layer of golf courses contains higher bacterial and fungal abundances than the soil. In our study, quantitative PCR was used to investigate total abundance of bacteria, fungi, and the turfgrass pathogen, Sclerotinia homoeocarpa (causal agent of dollar spot) in the thatch and soil of three golf courses on two sampling dates. Additionally, we compared the abundance of these organisms among roughs, fairways, and putting greens, which are under different management intensities. Our results demonstrate bacterial abundance was higher in May than in September, but not consistently higher in the thatch or soil among the three golf courses or management areas. Fungi, and specifically S. homoeocarpa, are more abundant in the thatch than in the soil. These results show the necessity for future turfgrass phytobiome studies to analyze both thatch and soil to obtain a complete picture of bacterial and fungal microbial community structure and dynamics on golf courses. Despite the differences in fungicide usage and management inputs, there were no differences in S. homoeocarpa abundance among the three management areas in the soil. S. homoeocarpa abundance was higher in the thatch on the conventional golf course fairway in September. These results may have important practical implications for development of integrated disease management strategies and for understanding the epidemiology of S. homoeocarpa on golf courses.
Modulation of TLR2 and TLR4 in Macrophages Following Trichinella Spiralis Infection

Summary Parasitic helminthes can suppress and/or regulate the host immune response to allow long-term survival and chronic infection where toll-like receptors (TLRs) expressed on macrophages play essential roles in response to parasitic infection. Semi-quantitative PCR and flow cytometry studies about the modulation of TLRs and cytokine profiles in macrophages following T. spiralis infection were performed. TLRs, MyD88 and NF-κB were up-regulated by T. spiralis infection and essential to the parasite life cycles. Cytokines profiles (IL-6, IL-10, IL-12, TNF-α) were modulated during T. spiralis infection. Results suggest that T. spiralis infection may regulate the expression of TLR4 on macrophages and TLR4/MyD88/NF-κB signaling pathways. This study provides further insights into the mechanisms of TLR-mediated post-inflammatory response during T. spiralis infection.
Geographic distribution and habitat use of Lepidoblepharis miyatai (Squamata: Sphaerodactylidae), with comments on the taxonomic status of the genus in northern Colombia

Geographic distribution and habitat use of Lepidoblepharis miyatai (Squamata: Sphaerodactylidae), with comments on the taxonomic status of the genus in northern Colombia. We present some ecological and biogeographic data on Lepidoblepharis miyatai, a small and endangered gecko endemic to the northwestern foothills of the Sierra Nevada de Santa Marta (SNSM), 31 years after its description. Based on museum specimens and feld observations, we recorded four new localities with confrmed presence of L. miyatai. We calculated the extent of occurrence and altitudinal distribution of this species reaching 21.3 km2 and from sea level to 360 m respectively. Lepidoblepharis miyatai inhabits plant formations of scrub thorn and tropical deciduous forest. Based on microhabitat data obtained from 88 individuals observed in “Las Tinajas Village” we can state a differential use of three substrates with predominant use of leaf-litter. We consider L. miyatai an endemic species of the northwestern sector of the SNSM with a distribution range limited to the south-west by the occurrence of L. sanctaemartae, and towards the east by a thus far undetermined Lepidoblepharis species (here called Lepidoblepharis cf. sanctaemartae). We do not register sympatry of L. miyatai with any other congener. Accordingly, we consider that the recent records of this species in the southeast sector of SNSM are erroneous, given that the specimens cited as L. miyatai of this zone correspond to Lepidoblepharis cf. sanctaemartae. Finally, a reevaluation of the conservation status of L. miyatai is needed, including precise information of its distribution.
Human microbiome and environmental disease

The importance of human microbiota and their genomes, human microbiome, in health and disease has been increasingly recognized. Human microbiome has tremendous impact in our pathophysiology by modulating metabolic functions, protecting against pathogens, and educating the immune system. In particular, human microbiome is a major player at the interface between humans and their environment and therefore is crucial to the development of environmental disease. In this article, we briefly summarize and interpret the recent advances in the understanding of the roles of human microbiome in environment-related health and disease, and call for a more systematic integration of human microbiome and environmental disease research within the framework of evolutionary medicine.