scholarly journals Genetic Characterisation of South African and Mozambican Bovine Rotaviruses Reveals a Typical Bovine-like Artiodactyl Constellation Derived through Multiple Reassortment Events

Pathogens ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1308
Author(s):  
Amy Strydom ◽  
Celeste M. Donato ◽  
Martin M. Nyaga ◽  
Simone S. Boene ◽  
Ina Peenze ◽  
...  
Keyword(s):  
South African ◽  
Illumina Miseq ◽  
Interspecies Transmission ◽  
African Countries ◽  
Double Stranded Rna ◽  
Bovine Rotavirus ◽  
Whole Genomes ◽  
Miseq Platform ◽  
Stool Samples ◽  
Animal Strains

This study presents whole genomes of seven bovine rotavirus strains from South Africa and Mozambique. Double-stranded RNA, extracted from stool samples without prior adaptation to cell culture, was used to synthesise cDNA using a self-annealing anchor primer ligated to dsRNA and random hexamers. The cDNA was subsequently sequenced using an Illumina MiSeq platform without prior genome amplification. All strains exhibited bovine-like artiodactyl genome constellations (G10/G6-P[11]/P[5]-I2-R2-C2-M2-A3/A11/A13-N2-T6-E2-H3). Phylogenetic analysis revealed relatively homogenous strains, which were mostly related to other South African animal strains or to each other. It appears that these study strains represent a specific bovine rotavirus population endemic to Southern Africa that was derived through multiple reassortment events. While one Mozambican strain, MPT307, was similar to the South African strains, the second strain, MPT93, was divergent from the other study strains, exhibiting evidence of interspecies transmission of the VP1 and NSP2 genes. The data presented in this study not only contribute to the knowledge of circulating African bovine rotavirus strains, but also emphasise the need for expanded surveillance of animal rotaviruses in African countries in order to improve our understanding of rotavirus strain diversity.

scholarly journals “A different gut microbiome linked to inflammation found in cirrhotic patients with and without hepatocellular carcinoma”

2017 ◽  
Author(s):  
Federico Piñero ◽  
Martín Vazquez ◽  
Patricia Baré ◽  
Cristian Rohr ◽  
Manuel Mendizabal ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Gut Microbiome ◽  
Illumina Miseq ◽  
Differential Abundance ◽  
Receptor Signalling ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Cirrhotic Patients ◽  
Stool Samples ◽  
Inflammatory Milieu

SUMMARYBackgroundNo specific microbiome in patients with hepatocellular carcinoma (HCC) has been reported to date.AimTo compare the gut microbiome found in cirrhotic patients with and without HCC.MethodsFrom 407 patients with Child Pugh A/B cirrhosis prospectively followed, 25 with HCC (cases) were matched with 25 without HCC (wo-HCC) in a 1:1 ratio according to age, gender, etiology, Child Pugh and severity of portal hypertension. In addition results were also compared with 25 healthy subjects. Faecal stool samples were collected noninvasively, aliquoted for DNA extraction and sequenced for the V3-V4 region of the microbial 16S rRNA (Illumina MiSeq Platform).ResultsThere were no significant clinical differences among cases and controls. We found a differential abundance in family members of Firmicutes with a 3-fold increased of Erysipelotrichaceae and a 5-fold decrease in family Leuconostocaceae in HCC when compared to wo-HCC controls. Genus Fusobacterium was found 5-fold decreased in HCC versus wo-HCC. The ratio bacteriodes/prevotella was increased in HCC due to the significant decrease in the genus prevotella. Genus Odoribacter and Butyricimonas were more differentialy abundant in HCC. This pattern has been previously associated with an inflammatory milieu with a putative increased activation of NOD-like receptor signalling pathways. A Random Forest model trained with differential abundant taxa correctly classifyed HCC individuals with an error of 22%.ConclusionsA pattern of microbiome linked to inflammation was observed in cirrhotic patients with HCC. These findings open the discussion whether or not microbiota has a physiopathologic role in HCC development in cirrhosis.

scholarly journals Gut Microbiome Alteration after Reboxetine Administration in Type-1 Diabetic Rats

2021 ◽  
Vol 9 (9) ◽  
pp. 1948
Author(s):  
Sinem Aydin ◽  
Ceren Ozkul ◽  
Nazlı Turan Yucel ◽  
Hulya Karaca
Keyword(s):  
Gut Microbiota ◽  
Illumina Miseq ◽  
Diabetic Rats ◽  
Clinical Settings ◽  
Illumina Miseq Platform ◽  
Noradrenaline Reuptake ◽  
Miseq Platform ◽  
Stool Samples ◽  
Study Type

Antidepressants are drugs commonly used in clinical settings. However, there are very limited studies on the effects of these drugs on the gut microbiota. Herein, we evaluated the effect of reboxetine (RBX), a selective norepinephrine (noradrenaline) reuptake inhibitor (NRI), on gut microbiota in both diabetic and non-diabetic rats. This is the first report of relation between reboxetine use and the gut microbiota to our knowledge. In this study, type-1 diabetes induced by using streptozotocin (STZ) and RBX was administered to diabetic rats and healthy controls for 14 days. At the end of the treatment, stool samples were collected. Following DNA extraction, amplicon libraries for the V3-V4 region were prepared and sequenced with the Illumina Miseq platform. QIIME was used for preprocessing and analysis of the data. As a result, RBX had a significant effect on gut microbiota structure and composition in diabetic and healthy rats. For example, RBX exposure had a pronounced microbial signature in both groups, with a low Firmicutes/Bacteroidetes ratio and low Lactobacillus levels. While another abundance phylum after exposure to RBX was Proteabacteria, other notable taxa in the diabetic group included Flavobacterium, Desulfovibrionaceae, Helicobacteriaceae, Campylobacterales, and Pasteurellacae when compared to the untreated group.

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

scholarly journals Conservation research output in sub-Saharan Africa is increasing, but only in a few countries

Oryx ◽  
2020 ◽  
pp. 1-10
Author(s):  
P. Christy Pototsky ◽  
Will Cresswell
Keyword(s):  
South African ◽  
Agricultural Land ◽  
Research Output ◽  
Sub Saharan Africa ◽  
Search Term ◽  
African Countries ◽  
Research Papers ◽  
North American Country ◽  
Conservation Research ◽  
Sub Saharan

Abstract We tested if peer-reviewed conservation research output has increased in sub-Saharan African countries over the last 30 years in response to increased development. We carried out a bibliometric analysis to identify the number of conservation research papers published by national authors of 41 sub-Saharan African countries during 1987–2017, to provide an index of national conservation research output. We identified country-specific development factors influencing these totals, using general linear modelling. There were positive relationships between conservation research output and population size, GDP, literacy rate, international tourism receipts and population growth rate, and negative relationships with urban population and agricultural land cover, in total explaining 77% of variation. Thirty-eight per cent of countries contributed < 30 conservation research papers (of 12,701) in 30 years. Analysis of trends in primary authorship in a random subsample of 2,374 of these papers showed that primary authorship by sub-Saharan African authors has increased significantly over time but is now at a lower rate than primary authorship for authors from countries outside the country associated with the search term, usually a European or North American country. Overall, 46% of papers had national primary authors, but 67% of these were South African. The results show that conservation research output in sub-Saharan Africa overall is increasing but only significantly in a few countries, and is still dominated by non-national scientists, probably as a result of a lack of socio-economic development.

Stability and Governability the Benign Effects of Party Dominance in South Africa

2020 ◽  
Vol 13 (1) ◽  
pp. 56-75
Author(s):  
Ainara Mancebo
Keyword(s):  
South Africa ◽  
South African ◽  
Trade Unions ◽  
African National Congress ◽  
The Other ◽  
Democratic Transitions ◽  
African Countries ◽  
National Congress ◽  
Independence Era ◽  
Party Dominance

A tripartite alliance formed by the African National Congress, the South African Communist Party and the Congress of South African Trade Unions has been ruling the country with wide parliamentarian majorities. The country remains more consensual and politically inclusive than any of the other African countries in the post-independence era. This article examines three performance’s aspects of the party dominance systems: legitimacy, stability and violence. As we are living in a period in which an unprecedented number of countries have completed democratic transitions, it is politically and conceptually important that we understand the specific tasks of crafting democratic consolidation.

scholarly journals Estimating the burden of cardiovascular risk in community dwellers over 40 years old in South Africa, Kenya, Burkina Faso and Ghana

2021 ◽  
Vol 6 (1) ◽  
pp. e003499
Author(s):  
Ryan G Wagner ◽  
Nigel J Crowther ◽  
Lisa K Micklesfield ◽  
Palwende Romauld Boua ◽  
Engelbert A Nonterah ◽  
...  
Keyword(s):  
Risk Factors ◽  
Risk Factor ◽  
South African ◽  
Sub Saharan Africa ◽  
African Countries ◽  
Cvd Risk ◽  
Genomic Studies ◽  
Sub Saharan ◽  
Context Specific ◽  
The Impact

IntroductionCardiovascular disease (CVD) risk factors are increasing in sub-Saharan Africa. The impact of these risk factors on future CVD outcomes and burden is poorly understood. We examined the magnitude of modifiable risk factors, estimated future CVD risk and compared results between three commonly used 10-year CVD risk factor algorithms and their variants in four African countries.MethodsIn the Africa-Wits-INDEPTH partnership for Genomic studies (the AWI-Gen Study), 10 349 randomly sampled individuals aged 40–60 years from six sites participated in a survey, with blood pressure, blood glucose and lipid levels measured. Using these data, 10-year CVD risk estimates using Framingham, Globorisk and WHO-CVD and their office-based variants were generated. Differences in future CVD risk and results by algorithm are described using kappa and coefficients to examine agreement and correlations, respectively.ResultsThe 10-year CVD risk across all participants in all sites varied from 2.6% (95% CI: 1.6% to 4.1%) using the WHO-CVD lab algorithm to 6.5% (95% CI: 3.7% to 11.4%) using the Framingham office algorithm, with substantial differences in risk between sites. The highest risk was in South African settings (in urban Soweto: 8.9% (IQR: 5.3–15.3)). Agreement between algorithms was low to moderate (kappa from 0.03 to 0.55) and correlations ranged between 0.28 and 0.70. Depending on the algorithm used, those at high risk (defined as risk of 10-year CVD event >20%) who were under treatment for a modifiable risk factor ranged from 19.2% to 33.9%, with substantial variation by both sex and site.ConclusionThe African sites in this study are at different stages of an ongoing epidemiological transition as evidenced by both risk factor levels and estimated 10-year CVD risk. There is low correlation and disparate levels of population risk, predicted by different risk algorithms, within sites. Validating existing risk algorithms or designing context-specific 10-year CVD risk algorithms is essential for accurately defining population risk and targeting national policies and individual CVD treatment on the African continent.

scholarly journals COMPUTATIONAL FLUID DYNAMICS STUDY OF DUSTY AIR FLOW OVER NACA 63415 AIRFOIL FOR WIND TURBINE APPLICATIONS

2017 ◽  
Vol 79 (7-3) ◽  
Author(s):  
Iham F. Zidane ◽  
Khalid M. Saqr ◽  
Greg Swadener ◽  
Xianghong Ma ◽  
Mohamed F. Shehadeh
Keyword(s):  
Numerical Simulation ◽  
Wind Turbine ◽  
South African ◽  
Stokes Equations ◽  
Lift Coefficient ◽  
Turbine Blades ◽  
Aerodynamic Performance ◽  
Accurate Estimation ◽  
African Countries ◽  
Sand Particles

Gulf and South African countries have enormous potential for wind energy. However, the emergence of sand storms in this region postulates performance and reliability challenges on wind turbines. This study investigates the effects of debris flow on wind turbine blade performance. In this paper, two-dimensional incompressible Navier-Stokes equations and the transition SST turbulence model are used to analyze the aerodynamic performance of NACA 63415 airfoil under clean and sandy conditions. The numerical simulation of the airfoil under clean surface condition is performed at Reynolds number 460×103, and the numerical results have a good consistency with the experimental data. The Discrete Phase Model has been used to investigate the role sand particles play in the aerodynamic performance degradation. The pressure and lift coefficients of the airfoil have been computed under different sand particles flow rates. The performance of the airfoil under different angle of attacks has been studied. Results showed that the blade lift coefficient can deteriorate by 28% in conditions relevant to the Gulf and South African countries sand storms. As a result, the numerical simulation method has been verified to be economically available for accurate estimation of the sand particles effect on the wind turbine blades.

scholarly journals A Rapid Bacteriophage DNA Extraction Method

2018 ◽  
Vol 1 (3) ◽  
pp. 27 ◽  
Author(s):  
Džiuginta Jakočiūnė ◽  
Arshnee Moodley
Keyword(s):  
Dna Extraction ◽  
Illumina Miseq ◽  
Extraction Methods ◽  
Resistant Bacteria ◽  
Simple Method ◽  
Antibiotic Resistant ◽  
Phage Dna ◽  
Specialized Equipment ◽  
Miseq Platform ◽  
Dna Extraction Methods

Bacteriophages (phages) are intensely investigated as non-antibiotic alternatives to circumvent antibiotic resistance development as well as last resort therapeutic options against antibiotic resistant bacteria. As part of gaining a better understanding of phages and to determine if phages harbor putative virulence factors, whole genome sequencing is used, for which good quality phage DNA is needed. Traditional phage DNA extraction methods are tedious and time consuming, requiring specialized equipment e.g., an ultra-centrifuge. Here, we describe a quick and simple method (under four hours) to extract DNA from double stranded DNA (dsDNA) phages at titers above 1.0 × 1010 plaque-forming units (PFU)/mL. This DNA was suitable for library preparation using the Nextera XT kit and sequencing on the Illumina MiSeq platform.

scholarly journals A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens

2018 ◽  
Vol 374 (1763) ◽  
pp. 20170395 ◽  
Author(s):  
Barnabas H. Daru ◽  
Elizabeth A. Bowman ◽  
Donald H. Pfister ◽  
A. Elizabeth Arnold
Keyword(s):  
Species Interactions ◽  
Fungal Endophytes ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Herbarium Specimens ◽  
Proof Of Concept ◽  
Ledum Palustre ◽  
Surface Contaminants ◽  
Symptomless Plant ◽  
Miseq Platform

Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome ( Andromeda polifolia and Ledum palustre subsp . groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years . We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

scholarly journals An Evaluative Study of Criminalistics: A Case of South African Counterfeiting and Knock-Off Menace

2021 ◽  
Vol 4 (2) ◽  
pp. 45-60
Author(s):  
Godfrey Thenga
Keyword(s):  
South Africa ◽  
South African ◽  
Human Life ◽  
Health Hazard ◽  
Capital Flight ◽  
Tax Revenue ◽  
African Countries ◽  
Counterfeit Goods ◽  
Evaluative Study ◽  
The World

Counterfeit goods are a health hazard to human life, environment and business. More so as the goods destroy the viability of legitimate businesses across the world. Counterfeit goods are characterized as a threat to the financial viability of legitimate businesses and has a dire impact on the tax revenue of countries, necessitating its effective and efficient policing for the financial wellbeing of countries. If not well managed, counterfeit goods could lead to unemployment, disinvestment and capital flight in countries. The available evidence reveals that even though counterfeit goods has dire consequences for the economic wellbeing of countries, its penalties in most African countries are less severe in comparison to penalties for other crimes. The sight of counterfeit goods in many places, such as on busy street corners and transportation terminals in the Southern parts of Africa, attests to its prevalence in the continent. Especially in South Africa as the country has become a transit point for contrabands. Post 1994, South Africa opened its borders to the world of branded and protected goods and this enabled rogue people to trade in counterfeit goods. Effective policing is hindered by the use of sophisticated skills and expertise that leads to counterfeit goods resembling genuine goods. Moreover, in South Africa, the problem persists despite the promulgation of the Counterfeit Goods Act 37 of 1997, thus questioning the effectiveness of the policing strategies in use to quell the problem.

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