Coronaviruses in avian species – review with focus on epidemiology and diagnosis in wild birds
subject: wild birds, poultry, coronavirus
description: Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution.
creator: Miłek Justyna, Blicharz-Domańska Katarzyna
source: Journal of Veterinary Research
publisher: Sciendo
date: 2018
language: EN
identifier: DOI: 10.2478/jvetres-2018-0035
coverage: Veterinary medicine

Distribution of the Ponto-Caspian Amphipods in Turkish Fresh Waters: An Overview
description: To date, 13 amphipod species [Dikerogammarus haemobaphes(Eichwald, 1841); D. istanbulensis Özbek & Özkan, 2011; D. gruberi Mateus & Mateus, 1990; Echinogammarus ischnusStebbing, 1899; Pontogammarus robustoides (Sars, 1894); P. maeoticus(Sowinsky, 1894); P. aestuarius(Derzhavin, 1924); Obesogammarus turcarum Stock, 1974; Amathillina cristata Sars, 1894; Chelicorophium curvispinum Sars, 1895; C. maeoticum(Sowinsky, 1898); C. robustum Sars, 1895 and Orchestia cavimana Heller, 1865] were reported from Turkey as the representatives of Ponto-Caspian amphipod fauna. Previous records and current distributional patterns of Ponto-Caspian amphipod crustaceans in Turkish inland waters were investigated. Three new localities were revealed as one of the southernmost points in distributional area of Pontogammarus robustoides (Sars, 1894).
creator: M. OZBEK
source: Mediterranean Marine Science
publisher: Hellenic Centre for Marine Research
date: 2011
language: EN
identifier: DOI: 10.12681/mms.44
coverage: Aquaculture. Fisheries. Angling

Primer design for complete sequencing of the Avastrovirus ORF2 gene
subject: PCR, Sequencing, Avastrovirus, Avian, ORF2
description: Avastrovirus infection is associated with enteric disease, nephritis, and hepatitis in birds. In this study, we present a protocol for the complete sequencing of the ORF2 gene of avian nephritis virus (ANV), chicken astrovirus (CAstV), and turkey astrovirus type 1 (TAstV-1) using a conventional Sanger technique. Previously and newly designed primer pairs targeting both the conserved flanking and internal regions of the ORF2 gene of these three viruses were used. The information derived from the astroviral sequences obtained in this study is fundamental for characterizing this virus and providing data regarding several aspects of disease epidemiology and prevention.
creator: Luis Ramiro Luna Espinoza, Laila Andreia Rodrigues Beserra, Rodrigo Martins Soares, Fabio Gregori
source: Semina: Ciências Agrárias
publisher: Universidade Estadual de Londrina
date: 2018
language: EN, PT
identifier: DOI: 10.5433/1679-0359.2018v39n1p411
coverage: Agriculture (General)

The Potential Influence of Value Added Tax Law Amendments on the Existence of E-Service Providing SMMEs in South Africa
subject: taxation, Value-added tax (VAT), electronic services, South Africa, tax practitioners, South African Revenue Services (SARS), Small Medium and Micro Enterprises (SMMEs)
description: In South Africa, almost all existing businesses are regarded as Small Medium and Micro Enterprises (SMMEs). Through legislation, the South African government has identified SMMEs as the best enablers to help with the achievement of certain core socio-economic objectives; particularly the creation of jobs and reduction of poverty levels. According to previous research studies these business entities are not achieving the latter socio-economic objectives; mainly as a result of their weak existence rate – up to 80% of these business entities fail within their first three years of existence. The latter is believed to stem from the realisation of economic factors – a major economic factor which adversely influences South African SMMEs is that of taxation. Over the years, more South African SMMEs have started to make use of the internet to conduct their respective business, which spurred the national government to make amendments to existing Value Added Tax (VAT) Laws by levying taxation on electronic services (e-services) provided by e-service suppliers. Hence, for this research study, the perception was formulated that the amendments made to VAT Laws will have an adverse influence on the existence of e-service providing South African SMMEs in the foreseeable future. Empirical research was conducted through means of obtaining quantitative data from registered South African Tax Practitioners based in the Cape Metropolis; all of whom had to adhere to strict delineation criterion. It was found that the amendments made to VAT Laws, by national government, will have an adverse influence on the existence of e-service providing South African SMMEs in the foreseeable future.
creator: Mogamat Riyaadh BARNES, Corne Truter VAN NIEKERK, Ayesha GOOL, William-John GROENER, Tracy LEE, Zubair MOOLA, Juan-Pierré BRUWER, Yolande SMIT
source: Expert Journal of Business and Management
publisher: Sprint Investify
date: 2016
language: EN
coverage: Business

Steroid Alkaloids from Holarrhena africana with Strong Activity against Trypanosoma brucei rhodesiense
subject: Holarrhena africana, Holarrhena fl oribunda, steroid alkaloid, Trypanosoma brucei rhodesiense, structure-activity relationship, anti-trypanosomal
description: In our continued search for natural compounds with activity against Trypanosoma brucei, causative agent of human African trypanosomiasis (HAT, “sleeping sickness”), we have investigated extracts from the leaves and bark of the West African Holarrhena africana (syn. Holarrhena floribunda; Apocynaceae). The extracts and their alkaloid-enriched fractions displayed promising in vitro activity against bloodstream forms of T. brucei rhodesiense (Tbr; East African HAT). Bioactivity-guided chromatographic fractionation of the alkaloid-rich fractions resulted in the isolation of 17 steroid alkaloids, one nitrogen-free steroid and one alkaloid-like non-steroid. Impressive activities (IC50 in µM) against Tbr were recorded for 3β-holaphyllamine (0.40 ± 0.28), 3α-holaphyllamine (0.37 ± 0.16), 3β-dihydroholaphyllamine (0.67 ± 0.03), N-methylholaphyllamine (0.08 ± 0.01), conessimine (0.17 ± 0.08), conessine (0.42 ± 0.09), isoconessimine (0.17 ± 0.11) and holarrhesine (0.12 ± 0.08) with selectivity indices ranging from 13 to 302. Based on comparison of the structures of this congeneric series of steroid alkaloids and their activities, structure-activity relationships (SARs) could be established. It was found that a basic amino group at position C-3 of the pregnane or pregn-5-ene steroid nucleus is required for a significant anti-trypanosomal activity. The mono-methylated amino group at C-3 represents an optimum for activity. ∆5,6 unsaturation slightly increased the activity while hydrolysis of C-12β ester derivatives led to a loss of activity. An additional amino group at C-20 engaged in a pyrrolidine ring closed towards C-18 significantly increased the selectivity index of the compounds. Our findings provide useful empirical data for further development of steroid alkaloids as a novel class of anti-trypanosomal compounds which represent a promising starting point towards new drugs to combat human African trypanosomiasis.
creator: Charles Okeke Nnadi, Ngozi Justina Nwodo, Marcel Kaiser, Reto Brun, Thomas J. Schmidt
source: Molecules
publisher: MDPI AG
date: 2017
language: EN
identifier: DOI: 10.3390/molecules22071129
coverage: Organic chemistry

RESULTS OF DETERMINING INDICATORS OF SALIVATION SPEED, MINERALIZED POTENTIAL, VISCOSITY AND PH OF ORAL FLUID IN CHILDREN WITH RECURRENT ARVI
subject: oral fluid, the rate of salivation, mineralized potential, pH, viscosity, acute respiratory viral infection
description: The article is devoted to studies the performance of oral fluid of children of 6-7 years, which often suffer from acute respiratory viral infections. Examination of 111 children with frequent acute respiratory viral infection and 89 healthy children revealed cariogenic situation in the mouth of sickly children, which is caused by the deterioration of the speed of salivation, mineralized potential, viscosity and pH of oral fluid in them. The results showed that the worst results of oral fluid parameters studied in children, who often suffer from ARVI. Our research has shown that children who often suffer acute respiratory viral infections, the rate of salivation is somewhat lower than in healthy children. Results of the study index MP children 6-7 years, both groups are almost identical. So the best indicator was in healthy children 6 years old - 2,51 ± 0,04 points, and the worst in children 7 years of age who are sick of SARS - 2,17 ± 0,12 points. Probable difference was observed only in average. We found that children who are sick of ARVI, the pH is lower than in healthy children. For example, in a group of healthy it varies from 6,64 ± 0,03 units to 6,65 ± 0.01, which corresponds to a weakly acidic value. In the group of children being ill its value - from 6,82 ± 0,01 units up to 6,97 ± 0,05 units, which is higher than in the healthy. Oral fluid viscosity index within the normal range in both groups of the study. But this figure is significantly higher in children with frequent episodes of acute respiratory viral infections like 6 or 7 years old - 1,60 ± 0,02 units and 1,76 ± 0,04 units respectively, in contrast to healthy children of the same age (1,31 ± 0,01 and 1,35 ± 0,02 units). Based on the results of the study can be argued that children who are sick of ARVI studied parameters worse than healthy. Consequently, children often suffer from acute respiratory viral infections studied indicators were worse than in healthy children, hence the presence of cariogeni…
creator: L. Kaskova, O. Pavlenkova
source: Український стоматологічний альманах
publisher: Ukrainian Medical Stomatological Academy
date: 2015
language: EN, RU, UK
coverage: Dentistry

Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
subject: trypanosomatidae, kraken taxonomic assignment tool, bowtie2 fast short reads aligner, ANCIENT DNA, parasitome, co-infection
description: Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect’s gut, and Lotmaria.
creator: Denis Sereno, Franck Dorkeld, Mohammad Akhoundi, Pascale Perrin
source: Genes
publisher: MDPI AG
date: 2018
language: EN
identifier: DOI: 10.3390/genes9080418
coverage: Genetics

Optimisation of qualitative and semi-quantitative detection of genetically modified crops by PCR
subject: PCR, qualitative detection, semi-quantitative detection, multiplex-PCR, Transgenic crops, maize MON810
description: For qualitative and semi-quantitative detection of genetically modified crops we selected the detection of the frequently used promoter 35S CaMV. To optimise the method we used two commercially available genotypes of maize from the company Monsanto (USA), i.e. the transgenic hybrid Bt-maize line MON810 and a genetically non-modified control (isogenic line to MON810). We tested the pri­mers and PCR programmes described by Greiner et al. (2005) and Hernandéz et al. (2005). When applying PCR methods of detection of Bt-maize the first step was to optimise the protocol for the detection of the maize genome and detection of the specific sites of genetically modified MON810 maize. For detection of the maize genome we selected the primers IVR1-F and IVR1-R (invertase gene) which verify the presence of the maize genome by a 226 bp product. For qualitative detection of the insert of Bt-maize MON810 the primer pairs VW01/VW03 (Greiner et al., 2005) and BT03/BT04 (Hernandéz et al., 2005) were used to detect the 35S CaMV promoter. Products of the size 178 bp and 280 bp, respectively, verify its presence. Based on the results of qualitative PCR we selected the primers VW01/VW03 for semi-quantitative detection of the amount of DNA of Bt-maize. For semi-quantitative PCR we have chosen sampling of the amplification product in the 30th cycle of the PCR reaction. In the genetically unmodified control a detection limit of 1% of admixture of Bt-maize was determined when using semi-quantitative PCR. The same primers as for semi-quantitative PCR were also used for multiplex PCR but with half the concentration of primers for standard PCR. This protocol however will have to be further optimised. The presented results introduce PCR methods for qualitative and semi-quantitative detection of DNA of the genetically modified Bt-maize MON810 which can also be used for other GM crops containing the 35S CaMV promoter. It could be suitable to use these methods for the qualitative detection and/or fo…
creator: Tomáš Vyhnánek, Pavel Hanáček
source: Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis
publisher: Mendel University Press
date: 2009
language: EN
identifier: DOI: 10.11118/actaun200957050313
coverage: Biology (General), Agriculture

Transmission of Severe Acute Respiratory Syndrome
subject: severe acute respiratory syndrome (SARS), Outbreak, Transmission, close contact, laboratory diagnosis, clinical virology
creator: Isao Arita, Kazunobu Kojima, Miyuki Nakane
source: Emerging Infectious Diseases
publisher: Centers for Disease Control and Prevention
date: 2003
language: EN
identifier: DOI: 10.3201/eid0909.030471
coverage: Infectious and parasitic diseases, Medicine

Surgical Helmets and SARS Infection
subject: Respiratory protective devices, severe acute respiratory syndrome, safety, Occupational, disease transmission, Patient-to-professional
description: Performance testing of two brands of surgical helmets indicated that their efficiency at in vivo filtration of sub–micrometer-sized particles is inadequate for their use as respirators. These helmets are not marketed for respiratory protection and should not be used alone for protection against severe acute respiratory syndrome when performing aerosol-generating procedures.
creator: James L. Derrick, Charles D. Gomersall
source: Emerging Infectious Diseases
publisher: Centers for Disease Control and Prevention
date: 2004
language: EN
identifier: DOI: 10.3201/eid1002.030764
coverage: Infectious and parasitic diseases, Medicine