The complete genome sequence of a South African isolate of grapevine virus F (GVF) is presented. It was first detected by metagenomic next-generation sequencing of field samples and validated through ...direct Sanger sequencing. The genome sequence of GVF isolate V5 consists of 7539 nucleotides and contains a poly(A) tail. It has a typical vitivirus genome arrangement that comprises five open reading frames (ORFs), which share only 88.96 % nucleotide sequence identity with the existing complete GVF genome sequence (JX105428).
A survey of viruses affecting grapevine in the wine regions of the Western Cape Province in South Africa was conducted. The survey determined the relative abundance of five different Grapevine ...leafroll-associated virus 3 (GLRaV-3) variants. Virus profiles were also determined for individual vines. A total of 315 plants were sampled and analysed over two growing seasons. Five GLRaV-3 variants were detected as either single or mixed infections, with GLRaV-3 variant groups II and VI being the most prominent as single infections and in combinations with each other and other variants. An analysis of the distribution of variants per region showed that single infections of variant groups II and VI occurred predominantly in certain regions, and were equally distributed in the red and white cultivars studied. The distribution of a recently identified, unclassified variant of GLRaV-3 (represented by isolates GH24 and GTG10) was included in the study. The overall analysis showed that infection with variant groups II and VI were the most abundant among the samples with 49.8 and 47.6 %, respectively, followed by variant group I, variants similar to isolate GH24 and variant group III with 16.2, 13.3 and 2.5 % infection, respectively. Mixed infections, representing 36 virus combinations, were found in 251 plants. The most abundant virus combination was GLRaV-3 with Grapevine virus E (GVE), found in 28 % of the plants. GLRaV-3 was the predominant virus detected in the samples with a frequency of 80 % detection, followed by GVE (57.4 %), Grapevine rupestris stem pitting-associated virus (GRSPaV) (36.8 %), Grapevine virus A (GVA) (19.3 %), Grapevine virus F (GVF) (16.25 %), Grapevine leafroll-associated virus 2 (GLRaV-2) (8.25 %), Grapevine leafroll-associated virus 1 (GLRaV-1) (1.58 % infection) and Grapevine leafroll-associated virus 4 (GLRaV-4 like) (0.6 %). Most of the plants tested were infected with multiple viruses. The complexity of virus populations detected in this study, highlights the need for detection methods able to identify all viruses and their variants in vineyards. The information generated in this study will assist in the development of reliable detection assays that will benefit the monitoring of disease spread and aid in the efficient management of Grapevine leafroll disease (GLD).
Thesis (MSc)--Stellenbosch University, 2015.
ENGLISH ABSTRACT: Vitis vinifera is the woody crop most susceptible to intracellular pathogens. Currently 70 pathogens;
infect grapevine, of which 63 are ...of viral origin. Grapevine leafroll-associated virus 3 (GLRaV-3);
is the type species of the genus Ampelovirus, family Closteroviridae. It is considered to be the;
primary causative agent of Grapevine leafroll disease (GLD) globally; however, the etiology of;
GLD is not completely understood. Here we report on the viral populations present in GLD;
symptomatic grapevines across the Western Cape province, South Africa. A widespread survey was;
performed to screen 315 grapevines for 11 grapevine-infecting viruses using RT-PCR. Additionally,;
GLRaV-3 variant groups were distinguished with high-resolution melt (HRM) curve analysis used;
in conjunction with real-time RT-PCR. Members of the family Closteroviridae were detected with;
the highest frequency, particularly GLRaV-3 that was detected in 87% of tested plants. Nextgeneration;
sequencing (NGS) is capable of detecting known and novel viruses without prior;
knowledge of viral sequences and when used in a metagenomic approach is able to detected viral;
populations within diseased vines. A total of 17 grapevine samples were subjected to NGS using;
either an Illumina MiSeq or HiSeq 2500 instrument to determine the virome within GLD vines.;
Collectively, more than 190 million reads were generated through NGS. Read datasets were;
trimmed and filtered for quality and subjected to both read-mapping and de novo assembly. Contigs;
assembled de novo were analyzed with BLAST (Basic Local Alignment Search Tool) against the;
NCBI (National Centre for Biotechnology Information) database and it was determined that;
GLRaV-3 was the best-represented virus, comprising 97.5% of the assembled contigs. Grapevine;
virus F (GVF) was detected for the first time in South African vineyards through de novo;
assemblies and the complete genome sequence validated through direct Sanger sequencing. The;
complete genome of GVF isolate V5 spans 7 539 nucleotides and shares 89.11% nucleotide identity;
to existing GVF genomes. The data generated through this study will assist in further understanding;
the etiology of GLD, support the current hypothesis of GLRaV-3 as the primary contributor to GLD,;
aid in understanding virus associations in diseased vines and potentially develop systems in which;
to control disease spread and symptom severity.
AFRIKAANSE OPSOMMING: Vitis vinifera is die houtagtige oes wat die mees vatbaarste is vir intrasellulêre patogene. Tans word;
wingerde deur 70 patogene geïnfekteer, waarvan 63 van virale oorsprong is. Grapevine leafrollassociated;
virus 3 (GLRaV-3) is die tipe spesie van die genus Ampelovirus, familie Closteroviridae.;
Dit word globaal beskou as die primêre oorsaak van Wingerd krulblaar-siekte (GLD), alhoewel die;
etiologie van GLD nie heeltemal begryp word nie. In hierdie verslag word die virale populasies;
teenwoordig in GLD simptomatiese wingerde oor die Wes-Kaap provinsie in Suid-Afrika;
gerapporteer. ‘n Wydverspreide opname was uitgevoer om 315 wingerde met 11 wingerdinfekterende;
virusse te ondersoek, deur gebruik te maak van tru-transkripsie polimerase ketting;
reaksie (PKR). Verder is variantgroepe van GLRaV-3 onderskei met hoë-resolusie smeltingskurweanalise,;
tesame met die gebruik van in-tyd tru-transkripsie PKR. Die hoogste frekwensie was van;
die lede van die familie Closteroviridae, veral GLRaV-3 wat in 87% van die ondersoekte plante;
gevind is. Nuwe-generasie volgorderbepaling (NGS) beskik oor die vermoë om bekende en nuwe;
virusse te herken in virale populasies in geaffekteerde wingerde sonder vorige kennis van virale;
volgorderbepalings en wanneer dit in ‘n metagenomiese benadering gebruik word kan die virale;
bevolkings binne siek wingerde ontdek. ‘n Totaal van 17 wingerd-steekproewe was blootgestel aan;
NGS deur die gebruik van of ‘n Illumina MiSeq of ‘n HiSeq 2500 instrument om die virome te;
bepaal van GLD wingerde. In totaal is meer 190 miljoen lesings gegenereer deur NGS. Hierdie data;
lesings was verwerk en gefilter vir kwaliteit om onderwerp te word vir beide kartering en de novo;
samestellings. Contigs verkry deur de novo samestellings was geanaliseer met BLAST (Basic;
Local Alignment Search Tool) teenoor die NCBI (National Centre for Biotechnology Information);
databasis en dit was vasgestel dat GLRaV-3 was die mees-verteenwoordigende virus, bestaande uit;
97.5% van die saamgestelde contigs. Grapevine virus F (GVF) was vir die eerste keer in Suid-;
Afrikaanse wingerde waargeneem deur de novo samestellings en die volledige genoom volgordger;
is geverifieer deur middel van direkte Sanger volgorderbepaling. Die volledige genoom van GVF;
isoleer V5 spanwydte van 7539 nukleotiedes en deel 89.11% nukleotied identiteite van bestaande;
GVF genome. Die gegenereerde data van hierdie studie sal bykomende begrip van die etiologie;
van GLD bystaan, die huidige hipotese van GLRaV-3 as die primêre bydraer tot GLD ondersteun,;
verhoogde begrip van virus-assosiasies in wingerdsiektes verseker en potensiële sisteme ontwikkel;
om siektes en simptome te beheer.
Thesis (Ph. D.)--University of Wisconsin--Madison, 1984.
Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references ...(leaves 106-112).
The onion thrips (Thrips tabaci L.) is one of the most serious insect pests of onions. Onions with glossy foliage (absence of distinct bloom) were described as thrips resistant many years ago but no ...glossy varieties have been released. Onion lines with the following phenotypes: nonglossy foliage with nonglossy scapes (Nonglossy, Ng1), glossy foliage with nonglossy scapes (Single glossy, Sg1), and glossy foliage with glossy scapes (Double glossy, Dg1) were used to establish F(,1), F(,2), F(,3) and BC(,1) populations for studying the inheritance of foliage and scape glossiness. A new intermediate (Int) phenotype with a gray streaked scape was recognized in segregating populations. The gene controlling nonglossy foliage (G1 locus) was shown to be dominant to glossy, as previously described, and epistatic to the glossy scape trait. Two loci were demonstrated as controlling scape glossiness and designated G1s(,1) and G1s(,2) for future reference. The dominant G1s(,1) allele (nonglossy) was shown to be epistatic to the G1s(,2) locus. The three loci give strong evidence of being linked, with G1s(,2) being further from G1 than is G1s(,1). Proposed genotypes are: Ng1, G1/-- --/-- --/--; Sg1, g1/g1 G1s(,1)/-- --/--; Int, g1/g1 g1s(,1)/g1s G1s(,2)/--; and Dg1, g1/g1 g1s(,1)/g1s(,1) g1s(,2)/g1s(,2). Based upon the number of thrips collected from onion umbels, glossy foliage onions are more resistant than nonglossy and Dg1 plants are more resistant than Sg1 plants. Evidence for the nonpreference (antixenosis) mechanism of resistance was demonstrated when greater numbers of adult thrips were collected from nonglossy seedlings than from glossy seedlings one week after infestation in a greenhouse isolation cage. Scanning electron microscopy of the epicuticular waxes revealed that wax crystals on nonglossy plants were abundant, primarily rods and toothed platelets, while wax crystals on glossy plants were sparse amorphous platelets only. In weight per cm('2), there was two and three times as much wax on nonglossy leaves and scapes as there was on those classified as glossy. Thin layer chromatography revealed that wax from nonglossy leaves or scapes was composed primarily of n-alkyl ketones and n-primary alcohols while wax of glossy leaves or scapes was primarily n-alkyl ketones and n-secondary alcohols.
The interaction of environmental bacteria with unicellular eukaryotes is generally considered a major driving force for the evolution of intracellular pathogens, allowing them to survive and ...replicate in phagocytic cells of vertebrate hosts. To test this hypothesis on a genome-wide level, we determined for the intracellular pathogen Mycobacterium marinum whether it uses conserved strategies to exploit host cells from both protozoan and vertebrate origin. Using transposon-directed insertion site sequencing (TraDIS), we determined differences in genetic requirements for survival and replication in phagocytic cells of organisms from different kingdoms. In line with the general hypothesis, we identified a number of general virulence mechanisms, including the type VII protein secretion system ESX-1, biosynthesis of polyketide lipids, and utilization of sterols. However, we were also able to show that M. marinum contains an even larger set of host-specific virulence determinants, including proteins involved in the modification of surface glycolipids and, surprisingly, the auxiliary proteins of the ESX-1 system. Several of these factors were in fact counterproductive in other hosts. Therefore, M. marinum contains different sets of virulence factors that are tailored for specific hosts. Our data imply that although amoebae could function as a training ground for intracellular pathogens, they do not fully prepare pathogens for crossing species barriers.
Simultaneous activation of β2- and β3-adrenoceptors (ARs) improves whole-body metabolism via beneficial effects in skeletal muscle and brown adipose tissue (BAT). Nevertheless, high-efficacy agonists ...simultaneously targeting these receptors whilst limiting activation of β1-ARs – and thus inducing cardiovascular complications – are currently non-existent. Therefore, we here developed and evaluated the therapeutic potential of a novel β2-and β3-AR, named ATR-127, for the treatment of obesity and its associated metabolic perturbations in preclinical models.
In the developmental phase, we assessed the impact of ATR-127's on cAMP accumulation in relation to the non-selective β-AR agonist isoprenaline across various rodent β-AR subtypes, including neonatal rat cardiomyocytes. Following these experiments, L6 muscle cells were stimulated with ATR-127 to assess the impact on GLUT4-mediated glucose uptake and intramyocellular cAMP accumulation. Additionally, in vitro, and in vivo assessments are conducted to measure ATR-127's effects on BAT glucose uptake and thermogenesis. Finally, diet-induced obese mice were treated with 5 mg/kg ATR-127 for 21 days to investigate the effects on glucose homeostasis, body weight, fat mass, skeletal muscle glucose uptake, BAT thermogenesis and hepatic steatosis.
Exposure of L6 muscle cells to ATR-127 robustly enhanced GLUT4-mediated glucose uptake despite low intramyocellular cAMP accumulation. Similarly, ATR-127 markedly increased BAT glucose uptake and thermogenesis both in vitro and in vivo. Prolonged treatment of diet-induced obese mice with ATR-127 dramatically improved glucose homeostasis, an effect accompanied by decreases in body weight and fat mass. These effects were paralleled by an enhanced skeletal muscle glucose uptake, BAT thermogenesis, and improvements in hepatic steatosis.
Our results demonstrate that ATR-127 is a highly effective, novel β2- and β3-ARs agonist holding great therapeutic promise for the treatment of obesity and its comorbidities, whilst potentially limiting cardiovascular complications. As such, the therapeutic effects of ATR-127 should be investigated in more detail in clinical studies.
•ATR-127 a safe dual β2-β3-AR agonist, demonstrates improved cardiovascular safety.•ATR-127 enhances skeletal muscle glucose uptake independently of cAMP.•ATR-127 markedly increases BAT glucose uptake and thermogenesis.•ATR-127 improves hepatic steatosis.•Prolonged ATR-127 treatment exhibits potent antiobesity and antidiabetic effects.
An adult female captive pygmy hippopotamus (Choeropsis liberiensis) was diagnosed with an oral anaplastic sarcoma. The tumor was surgically debulked and intralesional chemotherapy with mitomycin C ...(0.4 mg/cm3 of tumor) and cisplatin (1 mg/cm3 of tumor) was administered. Chemotherapeutic treatment proved difficult due to the risks of repeated anesthetics and unknown drug efficacies. Marked proliferation of the mass was observed during estrus, and chemotherapy was repeated as an experimental treatment to slow tumor progression in order for the animal to remain in the species breeding program. Tumor proliferation was detected during the first trimester of pregnancy; however, in the lactation period, the mass became quiescent. No adverse reactions to chemotherapeutic drugs were observed and the animal continues to be monitored for tumor progression. This is the first report of an anaplastic sarcoma and of chemotherapy use in a pygmy hippopotamus and it highlights logistical considerations for treating neoplasia in this species.
A large part of the variation in cognitive ability is known to be due to genetic factors. Researchers have tried to identify modifiers that influence the heritability of cognitive ability, indicating ...a genotype by environment interaction (G×E). To date, such modifiers include measured variables like income and socioeconomic status. The present paper focuses on G×E in cognitive ability where the environmental variable is an unmeasured environmental factor that is uncorrelated in family members. We examined this type of G×E in the GHCA-database (Haworth et al., Behav Genet 39:359–370,
2009
), which comprises data of 14 different cognition studies from four different countries including participants of different ages. Results indicate that for younger participants (4–13 years), the strength of E decreases across the additive genetic factor A, but that this effect reverts for older participants (17–34 years). However, a clear and general conclusion about the presence of a genuine G×E is hampered by differences between the individual studies with respect to environmental and genetic influences on cognitive ability.
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