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1.
J Phys Chem C Nanomater Interfaces ; 125(18): 10077-10089, 2021 May 13.
Article in English | MEDLINE | ID: mdl-34276857

ABSTRACT

Porosity in functional oxide nanorods is a recently discovered new type of microstructure, which is not yet fully understood and still under evaluation for its impact on applications in catalysis and gas/ion storage. Here we explore the shape and distribution of pores in ceria in three dimensions using a modified algorithm of geometric tomography as a reliable tool for reconstructing defective and strained nanoobjects. The pores are confirmed as "negative-particle" or "inverse-particle" cuboctahedral shapes located exclusively beneath the flat surface of the rods separated via a sub-5 nm thin ceria wall from the outside. New findings also comprise elongated "negative-rod" defects, seen as embryonic nanotubes, and pores in cube-shaped ceria. Furthermore, we report near-sintering secondary heat treatment of nanorods and cubes, confirming persistence of pores beyond external surface rounding. We support our experiments with molecular modeling and predict that the growth history of voids is via diffusion and aggregation of atomic point defects. In addition, we use density functional theory to show that the relative stability of pore (shape) increases in the order "cuboidal" < "hexagonal-prismatic" < "octahedral". The results indicate that by engineering voids into nanorods, via a high-temperature postsynthetic heat treatment, a potential future alternative route of tuning catalytic activities might become possible.

2.
Mol Biotechnol ; 61(2): 93-101, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30484144

ABSTRACT

Cassava brown streak disease (CBSD) has major impacts on yield and quality of the tuberous roots of cassava in Eastern and Central Arica. At least two Potyviridae species cause the disease: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Cloned viral genome sequences known as infectious clones (ICs) have been important in the study of other viruses, both as a means of standardising infectious material and characterising viral gene function. IC construction is often technically challenging for Potyviridae due to sequence instability in E. coli. Here, we evaluate three methods for the construction of infectious clones for CBSD. Whilst a simple IC for in vitro transcription was made for UCBSV isolate 'Kikombe', such an approach failed to deliver full-length clones for CBSV isolates 'Nampula' or 'Tanza', necessitating more complex approaches for their construction. The ICs successfully generated symptomatic infection in the model host N. benthamiana and in the natural host cassava. This shows that whilst generating ICs for CBSV is still a technical challenge, a structured approach, evaluating both in vitro and in planta transcription systems should successfully deliver ICs, allowing further study into the symptomology and virulence factors in this important disease complex.


Subject(s)
Cloning, Molecular/methods , Genome, Viral/genetics , Potyviridae/genetics , Virology/methods , DNA, Viral/genetics , Introns/genetics , Manihot/virology , Plant Diseases/virology , Potyviridae/isolation & purification , Potyviridae/pathogenicity , Nicotiana/virology
3.
Public Health ; 162: 135-146, 2018 Sep.
Article in English | MEDLINE | ID: mdl-30056313

ABSTRACT

OBJECTIVES: Hand injuries result in major healthcare costs from lack of productivity and disability. With rapid industrialization, the incidence of hand injuries is expected to rise in low- and middle-income countries (LMICs). However, estimates of burden and validated outcome tools are needed for effective resource allocation in the management of these injuries. STUDY DESIGN: We conducted a systematic review to evaluate the burden of hand injuries in LMICs according to Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines. METHODS: We searched PubMed, Scopus, Embase, Cochrane Library, PAIS International, African Index Medicus, Global Health, IMMEMR, IMSEAR, Wholis and Bdenf, Lilacs, Scielo, WPRIM, and WHO International Clinical Trials Registry Platform to detect eligible articles with no restrictions on length of follow-up, type of hand injury, or date. RESULTS: We included 17 articles after screening 933 eligible articles based on title, abstract, and full-text screening. There was significant heterogeneity and low quality of evidence. All included articles suggest that hand injuries were associated with work limitations for the majority of patients, and residual pain can further limit their activities. Direct and indirect costs related to treatment account for a major healthcare burden with limited evidence on estimates of long-term cost from disability. CONCLUSIONS: The present systematic review highlights the paucity of high-quality data on the epidemiology, management, and burden of hand injuries in LMICs. The data are heterogeneous, and comprehensive metrics are lacking. Because hand injuries can account for a significant proportion of injury-related disability, reducing the overall burden of hand injuries is of utmost importance.


Subject(s)
Developing Countries , Hand Injuries/epidemiology , Hand Injuries/prevention & control , Humans , Randomized Controlled Trials as Topic
4.
Anaesthesia ; 73(2): 195-204, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29150856

ABSTRACT

Our aim was to prospectively determine the predictive capabilities of SEPSIS-1 and SEPSIS-3 definitions in the emergency departments and general wards. Patients with National Early Warning Score (NEWS) of 3 or above and suspected or proven infection were enrolled over a 24-h period in 13 Welsh hospitals. The primary outcome measure was mortality within 30 days. Out of the 5422 patients screened, 431 fulfilled inclusion criteria and 380 (88%) were recruited. Using the SEPSIS-1 definition, 212 patients had sepsis. When using the SEPSIS-3 definitions with Sequential Organ Failure Assessment (SOFA) score ≥ 2, there were 272 septic patients, whereas with quickSOFA score ≥ 2, 50 patients were identified. For the prediction of primary outcome, SEPSIS-1 criteria had a sensitivity (95%CI) of 65% (54-75%) and specificity of 47% (41-53%); SEPSIS-3 criteria had a sensitivity of 86% (76-92%) and specificity of 32% (27-38%). SEPSIS-3 and SEPSIS-1 definitions were associated with a hazard ratio (95%CI) 2.7 (1.5-5.6) and 1.6 (1.3-2.5), respectively. Scoring system discrimination evaluated by receiver operating characteristic curves was highest for Sequential Organ Failure Assessment score (0.69 (95%CI 0.63-0.76)), followed by NEWS (0.58 (0.51-0.66)) (p < 0.001). Systemic inflammatory response syndrome criteria (0.55 (0.49-0.61)) and quickSOFA score (0.56 (0.49-0.64)) could not predict outcome. The SEPSIS-3 definition identified patients with the highest risk. Sequential Organ Failure Assessment score and NEWS were better predictors of poor outcome. The Sequential Organ Failure Assessment score appeared to be the best tool for identifying patients with high risk of death and sepsis-induced organ dysfunction.


Subject(s)
Organ Dysfunction Scores , Sepsis , Terminology as Topic , Adolescent , Adult , Aged , Aged, 80 and over , Cross Infection/mortality , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Multiple Organ Failure/etiology , Multiple Organ Failure/mortality , Predictive Value of Tests , Prevalence , Prognosis , Prospective Studies , ROC Curve , Sensitivity and Specificity , Sepsis/mortality , Treatment Outcome , Young Adult
5.
Clin Microbiol Infect ; 23(1): 47.e1-47.e10, 2017 Jan.
Article in English | MEDLINE | ID: mdl-27615723

ABSTRACT

OBJECTIVES: To identify important pathogen recognition receptor (PRR) pathways regulating innate immune responses and outcome in Staphylococcus aureus sepsis. METHODS: We analysed whether candidate PRR pathway genetic variants were associated with killed S. aureus-induced cytokine responses ex vivo and performed follow-up in vitro studies. We tested the association of our top-ranked variant with cytokine responses and clinical outcomes in a prospective multicentre cohort of patients with staphylococcal sepsis. RESULTS: An intronic TLR4 polymorphism and expression quantitative trait locus, rs1927907, was highly associated with cytokine release induced by stimulation of blood from healthy Thai subjects with S. aureus ex vivo. S. aureus did not induce TLR4-dependent NF-κB activation in transfected HEK293 cells. In monocytes, tumor necrosis factor (TNF)-α release induced by S. aureus was not blunted by a TLR4/MD-2 neutralizing antibody, but in a monocyte cell line, TNF-α was reduced by knockdown of TLR4. In Thai patients with staphylococcal sepsis, rs1927907 was associated with higher interleukin (IL)-6 and IL-8 levels as well as with respiratory failure. S. aureus-induced responses in blood were most highly correlated with responses to Gram-negative stimulants whole blood. CONCLUSIONS: A genetic variant in TLR4 is associated with cytokine responses to S. aureus ex vivo and plasma cytokine levels and respiratory failure in staphylococcal sepsis. While S. aureus does not express lipopolysaccharide or activate TLR4 directly, the innate immune response to S. aureus does appear to be modulated by TLR4 and shares significant commonality with that induced by Gram-negative pathogens and lipopolysaccharide.


Subject(s)
Inflammation/genetics , Sepsis/microbiology , Staphylococcal Infections/genetics , Staphylococcal Infections/microbiology , Toll-Like Receptor 4/metabolism , Adult , Cytokines/genetics , Cytokines/metabolism , Female , Gene Expression Regulation , Gene Knockdown Techniques , Genetic Predisposition to Disease , Genetic Variation , Humans , Inflammation/pathology , Male , Middle Aged , Thailand , Toll-Like Receptor 4/genetics
6.
Sci Rep ; 6: 27869, 2016 06 14.
Article in English | MEDLINE | ID: mdl-27298196

ABSTRACT

We report a class of amorphous thin film material comprising of transition (Fe) and Lanthanide metals (Dy and Tb) that show unique combination of functional properties. Films were deposited with different atomic weight ratio (R) of Fe to Lanthanide (Dy + Tb) using electron beam co-evaporation at room temperature. The films were found to be amorphous, with grazing incidence x-ray diffraction and x-ray photoelectron spectroscopy studies indicating that the films were largely oxidized with a majority of the metal being in higher oxidation states. Films with R = 0.6 were semiconducting with visible light transmission due to a direct optical band-gap (2.49 eV), had low resistivity and sheet resistance (7.15 × 10(-4) Ω-cm and ~200 Ω/sq respectively), and showed room temperature ferromagnetism. A metal to semiconductor transition with composition (for R < 11.9) also correlated well with the absence of any metallic Fe(0) oxidation state in the R = 0.6 case as well as a significantly higher fraction of oxidized Dy. The combination of amorphous microstructure and room temperature electronic and magnetic properties could lead to the use of the material in multiple applications, including as a transparent conductor, active material in thin film transistors for display devices, and in spin-dependent electronics.

7.
Radiat Res ; 185(5): 516-26, 2016 05.
Article in English | MEDLINE | ID: mdl-27135969

ABSTRACT

Cerium oxide nanoparticles (CNPs) have a unique surface regenerative property and can efficiently control reactive oxygen/nitrogen species. To determine whether treatment with CNPs can mitigate the delayed effects of lung injury after acute radiation exposure, CBA/J mice were exposed to 15 Gy whole-thorax radiation. The animals were either treated with nanoparticles, CNP-18 and CNP-ME, delivered by intraperitoneal injection twice weekly for 4 weeks starting 2 h postirradiation or received radiation treatment alone. At the study's end point of 160 days, 90% of the irradiated mice treated with high-dose (10 µM) CNP-18 survived, compared to 10% of mice in the radiation-alone (P < 0.0001) and 30% in the low-dose (100 nM) CNP-18. Both low- and high-dose CNP-ME-treated irradiated mice showed increased survival rates of 40% compared to 10% in the radiation-alone group. Multiple lung functional parameters recorded by flow-ventilated whole-body plethysmography demonstrated that high-dose CNP-18 treatment had a significant radioprotective effect on lethal dose radiation-induced lung injury. Lung histology revealed a significant decrease (P < 0.0001) in structural damage and collagen deposition in mice treated with high-dose CNP-18 compared to the irradiated-alone mice. In addition, significant reductions in inflammatory response (P < 0.01) and vascular damage (P < 0.01) were observed in the high-dose CNP-18-treated group compared to irradiated-alone mice. Together, the findings from this preclinical efficacy study clearly demonstrate that CNPs have both clinically and histologically significant mitigating and protective effects on lethal dose radiation-induced lung injury.


Subject(s)
Cerium/chemistry , Cerium/pharmacology , Lung Injury/prevention & control , Nanoparticles/chemistry , Radiation Injuries, Experimental/prevention & control , Animals , Body Weight/drug effects , Body Weight/radiation effects , Female , Lung/drug effects , Lung/pathology , Lung/radiation effects , Lung Injury/pathology , Lung Injury/physiopathology , Mice , Organ Size/drug effects , Organ Size/radiation effects , Radiation Injuries, Experimental/pathology , Radiation Injuries, Experimental/physiopathology , Respiration/drug effects , Respiration/radiation effects , Survival Analysis
8.
Indian J Cancer ; 53(1): 56-9, 2016.
Article in English | MEDLINE | ID: mdl-27146741

ABSTRACT

OBJECTIVES: To explore alternate modality of treatment in patients of advanced cancer cervix by neo-adjuvant chemotherapy (NACT) followed by External Beam Radiotherapy (ERT) and Brachytherapy (BT). Short- (6 months) and long- (12 months) term follow-up data from these patients were compared with the retrospective data from an urban cancer centre, where standard protocol of concurrent chemo-radiotherapy is practiced. MATERIALS AND METHODS: Two hundred patients of advanced cervical cancer, treated at our rural cancer centre between January 2007 and December 2007, were included in the study arm (Group A). These patients received three cycles of neo-adjuvant chemotherapy with Cisplatin, Bleomycin, and Vincristine before External-Beam Radiotherapy (EBT) followed by brachytherapy. Patients in the control arm (Group B) of an urban cancer centre, received EBT with weekly concomitant Cisplatin, followed by brachytherapy. Short- (6 months) and long- (12 months) term follow-up data from our patients were compared with the retrospective data from the urban cancer centre. RESULTS AND ANALYSIS: Complete response rate was comparatively higher among patients of Group A, also correspondingly proportion of patients showing progressive disease and stable disease was lower among them. Local treatment failure was 87.5% among patients from Group A and 94.4% in Group B patients. Concomitant chemoradiation (CRT) was associated with more GI toxicities. CONCLUSION: Our result suggests NACT arm is as effective as CRT arm in respect of complete response with less pelvic failure and G.I toxicities. Further follow-up data are needed before arriving at a definite conclusion.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Uterine Cervical Neoplasms/drug therapy , Adult , Bleomycin/administration & dosage , Brachytherapy , Chemoradiotherapy , Cisplatin/administration & dosage , Female , Humans , India , Middle Aged , Neoadjuvant Therapy , Rural Population , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/radiotherapy
9.
Cell Death Differ ; 21(10): 1622-32, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24902900

ABSTRACT

Evidence indicates that nitrosative stress and mitochondrial dysfunction participate in the pathogenesis of Alzheimer's disease (AD). Amyloid beta (Aß) and peroxynitrite induce mitochondrial fragmentation and neuronal cell death by abnormal activation of dynamin-related protein 1 (DRP1), a large GTPase that regulates mitochondrial fission. The exact mechanisms of mitochondrial fragmentation and DRP1 overactivation in AD remain unknown; however, DRP1 serine 616 (S616) phosphorylation is likely involved. Although it is clear that nitrosative stress caused by peroxynitrite has a role in AD, effective antioxidant therapies are lacking. Cerium oxide nanoparticles, or nanoceria, switch between their Ce(3+) and Ce(4+) states and are able to scavenge superoxide anions, hydrogen peroxide and peroxynitrite. Therefore, nanoceria might protect against neurodegeneration. Here we report that nanoceria are internalized by neurons and accumulate at the mitochondrial outer membrane and plasma membrane. Furthermore, nanoceria reduce levels of reactive nitrogen species and protein tyrosine nitration in neurons exposed to peroxynitrite. Importantly, nanoceria reduce endogenous peroxynitrite and Aß-induced mitochondrial fragmentation, DRP1 S616 hyperphosphorylation and neuronal cell death.


Subject(s)
Amyloid beta-Peptides/metabolism , Apoptosis/drug effects , Cerium/pharmacology , Mitochondria/pathology , Mitophagy/drug effects , Animals , Antioxidants/pharmacology , Dynamins/metabolism , Metal Nanoparticles , Mitochondrial Membranes/metabolism , Neurodegenerative Diseases/prevention & control , Neurons/pathology , Oxidative Stress/drug effects , Peroxynitrous Acid/chemistry , Peroxynitrous Acid/pharmacology , Phosphorylation , Rats , Rats, Sprague-Dawley , Reactive Nitrogen Species/metabolism
10.
J Obstet Gynaecol ; 34(3): 241-4, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24483234

ABSTRACT

A caesarean section at full dilatation (CSFD) can be technically demanding and has consistent association with increased intraoperative trauma. There is evidence that the incidence of caesarean sections at full dilation is on the rise. We report on a prospective study of 50 women undergoing CSFD using a fetal pillow (FP) to elevate the fetal head. Data were compared with historical controls of 124 women without FP use on uterine extensions, uterine incision delivery interval, blood loss, need for transfusion, operating time, length of stay, intensive care unit admission. The FP elevated the fetal head in all 50 women (p < 0.001). We found that patients in the FP group had a lower incidence of extensions (p = 0.03), shorter operating time (p < 0.001), uterine incision to delivery interval (p < 0.001) and shorter length of hospital stay (p < 0.001). Blood loss > 1,000 ml and admission to ICU was also lower but were not statistically significant. There were no significant differences in the fetal complications studied, APGAR scores, admission to neonatal intensive care unit, seizures, neonatal injury or death.


Subject(s)
Cesarean Section/instrumentation , Intraoperative Complications/prevention & control , Labor Stage, Second , Adolescent , Adult , Cesarean Section/statistics & numerical data , Female , Humans , India/epidemiology , Intraoperative Complications/epidemiology , Pregnancy , Prospective Studies , Young Adult
11.
J Mater Chem B ; 1(28): 3443-3450, 2013 Jul 28.
Article in English | MEDLINE | ID: mdl-32260934

ABSTRACT

A simple enzyme-free spectrophotometric detection of hydrogen peroxide is demonstrated based on its colorimetric reaction with oxygen deficient cerium oxide nanoparticles (CNPs). This colorimetric sensitivity of CNPs towards H2O2 increases significantly with decreasing crystallite size due to an increase in the surface area as well as the concentration of Ce3+ on the surface. The origin of this colorimetric reaction was studied using DFT that suggests the adsorption of peroxide and oxygen molecules on ceria nanoparticles creates new states in the electronic structure leading to transitions absorbing in the visible region of the electromagnetic spectrum. For detection, a single layer of nanoparticles was immobilized on transparent microscopic glass slides using self-assembled monolayers (SAMs) of poly(4-vinylpyridine) (PVP). Cluster-free and uniform immobilization of nanoparticles was confirmed from atomic force microscopy (AFM) and helium ion microscopy (HIM). UV-Visible absorption measurements showed a concentration dependent increase in absorbance from immobilized CNPs that were exposed to increasing concentrations (10-400 µM) of hydrogen peroxide. The immobilized CNPs can be baked at 80 °C after initial use to regenerate the sensor for reuse. The development of a direct, reusable, enzyme-free and dye-free peroxide sensing technology is possible and can be immediately applied in various areas, including biomedicine and national security.

12.
Br J Cancer ; 106(6): 1234-8, 2012 Mar 13.
Article in English | MEDLINE | ID: mdl-22333603

ABSTRACT

BACKGROUND: Triple-negative (TN) tumours are the predominant breast cancer subtype in BRCA1 mutation carriers. Recently, it was proposed that all individuals below 50 years of age with TN breast cancer should be offered BRCA testing. We have evaluated the BRCA1 mutation frequency and the implications for clinical practice of undertaking genetic testing in women with TN breast cancer. METHODS: We undertook BRCA1 mutation analysis in 308 individuals with TN breast cancer, 159 individuals from unselected series of breast cancer and 149 individuals from series ascertained on the basis of young age and/or family history. RESULTS: BRCA1 mutations were present in 45 out of 308 individuals. Individuals with TN cancer <50 years had >10% likelihood of carrying a BRCA1 mutation in both the unselected (11 out of 58, 19%) and selected (26 out of 111, 23%) series. However, over a third would not have been offered testing using existing criteria. We estimate that testing all individuals with TN breast cancer <50 years would generate an extra 1200 tests annually in England. CONCLUSION: Women with TN breast cancer diagnosed below 50 years have >10% likelihood of carrying a BRCA1 mutation and are therefore eligible for testing in most centres. However, implementation may place short-term logistical and financial burdens on genetic services.


Subject(s)
BRCA1 Protein/genetics , Breast Neoplasms/genetics , Genetic Testing , Age Factors , Breast Neoplasms/diagnosis , Breast Neoplasms/epidemiology , Breast Neoplasms/metabolism , DNA Mutational Analysis , Female , Genetic Association Studies , Humans , Incidence , Middle Aged , Mutation , Receptor, ErbB-2/metabolism , Receptors, Estrogen/metabolism , Receptors, Progesterone/metabolism
13.
J Phys Chem C Nanomater Interfaces ; 116(26): 14108-14114, 2012 Jul 05.
Article in English | MEDLINE | ID: mdl-23573300

ABSTRACT

The oxidation state switching of cerium in cerium oxide nanoparticles is studied in detail. The influence of synthesis medium, aging time and local environment on the oxidation state switching, between +3 and + 4, is analyzed by tracking the absorption edge using UV-Visible spectroscopy. It is observed that by tuning the local environment, the chemistry of the nanoparticles could be altered. These time dependent, environmentally induced changes likely contribute to inconsistencies in the literature regarding quantum-confinement effects for ceria nanoparticles. The results in this article indicate that there is a need to carry out comprehensive analysis of nanoparticles while considering the influence of synthesis and processing conditions, aging time and local environment.

14.
Nanoscale ; 3(3): 1090-101, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21180769

ABSTRACT

Fast, sensitive and discriminating detection of hydrogen at room temperature is crucial for storage, transportation, and distribution of hydrogen as an energy source. One dimensional nanowires of SnO2 are potential candidates for improved H2 sensor performance. The single directional conducting continuous nanowires can decrease electrical noise, and their large active surface area could improve the response and recovery time of the sensor. In this work we discuss synthesis and characterization of nanowire arrays made using nanosecond ultraviolet wavelength (266 nm) laser interference processing of ultrathin SnO2 films on SiO2 substrates. The laser energy was chosen to be above the melting point of the films. The results show that the final nanowire formation is dominated by preferential evaporation as compared to thermocapillary flow. The nanowire height (and hence wire aspect ratio) increased with increasing initial film thickness h0 and with increasing laser energy density Eo. Furthermore, a self-limiting effect was observed where-in the wire formation ceased at a specific final remaining thickness of SnO2 that was almost independent of h0 for a given Eo. To understand these effects, finite element modeling of the nanoscale laser heating was performed. This showed that the temperature rise under laser heating was a strong non-monotonic function of film thickness. As a result, the preferential evaporation rate varies as wire formation occurs, eventually leading to a shut-off of evaporation at a characteristic thickness. This results in the stoppage of wire formation. This combination of nanosecond pulsed laser experiments and thermal modeling shows that several unique synthesis approaches can be utilized to control the nanowire characteristics.


Subject(s)
Lasers , Nanostructures/chemistry , Nanostructures/ultrastructure , Tin Compounds/chemistry , Tin Compounds/radiation effects , Macromolecular Substances/chemistry , Macromolecular Substances/radiation effects , Materials Testing , Molecular Conformation/radiation effects , Nanostructures/radiation effects , Radiation Dosage , Surface Properties/drug effects
15.
J Virol Methods ; 163(2): 353-9, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19879299

ABSTRACT

Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10x cheaper (0.53 pounds sterling=US$0.80 per sample) than the RNeasy method (5.91 pounds sterling=US$8.86 per sample). A two-step RT-PCR (1.34 pounds sterling=US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (4.48 pounds sterling=US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100-400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7-1.7%, respectively. CBSV was detected at 10(-4)-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV.


Subject(s)
Manihot/virology , Plant Diseases/virology , Potyviridae/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/economics , Reverse Transcriptase Polymerase Chain Reaction/methods , Potyviridae/genetics , Reproducibility of Results , Sensitivity and Specificity
16.
Arch Virol ; 154(2): 297-314, 2009.
Article in English | MEDLINE | ID: mdl-19190853

ABSTRACT

The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high.


Subject(s)
Badnavirus/classification , Dioscorea/virology , Ecosystem , Plant Diseases/virology , Africa , Americas , Asia, Southeastern , Australia , Badnavirus/enzymology , Badnavirus/genetics , Dioscorea/classification , Genetic Variation , Melanesia , Molecular Sequence Data , Phylogeny , RNA-Directed DNA Polymerase/genetics , Recombination, Genetic , Viral Proteins/genetics
17.
Early Hum Dev ; 84(12): 783-5, 2008 Dec.
Article in English | MEDLINE | ID: mdl-18829186

ABSTRACT

Aicardi-Goutières syndrome (AGS) is a rare, genetically-determined encephalopathy whose importance from a neonatology perspective is magnified because of the risk of misdiagnosis as the sequelae of congenital infection. Molecular advances have shown that AGS can be caused by mutations in any one of at least five genes (four of which have been identified). A recent genotype-phenotype study has shown that a neonatal form of the disease, highly reminiscent of congenital infection, is seen particularly with TREX1 mutations. It seems likely that the enzymes defective in AGS are involved in digesting endogenous nucleic acids (DNA and RNA) produced during normal cell replication, and that a failure of this removal results in inappropriate triggering of the innate immune system. This hypothesis explains the remarkable phenotypic overlap of AGS with congenital infection, where a similar interferon alpha mediated innate immune response is triggered by viral, as opposed to self, nucleic acids.


Subject(s)
Encephalitis, Viral/diagnostic imaging , Heredodegenerative Disorders, Nervous System/diagnostic imaging , Proteins/genetics , Tomography, X-Ray Computed , Diagnosis, Differential , Encephalitis, Viral/congenital , Exodeoxyribonucleases , Heredodegenerative Disorders, Nervous System/genetics , Humans , Infant , Infant, Newborn , Male , Phenotype , Phosphoproteins , Syndrome
18.
Arch Virol ; 153(6): 1085-102, 2008.
Article in English | MEDLINE | ID: mdl-18483693

ABSTRACT

This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similar range to that reported within other DNA and RNA plant virus families.


Subject(s)
Caulimoviridae/classification , Caulimoviridae/genetics , Genome, Viral , RNA-Directed DNA Polymerase/genetics , Evolution, Molecular , Genetic Variation , Phylogeny , Sequence Analysis, Protein , Sequence Homology, Nucleic Acid
19.
Arch Virol ; 153(5): 877-89, 2008.
Article in English | MEDLINE | ID: mdl-18330495

ABSTRACT

Yam (Dioscorea spp.) samples (n = 690) from seven South Pacific Islands were screened for badnavirus infection by ELISA using two antisera to African badnaviruses. Positive readings were obtained for 26.4-34.6% of samples representing both known (D. bulbifera, D. nummularia and D. pentaphylla) and unreported host species (D. alata, D. esculenta, D. rotundata and D. trifida) in this region. Total DNAs were extracted from 25 ELISA-positive plants and 4 ELISA-negative controls and subjected to PCR amplification with badnavirus-specific primers targeting the reverse transcriptase (RT)-RNaseH genes. All 29 samples yielded the expected size PCR-product for badnaviruses, which were cloned and sequenced. Phylogenetic analyses of the resulting 45 partial (500-527 bp) RT-RNaseH sequences revealed 11 new sequence groups with <79% nucleotide identity to each other or any EMBL sequence. Three sequences (two groups) were highly divergent to the other nine new South Pacific yam badnavirus groups (47.9-57.2% identity) and probably represent either new Caulimoviridae genera or endogenous pararetrovirus sequences. Some sequence groups appeared specific to particular Dioscorea host species. Four 99.9% identical RT-RNaseH sequences possessing nine amino acid deletions from D. esculenta from three islands represent a putative integrated sequence group. The distribution of sequence groups across the islands indicates that badnaviruses have spread extensively between islands and continents through infected germplasm.


Subject(s)
Badnavirus/isolation & purification , Dioscorea/virology , Badnavirus/classification , Badnavirus/genetics , Badnavirus/pathogenicity , Base Sequence , DNA Primers/genetics , DNA, Viral/genetics , Enzyme-Linked Immunosorbent Assay , Genetic Variation , Pacific Islands , Phylogeny , Plant Diseases/virology , Polymerase Chain Reaction
20.
JOM (1989) ; 60(3): 33-37, 2008 Mar 01.
Article in English | MEDLINE | ID: mdl-20617106

ABSTRACT

The therapeutic application of nanomaterials has been a focus of numerous studies in the past decade. Due to its unique redox properties, cerium oxide (ceria) is finding widespread use in the treatment of medical disorders caused by the reactive oxygen intermediates (ROI). The radical-scavenging role of ceria nanoparticles (nanoceria) have been established, as well as the autocatalytic ability of nanoceria to regenerate under various environmental conditions. The synthesis of nanoceria in biocompatible media has also been reported along with cell viability in order to determine the potential use of nanoceria in biomedical applications.

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