scholarly journals New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

2022 ◽  
Vol 19 (1) ◽  
Author(s):  
Lien Gysens ◽  
Bert Vanmechelen ◽  
Maarten Haspeslagh ◽  
Piet Maes ◽  
Ann Martens
Keyword(s):  
Phylogenetic Trees ◽  
Wide Spectrum ◽  
Clinical Sample ◽  
Clinical Samples ◽  
Bovine Papillomavirus ◽  
Nanopore Sequencing ◽  
Veterinary Research ◽  
Equine Sarcoid ◽  
Potential Association ◽  
The One

Abstract Background Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in clinical presentation on the one hand and the host dependent clinical outcome of BPV-1 infection on the other hand indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. Methods In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. Results We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of them cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. Conclusions By generating a significant amount of complete-length BPV genomes, we succeeded to introduce next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

scholarly journals Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing

2021 ◽  
Vol 6 ◽  
pp. 241
Author(s):  
Ingra M. Claro ◽  
Mariana S. Ramundo ◽  
Thais M. Coletti ◽  
Camila A. M. da Silva ◽  
Ian N. Valenca ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Yellow Fever Virus ◽  
Rna Virus ◽  
Clinical Sample ◽  
Viral Metagenomics ◽  
Health Concern ◽  
Clinical Samples ◽  
Nanopore Sequencing ◽  
Emerging Viruses ◽  
Genome Coverage

Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5′ end of RNA Template) is a popular method for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, ‘SMART-9N’, and a version compatible with barcoded PCR primers available from Oxford Nanopore Technologies, ‘Rapid SMART-9N’, for the detection, characterization, and whole-genome sequencing of RNA viruses. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6e00 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.

Are Three Items Sufficient to Measure Sense of Coherence?

2018 ◽  
Vol 34 (4) ◽  
pp. 229-237 ◽  
Author(s):  
Francesca Chiesi ◽  
Andrea Bonacchi ◽  
Caterina Primi ◽  
Alessandro Toccafondi ◽  
Guido Miccinesi
Keyword(s):  
Sense Of Coherence ◽  
Convergent Validity ◽  
Clinical Sample ◽  
Clinical Samples ◽  
Depression Symptoms ◽  
Time Saving ◽  
Positive Role ◽  
Patients With Cancer ◽  
Measure Sense

Abstract. The present study aimed at evaluating if the three-item sense of coherence (SOC) scale developed by Lundberg and Nystrom Peck (1995) can be effectively used for research purpose in both nonclinical and clinical samples. To provide evidence that it represents adequately the measured construct we tested its validity in a nonclinical (N = 658) and clinical sample (N = 764 patients with cancer). Results obtained in the nonclinical sample attested a positive relation of SOC – as measured by the three-item SOC scale – with Antonovsky’s 13-item and 29-item SOC scales (convergent validity), and with dispositional optimism, sense of mastery, anxiety, and depression symptoms (concurrent validity). Results obtained in the clinical sample confirmed the criterion validity of the scale attesting the positive role of SOC – as measured by the three-item SOC scale – on the person’s capacity to respond to illness and treatment. The current study provides evidence that the three-item SOC scale is a valid, low-loading, and time-saving instrument for research purposes on large sample.

Investigation of duck plague virus in hoar areas of Bangladesh

2020 ◽  
Vol 26 (1-2) ◽  
pp. 73-78
Author(s):  
A Hossen ◽  
MH Rahman ◽  
MZ Ali ◽  
MA Yousuf ◽  
MZ Hassan ◽  
...  
Keyword(s):  
Cytopathic Effect ◽  
Clinical Sample ◽  
Chorioallantoic Membrane ◽  
Clinical Samples ◽  
Isolation And Identification ◽  
Duck Plague Virus ◽  
Pcr Method ◽  
Polymerase Chain ◽  
The Individual ◽  
Free Ranging

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78

Noticing and analysis of pedagogical practices in mathematics

2019 ◽  
Author(s):  
Yuri Morales López ◽  
Marianela Alpízar Vargas ◽  
Ana Lucía Alfaro Arce ◽  
Vicenç Font-Moll
Keyword(s):  
Classroom Management ◽  
Wide Spectrum ◽  
Math Education ◽  
Pedagogical Practices ◽  
Math Teachers ◽  
Education Activity ◽  
The One ◽  
Analysis Models ◽  
Teacher's Knowledge ◽  
Math Teacher

The purpose of this presentation is to show elements associated to the study and analysis of pedagogical practices used by mathematics teachers, taking into consideration different approaches and conceptions derived from theories related to the role of the math teacher. The project highlights the need to use different strategies to analyze the processes occurring in the activities and tasks organized and implemented by the teacher. One of the main tasks in teacher training is to promote the capacity to noticing on the pedagogical activity, where noticing is understood as an inherent process to improve the quality of classroom management. In addition, different analysis models should be compared using examples and experiential practices and the different theories and research projects developed in this field related to this type of analysis. Knowing what happens in the classroom is a task inherent to the math teacher. For sure, if the teacher does not understand or is even able to perceive what is happening in the class, improvement actions are very difficult to implement. Consequently, math teachers must develop the capability of analyzing their pedagogical activity and the related elements. It is not about isolating variables and looking for causal relationships, but rather about understanding the teacher’s activity as the center of the multiple situations occurring in the classroom, which may be known more in depth, if the attention is focused on the organization, ordering, and execution of the tasks planned by the teacher. It must also be understood that the competence of analyzing mentioned here is not an isolated activity without an effect. Such analysis must be approached from an active perspective where scenarios are generated to mitigate complex situations or to value an approach different than the one happening in the classroom. Being aware that there are many aspects to analyze (most likely almost everything that happens is analyzable), we must take a stand on which situations are highly related to what happens in our classroom and which could eventually happen. With such a wide spectrum, some questions that need to be addressed are: What is important in the math education activity and who defines what is important? What elements are of interest to math teachers? How does the analysis conducted relate to the different models of the teacher's knowledge? How does our previous experience influence the assessments we make? How do we distinguish elements of interest to analysis? What is the relationship between reflecting and analyzing? At what stages of the teacher’s activity is an analysis required? What is the ultimate purpose of analyzing teaching activities? What competencies or skills are related to the analysis? What types of analysis are appropriate (content, cognitive, media, among others)? How can we balance the actions derived from the analyses we conduct? From all these questions the most important one that can guide the study of this reflection would be: What should be assessed in pedagogical activities and what is the objective of analyzing such pedagogical activities in math education?

ANTIBIOTIC PROFILE AND ANTIBACTERIAL ACTIVITY OF COPPER OXIDE NANOPARTICLES AGAINST Pseudomonas fluorescens ISOLATED FROM WOUND INFECTION

2019 ◽  
Vol 9 (o3) ◽  
Author(s):  
Haider Qassim Raheem ◽  
Takwa S. Al-meamar ◽  
Anas M. Almamoori
Keyword(s):  
Antibacterial Activity ◽  
Copper Oxide ◽  
Pseudomonas Fluorescens ◽  
Wide Spectrum ◽  
Copper Oxide Nanoparticles ◽  
Morphological Properties ◽  
Clinical Samples ◽  
Oxide Nanoparticles ◽  
Cuo Nps ◽  
Disk Diffusion Assay

Fifty specimens were collected from wound patients who visited Al-Hilla Teaching Hospital. The samples were grown on Blood and MacConkey agar for 24-48 hr at 37oC. The bacterial isolates which achieved as a pure and predominant growth from clinical samples as Pseudomonas fluorescens, were identified using morphological properties and Vitek2 system. The anti-bacterial activity of copper oxide nanoparticles (CuO NPs) against was tested by (disk diffusion assay) using dilutions of (400, 200, 100, 50, 25, and 12.5‎µ‎g/ml). The (MIC and MBC) of each isolate was determined. CuO NPs shows wide spectrum antibacterial activity against tested bacteria with rise zone of inhibition diameter that is proportionate with the increase in nanoparticle concentration. The MIC of CuO NPs extended from 100-200‎µ‎g/ml and the MBC ranged from 200-400‎µ‎g/ml. The antibiotic profile was determined by Viteck 2 compact system (Biomérieux). CuO NPs‎ found highly effective and safe in P. fluorescens wounds infections comparing with used antibiotics.

scholarly journals X/XY Chromosome Mosaicism: Turner Syndrome and Other Clinical Conditions

2009 ◽  
Vol 63 (1-2) ◽  
pp. 1-4
Author(s):  
Irena Andriuškevičiūtė ◽  
Loreta Šalomskienė ◽  
Lina Jurkėnienė ◽  
Algimantas Sinkus
Keyword(s):  
Turner Syndrome ◽  
Y Chromosome ◽  
Wide Spectrum ◽  
Normal Male ◽  
Chromosome Mosaicism ◽  
Lymphocyte Cultures ◽  
Nosological Entity ◽  
The One ◽  
Clinical Conditions ◽  
Pierre Robin

X/XY Chromosome Mosaicism: Turner Syndrome and Other Clinical Conditions The 45,X/46,XY mosaicism shows a wide spectrum of phenotypes ranging from females with Turner syndrome, male or female pseudohermaphroditism, to appearently normal male development. Chromosome anomalies accompanying Turner syndrome were found in lymphocyte cultures of 236 patients. Chromosomal analysis revealed the karyotype 45,X in 118 (50.0%) patients. X monosomy mosaics or structural rearrangements of the X chromosome was established in 112 (47.5%) patients. The Y chromosome was found in six (2.5%) patients with typical features of Turner syndrome. In five mosaics 45,X/46,XY the proportion of the XY clone ranged from 46% to 76%. In one Turner syndrome patient only 47,XYY cells were found (solely blood culture investigated). In most cases of 45,X/46,XY mosaicism, the cause is considered to be the loss of the Y chromosome because of nondisjunction after normal disomic fertilisation. Five other patients with X/XY chromosome mosaicism showed mixed gonadal dysgenesis (two patients), one male pseudohermafroditism, one male with Pierre Robin syndrome, and one normal male phenotype. In two non Turner syndrome patients nondisjunction of the primary clone 46,XY was obvious and resulted in mosaicism 45,X/46,XY/47,XYY, the one patient contained dicentric Y. The similarities between X/XY Turner syndrome and other nosological entity of females possessing Y chromosome — the Swyer syndrome — are discussed.

scholarly journals Rapid electrochemical detection of coronavirus SARS-CoV-2

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Thanyarat Chaibun ◽  
Jiratchaya Puenpa ◽  
Tatchanun Ngamdee ◽  
Nimaradee Boonapatcharoen ◽  
Pornpat Athamanolap ◽  
...  
Keyword(s):  
Electrochemical Biosensor ◽  
Rolling Circle Amplification ◽  
Clinical Samples ◽  
Rolling Circle ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Sandwich Hybridization ◽  
Redox Active ◽  
One Step ◽  
The One

AbstractCoronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.

The Prevalence of Symptoms of Depression in An Australian General Population

1980 ◽  
Vol 14 (1) ◽  
pp. 65-71 ◽  
Author(s):  
D. G. Byrne
Keyword(s):  
Depressive Symptoms ◽  
General Population ◽  
Random Sample ◽  
Clinical Sample ◽  
Depression Scale ◽  
Clinical Samples ◽  
Demographic Differences ◽  
Symptoms Of Depression ◽  
The Subject ◽  
Depressive States

The prevalence of depressive symptoms was estimated in a random sample of an Australian general population by administration of the Zung Self-Rating Depression Scale (S.D.S.). Rates, calculated according to criteria derived from a previously studied clinical sample, were somewhat higher in this population than had been reported in similar studies elsewhere. It was reasoned that this finding related to the relative laxity of criteria employed in the present study. Socio-demographic influences on the reporting of depressive symptoms were evident, the most prominent of these being the sex of the subject. It was suggested that these influences may underlie socio-demographic differences in rates of recognized depressive states occurring within clinical samples.

scholarly journals Detection and characterisation of papillomavirus in skin lesions of giraffe and sable antelope in South Africa

2011 ◽  
Vol 82 (2) ◽  
Author(s):  
E. Van Dyk ◽  
A-M Bosman ◽  
E. Van Wilpe ◽  
J. H. Williams ◽  
R. G. Bengis ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Skin Lesions ◽  
Immunoperoxidase Staining ◽  
Bovine Papillomavirus ◽  
Virus Particles ◽  
Tissue Sections ◽  
Equine Sarcoid ◽  
Pcr Product ◽  
Papillomavirus Dna

Papillomavirus was detected electron microscopically in cutaneous fibropapillomas of a giraffe (Giraffa camelopardalis) and a sable antelope (Hippotragus niger). The virus particles measured 45 nm in diameter. Histopathologically, the lesions showed histopathological features similar to those of equine sarcoid as well as positive immunoperoxidase-staining of tissue sections for papillomavirus antigen. Polymerase chain reaction (PCR) detected bovine papillomavirus (BPV) DNA. Bovine papillomavirus-1 was characterised by real-time PCR in the sable and giraffe, and cloning and sequencing of the PCR product revealed a similarity to BPV-1. As in the 1st giraffe, the lesions from a 2nd giraffe revealed locally malignant pleomorphism, possibly indicating the lesional end-point of papilloma infection. Neither virus particles nor positively staining papillomavirus antigen could be demonstrated in the 2nd giraffe but papillomavirus DNA was detected by real-time PCR which corresponded with BPV-1 and BPV-2.

scholarly journals ANTIBACTERIAL RESISTANCE PATTERN OF PSEUDOMONAS AERUGINOSA ISOLATED FROM CLINICAL SAMPLES AT A GENERAL HOSPITAL IN PADANG, WEST SUMATRA, INDONESIA

2017 ◽  
Vol 10 (8) ◽  
pp. 158
Author(s):  
Rustini Rustini ◽  
Jamsari Jamsari ◽  
Marlina Marlina ◽  
Nasrul Zubir ◽  
Yori Yuliandra
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Resistance ◽  
Clinical Sample ◽  
Opportunistic Pathogen ◽  
Positive Control ◽  
Diffusion Method ◽  
Clinical Samples ◽  
Resistance Pattern ◽  
Tract Infections ◽  
Almost All

Objectives: Pseudomonas aeruginosa is an opportunistic pathogen that has an innate resistance to some antibiotics. This bacterium is one of the mostcommon causes of nosocomial infections that include surgical wound infections, burns, and urinary tract infections. The bacteria have been reportedlyresistant to many antibiotics and have developed multidrug resistance (MDR). The objective of the study was to determine the resistance pattern ofP. aeruginosa isolated from clinical samples of patients against some major antibiotics.Methods: Isolates of P. aeruginosa were obtained from clinical sample of urine, sputum, swabs, pus, feces, and blood and cultured in cetrimide agar. P.aeruginosa ATCC 27853 was used as a positive control. The antibacterial susceptibility testing was conducted against 13 antibiotics: Ceftazidime, cefotaxime,ceftriaxone, cefoperazone, ciprofloxacin, levofloxacin, ofloxacin, gentamicin, amikacin, piperacillin, ticarcillin, meropenem, and imipenem. The examinationwas carried out using agar diffusion method of Kirby-Bauer and following the standards from Clinical and Laboratory Standards Institute (CLSI).Results: The results showed that bacterial resistance was established against all tested antibiotics. The highest number of resistance was shownagainst ceftriaxone (44.21%), whereas the most susceptibility was exhibited against amikacin (only 9.47% of resistance). MDR P. aeruginosa (MDRPA)was detected on almost all clinical samples tested, except the feces. The sample with the highest percentage of MDRPA was the pus.Conclusion: The study concludes that the most effective antibiotic against P. aeruginosa is amikacin (91.51%), whereas the most resistance is exhibited to ceftriaxone (43.16%).

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