scholarly journals Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dan Wang ◽  
Liu Yang ◽  
Chao Ning ◽  
Jian-Feng Liu ◽  
Xingbo Zhao
Keyword(s):  
Genetic Relationships ◽  
Full Range ◽  
High Specificity ◽  
Vital Role ◽  
Reference Sequence ◽  
Specific Reference ◽  
Snp Calling ◽  
Specificity And Sensitivity ◽  
Reference Sequences ◽  
Genome Analyses

Abstract Background Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. In this study, we used three different types of reference sequences for mitogenome mapping, i.e., the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref), respectively, and compared the accuracy of mitogenome alignment and SNP calling among them, for the purpose of proposing the optimal reference sequence for mitochondrial DNA (mtDNA) analyses of specific populations Results Four pigs, representing three different breeds, were high-throughput sequenced, subsequently mapping reads to the reference sequences mentioned above, resulting in a largest mapping ratio and a deepest coverage without increased running time when aligning reads to a BS-ref. Next, single nucleotide polymorphism (SNP) calling was carried out by 18 detection strategies with the three tools SAMtools, VarScan and GATK with different parameters, using the bam results mapping to BS-ref. The results showed that all eighteen strategies achieved the same high specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref because of a low requirement for SNP calling tools and parameter choices. Conclusions This study showed that different reference sequences representing different genetic relationships to sample reads influenced mitogenome alignment, with the breed-specific reference sequences being optimal for mitogenome analyses, which provides a refined processing perspective for NGS data.

scholarly journals Breed-specific Reference Sequence Optimizes Mapping Accuracy of NGS Analyses for Pigs

2020 ◽  
Author(s):  
Dan Wang ◽  
Liu Yang ◽  
Chao Ning ◽  
Jian-Feng Liu ◽  
Xingbo Zhao
Keyword(s):  
Genetic Distances ◽  
Reference Sequence ◽  
Specific Reference ◽  
Snp Calling ◽  
Mapping Strategy ◽  
Specificity And Sensitivity ◽  
Reference Sequences ◽  
Genome Analyses ◽  
Next Generation Sequencing Ngs ◽  
Detection Strategies

Abstract Background: The reference sequence plays a key role in next-generation sequencing (NGS), which impacts the mapping quality during genome analyses. Especially for mitochondrion which contains plentiful amounts of innate DNA, the optimal reference sequence makes mitochondrial genome (mitogenome) alignment accurate and efficient. In this study, different mapping reference sequences, the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref) were compared to test the accuracy of mapping quality in the NGS analyses of pigs.Results: Four pigs from three breeds were high-throughput sequenced and subsequently mapped using three different reference mentioned above, which indicated that the BS-ref produced the largest number of mappable reads and coverages at acceptable run-times. After that, the SNP calling accuracy was evaluated by 18 detection strategies with three tools SAMtools, VarScan and GATK with different parameters under the BS-ref mapping strategy. Results showed that nine detection strategies achieved the same best specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref alignment strategy, with a low requirement for SNP calling tools and parameter choices. Conclusions: Overall, using the breed-specific reference sequences in NGS analyses optimized the mapping quality and the SNP calling accuracy. This study indicates that the different reference sequences which represent different genetic distances between reference sequences and samples in mitogenome alignments influence alignment quality.

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

2020 ◽  
Vol 20 (10) ◽  
pp. 831-840
Author(s):  
Weibin Li
Keyword(s):  
Pathogenic Bacteria ◽  
Genetic Diagnosis ◽  
Bloodstream Infections ◽  
High Specificity ◽  
Peptide Sequence ◽  
High Morbidity ◽  
Specificity And Sensitivity ◽  
Prospective Application ◽  
Small Molecule Therapeutics

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

scholarly journals SARS-CoV-2 specific antibody and neutralization assays reveal the wide range of the humoral immune response to virus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mikail Dogan ◽  
Lina Kozhaya ◽  
Lindsey Placek ◽  
Courtney Gunter ◽  
Mesut Yigit ◽  
...  
Keyword(s):  
Specific Antibody ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
High Specificity ◽  
Spike Protein ◽  
Humoral Immune ◽  
Specificity And Sensitivity ◽  
Wide Range ◽  
Specific Igg ◽  
Negative Controls

AbstractDevelopment of antibody protection during SARS-CoV-2 infection is a pressing question for public health and for vaccine development. We developed highly sensitive SARS-CoV-2-specific antibody and neutralization assays. SARS-CoV-2 Spike protein or Nucleocapsid protein specific IgG antibodies at titers more than 1:100,000 were detectable in all PCR+ subjects (n = 115) and were absent in the negative controls. Other isotype antibodies (IgA, IgG1-4) were also detected. SARS-CoV-2 neutralization was determined in COVID-19 and convalescent plasma at up to 10,000-fold dilution, using Spike protein pseudotyped lentiviruses, which were also blocked by neutralizing antibodies (NAbs). Hospitalized patients had up to 3000-fold higher antibody and neutralization titers compared to outpatients or convalescent plasma donors. Interestingly, some COVID-19 patients also possessed NAbs against SARS-CoV Spike protein pseudovirus. Together these results demonstrate the high specificity and sensitivity of our assays, which may impact understanding the quality or duration of the antibody response during COVID-19 and in determining the effectiveness of potential vaccines.

scholarly journals Highly Sensitive Fluorescent Detection of Acetylcholine Based on the Enhanced Peroxidase-Like Activity of Histidine Coated Magnetic Nanoparticles

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1207
Author(s):  
Hong Jae Cheon ◽  
Quynh Huong Nguyen ◽  
Moon Il Kim
Keyword(s):  
Magnetic Nanoparticles ◽  
High Sensitivity ◽  
High Specificity ◽  
Choline Oxidase ◽  
Fluorescent Detection ◽  
One Pot ◽  
Site Structure ◽  
Specificity And Sensitivity ◽  
Highly Sensitive ◽  
Peroxidase Mimics

Inspired by the active site structure of natural horseradish peroxidase having iron as a pivotal element with coordinated histidine residues, we have developed histidine coated magnetic nanoparticles (His@MNPs) with relatively uniform and small sizes (less than 10 nm) through one-pot heat treatment. In comparison to pristine MNPs and other amino acid coated MNPs, His@MNPs exhibited a considerably enhanced peroxidase-imitating activity, approaching 10-fold higher in catalytic reactions. With the high activity, His@MNPs then were exploited to detect the important neurotransmitter acetylcholine. By coupling choline oxidase and acetylcholine esterase with His@MNPs as peroxidase mimics, target choline and acetylcholine were successfully detected via fluorescent mode with high specificity and sensitivity with the limits of detection down to 200 and 100 nM, respectively. The diagnostic capability of the method is demonstrated by analyzing acetylcholine in human blood serum. This study thus demonstrates the potential of utilizing His@MNPs as peroxidase-mimicking nanozymes for detecting important biological and clinical targets with high sensitivity and reliability.

scholarly journals Serum MicroRNA Signature as a Diagnostic and Therapeutic Marker in Patients with Psoriatic Arthritis

2020 ◽  
Vol 47 (12) ◽  
pp. 1760-1767
Author(s):  
Sarah M. Wade ◽  
Trudy McGarry ◽  
Siobhan C. Wade ◽  
Ursula Fearon ◽  
Douglas J. Veale
Keyword(s):  
Psoriatic Arthritis ◽  
Characteristic Curve ◽  
High Specificity ◽  
Serum Samples ◽  
Rna Molecules ◽  
Serum Mirna ◽  
Serum Microrna ◽  
Specificity And Sensitivity ◽  
European League Against Rheumatism ◽  
Noninvasive Markers

ObjectiveMicroRNA (miRNA) are small endogenous regulatory RNA molecules that have emerged as potential therapeutic targets and biomarkers in autoimmunity. Here, we investigated serum miRNA levels in patients with psoriatic arthritis (PsA) and further assessed a serum miRNA signature in therapeutic responder versus nonresponder PsA patients.MethodsSerum samples were collected from healthy controls (HC; n = 20) and PsA patients (n = 31), and clinical demographics were obtained. To examine circulatory miRNA in serum from HC and PsA patients, a focused immunology miRNA panel was analyzed utilizing a miRNA Fireplex assay (FirePlex Bioworks Inc.). MiRNA expression was further assessed in responders versus nonresponders according to the European League Against Rheumatism response criteria.ResultsSix miRNA (miR-221-3p, miR-130a-3p, miR-146a-5p, miR-151-5p, miR-26a-5p, and miR-21-5p) were significantly higher in PsA compared to HC (all P < 0.05), with high specificity and sensitivity determined by receiver-operating characteristic curve analysis. Analysis of responder versus nonresponders demonstrated higher baseline levels of miR-221-3p, miR-130a-3p, miR-146a-5p, miR-151-5p, and miR-26a-5p were associated with therapeutic response.ConclusionThis study identified a 6-serum microRNA signature that could be attractive candidates as noninvasive markers for PsA and may help to elucidate the disease pathogenesis.

D-galactose catabolism in archaea: operation of the DeLey–Doudoroff pathway in Haloferax volcanii

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Julia-Beate Tästensen ◽  
Ulrike Johnsen ◽  
Andreas Reinhardt ◽  
Marius Ortjohann ◽  
Peter Schönheit
Keyword(s):  
Transcriptional Regulator ◽  
High Specificity ◽  
Comprehensive Analysis ◽  
Haloferax Volcanii ◽  
Knock Out ◽  
Genes Encoding ◽  
Functional Involvement ◽  
Genome Analyses ◽  
Galactose Dehydrogenase ◽  
Substrate Binding Protein

ABSTRACT The haloarchaeon Haloferax volcanii was found to grow on D-galactose as carbon and energy source. Here we report a comprehensive analysis of D-galactose catabolism in H. volcanii. Genome analyses indicated a cluster of genes encoding putative enzymes of the DeLey–Doudoroff pathway for D-galactose degradation including galactose dehydrogenase, galactonate dehydratase, 2-keto-3-deoxygalactonate kinase and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase. The recombinant galactose dehydrogenase and galactonate dehydratase showed high specificity for D-galactose and galactonate, respectively, whereas KDPGal aldolase was promiscuous in utilizing KDPGal and also the C4 epimer 2-keto-3-deoxy-6-phosphogluconate as substrates. Growth studies with knock-out mutants indicated the functional involvement of galactose dehydrogenase, galactonate dehydratase and KDPGal aldolase in D-galactose degradation. Further, the transcriptional regulator GacR was identified, which was characterized as an activator of genes of the DeLey–Doudoroff pathway. Finally, genes were identified encoding components of an ABC transporter and a knock-out mutant of the substrate binding protein indicated the functional involvement of this transporter in D-galactose uptake. This is the first report of D-galactose degradation via the DeLey–Doudoroff pathway in the domain of archaea.

scholarly journals Validity of the International Prostate Symptoms Score in predicting urinary retention after joint replacement

2019 ◽  
Vol 27 (3) ◽  
pp. 230949901986867 ◽  
Author(s):  
Alasdair JA Santini ◽  
Chetan A Jakaraddi ◽  
Fotis Polydoros ◽  
Sree Metikala
Keyword(s):  
Urinary Tract ◽  
Urinary Retention ◽  
Preoperative Evaluation ◽  
Age Groups ◽  
High Specificity ◽  
Logistic Regression Models ◽  
Prosthetic Joints ◽  
Specificity And Sensitivity ◽  
Urinary Tract Symptoms ◽  
Risk Patients

Postoperative urinary retention necessitating catheterization after major lower limb arthroplasty surgery adds to the patients’ postoperative discomfort and increases the risk of urinary tract infection with potential risk of transient bacteraemia and seeding of infection to prosthetic joints. Preoperative evaluation of patients with lower urinary tract symptoms may help to identify at-risk patients and the International Prostate Symptoms Score (IPSS) has been used as a screening tool to quantify the severity of symptoms in males. A prospective cohort of 303 patients undergoing total hip or knee arthroplasty was evaluated using the IPSS. Patients were categorized into three symptom groups (mild, moderate and severe based on scores of 0–7, 8–18 and greater than 18, respectively) and four age groups (<50 years, 51–60 years, 61–70 years and greater than 70 years). Twenty-six patients (8.6%) developed urinary retention and were catheterized postoperatively; of these, 16 were male and 10 were female. Statistical analysis using logistic regression models showed significant association between severe IPSS scores (>18) and urinary retention requiring catheterization in both males and females with both high specificity and sensitivity in the test in predicting postoperative catheterization. Hence, this test is a valid preoperative screen in predicting postoperative catheterization.

scholarly journals Effects of exposure of honey bee colonies to neonicotinoid seed–treated maize crops

2013 ◽  
Vol 57 (2) ◽  
pp. 199-208 ◽  
Author(s):  
Krystyna Pohorecka ◽  
Piotr Skubida ◽  
Piotr Semkiw ◽  
Artur Miszczak ◽  
Dariusz Teper ◽  
...  
Keyword(s):  
Zea Mays ◽  
Honey Bee ◽  
High Specificity ◽  
Negative Effects ◽  
Term Survival ◽  
Pollen Loads ◽  
Modified Quechers ◽  
Specificity And Sensitivity ◽  
Bee Colonies

Abstract The effects to honeybee colonies (Apis mellifera L.) during and after exposure to flowering maize (Zea mays L.), grown from seeds coated with clothianidin and imidacloprid was assessed in field-realistic conditions. The experimental maize crops were adjacent to the other flowering agriculture plants. Honey bee colonies were placed in three differently protected maize fields throughout the blooming period, and thereafter they were transferred to a stationary apiary. Samples of pollen loads, bee bread, and adult bees were collected and analyzed for neonicotinoid residues. To ensure high specificity and sensitivity of detection of the analyzed pesticides, a modified QuEChERS extraction method and liquid chromatography coupled with tandem mass spectrometry were used. Clothianidin was detected only in the samples of pollen loads. Their residue levels ranged from 10.0 to 41.0 ng/g (average 27.0 ng/g). Imidacloprid was found in no investigated sample. No negative effects of neonicotinoid seed-treated maize on the development and long-term survival of honey bee colonies were observed. The low proportion of Zea mays pollen in total bee-collected pollen during the maize flowering period was noted. The findings suggest that maize plants are less attractive forage for honey bees than phacelia (Phacelia tanacetifolia Benth.), buckwheat (Fagopyrum Mill.), white clover (Trifolium repens L.), goldenrod (Solidago L.), and vegetation from Brassicaceae family. The results indicate a possibility of reducing the risk of bees being exposed to the toxic effect of insecticidal dusts dispersed during maize sowing by seeding, in the areas surrounding maize crops, plants that bloom later in the year.

Multicolor enzyme-linked immunoassay method for visual readout of carbendazim

2021 ◽  
Author(s):  
Haoran Liu ◽  
Yiwen Wang ◽  
Ruijie Fu ◽  
Jing Zhou ◽  
Yanlin Liu ◽  
...  
Keyword(s):  
Immunosorbent Assay ◽  
High Specificity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Specificity And Sensitivity

Enzyme-linked immunosorbent assay (ELISA) with high specificity and sensitivity is one of the most popular techniques for detecting carbendazim (CBD), a commonly used benzimidazole fungicide in agriculture. However, the traditional...

scholarly journals Crude antigen from Taenia crassiceps cysticercus used as heterologous antigen in ELISA and in EITB for neurocysticercosis diagnosis of patients from Paraná-Brazil

2008 ◽  
Vol 51 (6) ◽  
pp. 1127-1137 ◽  
Author(s):  
João Carlos Minozzo ◽  
Juliana de Moura ◽  
Sérgio Monteiro Almeida ◽  
Vanete Thomaz-Soccol
Keyword(s):  
Public Health ◽  
Neurological Disorders ◽  
Indirect Elisa ◽  
Taenia Solium ◽  
High Specificity ◽  
Heterologous Antigen ◽  
Public Health Systems ◽  
Crude Antigen ◽  
Specificity And Sensitivity ◽  
Cysticercus Cellulosae

Neurocysticercosis (NCC), the cerebral presence of Taenia solium metacestode (Cysticercus cellulosae), is responsible for neurological disorders worldwide. In order to validate an immunodiagnosis for public-health patients in the State of Parana-Brazil, crude antigen of Taenia crassicepsmetacestode (Cysticercus longicollis) was used as an alternative heterologous antigen to be used in ELISA and in electroimmunotransfer blotting (EITB) for active and inactive NCC diagnosis. Indirect ELISA was able to discriminate between active and inactive samples and presented high specificity and sensitivity. Any immunodominant band was able to distinguish the NCC stages, although the EITB showed 100% specificity. The immunological results proved to be an important auxiliary toll for NCC diagnosis, mainly for public-health systems in developing countries, where either the neuroimage techniques are not accessible or the resources are scarce.

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