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Journal of Genetics 2021High-throughput genotyping has become more convenient and cost-effective due to recent advancements in next-generation sequencing (NGS) techniques. Numerous approaches... (Review)
Review
High-throughput genotyping has become more convenient and cost-effective due to recent advancements in next-generation sequencing (NGS) techniques. Numerous approaches exploring sequencing advances for genotyping have been developed over the past decade, which includes different variants of genotyping-by-sequencing (GBS), and restriction-site associated DNA sequencing (RAD-seq). Most of these methods are based on the reduced representation of the genome, which ultimately reduces the cost of sequencing by many folds. However, continuously lowering the cost of sequencing makes it more convenient to use whole genome-based approaches. In this regard, skim sequencing, where low coverage whole-genome sequencing is used for the identification of large numbers of polymorphic markers cost-effectively. In the present review, we have discussed recent technological advancements, applicability, and challenges of skim sequencing-based genotypic approaches for crop improvement programmes. Skim sequencing is being extensively used for genotyping in diverse plant species and has a wide range of applications, particularly in quantitative trait loci (QTL) mapping, genomewide association studies (GWAS), fine genetic map construction, and identification of recombination and gene conversion events in various breeding programmes. The cost-effectiveness, simplicity, and genomewide coverage will increase the application of skims sequencing-based genotyping. The article summarizes the protocol, uses, bioinformatics tools, its application, and future prospects of skim sequencing in crop improvement.
Topics: Crops, Agricultural; Genome, Plant; Genome-Wide Association Study; Genotype; Genotyping Techniques; High-Throughput Nucleotide Sequencing; Plant Breeding; Polymorphism, Single Nucleotide; Quantitative Trait Loci
PubMed: 34238778
DOI: No ID Found -
PloS One 2021Medical procedures that produce aerosolized particles are under great scrutiny due to the recent concerns surrounding the COVID-19 virus and increased risk for...
Medical procedures that produce aerosolized particles are under great scrutiny due to the recent concerns surrounding the COVID-19 virus and increased risk for nosocomial infections. For example, thoracostomies, tracheotomies and intubations/extubations produce aerosols that can linger in the air. The lingering time is dependent on particle size where, e.g., 500 μm (0.5 mm) particles may quickly fall to the floor, while 1 μm particles may float for extended lengths of time. Here, a method is presented to characterize the size of <40 μm to >600 μm particles resulting from surgery in an operating room (OR). The particles are measured in-situ (next to a patient on an operating table) through a 75mm aperture in a ∼400 mm rectangular enclosure with minimal flow restriction. The particles and gasses exiting a patient are vented through an enclosed laser sheet while a camera captures images of the side-scattered light from the entrained particles. A similar optical configuration was described by Anfinrud et al.; however, we present here an extended method which provides a calibration method for determining particle size. The use of a laser sheet with side-scattered light provides a large FOV and bright image of the particles; however, the particle image dilation caused by scattering does not allow direct measurement of particle size. The calibration routine presented here is accomplished by measuring fixed particle distribution ranges with a calibrated shadow imaging system and mapping these measurements to the in-situ imaging system. The technique used for generating and measuring these particles is described. The result is a three-part process where 1) particles of varying sizes are produced and measured using a calibrated, high-resolution shadow imaging method, 2) the same particle generators are measured with the in-situ imaging system, and 3) a correlation mapping is made between the (dilated) laser image size and the measured particle size. Additionally, experimental and operational details of the imaging system are described such as requirements for the enclosure volume, light management, air filtration and control of various laser reflections. Details related to the OR environment and requirements for achieving close proximity to a patient are discussed as well.
Topics: Aerosols; COVID-19; Humans; Operating Rooms; Particle Size
PubMed: 33819294
DOI: 10.1371/journal.pone.0249586 -
Cold Spring Harbor Protocols Nov 2020This protocol describes procedures for cloning blunt-ended DNA fragments into linearized plasmid vectors. To obtain the maximum number of "correct" ligation products...
This protocol describes procedures for cloning blunt-ended DNA fragments into linearized plasmid vectors. To obtain the maximum number of "correct" ligation products when cloning blunt-ended target fragments, the two components of DNA in the ligation reaction must be present at an appropriate ratio. If the molar ratio of plasmid vector to target DNA is too high, then the ligation reaction may generate an undesirable number of circular empty plasmids, both monomeric and polymeric; if too low, the ligation reaction may generate an excess of linear and circular homopolymers and heteropolymers of varying sizes, orientations, and compositions. For this reason, the orientation of the foreign DNA and the number of inserts in each recombinant clone must always be validated by restriction endonuclease mapping or some other means.
Topics: Bacteriophage T4; Buffers; Cloning, Molecular; DNA; DNA Ligases; DNA, Recombinant; Escherichia coli; Genetic Vectors; Plasmids; Viral Proteins
PubMed: 33139501
DOI: 10.1101/pdb.prot101246 -
Bioinformatics (Oxford, England) Oct 2021Optical mapping is a complementary technology to traditional DNA sequencing technologies, such as next-generation sequencing (NGS). It provides genome-wide,...
MOTIVATION
Optical mapping is a complementary technology to traditional DNA sequencing technologies, such as next-generation sequencing (NGS). It provides genome-wide, high-resolution restriction maps from single, stained molecules of DNA. It can be used to detect large and small structural variants, copy number variations and complex rearrangements. Optical mapping is affected by different kinds of errors in comparison with traditional DNA sequencing technologies. It is important to understand the source of these errors and how they affect the obtained data. This article proposes a novel approach to modeling errors in the data obtained from the Bionano Genomics Inc. Saphyr system with Direct Label and Stain (DLS) chemistry. Some studies have already addressed this issue for older instruments with nicking enzymes, but we are unaware of a study that addresses this new system.
RESULTS
The main result is a framework for studying errors in the data obtained from the Saphyr instrument with DLS chemistry. The framework's main component is a simulation that computes how major sources of errors for this instrument (a false site, a missing site and resolution errors) affect the distribution of fragment lengths in optical maps. The simulation is parametrized by variables describing these errors and we are using a differential evolution algorithm to evaluate parameters that best fit the data from the instrument. Results of the experiments manifest that this approach can be used to study errors in the optical mapping data analysis.
AVAILABILITY AND IMPLEMENTATION
Source codes supporting the presented results are available at: https://github.com/mvasinek/olgen-om-error-prediction. The data underlying this article are available on the Bionano Genomics Inc. website, at: https://bionanogenomics.com/library/datasets/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
PubMed: 33983386
DOI: 10.1093/bioinformatics/btab259 -
National Journal of Maxillofacial... 2021A large number of scientific articles have been published regarding impact of COVID-19 infection on dental practice, dental professionals, and the mode of spread of... (Review)
Review
A large number of scientific articles have been published regarding impact of COVID-19 infection on dental practice, dental professionals, and the mode of spread of infection via dental procedures. The present systematic review was planned with an aim of evidence mapping and quality analysis of published research on the dental aspects of COVID-19 infection. The protocol was registered at https://share.osf.io/registration/46221-C87-BA8. The search was performed in Scopus, PubMed, Cochrane, and Embase databases till 15th July 2020. There was no restriction of year of publication and language. All types of published articles related to Dentistry, Dentist, Dental practice, and Oral health education on COVID-19 were included. The Joanna Briggs Institute's (JBI) Critical Appraisal Tools were used for the risk of bias analysis of included studies. A total of 393 articles were short-listed and were checked for eligibility and finally, 380 articles were included. Among the 380 research articles published (till July 15, 2020), the majority of the included articles belonged to the lowermost strata of the evidence pyramid. There were 54 original research articles with no randomized clinical trial, systematic review or, meta-analysis pertaining to the dental perspective of COVID-19 infection. The level of available evidence about dentistry and COVID-19 infection is very low with a lack of researches of highest quality. The guidelines/recommendations for dental professionals, proposed by the different scientific organizations/societies regarding COVID-19 infection are only consensus-based necessitating the need to formulate evidence-based guidelines. There is a need to identify essential research questions and strengthen the study designs in most of the aspects related to the dentistry and COVID-19 pandemic.
PubMed: 34483571
DOI: 10.4103/njms.NJMS_237_20 -
Frontiers in Immunology 2023Bronchial asthma (asthma) is a chronic inflammatory disease of the airways, involving a variety of cells and cellular components, that manifests clinically as recurrent...
BACKGROUND
Bronchial asthma (asthma) is a chronic inflammatory disease of the airways, involving a variety of cells and cellular components, that manifests clinically as recurrent episodes of wheezing, shortness of breath, with or without chest tightness or cough, airway hyperresponsiveness, and variable airflow limitation. The number of people with asthma has reached 358 million worldwide and asthma causes huge economic loss. However, there is a subset of patients who are not sensitive to existing drugs and the existing drugs have many adverse effects. Therefore, it's important to find new drugs for asthma patients.
METHODS
Publications related to biologics in asthma published from 2000 to 2022 were retrieved from Web of Science Core Collection. The search strategies were as follows: topic: TS=(biologic* OR "biologic* product*" OR "biologic* therap*" OR biotherapy* OR "biologic* agent*" OR Benralizumab OR "MEDI-563" OR Fasenra OR "BIW-8405" OR Dupilumab OR SAR231893 OR "SAR-231893" OR Dupixent OR REGN668 OR "REGN-668" OR Mepolizumab OR Bosatria OR "SB-240563" OR SB240563 OR Nucala OR Omalizumab OR Xolair OR Reslizumab OR "SCH-55700" OR SCH55700 OR "CEP-38072" OR CEP38072 OR Cinqair OR "DCP-835" OR DCP835 OR Tezspire OR "tezepelumab-ekko" OR "AMG-157" OR tezspire OR "MEDI-9929" OR "MEDI-19929" OR MEDI9929 OR Itepekimab OR "REGN-3500"OR REGN3500 OR "SAR-440340"OR SAR440340 OR Tralokinumab OR "CAT-354" OR Anrukinzumab OR "IMA-638" OR Lebrikizumab OR "RO-5490255"OR "RG-3637"OR "TNX-650"OR "MILR1444A"OR "MILR-1444A"OR"PRO301444"OR "PRO-301444"OR Pitrakinra OR altrakincept OR "AMG-317"OR"AMG317" OR Etokimab OR Pascolizumab OR "IMA-026"OR Enokizumab OR "MEDI-528"OR "7F3COM-2H2" OR 7F3COM2H2 OR Brodalumab OR "KHK-4827" OR "KHK4827"OR "AMG-827"OR Siliq OR Ligelizumab OR "QGE-031" OR QGE031 OR Quilizumab OR Talizumab OR "TNX-901" OR TNX901 OR Infliximab OR Etanercept OR "PRS-060") AND TS=asthma*. The document type was set to articles and review articles and the language restriction was set to English. Three different analysis tools including one online platform, VOS viewer1.6.18, and CiteSpace V 6.1.R1 software were used to conduct this bibliometric study.
RESULTS
This bibliometric study included 1,267 English papers published in 244 journals from 2,012 institutions in 69 countries/regions. Omalizumab, benralizumab, mepolizumab, and tezepelumab in relation to asthma were the research hotspots in the field.
CONCLUSION
This study systematically uncovers a holistic picture of existing literature related to the biologic treatment of asthma over the past 20 years. We consulted scholars in order to understand key information in this field from the perspective of bibliometrics, which we believe may greatly facilitate future research in this field.
Topics: Humans; Omalizumab; Asthma; Biological Products; Bibliometrics
PubMed: 36845128
DOI: 10.3389/fimmu.2023.1034755 -
Journal of Neurosurgery Jun 2020Maximal safe resection of gliomas near motor pathways is facilitated by intraoperative mapping. The authors and other groups have described the use of bipolar or...
OBJECTIVE
Maximal safe resection of gliomas near motor pathways is facilitated by intraoperative mapping. The authors and other groups have described the use of bipolar or monopolar direct stimulation to identify functional tissue, as well as transcranial or transcortical motor evoked potentials (MEPs) to monitor motor pathways. Here, the authors describe their initial experience using all 3 modalities to identify, monitor, and preserve cortical and subcortical motor systems during glioma surgery.
METHODS
Intraoperative mapping data were extracted from a prospective registry of glioma resections near motor pathways. Additional demographic, clinical, pathological, and imaging data were extracted from the electronic medical record. All patients with new or worsened postoperative motor deficits were followed for at least 6 months.
RESULTS
Between January 2018 and August 2019, 59 operations were performed in 58 patients. Overall, patients in 6 cases (10.2%) had new or worse immediate postoperative deficits. Patients with temporary deficits all had at least Medical Research Council grade 4/5 power. Only 2 patients (3.4%) had permanently worsened deficits after 6 months, both of which were associated with diffusion restriction consistent with ischemia within the corticospinal tract. One patient's deficit improved to 4/5 and the other to 4/5 proximally and 3/5 distally in the lower limb, allowing ambulation following rehabilitation. Subcortical motor pathways were identified in 51 cases (86.4%) with monopolar high-frequency stimulation, but only in 6 patients using bipolar stimulation. Transcranial or cortical MEPs were diminished in only 6 cases, 3 of which had new or worsened deficits, with 1 permanent deficit. Insula location (p = 0.001) and reduction in MEPs (p = 0.01) were the only univariate predictors of new or worsened postoperative deficits. Insula location was the only predictor of permanent deficits (p = 0.046). The median extent of resection was 98.0%.
CONCLUSIONS
Asleep triple motor mapping is safe and resulted in a low rate of deficits without compromising the extent of resection.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Brain Mapping; Brain Neoplasms; Evoked Potentials, Motor; Female; Glioma; Humans; Intraoperative Neurophysiological Monitoring; Male; Middle Aged; Motor Cortex; Neurosurgical Procedures; Prospective Studies; Young Adult
PubMed: 32502996
DOI: 10.3171/2020.3.JNS193434 -
Dental Traumatology : Official... Feb 2021Evidence mapping of systematic reviews (SRs) systematically and comprehensively identifies, organizes, and summarizes the distribution of scientific evidence in a field.... (Meta-Analysis)
Meta-Analysis
BACKGROUND/AIMS
Evidence mapping of systematic reviews (SRs) systematically and comprehensively identifies, organizes, and summarizes the distribution of scientific evidence in a field. The aims of this study were to delineate domains in dental traumatology (DT), evaluate the existing SRs within the domains, and identify the paucity of evidence for future research.
METHODS
Domains and sub-domains of DT were established according to the methods of qualitative research. The protocol for evidence mapping was prepared as per the guidelines of GEM and PRISMA. The search strategy was formulated using words and MeSH terms in eight databases without restriction of languages and year of publication. Gray literature, protocol registries, and references of selected articles were also searched. Duplicates were removed, and the final selection of SRs was completed. Data extraction and quality analysis using the ROBIS tool and the PRISMA checklist were performed.
RESULTS
The overall search resulted in 64 SRs from 1999 to 2020 with 44 published in last six years. The highest number of SRs had been performed in the Prognostic domain (n = 19) followed by the domains of Epidemiology (n = 15), Therapeutics (n = 10), Oral Biology (n = 7), Diagnostics (n = 6), Preventive (n = 5), and Research Methods (n = 2). Within each domain, there were variabilities in the number of reviewers, a priori protocols, search limitations, risk of bias methods, and meta-analysis. Of the SRs, including 4 Cochrane reviews, 28.4% were inconclusive. A low risk of bias was found in 48.4% of the SRs. Among the registered and ongoing SRs, six were from the domain of epidemiology, two in the domain of therapeutics, five from prognostics, and one each in the domains of prevention and research methods.
CONCLUSION
The SRs in DT could be mapped in seven domains with variabilities in the methods. The majority had an a priori registered protocol and a low risk of reporting errors. Within the Epidemiology and Preventive domains, SRs were present in all the sub-domains with the majority demonstrating low-risk of bias (ROB). The domain of prognosis had SRs in most sub-domains but with a high ROB. Insufficient numbers of SRs were present in most sub-domains of the Diagnostics, Therapeutics, Research Methods and Oral Biology domains.
Topics: Bias; Research Design; Traumatology
PubMed: 32949064
DOI: 10.1111/edt.12606 -
Scientific Reports Jun 2023In developing countries, the prevalence of intestinal parasitic infection is still significant, particularly due to geographical and socioeconomic variables. The...
In developing countries, the prevalence of intestinal parasitic infection is still significant, particularly due to geographical and socioeconomic variables. The objective of this study was to map the distribution pattern of intestinal parasitic infection in a cohort of the Egyptian population, as well as to assess associated risk factors. A cross-sectional hospital-based study was conducted on 386 patients. A single fecal specimen was collected from the study individual and examined microscopically for the detection of parasitic infection. DNA was extracted from all samples and utilized to amplify Entamoeba histolytica complex species, Cryptosporidium species, Giardia intestinalis assemblages, and Blastocystis species using PCRs. Typing of Cryptosporidium species and Giardia intestinalis assemblages was performed using restriction enzymes RasI and HaeIII respectively. While Blastocystis spp. subtypes (ST) were identified through sequencing of PCR products and phylogenetic analysis. 59.6% (230/386) of the study patients were infected with one or more intestinal parasites, 87.4%; 201/230 of patients had mono-parasitic infections, and 12.6%; 29/230 had multiple-parasitic infections (P < 0.0001). The predominant protozoa were Blastocystis, followed by Entamoeba histolytica complex, and Giardia intestinalis both as mono-parasites and as part of multiple parasites. Molecular assays showed that Blastocystis ST3, Entamoeba dispar, Giardia intestinalis assemblage B, and Cryptosporidium hominis were the most prevalent species. Intestinal parasitic infection was significantly associated with age, gender, residence, and water source. Multi-parasitism showed that residency in a rural area was a risk factor (OR 4.49; 95% CI 1.51-13.37; P = 0.007). Egyptians residing in rural areas have a high prevalence of intestinal multi-parasitism. Therefore, to lessen the prevalence and effects of these infections in this group, effective and sustainable control methods, providing health education focusing on good personal hygiene habits, and providing a safe drinking water supply should be implemented.
Topics: Humans; Cryptosporidiosis; Cross-Sectional Studies; Phylogeny; Egypt; Cryptosporidium; Intestinal Diseases, Parasitic; Giardia lamblia; Blastocystis; Entamoeba histolytica
PubMed: 37340037
DOI: 10.1038/s41598-023-36320-z -
Genomics Jul 2019Single molecule analysis can help us study genomics efficiently. It involves studying single DNA molecules for genomic studies. DNA combing is one of such techniques...
Single molecule analysis can help us study genomics efficiently. It involves studying single DNA molecules for genomic studies. DNA combing is one of such techniques which allowed us to study single DNA molecules for multiple uses. DNA combing technology can be used to perform Fiber-FISH and optical mapping. Physical mapping of genomes can be studied by restriction digestion of combed DNA on glass slides. Restriction fragments can be arranged into optical maps by gathering fluorescent intensity data by CCD camera and image analysis by softwares. Physical mapping and DNA segment rearrangements can be studied by Fiber-FISH which involves application of probes on genomic DNA combed over glass slides. We developed a novel methodology involving combing solution optimization, denatured combed DNA and performed restriction digestion of combed DNA. Thus we provided an efficient and robust combing platform for its application in Fiber-FISH and optical mapping.
Topics: DNA, Single-Stranded; Humans; In Situ Hybridization, Fluorescence; Nucleic Acid Denaturation; Single Molecule Imaging
PubMed: 29550497
DOI: 10.1016/j.ygeno.2018.03.012