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3 Biotech Jul 2024The demand for food goods is rising along with the world population growth, which is directly related to the yield of agricultural crops around the world. However, a... (Review)
Review
The demand for food goods is rising along with the world population growth, which is directly related to the yield of agricultural crops around the world. However, a number of environmental factors, including floods, salinity, moisture, and drought, have a detrimental effect on agricultural production around the world. Among all of these stresses, drought stress (DS) poses a constant threat to agricultural crops and is a significant impediment to global agricultural productivity. Its potency and severity are expected to increase in the future years. A variety of techniques have been used to generate drought-resistant plants in order to get around this restriction. Different crop plants exhibit specific traits that contribute to drought resistance (DR), such as early flowering, drought escape (DE), and leaf traits. We are highlighting numerous methods that can be used to overcome the effects of DS in this review. Agronomic methods, transgenic methods, the use of sufficient fertilizers, and molecular methods such as clustered regularly interspaced short palindromic repeats (CRISPRs)-associated nuclease 9 (Cas9), virus-induced gene silencing (VIGS), quantitative trait loci (QTL) mapping, microRNA (miRNA) technology, and OMICS-based approaches make up the majority of these techniques. CRISPR technology has rapidly become an increasingly popular choice among researchers exploring natural tolerance to abiotic stresses although, only a few plants have been produced so far using this technique. In order to address the difficulties imposed by DS, new plants utilizing the CRISPR technology must be developed.
PubMed: 38846012
DOI: 10.1007/s13205-024-04020-8 -
PloS One 2024Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide....
Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles.
Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.
Topics: Humans; Quantitative Trait Loci; Ocimum basilicum; Plant Breeding; Chromosome Mapping; Phenotype; Genomics; Polymorphism, Single Nucleotide; Genetic Linkage
PubMed: 38593174
DOI: 10.1371/journal.pone.0299825 -
Nucleic Acids Research Jul 2023PlasMapper 3.0 is a web server that allows users to generate, edit, annotate and interactively visualize publication quality plasmid maps. Plasmid maps are used to plan,...
PlasMapper 3.0 is a web server that allows users to generate, edit, annotate and interactively visualize publication quality plasmid maps. Plasmid maps are used to plan, design, share and publish critical information about gene cloning experiments. PlasMapper 3.0 is the successor to PlasMapper 2.0 and offers many features found only in commercial plasmid mapping/editing packages. PlasMapper 3.0 allows users to paste or upload plasmid sequences as input or to upload existing plasmid maps from its large database of >2000 pre-annotated plasmids (PlasMapDB). This database can be searched by plasmid names, sequence features, restriction sites, preferred host organisms, and sequence length. PlasMapper 3.0 also supports the annotation of new or never-before-seen plasmids using its own feature database that contains common promoters, terminators, regulatory sequences, replication origins, selectable markers and other features found in most cloning plasmids. PlasMapper 3.0 has several interactive sequence editors/viewers that allow users to select and view plasmid regions, insert genes, modify restriction sites or perform codon optimization. The graphics for PlasMapper 3.0 have also been substantially upgraded. It now offers an interactive, full-color plasmid viewer/editor that allows users to zoom, rotate, re-color, linearize, circularize, edit annotated features and modify plasmid images or labels to improve the esthetic qualities of their plasmid map and textual displays. All the plasmid images and textual displays are downloadable in multiple formats. PlasMapper 3.0 is available online at https://plasmapper.ca.
Topics: Software; User-Computer Interface; Plasmids; Computers; Base Sequence; Internet
PubMed: 37099365
DOI: 10.1093/nar/gkad276 -
Environmental Pollution (Barking, Essex... Jul 2023Afforestation is an evergreen technology for restraining greenhouse gases (GHGs) emission and improving soil carbon sink in arid and semi-arid regions. Nonetheless, the...
Afforestation is an evergreen technology for restraining greenhouse gases (GHGs) emission and improving soil carbon sink in arid and semi-arid regions. Nonetheless, the long-term impact of woody forests irrigation using recycled wastewater resources remains inconclusive so far. For this purpose, the ecological risk benchmarks of potentially toxic elements (PTEs) were investigated on Eucalyptus forest plantation in order to gauge their bioavailability in the rhizospheric layer of Typic Torripsammentsoil and their accretion capacity in the biosphere. Water quality guidelines pointed to a moderate degree of restriction on use with elevated levels of PTEs. Notably, concentrations of As, B, Cd, Cr, Cu, Mn, Ni, V and Zn were above the permissible limits for irrigation. The geospatial mapping of PTEs concentration in soil pointed to elevated levels of most PTEs, particularly in the deforestated areas. Some of PTEs (Cd, Cu, Hg and Zn) showed values above the permissible limits. A spectrum of ecological risk indices showed considerable to high degree of contamination. Among PTEs, the water-soluble and exchangeable fractions showed high values of As, Cd and Hg (20.7, 17.2 and 11.0%, respectively). Sequential extraction showed variations among PTEs in their tendency to bind with different soil geochemical fractions: (i) carbonate (Cd, Zn and Cu), (ii) Fe-Mn oxides (Pb, Zn and Mn) and (iii) organic matter (B, Pb and Hg). Eight fungal species including Aspergillus flavus, Fusarium solani, Cephalosporimsp., Penicilliumsp., Rhizoctonia solani, Aspergillus niger, Botrytissp. and Verticilliumsp. were dominated in soil. Meanwhile, Agrobacteriumsp., phosphate solubilizing bacteria, nitrogen fixing bacteria and Escherichia coli were the dominant bacterial strains. Values of bioaccumulation index varied among PTEs, wherein B (5.15), Ni (1.98), Mn (1.62) and Cd (1.02) exhibited higher phytoextraction potentials. Other PTEs, however, exhibited values below 1.0 confirming their low phytoextraction potentials. Findings of this investigation, therefore, provide insights into biochemical signals of PTEs contamination in woody forest plantations and the urgent need to contextualize the large-scale utilization of recycled wastewater resources in such vulnerable areas.
Topics: Metals, Heavy; Wastewater; Eucalyptus; Cadmium; Lead; Mercury; Soil; Forests; Environmental Monitoring; Risk Assessment; Soil Pollutants
PubMed: 37121299
DOI: 10.1016/j.envpol.2023.121739 -
BMJ Open Jul 2023Matching-adjusted indirect comparison (MAIC) studies are a subtype of indirect comparison, which uses propensity score weighting to enhance comparability. This method...
Mapping the characteristics, concepts and methodologies of matching-adjusted indirect comparison studies assessing pharmacological therapies in oncology: a scoping review protocol.
INTRODUCTION
Matching-adjusted indirect comparison (MAIC) studies are a subtype of indirect comparison, which uses propensity score weighting to enhance comparability. This method adjusts aggregated data based on covariables from individual patient data from studies to produce population-adjusted indirect comparisons. Some national Health Technology Assessment agencies have recently received submissions containing MAIC models. However, there can be a lack of confidence in its estimates when they are poorly reported and inconsistent with other techniques. The objective of this study is to map the characteristics, concepts and methodology of MAIC studies used for pharmacological therapies in the field of oncology.
METHODS AND ANALYSIS
A scoping review methodology will be applied following the Joanna Briggs Institute framework and the results will be reported according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses Extension for Scoping Reviews. Studies that used MAIC to compare treatments in oncology conditions will be considered eligible. A systematic search will be conducted in PubMed, Embase and the Cochrane Library. No restriction of location or language will be applied. Study screening will be documented and presented in a Preferred Reporting Items for Systematic reviews and Meta-Analyses flow diagram. Data will be extracted and recorded on a predefined data form and will be presented in a tabular form accompanied by a descriptive summary.
ETHICS AND DISSEMINATION
No ethical approval is required for this study. The results of this scoping review will be disseminated through peer-reviewed publications.
Topics: Humans; Records; Academies and Institutes; Language; Medical Oncology; Mental Processes; Research Design; Systematic Reviews as Topic; Review Literature as Topic
PubMed: 37474190
DOI: 10.1136/bmjopen-2023-072156 -
World Journal of Urology Sep 2023The aim of this study was to investigate the overall sensitivity and specificity of indocyanine green (ICG)-near-infrared (NIR) fluorescence imaging in the detection of... (Meta-Analysis)
Meta-Analysis
Performance of indocyanine green in sentinel lymph node mapping and lymph node metastasis in penile cancer: systematic review, meta-analysis, and single-center experience.
PURPOSE
The aim of this study was to investigate the overall sensitivity and specificity of indocyanine green (ICG)-near-infrared (NIR) fluorescence imaging in the detection of sentinel lymph node metastasis (SLNM) in penile cancer.
METHODS
We searched PubMed, Embase, Web of Science, Scopus, and the Cochrane Library databases to identify manuscripts where ICG was intravenously administered prior to or during penile cancer surgery, with no restriction on language or publication status. The results extracted are presented as forest plots.
RESULTS
Seven studies were included in the analysis. The median sensitivity and specificity of ICG-NIR imaging for SLNM detection were 100 and 4%, respectively; the pooled sensitivity was 100.0% (95% confidence interval [CI] 97.0-100.0) and specificity was 2.0% (95% CI 1.0-3.0). There was no significant difference in the diagnostic results between different injection sites and doses in each experimental group.
CONCLUSION
To our knowledge, this meta-analysis is the first to summarize the diagnostic performance of ICG-NIR imaging for SLNM detection in penile cancer. ICG is sensitive in the imaging of SLN tissue, which can consequently improve the accuracy of lymph node detection. However, the specificity is very low.
Topics: Male; Humans; Lymphatic Metastasis; Indocyanine Green; Sentinel Lymph Node; Sentinel Lymph Node Biopsy; Penile Neoplasms; Lymph Nodes; Optical Imaging; Lymphadenopathy; Coloring Agents
PubMed: 37419973
DOI: 10.1007/s00345-023-04485-x -
JBI Evidence Synthesis Mar 2024The overarching aim of this scoping review is to describe and analyze the scope of use and reporting of Bayesian methods in meta-analyses in biomedical research.
OBJECTIVE
The overarching aim of this scoping review is to describe and analyze the scope of use and reporting of Bayesian methods in meta-analyses in biomedical research.
INTRODUCTION
The Bayesian approach provides a powerful and flexible framework for meta-analysis, particularly suited for dealing with complex, sparse, or heterogeneous data. Due to these advantages and its appeal, Bayesian methods have been increasingly used in many areas of biomedical research; however, their use in meta-analysis remains scarce.
INCLUSION CRITERIA
This review will include studies that used Bayesian methods for meta-analysis of primary studies in biomedical research.
METHODS
The proposed review will be conducted in accordance with the JBI methodology for scoping reviews. PubMed, Embase, CINAHL, and the Cochrane Database of Systematic Reviews will be searched to identify relevant full-text papers published since 2016 in English. No geographical restriction will be applied. Two reviewers will screen the articles and extract the data using a tool that will be pilot-tested and revised, as necessary. Analysis will involve frequency counts, narrative synthesis, and mapping concepts to propose an appropriate workflow. The details of the scoping review will be reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guideline.
REVIEW REGISTRATION
Open Science Framework https://osf.io/jenp4/.
Topics: Humans; Bayes Theorem; Biomedical Research; Databases, Factual; Systematic Reviews as Topic; Review Literature as Topic; Meta-Analysis as Topic
PubMed: 38328979
DOI: 10.11124/JBIES-23-00430 -
Frontiers in Genetics 2023Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read...
Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted , (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient's neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.
PubMed: 37811140
DOI: 10.3389/fgene.2023.1244983 -
Genes Oct 2023The main mechanism of innate immunity is the complement system. Its components include the protein products of the and genes, which are involved in the classical...
The main mechanism of innate immunity is the complement system. Its components include the protein products of the and genes, which are involved in the classical activation pathway as well as the inflammatory and cytolytic immune responses, respectively. The aim of this study was to determine the relationship between PCR-restriction fragment length polymorphism in (726T > C) and C5 (1044A > C) genes, and the values of hematological and biochemical blood indices in suckling crossbred (Polish Large White × Polish Landrace × Duroc × Pietrain) piglets (n = 473), considering their age (younger, 21 ± 3 days, n = 274; older, 35 ± 3 days, n = 199) and health status. The frequencies of the genotypes deviated from the Hardy-Weinberg expectations. Younger piglets, healthy piglets, piglets that deviated from physiological norms and older piglets with the TT genotype all had lower white and red blood cell indices. In piglets with the CC genotype, younger piglets, piglets that deviated from physiological norms and older piglets, a greater number and/or percentage of monocytes were recorded in the blood. Older piglets also showed an increase in the number of leukocytes and granulocytes, along with a tendency for a decrease in the percentage of lymphocytes in their blood. We concluded that a polymorphism in the gene may exhibit a functional association or genetic linkage with other genes involved in the process of erythropoiesis. Furthermore the relationship between the gene polymorphism and the number and/or percentage of monocytes in the blood may modify the body's defense abilities. Piglets with the CC genotype, having an increased number/proportion of these cells in their blood, probably display a weakened immune response to pathogens or a chronic stimulation of the immune system.
Topics: Animals; Swine; Polymorphism, Genetic; Polymorphism, Restriction Fragment Length; Chromosome Mapping; Genotype; Polymerase Chain Reaction
PubMed: 38002958
DOI: 10.3390/genes14112015 -
Journal of Cardiology Cases Apr 2024Non-reentrant fascicular tachycardia (NRFT) developed in a 6-year-old Japanese boy. Because of drug-resistant recurrences, he received catheter mapping and ablation at...
UNLABELLED
Non-reentrant fascicular tachycardia (NRFT) developed in a 6-year-old Japanese boy. Because of drug-resistant recurrences, he received catheter mapping and ablation at age 10 years. An electrocardiogram exhibited a superior left-axis deviation, a right bundle branch block-type configuration, and relatively narrow QRS with sharp R wave. It suggested verapamil-sensitive ventricular tachycardia (VT), but showed no sensitivity to verapamil or reentrant characteristics in the electrophysiological study. Detailed VT mapping determined the earliest presystolic Purkinje potential on the left posterior fascicle at the mid-ventricular septum. Radiofrequency current applications to the lesion led to his NRFT-free life without restriction.
LEARNING OBJECTIVES
Purkinje-related idiopathic ventricular tachycardias (VTs) are commonly due to reentrant mechanisms, and non-reentrant fascicular tachycardia (NRFT) is a rare form of idiopathic VT in adults. Although it is crucial to distinguish NRFT from reentrant VTs, there is no information about the electrophysiological studies and the treatment effect in pediatric-onset NRFT.
PubMed: 38646079
DOI: 10.1016/j.jccase.2023.12.002