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Methods in Molecular Biology (Clifton,... 2021Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were... (Review)
Review
Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.
Topics: Brassica napus; Crops, Agricultural; DNA, Plant; Diploidy; Disease Resistance; Genes, Plant; Genetic Markers; Haploidy; Homozygote; Hordeum; Isoenzymes; Molecular Biology; Plant Breeding; Plant Diseases; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Polymorphism, Single Nucleotide; Triticum
PubMed: 34270004
DOI: 10.1007/978-1-0716-1335-1_3 -
Current Environmental Health Reports Jun 2022Climate change (CC) is currently responsible for global weather extremes. These weather extremes could contribute to changes in the pattern of health problems. The... (Review)
Review
PURPOSE OF REVIEW
Climate change (CC) is currently responsible for global weather extremes. These weather extremes could contribute to changes in the pattern of health problems. The purpose of this review is to discuss the role of CC on remapping of hepatic diseases and the mechanisms of re-mapping.
RECENT FINDINGS
CC was found to have a major influence on the distribution and severity of hepatic diseases, such as outbreaks of vector-borne, water or food-borne, parasitic diseases, re-emerging of disappeared diseases, or emerging of new forms of infectious agents. Migration of infected people from endemic areas due to the CC disasters results in rapid dissemination of infectious diseases that leads to outbreaks or endemicity of diseases in new areas. CC could cause increasing chemical emissions, or change in its biodegradability, or restriction in its dispersion, such as PM, PAHs, heavy metals, mycotoxins, and aquatic toxins. Increase in the concentrations of these chemicals may have significant impacts in changing the health map of hepatic toxicity and liver cancer. The current review confirms the role of CC in changing the pattern of several liver health problems and remapping of these problems in several regions of the world. This review could be of high importance to the health decision-makers as an early alarm and prediction of hepatic health problems with the projected CC.
Topics: Animals; Climate Change; Communicable Diseases; Disease Outbreaks; Disease Vectors; Foodborne Diseases; Humans; Liver Diseases
PubMed: 35482218
DOI: 10.1007/s40572-022-00352-w -
BioRxiv : the Preprint Server For... Dec 2023Initial classification of acute leukemia involves the assignment of blasts to cell states within the hematopoietic hierarchy based on morphological and immunophenotypic...
Initial classification of acute leukemia involves the assignment of blasts to cell states within the hematopoietic hierarchy based on morphological and immunophenotypic features. Yet, these traditional classification approaches lack precision, especially at the level of immature blasts. Single-cell RNA-sequencing (scRNA-seq) enables precise determination of cell state using thousands of markers, thus providing an opportunity to re-examine present-day classification schemes of acute leukemia. Here, we developed a detailed reference map of human bone marrow hematopoiesis from 263,519 single-cell transcriptomes spanning 55 cellular states. Cell state annotations were benchmarked against purified cell populations, and in-depth characterization of gene expression programs underlying hematopoietic differentiation was undertaken. Projection of single-cell transcriptomes from 175 samples spanning acute myeloid leukemia (AML), mixed phenotype acute leukemia (MPAL), and acute erythroid leukemia (AEL) revealed 11 subtypes involving distinct stages of hematopoietic differentiation. These included AML subtypes with notable lymphoid or erythroid lineage priming, challenging traditional diagnostic boundaries between AML, MPAL, and AEL. Quantification of lineage priming in bulk patient cohorts revealed specific genetic alterations associated with this unconventional lineage priming. Integration of transcriptional and genetic information at the single-cell level revealed how genetic subclones can induce lineage restriction, differentiation blocks, or expansion of mature myeloid cells. Furthermore, we demonstrate that distinct cellular hierarchies can co-exist within individual patients, providing insight into AML evolution in response to varying selection pressures. Together, precise mapping of hematopoietic cell states can serve as a foundation for refining disease classification in acute leukemia and understanding response or resistance to emerging therapies.
PubMed: 38234771
DOI: 10.1101/2023.12.26.573390 -
Avicenna Journal of Medical... 2021The PX330 and the related PX459 plasmids are widely used for Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-mediated genome editing. Screening...
BACKGROUND
The PX330 and the related PX459 plasmids are widely used for Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-mediated genome editing. Screening for plasmids containing the correct sgRNA template insertion is one of the most important steps in this system. Different methods for screening the sgRNA inserts have been deployed. One such method is Restriction Enzyme (RE) mapping. Restriction enzyme mapping can be used to screen for numerous plasmid recombinants simultaneously.
METHODS
In this study, the sgRNA templates were initially cloned into the above PX459 plasmids. Subsequently, the accuracy of the constructs was determined by RE mapping.
RESULTS
This method was established to screen for sgRNA-bearing PX459 plasmids. However, numerous anomalies were detected after ligation of sgRNA templates into RE digested PX459 plasmids.
CONCLUSION
Our data suggest that RE mapping is only appropriate as an initial screen and that the identity of all plasmids with the correctly identified RE maps should be confirmed by Sanger sequencing.
PubMed: 34900150
DOI: No ID Found -
Functional & Integrative Genomics Sep 2023Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing... (Review)
Review
Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.
Topics: Humans; Trees; Genome-Wide Association Study; Plant Breeding; Chromosome Mapping; Alleles; Crops, Agricultural
PubMed: 37700096
DOI: 10.1007/s10142-023-01224-8 -
International Journal of Molecular... Jan 2023Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple...
Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.
Topics: Animals; Zea mays; Plant Breeding; Insecta; Genetic Variation; Genetic Association Studies
PubMed: 36768464
DOI: 10.3390/ijms24032138 -
World Journal of Clinical Cases Dec 2021Synthetic magnetic resonance imaging (MRI) MAGnetic resonance imaging compilation (MAGiC) is a new MRI technology. Conventional T1, T2, T2-fluid-attenuated inversion...
BACKGROUND
Synthetic magnetic resonance imaging (MRI) MAGnetic resonance imaging compilation (MAGiC) is a new MRI technology. Conventional T1, T2, T2-fluid-attenuated inversion recovery (FLAIR) contrast images, quantitative images of T1 and T2 mapping, and MAGiC phase sensitive inversion recovery (PSIR) Vessel cerebrovascular images can be obtained simultaneously through post-processing at the same time after completing a scan. In recent years, studies have reported that MAGiC can be applied to patients with acute ischemic stroke. We hypothesized that the synthetic MRI vascular screening scheme can evaluate the degree of cerebral artery stenosis in patients with acute ischemic stroke.
AIM
To explore the application value of vascular images obtained by synthetic MRI in diagnosing acute ischemic stroke.
METHODS
A total of 64 patients with acute ischemic stroke were selected and examined by MRI in the current retrospective cohort study. The scanning sequences included traditional T1, T2, and T2-FLAIR, three-dimensional time-of-flight magnetic resonance angiography (3D TOF MRA), diffusion-weighted imaging (DWI), and synthetic MRI. Conventional contrast images (T1, T2, and T2-FLAIR) and intracranial vessel images (MAGiC PSIR Vessel] were automatically reconstructed using synthetic MRI raw data. The contrast-to-noise ratio (CNR) values of traditional T1, T2, and T2-FLAIR images and MAGiC reconstructed T1, T2, and T2-FLAIR images in DWI diffusion restriction areas were measured and compared. MAGiC PSIR Vessel and TOF MRA images were used to measure and calculate the stenosis degree of bilateral middle cerebral artery stenosis areas. The consistency of MAGiC PSIR Vessel and TOF MRA in displaying the degree of vascular stenosis with computed tomography angiography (CTA) was compared.
RESULTS
Among the 64 patients with acute ischemic stroke, 79 vascular stenosis areas showed that the correlation between MAGiC PSIR Vessel and CTA ( = 0.90, < 0.01) was higher than that between TOF MRA and CTA ( = 0.84, < 0.01). With a degree of vascular stenosis > 50% assessed by CTA as a reference, the area under the receiver operating characteristic (ROC) curve of MAGiC PSIR Vessel [area under the curve (AUC) = 0.906, < 0.01] was higher than that of TOF MRA (AUC = 0.790, < 0.01). Among the 64 patients with acute ischemic stroke, 39 were scanned for traditional T1, T2, and T2-FLAIR images and MAGiC images simultaneously, and CNR values in DWI diffusion restriction areas were measured, which were: Traditional T2 = 21.2, traditional T1 = -6.7, and traditional T2-FLAIR = 11.9; and MAGiC T2 = 7.1, MAGiC T1 = -3.9, and MAGiC T2-FLAIR = 4.5.
CONCLUSION
The synthetic MRI vascular screening scheme for patients with acute ischemic stroke can accurately evaluate the degree of bilateral middle cerebral artery stenosis, which is of great significance to early thrombolytic interventional therapy and improving patients' quality of life.
PubMed: 35047594
DOI: 10.12998/wjcc.v9.i35.10828 -
Cell Stem Cell Mar 2022Deregulation of transcription is a hallmark of acute myeloid leukemia (AML) that drives oncogenic expression programs and presents opportunities for therapeutic...
Deregulation of transcription is a hallmark of acute myeloid leukemia (AML) that drives oncogenic expression programs and presents opportunities for therapeutic targeting. By integrating comprehensive pan-cancer enhancer landscapes with genetic dependency mapping, we find that AML-enriched enhancers encode for more selective tumor dependencies. We hypothesized that this approach could identify actionable dependencies downstream of oncogenic driver events and discovered a MYB-regulated AML-enriched enhancer regulating SEPHS2, a key component of the selenoprotein production pathway. Using a combination of patient samples and mouse models, we show that this enhancer upregulates SEPHS2, promoting selenoprotein production and antioxidant function required for AML survival. SEPHS2 and other selenoprotein pathway genes are required for AML growth in vitro. SEPHS2 knockout and selenium dietary restriction significantly delay leukemogenesis in vivo with little effect on normal hematopoiesis. These data validate the utility of enhancer mapping in target identification and suggest that selenoprotein production is an actionable target in AML.
Topics: Animals; Carcinogenesis; Enhancer Elements, Genetic; Humans; Leukemia, Myeloid, Acute; Mice; Oncogenes; Selenium
PubMed: 35108519
DOI: 10.1016/j.stem.2022.01.003 -
BMC Genomics May 2021The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this...
BACKGROUND
The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds.
RESULTS
We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes.
CONCLUSION
Despite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is 'better' than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research.
Topics: DNA Transposable Elements; Diatoms; Genomics; Haplotypes; Software
PubMed: 34030633
DOI: 10.1186/s12864-021-07666-3 -
Frontiers in Genetics 2019The largemouth bass is an important species, and its culture has risen sharply with the surge in fish aquaculture in China. Due to the lack of selective breeding...
The largemouth bass is an important species, and its culture has risen sharply with the surge in fish aquaculture in China. Due to the lack of selective breeding technology for the largemouth bass, the growth rate and disease resistance are low, its sexual maturation is slow, and other serious problems are contributing to a sharp decline in the safety and quality of largemouth bass products in recent decades. Therefore, comprehensive breeding programs to improve the economic performance and promote the modern industrial development of largemouth bass must be considered a priority. Here, a total of 152 adult largemouth bass, including two parents and 150 progenies, were selected to produce the genetic mapping family. Then, a high-density linkage map was constructed based on restriction site-associated DNA sequencing using 6,917 single-nucleotide polymorphisms (SNPs) located in 24 linkage groups (LGs). The total genetic length of the linkage map was 1,261.96 cM, and the length of each LG varied from 24.72 cM for LG02 to 117.53 cM for LG16, with an average length of 52.58 cM and an average SNP number of 286. Thirteen significant quantitative trait loci (QTLs) for sex determination were located on LG04, LG05, LG08, LG12, LG15, LG21, and LG23. An informative QTL cluster that included six QTLs was detected on LG12. However, one notable QTL, which accounted for 71.48% of the total phenotypic variation, was located in the region of 1.85 cM on LG05. In addition, 32 identified QTLs were related to growth, including body weight, body length, body height, and head length. The QTLs for these growth-related traits are located in 13 LG regions and have little effect on phenotypic variation. This high-density genetic linkage map will enable the fine-mapping of economic traits and support the future genome assembly of the largemouth bass. Additionally, our study will be useful for future selective culture of largemouth bass and could potentially be used in molecular-assisted breeding of largemouth bass for aquaculture.
PubMed: 31649731
DOI: 10.3389/fgene.2019.00960