Types Of Molecular Markers Research Articles

Molecular profiling of therapeutically important Alpinia and Kaempferia species using RAPD, ISSR, and SSR markers

Alpinia and Kaempferia species require precise identification and diversification to improve the accuracy in drug discovery and industrial demands. In this current study, four Alpinia species (Alpinia malaccensis, A. nigra, A. galanga and A. calcarata) and three Kaempferia species (Kaempferia galanga, K. rotunda and K. parishii) were selected for molecular profiling analysis. Three types of molecular markers (PCR based) such as RAPD, ISSR, and SSR were used to increase the accuracy of analysis. About 91 polymorphic loci were amplified in these 7 species using 9 RAPD primers out of 30. The resolving power (RP) was varied from 4.56 to 10.06 and the polymorphic information content (PIC) ranged between 0.8 and 0.93. Out of 40 ISSR primer 13 primers showed total 118 polymorphic loci. The maximum RP and PIC were 9.36 and 0.97 respectively. In case of SSR analysis, only 11 SSRs out of 35 showed 201 polymorphic loci. The RP were found between 3.12 and 17.86. The PIC in SSR primers were in between 0.78 and 0.97. This study indicated that unique banding pattern was observed in specific primers of each marker. D20, D18, and D8 primers were found as the best RAPD markers. (GA)8T, (GA)9T, and (GTGC)4 were the best ISSR markers which can produce distinct banding pattern. SSR2 and SSR14 have also successfully amplified in Alpinia and Kaempferia species with distinct banding pattern. Although SSR marker is more advance than other two but multiple markers based molecular profiling would have enough significance. This present study has enormous importance towards DNA fingerprinting study of different species of Alpinia and Kaempferia. The unique banding pattern in specific primer could be efficiently useful for species identification and future improvement of the taxa.

Using RAPD markers for Detection the genetic diversity of E. coli isolates from Kirkuk hospitals

300 samples from different infection sourcel for a patients and revisers in Azadi hospital, Kirkuk generic hospital, and children hospital, from various ages for both genders, to isolate Escherichia coli bacteria and diagnosis it, and study the genetic variety which distribution to clinical samples by (140) urine samples, (45) diarrhea samples, (40) wound swab, (40) burn swab, and (35) from otitis media infection.
 The growth isolation on the different cultural media was diagnosed from the appearance, microscopical, and cultural characteristics. The results the diagnosis showed that (75) clinical isolation about (38.65%) refers to E. coli bacteria distributed by (9) isolation at ratio (31%) from the burn swab, (6) isolation at ratio (26.1) from wound swab, (4) isolation from otitis media infection (19%), (13) isolation from the stool about (40.6%), and (43) isolation (84.3%) from the urinary tract infection (UTI).
 The sensitivity of the clinical and ecological isolations was studied for nine antibiotics from different antibiotics, broadly. Where the highest resistance for the antibiotics in the clinical isolations to both (ampicillin and cephalexin) reaching in the rate of (97.3%) and (92%), respectively. While the lowest resistance rate for the clinical isolations was to the (Amikacin) in the rate of (17.3%).
 It has been selected 24 clinical isolations, and 24 ecological isolations from E. coli isolations depending on here resistance to many of antibiotics. To study the genetic variation for these isolations and the genetic markers it has been used a type of molecular markers which is depending on PCR technical it is: randomly Amplified polymorphic DNA (RAPD).

The use of RAPD markers to Detect the genetic diversity of E. coli isolates from Kirkuk city environment

The environmental samples we were collected about 130 samples from the soil and water and were dividing to (71) , (59) water and soil samples resectively.
 The growth isolation on the different cultural media was diagnosed from the appearance, microscopically, and cultural characteristics.
 The results of the diagnosis for the environmental samples showed that (51) of the isolations refers to E. coli bacteria about (45.9%) divvied to 33 isolates from the water by (52.4%) and (18) isolates from the soil by (37.5%).
 The ecological isolates was studied against nine antibiotics, broadly the isolates variables wherefrom the resistance of the antibiotic. The highest resistance was to the antibiotic cephalexin which reach to (80.4%).while there was no resistance for antibiotics (Amikacin) and (5.5%) to chloramphenicol
 It has been selected 24 clinical isolations, and 24 ecological isolates from E. coli isolates depending on here resistance to many of antibiotics. To study the genetic variation for these isolates and the genetic markers it has been used a type of molecular markers which is depending on PCR technical it is: Randomly Amplified Polymorphic DNA (RAPD), and polymorphism bands then the observed data were enters to the computers for statistical analysis according to NTSYS-PC program, version 2.02 for this kind of the researches.

ГЕНЕТИЧЕСКАЯ ОЦЕНКА НОВОТАЛИЦКОЙ И ШЕБАЛИНСКОЙ ПОПУЛЯЦИЙ МАРАЛОВ

Currently, various approaches, including molecular genetic methods, are used to study the gene pool of different breeds and populations and to determine their genetic structure and diversity. The development of molecular genetic methods has opened up new possibilities for evaluating genetic diversity, determining population structure, and controlling the degree of inbreeding. One type of molecular genetic marker is microsatellites. The aim of the research was the genetic evaluation of the Novotalitskaya and Shebalinskaya maral populations using microsatellite markers. Molecular genetic studies were carried out in collaboration with the Bioengineering Laboratory of the Altai State University. Biological material from maral stags (ear concha cartilaginous tissue) was sampled in the branch “OS Novotalitskoe” of the Federal Altai Research Center of Agro- Biotechnologies (Charyshskiy District, Altai Region) and the LLC “Maral-Tolusoma” (Shebalinskiy District, Republic of Altai). Polymorphism in the maral populations was studied using five markers (ETH225, Haut14, ILSTS06, INRA35, and MM12). The number of alleles of these loci was found to vary from 7 (MM12) to 34 (ILSTS06) in the Novotalitskaya population, and from 8 (MM12) to 27 (ILSTS06, ETH225) in the Shebalinskaya population, with an average of 21.8 alleles in each. When analysing five loci, 109 alleles were found in each population. The most frequent genotypes in the Novotalitskaya population are 091/091 of the MM12 locus; in the Shebalinskaya population – 090/090 of the MM12 locus and 103/103 of the INRA35 locus. The heterozygosity of the microsatellite loci varies from 0.00 for the MM12 locus to 0.56 for the I LSTS06 locus (Novotalitskaya and Shebalinskaya populations), and 0.57 for the ETH225 locus (Novotalitskaya population). The analysis revealed a rather high level of inbreeding in the populations.

New genetic markers for <i>Burkholderia pseudomallei</i> strains typing

Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease in humans and animals that may be asymptomatic long-term and quickly develop to pneumonia and septicemia in immunocompromised state and due to predisposing factors. Melioidosis is endemic in countries with tropical and subtropical climates, where B. pseudomallei is a part of the soil and water microbiota of stagnant water bodies, as well as the plant rhizosphere. The recording of imported melioidosis cases in countries with temperate climate zone, along with the continued threat of using this pathogen as a bioterrorism agent, indicate the relevance of research aimed at developing modern methods for its diagnosing and typing. Current research in the intraspecific differentiation of pathogenic strains of infectious diseases tends to use two or more types of molecular markers. A promising direction for the B. pseudomallei strains genotyping is based on using a combination of VNTR loci, which provides a high discriminating ability of the method of multi-locus variable tandem repeat number analysis (MLVA), and slowly evolving single nucleotide polymorphisms (SNPs). The aim of this work was to identify new VNTR and SNP loci suitable for use as genetic markers in molecular typing of the melioidosis causative agent. 20 strains of B. pseudomallei from the collection of the Volgograd Plague Control Research Institute and whole genome sequences of 85 B. pseudomallei strains from the GenBank NCBI database were analyzed. While typing melioidosis causative agent strains from the GenBank NCBI database for 4 VNTR loci, 74 genotypes were identified, of which 64 were unique (HunterGaston index 0.997). It was found that the high allelic polymorphism of VNTR loci limited a potential to determine the geographical and phylogenetic relationships of B. pseudomallei isolates by using the MLVA-4 scheme, and the identified null alleles increased the risk of homoplasia. In this regard, the MLVA-4 scheme was supplemented with a VNTR marker in the BPSS1974 locus encoding a collagen-like protein as well as with SNP markers in the genes of lipid A biosynthesis lauroyl acyltransferase, RNA polymerase sigma factor RpoH, and glutamine amidotransferase. For amplification of the select loci, primers and probes were designed as part of the developed scheme, which were tested in the typing of B. pseudomallei collection strains. According to the results of a cluster analysis for 105 strains of the melioidosis causative agent, an integrated approach turned out to be optimal, allowing differentiation of strains within SNP groups based on VNTR profiles. The methodological approach developed for B. pseudomallei genetic typing, based on a comprehensive analysis of 4 SNP- and 5 MLVA-markers in our modification, allowed to differentiate strains according to the geographical regions of their origin and establish the clonal origin of isolates upon revealing cases of melioidosis.

MORPHOLOGICAL CHARACTERIZATION AND GENETIC DIVERSITY USING THE SSR TECHNIQUE IN SOME APPLE GENOTYPES

The scab is a widespread disease throughout the world causing large financial losses in apple production and needs to be controlled also by developing polygenic varieties with resistance to several races of the pathogen Venturia inaequalis by incorporation of two or more functionally different resistance genes. The studies for evidence of interest genes relating to the resistance of apple varieties to apple scab have been conducted using several types of molecular markers (SCAR, SSR, RAPD, ISSR etc.). In this experiment, using six SSR molecular markers (CH02b10, CH05e03, CH02d01, Hi07f01 and Hi07h02), was tracked the reveal of amplified fragments, corresponding to PCR products associated with resistance genes Rvi2, Rvi8, Rvi5 and Rvi11, but also the intraspecific diversity expressed at the molecular level of Romanian apple varieties, some of them having common genitors. The position of the amplified fragments on the agarose gel for the six SSR markers was located on similar values ranges to those published in various specialized papers, the size of the amplified fragments following to be evaluated by the sequencing step and published in a new paper as an addition to the results of this study.

CD73/NT5E is a Potential Biomarker for Cancer Prognosis and Immunotherapy for Multiple Types of Cancers.

Cluster of Differentiations 73 (CD73)/ecto-5'-nucleotidase (NT5E) is a novel type of immune molecular marker expressed on many tumor cells and involved in regulating the essential immune functions and affecting the prognosis of cancer patients. However, it is not clear how the NT5E is linked to the infiltration levels of the immune cells in pan-cancer patients and their final prognosis. This study explores the role of NT5E in 33 tumor types using GEPIA, TIMER, Oncomine, BioGPS databases, and several bioinformatic tools. The findings reveal that the NT5E is abnormally expressed in a majority of the types of cancers and can be used for determining the prognosis prediction ability of different cancers. Moreover, NT5E is significantly related to the infiltration status of numerous immune cells, immune-activated pathways, and immunoregulator expressions. Last, specific inhibitor molecules, like NORNICOTINE, AS-703026, and FOSTAMATINIB, which inhibit the expression of NT5E in various types of cancers, are screened with the CMap. Thus, it is proposed that NT5E can be utilized as a potential biomarker for predicting the prognosis of cancer patients and determining the infiltration of various immune cells in different types of cancers.

Мarker-assisted selection of ukrainian local chicken breeds. overview of research results

The article presents a complex system of using of different types of molecular genetic markers in marker-assisted selection of Ukrainian local chicken breeds of egg and combined productivity. The main stages of selection work with different chicken breeds of Ukrainian selection are given considering the results of genetic variability research and analysis of productivity parameters of chicken with different genotypes by a number of DNA-markers. According to the results of the research, prospective marker systems identified by the set of quantitative trait loci, allelic variants of which are associated with productivity indicators. The formulas of perspective genotypes according to the complex of quantitative trait loci for chickens of Birkivska Barvista line A, Poltava clay line 14 and Rhode Island Red line 38 are given. For chicken breeds of combined productivity, the formulas of the desired genotypes formed on the egg or meat direction.

Genome-wide meta-analysis of QTL for morphological related traits of flag leaf in bread wheat.

Flag leaf is an important organ for photosynthesis of wheat plants, and a key factor affecting wheat yield. In this study, quantitative trait loci (QTL) for flag leaf morphological traits in wheat reported since 2010 were collected to investigate the genetic mechanism of these traits. Integration of 304 QTLs from various mapping populations into a high-density consensus map composed of various types of molecular markers as well as QTL meta-analysis discovered 55 meta-QTLs (MQTL) controlling morphological traits of flag leaves, of which 10 MQTLs were confirmed by GWAS. Four high-confidence MQTLs (MQTL-1, MQTL-11, MQTL-13, and MQTL-52) were screened out from 55 MQTLs, with an average confidence interval of 0.82 cM and a physical distance of 9.4 Mb, according to the definition of hcMQTL. Ten wheat orthologs from rice (7) and Arabidopsis (3) that regulated leaf angle, development and morphogenesis traits were identified in the hcMQTL region using comparative genomics, and were speculated to be potential candidate genes regulating flag leaf morphological traits in wheat. The results from this study provides valuable information for fine mapping and molecular markers assisted selection to improve morphological characters in wheat flag leaf.

Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation.

It has been established that through binding to bone morphogenetic proteins (BMPs), bone morphogenetic protein receptor I B (BMPR1B) can mediate transforming growth factor β (TGF-β) signal transduction, and is involved in the regulation of several biological processes, such as bone and muscle formation and homeostasis, as well as folliculogenesis. Also known as FecB, BMPR1B has been reported as the major gene for sheep prolificacy. A number of previous studies have analyzed the relationship between single nucleotide polymorphisms (SNPs) in this gene and its related performance. In recent years, with the illustration of the effect of retrotransposon insertion on the expression of the proximal genes or phenotypic variation, retrotransposon insertion polymorphisms (RIPs) have been used as a novel type of molecular marker in the evaluation of evolution, population structure and breeding of plant and domestic animals. In this study, the RIPs in porcine BMPR1B gene were excavated, and thereafter verified using a comparative genome and polymerase chain reaction (PCR). The potential effects of phenotype, gene expression and functions related to RIPs were also explored. The results showed that 13 distinct RIPs were identified in introns of porcine BMPR1B. Among these, only BMPR1B-SINE-RIP9 and BMPR1B-LINE-RIP13 displayed a close relationship with the growth traits of Large White pigs. Moreover, the total number of BMPR1B-SINE+/+-RIP9 individuals born was found to be significantly higher than that of SINE−/− (p < 0.05). These two RIPs showed an obvious distribution pattern among Chinese indigenous breeds and Western commercial breeds. The expression of BMPR1B in ovaries of adult BMPR1B-SINE+/+-RIP9 Sushan pigs was found to be significantly higher in comparison to those of BMPR1B-SINE−/−-RIP9 (p < 0.05). SINE insertion of BMPR1B-SINE-RIP9 and LINE insertion of BMPR1B-LINE-RIP13 were observed to significantly increase the activity of Octamer binding transcription factor 4 (OCT4) minipromoter in CHO and C2C12 cells (p < 0.01). Therefore, these two RIPs could serve as useful molecular markers for modulating the growth or reproductive traits in assisted selection of pig breeding, while the mechanisms of the insertion function should be studied further.

Assessing and Evaluating the Scope and Constraints of Idylla Molecular Assays by Using Different Source Materials in Routine Diagnostic Settings.

For cancer treatment, diagnostics concerning tumor type and determination of molecular markers in short TAT is critical. The fully automated, real-time PCR-based molecular diagnostic Idylla assays are well established in many laboratories for qualitative detection, short TAT and routine screening of clinically relevant oncogenic mutations. According to the manufacturer, all IVD assays are recommended for use only with FFPE tissue samples of 5–10 µM dissections with at least 10% tumor content. In this study, we tested the performance and accuracy of the IVD assays along with the gene fusion assay (RUO) with different tissue/source materials like isolated DNA/RNA, cryomaterial, etc. The study also included testing archival FFPE tissue sections dating back from 20 years and a performance check for different pan-cancer samples individually. All the assays tested with FFPE sections and gDNA/RNA input showed above 96% accuracy and sensitivity, individually with 100% specificity. The Idylla assays also performed exceptionally well on the archival FFPE tissues, and the use of assays for other solid tumors was also remarkable. The performance test and accuracy of Idylla assays showed high efficiency with certain limitations. For the use of Idylla assays, both qualitative and quantitative applicability of different tumor source materials could produce efficient results in different diagnostic settings within a short TAT.

RABC: Rheumatoid Arthritis Bioinformatics Center.

Advances in sequencing technologies have led to the rapid growth of multi-omics data on rheumatoid arthritis (RA). However, a comprehensive database that systematically collects and classifies the scattered data is still lacking. Here, we developed the Rheumatoid Arthritis Bioinformatics Center (RABC, http://www.onethird-lab.com/RABC/),the first multi-omics data resource platform (data hub) for RA. There are four categories of data in RABC: (i) 175 multi-omics sample sets covering transcriptome, epigenome, genome, and proteome; (ii) 175 209 differentially expressed genes (DEGs), 105 differentially expressed microRNAs (DEMs), 18 464 differentially DNA methylated (DNAm) genes, 1764 KEGG pathways, 30 488 GO terms, 74 334 SNPs, 242 779 eQTLs, 105 m6A-SNPs and 18 491 669 meta-mQTLs; (iii) prior knowledge on seven types of RA molecular markers from nine public and credible databases; (iv) 127 073 literature information from PubMed (from 1972 to March 2022). RABC provides a user-friendly interface for browsing, searching and downloading these data. In addition, a visualization module also supports users to generate graphs of analysis results by inputting personalized parameters. We believe that RABC will become a valuable resource and make a significant contribution to the study of RA.

Molecular Markers in Breeding of Crops: Recent Progress and Advancements

A convectional plant breeder faces the challenge of how to more effectively and efficiently perform selection and accelerate breeding progress to satisfy the requirements of changing demands for crop cultivars. However, with the development and advancement of molecular marker technology, the fate of plant breeding has shifted from year to year. Recently, different types of molecular markers have been developed, and advancements in sequencing technologies have greatly increased plant improvement. To further our understanding of molecular markers, several reviews have been published in recent decades. However, with the advancement of newly emerging technologies and techniques, the reviewers did not discuss several recently emerged technologies and techniques in plant breeding. Therefore, this article is intended to be reviewed as an overview of recent breakthroughs in DNA markers and their applications in breeding of crops for early and senior researchers with little or no experience with molecular markers. The progress made in molecular plant breeding, genetics, genomic selection, gene pyramiding, MAS, and gene mapping has contributed to a deeper understanding of molecular markers, provided deeper insights into the variability available for crops, and considerably supplemented current breeding techniques. Next-generation sequencing technologies assist in the identification of novel molecular markers for complex and unstructured populations through genotyping-by-sequencing, gene mapping, QTL mapping, and association mapping. Altogether, the classification of molecular markers and their potential application in plants are discussed.

Morphological and Molecular Characterizations of Musa (ABB) 'Mali-Ong' in Thailand.

Simple SummaryThe banana cultivar Musa (ABB) ‘Mali-Ong’ is widely used in the processed food industry in Thailand, where it determines the quality of the products. However, the sub-cultivars of ‘Nam Wa Mali-Ong’ are almost indistinguishable, with few morphological differences and minimal genetic variation. This study used 77 morphological characteristics and two types of molecular markers to distinguish Nam Wa Mali-Ong from other cultivars. The study also assessed the genetic variation of nine ‘Nam Wa Mali-Ong’ clones and compared them with 10 other samples of bananas with different genomes or chromosome sets. The molecular markers grouped the ‘Nam Wa Mali-Ong’ samples. Four clones (A, B, D, and I) were superior and had higher bunch weights. This study will be useful for germplasm evaluation and future ‘Nam Wa Mali-Ong’ improvements.Musa (ABB) ‘Mali-Ong’ is an economically important banana cultivar in Thailand. We morphologically and molecularly characterized ‘Nam Wa Mali-Ong’. Leaf blade width was the only statistically different morphological character among the clones. To determine genetic variation, nine ‘Nam Wa Mali-Ong’ clones were compared with 10 samples of Musa ABB, AA, and BB cultivars by fingerprinting using seven pairs of sequence-related amplified polymorphism (SRAP) and eight inter simple sequence repeat (ISSR) markers. The SRAP and ISSR primers generated 65 and 76 amplicons, respectively, of which 57 (87.7%) and 62 (81.6%) amplicons, respectively, were polymorphic; the polymorphic information content was 0.28–0.49. The SRAP data revealed two distinct groups: Group I, comprising two subgroups (one including all ABB samples and the other containing the BB genome accessions), and Group II, comprising the AA genome accessions. The ISSR data revealed two groups: Group I, which incorporated the AA (Hom Champa) genome, and Group II, consisting of two subgroups: Subgroup A, comprising only the AA (Hom Chan) accessions, and subgroup B, comprising all the ABB accessions and wild banana M. balbisiana (BB genome). The ‘Nam Wa Mali-Ong’ samples clustered together, regardless of the markers used. SRAP and ISSR markers will be useful for germplasm evaluation and future Musa (ABB) improvements.

From STRs to SNPs via ddRAD-seq: Geographic assignment of confiscated tortoises at reduced costs.

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost‐effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD‐seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro‐area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re‐assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in‐situ of confiscated animals and their possible re‐allocation in the wild. Our methodological pipeline can easily be extended to other species.

Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales.

Although the power of genetic surveillance tools has been acknowledged widely, there is an urgent need in malaria endemic countries for feasible and cost-effective tools to implement in national malaria control programs (NMCPs) that can generate evidence to guide malaria control and elimination strategies, especially in the case of Plasmodium vivax. Several genetic surveillance applications (‘use cases’) have been identified to align research, technology development, and public health efforts, requiring different types of molecular markers. Here we present a new highly-multiplexed deep sequencing assay (Pv AmpliSeq). The assay targets the 33-SNP vivaxGEN-geo panel for country-level classification, and a newly designed 42-SNP within-country barcode for analysis of parasite dynamics in Vietnam and 11 putative drug resistance genes in a highly multiplexed NGS protocol with easy workflow, applicable for many different genetic surveillance use cases. The Pv AmpliSeq assay was validated using: 1) isolates from travelers and migrants in Belgium, and 2) routine collections of the national malaria control program at sentinel sites in Vietnam. The assay targets 229 amplicons and achieved a high depth of coverage (mean 595.7 ± 481) and high accuracy (mean error-rate of 0.013 ± 0.007). P. vivax parasites could be characterized from dried blood spots with a minimum of 5 parasites/µL and 10% of minority-clones. The assay achieved good spatial specificity for between-country prediction of origin using the 33-SNP vivaxGEN-geo panel that targets rare alleles specific for certain countries and regions. A high resolution for within-country diversity in Vietnam was achieved using the designed 42-SNP within-country barcode that targets common alleles (median MAF 0.34, range 0.01-0.49. Many variants were detected in (putative) drug resistance genes, with different predominant haplotypes in the pvmdr1 and pvcrt genes in different provinces in Vietnam. The capacity of the assay for high resolution identity-by-descent (IBD) analysis was demonstrated and identified a high rate of shared ancestry within Gia Lai Province in the Central Highlands of Vietnam, as well as between the coastal province of Binh Thuan and Lam Dong. Our approach performed well in geographically differentiating isolates at multiple spatial scales, detecting variants in putative resistance genes, and can be easily adjusted to suit the needs in other settings in a country or region. We prioritize making this tool available to researchers and NMCPs in endemic countries to increase ownership and ensure data usage for decision-making and malaria policy.

Screening of key methylation-driven genes CDO1 in breast cancer based on WGCNA.

With the rapid development of genomics and molecular biology, not only have biochemical indicators been used as tumour markers, but many new molecular markers have emerged. Epigenetic abnormalities are a new type of molecular marker, and DNA methylation is an important part of epigenetics. This study used weighted gene coexpression network analysis (WGCNA) to analyse key methylation-driven genes in breast cancer. The RNA-seq transcriptome data, DNA methylation data, and clinical information data of breast cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database, and the MethylMix R package was used to screen methylation-driven genes in breast cancer. The ClusterProfiler package and enrichplot package in R software were used to further analyse the function and signalling pathway of methylation-driven genes. Through univariate and multivariate Cox regression analyses, methylation-driver genes related to prognostic were obtained, a prognostic model was constructed and prognostic characteristics were analysed. The 17 methylation-driven genes related to prognosis were obtained by the WGCNA method in breast cancer, and the prognostic significance of these methylation-driven genes was determined by transcriptome and methylation combined survival analysis. Analysis of functions and signalling pathways showed that these genes were mainly enriched in biological processes and signalling pathway. Through univariate and multivariate Cox regression analyses, a prognostic model of 5 methylation-driven genes was constructed. The AUC of the receiver operating characteristic (ROC) curve of this model was 0.784, showing that the model had a good prediction effect. Based on WGCNA screening, it was found that only CDO1 was the key methylation-driven gene for prognosis in breast cancer, indicating that CDO1 may be an important indicator of the prognosis of breast cancer patients.

Biotechnological Initiative for Management of Mungbean Yellow Mosaic Virus in Mungbean (Vigna radiate L.)

Mungbean (Vigna radiate L.) is one of the most important legume crops of Asiatic region. The average yield of mungbean is quite low due to its susceptibility against mungbean yellow mosaic virus (MYMV). Mungbean yellow mosaic virus disease (MYMD) is caused by MYMV, which is transmitted through whitefly (Bemisia tabaci). The controlling of this devastating disease is mainly depends upon spraying of insecticides, which cause serious ill effect on humans and soil health. Breeding for its resistance is one of the best strategies for developing MYMV resistant genotypes in mungbean. Several types of molecular markers have been used in marker assisted breeding (MAB) in mungbean. Among them SSR markers are widely used and a plethora of scientific advocate the use of the SSR marker in developing MYMV resistance in mungbean. Recent advancements in functional genomics and gene editing technologies can further enhance our understanding of the molecular mechanisms underlying resistance to MYMV and hence facilitate the development of MYMV resistant mungbean genotypes.

Genetic diversity and relationship analyses of mango (Mangifera indica L.) germplasm resources with ISSR, SRAP, CBDP and CEAP markers

Forty-eight mango accessions were compared for genetic diversity and relationships based on four molecular marker assays, namely, inter-simple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP), CAAT-box derived polymorphism (CBDP), and cis-element amplified polymorphism (CEAP). Comparative analyses of the marker assays based on Nei's genetic diversity (H), Shannon's information index (I), polymorphism information content (PIC), the marker index (MI), and resolving power (Rp) revealed that (i) the CEAP markers provided the most information according to the PIC, MI and Rp values; (ii) the CBDP and ISSR markers exhibited valuable information according to the H and I values. The correlation values (r) of the Mantel test ranged from 0.334 (ISSR and CEAP) to 0.819 (CEAP and the combination of the four marker assays). The unweighted pair group method with arithmetic mean (UPGMA) cluster results showed that a single-marker assay can accurately reflect the genetic relationships of some mango samples but cannot accurately reflect the genetic relationships of all mango samples and that when multiple markers are used to evaluate the genetic relationships of mango germplasm resources, the results are more accurate than those of a single-marker assay. The combined cluster analysis of the molecular marker types shows higher discrimination according to genetic relationships. Nine mango accessions were suggested to be likely parental or sister lines based on the combination of the ISSR, SRAP, CBDP, and CEAP marker assays.

Neutrophil Death in Myeloproliferative Neoplasms: Shedding More Light on Neutrophils as a Pathogenic Link to Chronic Inflammation.

Neutrophils are an essential component of the innate immune response, but their prolonged activation can lead to chronic inflammation. Consequently, neutrophil homeostasis is tightly regulated through balance between granulopoiesis and clearance of dying cells. The bone marrow is both a site of neutrophil production and the place they return to and die. Myeloproliferative neoplasms (MPN) are clonal hematopoietic disorders characterized by the mutations in three types of molecular markers, with emphasis on Janus kinase 2 gene mutation (JAK2V617F). The MPN bone marrow stem cell niche is a site of chronic inflammation, with commonly increased cells of myeloid lineage, including neutrophils. The MPN neutrophils are characterized by the upregulation of JAK target genes. Additionally, MPN neutrophils display malignant nature, they are in a state of activation, and with deregulated apoptotic machinery. In other words, neutrophils deserve to be placed in the midst of major events in MPN. Our crucial interest in this review is better understanding of how neutrophils die in MPN mirrored by defects in apoptosis and to what possible extent they can contribute to MPN pathophysiology. We tend to expect that reduced neutrophil apoptosis will establish a pathogenic link to chronic inflammation in MPN.