Molecular Markers Research Articles

Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants.

Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.

Determining the residual volume in peritoneal dialysis using low molecular weight markers.

Variation in residual volume between peritoneal dialysis dwells creates uncertainty in ultrafiltration determination, dialysis efficiency, and poses a risk of overfill if the residual volume is large. Measuring the dilution of a marker molecule during fluid fill offers a convenient approach, however, estimation accuracy depends on the choice of dilution marker. We here evaluate the feasibility of creatinine and urea as dilution markers compared to albumin-based residual volumes and three-pore model estimations. This clinical, retrospective analysis comprises 56 residual volume estimations from 20 individuals, based on the dilution of pre-fill dialysate creatinine, urea and albumin concentrations during the dialysis fluid fill phase. Outcomes were compared individually. Bias induced by ultrafiltration, marker molecule mass-transfer and influence of fluid glucose contents was quantified using the three-pore model. Linear regression established conversion factors enabling conversion between the various marker molecules. Creatinine-based calculations overestimated residual volumes by 115 mL (IQR 89-149) in 1.5% dwells and 252 mL (IQR 179-313) in 4.25% glucose dwells. In hypertonic dwells, ultrafiltration was 52 mL (IQR 38-66), while intraperitoneal creatinine mass increased by 67% during fluid fill, being the leading cause of overestimation. Albumin-based volumes conformed strongly with three-pore model estimates. Correction factors effectively enabled marker molecule interchangeability. Mass-transfer of low molecular weight marker molecules is associated with residual volume overestimation. However, by applying correction factors, creatinine and urea dilution can still provide reasonable estimates, particularly when the purpose is to exclude the presence of a very large residual volume.

Pioneering Nit Gene Exploitation to Develop Molecular Diagnostic Assay forRapid Detection ofCotton Root Rot Incitant, Macrophomina phaseolina (Tassi) Goid, in Field Soil.

Cotton root rot caused by Macrophomina phaseolina pose a significant threat to cotton production, leading to substantial yield and quality losses. Early and accurate diagnosis of this pathogen in soil is crucial for effective disease management. Thisstudy presents a pioneering investigation into the utilization of the nit gene encoding nitrilase for the development of a molecular diagnostic assay aimed at the rapid detection of M. phaseolina in field soils. The methodology involved the design and validation of primers targeting the Nit gene sequence, followed by the optimization of PCR conditions for efficient amplification. Leveraging state-of-the-art molecular techniques, the assay offers a novel protocol to accurately identify the presence of M. phaseolina in soil with high sensitivity and specificity. The specificity of the designed primers was confirmed through PCR amplification using DNA from M. phaseolina and other related fungi. Sensitivity tests demonstrated that the PCR assay reliably detected M. phaseolina DNA at concentrations as low as 1 ng. Furthermore, the performance of the diagnostic assay was rigorously evaluated using field soil samples with a known status of M. phaseolina infection, demonstrating its reliability and efficacy in real-world scenarios. This study introduces a novel molecular marker for the detection of M. phaseolina and offers a rapid and efficient means for screening M. phaseolina in large soil samples with minimal time and manpower.

Synthesis of 64Cu-, 55Co-, and 68Ga-Labeled Radiopharmaceuticals Targeting Neurotensin Receptor-1 for Theranostics: Adjusting InVivo Distribution Using Multiamine Macrocycles.

The development of theranostic radiotracers relies on their binding to specific molecular markers of a particular disease and the use of corresponding radiopharmaceutical pairs thereafter. This study reports the use of multiamine macrocyclic moieties (MAs), as linkers or chelators, in tracers targeting the neurotensin receptor-1 (NTSR-1). The goal is to achieve elevated tumor uptake, minimal background interference, and prolonged tumor retention in NTSR-1-positive tumors. Methods: We synthesized a series of neurotensin antagonists bearing MA linkers and metal chelators. The MA unit is hypothesized to establish a strong interaction with the cell membrane, and the addition of a second chelator may enhance water solubility, consequently reducing liver uptake. Small-animal PET/CT imaging of [64Cu]Cu-DOTA-SR-3MA, [64Cu]Cu-NT-CB-NOTA, [68Ga]Ga-NT-CB-NOTA, [64Cu]Cu-NT-CB-DOTA, and [64Cu]Cu-NT-Sarcage was acquired at 1, 4, 24, and 48 h after injection using H1299 tumor models. [55Co]Co-NT-CB-NOTA was also tested in HT29 (high NTSR-1 expression) and Caco2 (low NTSR-1 expression) colorectal adenocarcinoma tumor models. Saturation binding assay and internalization of [55Co]Co-NT-CB-NOTA were used to test tracer specificity and internalization in HT29 cells. Results: In vivo PET imaging with [64Cu]Cu-NT-CB-NOTA, [68Ga]Ga-NT-CB-NOTA, and [55Co]Co-NT-CB-NOTA revealed high tumor uptake, high tumor-to-background contrast, and sustained tumor retention (≤48 h after injection) in NTSR-1-positive tumors. Tumor uptake of [64Cu]Cu-NT-CB-NOTA remained at 76.9% at 48 h after injection compared with uptake 1 h after injection in H1299 tumor models, and [55Co]Co-NT-CB-NOTA was retained at 60.2% at 24 h compared with uptake 1 h after injection in HT29 tumor models. [64Cu]Cu-NT-Sarcage also showed high tumor uptake with low background and high tumor retention 48 h after injection Conclusion: Tumor uptake and pharmacokinetic properties of NTSR-1-targeting radiopharmaceuticals were greatly improved when attached with different nitrogen-containing macrocyclic moieties. The study results suggest that NT-CB-NOTA labeled with either 64Cu/67Cu, 55Co/58mCo, or 68Ga (effect of 177Lu in tumor to be determined in future studies) and NT-Sarcage labeled with 64Cu/67Cu or 55Co/58mCo may be excellent diagnostic and therapeutic radiopharmaceuticals targeting NTSR-1-positive cancers. Also, the introduction of MA units to other ligands is warranted in future studies to test the generality of this approach.

MIPs: multi-locus intron polymorphisms in species identification and population genomics.

The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.

Synergistic effects of novel penicillin-binding protein 1A amino acid substitutions contribute to high-level amoxicillin resistance of Helicobacter pylori.

The growing resistance to amoxicillin (AMX)-one of the main antibiotics used in Helicobacter pylori eradication therapy-is an increasing health concern. Several mutations of penicillin-binding protein 1A (PBP1A) are suspected of causing AMX resistance; however, only a limited set of these mutations have been experimentally explored. This study aimed to investigate four PBP1A mutations (i.e., T558S, N562H, T593A, and G595S) carried by strain KIN76, a high-level AMX-resistant clinical H. pylori isolate with an AMX minimal inhibition concentration (MIC) of 2 µg/mL. We transformed a recipient strain 26695 with the DNA containing one to four mutation allele combinations of the pbp1 gene from strain KIN76. Transformants were subjected to genomic exploration and antimicrobial susceptibility testing. The resistance was transformable, and the presence of two to four PBP1A mutations (T558S and N562H, or T593A and G595S), rather than separate single mutations, was necessary to synergistically increase the AMX MIC up to 16-fold compared with the wild-type (WT) strain 26695. An AMX binding assay of PBP1A was performed using these strains, and binding was visualized by chasing Bocillin, a fluorescent penicillin analog. This revealed that all four-mutation allele-transformed strains exhibited decreased affinity to AMX on PBP1A than the WT. Protein structure modeling indicated that functional modifications occur as a result of these amino acid substitutions. This study highlights a new synergistic AMX resistance mechanism and establishes new markers of AMX resistance in H. pylori.IMPORTANCEThe development of resistance to antibiotics, including amoxicillin, is hampering the eradication of Helicobacter pylori infection. The identification of mechanisms driving this resistance is crucial for the development of new therapeutic strategies. We have demonstrated in vitro the synergistic role of novel mutations in the pbp1 gene of H. pylori that is suspected to drive amoxicillin resistance. Also deepening our understanding of amoxicillin resistance mechanisms, this study establishes new molecular markers of amoxicillin resistance that may be useful in molecular-based antibiotic susceptibility testing approaches for clinical practice or epidemiologic investigations.

Emerging concepts of migrasome: An up-and-coming organelle from biology to the clinic.

Since the migrasome concept was first proposed in 2015, extensive research has been conducted on these novel organelles, which grow on retracted fibers at the posterior end of migrating cells. Recently, molecular markers, biological functions, and clinical values based on the initial formation mechanism of migrasomes have emerged. Additionally, researchers are recognizing the significant role that migrasomes play in the pathological and diagnostic processes of clinical diseases. In this review, we summarize recent advances in the biology and clinical application of migrasomes and provide a comprehensive view of the prospective challenges surrounding their clinical application.

Molecular and Morphological Identification of Sarocladium Species Causing Sheath Rot of Rice in Thailand and Their Division into Physiological Races

Sheath rot and dirty panicle are some of the major diseases of rice in Thailand. The diseases are traditionally considered to be caused by the pathogen Sarocladium oryzae and damage and lower both the quantity and quality of rice grain. In this study, 32 fungal isolates collected from the central and northeastern regions of Thailand were analysed phylogenetically using three molecular markers (ITS, D1/D2 of 28S rDNA and ACT) and physiological races were determined on 10 differential rice cultivars. We found that S. oryzae is not the only causal agent of sheath rot in Thailand, but S. attenuatum was also found. Despite having similar morphological features, the phylogenetic analysis recognised 11 of 32 isolates as S. attenuatum and the remaining isolates as S. oryzae. This is the first report of S. attenuatum causing sheath rot of rice in Thailand in addition to S. oryzae. Evaluation of physiological races revealed high pathogenic diversity of the two species. Thus, 16 and 11 physiological races were recorded from 21 isolates of S. oryzae and 11 isolates of S. attenuatum, respectively. These results indicate that both S. oryzae and S. attenuatum are the causal agents of rice sheath rot and dirty panicle in Thailand and that they are pathologically diverse.

Gene pyramiding an advanced approach for disease management in rice: A review

Gene pyramiding is a vital strategy for varietal development in different crops. By using fewer generations than conventional breeding, molecular marker genotyping can streamline the gene pyramiding process. Enhancing the genetic foundation of resistance is crucial for reducing the burden of pesticide residues in the food chain, making it an effective strategy. The development of different pyramided lines carrying single or in combination of different diseases resistant genes in rice viz., Xa4, xa5, xa13, Xa21, and Xa38 for bacterial leaf blight; Pi1, Pi2, Pi9, Pi54, Pi46, and Pita for blast; qSBR7-1, qSBR11-1, and qSBR11-2 for sheath blight. The pyramided lines consist of either single or combinations of various resistance genes, which are instrumental in disease-resistant genetic improvement programs. These lines are utilized to develop profitable varieties that exhibit resistance to multiple diseases.

Association study of crude seed protein and fat concentration in a USDA pea diversity panel.

Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high-protein pea lines, exploring genetic architecture across environments, pinpointing genes and metabolic pathways associated with high protein, and documenting information for single nucleotide polymorphism (SNP)-based marker-assisted selection. From 2019 to 2021, a 487-accession pea diversity panel, More protein, More pea, More profit, was evaluated in a randomized complete block design. DNA was extracted for genomic analysis via genotype-by-sequencing. Phenotypic analysis included protein and fat measurements in seeds and flower color. Genome-wide association study (GWAS) used multiple models, and the Pathways Association Study Tool was used for metabolic pathway analysis. Significant associations were found between SNPs and pea seed protein and fat concentration. Gene Psat7g216440 on chromosome 7, which targets proteins to cellular destinations, including seed storage proteins, was identified as associated with SPC. Genes Psat4g009200, Psat1g199800, Psat1g199960, and Psat1g033960, all involved in lipid metabolism, were associated with fat concentration. GWAS also identified genes annotated for storage proteins associated with fat concentration, indicating a complex relationship between fat and protein. Metabolic pathway analysis identified 20 pathways related to fat and seven to protein concentration, involving fatty acids, amino acid and protein metabolism, and the tricarboxylic acid cycle. These findings will assist in breeding of high-protein, diverse pea cultivars, and SNPs that can be converted to breeder-friendly molecular marker assays are identified for genes associated with high protein.

Molecular evaluation and phenotypic screening of brown and orange rust in Saccharum germplasm.

Brazil is the largest global producer of sugarcane and plays a significant role-supplier of sugar and bioethanol. However, diseases such as brown and orange rust cause substantial yield reductions and economic losses, due decrease photosynthesis and biomass in susceptible cultivars. Molecular markers associated with resistance genes, such as Bru1 (brown rust) and G1 (orange rust), could aid in predicting resistant genotypes. In this study, we sought to associate the phenotypic response of 300 sugarcane accessions with the genotypic response of Bru1 and G1 markers. The field trials were conducted in a randomized block design, and five six-month-old plants per plot were evaluated under natural disease conditions. Genotypic information about the presence or absence of Bru1 (haplotype 1) and G1 gene was obtained after extraction of genomic DNA and conventional PCR. Of the total accessions evaluated, 60.3% (181) showed resistance to brown rust in the field, and of these, 70.7% (128) had the Bru1 gene present. Considering the field-resistant accessions obtained from Brazilian breeding programs (116), the Bru1 was present in 77,6% of these accessions. While alternative resistance sources may exist, Bru1 likely confers enduring genetic resistance in current Brazilian cultivars. Regarding the phenotypic reaction to orange rust, the majority of accessions, 96.3% (288), were field resistant, and of these, 52.7% (152) carried the G1 marker. Although less efficient for predicting resistance when compared to Bru1, the G1 marker could be part of a quantitative approach when new orange rust resistance genes are described. Therefore, these findings showed the importance of Bru1 molecular markers for the early selection of resistant genotypes to brown rust by genetic breeding programs.

Integrative description of two new species of the genus Mesobiotus (Eutardigrada, Macrobiotoidea) from Russia, with an updated phylogeny of the genus

In this study, we describe two new species of Mesobiotus based on morphological data collected through light and scanning electron microscopy. Descriptions include DNA sequences of four commonly used molecular markers (18S rDNA, 28S rDNA, ITS-2, and COI). Mesobiotus efa sp. nov. was discovered in North-West Russia and belongs to the group of species with smooth cuticle, harmsworthi-type OCA, typical Mesobiotus claws IV with unindented lunules, and egg chorion with reticulated processes in form of ‘sharp wide cones’ or ‘cones with long slender endings’, egg process bases with well-developed crone of dark thickenings without finger-like projections, and egg shell surface between the processes with ridges without reticulation, areolation or semi-areolation. It can be distinguished from all know species of this group by a unique combination of morphological and morphometric characters. Mesobiotus vulpinus sp. nov. was found in the Russian Far East, and is similar to Mesobiotus mauccii by having an egg chorion with polygonal relief. The new species can be distinguished from M. mauccii by having a narrower buccal tube, by details of oral cavity armature, and by longer egg chorion processes. Furthermore, we provide results of the phylogenetic analyses of the genus Mesobiotus conducted in this study.

Development of an efficient molecular-marker assisted selection strategy for berry color in grapevine

Marker-assisted selection (MAS) represents one of the most effective strategies to reduce costs and time in plant breeding programs. MAS benefits from the identification of markers in strong linkage disequilibrium (LD) with causative genes and from the development of fast, scalable, and reproducible screening techniques. In grape, berry color is a valuable trait, highly related to the sensory characteristics of fresh grape and wine quality.The present work aims to develop a MAS strategy to select skin color by High-Resolution Melting (HRM), a ‘close-tube’ method capable of detecting polymorphisms within PCR-amplified DNA fragments. To identify molecular markers associated with the berry skin color phenotypic trait, the total genome of 3 white-berry and 3 red-berry accessions were sequenced using Illumina technology and aligned to the reference genome PN40024 v4. The sequencing results revealed the presence of three highly polymorphic regions on chromosome 2 between 15 Kbp and 17 Kbp for red berry genotypes. HRM analyses were carried out on a total of 95 genotypes, 70 of which comprised a berry color segregating population: [‘Italia’ (white berry) x cv ‘Crimson Seedless’ (red berry)] and 25 genotypes belonging to a commercial grapevine germplasm collection consisting of 11 red and 14 white berry accessions. The HRM profiles of the three regions tested strongly correlated with the phenotypic trait of color.The results of this work represent an effective, fast, and reliable genotyping strategy that enables the discrimination of genotypes based on the presence or absence of berry pigmentation.

Increase in the Expression of Glucose Transporter 2 (GLUT2) on the Peripheral Blood Insulin-Producing Cells (PB-IPC) in Type 1 Diabetic Patients after Receiving Stem Cell Educator Therapy

Multicenter international clinical trials demonstrated the clinical safety and efficacy by using stem cell educator therapy to treat type 1 diabetes (T1D) and other autoimmune diseases. Previous studies characterized the peripheral blood insulin-producing cells (PB-IPC) from healthy donors with high potential to give rise to insulin-producing cells. PB-IPC displayed the molecular marker glucose transporter 2 (GLUT2), contributing to the glucose transport and sensing. To improve the clinical efficacy of stem cell educator therapy in the restoration of islet β-cell function, we explored the GLUT2 expression on PB-IPC in recent onset and longstanding T1D patients. In the Food and Drug Administration (FDA)-approved phase 2 clinical studies, patients received one treatment with the stem cell educator therapy. Peripheral blood mononuclear cells (PBMC) were isolated for flow cytometry analysis of PB-IPC and other immune markers before and after the treatment with stem cell educator therapy. Flow cytometry revealed that both recent onset and longstanding T1D patients displayed very low levels of GLUT2 on PB-IPC. After the treatment with stem cell educator therapy, the percentages of GLUT2+CD45RO+ PB-IPC were markedly increased in these T1D subjects. Notably, we found that T1D patients shared common clinical features with patients with other autoimmune and inflammation-associated diseases, such as displaying low or no expression of GLUT2 on PB-IPC at baseline and exhibiting a high profile of the inflammatory cytokine interleukin (IL)-1β. Flow cytometry demonstrated that their GLUT2 expressions on PB-IPC were also markedly upregulated, and the levels of IL-1β-positive cells were significantly downregulated after the treatment with stem cell educator therapy. Stem cell educator therapy could upregulate the GLUT2 expression on PB-IPC and restore their function in T1D patients, leading to the improvement of clinical outcomes. The clinical data advances current understanding about the molecular mechanisms underlying the stem cell educator therapy, which can be expanded to treat patients with other autoimmune and inflammation-associated diseases.

Exploring the potential of omics technologies in medicinal plant research: A review in Colombia

This review presents advances in the implementation of high-throughput sequencing and its application to the knowledge of medicinal plants. We conducted a bibliographic search of papers published in PubMed, Science Direct, Google Scholar, Scopus, and Web of Science databases and analyzed the obtained data using VOSviewer (version 1.6.19). Given that medicinal plants are a source of specialized metabolites with immense therapeutic values and important pharmacological properties, plant researchers around the world have turned their attention toward them and have begun to examine them widely. Recent advances in sequencing technologies have reduced cost and time demands and accelerated medicinal plant research. Such research leverages full genome sequencing, as well as RNA (ribonucleic acid) sequencing and the analysis of the transcriptome, to identify molecular markers of species and functional genes that control key biological traits, as well as to understand the biosynthetic pathways of bioactive metabolites and regulatory mechanisms of environmental responses. As such, the omics (e.g., transcriptomics, metabolomics, proteomics, and genomics, among others) have been widely applied within the study of medicinal plants, although their usage in Colombia is still few and, in some areas, scarce.

Development and identification of a novel wheat-Thinopyrum ponticum disomic substitution line DS5Ag(5D) with new genes conferring resistance to powdery mildew and leaf rust

BackgroundPowdery mildew (caused by Blumeria graminis f. sp. tritici (Bgt)) and leaf rust (caused by Puccinia triticina (Pt)) are prevalent diseases in wheat (Triticum aestivum L.) production. Thinopyrum ponticum (2n = 10x = 70, EeEeEbEbExExStStStSt) contains genes that confer high levels of resistance to these diseases.ResultsAn elite wheat-Th. ponticum disomic substitution line, DS5Ag(5D), was developed in the Bainong Aikang 58 (AK58) background. The line was assessed using genomic in situ hybridization (GISH), oligo-nucleotide probe multiplex (ONPM) fluorescence in situ hybridization (FISH), and molecular markers. Twenty eight chromosome-specific molecular markers were identified for the alien chromosome, and 22 of them were co-dominant. Additionally, SNP markers from the wheat 660 K SNP chip were utilized to confirm chromosome identification and they provide molecular tools for tagging the chromosome in concern. The substitution line demonstrated high levels of resistance to powdery mildew throughout its growth period and to leaf rust at the adult stage. Based on the resistance evaluation of five F5 populations between the substitution lines and wheat genotypes with different levels of sensitivity to the two diseases. Results showed that the resistance genes located on 5Ag confered stable resistance against both diseases across different backgrounds. Resistance spectrum analysis combined with diagnostic marker detection of known resistance genes of Th. ponticum revealed that 5Ag contained two novel genes, Pm5Ag and Lr5Ag, which conferred resistance to powdery mildew and leaf rust, respectively.ConclusionsIn this study, a novel wheat-Th. ponticum disomic substitution line DS5Ag(5D) was successfully developed. The Th. ponticum chromosome 5Ag contain new resistance genes for powdery mildew and leaf rust. Chromosomic—specific molecular markers were generated and they can be used to track the 5Ag chromosome fragments. Consequently, this study provides new elite germplasm resources and molecular markers to facilitate the breeding of wheat varieties that is resistant to powdery mildew and leaf rust.

Classification and prediction of drought and salinity stress tolerance in barley using GenPhenML

Genetic and agronomic advances consistently lead to an annual increase in global barley yield. Since abiotic stresses (physical environmental factors that negatively affect plant growth) reduce barley yield, it is necessary to predict barley resistance. Artificial intelligence and machine learning (ML) models are new and powerful tools for predicting product resilience. Considering the research gap in the use of molecular markers in predicting abiotic stresses, this paper introduces a new approach called GenPhenML that combines molecular markers and phenotypic traits to predict the resistance of barley genotypes to drought and salinity stresses by ML models. GenPhenML uses feature selection algorithms to determine the most important molecular markers. It then identifies the best model that predicts atmospheric resistance with lower MAE, RMSE, and higher R2. The results showed that GenPhenML with a neural network model predicted the salinity stress resistance score with MAE, RMSE and R2 values of 0.1206, 0.0308 and 0.9995, respectively. Also, the NN model predicted drought stress scores with MAE, RMSE and R2 values of 0.0727, 0.0105 and 0.9999, respectively. The GenPhenML approach was also used to classify barley genotypes as resistant and stress-sensitive. The results showed that the accuracy, accuracy and F1 score of the proposed approach for salinity and drought stress classification were higher than 97%.

A Novel Hand-held Multi-color Magnetic Particle Imaging Device based on Rapid Frequency Conversion.

Multi-color Magnetic Particle Imaging (MPI) technology offers high sensitivity and non-invasive imaging capabilities. It can simultaneously image multiple superparamagnetic iron oxide nanoparticles (SPIOs), facilitating more precise detection of multiple molecular markers in vivo. However, the fixed drive frequency of existing hand-held MPI devices makes it difficult to fully match the nonlinear magnetic response of different SPIOs, affecting the spatial resolution and quantitative accuracy of multi-color imaging. We designed a novel rapid frequency conversion based hand-held multi-color magnetic particle imaging (RFC-MPI) device. This device adjusts the drive frequency based on the nonlinear magnetic response of SPIOs at different frequencies, effectively expanding the system matrix information and thereby improving spatial resolution and multi-color imaging capabilities simultaneously. The device achieved a spatial resolution of 2 mm and an imaging speed of 1 frame/s. The scanning depth is 8 mm. It was used to scan a 22 cm x 22 cm area of a human-shaped phantom, verifying its potential for scanning humans. The ability of the device to identify and quantify SPIOs was validated using mice breast tumors. The quantitative accuracy during simultaneous imaging was determined to be 96.58%. Due to its innovative structural design and rapid frequency conversion method, the RFC-MPI device exhibits excellent in vivo imaging performance. Both simulation and phantom experiments have verified the effectiveness of the proposed method. The hand-held RFC-MPI device can effectively improve the spatial resolution and quantitative accuracy of multi-color MPI, laying the foundation for future clinical applications.

Pericytes recruited by CCL28 promote vascular normalization after anti-angiogenesis therapy through RA/RXRA/ANGPT1 pathway in lung adenocarcinoma

BackgroundIt has been proposed that anti-angiogenesis therapy could induce tumor "vascular normalization" and further enhance the efficacy of chemotherapy, radiotherapy, target therapy, and immunotherapy for nearly twenty years. However, the detailed molecular mechanism of this phenomenon is still obscure.MethodOverexpression and knockout of CCL28 in human lung adenocarcinoma cell line A549 and murine lung adenocarcinoma cell line LLC, respectively, were utilized to establish mouse models. Single-cell sequencing was performed to analyze the proportion of different cell clusters and metabolic changes in the tumor microenvironment (TME). Immunofluorescence and multiplex immunohistochemistry were conducted in murine tumor tissues and clinical biopsy samples to assess the percentage of pericytes coverage. Primary pericytes were isolated from lung adenocarcinoma tumor tissues using magnetic-activated cell sorting (MACS). These pericytes were then treated with recombinant human CCL28 protein, followed by transwell migration assays and RNA sequencing analysis. Changes in the secretome and metabolome were examined, and verification of retinoic acid metabolism alterations in pericytes was conducted using quantitative real-time PCR, western blotting, and LC–MS technology. Chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) was employed to validate the transcriptional regulatory ability and affinity of RXRα to specific sites at the ANGPT1 promoter.ResultsOur study showed that after undergoing anti-angiogenesis treatment, the tumor exhibited a state of ischemia and hypoxia, leading to an upregulation in the expression of CCL28 in hypoxic lung adenocarcinoma cells by the hypoxia-sensitive transcription factor CEBPB. Increased CCL28 could promote tumor vascular normalization through recruiting and metabolic reprogramming pericytes in the tumor microenvironment. Mechanistically, CCL28 modified the retinoic acid (RA) metabolism and increased ANGPT1 expression via RXRα in pericytes, thereby enhancing the stability of endothelial cells.ConclusionWe reported the details of the molecular mechanisms of "vascular normalization" after anti-angiogenesis therapy for the first time. Our work might provide a prospective molecular marker for guiding the clinical arrangement of combination therapy between anti-angiogenesis treatment and other therapies.

Altered ribosomal profile in acquired resistance and reversal associates with pathological response to chemotherapy in inflammatory breast cancer

Therapeutic resistance presents a significant hurdle in combating inflammatory breast cancer (IBC), adding to the complexity of its management. To investigate these mechanisms, we conducted a comprehensive analysis using transcriptomic and proteomic profiling in a preclinical model alone with correlates of treatment response in IBC patients. This included SUM149 cell lines derived from treatment-naïve patients, along with acquired drug resistance (rSUM149) and others in a state of resistance reversal (rrSUM149), aiming to uncover drug resistance networks. We identified specific ribosomal proteins associated with acquiring resistance. These correlated with elevated levels of molecular markers such as pERK, CDK1, XIAP, and SOD2. While resistance reversal in rrSUM149 cells largely normalized the expression profile, VIPER analysis revealed persistent alterations in ribosomal process-related proteins (AGO2, Exportin 1, RPL5), suggesting their continued involvement in drug resistance. Moreover, genes linked to ribosomal processes were significantly enriched (P < 0.001) among overexpressed genes in IBC patients (n = 87) who exhibited a pathological complete response (pCR) to neoadjuvant chemotherapy. Given the common hyperactivation of MAPK in IBC tumors, including rSUM149, we evaluated Merestinib, a multikinase inhibitor in clinical trials. It effectively targeted pERK and peIF4E pathways, suppressed downstream targets, induced cell death in drug-resistant rSUM149 cells, and showed synergistic effects with another tyrosine kinase inhibitor (Lapatinib) in parental cells. This underscores its significant impact on protein synthesis signaling, crucial for combating translational dependence in cancer cells. In summary, our study elucidates adaptive changes in IBC cells in response to therapy and treatment pauses, guiding precision medicine approaches for this challenging cancer type.