Yellow Gene Research Articles

Transcriptomic analysis reveals that methyl jasmonate confers salt tolerance in alfalfa by regulating antioxidant activity and ion homeostasis.

Alfalfa, a globally cultivated forage crop, faces significant challenges due to its vulnerability to salt stress. Jasmonates (JAs) play a pivotal role in modulating both plant growth and response to stressors. In this study, alfalfa plants were subjected to 150 mM NaCl with or without methyl jasmonate (MeJA). The physiological parameters were detected and a transcriptomic analysis was performed to elucidate the mechanisms underlying MeJA-mediated salt tolerance in alfalfa. Results showed that exogenous MeJA regulated alfalfa seed germination and primary root growth in a dose-dependent manner, with 5µM MeJA exerting the most efficient in enhancing salt tolerance. MeJA at this concentration elavated the salt tolerance of young alfalfa seedlings by refining plant growth, enhancing antioxidant capacity and ameliorating Na+ overaccumulation. Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. PageMan analysis revealed several significantly enriched categories altered by MeJA+NaCl treatment, compared with NaCl treatment alone, including genes involved in secondary metabolism, glutathione-based redox regulation, cell cycle, transcription factors (TFs), and other signal transductions (such as calcium and ROS). Further weighted gene co-expression network analysis (WGCNA) uncovered that turquoise and yellow gene modules were tightly linked to antioxidant enzymes activity and ion content, respectively. Pyruvate decar-boxylase (PDC) and RNA demethylase (ALKBH10B) were identified as the most central hub genes in these two modules. Also, some TFs-hub genes were identified by WGCNA in these two modules highly positive-related to antioxidant enzymes activity and ion content. MeJA triggered a large-scale transcriptomic remodeling, which might be mediated by transcriptional regulation through TFs or post-transcriptional regulation through demethylation. Our findings contributed new perspectives for understanding the underneath mechanisms by which JA-mediated salt tolerance in alfalfa.

Characterization and fine mapping of a yellow leaf gene regulating chlorophyll biosynthesis and chloroplast development in cotton (Gossypium arboreum)

Chlorophyll biosynthesis and chloroplast development are essential for photosynthesis and plant growth. Gossypium arboreum, a valuable source of genetic variation for cotton improvement, remains poorly studied for the mechanisms regulating chlorophyll biosynthesis and chloroplast development. Here we created a G. arboreum etiolated leaf and stuntedness (els) mutant that displayed a distinct yellow color of leaves, bracts and stems throughout the whole growth, where chlorophyll accumulation in leaves was reduced and chloroplast development was delayed. The GaCHLH gene, which encodes the H subunit of magnesium chelatase (Mg-chelatase), was screened by MutMap and KASP analysis. Compared to GaCHLH, the gene Gachlh of the mutant had a single nucleotide transition (G to A) at 1549 bp, which causes the substitution of a glycine (G) by a serine (S) at the 517th amino acid, resulting in an abnormal secondary structure of the Gachlh protein. GaCHLH-silenced SXY1 and ZM24 plants exhibited a lower GaCHLH expression level, a lower chlorophyll content, and the yellow-leaf phenotype. Gachlh expression affected the expression of key genes in the tetrapyrrole pathway. GaCHLH and Gachlh were located in the chloroplasts and that alteration of the mutation site did not affect the final target position. The BiFC assay result indicated that Gachlh could not bind to GaCHLD properly, which prevented the assembly of Mg-chelatase and thus led to the failure of chlorophyll synthesis. In this study, the Gachlh gene of G. arboreum els was finely localized and identified for the first time, providing new insights into the chlorophyll biosynthesis pathway in cotton.

Screening of Resistance Gene Analogue Marker(S) in Indian Bean [Lablab purpureus (L.) Sweet] against Yellow Mosaic Disease

In this study, 104 genotypes of Indian beans were evaluated against the yellow mosaic disease at College Farm, N. M. College of Agriculture, Navsari Agricultural University, Navsari during Rabi 2021–2022 (South Gujarat Heavy Rainfall Zone-II ), based on the disease rating scale (1–9). Out of the 104 genotypes of Indian beans, 33 genotypes showed resistance to the yellow mosaic disease, 14 genotypes showed moderate resistance, 17 genotypes showed moderate susceptibility, 29 genotypes showed susceptibility, and 11 genotypes showed highly susceptibility. The obtained sequence has a greatest identity of 95.05 percent with the full sequence of the dolichos yellow mosaic virus isolate AG segment DNA A with accession number MZ821026.1. As a result, the variant was given the accession number ON461886 and named dolichos yellow mosaic virus isolate NAU-RA coat protein gene segment DNA -A. In present investigation six resistant (P-19-169, V-19-15, V-19-35, GNIB-22, W-19-05, V-19-24) and six highly susceptible (P-19-176, W-19-60, P-19-127, V-19-11, W-19-58, V-19-106) Indian bean genotypes were screened by nine pairs of RGA primers. The amplicons were obtained in seven pairs of RGA primers, where five pairs of RGA primersRGA1FCG &RGA1R,VMYR1F & VMYR1R,YR4F & YR4R, RGAIB3 & RGAIB4, RGAIB5 & RGAIB6 amplified single band size of approximately 450 bp, 450 bp, 450 bp, 450 bp and 1050 bp respectively in resistant genotypes, while only two pairs of RGA primers CYR1F & CYR1R and RGAIB1 & RGAIB2 were found with prominent band of approximately 950bp and 350bp. According to the data from the current investigation, seven pairs of RGA markers have proven successful in differentiating between the resistant and highly susceptible genotypes of Indian beans. These RGA markers can be employed in investigations mapping resistance genes and validating markers with long-lasting YMV resistance.

Weighted Gene Co-Expression Network Analysis of red body color formation of crimson snapper, Lutjanus erythropterus

Crimson snapper (Lutjanus erythropterus) is a highly valued economic fish species, with its red body color being a crucial economic characteristic. A systematic study of skin pigmentation could offer insights into the mechanism of red coloration. In this study, we conducted the first network analysis of snapper transcriptomes during key developmental stages of pigmentation, identifying a cascade of cellular development and responsive gene modules and key genes, including eight developmental-specific modules. Among the four candidate hub genes (TNNT2, ROBO2, APBA2, and APOD), APOD was involved in pigmentation development. The network further revealed some key genes, such as TYRP1a, TYRP1b, PMEL, BCO1, BCO2, CYP2J2, CYP2J6, CYP3A4, PNPLA2, FABP6, ENPP7, and FFAR3, associated with melanin synthesis, carotenoids, and lipid metabolism. Our findings showed that pteridine and carotenoids were involved in yellow coloration after initial feeding, while yellow pigmentation-related genes (e.g., GCH1, PTS, SPR, CBR1, SCARB1, CD36, ABCA1, NpC1L1, etc.) had the same expression pattern at three days post-hatching (3 dph). At the red coloration emergence stage (45 dph), we observed an RNA level signal indicating the conversion of coloring substances from pteridine to carotenoids. These results substantially enhance understanding of the molecular mechanisms underlying pigmentation and skin color variation in L. erythropterus, providing a theoretical basis for improving of body coloration in economically cultured fish and genetic breeding of ornamental fish.

Ovariole-specific Yellow-g and Yellow-g2 proteins are required for fecundity and egg chorion rigidity in the red flour beetle, Tribolium castaneum

Most insects reproduce by laying eggs that have an eggshell/chorion secreted by follicle cells, which serves as a protective barrier for developing embryos. Thus, eggshell formation is vital for reproduction. Insect yellow family genes encode for secreted extracellular proteins that perform different, context-dependent functions in different tissues at various stages of development involving, for example, cuticle/eggshell coloration and morphology, molting, courtship behavior and embryo hatching. In this study we investigated the function of two of this family's genes, yellow-g (TcY-g) and yellow-g2 (TcY-g2), on the formation and morphology of the eggshell of the red flour beetle, Tribolium castaneum. Real-time PCR analysis revealed that both TcY-g and TcY-g2 were specifically expressed in the ovarioles of adult females. Loss of function produced by injection of double-stranded RNA (dsRNA) for either TcY-g or TcY-g2 gene resulted in failure of oviposition. There was no effect on maternal survival. Ovaries dissected from those dsRNA-treated females exhibited ovarioles containing not only developing oocytes but also mature eggs in their egg chambers. However, the ovulated eggs were collapsed and ruptured, resulting in swollen lateral oviducts and calyxes. TEM analysis showed that lateral oviducts were filled with electron-dense material, presumably from some cellular content leakage out of the collapsed eggs. In addition, morphological abnormalities in lateral oviduct epithelial cells and the tubular muscle sheath were evident. These results support the hypothesis that both TcY-g and TcY-g2 proteins are required for maintaining the rigidity and integrity of the chorion, which is critical for resistance to mechanical stress and/or rehydration during ovulation and egg activation in the oviducts of T. castaneum. Because Yellow-g and Yellow-g2 are highly conserved among insect species, both genes are potential targets for development of gene-based insect pest population control methods.

Characterization of tomato yellow leaf curl virus resistance genes and genetic variability in commercial tomato F1 hybrids

Tomato (Solanum lycopersicum L.) resistance to Tomato Yellow Leaf Curl Virus (TYLCV) is a major objective of breeding programs. Tomato breeders are now interested in the subsequent introgression of many resistance genes to increase resistance levels, expand resistance spectrum, and prolong the longevity of resistant cultivars. Many F1 hybrids are now multigene resistant. To select the best breeding materials, 15 commercial F1 tomato TYLCV-tolerant hybrids were evaluated for TYLCV resistance and productivity during the 2018 and 2019 fall seasons. Resistance genes were identified using gene-based molecular markers. Most hybrids have multiple heterozygous resistance genes. ‘Brivio’, ‘Dania’, ‘SV8320’, and ‘Tyrmes’ comprised resistance genes Ty-1/Ty-3, Ty-2, Ty-4, and ty-5. Thus, F1 hybrids exhibited moderate to mild symptoms, and viral replication was detected in their symptomless plants by PCR and qt-PCR. Genetic variability among hybrids, hybrid relationships, and inter-trait correlations were estimated based on phenotypes of TYLCV-tolerance, productivity, and fruit quality. Most traits had high estimates of genetic variance, genotypical coefficient of variance, and heritability. Genetic variability sufficed in selecting the best genotype. Based on multivariate analyses of principal components and hierarchical clusters, hybrids were highly diversified and divided into three clusters. Clusters 1 and 3 were better at TYLCV tolerance, yield, and fruit quality. Positive genotypical correlations were found between tolerance, total yield, and fruit quality (firmness, equatorial diameter, and TSS content). The use of ‘Brivio’, ‘Dania’, ‘SV8320’, and ‘Tyrmes’ will be very useful in TYLCV resistance breeding programs to pyramiding resistance genes by marker-assisted selection technique.

CRISPR/Cas9-Mediated genomic knock out of tyrosine hydroxylase and yellow genes in cricket Gryllus bimaculatus.

Gryllus bimaculatus is an emerging model organism in various fields of biology such as behavior, neurology, physiology and genetics. Recently, application of reverse genetics provides an opportunity of understanding the functional genomics and manipulating gene regulation networks with specific physiological response in G. bimaculatus. By using CRISPR/Cas9 system in G. bimaculatus, we present an efficient knockdown of Tyrosine hydroxylase (TH) and yellow-y, which are involved in insect melanin and catecholamine-biosynthesis pathway. As an enzyme catalyzing the conversion of tyrosine to 3,4-dihydroxyphenylalanine, TH confines the first step reaction in the pathway. Yellow protein (dopachrome conversion enzyme, DCE) is also involved in the melanin biosynthetic pathway. The regulation system and molecular mechanism of melanin biogenesis in the pigmentation and their physiological functions in G. bimaculatus hasn't been well defined by far for lacking of in vivo models. Deletion and insertion of nucleotides in target sites of both TH and Yellow are detected in both F0 individuals and the inheritable F1 progenies. We confirm that TH and yellow-y are down-regulated in mutants by quantitative real-time PCR analysis. Compared with the control group, mutations of TH and yellow-y genes result in defects in pigmentation. Most F0 nymphs with mutations of TH gene die by the first instar, and the only adult had significant defects in the wings and legs. However, we could not get any homozygotes of TH mutants for all the F2 die by the first instar. Therefore, TH gene is very important for the growth and development of G. bimaculatus. When the yellow-y gene is knocked out, 71.43% of G. bimaculatus are light brown, with a slight mosaic on the abdomen. The yellow-y gene can be inherited stably through hybridization experiment with no obvious phenotype except lighter cuticular color. The present loss of function study indicates the essential roles of TH and yellow in pigmentation, and TH possesses profound and extensive effects of dopamine synthesis in embryonic development in G. bimaculatus.

Yellow Petal locus GaYP promotes flavonol biosynthesis and yellow coloration in petals of Asiatic cotton (Gossypium arboreum)

Yellow Petal locus GaYP is located on chromosome 11 and encodes a Sg6 R2R3-MYB transcription factor, which promotes flavonol biosynthesis and yellow coloration in Asiatic cotton petals. Petal color is pivotal to ornamental value and reproduction of plants. Yellow coloration in plant petals is mainly attributed to colorants including carotenoids, aurones and some flavonols. To date, the genetic regulatory mechanism of flavonol biosynthesis in petals is still to be elucidated. Here, we employed Asiatic cottons with or without deep yellow coloration in petals to address this question. Multi-omic and biochemical analysis revealed significantly up-regulated transcription of flavonol structural genes and increased levels of flavonols, especially gossypetin and 6-hydroxykaempferol, in yellow petals of Asiatic cotton. Furthermore, the Yellow Petal gene (GaYP) was mapped on chromosome 11 by using a recombinant inbred line population. It was found that GaYP encoded a transcriptional factor belonging to Sg6 R2R3-MYB proteins. GaYP could bind to the promoter of flavonol synthase gene (GaFLS) and activate the transcription of downstream genes. Knocking out of GaYP or GaFLS homologs in upland cotton largely eliminated flavonol accumulation and pale yellow coloration in petals. Our results indicated that flavonol synthesis, up-regulated by the R2R3-MYB transcription activator GaYP, was the causative factor for yellow coloration of Asiatic cotton petals. In addition, knocking out of GaYP homologs also led to decrease in anthocyanin accumulation and petal size in upland cotton, suggesting that GaYP and its homologs might modulate developmental or physiological processes beyond flavonol biosynthesis.

Selection of introgressive wheat and triticale lines for grain quality and resistance to diseases for use in organic farming

17 introgressive lines and varieties of winter wheat and 2 lines of winter triticale (collection of the Kazakh Research Institute of Agriculture and Plant Growing) were studied to determine the possibility of their use in organic farming. The studies were conducted in 2021-2022 in the foothill zone of the south-east of the Republic of Kazakhstan on the basis of the research field stationary of the Kazakh Research Institute of Agriculture and Plant Growing. Analysis for genetically modified sources showed the absence of 35S and NOS regulatory elements in the samples. DNA identification by PCR to detect effective brown, stem and yellow rust genes ( Lr9, Lr26/Sr31/Yr9, Lr34/Yr18/ Sr57, Lr35/Sr39, Sr2, Sr36 ) made it possible to identify 4 samples (1633-40, 1675-170, 1723-11, 2041-7) with valuable Lr34/Yr18/Sr57/Pm38 genes and 1 sample (1127-7) with Lr26/Sr31/Yr9/Pm8 genes. Phytopathological assessment of the resistance of cereal crops was carried out on the natural background using the appropriate scales of recording the infestation of plants by brown stem rust and yellow rust. As a result, 9 samples resistant to 2 types of rust (brown and yellow) with reaction type R and zero percent were found (1127-7, 1675-170, 1676, 2005-13, 2041-13, 2046-1, KZ231, T-409-1, T-989-1). Stem rust in the years of research was not recorded. Grain quality assessment was carried out on the basis of the requirements of relevant GOSTs on the following parameters: grain nature, vitreousness, protein and gluten content, gluten quality. It was found that all the samples under consideration in terms of vitreousness and gluten content correspond to the class of strong wheat. Samples with high grain natures (≥800 g/l; 1674-27, 1675-149, 1675-170), protein content (≥16%; 2041-13, 2005-13, 2041-7, 1716-24, 1675-149, 1127-7, 1633-31, 1717-27, KZ231), quality and quantity of gluten (1127-7, KZ231) were selected. According to the results of comprehensive evaluation, 2 lines (1127-7, KZ231), which showed good resistance to 2 types of rust and high grain quality, were noted. These lines are recommended for use in organic farming.

The Genetic Mechanisms Underlying the Concerted Expression of the yellow and tan Genes in Complex Patterns on the Abdomen and Wings of Drosophila guttifera.

How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here, we sought to identify the genetic mechanisms that regulate the tan (t) gene in a multi-spotted pigmentation pattern on the abdomen and wings of Drosophila guttifera. Previously, we showed that yellow (y) gene expression completely prefigures the abdominal and wing pigment patterns of this species. In the current study, we demonstrate that the t gene is co-expressed with the y gene in nearly identical patterns, both transcripts foreshadowing the adult abdominal and wing melanin spot patterns. We identified cis-regulatory modules (CRMs) of t, one of which drives reporter expression in six longitudinal rows of spots on the developing pupal abdomen, while the second CRM activates the reporter gene in a spotted wing pattern. Comparing the abdominal spot CRMs of y and t, we found a similar composition of putative transcription factor binding sites that are thought to regulate the complex expression patterns of both terminal pigmentation genes y and t. In contrast, the y and t wing spots appear to be regulated by distinct upstream factors. Our results suggest that the D. guttifera abdominal and wing melanin spot patterns have been established through the co-regulation of y and t, shedding light on how complex morphological traits may be regulated through the parallel coordination of downstream target genes.

The Efficacity Investigation for Some Markers Detecting Yellow Rust Resistance Genes in Bread Wheat Varieties

Yellow rust is (Puccinia striiformis Westend. f. sp. tritici) is among the supreme diseases causing serious losses in wheat production. The chemical fungicides are commonly used in this disease-fighting. However, chemical control is not economical and also causes environmental pollution. Therefore, the use of resistant wheat varieties in production has critical importance. The resistance against yellow rust disease is expressed with Yr genes. In the breeding studies, knowing which parents include resistance genes provides a great advantage in the development of new resistant varieties. This study aims to determine the efficiency of markers used to detect resistance genes against yellow rust disease. The efficiency of molecular markers (Xgwm582, RgaYr10a, Xgwm413, Xgwm11, Wmc44, Barc101, Cfa2149, Sun104, Xgwm273) that are identified for nine genes (Yr9, Yr10, Yr15, Yr26, Yr29, Yr36, Yr48, Yr51, and YrCH52) providing resistance against yellow rust disease was investigated using PCR method. Twenty bread wheat varieties were used as material. Resistance gene profiles determined using PCR-based molecular markers and data obtained from registration information and field resistance data in the literature were analysed comparatively. As a result of the analysis, the efficiency/productivity of the markers defined for different resistance genes in detecting the resistance gene profile of wheat varieties was determined. Moreover, resistance gene profiles of varieties that are known resistance states in the field and sensitive varieties were compared. Genes that are prominent in providing resistance and detected with markers were determined and the efficiency of these genes was evaluated according to their homozygous/heterozygous states. It was concluded that the efficacy of markers such as RgaYr10a, Xgwm413, Barc101, and Cfa2149, which gave positive results in all wheat varieties, was low.

A synthetic peptide based on large yellow croaker (Larimichthys crocea) IFNG1R protein sequence has potential antimicrobial activity against Pseudomonas plecoglossicida

The overuse of antibiotics leads to the emergence of bacterial resistance, which poses a serious threat to aquaculture. Antimicrobial peptides (AMPs) display excellent antimicrobial activity and are thought to be the most feasible replacements for antibiotics. The usage of AMPs as feed additives has great application prospects in aquaculture. In this study, large yellow croaker interferon-γ related gene (IFNG1R) was cloned, and a 17-amino acids (aa) short peptide named SKL17-2 was synthesized based on its protein sequence. The synthesized SKL17-2 peptide possessed a strong antimicrobial activity against Pseudomonas plecoglossicida, which could cause visceral white nodules disease (VWND) in cultured marine fish, with a minimum inhibitory concentration (MIC) of 2 μM. SKL17-2 peptide also showed weak antimicrobial activities against other tested bacteria, indicating its narrow-spectrum antimicrobial activity. This suggested that SKL17-2 peptide may not kill probiotics in intestinal flora when used as the feed additive. Furthermore, SKL17-2 had broad temperature and pH stability, low cytotoxicity, and negligible hemolysis, indicating its good biosafety and stability. Mechanistically, the synthesized SKL17-2 peptide can form α-helical structure in a membrane environment and destroy P. plecoglossicida through membrane disruption. Thus, our data showed that SKL17-2 peptide may represent a potential feed additive used for prevention and treatment of VWND.

Identification of therapeutic targets and prognostic biomarkers in cholangiocarcinoma via WGCNA.

Cholangiocarcinoma (CCA) is a highly aggressive malignant tumor for which limited treatment methods and prognostic signatures are available. This study aims to identify potential therapeutic targets and prognostic biomarkers for CCA. Based on differentially expressed genes (DEGs) identified from The Cancer Genome Atlas (TCGA) data, our study identified key gene modules correlated with CCA patient survival by weighted gene coexpression network analysis (WGCNA). Cox regression analysis identified survival-related genes in the key gene modules. The biological properties of the survival-related genes were evaluated by CCK-8 and transwell assays. Then, these genes were used to construct a prognostic signature that was internally and externally validated. Additionally, by combining clinical characteristics with the gene-based prognostic signature, a nomogram for survival prediction was built. WGCNA divided the 1531 DEGs into four gene modules, and the yellow gene module was significantly associated with overall survival (OS) and histologic neoplasm grade. Our study identified the lncRNA AGAP2-AS1 and a novel gene, GOLGA7B, that are closely related to survival. GOLGA7B downregulation promoted the invasion, migration and proliferation of CCA cells, but AGAP2-AS1 had the opposite effect. AGAP2-AS1 and GOLGA7B were integrated into a gene-based prognostic signature, and both internal and external validation studies confirmed that this two-gene prognostic signature and nomogram could accurately predict CCA patient prognosis. AGAP2-AS1 and GOLGA7B are potential therapeutic targets and prognostic biomarkers for CCA.

The active Fe chelator proline-2'-deoxymugineic acid enhances peanut yield by improving soil Fe availability and plant Fe status.

Iron (Fe) deficiency restricts crop yields in calcareous soil. Thus, a novel Fe chelator, proline-2'-deoxymugineic acid (PDMA), based on the natural phytosiderophore 2'-deoxymugineic acid (DMA), was developed to solve the Fe deficiency problem. However, the effects and mechanisms of PDMA relevant to the Fe nutrition and yield of dicots grown under field conditions require further exploration. In this study, pot and field experiments with calcareous soil were conducted to investigate the effects of PDMA on the Fe nutrition and yield of peanuts. The results demonstrated that PDMA could dissolve insoluble Fe in the rhizosphere and up-regulate the expression of the yellow stripe-like family gene AhYSL1 to improve the Fe nutrition of peanut plants. Moreover, the chlorosis and growth inhibition caused by Fe deficiency were significantly diminished. Notably, under field conditions, the peanut yield and kernel micronutrient contents were promoted by PDMA application. Our results indicate that PDMA promotes the dissolution of insoluble Fe and a rich supply of Fe in the rhizosphere, increasing yields through integrated improvements in soil-plant Fe nutrition at the molecular and ecological levels. In conclusion, the efficacy of PDMA for improving the Fe nutrition and yield of peanut indicates its outstanding potential for agricultural applications.

Immune Subtypes and Immune Landscape Analysis of Endometrial Carcinoma.

Some patients with endometrial cancer (EC) suffer from limited survival benefits after immunotherapy, suggesting that there may be a specific pattern associated with immunotherapy. Immune-related genes were extracted from The Cancer Genome Atlas databases. We analyzed the differences among immune subtypes (ISs) in the distribution of the tumor mutational burden, chemotherapy-induced immune response markers, immune checkpoint-related genes, immunotherapy, and chemotherapy. We applied dimensionality reduction and defined the immune landscape of EC. Then, we used the Weighted Gene Co-Expression Network Analysis package to identify the coexpression modules of these immune genes. Finally, hub genes were selected and detected by quantitative PCR and immunohistochemistry. We obtained three ISs. There were differences in the distribution of the tumor mutational burden, chemotherapy-induced immune response markers, and immune checkpoint-related genes among the ISs. Regarding immunotherapy and chemotherapy, the IS2 subtypes were more sensitive to programmed cell death protein 1 inhibitors. In addition, different positions in the immune landscape map exhibited different prognostic characteristics, providing further evidence of the ISs. The IS2 subtypes were significantly positively correlated with yellow module gene list, indicating a good prognosis with high score. SIRPG and SLAMF1 were identified as the final characteristic genes. The quantitative PCR and immunohistochemistry results showed that the expression levels of SIRPG and SLAMF1 were low in human EC tissue. In this study, we identified three reproducible ISs of EC. The immune landscape analysis further revealed the intraclass heterogeneity of the ISs. SIRPG and SLAMF1 were identified to be associated with progression, suggesting that they may be novel immune-related biomarkers of EC.

Cytogenetic and genomic characterization of a novel tall wheatgrass-derived Fhb7 allele integrated into wheat B genome.

We identified and integrated the novel FHB-resistant Fhb7The2 allele into wheat B genome and made it usable in both common and durum wheat breeding programs without yellow flour linkage drag. A novel tall wheatgrass-derived (Thinopyrum elongatum, genome EE) Fhb7 allele, designated Fhb7The2, was identified and integrated into the wheat B genome through a small 7B-7E translocation (7BS·7BL-7EL) involving the terminal regions of the long arms. Fhb7The2 conditions significant Type II resistance to Fusarium head blight (FHB) in wheat. Integration of Fhb7The2 into the wheat B genome makes this wild species-derived FHB resistance gene usable for breeding in both common and durum wheat. By contrast, other Fhb7 introgression lines involving wheat chromosome 7D can be utilized only in common wheat breeding programs, not in durum wheat. Additionally, we found that Fhb7The2 does not have the linkage drag of the yellow flour pigment gene that is tightly linked to the decaploid Th. ponticum-derived Fhb7 allele Fhb7Thp. This will further improve the utility of Fhb7The2 in wheat breeding. DNA sequence analysis identified 12 single nucleotide polymorphisms (SNPs) in Fhb7The2, Fhb7Thp, and another Th. elongatum-derived Fhb7 allele Fhb7The1, which led to seven amino acid conversions in Fhb7The2, Fhb7Thp, and Fhb7The1, respectively. However, no significant variation was observed in their predicted protein configuration as a glutathione transferase. Diagnostic DNA markers were developed specifically for Fhb7The2. The 7EL segment containing Fhb7The2 in the translocation chromosome 7BS·7BL-7EL exhibited a monogenic inheritance pattern in the wheat genetic background. This will enhance the efficacy of marker-assisted selection for Fhb7The2 introgression, pyramiding, and deployment in wheat germplasm and varieties.

Investigation on Potential Biomarkers and Immune-Related Mechanisms of Ischemic Stroke

This study aimed to reveal the detailed immune-related mechanisms underlying ischemic stroke (IS) and identify new immune-associated biomarkers for clinical management. Differentially expressed genes (DEGs) between IS samples and normal controls were identified using the GSE16561 dataset. The feature genes of the immune cells were investigated using the GSE72642 dataset. Weighted correlation network analysis (WGCNA) was performed to reveal module genes, followed by an investigation of common DEGs and a functional enrichment analysis. Potential biomarkers were identified based on hub genes in protein-protein interaction networks and WGCNA. Finally, GSE158312 was used for biomarker verification. In total, 1230 DEGs were identified between the IS samples and normal controls. Seven clinically significant modules were identified using WGCNA. The yellow module genes were positively correlated with polymorphonuclear cells (PMNC), whereas the brown module genes were positively correlated with CD4+ T cells. Eight genes were selected as hub genes. These genes are mainly involved in functions such as the innate immune response. Upregulated TLR2 and ARG1 levels were significantly different between the two groups in the verification dataset. Our findings suggest ARG1 and TLR2 as novel biomarkers for IS. Upregulated TLR2 might play a role in IS development by participating in the innate immune response function.

Coat Protein Characterization of Mungbean yellow mosaic virus Infecting Blackgram (Vigna mungo L. Hepper) in Tamil Nadu

The Yellow Mosaic Disease is the main constraint for decreased yield in blackgram production. Coat protein gene of Mungbean yellow mosaic virus (MYMV) has been characterized and phylogenetic tree was constructed. The genomic DNA from diseased plants was collected and it was tested for it’s quality and quantity using a Nanodrop. The isolated DNA was subjected to polymerase chain reaction using begomovirus universal primers for preliminary confirmation of the virus. The samples amplified for universal primers were subjected for gene specific amplification using DNA A primers. The DNA A primers resulted in the amplification of the expected size of 1000 bp amplicon. The DNA fragments were sequenced and the sequence results of DNA A were compared with other sequences available in NCBI and it showed higher similarity with Mungbean yellow mosaic virus banglore coat protein gene (accession no: MK409376). The sequence was submitted in NCBI database and accession numbers were obtained. The phylogenetic tree was constructed using mega 11 software by comparing the selected strains with our isolate.

Bioinformatic identification and analysis of immune-related chromatin regulatory genes as potential biomarkers in idiopathic pulmonary fibrosis.

BackgroundIdiopathic pulmonary fibrosis (IPF) is a disease with a very poor prognosis. The search for new IPF biomarkers is particularly urgent due to the uncertainty of the mechanisms and treatment. Studies have shown that chromatin regulators (CRs) are involved in the development of IPF and are associated with tumor immunity. However, there are no studies on immune-related CRs in IPF. Therefore, we conducted a systematic study to analyze the expression levels and immune correlation of CRs in IPF tissues and normal tissues and to explore their potential as diagnostic biomarkers.MethodsGSE53845, GSE179781 and GSE24206 datasets from Gene Expression Omnibus (GEO) database were merged into an integrated dataset as the training set; GSE70866 was used as the validation dataset. The cr-related differentially expressed genes (DEGs) between normal and IPF tissues were identified using the “Limma” software package. Weighted gene co-expression network analysis (WGCNA) was performed using the “WGCNA” package to screen eigengenes, which were intersected with DEGs to identify hub genes. The “ggcorrplot” package was used to analyze the correlation between hub genes and immunity, and immune-related hub genes were defined as immHub. A logistic regression model was constructed using immHub as the independent variable and whether the diagnosis was IPF as the dependent variable.ResultsOne hundred and sixty-nine DEGs were identified between IPF and normal tissues. wGCNA identified 3 key modules in brown, green and yellow genes that were present in all 3 modules and met module membership (MM) >0.8 and gene significance (GS) >0.5 were called signature genes (n=390). Four intersecting genes were obtained by intersecting DEGs with signature genes (PADI4, IGFBP7, GADD45A, and SETBP1) all associated with immunity were defined as immHub genes Logistic regression models were constructed based on immHub genes. The area under the curve (AUC) of the ROC curve is used to evaluate the diagnostic accuracy of the logistic regression model for IPF. The AUC in the ROC analysis was 0.771 for the training dataset, and 0.759 for the validation dataset.ConclusionsPADI4, IGFBP7 and GADD45A may be biomarkers for IPF, which will provide assistance in the diagnosis, treatment and prognostic assessment of IPF patients, and provide an important basis for future studies on the relationship between CRs genes and IPF.

Comparative proteomic analysis reveals insights into the response of Cryptolaemus montrouzieri to bottom-up transfer of cadmium and lead across a multi-trophic food chain

Contamination of agro-ecosystems with heavy metals can affect the development and reproduction of insect natural enemies. This study reports a detailed Tandem Mass Tag based quantitative proteomic analysis of underlying mechanisms responsible for stress response of Cryptolaemus montrouzieri against heavy metals (cadmium (Cd) and lead (Pb)) transported across a multi-trophic food chain. A total of 6639 proteins were detected under Cd as well as Pb stress. In Pb versus the control cluster, 69 proteins (28 up-regulated and 41 down-regulated) were differentially expressed whereas 268 proteins were differentially expressed under Cd versus the control cluster, having 198 proteins up-regulated and 70 down-regulated proteins. The analysis of differentially expressed proteins showed that 27 proteins overlapped in both clusters representing the core proteome to Pb and Cd stress. The bioinformatics analysis demonstrated that these proteins were mapped to 57 and 99 pathways in Pb versus control and Cd versus control clusters, respectively. The functional classification by COG, GO and KEGG databases showed significant changes in protein expression by C. montrouzieri under Pb and Cd stress. The heavy metal stress (Pb and Cd) induced significant changes in expression of proteins like hexokinase (HK), succinyl-CoA, trypsin like proteins, cysteine proteases, cell division cycle proteins, and yellow gene proteins. The results provide detailed information on the protein expression levels of C. montrouzieri and will serve as basic information for future proteomic studies on heavy metal responses of insect predators within a multi-trophic food chain.