Screening Of Candidate Genes Research Articles

Identifying MTHFD1 and LGALS4 as Potential Therapeutic Targets in Prostate Cancer Through Multi-Omics Mendelian Randomization Analysis

Background: Prostate cancer remains one of the leading causes of cancer-related mortality in men worldwide. The treatment of it is currently based on surgical removal, radiotherapy, and hormone therapy. It is crucial to improve therapeutic prospects for the diagnosis and treatment of prostate cancer via drug target screening. Methods: We integrated eQTL data from the eQTLGen Consortium and pQTL data from UK Biobank Proteome Plasma Proteins (UKB-PPP) and deCODE health datasets. MR analyses (SMR, heterogeneity in dependent instruments (HEIDI), IVW, Wald ratio, weighted median, and MR-Egger) were used to screen candidate genes associated with prostate adenocarcinoma (PRAD) risk. Candidate genes were further verified through TCGA-based gene expression profile, survival analysis, and immune microenvironment evaluations. TIDE analysis was utilized to investigate gene immunotherapy response. Single-cell RNA sequencing data from the GSE176031 dataset were used to investigate the gene expression patterns. The Drug Bank, Therapeutic Target Database and Drug Signatures Database were utilized to predict targeted drugs for candidate genes. Results: MTHFD1 and LGALS4 were identified as promising therapeutic targets for PRAD, with evidence provided at multi-omics levels. LGALS4 was predominantly expressed in malignant cells and was correlated with enhanced immune checkpoint pathways, increased TIDE scores, and immunotherapy resistance. In contrast, MTHFD1was expressed in both tumor and microenvironmental cells and was associated with poor survival. Drug target prediction suggested that there are no currently approved drugs specifically targeting MTHFD1 and LGALS4. Conclusions: Our study identified MTHFD1 and LGALS4 as potential preventive targets for PRAD. However, future experiments are warranted to assess the utility and effectiveness of these candidate proteins.

Identification of potential biomarkers for hepatocellular carcinoma based on machine learning and bioinformatics analysis

Metastasis is the major cause of hepatocellular carcinoma (HCC) mortality. But the effective biomarkers for HCC metastasis remain underexplored. Here we integrated GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) datasets to screen candidate genes for hepatocellular carcinoma metastasis, a consensus metastasis-derived prognostic signature (MDPS) was constructed by machine learning. Based on the risk scores, HCC patients were stratified into high-risk and low-risk groups. Comprehensive analyses were conducted to investigate various aspects including survival outcomes, clinical characteristics, immune cell infiltration, as well as in vitro experiments. Together, we develop a comprehensive machine learning-based program for constructing a consensus MDPS including four genes (SPP1, TYMS, HMMR and MYCN). Our findings revealed that four genes could serve as efficient prognostic biomarkers and therapeutic targets in HCC. In addition, in vitro experiments showed that HMMR overregulation exacerbated tumor progression, including proliferation, migration and invasion.

Comprehensive Physiology, Cytology, and Transcriptomics Studies Reveal the Regulatory Mechanisms Behind the High Calyx Abscission Rate in the Bud Variety of Korla Pear (Pyrus sinkiangensis 'Xinnonglinxiang').

Whether the calyx tube of the Korla fragrant pear falls off seriously affects the fruit quality. 'Xinnonglinxiang' is a mutant variety of the Korla fragrant pear, which has a high calyx removal rate under natural conditions, and calyx tube fall seriously affects the fruit quality. The mechanism behind the high calyx removal rate of 'Xinnonglinxiang' remains unclear; thus, Korla fragrant pear (PT) and 'Xinnonglinxiang' (YB) with different degrees of calyx abscission were used as examples and the abscission areas of calyx tubes were collected in the early (21 April), middle (23 April), and late (25 April) shedding stages to explore the regulatory mechanism behind the abscission. The combination of the results of physiological, cytological, and transcriptomic methods indicated the highest number of differentially expressed genes (DEGs) in the middle of shedding. GO (Gene Ontology) enrichment analysis showed that the expression levels of genes related to the CEL (cellulase) and PG (polygalacturonase) activity functional pathways differed significantly in the two varieties during the three periods, whereas Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were significantly concentrated in the plant hormone signal transduction pathway in all three periods. The expression levels of genes related to the plant hormone signal transduction pathway differed significantly for the two varieties during calyx shedding. Five gene modules were obtained using Weighted Gene Co-Expression Network Analysis (WGCNA), and transcriptome data were correlated with five physiological index values. Two key modules that highly correlated with the Eth (ethylene) response were then screened, and 20 core genes were identified, with IRX10, IRX9, and OXI1 likely the hub genes that are involved in the regulation of calyx shedding in the YB variety. The obtained results provide reliable data for the screening of candidate genes for calyx shedding and analysis of the regulatory mechanism behind a high calyx shedding rate, providing a theoretical basis upon which the calyx shedding rate of fruits can be improved through genetic improvement.

Single-Cell Sequencing and Machine Learning Integration to Identify Candidate Biomarkers in Psoriasis: INSIG1.

Psoriasis represents a persistent, immune-driven inflammatory condition affecting the skin, characterized by a lack of well-established biologic treatments without adverse events. Consequently, the identification of novel targets and therapeutic agents remains a pressing priority in the field of psoriasis research. We collected single-cell RNA sequencing (scRNA-seq) datasets and inferred T cell differentiation trajectories through pseudotime analysis. Bulk transcriptome and scRNA-seq data were integrated to identify differentially expressed genes (DEGs). Machine learning was employed to screen candidate genes. Correlation analysis was used to predict the interactions between cells expressing insulin-induced gene 1 (INSIG1) and other immune cells. Finally, drug docking was performed on INSIG1, and the expression levels of INSIG1 in psoriasis were verified through clinical and in vivo experiments, and further in vivo experiments established the efficacy of tetrandrine in the treatment of psoriasis. T cells were initially categorized into seven states, with differentially expressed genes in T cells (TDEGs) identified and their functions and signaling pathways. INSIG1 emerged as a characteristic gene for psoriasis and was found to be downregulated in psoriasis and potentially negatively associated with T cells, influencing psoriasis fatty acid metabolism, as inferred from enrichment and immunoinfiltration analyses. In the cellular communication network, cells expressing INSIG1 exhibited close interactions with other immune cells through multiple signaling channels. Furthermore, drug sensitivity showed that tetrandrine stably binds to INSIG1, could be a potential therapeutic agent for psoriasis. INSIG1 emerges as a specific candidate gene potentially regulating the fatty acid metabolism of patients with psoriasis. In addition, tetrandrine shows promise as a potential treatment for the condition.

Human-specific epigenomic states in spermatogenesis

Infertility is becoming increasingly common, affecting one in six people globally. Half of these cases can be attributed to male factors, many driven by abnormalities in the process of sperm development. Emerging evidence from genome-wide association studies, genetic screening of patient cohorts, and animal models highlights an important genetic contribution to spermatogenic defects, but comprehensive identification and characterization of the genes critical for male fertility remain lacking. High divergence of gene regulation in spermatogenic cells across species poses challenges for delineating the genetic pathways required for human spermatogenesis using common model organisms. In this study, we leveraged post-translational histone modification and gene transcription data for 15,491 genes in four mammalian species (human, rhesus macaque, mouse, and opossum), to identify human-specific patterns of gene regulation during spermatogenesis. We combined H3K27me3 ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data to define epigenetic states for each gene at two stages of spermatogenesis, pachytene spermatocytes and round spermatids, in each species. We identified 239 genes that are uniquely active, poised, or dynamically regulated in human spermatogenic cells distinct from the other three species. While some of these genes have been implicated in reproductive functions, many more have not yet been associated with human infertility and may be candidates for further molecular and epidemiologic studies. Our analysis offers an example of the opportunities provided by evolutionary and epigenomic data for broadly screening candidate genes implicated in reproduction, which might lead to discoveries of novel genetic targets for diagnosis and management of male infertility and male contraception.

Genome-Wide Identification of Freezing-Responsive Genes in a Rapeseed Line NTS57 Tolerant to Low-Temperature.

Winter rapeseed is a high-oil crop that exhibits significant sensitivity to low temperatures, leading to a substantial reduction in production. Hence, it is of great significance to elucidate the genomic genetic mechanism of strong freezing-resistant winter rapeseed to improve their freezing-resistant traits. In this study, global transcriptome expression profiles of the freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained for the years 2015, 2016, and 2017 by RNA sequencing (RNA-seq). Most differentially expressed genes (DEGs) were involved in the plant hormone signal transduction, alpha-linolenic acid metabolism, protein processing, glutathione metabolism, and plant-pathogen interaction pathways. Antioxidant enzyme activities and lipid peroxidation levels were significantly positively and negatively correlated with overwintering rate (OWR), respectively. After freezing treatment, the formation of freezing resistance of NS was attributed to the increase in antioxidant enzyme activities and content of osmotic regulation substances, as well as the decrease in lipid peroxidation level. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and phenotypic verification indicated that heat stress transcription factor A2 (HSFA2) and 17.6 kDa class II heat shock protein (HSP17.6) participated in the response to freezing stress. This study will further refine the regulatory network of plants against freezing stress and help to screen candidate genes for improving plant freezing resistance.

The UBA1-STUB1 axis mediates cancer immune escape and resistance to checkpoint blockade.

How cancer cells escape immune surveillance and resist immune checkpoint blockade (ICB) remains to be fully elucidated. By screening candidate genes frequently gained in cancer, we identified expression of ubiquitin-like modifier activating enzyme 1 (UBA1) as being the most negatively correlated with signatures related to effector CD8+ T-cells. High UBA1 expression was strongly predictive of treatment resistance and poor survival in ICB cohorts. Functional studies revealed that UBA1 mediated immune escape to promote tumor growth. Immune profiling further showed that Uba1 overexpression or depletion markedly decreased or increased functional intratumoral CD8+ T-cells, respectively. Importantly, a selective UBA1 inhibitor, TAK-243, significantly synergized with ICB in multiple syngeneic models. Mechanistically, depletion or inactivation of the UBA1-STUB1 axis stabilized a key interferon pathway component (JAK1), enhanced IFN-signaling, and elevated key immune modulators, including CXCL9, CXCL10, and MHC class I. Our study warrants clinical evaluation of the combination of UBA1 inhibitors and ICB.

6615 Clinical features and genetic etiology of primary ovarian insufficiency in 46,XX children

Abstract Disclosure: F. Wang: None. X. Yin: None. X. Lan: None. P. Li: None. Purpose: The clinical features of primary ovarian insufficiency in 46,XX children were analyzed, the pathogenic genes of POI were screened, and the genetic etiology of primary ovarian insufficiency in children 46,XX was clarified. Method: The clinical data of 46,XX POI patients were collected, including uterine and ovarian ultrasound, serum follicle-stimulating hormone (FSH), estrogen, anti-mullerian hormone (AMH), chromosomal karyotype analysis, adrenal and thyroid function, and immune function. Whole exome sequencing (WES) and CNV were used to screen POI candidate genes. Novel mutations such as MCM8 gene were used to verify cell function. HE staining, immunohistochemistry, cell fluorescence, and Tunnel method were used to observe the changes in ovarian tissue structure. Construction overexpression plasmids of Mutant MCM8 gene in Hela cells. Result: 1. Clinical features of 46,XX POI: The age of onset of the children was 11.9∼16.1 years old. In addition to POI, the clinical phenotype showed height growth retardation. Among them, 4 cases were short stature, 3 cases were growth hormone deficiency, and 5 cases were backward in bone age. All of them showed elevated FSH (>25 IU/L), and 7 cases had low serum AMH (<0.5 ng/ml). 2.The Screening of POI candidate genes and pathogenicity analysis: 5 of the 10 children carried the mutations of the pathogenic genes with POI, that is, 2 cases (sisters of the same family) carried two novel heterozygous mutations of MCM8 gene, one infant carried two novel heterozygous mutations of CYP19A1 gene, and one case with delayed puberty carried one homozygous mutation of ZSW1M7 gene. 3.The MCM8 mutant were functionally validated: The sisters carried two novel mutations, namely p.C242R and p.S445*. The elder sister (the proband) showed POI, short stature and tumor susceptibility, while the younger sister showed a trend of gradual increase in FSH level and ovarian decline. The follicles of the proband disappeared and fibrous tissue proliferation, the MCM8 expression was lower, and the positive rate of cell apoptosis was higher than normal control. The downregulation of Bax and Capase3 expression in mutant MCM8 of Hela cell was delayed compared with wild type, indicating the persistence of apoptosis. Conclusion: 1. The clinical characteristics of 46,XX POI in children are ovarian hypoplasia, often combined with height growth retardation, biochemical manifestations of hypergonadotropic hypogonadism, decreased serum AMH, and karyotype 46,XX. 2.46,XX POI genetic etiology analysis found that five known POI-related pathogenic genes, namely CYP19A1, MCM8, and ZSW1M7, in which five novel mutations were identified.3.Mutant MCM8 promotes ovarian apoptosis by activating the Bcl-2/Bax/Caspase 3 pathway. Keywords: Primary ovarian insufficiency, short stature, apoptosis Presentation: 6/3/2024

Fermentative production of 3-hydroxypropionic acid by using metabolically engineered Klebsiella pneumoniae strains

3-Hydroxypropionic acid (3-HP) is an industrially important platform chemical for super-absorbent or biodegradable polymers. Its production via biological methods is expected to be more competitive than chemical methods. Klebsiella pneumoniae is the most promising host due to its innate capabilities for 3-HP and vitamin-B12 production, ease of culture, and ease of engineering. In this study, step-by-step metabolic engineering and fermentation technologies were used to enhance the production of 3-HP. K. pneumoniae-derived ydcW gene was overexpressed using a plasmid after screening candidate genes. Major competing pathways encoded by dhaT, yqhD, ldhA, glpK, poxB, and pta-ackA were blocked. Additionally, it was demonstrated that simultaneous reinforcement of two native aldehyde dehydrogenase encoded by the ydcW gene preferring NADPH and the puuC gene preferring NADH, synergistically improved 3-HP production. Additional reinforcement of the acs gene to reduce acetate accumulation resulted in 93.7 g/L of 3-HP with a yield of 0.42 g/g·glycerol over a 72-h fed-batch fermentation. This performance is deemed sufficient for industrial applications.

Comparative analysis of transcriptomics of Fasciola hepatica at different developmental stages.

This study explored the transcriptome differences in Fasciola hepatica at different developmental stages and identified functional genes related to growth and development during juvenile stages. DNBSEQ eukaryotic strand-specific transcriptome resequencing technology was used to sequence the transcriptomes of Fasciola hepatica eggs, juveniles, and adults. Additionally, the genes that were highly expressed during the juvenile stage were validated using qRT-PCR. The Q20 values of all three phases of sequencing were above 98%, and the Q30 values were above 94%. The differentially expressed genes (DEGs) in pairwise comparisons were analyzed by GO functional classification and the KEGG pathway database. Many immune-, growth-, and development-related pathways were found, which might be related to cell proliferation, development, and host immune evasion by Fasciola hepatica. In addition, five DEGs with high expression levels during the juvenile stage were identified: Cathepsin B, Glutathione S-transferase mu, heat shock protein 67B2, Kunitz-CH, and Legumain. Validation analyses revealed that these genes play key roles in maintaining normal growth, development, and immunological processes in liver Fasciola hepatica. RNA-seq was used to analyze the biological characteristics of the DEGs at different developmental stages concerning GO functional classification and KEGG metabolic pathways. Five DEGs with high expression during the juvenile stage were identified. These genes are related to the growth, development, and immune function of Fasciola hepatica, which provides a theoretical basis for subsequent research on the proteomics of Fasciola hepatica and the screening of candidate genes for early diagnosis.

Combining Transcriptomics and Proteomics to Screen Candidate Genes Related to Bovine Birth Weight.

We established transcriptome and proteome databases for low-birth-weight (LB) and high-birth-weight (HB) calf placentae, identifying key genes and proteins associated with birth weight through bioinformatics analyses that included functional enrichment and protein-protein interactions (PPIs). Both mRNA and protein levels were validated. A total of 1494 differentially expressed genes (DEGs) and 294 differentially expressed proteins (DEPs) were identified when comparing the LB group to the HB group. Furthermore, we identified 53 genes and proteins exhibiting significant co-expression across both transcriptomic and proteomic datasets; among these, 40 were co-upregulated, 8 co-downregulated, while 5 displayed upregulation at the protein level despite downregulation at the mRNA level. Functional enrichment analyses (GO and KEGG) and protein-protein interaction (PPI) analysis indicate that, at the transcriptional level, the primary factor contributing to differences in calf birth weight is that the placenta of the high-birth-weight (HB) group provides more nutrients to the fetus, characterized by enhanced nutrient transport (SLC2A1 and SLC2A11), energy metabolism (ACSL1, MICALL2, PAG2, COL14A1, and ELOVL5), and lipid synthesis (ELOVL5 and ELOVL7). In contrast, the placenta of the low-birth-weight (LB) group prioritizes cell proliferation (PAK1 and ITGA3) and angiogenesis. At the protein level, while the placentae from the HB group exhibit efficient energy production and lipid synthesis, they also demonstrate reduced immunity to various diseases such as systemic lupus erythematosus and bacterial dysentery. Conversely, the LB group placentae excel in regulating critical biological processes, including cell migration, proliferation, differentiation, apoptosis, and signal transduction; they also display higher disease immunity markers (COL6A1, TNC CD36, CD81, Igh-1a, and IGHG) compared to those of the HB group placentae. Co-expression analysis further suggests that increases in calf birth weight can be attributed to both high-efficiency energy production and lipid synthesis within the HB group placentae (ELOVL5, ELOVL7, and ACSL1), alongside cholesterol biosynthesis and metabolic pathways involving CYP11A1 and CYP17A1. We propose that ELOVL5, ELOVL7, ACSL1, CYP11A1, and CYP17A1 serve as potential protein biomarkers for regulating calf birth weight through the modulation of the fatty acid metabolism, lipid synthesis, and cholesterol levels.

Glycosyltransferase genes are associated with resistance to cyhalofop-butyl in a Chinese Echinochloa crus-galli population.

Echinochloa crus-galli is the most troublesome and widespread weed of most rice-growing regions of the world. Cyhalofop-butyl, a herbicide within the acetyl-CoA carboxylase (ACCase) chemical group, has been extensively used to control barnyardgrass in rice. The repeated exposure to cyhalofop-butyl has led to resistance evolution in E. crus-galli populations. In this study, we identified a population of E. crus-galli (R-HN) in a rice field in Hunan, China, that developed resistance to cyhalofop-butyl at 4.49-fold the recommended field dose. No known target mutation was detected in the ACCase gene of the R-HN population by ACCase sequencing compared to sensitive populations. Both cytochrome P450 (CYP450) and glutathione S-transferase (GST) inhibitors could not significantly reverse the resistance to cyhalofop-butyl. The nontarget-site resistance (NTSR) mechanism was investigated by transcriptome sequencing. Validation of the screened candidate genes by quantitative real-time (qRT)-PCR revealed that six glycosyltransferases (GTs) and four ATP-binding cassette (ABC) transporter genes were consistently upregulated in the R-HN population. Five GTs and one ABC transporter genes were constitutively upregulated after cyhalofop-butyl treatment in the R-HN population. Molecular docking results showed that the significant binding energy of GT79, GT75L6 and GT74E among all candidate genes. Thus, the GT genes appear to be directly implicated in NTSR to cyhalofop-butyl in the R-HN populations through metabolic enhancement, but their functional characterization needs to be studied. © 2024 Society of Chemical Industry.

Integrative metabolome and transcriptome analysis characterized methyl jasmonate-elicited flavonoid metabolites of Blumea balsamifera.

As a commonly used medicinal plant, the flavonoid metabolites of Blumea balsamifera and their association with genes are still elusive. In this study, the total flavonoid content (TFC), flavonoid metabolites and biosynthetic gene expression patterns of B. balsamifera after application of exogenous methyl jasmonate (MeJA) were scrutinized. The different concentrations of exogenous MeJA increased the TFC of B. balsamifera leaves after 48 h of exposure, and there was a positive correlation between TFC and the elicitor concentration. A total of 48 flavonoid metabolites, falling into 10 structural classes, were identified, among which flavones and flavanones were predominant. After screening candidate genes by transcriptome mining, the comprehensive analysis of gene expression level and TFC suggested that FLS and MYB may be key genes that regulate the TFC in B. balsamifera leaves under exogenous MeJA treatment. This study lays a foundation for elucidating flavonoids of B. balsamifera, and navigates the breeding of flavonoid-rich B. balsamifera varieties.

Molecular mechanism of reduced biological fitness of fludioxonil-resistant strains of Botrytis cinerea based on transcriptome analysis.

Fludioxonil is a fungicide used to control gray mold. However, the frequency of resistance in the field is low, and highly resistant strains are rarely isolated. The biological fitness of the resistant strain is lower than that of the wild strain. Therefore, the molecular mechanism underlying the decrease in the fitness of the fludioxonil-resistant strain of Botrytis cinerea was explored to provide a theoretical basis for resistance monitoring and management. Transcriptome analysis was performed on five different-point mutant resistant strains of fludioxonil, focusing on mining and screening candidate genes that lead to reduced fitness of the resistant strains and the functional verification of these genes. The differentially expressed genes (DEGs) of the five point-mutation resistant strains intersected with 1869 DEGs. Enrichment analysis showed that three downregulated genes (Bcin05g07030, Bcgad1, and Bcin03g05840) were enriched in multiple metabolic pathways and were downregulated in both domesticated strains. Bcin05g07030 and Bcin03g05840 were involved in mycelial growth and development, pathogenicity, and conidial yield, and negatively regulated oxidative stress and cell wall synthesis. Bcgad1 was involved in mycelial growth and development, conidial yield, oxidative stress, and cell wall synthesis. Furthermore, Bcin05g07030 was involved in osmotic stress and spore germination, whereas Bcin03g05840 and Bcgad1 negatively regulated osmotic stress and cell wall integrity. These results enable us to further understand the molecular mechanism underlying the decrease in the biological fitness of B. cinerea fludioxonil-resistant strains. © 2024 Society of Chemical Industry.

Факторы и уровень суммарного сердечно-сосудистого риска у населения северо-востока России

In northern regions, cardiovascular pathology tends to be more aggressive, is likely to occur at a young age already and often results in disability and even mortality among people who have not yet reached the retirement age. The aim of this study was to assess the structure and age-specific dynamics of basic factors able to cause cardiovascular diseases in men living in northern regions and the total cardiovascular risk. We conducted a one-center experimental cross-sectional comparative one-sample study of 116 men living in the north of the Magadan region. The complex study program included questioning, anthropometric examination, laboratory biochemical tests and molecular-genetic screening of candidate genes of essential hypertension (AGT (rs 4762), AGTR1 (rs5186), ADD1 (rs4961), NOS3 (rs2070744), and АСЕ (rs4340)). Genotyping was performed using real-time polymerase chain reaction. The total cardiovascular risk was calculated using the SCORE scale. The structure of basic risk factors that can cause cardiovascular diseases in men in the Magadan region includes both modifiable (smoking, obesity, essential hypertension, and dyslipidemia) and non-modifiable ones (climatic-geographic and genetic risk factors) in various age groups. With age, risk factors exert stronger influence on each other thus aggravating the clinical course of cardiovascular diseases and increasing risks of fatal cardiac events. This is especially important for northern regions where people are exposed to such non-modifiable risk factors as extreme climate. Moderate risk of cardiovascular diseases (according to the SCORE scale) was established for all men living in the North already at a young age. Therefore, a key task is to develop a strategy for active prevention of cardiovascular pathology that covers public at large starting from younger age groups.

Factors and level of the total cardiovascular risk for people in the north-eastern Russia

In northern regions, cardiovascular pathology tends to be more aggressive, is likely to occur at a young age already and often results in disability and even mortality among people who have not yet reached the retirement age. The aim of this study was to assess the structure and age-specific dynamics of basic factors able to cause cardiovascular diseases in men living in northern regions and the total cardiovascular risk. We conducted a one-center experimental cross-sectional comparative one-sample study of 116 men living in the north of the Magadan region. The complex study program included questioning, anthropometric examination, laboratory biochemical tests and molecular-genetic screening of candidate genes of essential hypertension (AGT (rs 4762), AGTR1 (rs5186), ADD1 (rs4961), NOS3 (rs2070744), and АСЕ (rs4340)). Genotyping was performed using real-time polymerase chain reaction. The total cardiovascular risk was calculated using the SCORE scale. The structure of basic risk factors that can cause cardiovascular diseases in men in the Magadan region includes both modifiable (smoking, obesity, essential hypertension, and dyslipidemia) and non-modifiable ones (climatic-geographic and genetic risk factors) in various age groups. With age, risk factors exert stronger influence on each other thus aggravating the clinical course of cardiovascular diseases and increasing risks of fatal cardiac events. This is especially important for northern regions where people are exposed to such non-modifiable risk factors as extreme climate. Moderate risk of cardiovascular diseases (according to the SCORE scale) was established for all men living in the North already at a young age. Therefore, a key task is to develop a strategy for active prevention of cardiovascular pathology that covers public at large starting from younger age groups.

Identification and Fine Mapping of a Mutant pv‐nts Gene Responsible for Dwarf and Thin Stem of Snap Bean (Phaseolus vulgaris L.)

ABSTRACTPlant height is one of the most important traits in the breeding of snap bean, which determines the planting density and the resistance to failure, which in turn affects its yield and quality. Therefore, studying the molecular mechanism of plant height in snap bean is an important measure to realize the improvement of snap bean. We obtained a dwarf, thin‐stemmed mutant nts (normal to slim) from a dwarf variety of snap bean A18 via 60CO‐γ‐ray treatment. We conducted phenotypic observations, endogenous hormone content measurements and genetic analyses of the dwarfing thin‐stemmed mutant nts and explored gene localization and candidate gene screening for the mutant trait in snap bean. Compared with wild‐type A18, nts mutant exhibited various abnormal phenotypes such as dwarfing, reduced branching, thinner top stem, reduced plant width, reduced number of leaf area and thousand grain weight and increased content of hormones such as indole‐3‐acetic acid (IAA) in the top stem. Genetic analysis indicated that the mutant trait was controlled by a single recessive nuclear gene, and the mutant gene was named pv‐nts. pv‐nts was localized to a 361.1‐kb segment on chromosome 8 as revealed by bovine serum albumin (BSA) hybrid pool sequencing and simple sequence repeat (SSR) molecular markers. Phvul.008G106300 (encoding LAX2 protein) was identified as a candidate gene corresponding to pv‐nts via gene function annotation. Phvul.008G106300 was significantly upregulated in nts mutant compared with wild‐type A18, which was consistent with the results of endogenous IAA levels. Sequence analysis showed that the Phvul.008G106300 gene in nts had a base mutation that altered the protein structure, thus causing the dwarfed, thin‐stemmed phenotype of cauliflower. Taken together, these results contribute to a better understanding of the genetic basis of dwarfing traits in snap bean.

A taxon-restricted duplicate of Iroquois3 is required for patterning the spider waist.

The chelicerate body plan is distinguished from other arthropod groups by its division of segments into 2 tagmata: the anterior prosoma ("cephalothorax") and the posterior opisthosoma ("abdomen"). Little is understood about the genetic mechanisms that establish the prosomal-opisthosomal (PO) boundary. To discover these mechanisms, we created high-quality genomic resources for the large-bodied spider Aphonopelma hentzi. We sequenced specific territories along the antero-posterior axis of developing embryos and applied differential gene expression analyses to identify putative regulators of regional identity. After bioinformatic screening for candidate genes that were consistently highly expressed in only 1 tagma (either the prosoma or the opisthosoma), we validated the function of highly ranked candidates in the tractable spider model Parasteatoda tepidariorum. Here, we show that an arthropod homolog of the Iroquois complex of homeobox genes is required for proper formation of the boundary between arachnid tagmata. The function of this homolog had not been previously characterized, because it was lost in the common ancestor of Pancrustacea, precluding its investigation in well-studied insect model organisms. Knockdown of the spider copy of this gene, which we designate as waist-less, in P. tepidariorum resulted in embryos with defects in the PO boundary, incurring discontinuous spider germ bands. We show that waist-less is required for proper specification of the segments that span the prosoma-opisthosoma boundary, which in adult spiders corresponds to the narrowed pedicel. Our results demonstrate the requirement of an ancient, taxon-restricted paralog for the establishment of the tagmatic boundary that defines Chelicerata.

Screening and analysis of candidate genes conferring alkalinity tolerance in rice (Oryza sativa L.) at the bud burst stage based on QTL-seq and RNA-seq

BackgroundSoil salinization is one of the key factors restricting the production of cropland. Once rice is subjected to alkali stress at the bud burst stage, the yield will suffer irreparable serious loss. Compared with salt tolerance, studies on QTL mapping and candidate gene analysis of rice alkali tolerance are limited. ResultsIn this study, we used the F2:3 population derived from the alkali-tolerant cultivar LD21 and the alkali-sensitive cultivar WL138 to construct an alkali-tolerant DNA mixing pool, and the BSA (Bulked Segregation Analysis) method was used for re-sequencing. The main QTL qRSLB9 controlling the relative shoot length of rice under alkali stress was mapped by QTL-seq. The candidate interval was narrowed to 346.5 kb by regional linkage mapping, which containing 6 DEGs screened through transcriptome sequencing. The qRT-PCR and candidate gene sequencing showed that LOC_Os09g24260 was most likely to control relative shoot length (RSL) in rice as a major gene who encodes the WD domain, G-beta repeat domain-containing protein. ConclusionsBased on these results, LOC_Os09g24260 was the candidate gene of qRSLB9 conferring alkalinity tolerance to rice at the bud burst stage. Our study provides valuable genetic information and materials for breeding new rice varieties with alkalinity tolerance.How to cite: Wang J, Bian J, Liu L, et al. Screening and analysis of candidate genes conferring alkalinity tolerance in rice (Oryza sativa L.) at the bud burst stage based on QTL-seq and RNA-seq. Electron J Biotechnol 2024;71. https://doi.org/10.1016/j.ejbt.2024.07.002.

Deciphering Trachinotus ovatus resistance to Streptococcus agalactiae:GWAS identification of key SNPs and candidate genes

The genetic basis of resistance in Trachinotus ovatus to Streptococcus agalactiae, a prevalent pathogen in warm-water fish, was explored in this study. T. ovatus, an economically significant marine fish, is widely distributed in tropical and subtropical oceans. This research involved the whole-genome resequencing of 200 T. ovatus individuals and a genome-wide association study (GWAS) to identify significant single nucleotide polymorphisms (SNPs) associated with resistance to S. agalactiae. Methods included infection experiments with S. agalactiae, quality control of DNA samples, high-throughput sequencing, SNP detection and quality control, analysis of population genetic structure, linkage disequilibrium (LD) analysis, GWAS, screening of candidate genes, and genotyping of significant SNPs. Results indicated a significant association of specific SNP loci with resistance in T. ovatus to S. agalactiae, notably SNP18597184 on chromosome LG9, associated with the NTRK3 and IFNK genes involved in neural development, survival, and immune response.