Gene Signal Transduction Research Articles

PARP1 Inhibition and Effect on Burn Injury-Induced Inflammatory Response and Cardiac Function.

Burn injury induces multiple signaling pathways leading to a significant inflammatory storm that adversely affects multiple organs, including the heart. Poly (ADP-ribose) polymerase inhibitor 1 (PARP1) inhibition, with specific agents such as N-(5,6-Dihydro-6-oxo-2-phenanthridinyl)-2-acetamide (PJ34), is effective in reducing oxidative stress and cytokine expression in the heart. We hypothesized that PARP1 inhibition would reduce inflammatory signaling and protect against burn injury-induced cardiac dysfunction. Male Sprague-Dawley rats (8 weeks old, 300 to 350 g) were randomly assigned to sham injury (Sham), 60% total body surface area burn (24 hours post burn), or 60% total body surface area burn with intraperitoneal administration of PJ34 (20 mg/kg, 24 hours post burn + PJ34) and sacrificed 24 hours after injury. Cardiac function was determined using Vevo 2100 echocardiography. Genetic expression of 84 specific toll-like receptor-mediated signal transduction and innate immunity genes were examined using microarray to evaluate cardiac tissue. Qiagen GeneGlobe Data Analysis Center was used to analyze expression, and genetic clustering was performed using TreeView V2.0.8 software. Real-time quantitative polymerase chain reaction was used to validate identified differentially expressed genes. Burn injury significantly altered multiple genes in the toll-like receptor signaling, interleukin-17 signaling, tumor necrosis factor signaling, and nuclear factor-κB signaling pathways and led to significant cardiac dysfunction. PARP1 inhibition with PJ34 normalized these signaling pathways to sham levels as well as improved cardiac function to sham levels. PARP1 inhibition normalizes multiple inflammatory pathways that are altered after burn injury and improves cardiac dysfunction. PARP1 pathway inhibition may provide a novel methodology to normalize multiple burn injury-induced inflammatory pathways in the heart.

Identification and Expression Analysis of Abscisic Acid Signal Transduction Genes in Hemp Seeds

Abscisic acid (ABA) is involved in regulating diverse biological processes, but its signal transduction genes and roles in hemp seed germination are not well known. Here, the ABA signaling pathway members, <i>PYL</i>, <i>PP2C</i> and <i>SnRK2</i> gene families, were identified from the hemp reference genome, including 7 <i>CsPYL</i> (pyrab-actin resistance1-like, ABA receptor), 8 <i>CsPP2CA</i> (group A protein phosphatase 2c), and 7 <i>CsSnRK2</i> (sucrose nonfermenting1-related protein kinase 2). The content of ABA in hemp seeds in germination stage is lower than that in non-germination stage. Exogenous ABA (1 or 10 μM) treatment had a significant regulatory effect on the selected <i>PYL</i>, <i>PP2C</i>, <i>SnRK2</i> gene families. <i>CsAHG3</i> and <i>CsHAI1</i> were most significantly affected by exogenous ABA treatment. Yeast two-hybrid experiments were performed to reveal that CsPYL5, CsSnRK2.2, and CsSnRK2.3 could interact with CsPP2CA7 and demonstrate that this interaction was ABA-independent. Our results indicated that <i>CsPYL5</i>, <i>CsSnRK2.2</i>, <i>CsSnRK2.3</i> and <i>CsPP2CA7</i> might involve in the ABA signaling transduction pathway of hemp seeds during the hemp seed germination stages. This study suggested that novel genetic views can be brought into investigation of ABA signaling pathway in hemp seeds and lay the foundation for further exploration of the mechanism of hemp seed germination.

1-Methylcyclopropene retards pak choi (Brassica rapasubsp. chinensis) yellowing via BcNAC055-, BcMYB44-, and BcOBF1-mediated regulation of the key chlorophyll degrading geneBcNYC1during storage at 20 °C

AbstractThe objective of this study was to investigate the molecular regulatory mechanism of 1-methylcyclopropene (1-MCP) treatment on leaf yellowing of pak choi during storage at 20 °C. In the present study, compared with the control and 10 μL/L ethylene-treated pak choi, 5.0 μL/L 1-MCP fumigation alleviated the yellowing process of pak choi as proved by the maintenance of higher levels of colour, chlorophyll content, and appearance. 1-MCP treatment decreased chlorophyll breakdown by downregulating the activity of chlorophyll-degrading enzymes (chlorophyll b reductase (CBR) and pheophytinase (PPH)) and the expression of their related genes (BcNYC1 and BcPPH). The application of 1-MCP also inhibited the transcript abundance of ethylene biosynthesis and signal transduction genes (BcACO, BcEIN3, and BcERF) and reduced ethylene production, thus helping to maintain the green colour of pak choi; however, ethylene treatment exerted the opposite function. Meanwhile, three transcription factors (BcNAC055, BcMYB44, and BcOBF1) were successfully cloned. Experiments performed using yeast one-hybrid assay, dual-luciferase reporter system and in vivo bioluminescence imaging assay, confirmed that BcNAC055, BcMYB44, and BcOBF1 directly bound to the BcNYC1 promoter. 1-MCP inhibited the expression levels of BcNAC055, BcMYB44, BcOBF1, and BcNYC1 during storage, while the application of ethylene activated their expression. In conclusion, 1-MCP downregulated the expression of the key chlorophyll degradation gene BcNYC1 by inhibiting the transcript level of its three positive regulators (BcNAC055, BcMYB44, and BcOBF1) and lowered the activity of chlorophyll-degrading enzyme CBR, thereby helping mitigate chlorophyll breakdown to retard leaf yellowing in pak choi. The results of this work extend our understanding of 1-MCP-delayed yellowing in postharvest pak choi.

Transcriptome Analysis Reveals the Molecular Mechanisms Associated with Flower Color Formation in Camellia japonica ‘Joy Kendrick’

Camellia japonica is a woody flower with high ornamental and economic value used for landscaping and as a pot plant. Floral colors are among the most important ornamental traits of flower plants, particularly multicolored flowers. The C. japonica cultivar ‘Joy Kendrick’ has multicolored flowers; the corolla is pink with darker red stripes, but the molecular mechanism underlying this trait is unknown. Here, pigment analysis showed that there are more anthocyanins accumulate in red petal regions than in pink areas, which may be key to formation of red stripes. Furthermore, transcriptome analysis revealed that anthocyanin biosynthesis, modification, and transporter genes are highly expressed in red stripes, consistent with the observed anthocyanin accumulation. In addition, many plant hormone signal transduction genes, particularly auxin, may contribute to the regulation of red stripe formation. This study provides broad insights into pigment accumulation and the regulatory mechanisms underlying floral color formation in C. japonica, and lays a foundation for breeding new C. japonica varieties.

One Health: Animal Models of Heritable Human Bleeding Diseases

Animal models of human and animal diseases have long been used as the lynchpin of experimental and clinical research. With the discovery and implementation of novel molecular and nano-technologies, cellular research now has advanced to assessing signal transduction pathways, gene editing, and gene therapies. The contribution of heritable animal models to human and animal health as related to hemostasis is reviewed and updated with the advent of gene editing, recombinant and gene therapies.

Implementation of multigene panel testing for breast and ovarian cancer in South Africa: A step towards excellence in oncology for the public sector.

Translation of genomic knowledge into public health benefits requires the implementation of evidence-based recommendations in clinical practice. In this study, we moved beyond BRCA1/2 susceptibility testing in breast and ovarian cancer patients to explore the application of pharmacogenetics across multiple genes participating in homologous recombination DNA damage repair. This involved the utilisation of next-generation sequencing (NGS) at the intersection of research and service delivery for development of a comprehensive genetic testing platform in South Africa. Lack of international consensus regarding risk categorization of established cancer susceptibility genes and the level of evidence required for prediction of drug response supported the development of a central database to facilitate clinical interpretation. Here we demonstrate the value of this approach using NGS to 1) determine the variant spectrum applicable to targeted therapy and implementation of prevention strategies using the 15-gene Oncomine™ BRCA Expanded Panel, and 2) searched for novel and known pathogenic variants in uninformative cases using whole exome sequencing (WES). Targeted NGS performed as a routine clinical service in 414 South African breast and/or ovarian cancer patients resulted in the detection of 48 actionable variants among 319 (15%) cases. BRCA1/2-associated cancers were identified in 70.8% of patients (34/48, including two double-heterozygotes), with the majority (35.3%, 12/34) representing known South African founder variants. Detection of actionable variants in established non-BRCA1/2 risk genes contributed 29% to the total percentage (14/48), distributed amongst ATM, CHEK2, BARD1, BRIP1, PALB2 and TP53. Experimental WES using a virtually constructed multi-cancer NGS panel in 16 genetically unresolved cases (and four controls) revealed novel protein truncating variants in the basal cell carcinoma gene PTCH1 (c.4187delG) and the signal transmission and transduction gene KIT (c.930delA) involved in crucial cellular processes. Based on these findings, the most cost-effective approach would be to perform BRCA1/2 founder variant testing at referral, followed by targeted multigene panel testing if clinically indicated and addition of WES in unresolved cases. This inventive step provides a constant flow of new knowledge into the diagnostic platform via a uniquely South African pathology-supported genetic approach implemented for the first time in this context to integrate research with service delivery.

In silico and in vitro approaches allow the identification of the Prosystemin molecular network

Tomato Prosystemin (ProSys), the precursor of Systemin, a small peptidic hormone, is produced at very low concentration in unchallenged plants, while its expression greatly increases in response to several different stressors triggering an array of defence responses. The molecular mechanisms that underpin such a wide array of defence barriers are not fully understood and are likely correlated with the intrinsically disordered (ID) structure of the protein. ID proteins interact with different protein partners forming complexes involved in the modulation of different biological mechanisms. Here we describe the ProSys-protein network that shed light on the molecular mechanisms underpinning ProSys associated defence responses. Three different approaches were used. In silico prediction resulted in 98 direct interactors, most clustering in phytohormone biosynthesis, transcription factors and signal transduction gene classes. The network shows the central role of ProSys during defence responses, that reflects its role as central hub. In vitro ProSys interactors, identified by Affinity Purification-Mass Spectrometry (AP-MS), revealed over three hundred protein partners, while Bimolecular Fluorescent Complementation (BiFC) experiments validated in vivo some interactors predicted in silico and in vitro. Our results demonstrate that ProSys interacts with several proteins and reveal new key molecular events in the ProSys-dependent defence response of tomato plant.

Novel Molecular Insights into Leukemic Evolution of Myeloproliferative Neoplasms: A Single Cell Perspective.

Myeloproliferative neoplasms (MPNs) are clonal disorders originated by the serial acquisition of somatic mutations in hematopoietic stem/progenitor cells. The major clinical entities are represented by polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), that are caused by driver mutations affecting JAK2, MPL or CALR. Disease progression is related to molecular and clonal evolution. PV and ET can progress to secondary myelofibrosis (sMF) but can also evolve to secondary acute myeloid leukemia (sAML). PMF is associated with the highest frequency of leukemic transformation, which represents the main cause of death. sAML is associated with a dismal prognosis and clinical features that differ from those of de novo AML. The molecular landscape distinguishes sAML from de novo AML, since the most frequent hits involve TP53, epigenetic regulators, spliceosome modulators or signal transduction genes. Single cell genomic studies provide novel and accurate information about clonal architecture and mutation acquisition order, allowing the reconstruction of clonal dynamics and molecular events that accompany leukemic transformation. In this review, we examine our current understanding of the genomic heterogeneity in MPNs and how it affects disease progression and leukemic transformation. We focus on molecular events elicited by somatic mutations acquisition and discuss the emerging findings coming from single cell studies.

Combined transcriptome and metabolome analysis revealed pathways involved in improved salt tolerance of Gossypium hirsutum L. seedlings in response to exogenous melatonin application

BackgroundSalinization is major abiotic stress limiting cotton production. Melatonin (MT) has been implicated in salt stress tolerance in multiple crops including upland cotton. Here, we explored the transcriptomic and metabolomic response of a salt-tolerant self-bred high-yielding cotton line SDS-01, which was exogenously sprayed with four MT concentrations (50, 100, 200, and 500 μM).ResultsHere we found that MT improves plant biomass and growth under salt stress. The combined transcriptome sequencing and metabolome profiling approach revealed that photosynthetic efficiency is improved by increasing the expressions of chlorophyll metabolism and antenna proteins in MT-treated seedlings. Additionally, linoleic acid and flavonoid biosynthesis were improved after MT treatment. The Na+/K+ homeostasis-related genes were increasingly expressed in salt-stressed seedlings treated with MT as compared to the ones experiencing only salt stress. Melatonin treatment activated a cascade of plant-hormone signal transduction and reactive oxygen scavenging genes to alleviate the detrimental effects of salt stress. The global metabolome profile revealed an increased accumulation of flavonoids, organic acids, amino acids and derivatives, saccharides, and phenolic acids in MT-treated seedlings. Interestingly, N, N′-Diferuloylputrescine a known antioxidative compound was highly accumulated after MT treatment.ConclusionCollectively, our study concludes that MT is a salt stress regulator in upland cotton and alleviates salt-stress effects by modulating the expressions of photosynthesis (and related pathways), flavonoid, ROS scavenging, hormone signaling, linoleic acid metabolism, and ion homeostasis-related genes.

Splicing Analysis Unveils Convergent Transcriptomic Pathways in U2AF1 S34 and Q157 Mutant Myeloid Neoplasia

Splicing factor mutations (SFMT) are frequent in MDS and their pathogenic consequences may include missplicing and changes in alternative splicing (AS). However, divergent sequence-sequence effects on misspliced genes were recorded in U2AF1MT at the two canonical hotspots (S34, Q157). Most of the current studies have been focused on the identification of distinctive features of splicing dysfunction between the two hotspots, unveiling various unique hotspot specific splicing events. Classical instances of missplicing events include those in ATG7,H2AFY and STRAP specific to U2AF1S34 MDS. However, whereas we and others have demonstrated certain unique clinical features of MDS patients carrying S34 vs Q1571, these two alterations produce a generally similar disease phenotype and likely rely on a common transformation mechanism. This conclusion suggests that missplicing events might converge in pathways relevant to MDS pathogenesis, which may be much more widespread than what is believed. While defining a topology of AS events (ASE), our analysis of the global landscape of RNA splicing in myeloid neoplasia (MN)2 also opened the possibility to search for subsets of patients sharing RNA splicing features and gene expression (GE). We now curated RNA-Seq data from diagnostic samples of 1258 MN patients by comparing RNA splicing profiles of clonal primary cells with S34 (n=19) and Q157 (n=26) (VAFs >10%, both) in search for overlapping ASE representing new cooperative mechanisms germane to leukemogenesis. ASE were filtered based on percent spliced in (PSI) (variation threshold > 0.01). Limma analysis for differential GE and PSI was applied. All data were analyzed on the genome assembly GRCh37/hg19. Patients without SFMT plus a cohort of 63 age-matched controls were used to detect exclusive ASE common in U2AF1 S34 and Q157. Pathway analysis showed an enrichment of chromatin remodeling, histone demethylases and signal transduction genes. A total of 17564 ASE were called with 30% (n=5106) of them found to be significant (qvalues ≤ .05 and inclusion level difference ≥ 5%). In-depth analysis of ASE showed that 70% of significant PSI changes resulted from exon skipping (ES) followed by intron retention (17%) and alternative 3′ and 5′ splice site events (14%). No significant mutually exclusive ASE was found. Considering that ES might result in truncated proteins and consequent lack of functional domains, we mapped ASE to protein domains. Top PSI changes which were common between S34 and Q157 were found in chromatin remodeling (EZH2,JMJD1C, ARID2/4B, CREBBP), O-linked β-N-acetylglucosamine transferase (OGT), a partner of TET2, GTPase activating (GNAS, ARHGAP9, HBS1L), RNA processing/ binding (RBM5, DDX21, DHX38,HNRNPM, PRPF3), unfolded protein response (XBP1), and ubiquitination (CUL3, NAE1, UBQLN1) genes. Lesions affecting chromosome 7 either structurally (cytogenetic alterations) or by mutations and CNV (EZH2 among others) are associated with adverse prognosis in MN. In total, 8% of the patients had deletion 7 and 4% carried EZH2MT. EZH2 mRNA expression levels were significantly lower in U2AF1MTvs controls (LFC=-0.88; P= 1e-11). Of note is that only 6 cases carried EZH2MT, of whom none harbored deletion 7. This suggests that EZH2 low expression levels might be due to other mechanisms. Looking at most relevant findings, we identified a significant and single ES (ex12) in EZH2 flanking the pre-SET domain (cysteine rich, CXC: aa503-605) crucial to maintain histone methyltransferase activity. Beside somatic mutations, EZH2 function can be altered by other mechanisms, e.g., cooperative mutations. The presence of an ES possibly suggests that an alternative mechanism of gene inactivation beside mutations in the CXC/SET domain and chromosome loss might play a role. Similarly, a CREBBP ES (ex11) was detected upstream the kinase inducible interacting (KIX) domain, a docking site for transcriptional activators (e.g., MLL, c-Myb sites). Finally, U2AF1MT have been also associated with deletion 20q or with a hyperactive long GNAS isoform. We found indeed an ES in GNAS and other GTPases, further emphasizing the broad dysfunctions in U2AF1 cooperative genes. In conclusion, our study describes convergent splicing features common to both U2AF1 S34 and Q157 to conceptualize the essential mechanisms contributing to clonal expansion due to lesions in U2AF1.

Characterization and expression analysis of key abscisic acid signal transduction genes during kiwifruit development

To characterise the regulation of abscisic acid (ABA) signal transduction during fruit development and ripening, we investigated the key genes involved in the ABA signalling pathway in kiwifruit (Actinidia chinensis), including 18 AcPYLs genes encoding ABA receptors, 7 AcPP2Cs genes encoding type 2C protein phosphatases, and 7 AcSnRK2s genes encoding members of the SNF1-related protein kinases 2 family identified in the kiwifruit reference genome. AcPYLs, AcPP2Cs, and AcSnRK2s from kiwifruit are putative homologues of the corresponding Arabidopsis and tomato proteins. Phylogenetic analysis revealed that AcPYLs and AcSnRK2s clustered into three subfamilies. Transcript levels indicated that the expression pattern of AcNCED4 was consistent with the ABA content of the pulp during kiwifruit development. Furthermore, the ABA content of the axile placenta was higher than that of the sarcocarp in kiwi pulp, and the expression of most ABA signal transduction genes, including AcPYLs, AcPP2Cs, and AcSnRK2s, was more predominant in the axile placenta. Moreover, AcPP2C3 was localised in the nucleus and could interact with all AcPYLs and AcSnRK2s in an ABA-independent manner, as revealed by subcellular localisation and yeast two-hybrid assays. These findings enhance our understanding of ABA signal transduction genes in kiwis, and provide the necessary background for further exploration of the molecular mechanisms at play during kiwifruit development.

Blood-derived deoxyribonucleic acid methylation clusters associate with adverse social exposures and endophenotypes of stress-related psychiatric illness in a trauma-exposed cohort of women.

Adverse social exposures (ASEs) such as low income, low educational attainment, and childhood/adult trauma exposure are associated with variability in brain region measurements of gray matter volume (GMV), surface area (SA), and cortical thickness (CT). These CNS morphometries are associated with stress-related psychiatric illnesses and represent endophenotypes of stress-related psychiatric illness development. Epigenetic mechanisms, such as 5-methyl-cytosine (5mC), may contribute to the biological embedding of the environment but are understudied and not well understood. How 5mC relates to CNS endophenotypes of psychiatric illness is also unclear. In 97 female, African American, trauma-exposed participants from the Grady Trauma Project, we examined the associations of childhood trauma burden (CTQ), adult trauma burden, low income, and low education with blood-derived 5mC clusters and variability in brain region measurements in the amygdala, hippocampus, and frontal cortex subregions. To elucidate whether peripheral 5mC indexes central nervous system (CNS) endophenotypes of psychiatric illness, we tested whether 73 brain/blood correlated 5mC clusters, defined by networks of correlated 5mC probes measured on Illumina's HumanMethylation Epic Beadchip, mediated the relationship between ASEs and brain measurements. CTQ was negatively associated with rostral middle frontal gyrus (RMFG) SA (β =-0.231, p = 0.041). Low income and low education were also associated with SA or CT in a number of brain regions. Seven 5mC clusters were associated with CTQ (pmin = 0.002), two with low education (pmin = 0.010), and three with low income (pmin = 0.007). Two clusters fully mediated the relation between CTQ and RMFG SA, accounting for 47 and 35% of variability, respectively. These clusters were enriched for probes falling in DNA regulatory regions, as well as signal transduction and immune signaling gene ontology functions. Methylome-network analyses showed enrichment of macrophage migration (p = 9 × 10-8), T cell receptor complex (p = 6 × 10-6), and chemokine-mediated signaling (p = 7 × 10-4) pathway enrichment in association with CTQ. Our results support prior work highlighting brain region variability associated with ASEs, while informing a peripheral inflammation-based epigenetic mechanism of biological embedding of such exposures. These findings could also serve to potentiate increased investigation of understudied populations at elevated risk for stress-related psychiatric illness development.

The Core Jasmonic Acid-Signalling Module CoCOI1/CoJAZ1/CoMYC2 Are Involved in Jas Mediated Growth of the Pollen Tube in Camellia oleifera.

Camellia oleifera is a woody edible oil species with late self-incompatibility characteristics. Previous transcriptome analysis showed that genes involved in jasmonic acid signal transduction were significantly different in self-and cross-pollinated pistils of Camellia oleifera. To investigate the relationship between jasmonate signal and self-incompatibility by studying the core genes of jasmonate signal transduction. The results showed that exogenous JA and MeJA at 1.0 mM significantly inhibited pollen tube germination and pollen tube elongation. and JA up-regulated CoCOI1, CoJAZ1, and CoMYC, the core genes of jasmonate signal transduction. Subcellular localization indicated that CoCOI1 and CoJAZ1 were located in the nucleus and CoMYC2 in the endoplasmic reticulum. The three genes exhibited tissue-specific expression pattern. CoCOI1 was significantly expressed in pollen, CoJAZ1 was significantly expressed in ovary, CoMYC2 was significantly expressed in filaments, but not in pollen. Furthermore, CoJAZ1 and CoMYC2 were highly expressing at 24 h in self-pollinated styles. These results suggested that JA signal transduction of C. oleifera was involved in the process of self-pollination, and thus in the process of plant defense. When pollen tubes grew slowly in the style, ovary may receive JA signal, which initiates the molecular mechanism of inhibiting the growth of self-pollinating pollen tubes.

Biochar-amended composting of lincomycin fermentation dregs promoted microbial metabolism and reduced antibiotic resistance genes

Improper disposal of antibiotic fermentation dregs poses a risk of releasing antibiotics and antibiotic resistant bacteria to the environment. Therefore, this study evaluated the effects of biochar addition to lincomycin fermentation dregs (LFDs) composting. Biochar increased compost temperature and enhanced organic matter decomposition and residual antibiotics removal. Moreover, a 1.5- to 17.0-fold reduction in antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was observed. Adding biochar also reduced the abundances of persistent ARGs hosts (e.g., Streptomyces, Pseudomonas) and ARG-related metabolic pathways and genes (e.g., ATP-binding cassette type-2 transport, signal transduction and multidrug efflux pump genes). By contrast, compost decomposition improved due to enhanced metabolism of carbohydrates and amino acids. Overall, adding biochar into LFDs compost reduced the proliferation of ARGs and enhanced microbial community metabolism. These results demonstrate that adding biochar to LFDs compost is a simple and efficient way to decrease risks associated with LFDs composting.

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress.

Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 –ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.

MPN-225 Next Generation Sequencing (NGS) in the Diagnosis, Prognosis and Features of the Disease in Ph-Negative Myeloproliferative Neoplasms.

Over the past decade NGS has expanded our understanding of the genomic landscape of hematological malignancies. New biomarkers discovered during NGS are now widely used in clinical practice to improve diagnosis, stratify patients into prognostic groups, and select targeted therapy for Ph-MPN patients. To assess possibilities of NGS in diagnosis and determination of prognostic features of disease course in Ph-MPN patients. The study included 36 patients from clinics in Moscow and St. Petersburg (17 men and 19 women), the median age was 55 (IQR 27-79) with diagnosed PV, ET, PMF, MDS, AML. A panel of 116 genes with an average reading depth of 200x or 1000x on MiSeq (Illumina) was used. NGS panel had a detection limit of 3% variant allele frequency. The clinical significance of mutations was determined using COSMIC and ClinVar. Genetic abnormalities were detected in all patients. On average, 10 mutations per one patient were revealed, including 4 somatic mutations in 92% (33/36) patients. In 70% (25/36), from 1 to 3 mutations with known clinical significance were found. In all patients without driver and somatic mutations (ASXL1, EZH2, etc.) and chromosomal aberrations, somatic mutations (both clinically significant and unknown clinical significance) were detected, that served as clonality confirmation. All patients were divided into two groups: 1) driver mutations, normal karyotype (16/36) (favorable prognosis) and 2) triple-negative mutational status (20/36) with additional patients having mutations in epigenetic regulators genes (4/36) (unfavorable prognosis). In the first group, NGS revealed additional mutations in 8/16 (50%) patients (ASXL1, EZH2, IDH1) and in 3/16 (19%) were noted mutations in TET2 gene. In an unfavorable group, additional mutations were also found in genes of epigenetic regulation (ASXL1, IDH1, SRSF2) and in signal transduction genes (RAS genes, PTPN11) and TET2. NGS data can confirm disease clonal nature, assess disease prognosis, and select target therapy for patients with Ph-negative myeloproliferative neoplasms. To get new information it is possible to expand the panel of sequenced genes, as well as study other genetic mechanisms underlying disease pathogenesis (e.g., changes in gene expression level, microRNAs, or transcription factors).

Integrated transcriptomic and metabolomic analyses of pak choi [Brassica pekinensis (Lour.) Rupr] response to combined stress of acid rain and cadmium-containing atmospheric fine particulate matter

Heavy metal-containing atmospheric particulate matter (PM) and acid rain (AR) trigger molecular alteration in plants, perturbing metabolites and damaging plant growth. However, the molecular mechanisms of plants under AR along with Cd-containing atmospheric fine particulate matter (PM2.5-Cd) stress remain unknown. In this study, integrated transcriptomics and metabolomics analyses of pak choi (Brassica pekinensis (Lour.) Rupr) exposed to AR (pH3.5) and PM2.5-Cd (500 μg·m−3) stress were performed. Metabolomics analyses revealed that AR-Cd stress mainly affected 42 metabolic pathways, including 451 differentially expressed metabolites (DEMs). RNA-seq identified 735 common differentially expressed genes (DEGs: 557 upregulated and 178 downregulated). Further analysis found several important DEGs (transcription factors, metabolic pathways genes, and signal transduction genes), including WRKY11, WRKY53, WRKY41, MYB73, NAC062, NAC046, HSFA4A, ABCC3, CAXs, GSTs, AZFs, PODs, PME41, CYP707A2, and CDPK32 implying that Cd chelate sequestration into the vacuoles, the antioxidant system, cell wall biosynthesis pathway, and calcium signaling play a critical role in AR damage and Cd detoxification. Conjoint revealed phenylpropanoid and flavonoid biosynthesis pathways with different metabolism patterns, including the key DEM, chlorogenic acids. The results obtained using multiple approaches provide a molecular-scale perspective on plant response to AR-Cd stress.

Interference of Dihydrocoumarin with Hormone Transduction and Phenylpropanoid Biosynthesis Inhibits Barnyardgrass (Echinochloa crus-galli) Root Growth.

Botanical compounds with herbicidal activity exhibit safety, low toxicity, and low chances of herbicide resistance development in plants. They have widespread applications in green agricultural production and the development of organic agriculture. In the present study, dihydrocoumarin showed potential as a botanical herbicide, and its phenotypic characteristics and mechanism of action were studied in barnyardgrass [Echinochloa crus-galli (L.) P.Beauv.] seedlings. The results indicated that dihydrocoumarin inhibited the growth of barnyardgrass without causing significant inhibition of rice seedling growth at concentrations ranging between 0.5 and 1.0 g/L. Additionally, dihydrocoumarin treatment could cause oxidative stress in barnyardgrass, disrupt the cell membrane, and reduce the root cell activity, resulting in root cell death. Transcriptomic analyses revealed that dihydrocoumarin could inhibit barnyardgrass normal growth by affecting the signal transduction of plant hormones. The results showed significant differential expression of plant hormone signal transduction genes in barnyardgrass. Additionally, dihydrocoumarin interfered with the expression of numerous phenylpropanoid biosynthesis genes in barnyardgrass that affect the production of various vital metabolites. We speculate that the barnyardgrass growth was suppressed by the interaction among hormones and phenylpropanoid biosynthesis genes, indicating that dihydrocoumarin can be applied as a bioherbicide to control barnyardgrass growth in rice transplanting fields.

Physiological and transcriptome analyses reveal the photosynthetic response to drought stress in drought-sensitive (Fengjiao) and drought-tolerant (Hanjiao) Zanthoxylum bungeanum cultivars.

As an important economical plant, Zanthoxylum bungeanum is widely cultivated in arid and semi-arid areas. The studies associated with photosynthesis under drought stress were widely carried out, but not yet in Z. bungeanum. Here, the photosynthesis of two Z. bungeanum cultivars (FJ, Z. bungeanum cv. “Fengjiao”; HJ, Z. bungeanum cv. “Hanjiao”) was analyzed under drought stress using physiological indicators and transcriptome data. Drought decreased stomatal aperture and stomatal conductance (Gsw), reduced transpiration rate (E) and sub-stomatal CO2 concentration (Ci), and lowered chlorophyll and carotenoid content, which reduced the net photosynthetic rate (Pn) of Z. bungeanum. The higher photosynthetic rate in HJ stemmed from its higher chlorophyll content, larger stomatal aperture and Gsw, and higher Ci. Weighted gene co-expression network analysis (WGCNA) identified several ABA signal transduction genes (PYL4, PYL9, and PYR1), LCH-encoding genes (LHCB4.3), and chlorophyll metabolism genes (CRD1, PORA, and CHLH). Additionally, seven transcription factor genes were identified as important factors regulating photosynthesis under drought conditions. In general, a photosynthetic response model under drought stress was built firstly in Z. bungeanum, and the key genes involved in photosynthesis under drought stress were identified. Therefore, the results in our research provide important information for photosynthesis under drought and provided key clues for future molecular breeding in Z. bungeanum.

Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization.

The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.