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KEY MESSAGE: A genetic linkage map representing proso millet genome was constructed with SSR markers, and a major QTL corresponding to plant height was mapped on chromosome 14 of this map. Proso millet (Panicum miliaceum L.) has the lowest water requirements of all cultivated cereal crops. However, the lack of a genetic map and the paucity of genomic resources for this species have limited the utility of proso millet for detailed genetic studies and hampered genetic improvement programs. In this study, 97,317 simple sequence repeat (SSR) markers were developed based on the genome sequence of the proso millet landrace Longmi 4. Using some of these markers in conjunction with previously identified SSRs, an SSR-based linkage map for proso millet was successfully constructed using a large mapping population (316 F2 offspring). In total, 186 SSR markers were assigned to 18 linkage groups corresponding to the haploid chromosomes. The constructed map had a total length of 3033.42 centimorgan (cM) covering 78.17% of the assembled reference genome. The length of the 18 linkage groups ranged from 88.89 cM (Chr. 15) to 274.82 cM (Chr. 16), with an average size of 168.17 cM. To our knowledge, this is the first genetic linkage map for proso millet based on SSR markers. Plant height is one of the most important traits in crop improvement. A major QTL was repeatedly detected in different environments, explaining 8.70-24.50% of the plant height variations. A candidate gene affecting auxin biosynthesis and transport, and ROS homeostasis regulation was predicted. Thus, the linkage map and QTL analysis provided herein will promote the development of gene mining and molecular breeding in proso millet.
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Panicum , Panicum/genética , Mapeo Cromosómico , Fenotipo , Repeticiones de Microsatélite , Ligamiento Genético , Genoma de PlantaRESUMEN
Pneumoconiosis is the most common occupational disease among coal miners, which is a lung disease caused by long-term inhalation of coal dust and retention in the lungs. The early stage of this disease is highly insidious, and pulmonary fibrosis may occur in the middle and late stages, leading to an increase in patient pain index and mortality rate. Currently, there is a lack of effective treatment methods. The pathogenesis of pneumoconiosis is complex and has many influencing factors. Although the characteristics of coal dust have been considered the main cause of different mechanisms of pneumoconiosis, the effects of coal dust composition, particle size and shape, and coal dust concentration on the pathogenesis of pneumoconiosis have not been systematically elucidated. Meanwhile, considering the irreversibility of pneumoconiosis progression, early prediction for pneumoconiosis patients is particularly important. However, there is no early prediction standard for pneumoconiosis among coal miners. This review summarizes the relevant research on the pathogenesis and prediction of pneumoconiosis in coal miners in recent years. Firstly, the pathogenesis of coal worker pneumoconiosis and silicosis was discussed, and the impact of coal dust characteristics on pneumoconiosis was analyzed. Then, the early diagnostic methods for pneumoconiosis have been systematically introduced, with a focus on image collaborative computer-aided diagnosis analysis and biomarker detection. Finally, the challenge of early screening technology for miners with pneumoconiosis was proposed.
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Minas de Carbón , Polvo , Humanos , Neumoconiosis , Antracosis/epidemiología , Exposición Profesional/efectos adversos , Biomarcadores , Carbón Mineral , Enfermedades Profesionales/etiología , Enfermedades Profesionales/epidemiologíaRESUMEN
Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.
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Ecosistema , Fabaceae , Suelo/química , ARN Ribosómico 16S/genética , Carbono/análisis , Conservación de los Recursos Naturales , Bacterias/genética , China , Fósforo/análisis , Potasio/análisis , Microbiología del SueloRESUMEN
BACKGROUND: The study of pathogenic mechanisms in adult asthma is often marred by a lack of precise information about the natural history of the disease. Children who have persistent wheezing (PW) during the first 6 years of life and whose symptoms start before age 3 years (PW+) are much more likely to have wheezing illnesses due to rhinovirus (RV) in infancy and to have asthma into adult life than are those who do not have PW (PW-). OBJECTIVE: Our aim was to determine whether nasal epithelial cells from PW+ asthmatic adults as compared with cells from PW- asthmatic adults show distinct biomechanistic processes activated by RV exposure. METHODS: Air-liquid interface cultures derived from nasal epithelial cells of 36-year old participants with active asthma with and without a history of PW in childhood (10 PW+ participants and 20 PW- participants) from the Tucson Children's Respiratory Study were challenged with a human RV-A strain (RV-A16) or control, and their RNA was sequenced. RESULTS: A total of 35 differentially expressed genes involved in extracellular remodeling and angiogenesis distinguished the PW+ group from the PW- group at baseline and after RV-A stimulation. Notably, 22 transcriptomic pathways showed PW-by-RV interactions; the pathways were invariably overactivated in PW+ patients, and were involved in Toll-like receptor- and cytokine-mediated responses, remodeling, and angiogenic processes. CONCLUSIONS: Asthmatic adults with a history of persistent wheeze in the first 6 years of life have specific biomolecular alterations in response to RV-A that are not present in patients without such a history. Targeting these mechanisms may slow the progression of asthma in these patients.
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Asma , Infecciones por Enterovirus , Infecciones por Picornaviridae , Adulto , Asma/diagnóstico , Niño , Preescolar , Células Epiteliales , Humanos , Fenotipo , Ruidos Respiratorios , Rhinovirus/genéticaRESUMEN
KEY MESSAGE: Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1-Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.
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Adaptación Fisiológica , Regulación de la Expresión Génica de las Plantas , Estudio de Asociación del Genoma Completo , Proteínas de Plantas/genética , Polimorfismo de Nucleótido Simple , Setaria (Planta)/fisiología , Genómica , Filogenia , Proteínas de Plantas/metabolismo , Setaria (Planta)/genéticaRESUMEN
BACKGROUND: Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet. RESULTS: In the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR. CONCLUSION: In this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance.
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Perfilación de la Expresión Génica/métodos , Panicum/crecimiento & desarrollo , Factores de Transcripción/genética , Secuenciación Completa del Genoma/métodos , Mapeo Cromosómico , Cromosomas de las Plantas/genética , Sequías , Evolución Molecular , Regulación de la Expresión Génica de las Plantas , Familia de Multigenes , Panicum/genética , Filogenia , Proteínas de Plantas/genética , Estrés FisiológicoRESUMEN
BACKGROUND: The endogenous lipid molecule sphingosine-1-phosphate (S1P) has received attention in the cardiovascular field due to its significant cardioprotective effects, as revealed in animal studies. The purpose of our study was to identify the distribution characteristics of S1P in systolic heart failure patients and the prognostic value of S1P for long-term prognosis. METHODS: We recruited 210 chronic systolic heart failure patients from June 2014 to December 2015. Meanwhile 54 healthy people in the same area were selected as controls. Plasma S1P was measured by liquid chromatography-tandem mass spectrometry. Patients were grouped according to the baseline S1P level quartiles, and restricted cubic spline plots described the association between S1P and all-cause death. Cox proportional hazard analysis was used to determine the relationship between category of S1P and all-cause death. RESULTS: Compared with the control group, the plasma S1P in chronic heart failure patients demonstrated a higher mean level (1.269 µmol/L vs 1.122 µmol/L, P = 0.006) and a larger standard deviation (0.441 vs 0.316, P = 0.022). Based on multivariable Cox regression with restricted cubic spline analysis, a non-linear and U-shaped association between S1P levels and the risk of all-cause death was observed. After a follow-up period of 31.7 ± 10.3 months, the second quartile (0.967-1.192 µml/L) with largely normal S1P levels had the lowest all-cause mortality and either an increase (adjusted HR = 2.368, 95%CI 1.006-5.572, P = 0.048) or a decrease (adjusted HR = 0.041, 95%CI 0.002-0.808, P = 0.036) predicted a worse prognosis. The survival curves showed that patients in the lowest quartile and highest quartile were at a higher risk of death. CONCLUSIONS: Plasma S1P levels in systolic heart failure patients are related to the long-term all-cause mortality with a U-shaped correlation. TRIAL REGISTRATION: CHiCTR, ChiCTR-ONC-14004463. Registered 20 March 2014.
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Insuficiencia Cardíaca Sistólica/sangre , Insuficiencia Cardíaca Sistólica/mortalidad , Lisofosfolípidos/sangre , Esfingosina/análogos & derivados , Adulto , Anciano , Causas de Muerte , Estudios de Cohortes , Femenino , Humanos , Masculino , Persona de Mediana Edad , Pronóstico , Modelos de Riesgos Proporcionales , Estudios Prospectivos , Esfingosina/sangreRESUMEN
Premature and incomplete drug release is the typical bottleneck of drug release in traditional chemotherapy. Synergistic therapies are highly desirable in medicine and biology because they can compensate for the drawbacks of single therapy and significantly enhance the therapeutic efficacy. Herein, a novel near infrared (NIR)-activated polymeric nanoplatform with upper critical solution temperature (UCST) was constructed for image-guided synergistic photothermal therapy (PTT) and chemotherapy. UCST-responsive amphiphilic block copolymers were synthesized by reversible addition-fragmentation chain-transfer (RAFT) polymerization and then co-assembled with IR780 and cabazitaxel (Cab) to form spherical nanoparticles (NPs). IR780/Cab dual-loaded UCST polymeric NPs can produce local heating upon NIR laser irradiation and further lead to the dissociation of cargo-loaded NPs and controlled release of Cab. IR780 plays the role of both a heating generator and an activator for "on-demand" drug release. The investigation of in vivo fluorescence and photothermal imaging clearly demonstrated tumor targeting. Notably, both in vitro and in vivo studies illustrated that the synergistic PTT and chemotherapy presented better anticancer efficacy than that of PTT and chemotherapy simplely combined. Thus, the well-defined polymeric nanoplatform opens a versatile and effective path to develop image-guided synergistic therapies for tumor treatment.
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Hipertermia Inducida , Indoles , Rayos Infrarrojos , Neoplasias Mamarias Experimentales/terapia , Nanopartículas , Fototerapia , Animales , Línea Celular Tumoral , Femenino , Indoles/química , Indoles/farmacología , Neoplasias Mamarias Experimentales/patología , Ratones , Ratones Endogámicos BALB C , Nanopartículas/química , Nanopartículas/uso terapéuticoRESUMEN
MOTIVATION: As 'omics' biotechnologies accelerate the capability to contrast a myriad of molecular measurements from a single cell, they also exacerbate current analytical limitations for detecting meaningful single-cell dysregulations. Moreover, mRNA expression alone lacks functional interpretation, limiting opportunities for translation of single-cell transcriptomic insights to precision medicine. Lastly, most single-cell RNA-sequencing analytic approaches are not designed to investigate small populations of cells such as circulating tumor cells shed from solid tumors and isolated from patient blood samples. RESULTS: In response to these characteristics and limitations in current single-cell RNA-sequencing methodology, we introduce an analytic framework that models transcriptome dynamics through the analysis of aggregated cell-cell statistical distances within biomolecular pathways. Cell-cell statistical distances are calculated from pathway mRNA fold changes between two cells. Within an elaborate case study of circulating tumor cells derived from prostate cancer patients, we develop analytic methods of aggregated distances to identify five differentially expressed pathways associated to therapeutic resistance. Our aggregation analyses perform comparably with Gene Set Enrichment Analysis and better than differentially expressed genes followed by gene set enrichment. However, these methods were not designed to inform on differential pathway expression for a single cell. As such, our framework culminates with the novel aggregation method, cell-centric statistics (CCS). CCS quantifies the effect size and significance of differentially expressed pathways for a single cell of interest. Improved rose plots of differentially expressed pathways in each cell highlight the utility of CCS for therapeutic decision-making. AVAILABILITY AND IMPLEMENTATION: http://www.lussierlab.org/publications/CCS/ CONTACT: yves@email.arizona.edu or piegorsch@math.arizona.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Resistencia a Antineoplásicos , Células Neoplásicas Circulantes/efectos de los fármacos , Análisis de Secuencia de ARN , Transcriptoma , Perfilación de la Expresión Génica , Humanos , Masculino , Neoplasias de la Próstata/tratamiento farmacológico , ARNRESUMEN
MOTIVATION: Understanding dynamic, patient-level transcriptomic response to therapy is an important step forward for precision medicine. However, conventional transcriptome analysis aims to discover cohort-level change, lacking the capacity to unveil patient-specific response to therapy. To address this gap, we previously developed two N-of-1-pathways methods, Wilcoxon and Mahalanobis distance, to detect unidirectionally responsive transcripts within a pathway using a pair of samples from a single subject. Yet, these methods cannot recognize bidirectionally (up and down) responsive pathways. Further, our previous approaches have not been assessed in presence of background noise and are not designed to identify differentially expressed mRNAs between two samples of a patient taken in different contexts (e.g. cancer vs non cancer), which we termed responsive transcripts (RTs). METHODS: We propose a new N-of-1-pathways method, k-Means Enrichment (kMEn), that detects bidirectionally responsive pathways, despite background noise, using a pair of transcriptomes from a single patient. kMEn identifies transcripts responsive to the stimulus through k-means clustering and then tests for an over-representation of the responsive genes within each pathway. The pathways identified by kMEn are mechanistically interpretable pathways significantly responding to a stimulus. RESULTS: In â¼9000 simulations varying six parameters, superior performance of kMEn over previous single-subject methods is evident by: (i) improved precision-recall at various levels of bidirectional response and (ii) lower rates of false positives (1-specificity) when more than 10% of genes in the genome are differentially expressed (background noise). In a clinical proof-of-concept, personal treatment-specific pathways identified by kMEn correlate with therapeutic response (p-value<0.01). CONCLUSION: Through improved single-subject transcriptome dynamics of bidirectionally-regulated signals, kMEn provides a novel approach to identify mechanism-level biomarkers.
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Perfilación de la Expresión Génica , Medicina de Precisión , Transcriptoma , Análisis por Conglomerados , Interpretación Estadística de Datos , Humanos , ARN MensajeroRESUMEN
MOTIVATION: The conventional approach to personalized medicine relies on molecular data analytics across multiple patients. The path to precision medicine lies with molecular data analytics that can discover interpretable single-subject signals (N-of-1). We developed a global framework, N-of-1-pathways, for a mechanistic-anchored approach to single-subject gene expression data analysis. We previously employed a metric that could prioritize the statistical significance of a deregulated pathway in single subjects, however, it lacked in quantitative interpretability (e.g. the equivalent to a gene expression fold-change). RESULTS: In this study, we extend our previous approach with the application of statistical Mahalanobis distance (MD) to quantify personal pathway-level deregulation. We demonstrate that this approach, N-of-1-pathways Paired Samples MD (N-OF-1-PATHWAYS-MD), detects deregulated pathways (empirical simulations), while not inflating false-positive rate using a study with biological replicates. Finally, we establish that N-OF-1-PATHWAYS-MD scores are, biologically significant, clinically relevant and are predictive of breast cancer survival (P < 0.05, n = 80 invasive carcinoma; TCGA RNA-sequences). CONCLUSION: N-of-1-pathways MD provides a practical approach towards precision medicine. The method generates the magnitude and the biological significance of personal deregulated pathways results derived solely from the patient's transcriptome. These pathways offer the opportunities for deriving clinically actionable decisions that have the potential to complement the clinical interpretability of personal polymorphisms obtained from DNA acquired or inherited polymorphisms and mutations. In addition, it offers an opportunity for applicability to diseases in which DNA changes may not be relevant, and thus expand the 'interpretable 'omics' of single subjects (e.g. personalome). AVAILABILITY AND IMPLEMENTATION: http://www.lussierlab.net/publications/N-of-1-pathways.
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Neoplasias de la Mama/mortalidad , Perfilación de la Expresión Génica/métodos , Análisis de Secuencia de ARN/métodos , Neoplasias de la Mama/genética , Neoplasias de la Mama/metabolismo , Interpretación Estadística de Datos , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Estimación de Kaplan-Meier , Medicina de PrecisiónRESUMEN
The causal and interplay mechanisms of Single Nucleotide Polymorphisms (SNPs) associated with complex diseases (complex disease SNPs) investigated in genome-wide association studies (GWAS) at the transcriptional level (mRNA) are poorly understood despite recent advancements such as discoveries reported in the Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTex). Protein interaction network analyses have successfully improved our understanding of both single gene diseases (Mendelian diseases) and complex diseases. Whether the mRNAs downstream of complex disease genes are central or peripheral in the genetic information flow relating DNA to mRNA remains unclear and may be disease-specific. Using expression Quantitative Trait Loci (eQTL) that provide DNA to mRNA associations and network centrality metrics, we hypothesize that we can unveil the systems properties of information flow between SNPs and the transcriptomes of complex diseases. We compare different conditions such as naïve SNP assignments and stringent linkage disequilibrium (LD) free assignments for transcripts to remove confounders from LD. Additionally, we compare the results from eQTL networks between lymphoblastoid cell lines and liver tissue. Empirical permutation resampling (p<0.001) and theoretic Mann-Whitney U test (p<10(-30)) statistics indicate that mRNAs corresponding to complex disease SNPs via eQTL associations are likely to be regulated by a larger number of SNPs than expected. We name this novel property mRNA hubness in eQTL networks, and further term mRNAs with high hubness as master integrators. mRNA master integrators receive and coordinate the perturbation signals from large numbers of polymorphisms and respond to the personal genetic architecture integratively. This genetic signal integration contrasts with the mechanism underlying some Mendelian diseases, where a genetic polymorphism affecting a single protein hub produces a divergent signal that affects a large number of downstream proteins. Indeed, we verify that this property is independent of the hubness in protein networks for which these mRNAs are transcribed. Our findings provide novel insights into the pleiotropy of mRNAs targeted by complex disease polymorphisms and the architecture of the information flow between the genetic polymorphisms and transcriptomes of complex diseases.
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Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , ARN Mensajero/genética , HumanosRESUMEN
RATIONALE: Lysocardiolipin acyltransferase (LYCAT), a cardiolipin-remodeling enzyme regulating the 18:2 linoleic acid pattern of mammalian mitochondrial cardiolipin, is necessary for maintaining normal mitochondrial function and vascular development. We hypothesized that modulation of LYCAT expression in lung epithelium regulates development of pulmonary fibrosis. OBJECTIVES: To define a role for LYCAT in human and murine models of pulmonary fibrosis. METHODS: We analyzed the correlation of LYCAT expression in peripheral blood mononuclear cells (PBMCs) with the outcomes of pulmonary functions and overall survival, and used the murine models to establish the role of LYCAT in fibrogenesis. We studied the LYCAT action on cardiolipin remodeling, mitochondrial reactive oxygen species generation, and apoptosis of alveolar epithelial cells under bleomycin challenge. MEASUREMENTS AND MAIN RESULTS: LYCAT expression was significantly altered in PBMCs and lung tissues from patients with idiopathic pulmonary fibrosis (IPF), which was confirmed in two preclinical murine models of IPF, bleomycin- and radiation-induced pulmonary fibrosis. LYCAT mRNA expression in PBMCs directly and significantly correlated with carbon monoxide diffusion capacity, pulmonary function outcomes, and overall survival. In both bleomycin- and radiation-induced pulmonary fibrosis murine models, hLYCAT overexpression reduced several indices of lung fibrosis, whereas down-regulation of native LYCAT expression by siRNA accentuated fibrogenesis. In vitro studies demonstrated that LYCAT modulated bleomycin-induced cardiolipin remodeling, mitochondrial membrane potential, reactive oxygen species generation, and apoptosis of alveolar epithelial cells, potential mechanisms of LYCAT-mediated lung protection. CONCLUSIONS: This study is the first to identify modulation of LYCAT expression in fibrotic lungs and offers a novel therapeutic approach for ameliorating lung inflammation and pulmonary fibrosis.
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1-Acilglicerol-3-Fosfato O-Aciltransferasa/genética , Aciltransferasas/genética , Mitocondrias/genética , Fibrosis Pulmonar/diagnóstico , Fibrosis Pulmonar/genética , Animales , Biomarcadores/metabolismo , Cardiolipinas/genética , Estudios de Cohortes , Modelos Animales de Enfermedad , Humanos , Fibrosis Pulmonar Idiopática/diagnóstico , Fibrosis Pulmonar Idiopática/genética , Hibridación in Situ , Leucocitos Mononucleares/metabolismo , Ratones , Mitocondrias/metabolismo , Valor Predictivo de las Pruebas , Fibrosis Pulmonar/enzimología , ARN Mensajero/metabolismo , Sensibilidad y Especificidad , Índice de Severidad de la EnfermedadRESUMEN
In this study, hydrochars were prepared at varying temperatures with distinct mixing ratio, and then the hydrochars were characterized and evaluated for heavy metals to ascertain its potential as a soil conditioner. The application of elevated temperatures resulted in a reduction in the yield of hydrochars, whereas the incorporation of coffee grounds led to an increase in the yield. The blended hydrochar displays elevated ash, fixed carbon, and diminished H/C, O/C, and (O + N)/C ratios, indicating enhanced stability in soil treatment and potential for enhanced soil fertility. The application of hydrothermal carbonization facilitated the stabilization of heavy metals within the sewage sludge, with the stabilizing effect being enhanced by the addition of coffee grounds. Following the application of SCC as a soil conditioner to the heavy metal-contaminated soil for a period of 90 days, it was observed that the heavy metals Cu, Cr, and Ni present in the contaminated soil underwent a transition from an unstable to a stable speciation. Of the treatments tested, AK15 was identified as the most effective, demonstrating a significant reduction in the risk of leaching and biotoxicity associated with Cu, Cr, and Ni in the contaminated soil.
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Cuticular waxes of plants impart tolerance to many forms of environmental stress and help shed dangerous human pathogens on edible plant parts. Although the chemical composition of waxes on a wide variety of important crops has been described, a detailed wax compositional analysis has yet to be reported for lettuce (Lactuca sativa L.), one of the most widely consumed vegetables. We present herein the leaf wax content and composition of 12 genetically diverse lettuce cultivars sampled across five time points during their vegetative growth phase in the field. Mean total leaf wax amounts across all cultivars varied little over 28 days of vegetative growth, except for a notable decrease in total waxes following a major precipitation event, presumably due to wax degradation from wind and rain. All lettuce cultivars were found to contain a unique wax composition highly enriched in 22- and 24-carbon length 1-alcohols (docosanol and tetracosanol, respectively). In our report, the dominance of these shorter chain length 1-alcohols as wax constituents represents a relatively rare phenotype in plants. The ecological significance of these dominant and relatively short 1-alcohols is still unknown. Although waxes have been a target for improvement of various crops, no such work has been reported for lettuce. This study lays the groundwork for future research that aims to integrate cuticular wax characteristics of field grown plants into the larger context of lettuce breeding and cultivar development.
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Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.
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Productos Agrícolas , Variación Genética , Genoma de Planta , Estudio de Asociación del Genoma Completo , Desequilibrio de Ligamiento , Productos Agrícolas/genética , Panicum/genética , Fenotipo , Sitios de Carácter Cuantitativo , Polimorfismo de Nucleótido Simple , Domesticación , Genómica/métodos , FitomejoramientoRESUMEN
BACKGROUND: The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. RESULTS: GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. CONCLUSIONS: Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.
Asunto(s)
Genoma de Planta , Setaria (Planta)/genética , Mapeo Cromosómico , Cromosomas de las Plantas , ADN de Plantas/genética , ADN Ribosómico/genética , Diploidia , Genómica/métodos , Proteínas de Homeodominio/genética , Hibridación in Situ/métodos , Filogenia , Proteínas de Plantas/genética , Poliploidía , Setaria (Planta)/clasificaciónRESUMEN
Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet.