Drought-Induced Root Pressure in Sorghum bicolor

Root pressure, also manifested as profusive sap flowing from cut stems, is a phenomenon in some species that has perplexed biologists for much of the last century. It is associated with increased crop production under drought, but its function and regulation remain largely unknown. In this study, we investigated the initiation, mechanisms, and possible adaptive function of root pressure in six genotypes of Sorghum bicolor during a drought experiment in the greenhouse. We observed that root pressure was induced in plants exposed to drought followed by re-watering but possibly inhibited by 100% re-watering in some genotypes. We found that root pressure in drought stressed and re-watered plants was associated with greater ratio of fine: coarse root length and shoot biomass production, indicating a possible role of root allocation in creating root pressure and adaptive benefit of root pressure for shoot biomass production. Using RNA-Seq, we identified gene transcripts that were up- and down-regulated in plants with root pressure expression, focusing on genes for aquaporins, membrane transporters, and ATPases that could regulate inter- and intra-cellular transport of water and ions to generate positive xylem pressure in root tissue.

Download Full-text

Potensi Produksi dan Mutu Benih serta Produksi Biomassa Sorghum bicolor Varietas Samurai 2 pada Umur Panen Berbeda sebagai Bahan Pakan

Jurnal Ilmu Nutrisi dan Teknologi Pakan ◽

10.29244/jintp.19.3.78-84 ◽

2021 ◽

Vol 19 (3) ◽

pp. 78-84

Author(s):

A Najam ◽

L Abdullah ◽

Panca dewi manu hara Karti ◽

S Hoeman

Keyword(s):

Sorghum Bicolor ◽

Seed Production ◽

Biomass Production ◽

Dry Matter ◽

Seed Viability ◽

Dry Weight ◽

Shoot Biomass ◽

Seed Moisture Content ◽

Seed Moisture ◽

Panicle Weight

Sorghum bicolor var. Samurai 2 can be used as raw material in silage production for ruminant feed. The problem encountered is the difficulty of obtaining certified seeds for commercial sorghum production. So that is necessary to do this research to investigate potential sorghum seed production and its quality of Sorghum bicolor var. Samurai 2. The study was conducted at University Research Station-Jonggol Animal Education and Research Unit, Bogor Agricultural University. The experimental design used was a randomized block design with 4 treatments and 5 replicates. Five individual plants were taken to measure the variables at each treatment set. The treatments consisted of different harvesting times, namely P95 (harvested 95 days after planting), P100, P105 and P110. The variables observed were dry weight of shelled seeds, seed weight per panicle, weight of panicle stalk, panicle weight, seed production per ha, seed moisture content, seed viability test, and shoot biomass production per ha. The results showed that seed production per ha, panicle dry matter weight, fresh seed moisture content, panicle stalk dry weight was not significantly different. Dry weight of shelled seeds, dry weight of seeds per panicle, panicle dry weight, seed viability, weight of biomass per ha were significantly different (p<0.05). The potential for the production of shelled seeds, dry matter of seeds per panicle was the best in the P105 and P110, the viability of the seeds in the P105 and shoot biomass production per ha in the P105. The potential for shelled seed production (4038 kg ha-1), seed dry weight per panicle (54.87 g panicle-1), seed viability (92.8%) and the best biomass production (55.88 tons ha-1) were in treatment P105. Key words: seed production, shoot biomass, Sorghum bicolor, viability

Download Full-text

Transcriptome Response of Metallicolous and a Non-Metallicolous Ecotypes of Noccaea goesingensis to Nickel Excess

Plants ◽

10.3390/plants9080951 ◽

2020 ◽

Vol 9 (8) ◽

pp. 951

Author(s):

Agnieszka Domka ◽

Piotr Rozpądek ◽

Rafał Ważny ◽

Roman Jan Jędrzejczyk ◽

Magdalena Hubalewska-Mazgaj ◽

...

Keyword(s):

Culture Medium ◽

Shoot Biomass ◽

Nickel Concentration ◽

Rna Seq ◽

Metal Transporters ◽

Expression Of Genes ◽

Starting Point ◽

Accumulation Capacity ◽

Transcriptome Response

Root transcriptomic profile was comparatively studied in a serpentine (TM) and a non-metallicolous (NTM) population of Noccaea goesingensis in order to investigate possible features of Ni hyperaccumulation. Both populations were characterised by contrasting Ni tolerance and accumulation capacity. The growth of the TM population was unaffected by metal excess, while the shoot biomass production in the NTM population was significantly lower in the presence of Ni in the culture medium. Nickel concentration was nearly six- and two-fold higher in the shoots than in the roots of the TM and NTM population, respectively. The comparison of root transcriptomes using the RNA-seq method indicated distinct responses to Ni treatment between tested ecotypes. Among differentially expressed genes, the expression of IRT1 and IRT2, encoding metal transporters, was upregulated in the TM population and downregulated/unchanged in the NTM ecotype. Furthermore, differences were observed among ethylene metabolism and response related genes. In the TM population, the expression of genes including ACS7, ACO5, ERF104 and ERF105 was upregulated, while in the NTM population, expression of these genes remained unchanged, thus suggesting a possible regulatory role of this hormone in Ni hyperaccumulation. The present results could serve as a starting point for further studies concerning the plant mechanisms responsible for Ni tolerance and accumulation.

Download Full-text

Compartmentalization of mRNAs in the giant, unicellular green algae Acetabularia acetabulum

10.1101/2020.09.18.303206 ◽

2020 ◽

Author(s):

Ina J. Andresen ◽

Russell J. S. Orr ◽

Kamran Shalchian-Tabrizi ◽

Jon Bråte

Keyword(s):

Cell Biology ◽

Intracellular Transport ◽

Rna Seq ◽

Acetabularia Acetabulum ◽

Its Gene ◽

Mrna Content ◽

Gene Transcripts ◽

Single Nucleus ◽

Post Transcriptional Regulation

AbstractAcetabularia acetabulum is a single-celled green alga previously used as a model species for studying the role of the nucleus in cell development and morphogenesis. The highly elongated cell, which stretches several centimeters, harbors a single nucleus located in the basal end. Although A. acetabulum historically has been an important model in cell biology, almost nothing is known about its gene content, or how gene products are distributed in the cell. To study the composition and distribution of mRNAs in A. acetabulum, we have used quantitative RNA-seq to sequence the mRNA content of four sections of adult A. acetabulum cells. We found that although mRNAs are present throughout the cell, there are large pools of distinct mRNAs localized to the different subcellular sections. Conversely, we also find that gene transcripts related to intracellular transport are evenly distributed throughout the cell. This distribution hints at post-transcriptional regulation and selective transport of mRNAs as mechanisms to achieve mRNA localization in A. acetabulum.

Download Full-text

Type III Collagen is Required for Adipogenesis and Actin Stress Fibre Formation in 3T3-L1 Preadipocytes

Biomolecules ◽

10.3390/biom11020156 ◽

2021 ◽

Vol 11 (2) ◽

pp. 156

Author(s):

Mohammad Al Hasan ◽

Patricia E. Martin ◽

Xinhua Shu ◽

Steven Patterson ◽

Chris Bartholomew

Keyword(s):

Quantitative Polymerase Chain Reaction ◽

Type Iii Collagen ◽

Type Iii ◽

Actin Stress Fibre ◽

Matrix Gene ◽

Gene Transcripts ◽

Polymerase Chain ◽

Oil Red O Staining ◽

Oil Red O

GPR56 is required for the adipogenesis of preadipocytes, and the role of one of its ligands, type III collagen (ColIII), was investigated here. ColIII expression was examined by reverse transcription quantitative polymerase chain reaction, immunoblotting and immunostaining, and its function investigated by knockdown and genome editing in 3T3-L1 cells. Adipogenesis was assessed by oil red O staining of neutral cell lipids and production of established marker and regulator proteins. siRNA-mediated knockdown significantly reduced Col3a1 transcripts, ColIII protein and lipid accumulation in 3T3-L1 differentiating cells. Col3a1−/− 3T3-L1 genome-edited cell lines abolished adipogenesis, demonstrated by a dramatic reduction in adipogenic moderators: Pparγ2 (88%) and C/ebpα (96%) as well as markers aP2 (93%) and oil red O staining (80%). Col3a1−/− 3T3-L1 cells displayed reduced cell adhesion, sustained active β-catenin and deregulation of fibronectin (Fn) and collagen (Col4a1, Col6a1) extracellular matrix gene transcripts. Col3a1−/− 3T3-L1 cells also had dramatically reduced actin stress fibres. We conclude that ColIII is required for 3T3-L1 preadipocyte adipogenesis as well as the formation of actin stress fibres. The phenotype of Col3a1−/− 3T3-L1 cells is very similar to that of Gpr56−/− 3T3-L1 cells, suggesting a functional relationship between ColIII and Gpr56 in preadipocytes.

Download Full-text

DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

Clinical Epigenetics ◽

10.1186/s13148-020-00957-8 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Monica del C. Gomez-Alonso ◽

Anja Kretschmer ◽

Rory Wilson ◽

Liliane Pfeiffer ◽

Ville Karhunen ◽

...

Keyword(s):

Dna Methylation ◽

Lipid Metabolism ◽

Population Based ◽

Total Serum ◽

Resonance Spectroscopy ◽

Metabolic Disturbances ◽

Cpg Sites ◽

Gene Transcripts

Abstract Background The discovery of robust and trans-ethnically replicated DNA methylation markers of metabolic phenotypes, has hinted at a potential role of epigenetic mechanisms in lipid metabolism. However, DNA methylation and the lipid compositions and lipid concentrations of lipoprotein sizes have been scarcely studied. Here, we present an epigenome-wide association study (EWAS) (N = 5414 total) of mostly lipid-related metabolic measures, including a fine profiling of lipoproteins. As lipoproteins are the main players in the different stages of lipid metabolism, examination of epigenetic markers of detailed lipoprotein features might improve the diagnosis, prognosis, and treatment of metabolic disturbances. Results We conducted an EWAS of leukocyte DNA methylation and 226 metabolic measurements determined by nuclear magnetic resonance spectroscopy in the population-based KORA F4 study (N = 1662) and replicated the results in the LOLIPOP, NFBC1966, and YFS cohorts (N = 3752). Follow-up analyses in the discovery cohort included investigations into gene transcripts, metabolic-measure ratios for pathway analysis, and disease endpoints. We identified 161 associations (p value < 4.7 × 10−10), covering 16 CpG sites at 11 loci and 57 metabolic measures. Identified metabolic measures were primarily medium and small lipoproteins, and fatty acids. For apolipoprotein B-containing lipoproteins, the associations mainly involved triglyceride composition and concentrations of cholesterol esters, triglycerides, free cholesterol, and phospholipids. All associations for HDL lipoproteins involved triglyceride measures only. Associated metabolic measure ratios, proxies of enzymatic activity, highlight amino acid, glucose, and lipid pathways as being potentially epigenetically implicated. Five CpG sites in four genes were associated with differential expression of transcripts in blood or adipose tissue. CpG sites in ABCG1 and PHGDH showed associations with metabolic measures, gene transcription, and metabolic measure ratios and were additionally linked to obesity or previous myocardial infarction, extending previously reported observations. Conclusion Our study provides evidence of a link between DNA methylation and the lipid compositions and lipid concentrations of different lipoprotein size subclasses, thus offering in-depth insights into well-known associations of DNA methylation with total serum lipids. The results support detailed profiling of lipid metabolism to improve the molecular understanding of dyslipidemia and related disease mechanisms.

Download Full-text

FOXO1 mitigates the SMAD3/FOXL2C134W transcriptomic effect in a model of human adult granulosa cell tumor

Journal of Translational Medicine ◽

10.1186/s12967-021-02754-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Christian Secchi ◽

Paola Benaglio ◽

Francesca Mulas ◽

Martina Belli ◽

Dwayne Stupack ◽

...

Keyword(s):

Granulosa Cell ◽

Chromatin Remodeling ◽

Granulosa Cell Tumor ◽

Cell Tumor ◽

Rna Seq ◽

Pathogenic Role ◽

Rare Type ◽

Cellular Models ◽

Genome Wide

Abstract Background Adult granulosa cell tumor (aGCT) is a rare type of stromal cell malignant cancer of the ovary characterized by elevated estrogen levels. aGCTs ubiquitously harbor a somatic mutation in FOXL2 gene, Cys134Trp (c.402C < G); however, the general molecular effect of this mutation and its putative pathogenic role in aGCT tumorigenesis is not completely understood. We previously studied the role of FOXL2C134W, its partner SMAD3 and its antagonist FOXO1 in cellular models of aGCT. Methods In this work, seeking more comprehensive profiling of FOXL2C134W transcriptomic effects, we performed an RNA-seq analysis comparing the effect of FOXL2WT/SMAD3 and FOXL2C134W/SMAD3 overexpression in an established human GC line (HGrC1), which is not luteinized, and bears normal alleles of FOXL2. Results Our data shows that FOXL2C134W/SMAD3 overexpression alters the expression of 717 genes. These genes include known and novel FOXL2 targets (TGFB2, SMARCA4, HSPG2, MKI67, NFKBIA) and are enriched for neoplastic pathways (Proteoglycans in Cancer, Chromatin remodeling, Apoptosis, Tissue Morphogenesis, Tyrosine Kinase Receptors). We additionally expressed the FOXL2 antagonistic Forkhead protein, FOXO1. Surprisingly, overexpression of FOXO1 mitigated 40% of the altered genome-wide effects specifically related to FOXL2C134W, suggesting it can be a new target for aGCT treatment. Conclusions Our transcriptomic data provide novel insights into potential genes (FOXO1 regulated) that could be used as biomarkers of efficacy in aGCT patients.

Download Full-text

Targeting HSPA1A in ARID2-deficient lung adenocarcinoma

National Science Review ◽

10.1093/nsr/nwab014 ◽

2021 ◽

Author(s):

Xue Wang ◽

Yuetong Wang ◽

Zhaoyuan Fang ◽

Hua Wang ◽

Jian Zhang ◽

...

Keyword(s):

Lung Cancer ◽

Lung Adenocarcinoma ◽

Genetically Engineered ◽

Malignant Progression ◽

Murine Models ◽

Rna Seq ◽

Potential Therapeutic Target ◽

Lung Cancers ◽

Integrative Analyses

Abstract Somatic mutations of the chromatin remodeling gene ARID2 are observed in about 7% of human lung adenocarcinoma (LUAD). However, the role of ARID2 in the pathogenesis of LUAD remains largely unknown. Here we find that ARID2 expression is decreased during the malignant progression of both human and mice LUAD. Using two KrasG12D-based genetically engineered murine models (GEMM), we demonstrate that ARID2 knockout significantly promotes lung cancer malignant progression and shortens the overall survival. Consistently, ARID2 knockdown significantly promotes cell proliferation in human and mice lung cancer cells. Through integrative analyses of Chip-Seq and RNA-Seq data, we find that Hspa1a is up-regulated by Arid2 loss. Knockdown of Hspa1a specifically inhibits malignant progression of Arid2-deficient but not Arid2-wt lung cancers in both cell lines as well as animal models. Treatment with Hspa1a inhibitor could significantly inhibit the malignant progression of lung cancer with Arid2 deficiency. Together, our findings establish ARID2 as an important tumor suppressor in LUAD with novel mechanistic insights, and further identify HSPA1A as a potential therapeutic target in ARID2-deficient LUAD.

Download Full-text

MBRS-17. EXAMINING THE ROLE OF LHX9 IN GROUP 3 MEDULLOBLASTOMA

Neuro-Oncology ◽

10.1093/neuonc/noaa222.533 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii401-iii401

Author(s):

Sarah Injac ◽

L Frank Huang ◽

Stephen Mack ◽

Frank Braun ◽

Yuchen Du ◽

...

Keyword(s):

Drug Repositioning ◽

Single Agent ◽

Xenograft Model ◽

Cell Killing ◽

Rna Seq ◽

Loss Of Function ◽

Novel Treatments ◽

Novel Approach ◽

Group 3

Abstract Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Despite major advances in our understanding of the biology of MB, novel treatments remain urgently needed. Using a chemical-genomics driven drug repositioning strategy, we identified the cardiac glycoside family of compounds as potential treatments for Group 3 MB. We subsequently demonstrated that single-agent treatment with digoxin prolongs survival in a patient-derived xenograft model (PDOX) of Group 3 MB to a degree comparable to radiation therapy, a mainstay in the treatment of MB. Finally, we examined the mechanism of digoxin-mediated cell killing using RNA-seq. This work identified LHX9, a member of the LIM homeobox family of transcription factors, as the gene most significantly down-regulated following treatment (Huang and Injac et al, Sci Trans Medicine, 2018). Homologs of LHX9 play key roles in cerebellar development via spatially and temporally restricted expression and LHX9 has been proposed as a core transcription factor (TF) in the regulatory circuitry of Group 3 tumors. Loss of function of other core TFs has been shown to impact MB growth. The role of LHX9 in MB, however, has not been previously experimentally evaluated. We now report that knockdown of LHX9 in MB-derived cell lines results in marked growth inhibition raising the possibility that loss of LHX9 plays a major role in digoxin-mediated cell killing and that LHX9 represents a key dependency required for the growth of Group 3 MB. Clinical targeting of core TFs would represent a novel approach to targeting this devastating disease.

Download Full-text