Microgreens have been used for raw consumption and are generally viewed as healthy food. This study aimed to optimize the yield parameters, shelf life, sensory evaluation and characterization of ...total aerobic bacteria (TAB), yeast and mold (Y&M), Escherichia coli, Salmonella spp., and Listeria spp. incidence in mungbean (Vigna radiata (L.) Wilczek), lentil (Lens culinaris Medikus subsp. culinaris), and Indian mustard (Brassica juncea (L.) Czern & Coss.) microgreens. In mungbean and lentil, seeding-density of three seed/cm2, while in Indian mustard, eight seed/cm2 were recorded as optimum. The optimal time to harvest mungbean, Indian mustard, and lentil microgreens were found as 7th, 8th, and 9th day after sowing, respectively. Interestingly, seed size was found highly correlated with the overall yield in both mungbeans (r2 = .73) and lentils (r2 = .78), whereas no such relationship has been recorded for Indian mustard microgreens. The target pathogenic bacteria such as Salmonella spp. and Listeria spp. were not detected; while TAB, Y&M, Shigella spp., and E. coli were recorded well within the limit to cause any human illness in the studied microgreens. Washing with double distilled water for two minutes has shown some reduction in the overall microbial load of these microgreens. The results provided evidence that microgreens if grown and stored properly, are generally safe for human consumption. This is the first study from India on the safety of mungbean, lentils, and Indian mustard microgreens.
Micro RNAs (miRNAs) are involved in diverse biological processes including adaptive response towards abiotic stresses. To unravel small RNAs and more specifically miRNAs that can potentially regulate ...determinants of abiotic stress tolerance, next generation sequencing of B. juncea seedlings subjected to high temperature, high salt and drought conditions was carried out. With the help of UEA sRNA workbench software package, 51 conserved miRNAs belonging to 30 miRNA families were identified. As there was limited genomic information available for B. juncea, we generated and assembled its genome sequence at a low coverage. Using the generated sequence and other publically available Brassica genomic/transcriptomic resources as mapping reference, 126 novel (not reported in any plant species) were discovered for the first time in B. juncea. Further analysis also revealed existence of 32 and 37 star sequences for conserved and novel miRNAs, respectively. The expression of selected conserved and novel miRNAs under conditions of different abiotic stresses was revalidated through universal TaqMan based real time PCR. Putative targets of identified conserved and novel miRNAs were predicted in B. rapa to gain insights into functional roles manifested by B. juncea miRNAs. Furthermore, SPL2-like, ARF17-like and a NAC domain containing protein were experimentally validated as targets of miR156, miR160 and miR164 respectively. Investigation of gene ontologies linked with targets of known and novel miRNAs forecasted their involvement in various biological functions.
Coleoptile is the small conical, short-lived, sheath-like organ that safeguards the first leaf and shoot apex in cereals. It is also the first leaf-like organ to senesce that provides nutrition to ...the developing shoot and is, therefore, believed to play a crucial role in seedling establishment in rice and other grasses. Though histochemical studies have helped in understanding the pattern of cell death in senescing rice coleoptiles, genome-wide expression changes during coleoptile senescence have not yet been explored. With an aim to investigate the gene regulation underlying the coleoptile senescence (CS), we performed a combinatorial whole genome expression analysis by sequencing transcriptome and miRNAome of senescing coleoptiles. Transcriptome analysis revealed extensive reprogramming of 3439 genes belonging to several categories, the most prominent of which encoded for transporters, transcription factors (TFs), signaling components, cell wall organization enzymes, redox homeostasis, stress response and hormone metabolism. Small RNA sequencing identified 41 known and 21 novel miRNAs that were differentially expressed during CS. Comparison of gene expression and miRNA profiles generated for CS with publicly available leaf senescence (LS) datasets revealed that the two aging programs are remarkably distinct at molecular level in rice. Integration of expression data of transcriptome and miRNAome identified high confidence 140 miRNA-mRNA pairs forming 42 modules, thereby demonstrating multi-tiered regulation of CS. The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.
Abstract
Diffuse Midline Glioma (DMG) is a highly aggressive form of brainstem cancer that primarily affects children, leading to a grim prognosis and limited treatment options. Despite extensive ...research efforts, many crucial aspects of DMG development and progression remain poorly understood. One significant knowledge gap lies in comprehending the invasive nature of DMG cells, which enables their escape from the primary tumor site and dissemination to other regions of the brain. Additionally, understanding the molecular basis that drives this invasive behavior is essential but remains largely unexplored, necessitating further investigation. To address these critical knowledge gaps, we have generated one of the largest single-cell multi-omic datasets ( >300,000 cells) specifically focusing on pons development in humans and its relation to DMG. This dataset provides a valuable resource for investigating the intricacies of tumorigenesis and the development of resistance to radiation therapy. Comprehensive analyses of this dataset shed light on the molecular events driving DMG progression and radiation resistance, ultimately paving the way for the discovery of novel therapeutic targets and the development of innovative strategies to combat this devastating pediatric cancer. In summary, our study aims to deepen our understanding of DMG by elucidating the mechanisms associated with histone mutations, unraveling the invasive behavior of DMG cells, and exploring the factors contributing to radiation resistance. Through these endeavors, we hope to make significant advancements in the field and improve the outcomes for patients affected by DMG.
Abstract BACKGROUND Diffuse Midline Glioma (DMG) is a incurable tumor affecting children. Recent genomic investigations have identified a recurrent H3K27M mutation which induces global alterations in ...histone methylation patterns and DNA methylation. These epigenetic modifications hint at pivotal roles in DMG pathogenesis, yet effective therapeutic strategies remain elusive, with median survival rates stagnant at approximately one year. This shortfall stems from two main factors: 1) Inadequate multiomics studies hindering our understanding of DMG evolution and tumor progression, and 2) Limited comprehension of the tumor microenvironment in DMG. METHODS To elucidate DMG’s clonal evolution, we adopted a comprehensive multi-region sampling approach, acquiring 33 specimens from seven patients. Whole-exome and transcriptome sequencing, alongside DNA methylation profiling, were performed. Additionally, we generated one of the most extensive single-cell multiomics datasets (>300,000 cells from 21 additional samples), with a focus on pre- and post-treatment, and dissemination effects in DMG. RESULTS Our analysis delineated a tumor-promoting microenvironment characterized by hypoxia and pro-inflammatory conditions, nurturing genomic alterations and specialized biological processes such as proliferation and epithelial-mesenchymal transition. Notably, a majority of immune cells exhibited M1-like polarization, bolstering pro-inflammatory programs within the tumor milieu. Subclones within the DMG cohort demonstrated dissemination potential, often exhibiting up-regulation of NOTCH, P53, and WNT beta-catenin signaling pathways. These findings suggest that DMG clones harboring dissemination capabilities outside the pons acquire additional phenotypic features, possibly mediated by epigenetic or transcriptional alterations, contributing to enhanced migratory and aggressive behaviors. CONCLUSIONS Our study unveils the parallel evolution of DMG at genetic, epigenetic, and transcriptional levels, unveiling novel subclonal phenotypes governing tumor behavior. Crucially, we identify critical environmental shifts such as hypoxia and inflammatory changes, coupled with specialized signaling programs, driving dissemination and resistance phenotypes. These insights may pave the way for generating accurate genetically mouse models and targeted therapeutic interventions to combat this challenging malignancy.
Brassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have ...been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de-novo assembly to discover B. juncea transcriptome associated with high temperature and drought stresses.
We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Many of these were responsive to high temperature, drought or both stresses. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families, respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes.
Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resource generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity.
Microgreens have been used for raw consumption and are generally viewed as healthy food. This study aimed to optimize the yield parameters, shelf life, sensory evaluation and characterization of ...total aerobic bacteria (TAB), yeast and mold (Y&M), Escherichia coli, Salmonella spp., and Listeria spp. incidence in mungbean (Vigna radiata (L.) Wilczek), lentil (Lens culinaris Medikus subsp. culinaris), and Indian mustard (Brassica juncea (L.) Czern & Coss.) microgreens. In mungbean and lentil, seeding-density of three seed/cm.sup.2, while in Indian mustard, eight seed/cm.sup.2 were recorded as optimum. The optimal time to harvest mungbean, Indian mustard, and lentil microgreens were found as 7.sup.th, 8.sup.th, and 9.sup.th day after sowing, respectively. Interestingly, seed size was found highly correlated with the overall yield in both mungbeans (r.sup.2 = .73) and lentils (r.sup.2 = .78), whereas no such relationship has been recorded for Indian mustard microgreens. The target pathogenic bacteria such as Salmonella spp. and Listeria spp. were not detected; while TAB, Y&M, Shigella spp., and E. coli were recorded well within the limit to cause any human illness in the studied microgreens. Washing with double distilled water for two minutes has shown some reduction in the overall microbial load of these microgreens. The results provided evidence that microgreens if grown and stored properly, are generally safe for human consumption. This is the first study from India on the safety of mungbean, lentils, and Indian mustard microgreens.
Repetitive mild traumatic brain injury (mTBI) in children and adolescents leads to acute and chronic neurologic sequelae and is linked to later life neurodegenerative disease. However, the biological ...mechanisms connecting early life mTBI to neurodegeneration remain unknown. Using an adolescent mouse repetitive closed head injury model that induces progressive cognitive impairment in males and anxiety in females in the absence of overt histopathology, we examined transcriptional and translational changes in neurons isolated from sham and injured brain in the chronic phase after injury. At 14 months, single-nuclei RNA sequencing of cortical brain tissue identified disruption of genes associated with neuronal proteostasis and evidence for disrupted ligand-receptor signaling networks in injured mice. Western blot analysis of isolated neurons showed evidence of inflammasome activation and downstream IL-1β processing, as previously demonstrated in acute CNS injury models, and accumulation of misfolded, hyperphosphorylated tau, and changes in expression of proteins suggestive of impaired translation in males but not in females. At 6 months, injured IL-1 receptor 1 (
) KO mice, which are protected from postinjury cognitive deficits, had decreased accumulation of pro-IL-1β and misfolded tau in cortex and cerebellum, suggesting that IL-1R1 is upstream of inflammasome priming (defined as increase in pro-IL-1β) and abnormal tau phosphorylation. Together, our findings provide evidence for neuronal inflammasome activation and impaired proteostasis as key mechanisms linking repetitive mTBI in adolescence to later life neurologic dysfunction and neurodegeneration.
Repetitive mild closed head injury in adolescent male mice leads to impaired proteostasis, tau phosphorylation, and inflammasome activation in neurons later in adulthood through mechanisms involving IL-1 receptor 1. The data are the first to link repetitive mild traumatic brain injury in adolescence to neurodegeneration and suggest molecular targets and pathways to prevent neurologic sequelae in the chronic period after injuries.
Microgreens have been used for raw consumption and are generally viewed as healthy food. This study aimed to optimize the yield parameters, shelf life, sensory evaluation and characterization of ...total aerobic bacteria (TAB), yeast and mold (Y&M), Escherichia coli, Salmonella spp., and Listeria spp. incidence in mungbean (Vigna radiata (L.) Wilczek), lentil (Lens culinaris Medikus subsp. culinaris), and Indian mustard (Brassica juncea (L.) Czern & Coss.) microgreens. In mungbean and lentil, seeding-density of three seed/cm.sup.2, while in Indian mustard, eight seed/cm.sup.2 were recorded as optimum. The optimal time to harvest mungbean, Indian mustard, and lentil microgreens were found as 7.sup.th, 8.sup.th, and 9.sup.th day after sowing, respectively. Interestingly, seed size was found highly correlated with the overall yield in both mungbeans (r.sup.2 = .73) and lentils (r.sup.2 = .78), whereas no such relationship has been recorded for Indian mustard microgreens. The target pathogenic bacteria such as Salmonella spp. and Listeria spp. were not detected; while TAB, Y&M, Shigella spp., and E. coli were recorded well within the limit to cause any human illness in the studied microgreens. Washing with double distilled water for two minutes has shown some reduction in the overall microbial load of these microgreens. The results provided evidence that microgreens if grown and stored properly, are generally safe for human consumption. This is the first study from India on the safety of mungbean, lentils, and Indian mustard microgreens.
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