L-2-hydroxyglutarate remodeling of the epigenome and epitranscriptome creates a metabolic vulnerability in kidney cancer models.

Tumor cells are known to undergo considerable metabolic reprogramming to meet their unique demands and drive tumor growth. At the same time, this reprogramming may come at a cost with resultant metabolic vulnerabilities. The small molecule L-2-hdroxyglutarate (L-2HG) is elevated in the most common histology of renal cancer. Similar to other oncometabolites, L-2HG has the potential to profoundly impact gene expression. Here, we demonstrate that L-2HG remodels amino acid metabolism in renal cancer cells through the combined effects on histone methylation and RNA N6-methyladenosine (m6A). The combined effects of L-2HG result in a metabolic liability that renders tumors cells reliant on exogenous serine to support proliferation, redox homeostasis, and tumor growth. In concert with these data, high L-2HG kidney cancers demonstrates reduced expression of multiple serine biosynthetic enzymes. Collectively, our data indicate that high L-2HG renal tumors could be specifically targeted by strategies that limit serine availability to tumors.

Transcriptome-wide quantitative profiling of PUS7-dependent pseudouridylation by nanopore direct long read RNA sequencing.

Pseudouridylation is a prevalent post-transcriptional RNA modification that impacts many aspects of RNA biology and function. The conversion of uridine to pseudouridine (Ψ) is catalyzed by the family of pseudouridine synthases (PUSs). Development of robust methods to determine PUS-dependent regulation of Ψ location and stoichiometry in low abundant mRNA is essential for biological and functional understanding of pseudouridylation. Here, we present a framework, NanoPsiPy, for identifying Ψ sites and quantify their levels in poly-A RNA at single-nucleotide resolution using direct RNA long-read Nanopore sequencing, based on the observation that Ψ can cause characteristic U-to-C basecalling errors in Nanopore direct RNA sequencing data. Our method was able to detect low and high stoichiometric Ψ sites in human mRNA. We validated our method by transcriptome-wide quantitative profiling of PUS7-dependent Ψ sites in poly-A RNA from a MYCN -amplified neuroblastoma cell line. We identified 8,625 PUS7-dependent Ψ sites in 1,246 mRNAs that encode proteins involved primarily in ribosome biogenesis, translation, and mitochondrial energy metabolism. Our work provides the first example of using direct RNA long-read Nanopore sequencing for transcriptome-wide quantitative profiling of mRNA pseudouridylation regulated by a PUS. We envision that our method will facilitate functional interrogation of PUSs in biological and pathological processes.

Application of ZnO Nanoparticles Encapsulated in Mesoporous Silica on the Abaxial Side of a Solanum lycopersicum Leaf Enhances Zn Uptake and Translocation via the Phloem.

Foliar application of nutrient nanoparticles (NPs) is a promising strategy for improving fertilization efficiency in agriculture. Phloem translocation of NPs from leaves is required for efficient fertilization but is currently considered to be feasible only for NPs smaller than a cell wall pore size exclusion limit of <20 nm. Using mass spectrometry imaging, we provide here the first direct evidence for phloem localization and translocation of a larger (∼70 nm) fertilizer NP comprised of ZnO encapsulated in mesoporous SiO2 (ZnO@MSN) following foliar deposition. The Si content in the phloem tissue of the petiole connected to the dosed leaf was ∼10 times higher than in the xylem tissue, and ∼100 times higher than the phloem tissue of an untreated tomato plant petiole. Direct evidence of NPs in individual phloem cells has only previously been shown for smaller NPs introduced invasively in the plant. Furthermore, we show that uptake and translocation of the NPs can be enhanced by their application on the abaxial (lower) side of the leaf. Applying ZnO@MSN to the abaxial side of a single leaf resulted in a 56% higher uptake of Zn as well as higher translocation to the younger (upper) leaves and to the roots, than dosing the adaxial (top) side of a leaf. The higher abaxial uptake of NPs is in alignment with the higher stomatal density and lower density of mesophyll tissues on that side and has not been demonstrated before.

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea.

Fungal infections are the inevitable limiting factor for productivity of tea. Transcriptome reprogramming recruits multiple regulatory pathways during pathogen infection. A comprehensive meta-analysis was performed utilizing previously reported, well-replicated transcriptomic datasets from seven fungal diseases of tea. The study identified a cumulative set of 18,517 differentially expressed genes (DEGs) in tea, implicated in several functional clusters, including the MAPK signaling pathway, transcriptional regulation, and the biosynthesis of phenylpropanoids. Gene set enrichment analyses under each pathogen stress elucidated that DEGs were involved in ethylene metabolism, secondary metabolism, receptor kinase activity, and various reactive oxygen species detoxification enzyme activities. Expressional fold change of combined datasets highlighting 2258 meta-DEGs shared a common transcriptomic response upon fungal stress in tea. Pervasive duplication events caused biotic stress-responsive core DEGs to appear in multiple copies throughout the tea genome. The co-expression network of meta-DEGs in multiple modules demonstrated the coordination of appropriate pathways, most of which involved cell wall organization. The functional coordination was controlled by a number of hub genes and miRNAs, leading to pathogenic resistance or susceptibility. This first-of-its-kind meta-analysis of host-pathogen interaction generated consensus candidate loci as molecular signatures, which can be associated with future resistance breeding programs in tea.

Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper].

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

Deciphering the role of alternative splicing as modulators of defense response in the MYMIV-Vigna mungo pathosystem.

Alternative splicing (AS) is a crucial regulatory mechanism that impacts transcriptome and proteome complexity under stressful situations. Although its role in abiotic stresses is somewhat understood, our understanding of the mechanistic regulation of pre-messenger RNA splicing in plant-pathogen interaction is meager. To comprehend this unexplored immune reprogramming mechanism, transcriptome profiles of Mungbean Yellow Mosaic India Virus (MYMIV)-resistant and susceptible Vigna mungo genotypes were analyzed for AS genes that may underlie the resistance mechanism. Results revealed a repertoire of AS-isoforms accumulated during pathogenic infestation, with intron retention being the most common AS mechanism. Identification of 688 differential alternatively spliced (DAS) genes in the resistant host elucidates its robust antiviral response, whereas 322 DAS genes were identified in the susceptible host. Enrichment analyses confirmed DAS transcripts pertaining to stress, signaling, and immune system pathways have undergone maximal perturbations. Additionally, a strong regulation of the splicing factors has been observed both at the transcriptional and post-transcriptional levels. qPCR validation of candidate DAS transcripts with induced expression upon MYMIV infection demonstrated a competent immune response in the resistant background. The AS-impacted genes resulted either in partial/complete loss of functional domains or altered sensitivity to micro-RNA-mediated gene silencing. A complex regulatory module, miR7517-ATAF2, has been identified in an aberrantly spliced ATAF2 isoform that exposes an intronic miR7517 binding site, thereby suppressing the negative regulator to enhance the defense reaction. The present study establishes AS as a noncanonical immune reprogramming mechanism that operates in parallel, thereby offering an alternative strategy for developing yellow mosaic-resistant V. mungo cultivars.

Engineering Catalytically Active Sites by Sculpting Artificial Edges on MoS2 Basal Plane for Dinitrogen Reduction at a Low Overpotential.

Engineering catalytically active sites have been a challenge so far and often relies on optimization of synthesis routes, which can at most provide quantitative enhancement of active facets, however, cannot provide control over choosing orientation, geometry and spatial distribution of the active sites. Artificially sculpting catalytically active sites via laser-etching technique can provide a new prospect in this field and offer a new species of nanocatalyst for achieving superior selectivity and attaining maximum yield via absolute control over defining their location and geometry of every active site at a nanoscale precision. In this work, a controlled protocol of artificial surface engineering is shown by focused laser irradiation on pristine MoS2 flakes, which are confirmed as catalytic sites by electrodeposition of AuNPs. The preferential Au deposited catalytic sites are found to be electrochemically active for nitrogen adsorption and its subsequent reduction due to the S-vacancies rather than Mo-vacancy, as advocated by DFT analysis. The catalytic performance of Au-NR/MoS2 shows a high yield rate of ammonia (11.43 × 10-8  mol s-1 cm-2 ) at a potential as low as -0.1 V versus RHE and a notable Faradaic efficiency of 13.79% during the electrochemical nitrogen reduction in 0.1 m HCl.

Impacts of Arctic diesel contamination on microbial community composition and degradative gene abundance during hydrocarbon biodegradation with and without nutrients: A case study of seven sub-Arctic soils.

Although a number of studies have assessed hydrocarbon degradation or microbial responses in petroleum contaminated soils, few have examined both and/or assessed impacts in multiple soils simultaneously. In this study petroleum hydrocarbon biodegradation and microbial activity was monitored in seven sub-Arctic soils at similar levels (∼3500-4000 mg/kg) of Arctic diesel (DSL), amended with moisture and nutrients (70 mg-N/kg, 78 mg-P/kg), and incubated at site-representative summer temperatures (∼7 °C) under water unsaturated conditions. Total petroleum hydrocarbon (TPH) biodegradation extents (42.7-85.4 %) at 50 days were slightly higher in nutrient amended (DSL + N,P) than unamended (DSL) systems in all but one soil. Semi-volatile (C10-C16) hydrocarbons were degraded to a greater extent (40-80 %) than non-volatile (C16-C24) hydrocarbons (20-40 %). However, more significant shifts in microbial diversity and relative abundance of genera belonging to Actinobacteria and Proteobacteria phyla were observed in DSL + N,P than in DSL systems in all soils. Moreover, higher abundance of the alkane degrading gene alkB were observed in DSL + N,P systems than in DSL systems for all soils. The more significant microbial community response in the DSL + N,P systems indicate that addition of nutrients may have influenced the microbial community involved in degradation of carbon sources other than the diesel compounds, such as the soil organic matter or degradation intermediates of diesel compounds. Nocardioides, Arthrobacter, Marmoricola, Pseudomonas, Polaromonas, and Massilia genera were present in high relative abundance in the DSL systems suggesting those genera contained hydrocarbon degraders. Overall, the results suggest that the extents of microbial community shifts or alkB copy number increases may not be closely correlated to the increase in hydrocarbon biodegradation and thus bioremediation performance between various treatments or across different soils.

Phylogenetic, structural, functional characterisation and effect of exogenous spermidine on rice (Oryza sativa) HAK transporters under salt stress.

The HAK (High-affinity K+ ) family members mediate K+ transport that confers normal plant growth and resistance against unfavourable environmental conditions. Rice (Oryza sativa L.) HAK transporters have been extensively investigated for phylogenetic analyses with other plants species with very few of them functionally characterised. But very little information is known about their evolutionary aspects, overall structural, functional characterisation, and global expression pattern of the complete HAK family members in response to salt stress. In this study, 27 rice transporters were phylogenetically clustered with different dicot and monocot family members. Subsequently, the exon-intron structural patterns, conserved motif analyses, evolutionary divergence based different substitution matrix, orthologous-paralogous relationships were studied elaborately. Structural characterisations included a comparative study of secondary and tertiary structure, post-translational modifications, correspondence analyses, normal mode analyses, K+ /Na+ binding affinities of each of the OsHAK gene members. Global expression profile under salt stress showed clade-specific expression pattern of the proteins. Additionally, five OsHAK genes were chosen for further expression analyses in root and shoot tissues of two rice varieties during short-term salinity in the presence and absence of exogenous spermidine. All the information can be used as first-hand data for dissecting the administrative role of rice HAK transporters under various abiotic stresses.

Hymenolepis diminuta Reduce Lactic Acid Bacterial Load and Induce Dysbiosis in the Early Infection of the Probiotic Colonization of Swiss Albino Rat.

Tapeworm infection continues to be an important cause of morbidity worldwide. Recent metagenomics studies have established a link between gut microbiota and parasite infection. The identification of gut probiotics is of foremost importance to explore its relationship and function with the parasite in the host. In this study, the gut content of hosts infected with tapeworm Hymenolepis diminuta and non-infected host gut were disected out to determine their Lactic acid bacterial (LAB) population in MRS agar and microbial community was analysed by metagenomics. The bacterial count was calculated on a bacterial counting chamber and their morphology was determined microscopically and biochemically. Further, to determine the safety profile antibiotic resistance test, antimicrobial, hemolytic activity, and adhesion capability were calculated. We found six dominant probiotic strains and a decrease in LAB load from 1.7-2.3 × 107 CFU/mL in the uninfected group to a range of 8.4 × 105 CFU/mL to 3.2 × 105 CFU/mL in the infected groups with respect to an increase in the parasite number from 10-18. In addition, we found a depletion in the probiotic relative abundance of Lactobacillus and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria, and Streptococcus. Phylogenetic analysis of the six probiotics revealed a close similarity with different strains of L. brevis, L. johnsonii, L. taiwansis, L. reuteri, L. plantarum, and L. pentosus. Thus, this study suggests that the parasite inhibits probiotic colonization in the gut during its early establishment of infection inside the host.

Accidental formalin poisoning in a child with acute fatal manifestations: A rare case report.

Formalin is a protoplasmic poison, which poses a potential occupational hazard among morticians, embalmers, pathologists, and hospital staff. The crystal-clear appearance of formalin can be easily mistaken for normal saline, local anesthetics, hydrogen peroxide, sodium hypochlorite, and spirit in health care facilities and water in domestic settings. However, accidental poisoning is extremely rare because of its low olfactory threshold, strong irritant nature, pungent taste, and odor. This is also evident from the scarce scientific literature on this topic. Here, we presented a case of accidental, fatal formalin ingestion by a 4-year-old child who succumbed to the poisoning within 12 h of ingestion. The case presented here is unique because of its rarity in causing accidental poisoning by ingestion and first of its kind in a child.

Idiopathic Pericardial Ossification Causing Chronic Constrictive Pericarditis.

BACKGROUND: Chronic constrictive pericarditis (CCP) is usually caused by the fibroinflammatory reaction of the visceral and parietal pericardium that encase the heart. The cause of CCP is various including tuberculosis, trauma, prior surgery, radiation, and malignancy. MATERIAL AND METHODS: We examined the pericardiectomy specimen of a case of CCP in a 17-year-old boy. RESULTS: The histopathology of the pericardium revealed pericardial ossification bony remodeling and hematopoiesis within the intertrabecular marrow spaces. No granulomatous or neoplastic etiology was identified. CONCLUSION: Idiopathic pericardial ossification can cause CCP in pediatric patients.

Umbilical Hernia as Forerunner of Primary Umbilical Endometriosis: A Case Report.

Umbilical endometriosis is a type of cutaneous endometriosis that usually follows laparoscopic or surgical procedures that involve the umbilicus. Primary umbilical endometriosis (PUE) is an extremely rare condition and its association with an umbilical hernia is an equally rare condition. To date, only very few cases of PUE with umbilical hernia association have been reported in the medical literature. Report herein is a case of PUE associated with an umbilical hernia who presented with classical umbilical nodule symptoms with cyclical pain and bleeding due to menstruation. The patient underwent omphalectomy with abdominal wall defect repair using prosthetic mesh. The diagnosis was confirmed by histopathological examination of the excised umbilical nodule. This case report highlights a rare entity that should be considered as a differential diagnosis in females of the reproductive age group that presents with the umbilical nodule.

The TGF-ß/HDAC7 axis suppresses TCA cycle metabolism in renal cancer.

Mounting evidence points to alterations in mitochondrial metabolism in renal cell carcinoma (RCC). However, the mechanisms that regulate the TCA cycle in RCC remain uncharacterized. Here, we demonstrate that loss of TCA cycle enzyme expression is retained in RCC metastatic tissues. Moreover, proteomic analysis demonstrates that reduced TCA cycle enzyme expression is far more pronounced in RCC relative to other tumor types. Loss of TCA cycle enzyme expression is correlated with reduced expression of the transcription factor PGC-1α, which is also lost in RCC tissues. PGC-1α reexpression in RCC cells restores the expression of TCA cycle enzymes in vitro and in vivo and leads to enhanced glucose carbon incorporation into TCA cycle intermediates. Mechanistically, TGF-ß signaling, in concert with histone deacetylase 7 (HDAC7), suppresses TCA cycle enzyme expression. Our studies show that pharmacologic inhibition of TGF-ß restores the expression of TCA cycle enzymes and suppresses tumor growth in an orthotopic model of RCC. Taken together, this investigation reveals a potentially novel role for the TGF-ß/HDAC7 axis in global suppression of TCA cycle enzymes in RCC and provides insight into the molecular basis of altered mitochondrial metabolism in this malignancy.

Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses.

MAIN CONCLUSION: Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses. GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.

Uptake and Translocation of Mesoporous SiO2-Coated ZnO Nanoparticles to Solanum lycopersicum Following Foliar Application.

Nanoparticles composed of ZnO encapsulated in a mesoporous SiO2 shell (nZnO@SiO2) with a primary particle diameter of ∼70 nm were synthesized for delivery of Zn, a micronutrient, by foliar uptake. Compared to the rapid dissolution of bare nZnO (90% Zn dissolution after 4 h) in a model plant media (pH = 5), nZnO@SiO2 released Zn more slowly (40% Zn dissolution after 3 weeks), thus enabling sustained Zn delivery over a longer period. nZnO@SiO2, nZnO, and ZnCl2 were exposed to Solanum lycopersicum by dosing 40 µg of Zn micronutrient (in a 20 µL suspension) on a single leaf. No Zn uptake was observed for the nZnO treatment after 2 days. Comparable amounts of Zn uptake were observed 2 days after ZnCl2 (15.5 ± 2.4 µg Zn) and nZnO@SiO2 (11.4 ± 2.2 µg Zn) dosing. Single particle inductively coupled plasma mass spectrometry revealed that for foliar applied nZnO@SiO2, almost all of the Zn translocated to upper leaves and the stem were in nanoparticulate form. Our results suggest that the SiO2 shell enhances the uptake of ZnO nanoparticles in Solanum lycopersicum. Sustained and controlled micronutrient delivery in plants through foliar application will reduce fertilizer, energy, and water use.

Pre-bypass levosimendan in ventricular dysfunction-effect on right ventricle.

BACKGROUND: Levosimendan is an effective calcium sensitizer with complementary mechanisms of action: calcium sensitization and opening of adenosine triphosphate-dependent potassium channels, both on the sarcolemma of the smooth muscle cells in the vasculature and on the mitochondria of cardiomyocytes. Levosimendan has a long-acting metabolite with a half-life of approximately 80 h. There have been a few small studies on this drug regarding right ventricular function. In view of this, we investigated the effect of levosimendan on right ventricular function in patients with coronary artery disease. METHODS: This was a prospective, randomized, double-blind study on 50 patients with coronary artery disease and severe left ventricular dysfunction (left ventricular ejection fraction ≤35%) undergoing elective off-pump coronary artery bypass. RESULTS: Levosimendan had an inotropic effect on right ventricular myocardium and a vasodilatory effect on blood vessels. It caused a decline in pulmonary vascular resistance (p < 0.018), right ventricular systolic pressure (p < 0.001), and pulmonary artery systolic pressure (p < 0.001), and improved right ventricular diastolic function as shown by the decrease in right ventricular Tei index (p < 0.001), right ventricular end-diastolic pressure, and the ratio of early diastolic tricuspid inflow to tricuspid lateral annular velocity (p < 0.006). However, we found no beneficial effects on intensive care unit or hospital stay (p = 0.164, p = 0.349, respectively) nor a mortality benefit. CONCLUSIONS: Levosimendan has salutary effects on right ventricular function in patients with severe left ventricular dysfunction undergoing coronary artery bypass, in terms of improved hemodynamic parameters.

Teleological role of L-2-hydroxyglutarate dehydrogenase in the kidney.

L-2-hydroxyglutarate (L-2HG) is an oncometabolite found elevated in renal tumors. However, this molecule might have physiological roles that extend beyond its association with cancer, as L-2HG levels are elevated in response to hypoxia and during Drosophila larval development. L-2HG is known to be metabolized by L-2HG dehydrogenase (L2HGDH), and loss of L2HGDH leads to elevated L-2HG levels. Despite L2HGDH being highly expressed in the kidney, its role in renal metabolism has not been explored. Here, we report our findings utilizing a novel CRISPR/Cas9 murine knockout model, with a specific focus on the role of L2HGDH in the kidney. Histologically, L2hgdh knockout kidneys have no demonstrable histologic abnormalities. However, GC-MS metabolomics demonstrates significantly reduced levels of the TCA cycle intermediate succinate in multiple tissues. Isotope labeling studies with [U-13C] glucose demonstrate that restoration of L2HGDH in renal cancer cells (which lowers L-2HG) leads to enhanced incorporation of label into TCA cycle intermediates. Subsequent biochemical studies demonstrate that L-2HG can inhibit the TCA cycle enzyme α-ketoglutarate dehydrogenase. Bioinformatic analysis of mRNA expression data from renal tumors demonstrates that L2HGDH is co-expressed with genes encoding TCA cycle enzymes as well as the gene encoding the transcription factor PGC-1α, which is known to regulate mitochondrial metabolism. Restoration of PGC-1α in renal tumor cells results in increased L2HGDH expression with a concomitant reduction in L-2HG levels. Collectively, our analyses provide new insight into the physiological role of L2HGDH as well as mechanisms that promote L-2HG accumulation in disease states.