ABSTRACT
Lipids contribute to the structure, development, and function of healthy brains. Dysregulated lipid metabolism is linked to aging and diseased brains. However, our understanding of lipid metabolism in aging brains remains limited. Here we examined the brain lipidome of mice across their lifespan using untargeted lipidomics. Co-expression network analysis highlighted a progressive decrease in 3-sulfogalactosyl diacylglycerols (SGDGs) and SGDG pathway members, including the potential degradation products lyso-SGDGs. SGDGs show an age-related decline specifically in the central nervous system and are associated with myelination. We also found that an SGDG dramatically suppresses LPS-induced gene expression and release of pro-inflammatory cytokines from macrophages and microglia by acting on the NF-κB pathway. The detection of SGDGs in human and macaque brains establishes their evolutionary conservation. This work enhances interest in SGDGs regarding their roles in aging and inflammatory diseases and highlights the complexity of the brain lipidome and potential biological functions in aging.
Subject(s)
Aging , Lipids , Animals , Humans , Mice , Aging/genetics , Anti-Inflammatory Agents , Brain/metabolism , Microglia/metabolism , NF-kappa B/metabolismABSTRACT
Sensory signals detected by olfactory sensory organs are critical regulators of animal behavior. An accessory olfactory organ, the vomeronasal organ, detects cues from other animals and plays a pivotal role in intra- and inter-species interactions in mice. However, how ethologically relevant cues control mouse behavior through approximately 350 vomeronasal sensory receptor proteins largely remains elusive. The type 2 vomeronasal receptor-A4 (V2R-A4) subfamily members have been repeatedly detected from vomeronasal sensory neurons responsive to predator cues, suggesting a potential role of this receptor subfamily as a sensor for predators. This review focuses on this intriguing subfamily, delving into its receptor functions and genetic characteristics.
Subject(s)
Olfactory Bulb , Vomeronasal Organ , Mice , Animals , Olfactory Bulb/physiology , Sensory Receptor Cells/metabolism , Vomeronasal Organ/metabolismABSTRACT
Homovanillic acid (HVA) and 5-hydroxyindoleacetic acid (5-HIAA) are the urinary metabolites of dopamine (DA) and serotonin (5-HA), respectively. We aimed to develop an extraction method for the determination of HVA and 5-HIAA, using strong anionic exchange cartridges combined with HPLC with electrochemical detection, and apply it to measure the levels of HVA and 5-HIAA in children living near a ferro-manganese alloy plant in Simões Filho, Brazil. The validated method showed good selectivity, sensitivity, precision, and accuracy. The limits of detection (LOD) were 4 and 8 µmol/L for 5-HIAA and HVA, respectively, in urine. Recoveries ranged from 85.8 to 94%. The coefficients of determination (R2 ) of the calibration curves were greater than 0.99. Spot urine samples of 30 exposed children and 20 nonexposed ones were processed accordingly. The metabolite levels in exposed and reference children were within the physiological ranges. The medians (range) for 5-HIAA and HVA of the exposed ones were 36.4 µmol/L (18.4-58.0) and 32.9 µmol/L (Subject(s)
Dopamine
, Manganese
, Humans
, Child
, Homovanillic Acid/urine
, Hydroxyindoleacetic Acid
, Chromatography, High Pressure Liquid/methods
, Dopamine/metabolism
ABSTRACT
BACKGROUND AND PURPOSE: Lead (Pb) is used as a flux in the glazing process of pottery utensils in several regions of the world. It can affect the nervous and hematopoietic systems; in addition, it is classified as a probable human carcinogen. This work aims to evaluate Pb exposure of potters and describe the main determinants of elevated blood Pb (PbB) levels in this group of workers. METHODS: This is a cross-sectional study with potters of Maragogipinho Village, Bahia, Brazil, of both sexes, aged 16-72 years (n = 85). Non-exposed workers of the same age range residing in the urban area of Aratuípe town were also recruited (n = 50). We evaluated Pb dust deposition rates (PbDrt) in pottery workshops and PbB levels. All Pb measurements were performed by Graphite Furnace Atomic Absorption Spectrometry. RESULTS: The median of PbB (min-max) and geometric mean (SD) PbDrt for the exposed group were 7.9 (0.9-49.8) µg/dL and 1463 (± 290,000) µg/m2/30 days, respectively. For the control group, levels were 1.5 (0.1-19.8) µg/dL and 82 (46) µg/m2 30 days, respectively. CONCLUSION: The data found showed an excessive exposure among artisans, exceeding occupationally safe levels and those reported in the literature. It is important to implement occupational hygiene measures and improvements of the working conditions of these labors, especially the replacement of lead oxide in the pottery-glazing process.
Subject(s)
Ceramics , Dust/analysis , Lead/analysis , Occupational Exposure/analysis , Adolescent , Adult , Aged , Brazil , Cross-Sectional Studies , Environmental Monitoring , Female , Humans , Lead/blood , Male , Middle Aged , Risk Factors , Young AdultABSTRACT
Lead (Pb) exposure compromises heme synthesis by inhibiting ferrochelatase, forming zinc-protoporphyrin (ZnPP). This study aims to validate a method for the determination of ZnPP by HPLC with fluorescence detection and apply this method to evaluate the extent of Pb exposure of artisanal pottery workers. Extraction procedures were tested using both nonacid and acid liquid-liquid extraction. The former presented a better chromatogram and recovery results. The validated method yielded a good resolution of ZnPP and its free form peaks with acceptable precision and accuracy. Total run time was 15 min and ZnPP peak retention time was 5.6 min. We applied this method to evaluate 39 potters (90% male), mean age 40 years (9-80). The medians (ranges) of blood lead, ZnPP and hemoglobin were 16.0 µg/dl (2.2-71.5), 12.6 µg/dl (4.6-279.8) and 15.1 g/dl (11.0-17.8), respectively. Significant differences were observed for blood lead according to gender, age range (>40 years), direct handling of lead oxide and years of occupation. Significantly higher levels of ZnPP were observed in male potters involved with lead glazing activity. The validated method was shown to be simple with one-step nonacid extraction, good sensitivity, reproducibility and accuracy. Our data shows that these laborers are dangerously exposed to Pb, reflecting the effect on the heme synthesis.
Subject(s)
Chromatography, High Pressure Liquid/methods , Lead/blood , Occupational Exposure/analysis , Protoporphyrins/blood , Adolescent , Adult , Aged , Aged, 80 and over , Biomarkers/blood , Child , Female , Hemoglobins/analysis , Humans , Linear Models , Male , Middle Aged , Reproducibility of Results , Sensitivity and Specificity , Spectrometry, Fluorescence , Young AdultABSTRACT
Obesity may be counteracted by increased energy expenditure. Circulating molecules act in the adipose tissue to influence brown and beige adipocyte function, differentiation, and thermogenic capacity, which in turn affects substrate utilization and impacts energy balance at the organismal level. These molecules have been envisioned as biomarkers and potential candidates for pharmacological interventions to treat obesity. Here we summarize studies that demonstrate the roles of endogenous circulating molecules of a wide variety in regulating the thermogenic potential of brown and beige fat cells. This review describes the state-of-the-art in the field and helps researchers to prioritize their targets in future studies.
Subject(s)
Adipocytes/cytology , Adipocytes/metabolism , Cell Differentiation , Animals , Inflammation Mediators/blood , Inflammation Mediators/metabolism , Lipids/blood , MicroRNAs/blood , MicroRNAs/metabolism , Mitochondria/metabolism , Peptide Hormones/blood , Peptide Hormones/metabolism , Thermogenesis , Uncoupling Protein 1/metabolismABSTRACT
BACKGROUND: The B subunit of Escherichia coli heat-labile enterotoxin (LTB) is a potent mucosal immune adjuvant. However, there is little information about LTB's potential as a parenteral adjuvant. OBJECTIVES: We aimed at evaluating and better understanding rLTB's potential as a parenteral adjuvant using the fused R1 repeat of Mycoplasma hyopneumoniae P97 adhesin as an antigen to characterise the humoral immune response induced by this construct and comparing it to that generated when aluminium hydroxide is used as adjuvant instead. METHODS: BALB/c mice were immunised intraperitoneally with either rLTBR1 or recombinant R1 adsorbed onto aluminium hydroxide. The levels of systemic anti-rR1 antibodies (total Ig, IgG1, IgG2a, and IgA) were assessed by enzyme-linked immunosorbent assay (ELISA). The ratio of IgG1 and IgG2a was used to characterise a Th1, Th2, or mixed Th1/Th2 immune response. FINDINGS: Western blot confirmed rR1, either alone or fused to LTB, remained antigenic; anti-cholera toxin ELISA confirmed that LTB retained its activity when expressed in a heterologous system. Mice immunised with the rLTBR1 fusion protein produced approximately twice as much anti-rR1 immunoglobulins as mice vaccinated with rR1 adsorbed onto aluminium hydroxide. Animals vaccinated with either rLTBR1 or rR1 adsorbed onto aluminium hydroxide presented a mixed Th1/Th2 immune response. We speculate this might be a result of rR1 immune modulation rather than adjuvant modulation. Mice immunised with rLTBR1 produced approximately 1.5-fold more serum IgA than animals immunised with rR1 and aluminium hydroxide. MAIN CONCLUSIONS: The results suggest that rLTB is a more powerful parenteral adjuvant than aluminium hydroxide when administered intraperitoneally as it induced higher antibody titres. Therefore, we recommend that rLTB be considered an alternative adjuvant, even if different administration routes are employed.
Subject(s)
Adhesins, Bacterial/immunology , Adjuvants, Immunologic/administration & dosage , Bacterial Toxins/administration & dosage , Enterotoxins/administration & dosage , Escherichia coli Proteins/administration & dosage , Mycoplasma hyopneumoniae/immunology , Pneumonia of Swine, Mycoplasmal/prevention & control , Aluminum Hydroxide , Animals , Bacterial Toxins/immunology , Enterotoxins/immunology , Enzyme-Linked Immunosorbent Assay , Escherichia coli Proteins/immunology , Female , Mice , Mice, Inbred BALB C , Pneumonia of Swine, Mycoplasmal/immunology , SwineABSTRACT
Numerous studies have shown that many works of art from the Renaissance period contain hidden symbols and codes that could have religious, mathematical and/or pagan significance and even anatomical allusions. In this context, the present manuscript offers new evidence that the great genius of anatomy, Michelangelo Buonarroti (1475-1564), included pagan symbols associated with female anatomy in the funerary monuments found in the Sagrestia Nuova/Medici Chapel (1519-1533) in Florence, Italy. The interpretation of the symbols provided in this study will interest those with a passion for the history of anatomy. Clin. Anat. 30:572-577, 2017. © 2017 Wiley Periodicals, Inc.
Subject(s)
Anatomy/history , Famous Persons , Genitalia, Female/anatomy & histology , Symbolism , Female , History, 16th Century , HumansABSTRACT
Fossil fuel combustion and many industrial processes generate gaseous emissions that contain a number of toxic organic pollutants and carbon dioxide (CO2) which contribute to climate change and atmospheric pollution. There is a need for green and sustainable solutions to remove air pollutants, as opposed to conventional techniques which can be expensive, consume additional energy and generate further waste. We developed a novel integrated bioreactor combined with recyclable iron oxide nano/micro-particle adsorption interfaces, to remove CO2, and undesired organic air pollutants using natural particles, while generating oxygen. This semi-continuous bench-scale photo-bioreactor was shown to successfully clean up simulated emission streams of up to 45% CO2 with a conversion rate of approximately 4% CO2 per hour, generating a steady supply of oxygen (6mmol/hr), while nanoparticles effectively remove several undesired organic by-products. We also showed algal waste of the bioreactor can be used for mercury remediation. We estimated the potential CO2 emissions that could be captured from our new method for three industrial cases in which, coal, oil and natural gas were used. With a 30% carbon capture system, the reduction of CO2 was estimated to decrease by about 420,000, 320,000 and 240,000 metric tonnes, respectively for a typical 500MW power plant. The cost analysis we conducted showed potential to scale-up, and the entire system is recyclable and sustainable. We further discuss the implications of usage of this complete system, or as individual units, that could provide a hybrid option to existing industrial setups.
Subject(s)
Air Pollutants/analysis , Air Pollution/prevention & control , Bioreactors , Carbon Dioxide/analysis , Metals/analysis , Nanoparticles/chemistry , Air Pollutants/chemistry , Carbon Dioxide/chemistry , Metals/chemistryABSTRACT
PURPOSE: Beneficial effects of green tea (GT) polyphenols against obesity have been reported. However, until this moment the molecular mechanisms of how green tea can modulate obesity and regulates fat metabolism, particularly in adipose tissue, remain poorly understood. The aim of this study was to evaluate the role of GT extract in the adipose tissue of obese animals and its effect on weight gain, metabolism and function (de novo lipogenesis and lipolysis), and the involvement of AMP-activated protein kinase (AMPK). METHODS AND RESULTS: Male Wistar rats were treated with GT by gavage (12 weeks/5 days/week; 500 mg/kg of body weight), and obesity was induced by cafeteria diet (8 weeks). Here, we show that obese rats treated with GT showed a significant reduction in indicators of obesity such as hyperlipidemia, fat synthesis, body weight, and fat depots as compared to those treated with standard control diet. AMPK was induced in adipose tissue in rats that were treated with GT and likely restored insulin sensitivity, increased mRNA expression of GLUT4, reducing the concentrations of plasma and liver lipid content, also stimulating fatty acid oxidation in the same tissue. Importantly, repression of de novo lipogenesis in the adipose tissue, reduced lipid droplets in the liver, and the development of insulin resistance in diet-induced obese rats were accompanied by AMPK activation. CONCLUSION: Our study identified that metabolic changes caused by GT intake induced AMPK activation and modulate the expression of genes involved in metabolism, particularly in adipose tissue, thus offering a therapeutic strategy to combat insulin resistance, dyslipidemia, and obesity in rats.
Subject(s)
AMP-Activated Protein Kinases/metabolism , Adipose Tissue, White/drug effects , Obesity/metabolism , Plant Extracts/pharmacology , Polyphenols/pharmacology , Tea/chemistry , Adipose Tissue, White/metabolism , Alanine Transaminase/blood , Animals , Antioxidants/analysis , Antioxidants/pharmacology , Aspartate Aminotransferases/blood , Blood Glucose/metabolism , Caffeine/analysis , Caffeine/pharmacology , Cytokines/blood , Flavonoids/analysis , Flavonoids/pharmacology , Glucose Tolerance Test , Insulin Resistance , Lipids/blood , Lipogenesis/drug effects , Lipolysis/drug effects , Liver/drug effects , Liver/metabolism , Male , Plant Extracts/chemistry , Rats , Rats, Wistar , Weight Gain/drug effectsABSTRACT
A number of published articles have suggested that each element of Renaissance art contains an inner meaning. Some of these elements include the choice of theme and protagonists, faces selected for the characters, colors used, species of flowers and trees chosen, animals depicted, positions of the elements, posture of the characters and their gestures, juxtapositions in the scenes, and even the very scenario or landscape. All of these elements are thought to have hidden meanings. In this context, this manuscript presents a new hypothesis suggesting that Michelangelo Buonarroti (1475-1564) may have concealed symbols associated with female anatomy in the ceiling of the Sistine Chapel (painted 1508-1512) in Rome. Thus, this paper is useful to better understand the history of anatomy and corroborates recent descriptions that have suggested the possible existence of anatomic figures concealed in many of Michelangelo's works. Clin. Anat. 29:911-916, 2016. © 2016 Wiley Periodicals, Inc.
Subject(s)
Ceramics , Famous Persons , Genitalia, Female/anatomy & histology , Paintings , Symbolism , Female , HumansABSTRACT
The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 µM to 230 mM and <0.2 nM to 580 µM, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (≥126 nM). They included cadmium, manganese, and cobalt, which were 1,300- to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed.
Subject(s)
Denitrification , Groundwater/chemistry , Groundwater/microbiology , Molybdenum/metabolism , Nitrates/metabolism , Pseudomonas stutzeri/metabolism , Coenzymes/metabolism , Nitrate Reductase/metabolism , Pseudomonas stutzeri/growth & development , TennesseeABSTRACT
Art and anatomy were particularly closely intertwined during the Renaissance period and numerous painters and sculptors expressed themselves in both fields. Among them was Michelangelo Buonarroti (1475-1564), who is renowned for having produced some of the most famous of all works of art, the frescoes on the ceiling and on the wall behind the altar of the Sistine Chapel in Rome. Recently, a unique association was discovered between one of Michelangelo's most celebrated works (The Creation of Adam fresco) and the Divine Proportion/Golden Ratio (GR) (1.6). The GR can be found not only in natural phenomena but also in a variety of human-made objects and works of art. Here, using Image-Pro Plus 6.0 software, we present mathematical evidence that Michelangelo also used the GR when he painted Saint Bartholomew in the fresco of The Last Judgment, which is on the wall behind the altar. This discovery will add a new dimension to understanding the great works of Michelangelo Buonarroti.
Subject(s)
Anatomy/history , Catholicism/history , Paintings/history , Famous Persons , History, 16th Century , Humans , Italy , Male , Mathematical Concepts , SoftwareABSTRACT
Michelangelo Buonarroti (1475-1564) was a master anatomist as well as an artistic genius. He dissected numerous cadavers and developed a profound understanding of human anatomy. Among his best-known artworks are the frescoes painted on the ceiling of the Sistine Chapel (1508-1512), in Rome. Currently, there is some debate over whether the frescoes merely represent the teachings of the Catholic Church at the time or if there are other meanings hidden in the images. In addition, there is speculation regarding the image of the brain embedded in the fresco known as "The Creation of Adam," which contains anatomic features of the midsagittal and lateral surfaces of the brain. Within this context, we report our use of Image Pro Plus Software 6.0 to demonstrate mathematical evidence that Michelangelo painted "The Creation of Adam" using the Divine Proportion/Golden Ratio (GR) (1.6). The GR is classically associated with greater structural efficiency and is found in biological structures and works of art by renowned artists. Thus, according to the evidence shown in this article, we can suppose that the beauty and harmony recognized in all Michelangelo's works may not be based solely on his knowledge of human anatomical proportions, but that the artist also probably knew anatomical structures that conform to the GR display greater structural efficiency. It is hoped that this report will at least stimulate further scientific and scholarly contributions to this fascinating topic, as the study of these works of art is essential for the knowledge of the history of Anatomy.
Subject(s)
Famous Persons , Neuroanatomy/history , Paintings/history , History, 15th Century , History, 16th Century , Humans , ItalyABSTRACT
Animals have the innate ability to select optimal defensive behavioral outputs with an appropriate intensity in response to predator threat in specific contexts. Such innate behavioral decisions are thought to be computed in the medial hypothalamic nuclei that contain neural populations directly controlling defensive behavioral outputs. The vomeronasal organ (VNO) is one of the major sensory input channels through which predator cues are detected with ascending inputs to the medial hypothalamic nuclei, especially to the ventromedial hypothalamus (VMH), through the medial amygdala (MeA) and bed nucleus of the stria terminalis (BNST). Here, we show that cat saliva contains predator cues that signal imminence of predator threat and regulate the robustness of freezing behavior through the VNO in mice. Cat saliva activates neurons expressing the V2R-A4 subfamily of sensory receptors, suggesting the existence of specific receptor groups responsible for freezing behavior induced by the predator cues. The number of VNO neurons activated in response to saliva correlates with the freshness of saliva and the intensity of freezing behavior, while the downstream neurons in the accessory olfactory bulb (AOB) and defensive behavioral circuit are quantitatively equally activated by fresh and old saliva. Strikingly, however, only the number of VMH neurons activated by fresh saliva positively correlates with the intensity of freezing behavior. Detailed analysis of the spatial distribution of fresh and old saliva-responding neurons revealed a neuronal population within the VMH that is more sensitive to fresh saliva than old saliva. Taken together, this study demonstrates that predator cues in cat saliva change over time and differentially activate the sensory-to-hypothalamus defensive behavioral pathway to modulate behavioral outputs.
ABSTRACT
This study investigated the occurrence of aflatoxins (B1, B2, G1, and G2) in maize flour produced in Mozambique and to assess the associated carcinogenic risk. At different opportunities, 30 samples of maize flour were collected in five flour processing factories. These were determined by high-performance liquid chromatography (HPLC) with fluorescence detection. AFB1 concentrations ranged from 0.25 to 0.33 µg kg-1. The levels of total aflatoxins ranged from 0.55 to 1.05 µg kg-1, with a mean of 0.89 µg kg-1, for which maximum limits (MLs) are 10 and 4 µg kg-1 for Mozambique and the European Union, respectively. The calculated Margin of Exposure (MOE) for men and women was 243 and 231, respectively, so several folds below the risk cut-off level, indicating that consumption of such maize flour poses a potential risk of hepatocarcinoma related to aflatoxin exposure due to high intake of this food, a staple diet in most African countries.
Subject(s)
Aflatoxins , Flour , Food Contamination , Zea mays , Zea mays/chemistry , Mozambique , Aflatoxins/analysis , Flour/analysis , Humans , Food Contamination/analysis , Risk Assessment , Chromatography, High Pressure Liquid , Female , Male , Aflatoxin B1/analysis , Liver Neoplasms/chemically inducedABSTRACT
Upstream open reading frames (uORFs) are cis-acting elements that can dynamically regulate the translation of downstream ORFs by suppressing downstream translation under basal conditions and, in some cases, increasing downstream translation under stress conditions. Computational and empirical methods have identified uORFs in the 5'-UTRs of approximately half of all mouse and human transcripts, making uORFs one of the largest regulatory elements known. Because the prevailing dogma was that eukaryotic mRNAs produce a single functional protein, the peptides and small proteins, or microproteins, encoded by uORFs were rarely studied. We hypothesized that a uORF in the SLC35A4 mRNA is producing a functional microprotein (SLC35A4-MP) because of its conserved amino acid sequence. Through a series of biochemical and cellular experiments, we find that the 103-amino acid SLC35A4-MP is a single-pass transmembrane inner mitochondrial membrane (IMM) microprotein. The IMM contains the protein machinery crucial for cellular respiration and ATP generation, and loss of function studies with SLC35A4-MP significantly diminish maximal cellular respiration, indicating a vital role for this microprotein in cellular metabolism. The findings add SLC35A4-MP to the growing list of functional microproteins and, more generally, indicate that uORFs that encode conserved microproteins are an untapped reservoir of functional microproteins.
Subject(s)
Mitochondrial Membranes , Mitochondrial Proteins , Nucleotide Transport Proteins , Open Reading Frames , Humans , 5' Untranslated Regions/genetics , Amino Acid Sequence , Mitochondria/metabolism , Mitochondria/genetics , Mitochondrial Membranes/metabolism , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Open Reading Frames/genetics , Protein Biosynthesis , RNA, Messenger/genetics , RNA, Messenger/metabolism , Nucleotide Transport Proteins/genetics , Nucleotide Transport Proteins/metabolism , HEK293 CellsABSTRACT
Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS.
Subject(s)
Data Mining/methods , Databases, Protein , Metabolome/physiology , Models, Biological , Protein Interaction Mapping/methods , Proteome/metabolism , Signal Transduction/physiology , Algorithms , Animals , Computer Simulation , Humans , Periodicals as Topic , PhenotypeABSTRACT
Compounds derived from plants have been widely studied in the context of metabolic diseases and associated clinical conditions. In this regard, although the effects of Camellia sinensis plant, from which various types of teas, such as green tea, originate, have been vastly reported in the literature, the mechanisms underlying these effects remain elusive. A deep search of the literature showed that green tea's action in different cells, tissues, and diseases is an open field in the research of microRNAs (miRNAs). miRNAs are important communicator molecules between cells in different tissues implicated in diverse cellular pathways. They have emerged as an important linkage between physiology and pathophysiology, raising the issue of polyphenols can act also by changing miRNA expression. miRNAs are short, non-coding endogenous RNA, which silence the gene functions by targeting messenger RNA (mRNA) through degradation or translation repression. Therefore, the aim of this review is to present the studies that show the main compounds of green tea modulating the expression of miRNAs in inflammation, adipose tissue, skeletal muscle, and liver. We provide an overview of a few studies that have tried to demonstrate the role of miRNAs associated with the beneficial effects of compounds from green tea. We have emphasized that there is still a considerable gap in the literature investigating the role and likely involvement of miRNAs in the extensive beneficial health effects of green tea compounds already described, indicating miRNAs as potential polyphenols' mediators with a promising field to be investigated.
Subject(s)
Camellia sinensis , MicroRNAs , Tea , MicroRNAs/genetics , MicroRNAs/metabolism , Polyphenols/pharmacology , Polyphenols/metabolism , Camellia sinensis/genetics , Camellia sinensis/metabolism , RNA, Messenger/metabolismABSTRACT
The ultrasound characteristics of thyroid nodules guide the evaluation of thyroid cancer in patients with thyroid nodules. However, the characteristics of thyroid nodules are often documented in clinical narratives such as ultrasound reports. Previous studies have examined natural language processing (NLP) methods in extracting a limited number of characteristics (<9) using rule-based NLP systems. In this study, a multidisciplinary team of NLP experts and thyroid specialists, identified thyroid nodule characteristics that are important for clinical care, composed annotation guidelines, developed a corpus, and compared 5 state-of-the-art transformer-based NLP methods, including BERT, RoBERTa, LongFormer, DeBERTa, and GatorTron, for extraction of thyroid nodule characteristics from ultrasound reports. Our GatorTron model, a transformer-based large language model trained using over 90 billion words of text, achieved the best strict and lenient F1-score of 0.8851 and 0.9495 for the extraction of a total number of 16 thyroid nodule characteristics, and 0.9321 for linking characteristics to nodules, outperforming other clinical transformer models. To the best of our knowledge, this is the first study to systematically categorize and apply transformer-based NLP models to extract a large number of clinical relevant thyroid nodule characteristics from ultrasound reports. This study lays ground for assessing the documentation quality of thyroid ultrasound reports and examining outcomes of patients with thyroid nodules using electronic health records.