Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis

Comparison of logistic regression, SVM and random forest performance in the plasma training data set. Table S2. Pathway significance and relative log fold changes in our metabolomics data and TCGA breast cancer RNA-Seq data. Table S3. Detected metabolites and their differential test results among the two models. a All-stage diagnosis model. b Early-stage diagnosis model. Table S4. Single-variate logistic analysis of metabolites or pathways selected as features in the metabolite-based or pathway-based early-stage diagnosis model. Table S5. Comparison of pathway features in the full-size (101 input pathways) and half-size (51 input pathways) pathway-based early-stage diagnosis models. (DOCX 34 kb

A Metabolomics-Based Strategy for the Quality Control of Traditional Chinese Medicine: Shengmai Injection as a Case Study

Quality control of traditional Chinese medicines (TCMs) used clinically is becoming a challenge and has limited the development of TCM due to the high variability in concentration levels of active ingredients and markers as well as the lack of well-established criteria. Using Shengmai injection, which is a well-established TCM, as an example, we developed an integrated profiling approach that simultaneously captures the entire spectrum of ingredients and quantitatively determines the levels of seven key ingredients in the TCM product. A multivariate statistical model was constructed to establish a “seven-marker-” based quality standard that qualified the majority of samples in this study. This newly developed strategy showed that a panel of key ingredients or markers in the TCM product were relatively consistent within a statistically acceptable range. Therefore, this metabolomics-based approach will complement the current quality control standard using the concentration of several key ingredients or their total content and help improve the consistency and clinic efficacy of TCM products

Urine Metabolite Profiling Offers Potential Early Diagnosis of Oral Cancer

Oral cancer is the sixth most common human cancer, with a high morbidity rate and an overall 5-year survival rate of less than 50%. It is often not diagnosed until it has reached an advanced stage. Therefore, an early diagnostic and stratification strategy is of great importance for oral cancer. In the current study, urine samples of patients with oral squamous cell carcinoma (OSCC, n = 37), oral leukoplakia (OLK, n = 32) and healthy subjects (n = 34) were analyzed by gas chromatography-mass spectrometry (GC–MS). Using multivariate statistical analysis, the urinary metabolite profiles of OSCC, OLK and healthy control samples can be clearly discriminated and a panel of differentially expressed metabolites was obtained. Metabolites, valine and 6-hydroxynicotic acid, in combination yielded an accuracy of 98.9%, sensitivity of 94.4%, specificity of 91.4%, and positive predictive value of 91.9% in distinguishing OSCC from the controls. The combination of three differential metabolites, 6-hydroxynicotic acid, cysteine, and tyrosine, was able to discriminate between OSCC and OLK with an accuracy of 92.7%, sensitivity of 85.0%, specificity of 89.7%, and positive predictive value of 91.9%. This study demonstrated that the metabolite markers derived from this urinary metabolite profiling approach may hold promise as a diagnostic tool for early stage OSCC and its differentiation from other oral conditions

Management of Hepatic Encephalopathy by Traditional Chinese Medicine

In spite of the impressive progress in the investigation of hepatic encephalopathy (HE), the complex mechanisms underlying the onset and deterioration of HE are still not fully understood. Currently, none of the existing theories provide conclusive explanations on the symptoms that link liver dysfunction to nervous system disorders and clinical manifestations. This paper summarized the diagnostic and therapeutic approaches used for HE in modern medicine and traditional Chinese medicine and provided future perspective in HE therapies from the viewpoint of holistic and personalized Chinese medicine

Management of Hepatic Encephalopathy by Traditional Chinese Medicine

In spite of the impressive progress in the investigation of hepatic encephalopathy (HE), the complex mechanisms underlying the onset and deterioration of HE are still not fully understood. Currently, none of the existing theories provide conclusive explanations on the symptoms that link liver dysfunction to nervous system disorders and clinical manifestations. This paper summarized the diagnostic and therapeutic approaches used for HE in modern medicine and traditional Chinese medicine and provided future perspective in HE therapies from the viewpoint of holistic and personalized Chinese medicine

Waterborne Manganese Exposure Alters Plasma, Brain, and Liver Metabolites Accompanied by Changes in Stereotypic Behaviors

Overexposure to waterborne manganese (Mn) is linked with cognitive impairment in children and neurochemical abnormalities in other experimental models. In order to characterize the threshold between Mn-exposure and altered neurochemistry, it is important to identify biomarkers that positively correspond with brain Mn-accumulation. The objective of this study was to identify Mn-induced alterations in plasma, liver, and brain metabolites using liquid/gas chromatography–time of flight–mass spectrometry metabolomic analyses; and to monitor corresponding Mn-induced behavior changes. Weanling Sprague–Dawley rats had access to deionized drinking water either Mn-free or containing 1 g Mn/L for 6 weeks. Behaviors were monitored during the sixth week for a continuous 24 h period while in a home cage environment using video surveillance. Mn-exposure significantly increased liver, plasma, and brain Mn concentrations compared to control, specifically targeting the globus pallidus (GP). Mn significantly altered 98 metabolites in the brain, liver, and plasma; notably shifting cholesterol and fatty acid metabolism in the brain (increased oleic and palmitic acid; 12.57 and 15.48 fold change (FC), respectively), and liver (increased oleic acid, 14.51 FC; decreased hydroxybutyric acid, - 14.29 FC). Additionally, Mn-altered plasma metabolites homogentisic acid, chenodeoxycholic acid, and aspartic acid correlated significantly with GP and striatal Mn. Total distance traveled was significantly increased and positively correlated with Mn-exposure, while nocturnal stereotypic and exploratory behaviors were reduced with Mn-exposure and performed largely during the light cycle compared to unexposed rats. These data provide putative biomarkers for Mn-neurotoxicity and suggest that Mn disrupts the circadian cycle in rats

Metabolic Substrates Exhibit Differential Effects on Functional Parameters of Mouse Sperm Capacitation

Although substantial evidence exists that sperm ATP production via glycolysis is required for mammalian sperm function and male fertility, conflicting reports involving multiple species have appeared regarding the ability of individual glycolytic or mitochondrial substrates to support the physiological changes that occur during capacitation. Several mouse models with defects in the signaling pathways required for capacitation exhibit reductions in sperm ATP levels, suggesting regulatory interactions between sperm metabolism and signal transduction cascades. To better understand these interactions, we conducted quantitative studies of mouse sperm throughout a 2-h in vitro capacitation period and compared the effects of single substrates assayed under identical conditions. Multiple glycolytic and nonglycolytic substrates maintained sperm ATP levels and comparable percentages of motility, but only glucose and mannose supported hyperactivation. These monosaccharides and fructose supported the full pattern of tyrosine phosphorylation, whereas nonglycolytic substrates supported at least partial tyrosine phosphorylation. Inhibition of glycolysis impaired motility in the presence of glucose, fructose, or pyruvate but not in the presence of hydroxybutyrate. Addition of an uncoupler of oxidative phosphorylation reduced motility with pyruvate or hydroxybutyrate as substrates but unexpectedly stimulated hyperactivation with fructose. Investigating differences between glucose and fructose in more detail, we demonstrated that hyperactivation results from the active metabolism of glucose. Differences between glucose and fructose appeared to be downstream of changes in intracellular pH, which rose to comparable levels during incubation with either substrate. Sperm redox pathways were differentially affected, with higher levels of associated metabolites and reactive oxygen species generated during incubations with fructose than during incubations with glucose

Fine Mapping of a Novel Heading Date Gene, TaHdm605, in Hexaploid Wheat

The heading date is critical in determining the adaptability of plants to specific natural environments. Molecular characterization of the wheat genes that regulate heading not only enhances our understanding of the mechanisms underlying wheat heading regulation but also benefits wheat breeding programs by improving heading phenotypes. In this study, we characterized a late heading date mutant, m605, obtained by ethyl methanesulfonate (EMS) mutation. Compared with its wild-type parent, YZ4110, m605 was at least 7 days late in heading when sown in autumn. This late heading trait was controlled by a single recessive gene named TaHdm605. Genetic mapping located the TaHdm605 locus between the molecular markers cfd152 and barc42 on chromosome 3DL using publicly available markers and then further mapped this locus to a 1.86 Mb physical genomic region containing 26 predicted genes. This fine genetic and physical mapping will be helpful for the future map-based cloning of TaHdm605 and for breeders seeking to engineer changes in the wheat heading date trait

Observation of Blackbody Radiation Enhanced Superradiance in Ultracold Rydberg Gases

An ensemble of excited atoms can synchronize emission of light collectively in a process known as superradiance when its characteristic size is smaller than the wavelength of emitted photons. The underlying superradiance depends strongly on electromagnetic (photon) fields surrounding the atomic ensemble. High mode densities of microwave photons from 300 K blackbody radiation (BBR) significantly enhance decay rates of Rydberg states to neighbouring states, enabling superradiance that is not possible with bare vacuum induced spontaneous decay. Here we report observations of the superradiance of ultracold Rydberg atoms embedded in a bath of room-temperature photons. The temporal evolution of the Rydberg |nD to |(n + 1)P superradiant decay of Cs atoms (n the principal quantum number) is measured directly in free space. Theoretical simulations confirm the BBR enhanced superradiance in large Rydberg ensembles. We demonstrate that the van der Waals interactions between Rydberg atoms change the superradiant dynamics and modify the scaling of the superradiance. In the presence of static electric fields, we find that the superradiance becomes slow, potentially due to many-body interaction induced dephasing. Our study provides insights into many-body dynamics of interacting atoms coupled to thermal BBR, and might open a route to the design of blackbody thermometry at microwave frequencies via collective, dissipative photon-atom interactions