Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

Tutorial: Capillary Electrophoresis

In recent years a number of exciting developments have emerged in the area of scientific computational tools for classroom use. Computer Algebra Systems (CASs), for example, Maple, are at the forefront of this arena. Such tools have been long sought by teachers of physical chemistry, inherently a mathematics intensive subject. With a CAS at hand, students can look forward to taking college science courses, like physical chemistry, without the usual mathematics anxiety. These tools can be used to do numerical and symbolic mathematics including calculus and linear algebra. In addition, they have wonderful graphics capabilities that include three-dimensional plots, contour plots, and animations. This paper describes the implementation of Maple in two junior-level physical chemistry courses. The materials used for beginning workshops are presented here and additional examples of Maples graphic and algebraic capabilities are described.     

Folded chain crystals as micro-phases

Summary A thermodynamic treatment of homo-polymer systems out of linear chains with folded chain crystals is developed outgoing from appropriate models for single component systems. An expansion of thermodynamics to multi-micro-phase systems the structure of which is partially or totaly frozen is indispensable. General properties of melt crystallized homopolymers with folded chain crystals can be recognized indeed when the thermodynamic formalisms developed are applied.

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Zusammenfassung Das Schmelzen in polymeren Einteilchensystemen mit Faltungskristallen einheitlicher Dicke kann thermodynamisch als Umwandlung 1. Ordnung in einer Richtung behandelt werden, wenn die Faltungslänge bis zur Umwandlungstemperatur konstant bleibt (Faltungslänge als innerer Zusatzparameter). Eine wesentliche begriffliche Erweiterung ist für eine phänomenologische Beschreibung mit den Mitteln der Thermodynamik unumgänglich, wenn eine Faltungskristallit-Dickenverteilung existiert, weil dann prinzipiell nur noch partielle Koexistenz bestimmter Fraktionen metastabiler autonomer Mikrophasen mit der Schmelze möglich ist. Partielles Aufschmelzen und Rektistallisation können so dann auch in Betracht genommen werden. Die entwickelten Konzeptionen bewähren sich in der Anwendung auf bekannte Experimente.

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Notation g ^c (y);g ^m (Y) molar Gibbs-free energy of a chain of a lengthy within an extended chain crystal and the melt rsp - g _o ^c ;g _o ^m molar free enthalpy of the unit in the crystal lattice and the melt rsp - g(y,y, f) molar Gibbs-function of an ideally folded chain crystal with the fold heighty _f - gco(y, y _ef,y _f) molar free enthalpy of the crystal corey _co - g ₀ ^ex ((y_ef) excess free enthalpy of the longitudinal layers of folded chain crystals - g ^f(y_ef,g _o ^ex ) molar free enthalpy of the longitudinal layers of the folded chain crystals - g ^tot molar free enthalpy of a chain of the lengthy within a folded chain crystal with longitudinal layers - h _o ^1c ,h _o ^m molar enthalpy of the chain unit within the crystal lattice and the melt rsp - h =h _o ^m -h _o ^c molar heat of fusion of the unit - C _p=C _p ^m -C _p ^c difference of the molar specific heat of a unit within the melt and within the chain crystal - h ^D molar defect enthalpy of local defects within the crystal lattice - h ^D molar defect enthalpy of the unit - s _o ^c ,s _o ^m molar entropy of the chain unit within the crystal lattice and the melt rsp - s _c ^m conformational entropy of a chain in the melt - s _gk conformational entropy of a chain of lengthy within a super-lattice as indicated in figure 5, - s molar entropy of fusion of the melt - s _n ^c nematic configurational entropy - T absolute temperature - T _M melting temperature of extended chain crystals of infinite size - T _M(y) melting temperature of extended chain crystals containing only chains of the lengthy - T _M (y, y _f) melting temperatureof folded chain crystals of the thicknessy _f composed of chains of the lengthy - T _M(y _f) melting temperature of folded chain crystals of the thicknessy _fy - _eh excess free enthalpy of the chain ends occupying crystallographic places - _ef excess free enthalpy of a single fold loop - z coordination number of the lattice - 7 Euler's constant - R Boltzmann's constant - y number of chain units - y _f height of lamelliform folded chain crystals - f=(y/y _f - 1) number of fold loops of a chain of a lengthy when being built into a folded chain crystal of the thicknessy _f - y _co thickness of the crystal core of the simplified twophase model - y _et average thickness of the surface layers of folded chain crystals - N _c number of crystallized units of a chain of the lengthy - x _c molar number of crystallized units of a chain of the lengthy - x _nc molar number of noncrystallized units - excess free enthalpy parameter - (y _f) thickness distribution of the fold heightsy _f With 15 figures and 2 tables     

Über 1-Alkyl-bzw. 1-Aryl-dihydro-6-methyl-2(1H)-pyrimidinthione

The title compounds7 are formed in a general reaction by heating β-isothiocyanoketones3 with primary amines in inert solvents, or by thermal elimination of water from tetrahydro-6-hydroxy-6-methyl-2(1H)-pyrimidinethiones5, also in inert solvents. The 1-alkyl compounds can also be prepared under similar conditions from α,β-unsaturated ketones by reaction with alkylammonium rhodanides. The NMR-spectra show that the 1-substituted dihydro-6-methyl-2(1H)-pyrimidinethiones are in tautomeric equilibrium with the tetrahydro-6-methylene-2(1H)-pyrimidinethiones13. The reactivity of 1-alkyl and 1-aryldihydro-6-methyl-2(1H)-pyrimidinethiones is similar to that of dihydro-4,4,6-trimethyl-2(1H)-pyrimidinethione7 j, although their ring stability is certainly less.     

Beiträge zur Chemie des Sulfamids, 1. Mitt.: Zur Konstitution des Disilber-sulfamids

According to spectroscopic (IR, broadline proton NMR) and chemical (alkylation) investigations of disilver sulphamide the following molecular structure is assumed: $$\begin{gathered} O \hfill \\ || \hfill \\ H_2 N\_\_S\_\_NAg| \hfill \\ OAg \hfill \\ \end{gathered}$$ From the IR and NMR data deduction concerning the nature of the chemical bonds in this compound is possible. The instability of the still unknown mono-and trisilver sulphamide is discussed with regard to the structure of disilver sulphamide.     

Synthesis, crystal structure and magnetic property of the novel dinuclear nickel(II) complex with 4-(p-methoxyphenyl)-3,5-bis(pyridine-2-yl)-1,2,4-triazole

A novel dinuclear nickel(II) complex, [Ni₂(MOBPT)₂Cl₂(H₂O)₂]Cl₂ · 7H₂O (MOBPT = 4-(p-methoxyphenyl) −3,5-bis(pyridine-2-yl)-1,2,4-triazole), has been synthesized and characterized by elemental analysis, IR and single crystal X-ray diffraction methods. The crystal structure determination shows that the dinuclear Ni₂N₈ unit is almost planer in which each Ni^II ion is coordinated by four nitrogen atoms from MOBPT equatorially and a water molecule and a chloride ion axially in a distorted octahedral geometry. Magnetic measurements reveal a relatively weak antiferromagnetic exchange in the complex.     

A small molecule with osteogenesis-inducing activity in multipotent mesenchymal progenitor cells

Purmorphamine, which is a 2,6,9-trisubstituted purine compound, was discovered through cell-based high-throughput screening from a heterocycle combinatorial library. It differentiates multipotent mesenchymal progenitor cells into an osteoblast lineage. It will serve as a unique chemical tool to study the molecular mechanisms of osteogenesis of stem cells and bone development.     

Near-infrared fluorimetric determination of nucleic acids by shifting the ion-association equilibrium between heptamethylene cyanine and Alcian blue 8GX

A new method based on near-infrared (near-IR) fluorescence recovery, employing a two-reagent system which is composed of an anionic heptamethylene cyanine (HMC) and a polycationic phthalocyanine dye, Alcian blue 8GX, is presented for the determination of nucleic acids. With a maximum excitation wavelength at 766 nm and a maximum emission wavelength at 796 nm, the fluorescence recovery is linear with the concentration of nucleic acids added. Factors including the acidity of the medium, the reaction time, the optimal ratio of the two reagents, as well as the influence of foreign substance were all investigated. Meanwhile, the mechanism of fluorescence recovery was also studied. Under the optimal conditions, the linear ranges of the calibration curves were 10-250 ng ml⁻¹ for calf thymus DNA (CT DNA) and 10-200 ng ml⁻¹ for yeast RNA. The detection limits were 6.8 ng ml⁻¹ for CT DNA and 6.3 ng ml⁻¹ for yeast RNA, respectively. The method has been applied to the analysis of practical samples and the recovery results were satisfactory.     

Optical properties of ZnO and ZnO:In nanorods assembled by sol-gel method

Self-assembled zinc oxide (ZnO) and indium-doping zinc oxide (ZnO:In) nanorod thin films were synthesized on quartz substrates without catalyst in aqueous solution by sol-gel method. The samples were characterized by x-ray diffraction (XRD), scanning electron microscope (SEM), Raman-scattering spectroscopy, room-temperature photoluminescence (PL) spectra, and temperature-dependent PL spectra measurements. XRD and Raman spectra illustrated that there were no single In2O3 phase in ZnO lattice after indium doping. The PL spectra of ZnO showed a strong UV emission band located at 394 nm and a very weak visible emission associated with deep-level defects. Indium incorporation induced the shift of optical band gap, quenching of the near-band-edge photoluminescence and enhanced LO mode multiphonon resonant Raman scattering in ZnO crystals at different temperatures. Abnormal temperature dependence of UV emission integrated intensity of ZnO and ZnO:In samples is observed. The local state emission peak of ZnO:In samples at 3.37 eV is observed in low-temperature PL spectra. The near-band-edge emission peak at room temperature was a mixture of excitons and impurity-related transitions for both of two samples.