Fundamental Molecules Research Articles

A primer on molecular biology for imagers: IV. Concepts and basic methods in molecular biology 1

In this review article series so far, we have covered the three fundamental molecules: DNA, RNA, and proteins, and some of the basic processes inside the cell that these molecules are part and parcel of ( 1 Pandit S.D. Bednarski M. Li K.C. Review article series. A primer on molecular biology for imagers: I. DNA, how does it work?. Acad Radiol. 2003; 10: 1215-1223 Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar , 2 Pandit S.D. Li K.C. Review article series. A primer on molecular biology for imagers. II. Transcription and gene expression. Acad Radiol. 2004; 11: 333-344 Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar , 3 Pandit S.D. Li K.C. Review article series. A primer on molecular biology for imagers: III. Proteins: structure and function. Acad Radiol. 2004; 11: 448-461 Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar ). The challenge for us in terms of writing a review article on “methods in molecular biology” is how to make it interesting and not a drab rendition of procedures, many examples of which are already available. Keeping this in mind, we have covered some of the very basic procedures that a radiologist, molecular imager, chemist, or physicist as a part of a multi-disciplinary team in molecular imaging would be required to know. We have attempted to emphasize the principles behind the molecular biology protocols rather than the procedures themselves.

A primer on molecular biology for imagers: IV. concepts and basic methods in molecular biology 1

In this review article series so far, we have covered the three fundamental molecules: DNA, RNA, and proteins, and some of the basic processes inside the cell that these molecules are part and parcel of (1,2,3). The challenge for us in terms of writing a review article on “methods in molecular biology” is how to make it interesting and not a drab rendition of procedures, many examples of which are already available. Keeping this in mind, we have covered some of the very basic procedures that a radiologist, molecular imager, chemist, or physicist as a part of a multi-disciplinary team in molecular imaging would be required to know. We have attempted to emphasize the principles behind the molecular biology protocols rather than the procedures themselves.

Molecular Pathology of Angiogenesis, Abstract 139, State-of-the-art lecture

Lymph node metastasis is an essential determinant for stage and clinical management of non-small cell lung cancer (NSCLC). The vascular endothelial growth factors (VEGFs) and receptors (VEGFRs) are fundamental molecules in angiogenesis and lymphangiogenesis. We aimed to explore the correlations between nodal metastasis and the expression of VEGFs and VEGFRs in tumor cells and in tumor-related stroma.Tumor tissue samples from 335 resected patients with stage I–IIIA NSCLC were obtained and tissue microarrays were constructed from duplicate cores of tumor cells and surrounding stromal tissue from each resected specimen. Immunohistochemistry was used to evaluate the expression of VEGF-A, VEGF-C, and VEGF-D and VEGFR-1, VEGFR-2 and VEGFR-3.There were 232 N0 and 103 N+ patients (76 N1, 27 N2). In multivariate analyses, low stromal VEGF-A expression (P = 0.018) is associated with N+ status. In tumor cells, strong correlations exist between high VEGF-A expression (P = 0.032) and N+ status, and high VEGFR-3 expression (P < 0.001) and N2-status.The converse impact by stromal VEGF-A versus tumor cell VEGF-A expression on nodal metastasis may allude the importance of the tumor–stroma interaction when trying to understand lymphatic metastasis in NSCLC.

Quantitative assessment of tumor oxygen dynamics: molecular imaging for prognostic radiology.

One of the fundamental molecules governing the survival of mammalian cells is oxygen. Oxygen has gained particular significance in tumor developmental biology and oncology. An increasingly diverse array of methods is now available to characterize tumor oxygenation. This Prospect will consider a new method, Fluorocarbon Relaxometry using Echo planar imaging for Dynamic Oxygen Mapping (FREDOM), which we have recently developed for oximetry, examine application to a specific therapeutic example and place this technique in the context of other approaches.

Toward a More Accurate Silicon Stereochemistry: An Electron Diffraction Study of the Molecular Structure of Tetramethylsilane

The present electron diffraction study of the molecular structure of tetramethylsilane, augmented with theoretical calculations, answers the need for accurate and detailed information on the most fundamental molecules containing silicon. The Si—C bond length is r g = 1.877 ± 0.004 A, in perfect agreement with a previous study (Beagley, B.; Monaghan, J. J.; Hewitt, T. G. J. Mol. Struct. 1971 8 401). The C—H bond length is r g= 1.110 ± 0.003 A and the Si—C—H angle is 111.0 ± 0.2°. The experimental data are consistent with a model of T d symmetry and staggered methyl conformation. The barrier to methyl rotation is estimated to be 5.7 ± 2.0 kJ mol−1 on the basis of the experimentally observed average torsion of the methyl groups.

Theoretical results which strengthen the hypothesis of electroweak bioenantioselection

It is shown via a large series of numerical tests on two fundamental organic molecules, the $L\ensuremath{-}\ensuremath{\alpha}$-amino acid L-valine and the sugar precursor hydrated D-glyceraldheyde, that the ab initio calculation of the parity-violating energy shift, at the random-phase approximation level of accuracy, provides results that are about one order of magnitude larger than those obtained by means of less accurate methods employed previously. These findings would make more plausible the hypothesis of electroweak selection of natural enantiomers via the Kondepudi-Nelson scenario, or could imply that Salam phase-transition temperature is higher than previously inferred: accordingly, the hypothesis of terrestrial origin of life would become more realistic.

Understanding structure and reactivity of new fundamental inorganic molecules: metal sulfides, metallocarbohedrenes, and nitrogenase

A large number of new and unexpected molecules, fundamentally inorganic and containing just metal and sulfur, or metal and carbon, can be synthesised in the gas phase, and their reactivities investigated. In the absence of bulk samples and definitive characterisation data they can be very profitably investigated using density functional calculations. A valuable perspective places these new and unprotected molecules in the context of related non-molecular solids, and terminally ligated molecules. The Fe7MoS9 cluster which effects the mild reduction of N2 at the active site of nitrogenase is similarly undercoordinated, floppy, and reactive. Density functional calculations reveal the characteristics of the Fe7MoS9 site and elucidate postulated mechanisms for the reduction.

Reproduction of ab initio electrostatic potential with classical fractional point charges.

New additional charge sets, which were added to correct the electrostatic potential (ESP) values on the van der Waals molecular surface using Mulliken net atomic charges, were found to reproduce ab initio ESP with the STO-3G basis set. The charge sets were obtained for fundamental small molecules (water, ammonia. methane. ethane, and benzene). Lone pair regions of oxygen and nitrogen atoms show remarkable improvement, while pi electrons do not contribute much to ESP. The present work opens a way for treating large molecules of biological interest.

Two-photon MPI spectroscopy of alkyl iodides

The two-photon resonant multiphoton ionization (MPI) spectra of methyl iodide, methyl iodide-d 3, ethyl, propyl, and butyl iodide are reported in the 49 000-55 000 cm −1 region. Four separate transitions to excited states labeled Δ, Π, Σ, Π in increasing energy are expected in this range which result from the excitation of an iodine 5pπ electron to the 6s molecular Rydberg orbital. Two-photon spectroscopy with its different selection rules and unique dependence on the laser polarization is shown to significantly advance the understanding of these transitions. In particular, laser polarization studies identify a state which is strongly two-photon allowed but absent in the UV absorption spectrum as the Σ state. Rotational contours indicate a large geometry change takes place in this transition. The two Π states appear strongly in both the one-and two-photon spectrum. Polarization analysis confirms their electronic symmetry assignment in addition to distinguishing vibronic bands arising from nontotally symmetric vibrations. No evidence is found for the Δ state in the multiphoton ionization spectrum, due to either a small two-photon cross section or a low probability of ionization following the initial two-photon transition. Further complications and characteristics of single laser MPI spectroscopy in the study of two-photon absorption in methyl iodide and other fundamental molecules are discussed.

Energy transfer of argon excited diatomic molecules

Argon excited diatomic molecules Ar*2(3𝒥+u)were produced by irradiating argon gas with short electron beam pulses. The kinetic behavior was studied by monitoring the time dependence of the 987.6 nm absorption band due to Ar*2 under various conditions.The method is largely different from the vacuum UV emission spectroscopy used previously in such kinetic studies. Ar*2 was found to be produced by a three-body reaction with a rate constant of (1.0±0.3) ×10−32 cm 6 sec−1. Then, the rate constants and cross sections of energy transfer were determined for 12 fundamental acceptor molecules. The theoretical formula proposed previously for Penning ionization was applied to energy transfer between Ar*2 cross sections given by the formula have the values comparable to the observed ones.

Recent Advances in Studies of Molecular Transition Probabilities

The development of high power electron excitation applied in the High Frequency Deflection technique has enabled time resolved precision spectroscopy to be performed with a resolving power as high as 1:105. This is typically a two orders of magnitude higher resolution than what is commonly achieved using other approaches and this has created new possibilities of studying hitherto unknown properties of fundamental molecules. Thus a great number of time resolved studies of individual rotational levels including resolved spin-orbit and Λ components show that radiationless destructions of molecules are much more common in nature than earlier believed implying a violation of the Born Oppenheimer approximation which demands new theoretical treatments of molecular structure. Among important applications of the radiationless processes should be mentioned determinations of dissociation energies with superior accuracy and molecular formation rates. An extensive programme for theoretical studies of the obtained results is in progress in collaboration with the quantum chemistry groups in Århus and Uppsala. This programme also includes precision estimates of oscillator strengths with applications to molecular abundance estimates and to laser physics.

Electronic Structures and Spectra of Quinarene Molecules

Abstract The electronic structures and spectra of fundamental quinarene molecules, 1–9 (Fig. 1) and some of their diphenyl derivatives (Fig. 2) have been studied by using the variable bond-length SCF LCAO-π-MO CI method.

The system albite‐wollastonite‐nepheline

A study has been made of the high‐temperature equilibrium‐relations, at atmospheric pressure, of the three silicates sodium aluminium polysilicate, calcium metasilicate, and sodium aluminium orthosilicate. These constitute the fundamental molecules of the rock‐forming minerals‐albite, wollastonite, and nepheline, respectively. The system forms a plane in the quaternary system soda‐lime‐alumina‐silica. As a preliminary to the study, two of the limiting systems were investigated, namely, nepheline‐wollastonlte and albite‐wollastonite. The three minerals concerned do not form a true ternary system, there being a plagioclase field instead of one of albite. The minimum‐temperature point of the entire system is the albite‐nepheline eutectic.