Label-free differentiation of human pituitary adenomas by FT-IR spectroscopic imaging

Fourier transform infrared (FT-IR) spectroscopic imaging has been used to characterize different types of pituitary gland tumors and normal pituitary tissue. Freshly resected tumor tissue from surgery was prepared as thin cryosections and examined by FT-IR spectroscopic imaging. Tissue types were discriminated via k-means cluster analysis and a supervised classification algorithm based on linear discriminant analysis. Spectral classification allowed us to discriminate between tumor and non-tumor cells, as well as between tumor cells that produce human growth hormone (hGH+) and tumor cells that do not produce that hormone (hGH−).The spectral classification was compared and contrasted with a histological PAS and orange G stained image. It was further shown that hGH+ pituitary tumor cells show stronger amide bands than tumor cells that do not produce hGH. This study demonstrates that FT-IR spectroscopic imaging can not only potentially serve as a fast and objective approach for discriminating pituitary gland tumors from normal tissue, but that it can also detect hGH-producing tumor cells.     

Application of genetic algorithms in molecular modeling

A genetic algorithm has been developed for molecular mechanics calculations. It has been proved to be a robust and efficient structure optimization technique. Because it uses randomly generated starting structures and stochastic operators, the resulting structures are not subjected to the chemist's bias. © 1994 by John Wiley & Sons, Inc.     

Kinetics of phase changes in large molecular clusters

A method has been devised to study the kinetics of phase changes in an unfamiliar regime of extreme undercooling and rate of transformation. We show how electron diffraction can monitor the time evolution of phase changes in molecular clusters condensed from the vapor in supersonic flow. Transitions taking place in microseconds are readily followed. Examples include solid state transformations as well as the freezing of liquid clusters. Aspects of the experiment making it possible to observe familiar transitions under highly unusual conditions will be discussed along with some advantages of the new technique.     

The dynamics of phase changes in molecular clusters

The significant advantages offered by systems of molecular clusters in the study of homogeneous nucleation are discussed. Determinations of nucleation rates in clusters can be followed experimentally in supersonic jets or computationally in molecular dynamics simulations. Extraordinarily high rates may be encountered, both in freezing and in solid-state transitions. From such information can be inferred the interfacial free energies, σ_sl and σ_SS, mechanisms of solid-state transitions. and an explanation of why certain crystalline phases not found in bulk systems can be seen in large molecular clusters.     

Solvent induced molecular magnetic changes observed in single-crystal-to-single-crystal transformation

Single-crystal-to-single-crystal (SCSC) transformations have recently been found in some molecular magnets, which involve rearrangement or dynamic movement of molecular components of the crystals. Various stimuli such as guest removal, guest exchange, ligand exchange as well as redox reactions may induce SCSC transformations. To date, only a few molecular magnets are known to exhibit SCSC transformations, which often show high-dimensional robust structures. This review mainly focuses on magnetic complexes that are robust enough to experience SCSC transformations and show magnetic changes induced by solvents in due course. This contribution is organized according to the means of solvent treatment of molecular magnets, aiming at revealing magneto-structural correlation in such SCSC transformations.     

Analysis of molecular shape changes along reaction paths

In this work, a detailed discussion and illustrative example are given for a new conceptual approach to the notion of similarity between nuclear configurations. We analyze the changes in molecular shape, as described by a topological characterization of molecular envelope surfaces, along reaction paths. This approach provides an independent definition of formal species along the path, defined in terms of molecular shape, rather than based on the curvature properties of the potential energy function. The two approaches are compared in this work, using the [1,3] hydrogen-shift in formic acid as an illustrative example. The reaction is studied at SCF and MP 2 ab initio levels. Although the actual reaction paths are different, the molecular shape changes encountered along them are similar, indicating that the essential shape changes provide chemical information on a more fundamental level than do detailed reaction paths.     

Sequence‐related amplified polymorphism,an effective molecular approach for studying genetic variation in Fasciola spp. of human and animal health significance

In the present study, a recently described molecular approach, namely sequence‐related amplified polymorphism (SRAP), which preferentially amplifies ORFs, was evaluated for the studies of genetic variation among Fasciola hepatica, Fasciola gigantica and the “intermediate” Fasciola from different host species and geographical locations in mainland China. Five SRAP primer combinations were used to amplify 120 Fasciola samples after ten SRAP primer combinations were evaluated. The number of fragments amplified from Fasciola samples using each primer combination ranged from 12 to 20, with an average of 15 polymorphic bands per primer pair. Fifty‐nine main polymorphic bands were observed, ranging in size from 100 to 2000 bp, and SRAP bands specific to F. hepatica or F. gigantica were observed. SRAP fragments common to F. hepatica and the “intermediate” Fasciola, or common to F. gigantica and the “intermediate” Fasciola were identified, excised and confirmed by PCR amplification of genomic DNA using primers designed based on sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair‐group method with arithmetic averages clustering algorithm categorized all of the examined representative Fasciola samples into three groups, representing the F. hepatica, the “intermediate” Fasciola, or the F. gigantica. These results demonstrated the usefulness of the SRAP technique for revealing genetic variability between F. hepatica, F. gigantica and the “intermediate” Fasciola, and also provided genomic evidence for the existence of the “intermediate” Fasciola between F. hepatica and F. gigantica. This technique provides an alternative and a useful tool for the genetic characterization and studies of genetic variability in parasites.     

Analysis of the genetic algorithm method of molecular conformation determination

Many important problems in chemistry require knowledge of the 3-D conformation of a molecule. A commonly used computational approach is to search for a variety of low-energy conformations. Here, we study the behavior of the genetic algorithm (GA) method as a global search technique for finding these low-energy conformations. Our test molecule is cyclic hexaglycine. The goal of this study is to determine how to best utilize GAs to find low-energy populations of conformations given a fixed amount of CPU time. Two measures are presented that help monitor the improvement in the GA populations and their loss of diversity. Different hybrid methods that combine coarse GA global search with local gradient minimization are evaluated. We present several specific recommendations about trade-offs when choosing GA parameters such as population size, number of generations, rate of interaction between subpopulations, and combinations of GA and gradient minimization. In particular, our results illustrate why approaches that emphasize convergence of the GA can actually decrease its effectiveness as a global conformation search method. © John Wiley & Sons, Inc.     

Self-organization of molecular systems and evolution of the genetic apparatus

The aim of the work described in this report is to find pathways leading to self-organization of molecular systems. The idea is not to trace the historical pathway of evolution but to describe a model whose experimental verification should help to clarify the important principles of evolution. The difficulty of accepting the origin of living organisms as a physico-chemical phenomenon and the deeply rooted notion that a system of such complexity as the genetic apparatus could never be the outcome of processes based solely on the known laws of physics have influenced philosophical thinking very strongly. This study is also intended as an attempt to overcome this psychological problem by systematic pursuit of a model pathway composed of many, readily comprehensible steps. A process thus becomes understandable which cannot be grasped as a whole, and is therefore alien to our conceptual habits.     

Heat-induced changes to lipid molecular structure in Vimy flaxseed: spectral intensity and molecular clustering

Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed (Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH(3) asymmetric (ca. 2959 cm(-1)), CH(2) asymmetric (ca. 2928 cm(-1)), CH(3) symmetric (ca. 2871 cm(-1)) and CH(2) symmetric (ca. 2954 cm(-1)) functional groups, lipid carbonyl CO ester group (ca. 1745 cm(-1)), lipid unsaturation group (CH attached to CC) (ca. 3010 cm(-1)) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120°C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease (P<0.05) in the CH(2) asymmetric to CH(3) asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects (P<0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH(2) asymmetric to CH(3) asymmetric stretching vibration intensity. Autoclaving had no significant effect (P>0.05) on lipid carbonyl CO ester group and lipid unsaturation group (CH attached to CC) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH(3) and CH(2) asymmetric and symmetric region (ca. 2988-2790 cm(-1)). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.     

Optimization of a genetic algorithm for searching molecular conformer space

We present two sets of tunings that are broadly applicable to conformer searches of isolated molecules using a genetic algorithm (GA). In order to find the most efficient tunings for the GA, a second GA--a meta-genetic algorithm--was used to tune the first genetic algorithm to reliably find the already known a priori correct answer with minimum computational resources. It is shown that these tunings are appropriate for a variety of molecules with different characteristics, and most importantly that the tunings are independent of the underlying model chemistry but that the tunings for rigid and relaxed surfaces differ slightly. It is shown that for the problem of molecular conformational search, the most efficient GA actually reduces to an evolutionary algorithm.     

Thermal-induced changes in molecular magnets based on prussian blue analogues

The thermal-induced changes in molecular magnets based on Prussian blue analogues, M(3)[Fe(CN)(6)](2).xH(2)O (M = Mn, Co, Ni, Cu, Zn, and Cd), were studied from infrared, X-ray diffraction, thermo-gravimetric, M?ssbauer, and magnetic data. Upon being heated, these materials loose the crystalline water that enhances the interaction between the metal centers, as has been detected from M?ssbauer spectroscopy data. At higher temperatures, a progressive decomposition process takes place, liberating CN(-) groups, which reduces the iron atom from Fe(III) to Fe(II) to form hexacyanoferrates(II). The exception corresponds to the cobalt compound that undergoes an inner charge transfer to form Co(III) hexacyanoferrate(II). In the case of zinc ferricyanide, the thermal decomposition is preceded by a structural transformation, from cubic to hexagonal. For M = Co, Ni, Cu, and Zn the intermediate reaction product corresponds to a solid solution of M(II) ferricyanide and ferrocyanide. For M = Mn and Cd the formation of a solid solution on heating was not detected. The crystal frameworks of the initial M(II) ferricyanide and of the formed M(II) ferrocyanide are quite different. In annealed Mn(II) ferricyanide samples, an increasing anti-ferromagnetic contribution on heating, which dominates on the initial ferrimagnetic order, was observed. Such a contribution was attributed to neighboring Mn(II) ions linked by aquo bridges. In the anhydrous annealed sample such interaction disappears. This effect was also studied in pure Mn(II) ferrocyanide. The occurrence of linkage isomerism and also the formation of Ni(III), Cu(III), and Zn(III) hexacyanoferrates(II) were discarded from the obtained experimental evidence.     

Changes in molecular properties with changes in molecular geometry: A partitioning into electronic and nuclear components

Most one-electron properties vary with changes in molecular conformation. Although the nuclear component remains constant for some of the one-electron property changes and thus the overall change depends only on the electronic change this result is not general. Often the change in the nuclear component dominates the overall change in a molecular property. An analysis of the changes in a number of one-electron properties with changes in molecular geometry in terms of the changes in the nuclear and the electronic components is presented. The inversion of ammonia and the torsion of ethane were chosen as important examples of conformational changes and the changes in molecular one-electron properties studied.     

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems

We propose a molecular simulation method using genetic algorithm (GA) for biomolecular systems to obtain ensemble averages efficiently. In this method, we incorporate the genetic crossover, which is one of the operations of GA, to any simulation method such as conventional molecular dynamics (MD), Monte Carlo, and other simulation methods. The genetic crossover proposes candidate conformations by exchanging parts of conformations of a target molecule between a pair of conformations during the simulation. If the candidate conformations are accepted, the simulation resumes from the accepted ones. While conventional simulations are based on local update of conformations, the genetic crossover introduces global update of conformations. As an example of the present approach, we incorporated genetic crossover to MD simulations. We tested the validity of the method by calculating ensemble averages and the sampling efficiency by using two kinds of peptides, ALA3 and (AAQAA)₃. The results show that for ALA3 system, the distribution probabilities of backbone dihedral angles are in good agreement with those of the conventional MD and replica-exchange MD simulations. In the case of (AAQAA)₃ system, our method showed lower structural correlation of α-helix structures than the other two methods and more flexibility in the backbone ψ angles than the conventional MD simulation. These results suggest that our method gives more efficient conformational sampling than conventional simulation methods based on local update of conformations. © 2018 Wiley Periodicals, Inc.     

Immunological and molecular genetic analysis of the cellulase component fromPenicillium funiculosum

Following immunization of rabbits, the antiserum was initially analyzed for antiendoglucanase activity using dot-blot ELISA methods. When compared with the preimmune serum, the antiserum showed strong response even at 25 ng concentration. The specificity of the polyclonal antibodies, raised against the partially purified endoglucanase component of Penicillium funiculosum, was determined by Oüchterlony double diffusion. Rocket electrophoresis confirmed the presence of only two types of antigens in the serum. The two rockets obtained were attributable to endo I and the merging of immunologically identical (but mobility wise different) endo II and endo III. This antibody preparation was used as a probe. The deduced M1 of the cloned E. coli endo I was found to be 58 Kd by Western blotting.     

Sampling small-scale and large-scale conformational changes in proteins and molecular complexes

Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.     

Detection of irradiated food by the changes in protein molecular mass distribution

Protein constituents were extracted from chicken drumstick and chicken white meat, separated according to the molecular mass (Mm), using discontinuous SDS–polyacrylamide electrophoresis (SDS–PAGE) and quantified by scanning densitometry. The obtained profiles were compared with the profiles corresponding to the meat samples which were irradiated at −20, +4, and +20°c. It was observed that the irradiation of chicken white meat led to protein scission which was partially unselective (e.g. the amount of proteins whose Mm>20 kDa decreased, while the amount of those whose Mm<20 kDa increased), and partially selective (e.g. the appearance of Mm16 kDa fragment). In the case of chicken drumstick meat the irradiation caused both protein scission and protein cross-linking (unselective and selective, and appearance of 16 kDa fragment). However, in the case of aerated dehydrated egg white proteins, irradiation led only to unselective protein scission. The obtained results are discussed in view of possible application of discontinuous analytical SDS–PAGE combined with laser scanning densitometry for detection of previously irradiated foodstuff.