Developing a coordinate-based strategy to support cognitive targeted prostate biopsies and correlative spatial-histopathological outcome analysis / 亚洲男科学杂志(英文版)

Lack of investment for magnetic resonance (MR) fusion systems is an obstacle to deliver targeted prostate biopsies within the prostate cancer diagnostic pathway. We developed a coordinate-based method to support cognitive targeted prostate biopsies and then performed an audit on cancer detection and the location of lesions. In each patient, the prostate is considered as two separate hemiprostates, and each hemiprostate is divided into 4 × 4 × 4 units. Each unit is therefore defined by a three-dimensional coordinate. We prospectively applied our coordinates approach to target 106 prostatic lesions in 93 men. Among 45 (of 106; 42.5%) lesions positive for cancer, 27 lesions (60.0%) harbored clinically significant disease. PSA density was significantly higher in patients with proven cancer (median: 0.264 ng ml

Charge-Shift Bonding: A New and Unique Form of Bonding.

Charge-shift bonds (CSBs) constitute a new class of bonds different than covalent/polar-covalent and ionic bonds. Bonding in CSBs does not arise from either the covalent or the ionic structures of the bond, but rather from the resonance interaction between the structures. This Essay describes the reasons why the CSB family was overlooked by valence-bond pioneers and then demonstrates that the unique status of CSBs is not theory-dependent. Thus, valence bond (VB), molecular orbital (MO), and energy decomposition analysis (EDA), as well as a variety of electron density theories all show the distinction of CSBs vis-à-vis covalent and ionic bonds. Furthermore, the covalent-ionic resonance energy can be quantified from experiment, and hence has the same essential status as resonance energies of organic molecules, e.g., benzene. The Essay ends by arguing that CSBs are a distinct family of bonding, with a potential to bring about a Renaissance in the mental map of the chemical bond, and to contribute to productive chemical diversity.

Hydrogen bonding from a valence bond theory perspective: the role of covalency.

A valence bond theory based method has been developed to decompose hydrogen bond energies into contributions from geometry, electrostatics, polarization and charge transfer. This decomposition method has been carried out for F-HFH, F-HOH2, F-HNH3, HO-HOH2, HO-HNH3, and H2N-HNH3. Localized valence bond self-consistent field (L-VBSCF) and localized breathing orbital valence bond (L-BOVB) calculations were performed at the PBEPBE/aug-cc-pVDZ optimized geometries. It is shown that inclusion of valence bond structures that explicitly include charge transfer account for at least 32% (likely over half) of the hydrogen bond energy of all systems studied, indicating the dominant role of covalency. This is in agreement with calculated bond lengths, geometry deformation energies, and polarization energies. Electrostatic effects were found to play only a minor role in contrast to some widely held ideas regarding the nature of hydrogen bonding.

Expanding the toolbox for Trypanosoma cruzi: A parasite line incorporating a bioluminescence-fluorescence dual reporter and streamlined CRISPR/Cas9 functionality for rapid in vivo localisation and phenotyping.

BACKGROUND: Infection with Trypanosoma cruzi causes Chagas disease, a major public health problem throughout Latin America. There is no vaccine and the only drugs have severe side effects. Efforts to generate new therapies are hampered by limitations in our understanding of parasite biology and disease pathogenesis. Studies are compromised by the complexity of the disease, the long-term nature of the infection, and the fact that parasites are barely detectable during the chronic stage. In addition, functional dissection of T. cruzi biology has been restricted by the limited flexibility of the genetic manipulation technology applicable to this parasite. METHODOLOGY/PRINCIPAL FINDINGS: Here, we describe two technical innovations, which will allow the role of the parasite in disease progression to be better assessed. First, we generated a T. cruzi reporter strain that expresses a fusion protein comprising red-shifted luciferase and green fluorescent protein domains. Bioluminescence allows the kinetics of infection to be followed within a single animal, and specific foci of infection to be pinpointed in excised tissues. Fluorescence can then be used to visualise individual parasites in tissue sections to study host-parasite interactions at a cellular level. Using this strategy, we have been routinely able to find individual parasites within chronically infected murine tissues for the first time. The second advance is the incorporation of a streamlined CRISPR/Cas9 functionality into this reporter strain that can facilitate genome editing using a PCR-based approach that does not require DNA cloning. This system allows the rapid generation of null mutants and fluorescently tagged parasites in a background where the in vivo phenotype can be rapidly assessed. CONCLUSIONS/SIGNIFICANCE: The techniques described here will have multiple applications for studying aspects of T. cruzi biology and Chagas disease pathogenesis previously inaccessible to conventional approaches. The reagents and cell lines have been generated as a community resource and are freely available on request.

Expanding the toolbox for Trypanosoma cruzi: A parasite line incorporating a bioluminescence-fluorescence dual reporter and streamlined CRISPR/Cas9 functionality for rapid in vivo localisation and phenotyping

Background Infection with Trypanosome cruzi causes Chagas disease, a major public health problem throughout Latin America. There is no vaccine and the only drugs have severe side effects. Efforts to generate new therapies are hampered by limitations in our understanding of parasite biology and disease pathogenesis. Studies are compromised by the complexity of the disease, the long-term nature of the infection, and the fact that parasites are barely detectable during the chronic stage. In addition, functional dissection of T. cruzi biology has been restricted by the limited flexibility of the genetic manipulation technology applicable to this parasite. Methodology/Principal findings Here, we describe two technical innovations, which will allow the role of the parasite in disease progression to be better assessed. First, we generated a T. cruzi reporter strain that expresses a fusion protein comprising red-shifted luciferase and green fluorescent protein domains. Bioluminescence allows the kinetics of infection to be followed within a single animal, and specific foci of infection to be pinpointed in excised tissues. Fluorescence can then be used to visualise individual parasites in tissue sections to study host-parasite interactions at a cellular level. Using this strategy, we have been routinely able to find individual parasites within chronically infected murine tissues for the first time. The second advance is the incorporation of a streamlined CRISPR/Cas9 functionality into this reporter strain that can facilitate genome editing using a PCR-based approach that does not require DNA cloning. This system allows the rapid generation of null mutants and fluorescently tagged parasites in a background where the in vivo phenotype can be rapidly assessed. Conclusions/Significance The techniques described here will have multiple applications for studying aspects of T. cruzi biology and Chagas disease pathogenesis previously inaccessible to conventional approaches. The reagents and cell lines have been generated as a community resource and are freely available on request.

Expanding the toolbox for Trypanosoma cruzi: a parasite line incorporating a bioluminescence-fluorescence dual reporter and streamlined CRISPR/Cas9 functionality for rapid in vivo localisation and phenotyping

Background Infection with Trypanosome cruzi causes Chagas disease, a major public health problem throughout Latin America. There is no vaccine and the only drugs have severe side effects. Efforts to generate new therapies are hampered by limitations in our understanding of parasite biology and disease pathogenesis. Studies are compromised by the complexity of the disease, the long-term nature of the infection, and the fact that parasites are barely detectable during the chronic stage. In addition, functional dissection of T. cruzi biology has been restricted by the limited flexibility of the genetic manipulation technology applicable to this parasite. Methodology/Principal findings Here, we describe two technical innovations, which will allow the role of the parasite in disease progression to be better assessed. First, we generated a T. cruzi reporter strain that expresses a fusion protein comprising red-shifted luciferase and green fluorescent protein domains. Bioluminescence allows the kinetics of infection to be followed within a single animal, and specific foci of infection to be pinpointed in excised tissues. Fluorescence can then be used to visualise individual parasites in tissue sections to study host-parasite interactions at a cellular level. Using this strategy, we have been routinely able to find individual parasites within chronically infected murine tissues for the first time. The second advance is the incorporation of a streamlined CRISPR/Cas9 functionality into this reporter strain that can facilitate genome editing using a PCR-based approach that does not require DNA cloning. This system allows the rapid generation of null mutants and fluorescently tagged parasites in a background where the in vivo phenotype can be rapidly assessed. Conclusions/Significance The techniques described here will have multiple applications for studying aspects of T. cruzi biology and Chagas disease pathogenesis previously inaccessible to conventional approaches. The reagents and cell lines have been generated as a community resource and are freely available on request.

Charge-Shift Corrected Electronegativities and the Effect of Bond Polarity and Substituents on Covalent-Ionic Resonance Energy.

Bond dissociation energies and resonance energies for HnA-BHm molecules (A, B = H, C, N, O, F, Cl, Li, and Na) have been determined in order to re-evaluate the concept of electronegativity in the context of modern valence bond theory. Following Pauling's original scheme and using the rigorous definition of the covalent-ionic resonance energy provided by the breathing orbital valence bond method, we have derived a charge-shift corrected electronegativity scale for H, C, N, O, F, Cl, Li, and Na. Atomic charge shift character is defined using a similar approach resulting in values of 0.42, 1.06, 1.43, 1.62, 1.64, 1.44, 0.46, and 0.34 for H, C, N, O, F, Cl, Li, and Na, respectively. The charge-shift corrected electronegativity values presented herein follow the same general trends as Pauling's original values with the exception of Li having a smaller value than Na (1.57 and 1.91 for Li and Na respectively). The resonance energy is then broken down into components derived from the atomic charge shift character and polarization effects. It is then shown that most of the resonance energy in the charge-shift bonds H-F, H3C-F, and Li-CH3 and borderline charge-shift H-OH is associated with polarity rather than the intrinsic atomic charge-shift character of the bonding species. This suggests a rebranding of these bonds as "polar charge-shift" rather than simply "charge-shift". Lastly, using a similar breakdown method, it is shown that the small effect the substituents -CH3, -NH2, -OH, and -F have on the resonance energy (<10%) is mostly due to changes in the charge-shift character of the bonding atom.

Effect of Lone Pairs on Molecular Resonance Energy.

In an effort to understand the theoretical parameters of charge-shift bonding, computational experiments have been designed to elucidate the factors effecting molecular resonance energy. Valence bond theory calculations have been used to calculate resonance energies of homonuclear bonds in the series [HnX-XHn]Z, where n = 0-3 and Z = 2n - 6, 2n - 4, 2n - 2, and 2n for X = C, N, O, and F, respectively. It is shown that the resonance energy decreases as the number of lone pairs increases. Calculated orbital contraction coefficients show that this unexpected result is due to the dominance of orbital size over the lone-pair effect. These results are irrespective of the HXX bond angles. It is also shown that the resonance energy increases with decreasing HXX bond angles due to the increase in p character in the bonding orbital.

A valence bond study of three-center four-electron pi bonding: electronegativity vs electroneutrality.

Three-center four-electron (3c4e) pi bonding systems analogous to that of the ozone molecule have been studied using modern valence bond theory. Molecules studied herein consist of combinations of first row atoms C, N, and O with the addition of H atoms where appropriate in order to preserve the 3c4e pi system. Breathing orbital valence bond (BOVB) calculations were preformed at the B3LYP/6-31G**-optimized geometries in order to determine structural weights, pi charge distributions, resonance energies, and pi bond energies. It is found that the most weighted VB structure depends on atomic electronegativity and charge distribution, with electronegativity as the dominant factor. By nature, these systems are delocalized, and therefore, resonance energy is the main contributor to pi bond energies. Molecules with a single dominant VB structure have low resonance energies and therefore low pi bond energies.

Proposed reaction mechanisms for selenium UV photolysis vapor generation by computational methods.

The production of volatile analyte species by UV photolysis in the presence of low-molecular-weight organic acids as an alternative to chemical vapor generation has been of recent interest. The mechanism of this process is not well understood. Proposed mechanisms often involve photolytic cleavage of the organic acid as the initial step. Evidence suggests that this may not be the dominant route for UV photolysis vapor generation. In this work computational methods were applied to determine a possible alternative mechanism in the absence of free-radical production. The proposed mechanism specifically focused on selenium vapor generation. An energetically favored mechanism was found for UV photolysis of inorganic selenium in the presence of formic and acetic acids which is consistent with previously reported experimental results.

What accounts for the difference between singlet phenylphosphinidene and singlet phenylnitrene in reactivity toward ring expansion?

(8/8)CASSCF and (8/8)CASPT2 calculations have been performed in order to investigate the potential surface for the ring expansion of the (1)A(2) state of phenylphosphinidene (1c) to 1-phospha-1,2,4,6-cycloheptatetraene (3c). Unlike the comparable ring expansion of the (1)A(2) state of phenylnitrene (1b) to 1-aza-1,2,4,6-cycloheptatetraene (3b), ring expansion of 1c to 3c is computed to be quite endothermic. Nevertheless, cyclization of 1c, to form the bicyclic intermediate 2c in the ring expansion reaction, is computed to be only slightly more endothermic than the comparable cyclization reaction of 1b to 2b. The origins of these differences between the ring expansion reactions of 1b and 1c have been elucidated through the calculation of the energies of relevant isodesmic reactions.