In silico Mechanics of Stem Cells Intramyocardially Transplanted with a Biomaterial Injectate for Treatment of Myocardial Infarction.

PURPOSE: Biomaterial and stem cell delivery are promising approaches to treating myocardial infarction. However, the mechanical and biochemical mechanisms underlying the therapeutic benefits require further clarification. This study aimed to assess the deformation of stem cells injected with the biomaterial into the infarcted heart. METHODS: A microstructural finite element model of a mid-wall infarcted myocardial region was developed from ex vivo microcomputed tomography data of a rat heart with left ventricular infarct and intramyocardial biomaterial injectate. Nine cells were numerically seeded in the injectate of the microstructural model. The microstructural and a previously developed biventricular finite element model of the same rat heart were used to quantify the deformation of the cells during a cardiac cycle for a biomaterial elastic modulus (Einj) ranging between 4.1 and 405,900 kPa. RESULTS: The transplanted cells' deformation was largest for Einj = 7.4 kPa, matching that of the cells, and decreased for an increase and decrease in Einj. The cell deformation was more sensitive to Einj changes for softer (Einj ≤ 738 kPa) than stiffer biomaterials. CONCLUSIONS: Combining the microstructural and biventricular finite element models enables quantifying micromechanics of transplanted cells in the heart. The approach offers a broader scope for in silico investigations of biomaterial and cell therapies for myocardial infarction and other cardiac pathologies.

Effect of biomaterial stiffness on cardiac mechanics in a biventricular infarcted rat heart model with microstructural representation of in situ intramyocardial injectate.

Intramyocardial delivery of biomaterials is a promising concept for treating myocardial infarction. The delivered biomaterial provides mechanical support and attenuates wall thinning and elevated wall stress in the infarct region. This study aimed at developing a biventricular finite element model of an infarcted rat heart with a microstructural representation of an in situ biomaterial injectate, and a parametric investigation of the effect of the injectate stiffness on the cardiac mechanics. A three-dimensional subject-specific biventricular finite element model of a rat heart with left ventricular infarct and microstructurally dispersed biomaterial delivered 1 week after infarct induction was developed from ex vivo microcomputed tomography data. The volumetric mesh density varied between 303 mm-3 in the myocardium and 3852 mm-3 in the injectate region due to the microstructural intramyocardial dispersion. Parametric simulations were conducted with the injectate's elastic modulus varying from 4.1 to 405,900 kPa, and myocardial and injectate strains were recorded. With increasing injectate stiffness, the end-diastolic median myocardial fibre and cross-fibre strain decreased in magnitude from 3.6% to 1.1% and from -6.0% to -2.9%, respectively. At end-systole, the myocardial fibre and cross-fibre strain decreased in magnitude from -20.4% to -11.8% and from 6.5% to 4.6%, respectively. In the injectate, the maximum and minimum principal strains decreased in magnitude from 5.4% to 0.001% and from -5.4% to -0.001%, respectively, at end-diastole and from 38.5% to 0.06% and from -39.0% to -0.06%, respectively, at end-systole. With the microstructural injectate geometry, the developed subject-specific cardiac finite element model offers potential for extension to cellular injectates and in silico studies of mechanotransduction and therapeutic signalling in the infarcted heart with an infarct animal model extensively used in preclinical research.

Changes in serum PSA after endoscopic enucleation of the prostate are predictive for the future diagnosis of prostate cancer.

PURPOSE: After Endoscopic Enucleation of the Prostate (EEP) for benign prostatic obstruction (BPO), men remain at risk for prostate cancer (PCa). Significant PSA changes occur after enucleation, which interfere with later screening for PCa. It remains unclear which patients need further diagnostic investigations for PCa after EEP. The goal of this study was to identify an independent predictor for PCa diagnosis after Holmium Laser Enucleation of the Prostate (HoLEP) in patients whose HoLEP resection specimen did not show PCa. METHODS: Data of 773 patients who underwent HoLEP for BPO between 2010 and 2018 in a referral center were analyzed. Exclusion criteria were PCa detection in the HoLEP specimen or absence of post-operative PSA values. Patients were divided in a PCa group and Control group depending on whether or not PCa was detected during follow-up after HoLEP. The predictive value for future diagnosis of PCa of different forms of PSA-change after HoLEP was analyzed by multivariate Cox regression and ROC analysis. RESULTS: Overall, 24 (4.2%) patients developed PCa after HoLEP. At 5 year follow-up, the PCa-free survival rate was 85%. First post-operative PSA was an independent predictor of PCa diagnosis after HoLEP (HR 1.106, 95% CI 1.074-1.139, p < 0.001, ROC AUC 0.903) with an optimal cut-off value of 1.73 ng/ml (sensitivity 83.3%, specificity 82.3%). CONCLUSIONS: For patients who underwent HoLEP for BPO, post-operative PSA after HoLEP is an independent predictor for future PCa diagnosis. When PSA is > 1.73 ng/ml within the first year after HoLEP, rigorous follow-up and diagnostic investigations for PCa are indicated.

EFFICACY OF FUNGICIDES AGAINST CALONECTRIA PAUCIRAMOSA IN POT AZALEA.

Calonectria (formerly Cylindrocladium) infection of pot azalea (Rhododendron simsii Planch) is an important disease problem in which usually one or two of the four plants per pot show progressing leaf and especially stem lesions, leading to mortality of the respective plant and rendering the pot unmarketable. This may occur in a later stage of the growing season, leading to significant commercial losses. The main objective of this study was to test a range of fungicides for their efficacy against this pathogen. To test the fungicides, a bioassay was first developed in which mycelium and conidiospores of the pathogen were produced on Potato Dextrose Agar, blended in water, and dilutions of the resulting suspension inoculated at the base of 11-week-old cuttings three weeks after they had been trimmed. Disease progression was monitored up to 7 weeks post inoculation and a disease index on a scale of 0 to 3 was established. In the actual efficacy trial, the following fungicides (with corresponding active ingredient(s)) were tested as preventive treatments: Topsin M 70 WG (thiophanate-methyl), Sporgon (prochloraz), Signum (boscalid+pyraclostrobin), Switch (cyprodinyl+fludioxonil), Flint 50WG (trifloxystrobin), Ortiva Top (azoxystrobin+difenoconazole) and Fungaflor (imazalil). Disease expression started after about 2 weeks, increased approximately 1 index level, and leveled off 5 weeks after inoculation. The best control was observed with Sporgon, Ortiva Top and Signum. Switch produced intermediate effects and insufficient control was observed with Topsin, Flint and Fungaflor. These results explain why specific standard fungicide treatments, such as those with Topsin, fail to control the disease, while they can be effective against a different Calonectria species such as C. pseudonaviculata, the cause of boxwood blight.

THE EFFECT OF COLD STORAGE OF POTTED AZALEA ON BROAD MITE INFECTION.

In potted azalea (Rhododendron simsii hybrids) the broad mite Polyphagotarsonemus latus (Banks) is considered a severe pest with an important economic impact. Although chemical control is available, permitted acaricides are limited and have a restricted number of applications. Therefore, growers have a keen interest in alternative control measures. Recently, research on the behaviour and population dynamics of P. latus on azalea leaf disks stored at different temperatures indicated that survival and reproductive capacity of broad mite is reduced drastically when temperature drops below 7°C. In Flanders, storage of azalea plants at 3°C is common practice to pause flower development (in function of the date that plants have to be ready for sale) before forcing them to flower in a heated greenhouse. Hence, an experiment was set-up to verify and quantify the effect of cold storage of azalea on broad mite infection. Azalea plants were infected with P. latus and stored at 3°C for 2, 3 or 4 weeks. Then, plants were transferred to a heated greenhouse for 2 weeks to check whether surviving female broad mites were still able to reproduce. The number of P. latus on azalea was assessed before cold treatment, immediately after treatment, and 2 weeks after transfer to the heated greenhouse. Results confirmed that cold storage can play a role in broad mite control as the P. latus population was significantly reduced (up to 90%) immediately after treatment. A further decrease in the number of P. latus during storage in the heated greenhouse indicated that cold treatment during 4 weeks had also an effect on the reproduction capacity of P. latus. We conclude that cold storage of azalea plants (at least 4 weeks at maximum 3°C) should be considered as an additional and alternative control method for P. latus at the end of the azalea production cycle.

Development and usability of a computer-tailored pedometer-based physical activity advice for breast cancer survivors.

This observational study aimed to adapt a computer-tailored step advice for the general population into a feasible advice for breast cancer survivors and to test its usability. First, several adaptations were made to the original design (adding cancer-related physical activity (PA) barriers and beliefs, and self-management strategies to improve survivors' personal control). Second, the adapted advice was evaluated in two phases: (1) a usability testing in healthy women (n = 3) and survivors (n = 6); and (2) a process evaluation during 3 weeks in breast cancer survivors (n = 8). Preliminary usability testing revealed no problems during logging-in; however, three survivors misinterpreted some questions. After refining the questionnaire and advice, survivors evaluated the advice as interesting, attractive to read, comprehensible and credible. Inactive survivors found the advice novel, but too long. The process evaluation indicated that the majority of the women (n = 5/8) reported increased steps. Monitoring step counts by using a pedometer was perceived as an important motivator to be more active. To conclude, this study provides initial support for the usability and acceptability of a computer-tailored pedometer-based PA advice for breast cancer survivors. After testing efficacy and effectiveness of this intervention, this tool can broaden the reach of PA promotion in breast cancer survivors.

Comparison of the blood supply to the articular-epiphyseal growth complex in horse vs. pony foals.

REASONS FOR PERFORMING STUDY: To increase understanding of why the prevalence of clinical/radiographic osteochondrosis (OC) dissecans is high in horses and low in ponies. OBJECTIVES: To investigate whether the clinical difference in OC occurrence between horses and ponies could partly be explained by a difference in: 1) number of patent vessels in the epiphyseal growth cartilage; 2) duration of the presence of patent cartilage canals; or 3) growth cartilage thickness at predilection sites for OC. The hypothesis was that pony foals would have fewer cartilage canals, shorter duration of blood supply and thinner growth cartilage than horse foals. STUDY DESIGN: Observational, cross-sectional study. METHODS: Nine Standardbred foals (horse group) 1-49 days old and 11 Norwegian Fjord foals (pony group) 1-62 days old were included. A total of 15 anatomical locations in the tarsocrural and metatarsophalangeal joints were examined by one or more of the following techniques: arterial perfusion; photography of cleared specimens; microcomputed tomography; radiography; and histology. The number of cartilage canals was counted. Cartilage thickness was measured. Duration of blood supply was assessed in histological sections. RESULTS: Of the 3 common predilection sites for OC investigated, there were significantly fewer vessels (P = 0.003) and thinner cartilage (P = 0.002) at the distal lateral trochlear ridge of the talus in the pony group. There was no difference in the duration of presence of cartilage canals between the groups. CONCLUSION: The hypothesis that pony foals would have fewer cartilage canals and thinner growth cartilage than horse foals was confirmed for the lateral trochlear ridge of the talus. The current results may contribute towards an explanation for the low prevalence of OC at the distal lateral trochlear ridge of the talus in pony foals.

Cold storage to overcome dormancy affects the carbohydrate status and photosynthetic capacity of Rhododendron simsii.

Global warming leads to increasing irregular and unexpected warm spells during autumn, and therefore natural chilling requirements to break dormancy are at risk. Controlled cold treatment can provide an answer to this problem. Nevertheless, artificial cold treatment will have consequences for carbon reserves and photosynthesis. In this paper, the effect of dark cold storage at 7 °C to break flower bud dormancy in the evergreen Rhododendron simsii was quantified. Carbohydrate and starch content in leaves and flower buds of an early ('Nordlicht'), semi-early ('M. Marie') and late ('Mw. G. Kint') flowering cultivar showed that carbon loss due to respiration was lowest in 'M. Marie', while 'Mw. G. Kint' was completely depleted of starch reserves at the end of cold treatment. Gene isolation resulted in a candidate gene for sucrose synthase (SUS) RsSus, which appears to be homologous to AtSus3 and had a clear increase in expression in leaves during cold treatment. Photosynthesis measurements on 'Nordlicht' and the late-flowering cultivar 'Thesla' showed that during cold treatment, dark respiration decreased 58% and 63%, respectively. Immediately after cold treatment, dark respiration increased and stabilised after 3 days. The light compensation point followed the same trend as dark respiration. Quantum efficiency showed no significant changes during the first days after cold treatment, but was significantly higher than in plants with dormant flower buds at the start of cold treatment. In conclusion, photosynthesis stabilised 3 days after cold treatment and was improved compared to the level before cold treatment.

EDART, a discrete algebraic reconstructing technique for experimental data obtained with high resolution computed tomography.

A novel reconstruction method is presented to improve the image quality of three dimensional (3D) datasets for samples consisting of only one material and surrounding air, obtained with high resolution X-ray Computed Tomography (µCT). It combines discrete tomography with iterative reconstruction algorithms, it is applicable for routine µCT applications and is referred to as the Experimental Discrete Algebraic Reconstruction Technique (EDART). A fast and intuitive method to estimate the attenuation coefficient and segmentation threshold, in case these are unknown, is included. Experimental results illustrate that EDART allows the improvement of the reconstruction quality as compared to standard iterative reconstruction when few projections are available, without significantly increasing the reconstruction time.

CLIMATE CONDITIONS AFFECTING THE WITHIN-PLANT SPREAD OF BROAD MITES ON AZALEA.

The broad mite Polyphagotarsonemus latus (Banks) is considered a major pest in potted azalea, Flanders' flagship ornamental crop of Rhododendron simsii hybrids. In addition to severe economic damage, the broad mite is dreaded for its increasing resistance to acaricides. Due to restrictions in the use of broad spectrum acaricides, Belgian azalea growers are left with only three compounds, belonging to two mode of action groups and restricted in their number of applications, for broad mite control: abamectin, milbemectin and pyrethrin. Although P. latus can be controlled with predatory mites, the high cost of this system makes it (not yet) feasible for integration into standard azalea pest management systems. Hence, a maximum efficacy of treatments with available compounds is essential. Because abamectin, milbemectin and pyrethrin are contact acaricides with limited trans laminar flow, only broad mites located on shoot tips of azalea plants will be controlled after spraying. Consequently, the efficacy of chemical treatments is influenced by the location and spread of P. latus on the plant. Unfortunately, little is known on broad mites' within-plant spread or how it is affected by climatic conditions like temperature and relative humidity. Therefore, experiments were set up to verify whether climate conditions have an effect on the location and migration of broad mites on azalea. Broad mite infected azalea plants were placed in standard growth chambers under different temperature (T:2.5-25°C) and relative humidity (RH:55-80%) treatments. Within-plant spread was determined by counting mites on the shoot tips and inner leaves of azalea plants. Results indicate that temperature and relative humidity have no significant effect on the within-plant spread of P. latus. To formulate recommendations for optimal spray conditions to maximize the efficacy of broad mite control with acaricides, further experiments on the effect of light intensity and rain are scheduled.

Cold storage to overcome dormancy affects the carbon balance of azalea.

Flower bud dormancy in azalea (Rhododendron simsii) is broken by artificial cold treatment and this will have its consequences on carbon reserves and photosynthesis. The effect of cold storage at 7 °C on carbohydrate and starch content in leaves and flower buds of an early ('Nordlicht') and semi-early ('M. Marie) flowering cultivar was quantified. Carbon loss due to respiration was lowest for 'M. Marie'. Photosynthetic measurements on 'Nordlicht' showed that photosynthesis 3 days after cold treatment (plants ready to flower) was improved compared to before cold treatment (plants with dormant flower buds).

An exploratory study of contrast agents for soft tissue visualization by means of high resolution X-ray computed tomography imaging.

High resolution X-ray computed tomography (CT), or microCT, is a promising and already widely used technique in various scientific fields. Also for histological purposes it has great potential. Although microCT has proven to be a valuable technique for the imaging of bone structures, the visualization of soft tissue structures is still an important challenge due to their low inherent X-ray contrast. One way to achieve contrast enhancement is to make use of contrast agents. However, contrary to light and electron microscopy, knowledge about contrast agents and staining procedures is limited for X-ray CT. The purpose of this paper is to identify useful X-ray contrast agents for soft tissue visualization, which can be applied in a simple way and are also suited for samples larger than (1 cm)(3) . And 28 chemical substances have been investigated. All chemicals were applied in the form of concentrated aqueous solutions in which the samples were immersed. First, strips of green Bacon were stained to evaluate contrast enhancement between muscle and adipose tissue. Furthermore it was also tested whether the contrast agents remained fixed in the tissue after staining by re-immersing them in water. Based on the results, 12 contrast agents were selected for further testing on postmortem mice hind legs, containing a variety of different tissues, including muscle, fat, bone, cartilage and tendons. It was evaluated whether the contrast agents allowed a clearer distinction between the different soft tissue structures present. Finally also penetration depth was measured. And 26 chemicals resulted in contrast enhancement between muscle and adipose tissue in the Bacon strips. Mercury(II)chloride (HgCl2 ), phosphotungstic acid (PTA), phosphomolybdic acid (PMA) and ammonium orthomolybdate ((NH4 )2 MoO4 ) remained fixed after re-immersion in water. The penetration tests showed that potassium iodide (KI) and sodium tungstate can be most efficiently used for large samples of the order of several tens of cm(3) . PMA, PTA, HgCl2 and also to a lesser extent Na2 WO4 and (NH4 )2 MoO4 allowed a clearer distinction between the different soft tissue structures present.

Accurate spin-orbit and spin-other-orbit contributions to the g-tensor for transition metal containing systems.

In this paper an overview is presented of several approximations within Density Functional Theory (DFT) to calculate g-tensors in transition metal containing systems and a new accurate description of the spin-other-orbit contribution for high spin systems is suggested. Various implementations in a broad variety of software packages (ORCA, ADF, Gaussian, CP2K, GIPAW and BAND) are critically assessed on various aspects including (i) non-relativistic versus relativistic Hamiltonians, (ii) spin-orbit coupling contributions and (iii) the gauge. Particular attention is given to the level of accuracy that can be achieved for codes that allow g-tensor calculations under periodic boundary conditions, as these are ideally suited to efficiently describe extended condensed-phase systems containing transition metals. In periodic codes like CP2K and GIPAW, the g-tensor calculation schemes currently suffer from an incorrect treatment of the exchange spin-orbit interaction and a deficient description of the spin-other-orbit term. In this paper a protocol is proposed, making the predictions of the exchange part to the g-tensor shift more plausible. Focus is also put on the influence of the spin-other-orbit interaction which becomes of higher importance for high-spin systems. In a revisited derivation of the various terms arising from the two-electron spin-orbit and spin-other-orbit interaction (SOO), new insight has been obtained revealing amongst other issues new terms for the SOO contribution. The periodic CP2K code has been adapted in view of this new development. One of the objectives of this study is indeed a serious enhancement of the performance of periodic codes in predicting g-tensors in transition metal containing systems at the same level of accuracy as the most advanced but time consuming spin-orbit mean-field approach. The methods are first applied on rhodium carbide but afterwards extended to a broad test set of molecules containing transition metals from the fourth, fifth and sixth row of the periodic table. The set contains doublets as well as high-spin molecules.

Physical activity levels and supportive care needs for physical activity among breast cancer survivors with different psychosocial profiles: a cluster-analytical approach.

The transition from breast cancer patient to survivor is associated with many treatment-related and psychosocial factors, which can influence health behaviour and associated needs. First, this study aimed to identify clusters of treatment-related and psychosocial factors among breast cancer survivors. Second, clusters' physical activity levels and care needs for physical activity were evaluated. Breast cancer survivors (n= 440; 52 ± 8 years) (3 weeks to 6 months post treatment) completed self-reports on physical and psychological symptoms; illness representations; social support and coping; physical activity and care needs for physical activity. Analyses identified four clusters: (1) a low distress-active approach group; (2) a low distress-resigned approach group; (3) a high distress-active approach group; and (4) a high distress-emotional approach group. Physical activity levels were higher in the low distress groups than in the high distress-emotional approach group. However, women with low distress and an active approach reported equal care needs for physical activity than women with high distress and an emotional approach. These findings suggest that care needs for physical activity are unrelated to distress and actual physical activity levels. The results emphasise the importance of screening for needs and provide a framework supporting the referral of breast cancer survivors to tailored interventions.

The potential role of quorum-sensing peptides in oncology.

Cancer is a leading cause of death worldwide, with a limited cure rate and late diagnosis for certain types of cancer (e.g. pancreatic cancer). As this disease presents an enormous challenge for scientists, new paradigms in oncology are needed to defeat this serious disease. Currently, several peptide drugs are investigated for their preventive, diagnostic and therapeutic properties in oncology, with already 15 peptide drugs marketed for cancer therapy. However, we suggest that quorum-sensing peptide agonists and antagonists can be used in oncology as well, resulting in a larger potential peptide space. This hypothesis is based on (1) the recent evidence of prokaryote-eukaryote signalling by the use of quorum-sensing signalling molecules, (2) the apoptotic phenomenon seen in bacteria, (3) the clear similarities between the bacterial quorum-sensing mechanisms and the metastatic process tumor cells initiate, (4) the multiple receptor targeting and (5) the possibility of pharmacologic manipulation of peptides, resulting in increased receptor targeting. Up till now, however, the use of quorum-sensing signalling peptides in oncology has not yet been investigated, despite the urgent need for new insights in oncology and the promising perspectives.

Assessment of periodic and cluster-in-vacuo models for first principles calculation of EPR parameters of paramagnetic defects in crystals: Rh2+ defects in NaCl as case study.

In order to find a reliable and efficient calculation scheme for electron paramagnetic resonance (EPR) spectroscopic parameters for transition metal complexes in ionic solids from first principles, periodic and finite cluster-in-vacuo density functional theory (DFT) simulations are performed for g tensors, ligand hyperfine tensors (A), and quadrupole tensors (Q) for Rh(2+)-related centers in NaCl. EPR experiments on NaCl:Rh single crystals identified three Rh(2+) monomer centers, only differing in the number of charge compensating vacancies in their local environment, and one dimer center. Periodic and cluster calculations, both based on periodically optimized structures, are able to reproduce experimentally observed trends in the ligand A and Q tensors and render very satisfactory numerical agreement with experiment. Taking also computation time into account as a criterion, a full periodic approach emerges as most appropriate for these parameters.The g tensor calculations, on the other hand, prove to be insufficiently accurate for model assessment. The calculations also reveal parameters of the complexes which are not directly accessible through experiments, in particular related to their geometry.

Contribution of VANGL2 mutations to isolated neural tube defects.

Vangl2 was identified as the gene defective in the Looptail (Lp) mouse model for neural tube defects (NTDs). This gene forms part of the planar cell polarity (PCP) pathway, also called the non-canonical Frizzled/Dishevelled pathway, which mediates the morphogenetic process of convergent extension essential for proper gastrulation and neural tube formation in vertebrates. Genetic defects in PCP signaling have strongly been associated with NTDs in mouse models. To assess the role of VANGL2 in the complex etiology of NTDs in humans, we resequenced this gene in a large multi-ethnic cohort of 673 familial and sporadic NTD patients, including 453 open spina bifida and 202 closed spinal NTD cases. Six novel rare missense mutations were identified in seven patients, five of which were affected with closed spinal NTDs. This suggests that VANGL2 mutations may predispose to NTDs in approximately 2.5% of closed spinal NTDs (5 in 202), at a frequency that is significantly different from that of 0.4% (2 in 453) detected in open spina bifida patients (p = 0.027). Our findings strongly implicate VANGL2 in the genetic causation of spinal NTDs in a subset of patients and provide additional evidence for a pathogenic role of PCP signaling in these malformations.

Microdosing in early lead discovery.

Microdosing provides a tool to enhance drug development by initiating human studies prior to Phase I studies. The purpose is to assist in the go versus no-go decision-making process and to eliminate early ineffective compounds from the drug pipeline. Selection of multiple potential leads can be performed at the clinical stage instead of in preclinical studies. The microdosing approach can be easily used for a molecularly targeted potential drug compound with a known mechanism of action. It provides useful data regarding accessibility and biodistribution that can be used in many estimations benefiting the development of the molecule. In addition, steady state and genetic investigations are becoming possible. Microdosing has a sparing effect on timelines and costs, however, the real importance is not yet known because, although it is known to be widely performed, only a few original reports have been published.

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules.

In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [ J. Chem. Phys. 2007 , 126 ( 22 ), 224102. ]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.

Identification and conformational study of stable radiation-induced defects in sucrose single crystals using density functional theory calculations of electron magnetic resonance parameters.

One of the major stable radiation-induced radicals in sucrose single crystals (radical T2) has been identified by means of density functional theory (DFT) calculations of electron magnetic resonance parameters. The radical is formed by a net glycosidic bond cleavage, giving rise to a glucose-centered radical with the major part of the spin density residing at the C 1 carbon atom. A concerted formation of a carbonyl group at the C 2 carbon accounts for the relatively small spin density at C 1 and the enhanced g factor anisotropy of the radical, both well-known properties of this radical from several previous experimental investigations. The experimentally determined and DFT calculated proton hyperfine coupling tensors agree very well on all accounts. The influence of the exact geometrical configuration of the radical and its environment on the tensors is explored in an attempt to explain the occurrence and characteristics of radical T3, another major species that is most likely another conformation of T2. No definitive conclusions with regard to the actual structure of T3 could be arrived at from this study. However, the results indicate that, most likely, T3 is identical in chemical structure to T2 and that changes in the orientation of neighboring hydroxy groups or changes in the configuration of the neighboring fructose ring can probably not account for the type and size of the discrepancies between T2 and T3.