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PubMed1991

Three-dimensional folding of Tetrahymena thermophila rRNA IVS sequence: a proposal.

We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the theoretical analysis with a computer method previously proposed, to find optimal free energy secondary structures with the required features, under the suitable constrains. Then we tried folding the obtained secondary structures, in low resolution tertiary models, which kept up the proximity of the catalytic sites also in the space. The proposed tertiary folding seems to provide for a better explanation to the transesterification mechanisms and moreover it is in good agreement with the experimental data (activity of mutants, enzymatic cleavages, phylogenetically conserved regions).

Animals↗
PubMed2002

Involvement of state transitions in the switch between linear and cyclic electron flow in Chlamydomonas reinhardtii.

The energetic metabolism of photosynthetic organisms is profoundly influenced by state transitions and cyclic electron flow around photosystem I. The former involve a reversible redistribution of the light-harvesting antenna between photosystem I and photosystem II and optimize light energy utilization in photosynthesis whereas the latter process modulates the photosynthetic yield. We have used the wild-type and three mutant strains of the green alga Chlamydomonas reinhardtii--locked in state I (stt7), lacking the photosystem II outer antennae (bf4) or accumulating low amounts of cytochrome b6f complex (A-AUU)--and measured electron flow though the cytochrome b6f complex, oxygen evolution rates and fluorescence emission during state transitions. The results demonstrate that the transition from state 1 to state 2 induces a switch from linear to cyclic electron flow in this alga and reveal a strict cause-effect relationship between the redistribution of antenna complexes during state transitions and the onset of cyclic electron flow.

Animals↗
PubMed1983

Calcium-free cardioplegia--pro.

Preischaemic doubling of the myocardial buffer capacity optimizes the energy supply of the ischaemic heart by anaerobic glycolysis. For osmotic reasons this method of improving ischaemia tolerance can only be realized in combination with cardioplegia by extracellular Na+ and Ca2+ reduction. The cardioplegic solution 'HTK' which has been developed according to these considerations. (1) delays the decay velocity of myocardial ATP by a factor of 7-8 in comparison with pure ischaemia; (2) leads to a good myocardial recovery with regard to metabolic, morphological, and functional criteria after an ischaemic stress of 300 min at 23 +/- 1 degrees C--especially after the addition of quinine; (3) is considerably reduced in its protective efficacy by adding 50 mumol l-1 Ca2+; (4) causes a calcium paradox if it is infused for 30 min at 35 degrees C; this does not happen if it is infused for 60 min at 25 degrees C or for 120 min at 15 degrees C; on adding 50 mumol l-1 Ca2+ to the solution the risk of a calcium paradox is significantly reduced, even after infusion for 35 min at 35 degrees C; (5) effects an evident delay of recovery, if a continuous ischaemic stress of 300 min at 23 degrees +/- 1 degree C is reduced to 3 X 100 min of ischaemia at 17 +/- 1 degrees C by intermittent cardioplegic reperfusion; (6) considerably improves the myocardial recovery even after intermittent cardioplegia if 50 mumol l-1 Ca2+ are added or Mg2+ is reduced from 9 to 4 mmol l-12. The metabolic, morphological, and functional results are equivalent to those after 300 min of continuous ischaemia. Further investigations must show to what extent the 'membrane stabilizing effect' of [Ca2+]o can be achieved by taking advantage of mutual ionic interaction on the level of plasmalemma (e.g. H+-Mg2+-Ca2+) or by adding membrane effective substances (quinine).

Animals↗
PubMed1993

The dietary requirement of young rainbow trout (Oncorhynchus mykiss) for folic acid.

We sought to determine the dietary folic acid requirement of young rainbow trout using growth indices supported by measurements of tissue folate concentrations. The investigation was conducted with purified diets that had, by assay, basal folic acid levels of 0.08 and 0.16 mg/kg in the first and second, respectively, of two experiments. Each experiment was started with fry (initial mean weight, 1.4 and 2.8 g/fish in Experiments 1 and 2, respectively) and was conducted at a water temperature of 15 degrees C. Experiment 1 lasted 18 wk and Experiment 2 lasted 16 wk. Recovery tests (of 8 wk duration, performed on fish fed the unsupplemented diet) and pair-feeding showed that the unsupplemented diet led to a folate-specific deficiency condition in which the main hematological abnormality was the appearance of misshapen nuclei in a small proportion (2.3%) of erythrocytes. Dietary requirements were shown not to exceed 0.3 and 0.6 mg folic acid/kg (17 and 33 micrograms/MJ digestible energy) for optimizing survival and growth indices, respectively. We conclude that the dietary folate requirement of the trout is comparable to that of other vertebrates for the purpose of achieving maximal weight gain.

Analysis of Variance↗
PubMedDate not supplied

Circuit weight training in cardiac patients: determining optimal workloads for safety and energy expenditure.

BACKGROUND: While most studies suggest circuit weight training (CWT) to be safe in cardiac rehabilitation populations, few investigators have controlled variables known to impact CWT intensity. Therefore, the purposes of this study were to determine the energy cost and evaluate safety of cardiac patients while varying rest interval duration and lifting load in a CWT format. METHODS: Nine male subjects with documented coronary artery disease had maximal oxygen uptake (VO2max), one-repetition maximum (1-RM), and body composition tested. In random order and on separate days, 4 CWT sessions using either 40% or 60% of the 1-RM, and either 30 or 60 seconds of rest between stations were completed. Energy cost, heart rate (HR), blood pressure (BP), and rate-pressure product (RPP) were measured. Data were analyzed with a repeated measures analysis of variance, and Tukey's post-hoc test was performed when significant results were found. The alpha level was set at < .05. RESULTS: Subjects exercised at 25% to 32% of VO2max (58%-67% of HRmax) during CWT. The HR and RPP responses were lower during all CWT protocols than at 85% of the treadmill VO2max. No subject displayed any ST-segment depression or angina during CWT. The 40%-60-second protocol had an energy cost (2.98 kcal/min) that was lower (P < .05) than the other protocols (3.48-3.81 kcal/min). Increasing the lifting load resulted in increases (P < .05) in energy cost, and decreasing the rest interval increased energy cost only during the 40% 1-RM protocols. CONCLUSIONS: Results indicate that CWT protocols of varied intensity are safe for cardiac patients when compared to treadmill exercise, and changes in rest interval duration and load can impact the energy cost.

Aged↗
PubMed2025

STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features.

The adaptive immune system monitors cellular integrity by recognizing short peptides from intracellular proteins presented on Major Histocompatibility Complex class I (MHC-I) molecules, collectively termed peptide-MHC complexes (pMHC), enabling detection of foreign or mutated proteins. With the rising importance of immunotherapies targeting neoantigens in cancers, the ability to accurately predict which peptides will bind to the diverse population of MHC alleles is critically important. Current computational methods for pMHC-I prediction fall broadly into sequence-based methods, which rely heavily on large training datasets, and structure-based methods that leverage structural modeling and energetics of pMHC binding. While sequence-based methods have been popularly used, their performance is dependent on the size and quality of training data. On the other hands, while structure-based approaches can generalize better across diverse MHC alleles, they traditionally depend on identifying a single global minimum energy conformation, an assumption that often fails due to the inherent binding promiscuity of MHC-I molecules. To address these limitations, we developed a STRUMP-I (STRUcture-based pMHC Prediction (for class I)), a novel pMHC binding prediction tool that directly leverages a broad set of force-field-derived energy terms as machine-learning features. STRUMP-I achieves performance comparable to state-of-the-art sequence-based models while significantly outperforming them on MHC alleles with limited representation in training data. Furthermore, STRUMP-I demonstrates strong synergy when integrated with sequence-based methods, notably enhancing prediction precision. The robustness and generalizability of STRUMP-I were confirmed by evaluating its predictive performance on independent, previously unseen datasets, including an experimentally validated cancer neoantigen dataset. This combined approach advances our capability to reliably identify clinically relevant neoantigen targets. The source code and trained models are available at https://github.com/yoonjoolab/STRUMP-I.

energy optimization↗
PubMed2004

Three-dimensional bubble clusters: shape, packing, and growth rate.

We consider three-dimensional clusters of equal-volume bubbles packed around a central bubble and calculate their energy and optimal shape. We obtain the surface area and bubble pressures to improve on existing growth laws for three-dimensional bubble clusters. We discuss the possible number of bubbles that can be packed around a central one: the "kissing problem," here adapted to deformable objects.

Journal Article↗
PubMed2006

Learning-based deformable registration of MR brain images.

This paper presents a learning-based method for deformable registration of magnetic resonance (MR) brain images. There are two novelties in the proposed registration method. First, a set of best-scale geometric features are selected for each point in the brain, in order to facilitate correspondence detection during the registration procedure. This is achieved by optimizing an energy function that requires each point to have its best-scale geometric features consistent over the corresponding points in the training samples, and at the same time distinctive from those of nearby points in the neighborhood. Second, the active points used to drive the brain registration are hierarchically selected during the registration procedure, based on their saliency and consistency measures. That is, the image points with salient and consistent features (across different individuals) are considered for the initial registration of two images, while other less salient and consistent points join the registration procedure later. By incorporating these two novel strategies into the framework of the HAMMER registration algorithm, the registration accuracy has been improved according to the results on simulated brain data, and also visible improvement is observed particularly in the cortical regions of real brain data.

Algorithms↗
PubMed2006

Statistical potential for assessment and prediction of protein structures.

Protein structures in the Protein Data Bank provide a wealth of data about the interactions that determine the native states of proteins. Using the probability theory, we derive an atomic distance-dependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein Energy, or DOPE). DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. The DOPE potential was extracted from a nonredundant set of 1472 crystallographic structures. We tested DOPE and five other scoring functions by the detection of the native state among six multiple target decoy sets, the correlation between the score and model error, and the identification of the most accurate non-native structure in the decoy set. For all decoy sets, DOPE is the best performing function in terms of all criteria, except for a tie in one criterion for one decoy set. To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo-electron microscopy mass density maps combined with comparative protein structure modeling, DOPE was incorporated into the modeling package MODELLER-8.

Computational Biology↗
PubMed2006

Minimal requirements for oxygen sensing by the aerotaxis receptor Aer.

The PAS and HAMP domain superfamilies are signal transduction modules found in all kingdoms of life. The Aer receptor, which contains both domains, initiates rapid behavioural responses to oxygen (aerotaxis) and other electron acceptors, guiding Escherichia coli to niches where it can generate optimal cellular energy. We used intragenic complementation to investigate the signal transduction pathway from the Aer PAS domain to the signalling domain. These studies showed that the HAMP domain of one monomer in the Aer dimer stabilized FAD binding to the PAS domain of the cognate monomer. In contrast, the signal transduction pathway was intra-subunit, involving the PAS and signalling domains from the same monomer. The minimal requirements for signalling were investigated in heterodimers containing a full-length and truncated monomer. Either the PAS or signalling domains could be deleted from the non-signalling subunit of the heterodimer, but removing 16 residues from the C-terminus of the signalling subunit abolished aerotaxis. Although both HAMP domains were required for aerotaxis, signalling was not disrupted by missense mutations in the HAMP domain from the signalling subunit. Possible models for Aer signal transduction are compared.

Carrier Proteins↗
PubMed1991

The solution structure of a monomeric insulin. A two-dimensional 1H-NMR study of des-(B26-B30)-insulin in combination with distance geometry and restrained molecular dynamics.

The solution conformation of des-(B26-B30)-insulin (DPI) has been investigated by 1H-NMR spectroscopy. A set of 250 approximate interproton distance restraints, derived from two-dimensional nuclear Overhauser enhancement spectra, were used as the basis of a structure determination using distance geometry (DG) and distance-bound driven dynamics (DDD). Sixteen DG structures were optimized using energy minimization (EM) and submitted to short 5-ps restrained molecular dynamics (RMD) simulations. A further refinement of the DDD structure with the lowest distance errors was done by energy minimization, a prolonged RMD simulation in vacuo and a time-averaged RMD simulation. An average structure was obtained from a trajectory generated during 20-ps RMD. The final structure was compared with the des-(B26-B30)-insulin crystal structure refined by molecular dynamics and the 2-Zn crystal structure of porcine insulin. This comparison shows that the overall structure of des-(B26-B30)-insulin is retained in solution with respect to the crystal structures with a high flexibility at the N-terminal part of the A chain and at the N-terminal and C-terminal parts of the B chain. In the RMD run a high mobility of Gly A1, Asn A21 and of the side chain of Phe B25 is noticed. One of the conformations adopted by des-(B26-B30)-insulin in solution is similar to that of molecule 1 (Chinese nomenclature) in the crystal structure of porcine insulin.

Amino Acid Sequence↗
PubMedDate not supplied

Laser lithotripsy for treatment of canine uroliths.

OBJECTIVE: To confirm in vivo optimal laser energy settings previously determined in vitro for lithotripsy, to develop a technique for Ho:YAG laser lithotripsy, and to evaluate acute and chronic tissue effects of laser lithotripsy. STUDY DESIGN: Prospective, randomized preclinical trial. ANIMALS OR SAMPLE POPULATION: Nineteen intact, adult male dogs. METHODS: Via cystotomy, a single urolith was inserted into the urethra to the level of the base of the os penis to simulate obstruction. Uroliths (calcium oxalate, urate, or magnesium ammonium phosphate) were fragmented by Ho:YAG laser, in contact mode through a 320 micro optic fiber, passed through the operating channel of a 2.8 mm flexible endoscope. The time and total energy to fragmentation were recorded. Dogs were euthanatized immediately after lithotripsy (3 dogs) or at 3 days (7 dogs), and urethral lesions and any stone remnants were evaluated. Urethral integrity was also evaluated in 9 other dogs by endoscopy on day 10; these were also monitored clinically for 30 days. RESULTS: The mean time for adequate fragmentation was 166.7 seconds (range, 47-494.5 seconds). The mean+/-SD energy used was 1418+/-851.2 J. In part 1, 2 dogs were obstructed with urolith fragments at necropsy. Eight dogs had minimal (<30 mg) or no urolith material evident within the urethra. Four dogs had gross focal or circumferential erosion, ulceration, or hemorrhage of the urethral mucosa. Lesions were not associated with the site of laser irradiation in 2 dogs. In dogs observed for 30 days, hematuria, pollakiuria, and stranguria that were observed after lithotripsy, resolved in all affected dogs by day 5. No mucosal lesions were observed by endoscopy and none of the dogs became obstructed. CONCLUSION: Laser lithotripsy with the Ho:YAG laser in contact mode successfully fragmented obstructive uroliths in male dogs. CLINICAL RELEVANCE: Laser lithotripsy may be a clinically relevant technique for treatment of urolithiasis in male dogs; clinical studies to evaluate long-term effects on urethral mucosa and the role of repeat treatment for recurrence are indicated.

Animals↗
PubMed1992

Dynamic effects of carotid sinus baroreflex on ventriculoarterial coupling studied in anesthetized dogs.

We evaluated dynamic effects of the carotid sinus baroreflex on ventriculoarterial coupling. In seven anesthetized, vagotomized dogs, we bilaterally isolated carotid sinuses and randomly changed carotid sinus pressure while measuring aortic pressure, aortic flow, and left ventricular pressure. Estimating left ventricular end-systolic elastance (Ees) and effective arterial elastance (Ea) on a beat-to-beat basis, we determined transfer functions from the carotid sinus pressure to Ees (HEes) and from the carotid sinus pressure to Ea (HEa) over the frequency range spanning 0.002-0.25 Hz. Both HEes and HEa exhibited characteristics of a second-order low-pass filter. The gains of HEes and HEa were 0.085 +/- 0.065 (mean +/- SD) and 0.081 +/- 0.049 mm Hg/ml/mm Hg, respectively. There were no significant differences in natural frequencies (0.039 +/- 0.013 versus 0.039 +/- 0.007 Hz) or damping ratios (0.65 +/- 0.11 versus 0.64 +/- 0.24). The results indicated that the carotid sinus baroreflex dynamically altered Ees and Ea to the same extent in the process of stabilizing arterial pressure. Because the arterial system extracts maximal external work from a given heart when Ea equals Ees, the carotid sinus baroreflex appeared to be designed to regulate the ventricular and arterial properties to optimize the energy transmission from the left ventricle to the arterial system in anesthetized, vagotomized dogs.

Anesthesia↗
PubMed2001

Using beta-cell growth factors to enhance human pancreatic Islet transplantation.

This is a particularly exciting time in the field of pancreatic islet growth, development, and survival. The recent publication of a study demonstrating that human pancreatic islet transplantation is both technically and immunologically feasible has highlighted the need for large supplies of pancreatic islets or pancreatic beta cells for larger-scale islet transplantation in patients with diabetes. This, together with a rapid expansion in the past several years of the understanding of mechanisms of islet growth, development, and survival, has accelerated and invigorated efforts to therapeutically harness the cellular mechanisms responsible for pancreatic beta-cell proliferation, survival, and development and to take advantage of this new knowledge to enhance the availability, survival, and function of pancreatic beta cells in human islet transplantation for diabetes mellitus. Here, we briefly review the confluence of events that have provided optimism and energy to the islet transplant field, and we focus on peptide growth factors that eventually may be deployed in the effort to augment islet mass and function in patients with diabetes.

Animals↗
PubMed2007

Feasibility of breast preserving therapy with single fraction in situ radiotherapy delivered intraoperatively.

BACKGROUND: Accelerated partial breast irradiation (APBI) has gained widespread interest as a means of improving the convenience and availability of breast conserving radiotherapy. Intraoperative radiation therapy (IORT) is an APBI technique that delivers breast radiotherapy as a single dose at the time of partial mastectomy. We adapted the technique of Veronesi to deliver IORT prior to tumor excision to improve delivery to the region at risk and reduce the volume of normal tissue irradiated. METHODS: Patients age >or=55 with ultrasonographically defined tumors <or=3 cm and invasive ductal carcinoma confirmed by core biopsy were eligible. Pre-operative ultrasound was performed at the time of needle localization and radiocolloid injection. IORT treatment planning was performed prior to surgery using ultrasound tumor definition, selecting cone size and electron energy to optimize dose distribution. In the operating room, the surgeon retracted the skin over the tumor, cone was placed and radiotherapy delivered. Standard partial mastectomy was then performed. RESULTS: Twenty-three patients were enrolled in the study. Eighteen patients completed IORT with 10 patients having successful IORT no additional local therapy necessary. In five patients, the intraoperative radiation therapy served as the boost and in three patients unsuspected larger tumors or multicentric disease necessitated a mastectomy. The majority of patients had a good to excellent cosmetic result. CONCLUSIONS: Single fraction in situ IORT prior to partial mastectomy is feasible for patients with small breast cancers in achieving a good to excellent cosmetic result. Based on this early preliminary data, we plan to expand our feasibility trial.

Aged↗
PubMed2004

[KiBank: a database for computer-aided drug design based on protein-chemical interaction analysis].

KiBank is a database for computer-aided drug design and consists of binding affinities and chemical and target protein structures. Each chemical or protein structure with hydrogen atoms added was optimized by energy minimization and stored in PDB or MDL MOL file format, so that the structural data can be directly used for in silico binding studies. To describe the extent of inhibition, the inhibition constant (K(i)) value is used to simplify comparisons of strengths among chemical-protein bindings. As of April 2004, KiBank contained 142 proteins, over 5000 chemicals, and over 6000 binding affinity values that were published in peer-reviewed journals. The binding affinity values are currently mostly for membrane and nuclear receptors but are soon being expanded to other drug targets. KiBank is updated daily and can be accessed on the Web at http://kibank.iis.u-tokyo.ac.jp/at no charge.

Computer-Aided Design↗
PubMed2005

The association of tetrameric acetylcholinesterase with ColQ tail: a block normal mode analysis.

Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists as tetramers associated with the proline-rich attachment domain (PRAD) of either collagen-like Q subunit (ColQ) or proline-rich membrane-anchoring protein. Crystallographic studies have revealed that different tetramer forms may be present, and it is not clear whether one or both are relevant under physiological conditions. Recently, the crystal structure of the tryptophan amphiphilic tetramerization (WAT) domain of AChE associated with PRAD ([WAT]4PRAD), which mimics the interface between ColQ and AChE tetramer, became available. In this study we built a complete tetrameric mouse [AChE(T)]4-ColQ atomic structure model, based on the crystal structure of the [WAT]4PRAD complex. The structure was optimized using energy minimization. Block normal mode analysis was done to investigate the low-frequency motions of the complex and to correlate the structure model with the two known crystal structures of AChE tetramer. Significant low-frequency motions among the catalytic domains of the four AChE subunits were observed, while the [WAT]4PRAD part held the complex together. Normal mode involvement analysis revealed that the two lowest frequency modes were primarily involved in the conformational changes leading to the two crystal structures. The first 30 normal modes can account for more than 75% of the conformational changes in both cases. The evidence further supports the idea of a flexible tetramer model for AChE. This model can be used to study the implications of the association of AChE with ColQ.

Acetylcholinesterase↗