LET dependence of the response of a PTW-60019 microDiamond detector in a 62 MeV proton beam

This study was initiated following conclusions from earlier experimental work, performed in a low-energy carbon ion beam, indicating a significant LET dependence of the response of a PTW-60019 microDiamond detector. The purpose of this paper is to present a comparison between the response of the same PTW-60019 microDiamond detector and an IBA Roos-type ionization chamber as a function of depth in a 62 MeV proton beam. Even though proton beams are considered as low linear energy transfer (LET) beams, the LET value increases slightly in the Bragg peak region. Contrary to the observations made in the carbon ion beam, in the 62 MeV proton beam good agreement is found between both detectors in both the plateau and the distal edge region. No significant LET dependent response of the PTW-60019 microDiamond detector is observed consistent with other findings for proton beams in the literature, despite this particular detector exhibiting a substantial LET dependence in a carbon ion beam.     

Cysteine 62 of Bax is critical for its conformational activation and its proapoptotic activity in response to H2O2-induced apoptosis

Bax is activated and translocated onto mitochondria to mediate cytochrome c release and apoptosis. The molecular mechanisms of Bax activation during apoptosis remain a subject of debate. We addressed the question of whether reactive oxygen species could directly activate Bax for its subsequent translocation and apoptosis. Using the SW480 human colon adenocarcinoma cell line stably expressing Bax fused to GFP, we showed that H2O2 induces Bax conformational change, mitochondrial translocation, and subsequent oligomerization at mitochondria. We found that H2O2-induced Bax activation is dependent on the conserved cysteine residue 62 of Bax. Mutation of cysteine 62, but not cysteine 126, to serine or alanine abolished its activation by H2O2 but not other death stimuli, both in SW480 and Bax-deficient HCT116 cells, whereas wild type Bax sensitizes these cells to apoptosis. Cysteines of Bax could chemically react with H2O2. Mutation of Bax BH3 domain in the presence of cysteine 62 also abolished Bax proapoptotic activity. We conclude that reactive oxygen species could be a direct signal for Bax activation by reacting with cysteine residues. Our results identify a critical role of cysteine 62 in oxidative stress-induced Bax activation and subsequent apoptosis.     

Use of residue pairs in protein sequence-sequence and sequence-structure alignments

Two new sets of scoring matrices are introduced: H2 for the protein sequence comparison and T2 for the protein sequence-structure correlation. Each element of H2 or T2 measures the frequency with which a pair of amino acid types in one protein, k-residues apart in the sequence, is aligned with another pair of residues, of given amino acid types (for H2) or in given structural states (for T2), in other structurally homologous proteins. There are four types, corresponding to the k-values of 1 to 4, for both H2 and T2. These matrices were set up using a large number of structurally homologous protein pairs, with little sequence homology between the pair, that were recently generated using the structure comparison program SHEBA. The two scoring matrices were incorporated into the main body of the sequence alignment program SSEARCH in the FASTA package and tested in a fold recognition setting in which a set of 107 test sequences were aligned to each of a panel of 3,539 domains that represent all known protein structures. Six procedures were tested; the straight Smith-Waterman (SW) and FASTA procedures, which used the Blosum62 single residue type substitution matrix; BLAST and PSI-BLAST procedures, which also used the Blosum62 matrix; PASH, which used Blosum62 and H2 matrices; and PASSC, which used Blosum62, H2, and T2 matrices. All procedures gave similar results when the probe and target sequences had greater than 30% sequence identity. However, when the sequence identity was below 30%, a similar structure could be found for more sequences using PASSC than using any other procedure. PASH and PSI-BLAST gave the next best results.     

The cerebellar nodulus/uvula integrates otolith signals for the translational vestibulo-ocular reflex

BACKGROUND: The otolith-driven translational vestibulo-ocular reflex (tVOR) generates compensatory eye movements to linear head accelerations. Studies in humans indicate that the cerebellum plays a critical role in the neural control of the tVOR, but little is known about mechanisms of this control or the functions of specific cerebellar structures. Here, we chose to investigate the contribution of the nodulus and uvula, which have been shown by prior studies to be involved in the processing of otolith signals in other contexts. METHODOLOGY/PRINCIPAL FINDINGS: We recorded eye movements in two rhesus monkeys during steps of linear motion along the interaural axis before and after surgical lesions of the cerebellar uvula and nodulus. The lesions strikingly reduced eye velocity during constant-velocity motion but had only a small effect on the response to initial head acceleration. We fit eye velocity to a linear combination of head acceleration and velocity and to a dynamic mathematical model of the tVOR that incorporated a specific integrator of head acceleration. Based on parameter optimization, the lesion decreased the gain of the pathway containing this new integrator by 62%. The component of eye velocity that depended directly on head acceleration changed little (gain decrease of 13%). In a final set of simulations, we compared our data to the predictions of previous models of the tVOR, none of which could account for our experimental findings. CONCLUSIONS/ SIGNIFICANCE: Our results provide new and important information regarding the neural control of the tVOR. Specifically, they point to a key role for the cerebellar nodulus and uvula in the mathematical integration of afferent linear head acceleration signals. This function is likely to be critical not only for the tVOR but also for the otolith-mediated reflexes that control posture and balance.     

Index selection with nonlinear profit function as a tool to achieve simultaneous genetic gain

Summary Simultaneous improvement of several, and often negatively correlated, traits is frequently a desired objective in forest tree breeding. A profit function that includes a combination of both linear weights and weights for the cross-products of trait combinations facilitates the construction of a linear index, with an attractive response in all traits. A detailed algorithm for finding the index coefficients is provided, along with three examples of applications in tree breeding. The index is also a powerful tool in optimizing the selection for a ratio of two traits. It is argued that a more equal progress in several traits provides a safetey net when faced with economic uncertainties. The provided algorithm eliminates the need for direct search techniques. Existence of a dual set of linear weights means that the statistical properties of the index based on nonlinear profit functions are identical to those of the classical Smith-Hazel type of index.     

Dose-response time modelling for highly pathogenic avian influenza A (H5N1) virus infection

Aims: To develop time‐dependent dose–response models for highly pathogenic avian influenza A (HPAI) of the H5N1 subtype virus. Methods and Results: A total of four candidate time‐dependent dose–response models were fitted to four survival data sets for animals (mice or ferrets) exposed to graded doses of HPAI H5N1 virus using the maximum‐likelihood estimation. A beta‐Poisson dose–response model with the N₅₀ parameter modified by an exponential‐inverse‐power time dependency or an exponential dose–response model with the k parameter modified by an exponential‐inverse time dependency provided a statistically adequate fit to the observed survival data. Conclusions: We have successfully developed the time‐dependent dose–response models to describe the mortality of animals exposed to an HPAI H5N1 virus. The developed model describes the mortality over time and represents observed experimental responses accurately. Significance and Impact of the Study: This is the first study describing time‐dependent dose–response models for HPAI H5N1 virus. The developed models will be a useful tool for estimating the mortality of HPAI H5N1 virus, which may depend on time postexposure, for the preparation of a future influenza pandemic caused by this lethal virus.     

Information in Observation Under the Correlated Linear Model

In this paper we propose a measure of information in a set of observations under a given design and the linear model with the observations being correlated. We then compare the different sets of observations with respect to the information measure in the situations where the underlying designs are nested and split-plot. AMS 1970 Subject Classification: Secondary 62J05, 62J10, 62K05, 62K10, 62K15, 62K99.     

Autophagy substrate SQSTM1/p62 regulates chromatin ubiquitination during the DNA damage response

The importance of autophagy in the DNA damage repair process is clear; however, the detailed molecular mechanism is still largely unknown. Here we found that DNA damage-induced histone H2A ubiquitination is suppressed in autophagy-deficient cells in a SQSTM1/p62 dependent manner. SQSTM1 binds and inhibits E3 ligase RNF168s activity, which is essential for H2A ubiquitination. As a result, several important factors for DNA repair cannot be recruited to the sites of DNA double-strand breaks (DSBs) in autophagy-deficient cells, leading to diminished DNA repair and increased sensitivity of cells to radiation.     

The type of interaction of histone H5 wo ith DNA changes significantly at various stages of chromatin condensation

Histones were covalently bound to DNA by dimethylsulfate-induced crosslinking and DNA-contacting peptides of histone H5, thus modified, were mapped by a combination of peptide cleavage reactions and peptide gel electrophoresis. In the nucleosome, the only strong crosslinking point is His-25 which resides near the ends of nucleosomal DNA. This contact point persists throughout different steps of chromatin condensation--decondensation. In decondensed chromatin, it is supplemented by the contact with DNA of the N-terminus of the histone H5 molecule. The high level of chromatin condensation existing in the nuclei or induced by bivalent cations results in a new and considerably stronger crosslinking point His-62, which is also characteristic for cooperative H5-DNA complexes. This structural change is observed only on oligonucleosomal chains containing no less than 3 contiguous nucleosomes, and is absent in isolated mono- or dinucleosomes. We propose that the formation of the 30-nm chromatin fibre, typical for the nuclei, is accomplished in part by the histone H5-linker DNA cooperative interactions, manifested by strong His-62--linker DNA contact.     

Relative limb strength and locomotion in Homo habilis

The Homo habilis OH 62 partial skeleton has played an important, although controversial role in interpretations of early Homo locomotor behavior. Past interpretive problems stemmed from uncertain bone length estimates and comparisons using external bone breadth proportions, which do not clearly distinguish between modern humans and apes. Here, true cross-sectional bone strength measurements of the OH 62 femur and humerus are compared with those of modern humans and chimpanzees, as well as two early H. erectus specimens-KNM-WT 15000 and KNM-ER 1808. The comparative sections include two locations in the femur and two in the humerus in order to encompass the range of possible section positions in the OH 62 specimens. For each combination of section locations, femoral to humeral strength proportions of OH 62 fall below the 95% confidence interval of modern humans, and for most comparisons, within the 95% confidence interval of chimpanzees. In contrast, the two H. erectus specimens both fall within or even above the modern human distributions. This indicates that load distribution between the limbs, and by implication, locomotor behavior, was significantly different in H. habilis from that of H. erectus and modern humans. When considered with other postcranial evidence, the most likely interpretation is that H. habilis, although bipedal when terrestrial, still engaged in frequent arboreal behavior, while H. erectus was a completely committed terrestrial biped. This adds to the evidence that H. habilis (sensu stricto) and H. erectus represent ecologically distinct, parallel lineages during the early Pleistocene.     

Temporal development of hippocampal cell death is dependent on tissue strain but not strain rate

Deformation of brain tissue in response to mechanical loading of the head is the root-cause of traumatic brain injury (TBI). Even below ultimate failure limits, deformation activates pathophysiological cascades resulting in delayed cell death. Injury response of soft tissues, such as the chest and spinal cord, is dependent on the product of deformation and velocity, a parameter termed the viscous criterion. We set out to test if hippocampal cell death could be predicted by a similar combination of strain and strain rate and if the viscous criterion was valid for hippocampus. Quantitative prediction of the brain's biological response to mechanical stimuli is difficult to achieve in animal models of TBI, so we utilized an in vitro model of TBI based on hippocampal slice cultures. We quantified the temporal development of cell death after precisely controlled deformations for 30 combinations of strain (0.05-0.50) and strain rate (0.1-50s(-1)) relevant to TBI. Loading conditions for a subset of cultures were verified by analysis of high-speed video. Cell death was found to be significantly dependent on time-post injury, on strain magnitude, and to a lesser extent, on anatomical region by a repeated-measures, three-way ANOVA. The responses of the CA1 and CA3 regions of the hippocampus were not statistically different in contrast to some in vivo TBI studies. Surprisingly, cell death was not dependent on strain rate leading us to conclude that the viscous criterion is not a valid predictor for hippocampal tissue injury. Given the large data set and extensive combinations of biomechanical parameters, predictive mathematical functions relating independent variables (strain, region, and time post-injury) to the resultant cell death were defined. These functions can be used as tolerance criteria to equip finite element models of TBI with the added capability to predict biological consequences.     

Projected [<Superscript>1</Superscript>H,<Superscript>15</Superscript>N]-HMQC-[<Superscript>1</Superscript>H,<Superscript>1</Superscript>H]-NOESY for large molecular systems: application to a 121 kDa protein-DNA complex

We present a projected [¹H,¹⁵N]-HMQC-[¹H,¹H]-NOESY experiment for observation of NOE interactions between amide protons with degenerate ¹⁵N chemical shifts in large molecular systems. The projection is achieved by simultaneous evolution of the multiple quantum coherence of the nitrogen spin and the attached proton spin. In this way NOE signals can be separated from direct-correlation peaks also in spectra with low resolution by fully exploiting both ¹H and ¹⁵N frequency differences, such that sensitivity can be increased by using short maximum evolution times. The sensitivity of the experiment is not dependent on the projection angle for projections up to 45° and no additional pulses or delays are required as compared to the conventional 2D [¹H,¹⁵N]-HMQC-NOESY. The experiment provides two distinct 2D spectra corresponding to the positive and negative angle projections, respectively. With a linear combination of 1D cross-sections from the two projections the unavoidable sensitivity loss in projection spectra can be compensated for each particular NOE interaction. We demonstrate the application of the novel projection experiment for the observation of an NOE interaction between two sequential glycines with degenerate ¹⁵N chemical shifts in a 121.3 kDa complex of the linker H1 histone protein with a 152 bp linear DNA.     

Anomalous oxidation of MDL 73,404 by horseradish peroxidase

3,4-Dihydro-6-hydroxy-N,N,N-2,5,7,8-heptamethyl-2H-1-benzopyran-2-ethanaminium-4-methylbenzene sulfonate (MDL 73,404) is a cardioselective water-soluble quaternary ammonium analogue of Vitamin E which is synthesized to augment the antioxidant defence in situations of free radical injury such as myocardial infarction/reperfusion. Its oxidation by any peroxidative enzyme has not been studied kinetically. This paper describes its enzymatic oxidation by horseradish peroxidase (HRP). The activity was followed spectrophotometrically at 255nm, and the experimental results were simulated using the program "KINETIC 3.1" for Windows 3.x. The MDL 73,404 was oxidized by horseradish peroxidase in the presence of H2O2 to its corresponding MDL 73,404 quinone. During this oxidation, the horseradish peroxidase showed an unexpectedly slow kinetic response with time, which contrast with the linear product accumulation curve measured with 2,2'-azino-bis-(3-estilbenzotiazol-6-sulfonic acid) (ABTS). This response was dependent on the respective concentrations of enzyme, MDL 73,404 and H2O2. However, when the enzyme was incubated with H2O2, the slow kinetic response disappeared and a lag period was observed. Furthermore, when p-coumaric acid (PCA) was added, the activity increased and the slow kinetic response became a straight line. In order to explain this anomalous behaviour, a kinetic model has been proposed and its differential equations simulated. From the correlation between experimental and simulated results it is concluded that MDL 73,404 can act as a slow response substrate for peroxidase, probably due to the presence of a quaternary ammonium side chain that confers on it a slow capacity to convert compound III into ferriperoxidase.     

Prediction of variability in CYP3A4 induction using a combined 1H NMR metabonomics and targeted UPLC-MS approach

The activity of Cytochrome P450 3A4 (CYP3A4) enzyme is associated with many adverse or poor therapeutic responses to drugs. We used (1)H NMR-based metabonomics to identify a metabolic signature associated with variation in induced CYP3A4 activity. A total of 301 female twins, aged 45--84, participated in this study. Each volunteer was administered a potent inducer of CYP3A4 (St. John's Wort) for 14 days and the activity of CYP3A4 was quantified through the metabolism of the exogenously administered probe drug quinine sulfate (300 mg). Pre- and postintervention fasting urine samples were used to obtain metabolite profiles, using (1)H NMR spectroscopy, and were analyzed using UPLC--MS to obtain a marker for CYP3A4 induction, via the ratio of 3-hydroxyquinine to quinine (3OH-Q:Q). Multiple linear regression was used to build a predictive model for 3OH-Q:Q values based on the preintervention metabolite profiles. A combination of seven metabolites and seven covariates showed a strong (r = 0.62) relationship with log(3OH-Q:Q). This regression model demonstrated significant (p < 0.00001) predictive ability when applied to an independent validation set. Our results highlight the promise of metabonomics for predicting CYP3A4-mediated drug response.     

A simple procedure to weight empirical potentials in a fitness function so as to optimize its performance in ab initio protein-folding problem

In an approach to the protein folding problem by a Genetic Algorithm, the fitness function plays a critical role. Empirical potentials are generally used to build the fitness function, and they must be weighted to obtain a valuable one. The weights are generally found by the comparison with a set of misfolded structures (decoys), but a dependence of the obtained fitness generally arises on the used decoys. Here we describe a general procedure to find out, from a given set of potentials, their better linear combination that could either identify the wild structure or prove their powerlessness. We use topological considerations over the hyperspace of the potentials, and a multiple linear inequalities solver. The iterated method flows through the following steps: it determines a direction in the hyperspace of the potentials, which identifies the native structure as a vertex among a set of misfolded decoys. A multiple linear inequalities solver obtains the direction. A Genetic Algorithm, tailored to the specific problem, uses the fitness function defined by this direction and generally reaches a new structure better than the experimental one, which is added to the ensemble. The decoys so generated are not dependent on a deterministic criterion. This iterative procedure can be stopped either by identifying an effective fitness function or by proving the impossibility of its achievement. In order to test the method under the hardest conditions, we choose numerous and heterogeneous quantities as components of the fitness function. This method could be a useful tool for the scientific community in order to test any fitness proposed and to recognize the most important components on which it is built.     

Structural and functional dissection of Sec62p, a membrane-bound component of the yeast endoplasmic reticulum protein import machinery.

SEC62 is required for the import of secretory protein precursors into the endoplasmic reticulum (ER) of Saccharomyces cerevisiae. The DNA sequence of SEC62 predicts a 32-kDa polypeptide with two potential membrane-spanning segments. Two antisera directed against different portions of the SEC62 coding region specifically detected a 30-kDa polypeptide in cell extracts. A combination of subcellular fractionation, detergent and alkali extraction, and indirect immunofluorescence studies indicated that Sec62p is intimately associated with the ER membrane. Protease digestion of intact microsomes and analysis of the oligosaccharide content of a set of Sec62p-invertase hybrid proteins suggested that Sec62p spans the ER membrane twice, displaying hydrophilic amino- and carboxy-terminal domains towards the cytosol. Sec62p-invertase hybrid proteins that lack the Sec62p C terminus failed to complement the sec62-l mutation and dramatically inhibited the growth of sec62-l cells at a normally permissive temperature. The inhibitory action of toxic Sec62p-invertase hybrids was partially counteracted by the overexpression of Sec63p. Taken together, these data suggest that the C-terminal domain of Sec62p performs an essential function and that the N-terminal domain associates with other components of the translocation machinery, including Sec63p.     

Stimulation of Na+/H+ antiport activity by epidermal growth factor and insulin occurs without activation of protein kinase C

Addition of phorbol 12, 13 dibutyrate (PBt2) or a combination of epidermal growth factor (EGF) and insulin to quiescent cultures of Swiss 3T3 cells increased intracellular pH in a Na+-dependent fashion. In contrast to PBt2, EGF plus insulin failed to stimulate protein kinase C and elicited the ionic response in cells lacking this enzyme. We suggest that the stimulation of the Na+/H+ antiport in Swiss 3T3 cells is mediated by at least two separate pathways, only one of which is dependent upon the activation of protein kinase C.     

The effect of propylbenzilylcholine mustard on contraction and radioligand binding parameters of muscarinic receptors in guinea pig ileum

The receptor occupancy-biological effect relationship for muscarinic receptors in guinea pig ileal smooth muscle has been studied by comparison of radioligand binding and contractile response. Muscarinic receptors in homogenates of ileal smooth muscle were labeled with [3H]-1-Quinuclidinyl benzilate. Treatment with propylbenzilylcholine mustard (PrBCM), to inactivate irreversibly muscarinic receptors, caused a large dose dependent rightward shift of the dose-response curve to three agonistic furtrethonium derivatives with a concomitant decrease in maximal response. Using those data, the fraction of receptors remaining unoccupied (q-values) and "true affinity constants" (-log KA-values) were calculated. Exposure to 20 or 60 nM PrBCM for 15 minutes resulted in a 39% and a 61% reduction in specific [3H]-1-Quinuclidinyl benzilate binding sites respectively to be compared with a 62% and a 85% decrease expected from calculated q-values. KA-values for the methyl and ethyl derivative agreed well with the dissociation constants for the high affinity agonist sites determined from displacement of [3H-]-1-Quinuclidinyl benzilate. The KA-value for the propylfurtrethonium corresponds to the low affinity agonist dissociation constant. The fraction of receptors in the high affinity agonist state differs considerably for the three furtrethonium derivatives investigated. Neither the fraction of receptors in the high affinity agonist state, nor the ratio of dissociation constants for these states is affected by the alkylation of 85% of the functional muscarinic receptors. The inactivation of components of the effector system by PrBCM seems unlikely.     

Characterization of phosphorylation sites on histone H1 isoforms by tandem mass spectrometry

Histone H1 isoforms isolated from asynchronously grown HeLa cells were subjected to enzymatic digestion and analyzed by nano-flow reversed-phase high performance liquid chromatography (RP-HPLC) tandem mass spectrometry (MS/MS) on both quadrupole ion trap and linear quadrupole ion trap-Fourier transform ion cyclotron resonance mass spectrometers. We have observed all five major isoforms of histone H1 (H1.1, H1.2, H1.3, H1.4, and H1.5) as well as a lesser studied H1, isoform H1.X. MS/MS experiments confirmed N-terminal acetylation on all isoforms plus a single internal acetylation site. Immobilized metal affinity chromatography in combination with tandem mass spectrometry was utilized to identify 19 phosphorylation sites on the five major H1 isoforms plus H1.X. Fourteen of these phosphorylation sites were located on peptides containing the cyclin dependent kinase (CDK) consensus motif (S/T)-P-X-Z (where X is any amino acid and Z is a basic amino acid). Five phosphorylation sites were identified in regions that did not fit the consensus CDK motif. One of these phosphorylation sites was found on the serine residue on the H1.4 peptide KARKSAGAAKR. The adjacent lysine residue to the phosphoserine was also shown to be methylated. This finding raises the question of whether the hypothesized "methyl/phos" switch could be extended to linker histones, and not exclusive to core histones.