Computational investigation on microsolvation of the osmolyte glycine betaine [GB (H2O)1-7]

The preferential interactions of glycine betaine (GB) with solvent components and the effect of solvent on its stability have been examined. In particular, the microsolvation of organic osmolyte and widely important osmoprotectant in nature as glycine betaine has been reported by using M06 method. A number of configurations (b_X (a-z)) of the clusters for one to seven water molecules (×?=?1-7) have been considered for the microsolvation. Structures of stable conformers are obtained and denoted as b1a, b2a, b3a, b4a, b5a, b6a and b7a. It is observed from the interaction energy difference (?E) that only seven water molecules can be accommodated in the first solvation shell to stabilize GB. It is also observed that the calculated relative energy using M06 is in close agreement with calculations at the MP2 level of theory.

Monetary Valuation of Emissions in Implementing Environmental Policy

At various levels of environmental policy making there is a demand to translate polluting emissions into monetary units. In the so-called reduction cost approach, based upon policy targets, polluting emissions are expressed in monetary terms by determination of the marginal unit reduction cost at the emission target level. This approach provides shadow prices for emissions by which it can be established whether a certain measure or technology belongs to the most efficient set of measures by which the policy targets can be reached. This article argues that, if clear (generic) government targets such as national emission reduction targets exist for an emission, shadow prices derived by this method are to be preferred to shadow prices derived by other methods for decisions at the project (implementation) level. By application of the reduction cost approach, implementation decisions can be made that are both cost-effective and consistent with government policy.     

Chemical composition and serological analysis of the cell wall of Peptostreptococcus

Bahn, Arthur N. (Northwestern University, Chicago, Ill.), Patrick C. Y. Kung, and James A. Hayashi. Chemical composition and serological analysis of the cell wall of Peptostreptococcus. J. Bacteriol. 91:1672-1676. 1966.-Chemical and serological analyses were made of the cell wall of Peptostreptococcus to characterize taxonomically this genus of anaerobic streptococci. Cell wall hydrolysates of P. putridus strains 06 and 85, P. intermedius strains 11 and 87, and P. elsdenii strain B-159 were prepared, and the cell wall sugars were measured quantitatively by paper chromatography. Strain 85 contained only glucose, whereas strain 06 contained 93% glucose and 7% mannose. Strain 87 contained only rhamnose, and strain 11 contained approximately equal amounts of glucose and rhamnose. Strain B-159 differed from all the other strains in having a low (3.1%) content of total carbohydrate, consisting of rhamnose, galactose, and glucose. Quantitative amino acid analyses showed that the major amino compounds present in the cell wall were glutamic and aspartic acids, alanine, lysine, muramic acid, glucosamine, and galactosamine. Strains 06 and 85 possessed this complement of amino compounds, but strains 11 and 87 had relatively little aspartic acid. Strain B-159 was markedly different in having a high content of glycine and diaminopimelic acid, with only traces of lysine; it was the only strain in which teichoic acid was found. Serological analyses were made with the use of cell wall extracts as antigenic material and with homologous antisera, as well as streptococcal group antisera for groups A through S. The only strong agglutination was obtained between strain 87 antigen and group C antisera; weak agglutination was obtained with 87 against N, O, and K, and between strain 11 and groups E and F. All other antisera gave negative reactions. It is concluded that strain B-159 does not belong to the genus Peptostreptococcus, that strains 06 and 85 are members of P. putridus, and that strains 11 and 87 may be members of two different genera.     

Immunohistochemical identification of reserve cells of the endocervical canal by monoclonal antibodies EE21-06d

Expression of cytokeratin polypeptides characteristic of squamous epithelium was studied in reserve cells of cervical canal obtained from 8 women by the immunofluorescence method with the help of monoclonal antibodies EE21-06d (MAB). MAB EE21-06d were shown to detect individual reserve cells as well as their hyperplasia foci without staining columnar cells.     

Characterization and cross-amplification of 13 microsatellite loci in the northern pine processionary moth, Thaumetopoea pinivora (Lepidoptera: Notodontidae)

Thirteen polymorphic microsatellite loci were developed for the northern pine processionary moth (Thaumetopoea pinivora) and tested for cross-amplification in seven other species within the Thaumetopoea family. Number of alleles ranged from two to 10 when at least 28 individuals from one population were screened and one locus, Thapin06, appears to be sex linked. Expected heterozygosity ranged from 0.094 to 0.856 and observed heterozygosity ranged from 0.097 to 0.806. Amplification success varied between sister species, with two up to seven loci being successfully amplified. The described loci will be valuable for studying the population genetic structure and dispersal behaviour of this forest pest.     

Bimodal loop-loop interactions increase the affinity of RNA aptamers for HIV-1 RNA structures

Multiple loop-loop interactions between adjacent RNA hairpins regulate gene expression in different organisms. To demonstrate that such natural interactions could be mimicked for generating RNA ligands that are able to recognize simultaneously at least two structured RNA targets, a double kissing complex model was designed. The target consisted of two HIV-1 transactivating responsive (TAR) RNA variants, BRU and MAL, connected by a non-nucleotidic linker. The double ligand was generated by combining the corresponding hairpin aptamers, R06BRU and R06MAL, identified previously by in vitro selection [Ducongé, F., and Toulmé, J. J (1999) RNA 5, 1605-1614]. The resulting interaction was analyzed by thermal denaturation monitored by UV spectroscopy, electrophoretic mobility shift assays (EMSAs), and surface plasmon resonance (SPR) experiments. The bimodal complex was characterized by a binding equilibrium constant increased by at least 1 order of magnitude compared to that of the complexes between the individual parent hairpins. This resulted from a slower dissociation rate. We then made use of such a strategy for targeting two structured functional motifs of the folded 5' untranslated region (5'UTR) of HIV-1. Two bivalent RNA ligands were designed that targeted simultaneously the TAR and dimerization initiation site (DIS) hairpins or the TAR and poly(A) ones. The results show that these ligands also displayed enhanced affinity for their target compared to the individual molecules. The work reported here suggests that bimodal structured RNA ligands might provide a way of increasing the affinity of aptamers for folded RNA targets.     

Use of the Brown-Roberts-Wells stereotactic frame for functional neurosurgery

The Brown-Roberts-Wells (BRW) stereotactic unit has proven itself to be a highly accurate instrument for biopsying or locating pathologic intracranial lesions based on CT scan information. We utilized the BRW frame to select 18 target sites in 12 patients undergoing functional stereotactic procedures. Two patients had bilateral cingulumotomies, 5 had thalamotomies for movement disorders, and 5 underwent electrode implantations for the treatment of chronic pain. Stereotactic frame settings were determined using a positive contrast ventriculogram, orthogonal radiographs, and a computer program provided with the BRW system. In addition, attempts were made to select targets based on CT scan landmarks alone, and these were compared to those derived using ventriculography. We found the BRW frame to be a satisfactory device for performing functional neurosurgical procedures based on ventriculographic landmarks. Coordinates derived from CT scans were similar to those obtained with ventriculography, but were not accurate enough to permit the use of CT scanning as the sole means of target identification. Although future improvements in imaging techniques and computer software are likely to occur, our experience supports ventriculography as the current method of choice for the precise localization of functional targets with the BRW stereotactic system.     

Fatigue strength: effect of welding type and joint design executed in Ti-6Al-4V structures

doi: 10.1111/j.1741‐2358.2011.00598.x
Fatigue strength: effect of welding type and joint design executed in Ti‐6Al‐4V structures Background: This study evaluated the fatigue strength of Ti‐6Al‐4V‐machined structures submitted to laser (L)‐welding and TIG (TIG)‐welding procedures, varying the joint designs. Materials and methods: Seventy dumbbell rods were machined in Ti‐6Al‐4V alloy with central diameters of 3.5 mm. The specimens were sectioned and welded using TIG or L and three joint designs {‘I’ design, varying welding distances [0.0 mm (I00) or 0.6 mm (I06)], or ‘X’ [X] design}. The combinations of variables created six groups, which, when added to the intact group, made a total of seven groups (n = 10). L was executed as follows: 360 V/8 ms (X) and 390 V/9 ms (I00 and I06), with focus and frequency regulated to zero. TIG was executed using 2:2 (X) and 3:2 (I00 and I06) as welding parameters. Joints were finished, polished and submitted to radiographic examination to be analysed visually for the presence of porosity. The specimens were then subjected to mechanical cyclic tests, and the number of cycles completed until failure was recorded. The fracture surface was examined using a scanning electron microscope. Results: The Kruskal–Wallis and Dunn test (α = 0.05) indicated that the number of cycles resisted for fracture was higher to X for both welding procedures. To L, I06 was as resistant as X. The Mann–Whitney U‐test (α = 0.05) indicated that L joints were more resistant than TIG to I00 and I06. Spearman’s correlation coefficient (α = 0.05) indicated a negative correlation between the number of cycles and presence of porosity. Conclusion: Thus, to weld Ti‐6Al‐4V structures, the best condition is X, independent of the welding method employed.     

Stability of the transformants obtained by phage particle-mediated gene transfer

Recombinant lambda phage DNA, encapsulated in phage particles and coprecipitated with calcium phosphate, efficiently transforms cultured mammalian cells without a requirement for carrier DNA. The present paper analyzes the stability of the transformants obtained by the phage transfer method. lambda phage particles containing recombinant DNA that includes the thymidine kinase (TK) gene of herpes simplex virus type 1 as a selective marker were introduced into Ltk- cells deficient in TK activity, and TK+ transformants were selected in HAT medium. To test the stability of the TK+ phenotype of the transformants, seven individual transformant clones were isolated, cultured in HAT selective medium and then in non-selective medium for various lengths of time. After such culture, transformants were allowed to develop colonies in both selective and non-selective medium. For all seven transformant clones, the numbers of colonies obtained in the two types of medium were almost identical, irrespective of whether or not each transformant clone had been previously cultured for 15 to 50 days in non-selective medium. This result suggests that most transformants obtained by the phage transfer method maintain the TK+ phenotype stably, for at least 50 days, when grown in non-selective medium.     

Visual contrast thresholds in the cod Gadus morhua L.

The contrast discrimination of Gadus morhua L. was studied by means of a cardiac conditioning technique. Fish were trained to respond to a projected pattern of spots and the contrast of pattern and background then reduced until the minimum contrast required to elicit a response was established. This was repeated at seven different background light levels to cover the range of light conditions naturally encountered by the cod. The minimum detectable contrast decreased with increasing light level to a minimum of around 2.0%. The contrast threshold curve showed a discontinuity at a light level of approximately 8.0 × 10^-6 W sr^-1 m^-2. This was thought to be linked to the change from photopic to scotopic vision. Significant differences were found in cod taken from two different locations. Overall, cod contrast detection compared very favourably with figures available for other species including man. Using the obtained contrast discrimination figures some estimates were made of the cod sighting distance of hypothetical targets under natural conditions.     

Protein structure prediction assisted with sparse NMR data in CASP13

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and ¹⁵N-¹H residual dipolar coupling data, typical of that obtained for ¹⁵N,¹³C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.     

A soft docking algorithm for predicting the structure of antibody-antigen complexes

An efficient soft docking algorithm is described for predicting the mode of binding between an antibody and its antigen based on the three-dimensional structures of the molecules. The basic tools are the "simplified protein" model and the docking algorithm of Wodak and Janin. The side-chain flexibility of Arg, Lys, Asp, Glu, and Met residues on the protein surface is taken into account. A combined filtering technique is used to select candidate binding modes. After energy minimization, we calculate a scoring function, which includes electrostatic and desolvation energy terms. This procedure was applied to targets 04, 05, and 06 of CAPRI, which are complexes of three different camelid antibody VHH variable domains with pig alpha-amylase. For target 06, two native-like structures with a root-mean-square deviation < 4.0 A relative to the X-ray structure were found within the five top ranking structures. For targets 04 and 05, our procedure produced models where more than half of the antigen residues forming the epitope were correctly predicted, albeit with a wrong VHH domain orientation. Thus, our soft docking algorithm is a promising tool for predicting antibody-antigen recognition.     

Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor

MOTIVATION: Identifying protein enzymatic or pharmacological activities are important areas of research in biology and chemistry. Biological and chemical databases are increasingly being populated with linkages between protein sequences and chemical structures. There is now sufficient information to apply machine-learning techniques to predict interactions between chemicals and proteins at a genome scale. Current machine-learning techniques use as input either protein sequences and structures or chemical information. We propose here a method to infer protein-chemical interactions using heterogeneous input consisting of both protein sequence and chemical information. RESULTS: Our method relies on expressing proteins and chemicals with a common cheminformatics representation. We demonstrate our approach by predicting whether proteins can catalyze reactions not present in training sets. We also predict whether a given drug can bind a target, in the absence of prior binding information for that drug and target. Such predictions cannot be made with current machine-learning techniques requiring binding information for individual reactions or individual targets.     

Homeliness is in the disgust sensitivity of the beholder: relatively unattractive faces appear especially unattractive to individuals higher in pathogen disgust

Pathogen-relevant variables (e.g., regional variation in pathogen prevalence, individual differences in sensitivity to pathogen disgust) have been found to be associated with judgments and preferences surrounding physical attractiveness, in line with the view that certain morphological features and configurations indicate health and/or immunocompetence. In three studies, we administered the three-domain disgust scale and obtained ratings of attractiveness of faces to examine whether associations emerged between perceivers' disgust sensitivity and their ratings of attractive and/or unattractive targets. The results across the three studies showed that for unattractive targets, perceivers higher in pathogen disgust tended to assign lower attractiveness ratings; for attractive targets, pathogen disgust was uncorrelated with attractiveness ratings. Sexual disgust and moral disgust were not associated with perceptions of unattractive or attractive target faces. These results indicate that disgust-dependent attractiveness perceptions may motivate avoidance of potentially unfit interaction partners.     

Immunogenic complexes of the soluble surface antigens of Sh. sonnei]

The comparative study of the immunogenic properties of Sh. sonnei (phases I and II) soluble surface antigens obtained by the modified method of aqueous-saline extraction and Sh. sonnei (phase I) antigen obtained by Boivin's method was made with the use of the keratoconjunctival test in guinea pigs. The protective activity of a high molecular fraction obtained by the fractionation of phase I soluble surface antigens in Sepharose 4B was studied. Boivin's antigen, when used for immunization in optimum doses, was found to have pronounced protective properties, whereas phase II soluble surface antigens showed no protective activity. A high molecular fraction obtained from phase I soluble surface antigen was found to be the most immunogenic. Protective activity was largely connected with protein antigen. The question whether protein antigen was an independent protective antigen or whether it constituted a part of a complex which determined the protective activity of a high molecular fraction remained unsolved.     

中国部分地区马铃薯寄主上致病疫霉SSR基因型分析

利用两对SSR引物对两个基因座Pi4B和Pi4G进行了PCR扩增,测定了中国部分地区66个致病疫霉Phyophthora infestans(马铃薯晚疫病菌)菌株和2个参考菌株的SSR基因型,并对菌株的基因型进行了鉴定和命名.在被测定的66个致病疫霉菌株中,共产生了7种SSR基因型D-03,D-05,D-06,G-02,H-01,F-01和F-06,其中F-06为本研究新命名的基因型.F-01基因型菌株53个,占总菌株数目的80.3%,该基因型为中国致病疫霉的优势基因型.在对两个基因座Pi4B和Pi4G产生的等位基因统计分析发现基因座Pi4B产生的多样性比Pi4G高.对SSR数据揭示的河北、黑龙江和云南3个不同省份致病疫霉遗传多样性的比较发现,河北省和黑龙江省致病疫霉遗传多样性几乎相同,然而与云南省致病疫霉有较大的遗传差异.此外,发现致病疫霉SSR基因型与其对甲霜灵抗性无相关性.     

The application of rate dialysis to the determination of free steroids in plasma

Rate dialysis is used to obtain the free steroid fraction in undiluted plasma at 37°C. The free steroid fraction is determined from the rate at which a small amount of tritiated steroid diffuses from plasma on one side of a semipermeable membrane into an identical plasma sample on the other side which lacks radioactive steroid. The method may be generally applicable to steroids since the cell permeability constant, which is a function of the volume of the dialysis cell and the area and diffusion properties of the membrane, was similar for seven steroids tested. The method requires only 0.3 ml of plasma, is simple and economical to perform, and enables up to 120 determinations to be made in one day. The free fractions of cortisol, progesterone, and estradiol-17β were measured in plasma pooled from pregnant and non-pregnant women and pregnant and lactating sows. The results were compared with those obtained for the same plasma pools by centrifugal ultrafiltration.     

Magnetic resonance imaging stereotaxy: recognition and utilization of the commissures

Magnetic Resonance Imaging (MRI) offers a non-invasive method to visualize the intracerebral structures. Coupled to a compatible stereotactic frame and software, MRI can be used to determine the coordinates of intracranial targets. Coordinates of the anterior commissure, posterior commissure, targets and intercommissural distance were obtained from positive contrast ventriculography and by MRI in 6 patients undergoing stereotactic localization prior to the implantation of stimulating thalamic electrodes for pain control. The correlation of coordinates and measurements obtained with ventriculography and MRI is +/- 1 mm in most measurements, but up to 3 mm in 2 cases. Magnetic resonance stereotaxy allows non-invasive and precise localization of intracerebral targets, but does not yet allow its routine use with confidence. Further understanding of distortion and artifacts and corrections of these is mandatory.     

The impact of training schedules on the sleep and fatigue of elite athletes

In any sport, successful performance requires a planned approach to training and recovery. While sleep is recognized as an essential component of this approach, the amount and quality of sleep routinely obtained by elite athletes has not been systematically evaluated. Data were collected from 70 nationally ranked athletes from seven different sports. Athletes wore wrist activity monitors and completed self-report sleep/training diaries for 2 weeks during normal training. The athletes also recorded their fatigue level prior to each training session using a 7-point scale. On average, the athletes spent 08:18?±?01:12?h in bed, fell asleep at 23:06?±?01:12?h, woke at 6:48?±?01:30?h and obtained 06:30?±?01:24?h of sleep per night. There was a marked difference in the athletes’ sleep/wake behaviour on training days and rest days. Linear mixed model analyses revealed that on nights prior to training days, time spent in bed was significantly shorter (p?=?0.001), sleep onset and offset times were significantly earlier (p?<?0.001) and the amount of sleep obtained was significantly less (p?=?0.001), than on nights prior to rest days. Moreover, there was a significant effect of sleep duration on pre-training fatigue levels (p?≤?0.01). Specifically, shorter sleep durations were associated with higher levels of pre-training fatigue. Taken together, these findings suggest that the amount of sleep an elite athlete obtains is dictated by their training schedule. In particular, early morning starts reduce sleep duration and increase pre-training fatigue levels. When designing schedules, coaches should be aware of the implications of the timing of training sessions for sleep and fatigue. In cases where early morning starts are unavoidable, countermeasures for minimizing sleep loss – such as strategic napping during the day and correct sleep hygiene practices at night – should be considered.     

On the location of active serines of membrane acetylcholinesterase studied by the ESR method.

1. An attempt was made to find out the causes of the discrepancy between the ESR spectra of membrane acetylcholinesterase (EC 3.1.1.7) obtained by Morrisett and co-workers and those obtained by the present authors. 2. In order to see whether the discrepancy was due to the different spin-labeling procedures, the same membrane acetylcholinesterase preparations were spin-labeled with the same compound, using the two different spin-labeling procedures. The enzyme activity was determined with pH-static titration and the ESR spectra recorded. 3. It was found that after spin-labeling according to Morrisett and co-workers, there were from 10-100 times more spin-label molecules bound to the enzyme preparations than there were active serines in them. 4. Using the method of Morrisett and co-workers, the majority of spin-label molecules was found to be bound to sites outside the active serines whereas the spin-labeling procedures of the present authors proved to be selective for active serines; the discrepancy in ESR spectra is explained.