Antibody side chain conformations are position‐dependent

Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone‐dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody‐specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position‐dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ₁ and accuracy (78.7% and 64.8%) compared to three leading backbone‐dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain–side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears .     

Food safety through the meat supply chain

Food poisoning in humans can be caused by many different bacterial genera. While the incidence of food poisoning in England, Wales and Scotland from Salmonella has reached a plateau, there has been an increase in the incidence from Campylobacter. The incidence from Escherichia coli O157:H7 rose to 1997 but declined slightly in 1998 (data from the Public Health Laboratory Service and the Scottish Centre for Infection and Environmental Health). This organism has a high virulence in humans and a very low infective dose. Infection can produce a wide range of responses, including death. The low infective dose presents a major threat. The organism is relatively heat-sensitive and the cooking of food products to achieve a centre core temperature of 70 degrees C for 2 min is sufficient to destroy it. It is relatively acid-tolerant and will survive for several weeks at pH 4.2. Several foodstuffs, as well as water, have been implicated in world-wide outbreaks. The E. coli O157:H7 food-borne outbreak in Lanarkshire in 1996 led to 21 fatalities. The Pennington Group report, issued in April 1997, reported on the circumstances leading to this outbreak, the implications for food safety and the lessons to be learnt. Four areas covered within the Pennington Group report specific to meat hygiene are reviewed in this paper. On-farm practices must ensure the presentation of clean animals for slaughter. There is a requirement for the development and introduction of risk assessment techniques based upon Hazard Analysis of Critical Control Points in abattoirs, and the Meat and Livestock Commission (MLC) is producing a manual for use by the abattoir sector. The Pennington report stated that there was a need for research into the potential use of end-process treatments such as steam pasteurization. The MLC is involved in evaluating such a system. Meat production premises and butchers' shops in England are introducing HACCP through an MLC scheme funded by the Department of Health. At the point of consumption, food safety is improved by the provision of practical guidelines regarding the handling of meat and meat products. These are distributed at retail outlets and communicated to secondary schools via MLC's educational publications.     

Efficacy and safety of new medicines: a human focus

The introduction of safe and effective new medicines is proving ever more difficult, a problem arguably due at least in part to over-reliance on experimental animal-based test systems. In light of the increasing awareness of the lack of predictiveness of such non-human approaches, the necessity to focus on human-based test methods is clear. There has been considerable progress in human in vivo (microdosing) and in silico approaches, primarily to identify ADMET issues, however, in vitro functional studies using human tissues are receiving inadequate attention. The potential scope of human tissue-based research is considerable, but much methodological development is required, which necessitates an increased willingness on the part of the Pharma industry to support it. This approach also requires considerably improved access to the cells and tissues themselves. While current acquisition is almost exclusively from surgery and post mortem, the range of tissue types, the quantity, quality and frequency of supply will remain inadequate to support human tissue as a key component of pre-clinical efficacy and safety testing. Additional routine access to non-transplantable tissues from organ donors for research purposes would be of inestimable value, but in order to realise this, true collaboration will be required between NHS, the Pharma and biotech industries, and the general public.     

Energy dependent changes in the cytochromes of the mitochondrial respiratory chain

In intact mitochondria a stoichiometric coupling exists between cytochrome a₃ and the hydrolysis of adenosine triphosphate (ATP). In each case the modification of one cytochrome a₃ (measured as a spectral change) is coupled to the hydrolysis of one ATP molecule. When both cytochromes a₃ and a are reduced the measured equilibrium constant is 0.06 m^?1 but this constant is 10³ M^?1 when both cytochromes are oxidized. When the sixth ligand for cytochrome a₃ is an externally added ligand (HCN, H₂S, CO, NO) the equilibrium constant is different for each ligand, suggesting that the ATP induced modification is of the fifth ligand but that it is energetically dependent on the chemical nature of the sixth ligand. The measured half-reduction potentials for cytochromes a₃ and b_T are dependent on the concentrations of added ATP, adenosine diphosphate (ADP), and orthophosphate. The relationship is consistent with a ligand exchange mechanism in which the ligand on the cytochrome is dependent on the phosphate potential ($\text{ATP}\text{ADP}$ × P_i). The equilibrium constants obtained by the ligand exchange treatment of the E_m values for cytochrome a₃ are consistent with those obtained by direct measurement of the equilibrium constants for the spectrally measured changes.     

Evaluation of newly developed devices for denture placement and removal in the dependent elderly

doi: 10.1111/j.1741‐2358.2011.00547.x Evaluation of newly developed devices for denture placement and removal in the dependent elderly Objective: The purpose of this study was to subjectively evaluate the utility of newly developed denture placement and removal devices. Objective observations were also made to support the evidence. Materials and method: Twenty‐one subjects were instructed to place and remove their dentures with and without the devices. We evaluated the device based on a questionnaire. Objective observations were based on a 2‐D image analysis. We analysed three factors: the time, the area and the circumference required to insert and remove the dentures. Results: Image analysis showed that the effectiveness and ease with which the subject used the device significantly improved with practice. The questionnaire data showed that a majority of the subjects appreciated the device after the first and second time. While there was no significant decrease in time required to place and remove dentures even with the device, the area and circumference of the movement on 2‐D images were significantly reduced. Conclusion: In this study, the utility of denture placement and removal devices was evaluated both subjectively and objectively. Our data reveal that the device is effective in the elderly. Further minor improvement in the device might be required to increase its effectiveness.     

Supply chain surplus: comparing conventional and sustainable supply chains

In this paper, we first define sustainable supply chain, and its value, as a paradigm which pursues the maximization of supply chain profitability while taking its environmental and societal responsibilities. Secondly, we compare the supply chain surplus between the conventional and sustainable supply chains by means of adopting the basic economic analysis based on the concept of externality and social surplus in welfare economics. Through the proposed analysis, we show the possibility of sustainable supply chains which can provide more supply chain surplus to the companies. Finally, some limitations of this paper and future research directions are also presented.     

Fermentative production of branched chain amino acids: a focus on metabolic engineering

The branched chain amino acids (BCAAs), l-valine, l-leucine, and l-isoleucine, have recently been attracting much attention as their potential to be applied in various fields, including animal feed additive, cosmetics, and pharmaceuticals, increased. Strategies for developing microbial strains efficiently producing BCAAs are now in transition toward systems metabolic engineering from random mutagenesis. The metabolism and regulatory circuits of BCAA biosynthesis need to be thoroughly understood for designing system-wide metabolic engineering strategies. Here we review the current knowledge on BCAAs including their biosynthetic pathways, regulations, and export and transport systems. Recent advances in the development of BCAA production strains are also reviewed with a particular focus on l-valine production strain. At the end, the general strategies for developing BCAA overproducers by systems metabolic engineering are suggested.     

The impact of operations redesign on the safety stock investment in supply chains

This study is motivated by a real problem encountered in the manufacturing and distribution process at a local electronic manufacturer of security devices. We investigate the impact of operations redesign (i.e., operations merging) on the cost of safety stock in a supply chain. A simple safety stock method is used to derive a model for estimating safety stock levels. Our result shows that operations redesign can have a significant impact on safety stock investment. We extend and complement the existing literature in the following aspects: (i) we address the issue of safety stock deployment, i.e., we not only investigate the problem of how many operations should be delayed, but also determine which operations need to be delayed, (ii) we provide an efficient heuristic algorithm to determine which operations need to be merged, and (iii) we find the optimal operations redesign strategies under some special cases. Our analysis also reveals some important conditions and insights for better operations redesign, which enable us not only to decide when an operations redesign is appropriate, but also to suggest the scale and the format of the operations redesign.     

Structure refinement of protein model decoys requires accurate side‐chain placement

In this study, the application of temperature‐based replica‐exchange (T‐ReX) simulations for structure refinement of decoys taken from the I‐TASSER dataset was examined. A set of eight nonredundant proteins was investigated using self‐guided Langevin dynamics (SGLD) with a generalized Born implicit solvent model to sample conformational space. For two of the protein test cases, a comparison of the SGLD/T‐ReX method with that of a hybrid explicit/implicit solvent molecular dynamics T‐ReX simulation model is provided. Additionally, the effect of side‐chain placement among the starting decoy structures, using alternative rotamer conformations taken from the SCWRL4 modeling program, was investigated. The simulation results showed that, despite having near‐native backbone conformations among the starting decoys, the determinant of their refinement is side‐chain packing to a level that satisfies a minimum threshold of native contacts to allow efficient excursions toward the downhill refinement regime on the energy landscape. By repacking using SCWRL4 and by applying the RWplus statistical potential for structure identification, the SGLD/T‐ReX simulations achieved refinement to an average of 38% increase in the number of native contacts relative to the original I‐TASSER decoy sets and a 25% reduction in values of C_α root‐mean‐square deviation. The hybrid model succeeded in obtaining a sharper funnel to low‐energy states for a modeled target than the implicit solvent SGLD model; yet, structure identification remained roughly the same. Without meeting a threshold of near‐native packing of side chains, the T‐ReX simulations degrade the accuracy of the decoys, and subsequently, refinement becomes tantamount to the protein folding problem. Proteins 2013. 2012 Published by Wiley Periodicals, Inc.     

Elucidation of calpain dependent phosphorylation of myosin light chain in human platelets

Newly synthetized calpain inhibitors (CI-I approximately III) were used to prove potential participation of calpain in protein phosphorylation. CIs were about 1,000 times more potent against platelet calpain I than N-ethyl-maleimide (NEM) and an epoxy succinate derivative (E-64). CI-II inhibited 20K (myosin light chain) and 47K phosphorylation of Ca2+-stimulated lysed platelets as well as protein degradation (actin binding protein, P235). Both myosin light chain kinase (MLCK) and C-kinase dependent phosphorylation of 20K were inhibited by CI-II as demonstrated in phosphopeptides mapping. Electropermeabilized platelets (EP) were employed to examine the effects of CI-II on Ca2+ mediated reactions in non-lysed platelets. Phosphorylation of 20K and 47K induced by Ca2+ addition to EP was inhibited by CI-II, though secretory response was not modified. Only MLCK dependent phosphorylation of 20K was observed in Ca2+-activated EP, which was inhibited by CI-II. Collectively, the data indicated that calpain may activate both MLCK and C-kinase to phosphorylate 20K by partial proteolysis.     

Cytoplasmic dynein intermediate chain and heavy chain are dependent upon each other for microtubule end localization in Aspergillus nidulans

The multisubunit microtubule motor, cytoplasmic dynein, targets to various subcellular locations in eukaryotic cells for various functions. The cytoplasmic dynein heavy chain (HC) contains the microtubule binding and ATP binding sites for motor function, whereas the intermediate chain (IC) is implicated in the in vivo targeting of the HC. Concerning any targeting event, it is not known whether the IC has to form a complex with the HC for targeting or whether the IC can target to a site independently of the HC. In the filamentous fungus Aspergillus nidulans, the dynein HC is localized to the ends of microtubules near the hyphal tip. In this study, we demonstrate that our newly identified dynein IC in A. nidulans is also localized to microtubule ends and is required for HC's localization to microtubule ends in living cells. With the combination of two reagents, an HC loss-of function mutant and the green fluorescent protein (GFP)-fused IC that retains its function, we show that the IC's localization to microtubule ends also requires HC, suggesting that cytoplasmic dynein HC-IC complex formation is important for microtubule end targeting. In addition, we show that the HC localization is not apparently altered in the deletion mutant of NUDF, a LIS1-like protein that interacts directly with the ATP-binding domain of the HC. Our study suggests that, although HC-IC association is important for the targeting of dynein to microtubule ends, other essential components, such as NUDF, may interact with the targeted dynein complex to produce full motor activities in vivo.     

Replication fork and SeqA focus distributions in Escherichia coli suggest a replication hyperstructure dependent on nucleotide metabolism

Replication from the origin of Escherichia coli has traditionally been visualized as two replisomes moving away from each other, each containing a leading and a lagging strand polymerase. Fluorescence microscopy studies of tagged polymerases or forks have, however, indicated that the polymerases may be confined to a single location (or a few locations in cells with overlapping replication cycles). Here, we have analysed the exact replication patterns of cells growing with four different growth and replication rates, and compared these with the distributions of SeqA foci. The SeqA foci represent replication forks because the SeqA protein binds to the newly formed hemimethylated DNA immediately following the forks. The results show that pairs of forks originating from the same origin stay coupled for most of the cell cycle and thus support the replication factory model. They also suggest that the factories consisting of four polymerases are, at the time immediately after initiation, organized into higher order structures consisting of eight or 12 polymerases. The organization into replication factories was lost when replication forks experienced a limitation in the supply of nucleotides or when the thymidylate synthetase gene was mutated. These results support the idea that the nucleotide synthesis apparatus co-localizes with the replisomes forming a 'hyperstructure' and further suggest that the integrity of the replication factories and hyperstructures is dependent on nucleotide metabolism.     

Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Terahertz absorption spectra of alanine polypeptides in water were simulated with classical molecular dynamics at 310 K. Vibrational modes and oscillator strengths were calculated based on a quasi-harmonic approximation. Absorption spectra of Ala_n (n = 5, 15, 30) with different chain lengths and Ala₁₅ in coiled and helical conformations were studied in 10–40 cm^? 1 bandwidth. Simulation results indicated both the chain length and the conformation have significant influences on THz spectra of alanine polypeptides. With the increase of chain length, the average THz absorption intensity increases. Compared with the helical Ala₁₅ polypeptide, the THz spectra of coiled one shows stronger absorption peaks. These results were explained from different numbers of hydrogen bonds formed between polypeptides and the surrounding water molecules.     

Current status and future directions of post-marketing vaccine safety monitoring with focus on USA and Europe

Vaccine safety research is a key component of public health programs. Regulatory agencies need to be able to make informed decisions. Public health authorities need to respond to vaccine concerns before they turn into large scale scares reducing vaccine uptake and derailing immunization programs. Several post-licensure vaccine safety monitoring systems have been established in the USA and Europe, and methods such as rapid cycle analysis have been developed for real-time detection and analysis of safety issues. Accurate and reliable vaccine product testing and monitoring requires high quality data of populations of 100 million and above depending on the frequency of the event, vaccine coverage, and the time pressure during which data need to be generated. This requires post-licensure safety studies utilizing large linked population based databases of exposure and outcomes. Harmonized methods for development and linkage of these databases across countries need to be further developed, validated and implemented. Concerted action between the US and Europe could move vaccine safety monitoring to today's level of requirements globally and should be pursued.