The influence of nearest neighbours on the efficiency of coaxial stacking at contiguous stacking hybridization of oligodeoxyribonucleotides

Contiguous stacking hybridization of oligodeoxyribonucleotides with a stem of preformed minihairpin structure of a DNA template was studied with the use of UV-melting technique. It was shown that the free-energy of the coaxial stacking interaction (deltaG degrees ST at 37 degrees C, 1 M NaCl, pH 7.4) at the complementary interface XA*pTY/ZATV (an asterisk stands for a nick) strongly depends on the type of nearest neighbor bases X and Y flanking the nicked dinucleotide step. The maximum efficiency of the coaxial stacking was observed for the PuA*pTPy/PuATPy interface, whereas the minimum efficiency was obtained for the PyA*pTPu/PyATPu interface. A 5'-phosphate residue in the nick enhances the coaxial stacking. In dependence on duplex structure the observed efficiency of A*T/AT coaxial stacking varied from (- 0.97 kcal/mol) for unphosphorylated TA*TA/TATA interface to three-fold higher value (- 2.78 kcal/mol) for GA*pTT/AATC interface.     

A chassis exchange terminal to reduce truck congestion at container terminals

Truck congestion for container terminals seems to be a worldwide unwanted phenomenon. In this paper we present and analyze a chassis exchange terminal concept to reduce the congestion. The terminal works as a kind of extended gate of a group of traditional container terminals. During the night containers are collected from these container terminals using chassis (or trailers). In daytime these containers on chassis are then collected and exchanged with export containers also on chassis. By exchanging the chassis we avoid extra handling of containers. As connecting and disconnecting to a chassis can be done in a short time, the chassis exchange terminal increases handling capacity substantially during peak hours. In this paper we analyze the concept for the Maasvlakte container terminals in Rotterdam. We investigate both the effect on waiting time, as well as the environmental effects.     

Evaluating the contribution of base stacking during translesion DNA replication

Despite the nontemplating nature of the abasic site, dAMP is often preferentially inserted opposite the lesion, a phenomenon commonly referred to as the "A-rule". We have evaluated the molecular mechanism accounting for this unique behavior using a thorough kinetic approach to evaluate polymerization efficiency during translesion DNA replication. Using the bacteriophage T4 DNA polymerase, we have measured the insertion of a series of modified nucleotides and have demonstrated that increasing the size of the nucleobase does not correlate with increased insertion efficiency opposite an abasic site. One analogue, 5-nitroindolyl-2'-deoxyriboside triphosphate, was unique as it was inserted opposite the lesion with approximately 1000-fold greater efficiency compared to that for dAMP insertion. Pre-steady-state kinetic measurements yield a kpol value of 126 s(-1) and a Kd value of 18 microM for the insertion of 5-nitroindolyl-2'-deoxyriboside triphosphate opposite the abasic site. These values rival those associated with the enzymatic formation of a natural Watson-Crick base pair. These results not only reiterate that hydrogen bonding is not necessary for nucleotide insertion but also indicate that the base-stacking and/or desolvation capabilities of the incoming nucleobase may indeed play the predominant role in generating efficient DNA polymerization. A model accounting for the increase in catalytic efficiency of this unique nucleobase is provided and invokes pi-pi stacking interactions of the aromatic moiety of the incoming nucleobase with aromatic amino acids present in the polymerase's active site. Finally, differences in the rate of 5-nitroindolyl-2'-deoxyriboside triphosphate insertion opposite an abasic site are measured between the bacteriophage T4 DNA polymerase and the Klenow fragment. These kinetic differences are interpreted with regard to the differences in various structural components between the two enzymes and are consistent with the proposed model for DNA polymerization.     

Variable impact transportation (VIT) model for energy and environmental impact of hauling truck operation

Purpose

Fuel economy and emissions of heavy-duty trucks greatly vary based on vehicular/environmental conditions. Large-scale infrastructure construction projects require a large amount of material/equipment transportation. Single-parameter generic hauling models may not be the best option for an accurate estimation of hauling contribution in life cycle assessment (LCA) involving construction projects; therefore, more precise data and parameterized models are required to represent this contribution. This paper discusses key environmental/operational variables and their impact on transportation of materials and equipment; a variable-impact transportation (VIT) model accounting for these variables was developed to predict environmental impacts of hauling.

Methods

The VIT model in the form of multi-nonlinear regression equations was developed based on simulations using the U.S. Environmental Protection Agency (EPA)’s Motor Vehicle Emission Simulator (MOVES) to compute all the impact categories in EPA’s TRACI 2.1 and energy consumption of transportation. Considering actual driving cycles of hauling trucks recorded during a pavement rehabilitation project, the corresponding environmental impacts were calculated, and sensitivity analyses were performed. In addition, an LCA case study based on historical pavement reconstruction projects in Illinois was conducted to analyze the contribution of transportation and variability of its impacts during the pavements’ life cycle.

Results and discussion

The importance of vehicle driving cycles was realized from simulation results. The case study results showed that considering driving cycles using the VIT model could increase the contribution of hauling in total life cycle Global Warming Potential (GWP) and total life cycle GWP itself by 2–4 and 3–5%, respectively. In addition to GWP, ranges of other hauling-related impact categories including Smog, Ozone Depletion, Acidification, and Primary Energy Demand from fuel were presented based on the case study. Ozone Depletion ranged from 9 to 45%, and Smog ranged from 11 to 48% of the total relevant life cycle impacts. The GWP contribution of hauling in pavement LCA ranged between 5 and 32%. The results indicate that the contribution of hauling transportation can be significant in pavement LCA.

Conclusions

For large-scale roadway infrastructure construction projects that need a massive amount of material transportation, high fidelity models and data should be used especially for comparative LCAs that can be used as part of decision making between alternatives. The VIT model provides a simple analytical platform to include the critical vehicular/operational variables without any dependence on an external software; the model can also be incorporated in those studies where some of the transportation activity data are available.

     

Evaluating the environmental impact of debit card payments

Purpose

Consumers in the Netherlands made more than 3.2 billion debit card transactions at points-of-sale in 2015, corresponding to over half of all point-of-sale payments in that year. This study provides insights into the environmental impact of debit card transactions based on a life cycle assessment (LCA). In addition, it identifies several areas within the debit card payment chain where the environmental impact can be reduced.

Methods

The debit card payment system can be divided into three subsystems: debit cards, payment terminals, and data centers used for transaction processing. Input data for all elements within each subsystem (manufacturing, transport, energy use, and disposal) were retrieved from interviews and literature study. Seven key companies and authorities within the debit card system such as the Dutch Payments Association, two banks, two data centers, one payment terminal producer and a recycling company contributed data. The analysis is conducted using SimaPro, the Ecoinvent 3.0 database and the ReCiPe endpoint (H) impact assessment method.

Results and discussion

One Dutch debit card transaction in 2015 is estimated to have an absolute environmental impact of 470 μPt. Within the process chain of a debit card transaction, the relative environmental impact of payment terminals is dominant, contributing 75% of the total impact. Terminal materials (37%) and terminal energy use (27%) are the largest contributors to this share, while the remaining impact comprises data center (11%) and debit card (15%) subsystems. For data centers, this impact mainly stems from their energy use. Finally, scenario analyses show that a significant decrease (44%) in the environmental impact of the entire debit card payment system could be achieved by stimulating the use of renewable energy in payment terminals and data centers, reducing the standby time of payment terminals and increasing the lifetimes of debit cards.

Conclusions

For the first time, the environmental consequences of electronic card payment systems are evaluated. The total environmental impact of debit card transactions in the Netherlands is relatively modest compared to the impact of cash payments, which are the closest substitute of debit card payments at the point-of-sale. Scenario analysis indicates that the environmental impact can be reduced by 44%.

     

Immunogenicity of therapeutic proteins. Part 2: impact of container closures

Immunogenicity as a potential consequence of therapeutic protein administration is increasingly being scrutinized in the biopharmaceuticals industry, particularly with the imminent introduction of biosimilar products. Immunogenicity is an important safety aspect requiring rigorous investigation to fully appreciate its impact. Factors involved in product handling, such as storage temperature, light exposure, and shaking, have been implicated in immunogenicity, while container closure systems are no less important. Intended to provide a stable environment for the dosage form, container closures may also interact with a product, affecting performance and potentially enhancing immunogenicity. Glass surfaces, air-liquid interfaces, and lubricants can mediate protein denaturation, while phthalates in plastics and latex rubber are sources of extractables and leachates that may contaminate a product, causing allergic reactions and increasing immunogenicity. The manufacture of therapeutic proteins therefore requires rigorous safety evaluations not just in the context of the product, but also product containment.     

Evaluating the impact of topological protein features on the negative examples selection

Background

Supervised machine learning methods when applied to the problem of automated protein-function prediction (AFP) require the availability of both positive examples (i.e., proteins which are known to possess a given protein function) and negative examples (corresponding to proteins not associated with that function). Unfortunately, publicly available proteome and genome data sources such as the Gene Ontology rarely store the functions not possessed by a protein. Thus the negative selection, consisting in identifying informative negative examples, is currently a central and challenging problem in AFP. Several heuristics have been proposed through the years to solve this problem; nevertheless, despite their effectiveness, to the best of our knowledge no previous existing work studied which protein features are more relevant to this task, that is, which protein features help more in discriminating reliable and unreliable negatives.

Results

The present work analyses the impact of several features on the selection of negative proteins for the Gene Ontology (GO) terms. The analysis is network-based: it exploits the fact that proteins can be naturally structured in a network, considering the pairwise relationships coming from several sources of data, such as protein-protein and genetic interactions. Overall, the proposed protein features, including local and global graph centrality measures and protein multifunctionality, can be term-aware (i.e., depending on the GO term) and term-unaware (i.e., invariant across the GO terms). We validated the informativeness of each feature utilizing a temporal holdout in three different experiments on yeast, mouse and human proteomes: (i) feature selection to detect which protein features are more helpful for the negative selection; (ii) protein function prediction to verify whether the features considered are also useful to predict GO terms; (iii) negative selection by applying two different negative selection algorithms on proteins represented through the proposed features.

Conclusions

Term-aware features (with some exceptions) resulted more informative for problem (i), together with node betweenness, which is the most relevant among term-unaware features. The node positive neighborhood instead is the most predictive feature for the AFP problem, while experiment (iii) showed that the proposed features allow negative selection algorithms to select effectively negative instances in the temporal holdout setting, with better results when nonlinear combinations of features are also exploited.

     

Evaluating the impact of population bottlenecks in experimental evolution

Experimental evolution involves severe, periodic reductions in population size when fresh media are inoculated during serial transfer. These bottlenecks affect the dynamics of evolution, reducing the probability that a beneficial mutation will reach fixation. We quantify the impact of these bottlenecks on the evolutionary dynamics, for populations that grow exponentially between transfers and for populations in which growth is curbed by a resource-limited environment. We find that in both cases, mutations that survive bottlenecks are equally likely to occur, per unit time, at all times during the growth phase. We estimate the total fraction of beneficial mutations that are lost due to bottlenecks during experimental evolution protocols and derive the "optimal" dilution ratio, the ratio that maximizes the number of surviving beneficial mutations. Although more severe dilution ratios are often used in the literature, we find that a ratio of 0.1-0.2 minimizes the chances that rare beneficial mutations are lost. Finally, we provide a number of useful approximate results and illustrate our approach with applications to experimental evolution protocols in the literature.     

Evaluating energy efficiency of site-specific tillage in maize in NE Italy

This paper examine the efficiency of energy use of three conservation tillage practices (SST - sub-soil tillage; MT - minimum tillage; and NT - no tillage) performed within two management zones, previously identified in a field according to the stability of yield variability. Experiments were carried out in 2003 in NE Italy, on a farm near Rovigo, on a 8-ha field with clay soil, in maize (Zea mays, L.). The purpose of the paper is (i) to investigate the energy variability due to these tillage practices performed spatially within two management zones and (ii) to analyze the long-term energetic efficiency for each tillage practice. The energy balance was highest for SST with respect to MT and NT, due to labor and fuel consumption rates. The energy balance was influenced by the spatial pattern of yield, with appreciable differences between practices in terms of both the conversion index of energy for tillage (9.0, 12.6 and 22.8GJha(-1) for SST, MT and NT, respectively) and the energy use efficiency for tillage (8.0, 11.6, 21.8GJha(-1) for SST, MT and NT, respectively). Based on the simulated data and the calibration results, SALUS model proved to be a good tool for analyzing long-term effects of tillage practices on yield. The NT treatment showed the best efficiency over years, due to the low inputs in comparison with the output level.     

Evaluating the epidemiological impact of national control programmes for helminths

During the past decade, there has been renewed commitment to programmes for helminth control, and several international initiatives have been launched. Scientific evaluation of large-scale interventions to reduce the incidence of infection and associated morbidity and mortality is vital, not only to demonstrate health benefits, but also to assess cost-effectiveness to show that monies from donor agencies have been used wisely. Using the example of schistosomiasis, this article outlines a framework for the evaluation of the impact of national control programmes, highlighting the important epidemiological and practical issues that must be addressed.     

Solvent influence on base stacking.

In this paper we present a detailed analysis of the base-stacking phenomenon in different solvents, using nanosecond molecular dynamics simulations. The investigation focuses on deoxyribo- and ribodinucleoside monophosphates in aqueous and organic solutions. Organic solvents with a low dielectric constant, such as chloroform, and solvents with intermediate dielectric constants, such as dimethyl sulfoxide and methanol, were analyzed. This was also done for water, which is highly polar and has a high dielectric constant. Structural parameters such as the sugar puckering and the base-versus-base orientations, as well as the energetics of the solute-solvent interactions, were examined in the different solvents. The obtained data demonstrate that base stacking is favored in the high dielectric aqueous solution, followed by methanol and dimethyl sulfoxide with intermediate dielectric constants, and chloroform, with a low dielectric constant.     

Morphological structures of elite Karateka and their impact on technical and fighting efficiency

The aim of the study was to identify the morphological structures that determine achievement of top results in karate. The study included a sample of 85 karateka competing as senior category athletes within the Croatian Karate Society, aged 18-29 years. Sixteen morphological parameters were used; technical efficiency was assessed using 8 variables, i.e. evaluation of particular karate techniques, whereas fighting efficiency was estimated on the basis of results achieved at a number of contests. Factorial analysis of morphological space revealed the presence of four major factors: factor of muscle mass, followed by skeleton transverse dimensionality, factor of skeleton longitudinal dimensionality, factor of subcutaneous adipose tissue, and factor of shoulder width determining optimal trunk proportions (athlete type) in karateka. Regression analysis showed the isolated group of morphological factors to significantly determine both technical and fighting efficiency of karate athletes. Generally, skeleton longitudinality and muscle mass, followed by skeleton transverse dimensionality were found to exert favorable effects, and adipose tissue unfavorable effects according to both criteria. Also, each individual morphological factor influenced the performance of every karate technique applied. Adipose tissue had greatest unfavorable impact, whereas shoulder width and muscle mass had favorable impact on the performance of arm techniques (kicking). Considering performance of leg techniques, skeleton longitudinality had highest favorable impact, and adipose tissue greatest unfavorable impact. Of the techniques applied, combined karate kicks, i.e. jaku zuki-mawashi geri and kizame zuki-jaku zuki were found to be the best predictors of fighting efficiency.     

The impact of DNA topology on polyplex uptake and transfection efficiency in mammalian cells

The effect of DNA vector topology when complexed to poly-l-lysine (PLL) and its quantification in transfection efficiency has not been fully addressed even though it is thought to be of importance from both production and regulatory viewpoints. This study investigates and quantifies cell uptake followed by transfection efficiency of PLL:DNA complexes (polyplexes) in Chinese hamster ovary (CHO) cells and their dependence on DNA topology. PLL is known for its ability to condense DNA and serve as an effective gene delivery vehicle. Characterization of PLL conjugated to a 6.9 kb plasmid was carried out. Dual labeling of both the plasmid DNA (pDNA) and PLL enabled quantitative tracking of the complexed as well as dissociated elements, within the cell, and their dependence on DNA topology. Polyplex uptake was quantified by confocal microscopy and image analysis. Supercoiled (SC) pDNA when complexed with PLL, forms a polyplex with a mean diameter of 139.06 nm (±0.84% relative standard error [RSE]), whereas open circular (OC) and linear-pDNA counterparts displayed mean diameters of 305.54 (±3.2% RSE) and 841.5 nm (±7.2% RSE) respectively. Complexes containing SC-pDNA were also more resistant to nuclease attack than its topological counterparts. Confocal microscope images reveal how the PLL and DNA remain bound post transfection. Quantification studies revealed that by 1 h post transfection 61% of SC-pDNA polyplexes were identified to be associated with the nucleus, in comparison to OC- (24.3%) and linear-pDNA polyplexes (3.5%) respectively. SC-pDNA polyplexes displayed the greatest transfection efficiency of 41% which dwarfed that of linear-pDNA polyplexes of 18.6%. Collectively these findings emphasize the importance of pDNA topology when complexed with PLL for gene delivery with the SC-form being a key pre-requisite.     

Evaluating the impact of substrate and product concentration on a whole-cell biocatalyst during a Baeyer-Villiger reaction

The presence of high concentrations of substrate or product may impede the optimal functioning of a biocatalyst, more so in the case of whole cell biocatalysts where the metabolic status of the cells may be compromised. In this article we investigate these effects using as an example the Baeyer–Villiger oxidation of racemic bicyclo[3.2.0]hept-2-en-6-one to yield (?)-1(S),5(R)-2-oxabicyclo[3.3.0]oct-6-en-3-one and (?)-1(R),5(S)-3-oxabicyclo[3.3.0]oct-6-en-2-one by CHMO expressed in Escherichia coli TOP10. Multi parameter flow cytometry was used to illustrate that substrate (racemic bicyclo[3.2.0]hept-2-en-6-one) associated cell damage was concentration dependent. One of the two regio-isomeric products [(-)-1(S),5(R)-2-oxabicyclo[3.3.0]oct-6-en-3-one] was also used to identify that product associated cell damage was time dependent. In addition, both substrate and product concentrations affected the observed reaction rate.     

Entropy-assisted stacking of thylakoid membranes

Chloroplasts in plants and some green algae contain a continuous thylakoid membrane system that is structurally differentiated into stacked granal membranes interconnected by unstacked thylakoids, the stromal lamellae. Experiments were conducted to test the hypothesis that the thermodynamic tendency to increase entropy in chloroplasts contributes to thylakoid stacking to form grana. We show that the addition of bovine serum albumin or dextran, two very different water-soluble macromolecules, to a suspension of envelope-free chloroplasts with initially unstacked thylakoids induced thylakoid stacking. This novel restacking of thylakoids occurred spontaneously, accompanied by lateral segregation of PSII from PSI, thereby mimicking the natural situation. We suggest that such granal formation, induced by the macromolecules, is partly explained as a means of generating more volume for the diffusion of macromolecules in a crowded stromal environment, i.e., greater entropy overall. This mechanism may be relevant in vivo where the stroma has a very high concentration of enzymes of carbon metabolism, and where high metabolic fluxes are required.     

Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms

Genotype imputation is potentially a zero-cost method for bridging gaps in coverage and power between genotyping platforms. Here, we quantify these gains in power and coverage by using 1,376 population controls that are from the 1958 British Birth Cohort and were genotyped by the Wellcome Trust Case-Control Consortium with the Illumina HumanHap 550 and Affymetrix SNP Array 5.0 platforms. Approximately 50% of genotypes at single-nucleotide polymorphisms (SNPs) exclusively on the HumanHap 550 can be accurately imputed from direct genotypes on the SNP Array 5.0 or Illumina HumanHap 300. This roughly halves differences in coverage and power between the platforms. When the relative cost of currently available genome-wide SNP platforms is accounted for, and finances are limited but sample size is not, the highest-powered strategy in European populations is to genotype a larger number of individuals with the HumanHap 300 platform and carry out imputation. Platforms consisting of around 1 million SNPs offer poor cost efficiency for SNP association in European populations.