A comprehensive evaluation of assembly scaffolding tools

Background

Genome assembly is typically a two-stage process: contig assembly followed by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the focus of reported assembly statistics; longer scaffolds greatly facilitate the use of genome sequences in downstream analyses, and it is appealing to present larger numbers as metrics of assembly performance. However, scaffolds are highly prone to errors, especially when generated using short reads, which can directly result in inflated assembly statistics.

Results

Here we provide the first independent evaluation of scaffolding tools for second-generation sequencing data. We find large variations in the quality of results depending on the tool and dataset used. Even extremely simple test cases of perfect input, constructed to elucidate the behaviour of each algorithm, produced some surprising results. We further dissect the performance of the scaffolders using real and simulated sequencing data derived from the genomes of Staphylococcus aureus, Rhodobacter sphaeroides, Plasmodium falciparum and Homo sapiens. The results from simulated data are of high quality, with several of the tools producing perfect output. However, at least 10% of joins remains unidentified when using real data.

Conclusions

The scaffolders vary in their usability, speed and number of correct and missed joins made between contigs. Results from real data highlight opportunities for further improvements of the tools. Overall, SGA, SOPRA and SSPACE generally outperform the other tools on our datasets. However, the quality of the results is highly dependent on the read mapper and genome complexity.     

A comprehensive proteomic approach to identifying capacitation related proteins in boar spermatozoa

Background

Mammalian spermatozoa must undergo capacitation, before becoming competent for fertilization. Despite its importance, the fundamental molecular mechanisms of capacitation are poorly understood. Therefore, in this study, we applied a proteomic approach for identifying capacitation-related proteins in boar spermatozoa in order to elucidate the events more precisely. 2-DE gels were generated from spermatozoa samples in before- and after-capacitation. To validate the 2-DE results, Western blotting and immunocytochemistry were performed with 2 commercially available antibodies. Additionally, the protein-related signaling pathways among identified proteins were detected using Pathway Studio 9.0.

Result

We identified Ras-related protein Rab-2, Phospholipid hydroperoxide glutathione peroxidase (PHGPx) and Mitochondrial pyruvate dehydrogenase E1 component subunit beta (PDHB) that were enriched before-capacitation, and NADH dehydrogenase 1 beta subcomplex 6, Mitochondrial peroxiredoxin-5, (PRDX5), Apolipoprotein A-I (APOA1), Mitochondrial Succinyl-CoA ligase [ADP-forming] subunit beta (SUCLA2), Acrosin-binding protein, Ropporin-1A, and Spermadhesin AWN that were enriched after-capacitation (>3-fold) by 2-DE and ESI-MS/MS. SUCLA2 and PDHB are involved in the tricarboxylic acid cycle, whereas PHGPx and PRDX5 are involved in glutathione metabolism. SUCLA2, APOA1 and PDHB mediate adipocytokine signaling and insulin action. The differentially expressed proteins following capacitation are putatively related to sperm functions, such as ROS and energy metabolism, motility, hyperactivation, the acrosome reaction, and sperm-egg interaction.

Conclusion

The results from this study elucidate the proteins involved in capacitation, which may aid in the design of biomarkers that can be used to predict boar sperm quality.     

Analysis of the potential for a comprehensive approach towards LCA and EMS in Japan

Sustainable development can only be achieved if industry adoptsboth product related and organisation related environmental management tools, such as Life Cycle Assessment (LCA) and Environmental Management Systems (EMS). In Japan, EMS (ISO 14001) is more widely applied than LCA (ISO 14040). Therefore,one means by which Japanese industries could be motivated to adopt and use LCA is to relate LCA-activities to the policies and instruments of ISO 14001. The potential of such a comprehensive approach was analysed by a survey of 270 Japanese enterprises (response rate 45%). The results indicate that 19% of the responding representatives had responsibilities for both LCA and EMS, while the remaining only work in one of both fields. A statement in the company’s/ plant’s Environmental Policy of ISO 14001, stating that LCA is to be used as part of the EMS, was found in 42% of all companies. A surprising number (39%) either already use, or plan to use, LCA and EMS as combinated/integrated tools. A strong argument for the establishment of a comprehensive approach can be seen in the perception of the usefulness of LCA, which was rated significantly higher in companies that acknowledged the complementary potential of LCA and EMS.     

Connectivity and invasive species management: towards an integrated landscape approach

Invasive plants and animals are a major cause of global biodiversity loss. Invasive Species Management (ISM) helps conserve localized populations and ecosystems, but rarely have its potential benefits been explored at the landscape scale. We explore how ISM can enhance landscape connectivity, and how its incorporation into conservation planning algorithms could help design optimal reserve networks. Conversely, conservation planning and connectivity modelling can optimize targeting of ISM, achieving benefits for a wider range of taxa and ecological processes, without the need for additional resources. Empirical research must investigate the spatial pattern of benefits from ISM, and when to target priority conservation sites or the areas (matrix) between them. By bolstering populations within—and increasing connectivity between—focal patches, ISM should move beyond conserving individual sites to creating functionally connected networks of conservation areas.     

A comprehensive environmental assessment of petrochemical solvent production

Background, aim, and scope  Organic solvents are used in large quantities in the chemical, metal and electronics industries as well as in many consumer products, such as coatings or paints, and are therefore among the most important chemicals. The petrochemical production of organic solvents is a relevant environmental issue because fossil resources are needed (crude oil and natural gas), synthesis processes are energy-intensive and cause considerable amounts of emissions. So far, comprehensive data on the environmental impact are rather scarce. The aim of this paper is to therefore present a systematical environmental assessment of the main petrochemical solvent production routes using the Life Cycle Assessment (LCA) method. Methods  Fifty organic solvents were selected covering the most important representatives from the various chemical groups (e.g., alcohols, esters, ketones). To conduct the LCA, 40 new Life Cycle Inventories (LCI) were established and existing LCI were improved. The petrochemical solvent production was structured into four production routes. In these production routes, the single chemical unit processes (e.g. esterification, carbonylation or hydrogenation) were analyzed in order to determine characteristic environmental impacts. Results and discussion  The four solvent production routes including the unit processes and intermediates are presented. Additionally, energy profiles of these production routes are shown using the Cumulative Primary Energy Demand (CED) as an indicator for the environmental impact. The results were cross-checked with the Global Warming Potential and the Eco-indicator 99 method and good correlations were found. Processes that show high environmental impacts are the dehydration of butylene glycol to tetrahydrofuran, the carbonylation of methanol to methyl formate, the hydrogenation of acetone to methyl isobutyl ketone, and the Reppe synthesis of formaldehyd/acetylene to butylene glycol. Based on the energy profiles, ranges of environmental impacts are determined for all unit processes. On the one hand, esterification and alkylation processes cause high CED values because complex ancillaries are needed and hydroformylation and carbonylation processes are energy-intensive. On the other hand, in hydration, hydrogenation, hydrolysis, and oxidation processes, ancillaries with low CED are added to the chemical structure that result in low CED ranges for these unit processes. Dehydrogenation and molecular sieve separation processes seem to be energy efficient and no ancillaries are required. Therefore, these unit processes cause the lowest CED values. Perspectives  Subject of further research in this field should be the environmental analysis of further process steps that include the presented unit processes and a subsequent statistical analysis in order to derive reliable data ranges for all unit processes. Such statistically robust ranges could be used in the approximation of missing life-cycle inventory data of other chemical products and intermediates. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biospheric foundations of the ecosystem approach to environmental management

The ecosystem approach to environmental management inter-relates social, economic and environmental factors. Its incorporation into the Great Lakes Water Quality Agreement of 1978 changed the focus of the Agreement from water in a political context to politics in an ecosystem context. Because ecosystems are open and dependent on Biospheric processes for their continued operation, the Biosphere (global ecosystem) emerges as a globally integrating factor in ecosystem management. Influences leading to development of the ecosystem approach in the Great Lakes Basin included: a politically shared resource in jeopardy, pollution, a common drinking water source, common enemies, advances in ecosystem theory, citizen groups, international political institutions, common economic and cultural ties, and a sense of crisis. A rationale is presented for viewing nations as politically defined ecosystems.     

A natural product inspired hybrid approach towards the synthesis of novel pentamidine based scaffolds as potential anti-parasitic agents

A natural product inspired molecular hybridization approach led us to a series of novel pentamidine based pyrimidine and chalcone scaffolds. All the hybrids were evaluated for their anti-leishmanial potential. Most of the screened compounds have showed significant in vitro anti-leishmanial activity with less cytotoxicity in comparison to the standard drugs (pentamidine, sodium stibogluconate, and miltefosine). Additionally, anti-malarial screening of these compounds was also done and four compounds have shown superior activity against chloroquine resistance strain (K1) of Plasmodium falciparum.     

A modelling approach towards epidermal homoeostasis control

In order to grasp the features arising from cellular discreteness and individuality, in large parts of cell tissue modelling agent-based models are favoured. The subclass of off-lattice models allows for a physical motivation of the intercellular interaction rules. We apply an improved version of a previously introduced off-lattice agent-based model to the steady-state flow equilibrium of skin. The dynamics of cells is determined by conservative and drag forces, supplemented with delta-correlated random forces. Cellular adjacency is detected by a weighted Delaunay triangulation. The cell cycle time of keratinocytes is controlled by a diffusible substance provided by the dermis. Its concentration is calculated from a diffusion equation with time-dependent boundary conditions and varying diffusion coefficients. The dynamics of a nutrient is also taken into account by a reaction-diffusion equation. It turns out that the analysed control mechanism suffices to explain several characteristics of epidermal homoeostasis formation. In addition, we examine the question of how in silico melanoma with decreased basal adhesion manage to persist within the steady-state flow equilibrium of the skin. Interestingly, even for melanocyte cell cycle times being substantially shorter than for keratinocytes, tiny stochastic effects can lead to completely different outcomes. The results demonstrate that the understanding of initial states of tumour growth can profit significantly from the application of off-lattice agent-based models in computer simulations.     

A comprehensive approach for drug safety assessment

A comprehensive, multidisciplinary approach is proposed here for the development of a drug with an acceptable safety profile. Key parameters to be considered for drug safety evaluation based on this comprehensive approach include the following: (1) Pharmacology: Possible toxicity due to drug-target interactions, including interactions with unintended molecular targets, or with molecular targets in unintended organs. (2) Chemistry: Chemical scaffolding and side-chains with safety concerns. (3) Toxicology: Toxicity in animals in vivo, and in relevant animal and human cells in culture. (4) Drug metabolism and pharmacokinetics: Safety concerns due to toxification or detoxification, organ distribution, clearance and pharmacokinetic drug-drug interactions. (5) Risk factors: Physiological, environmental and genetic factors that may enhance a patient's susceptibility. It is proposed that this integrated, multidisciplinary approach to safety evaluation may enhance the accuracy of the prediction of drug safety and thereby the efficiency of drug development.     

Preliminary approach towards construction of peptide libraries as potential tools for diagnosis of malignant thyroid tumors

INTRODUCTION: Cancer of thyroid gland is the most common malignancy of the endocrine system. The treatment improvement could be achieved by early diagnosis. The aim of the study was to identify cancer specific antigenes with use of peptide libraries. MATERIAL AND METHODS: The material from 6 patients with thyroid cancer (4 with papillary cancer, 1 with follicular cancer and 1 with oxyphilic tumor) were analyzed. It was performed with use of lipophylic peptide libraries by direct comparison of staining of specimens prepared from normal and malignant tissue. RESULTS: Preliminary results confirm practical value of peptide libraries in early diagnostics of thyroid cancer. CONCLUSIONS: It is important to optimize construction of peptide libraries by using different staining agents hydrolyzed by proteases.     

Protein engineering towards natural product synthesis and diversification

A dazzling array of enzymes is used by nature in making structurally complex natural products. These enzymes constitute a molecular toolbox that may be used in the construction and fine-tuning of pharmaceutically active molecules. Aided by technological advancements in protein engineering, it is now possible to tailor the activities and specificities of these enzymes as biocatalysts in the production of both natural products and their unnatural derivatives. These efforts are crucial in drug discovery and development, where there is a continuous quest for more potent agents. Both rational and random evolution techniques have been utilized in engineering these enzymes. This review will highlight some examples from several large families of natural products.     

A new approach for environmental risk assessment

Environmental problems, such as global warming, the limited supply of sustainable energy, the depletion of natural resources, hazardous emissions released into the atmosphere and waste, are increasing global concerns. Therefore, individuals, communities, and businesses need to address environmental protection and sustainability. Environmental impact assessments are needed to identify, mitigate, and control aspects that affect the environment or a company's products, services, or activities. In this study, a general environmental aspect and impact assessment approach, which can be applied to any company that is involved in the production or service sector, is created. An environmental impact pattern that consists of 10 main and 32 sub-categories was formed based on the ISO 14001, environmental studies and field applications. The developed approach was applied to the dyeing units of a manufacturing firm. Sixteen environmental aspects were identified and assessed using the environmental impact template via the environmental failure mode and effect analysis (E-FMEA) method. The developed-approach can be applied to each sector, which will enable us to perform a detailed analysis of the environmental aspects in the environmental impact category. This approach provides a checklist for the environmental impact studies of businesses and has been pioneered as an effective method for company resources to improve their environmental performance.     

A biomimetic approach towards synthesis of zinc oxide nanoparticles

Using natural processes as inspiration, the present study demonstrates a positive correlation between zinc metal tolerance ability of a soil fungus and its potential for the synthesis of zinc oxide (ZnO) nanoparticles. A total of 19 fungal cultures were isolated from the rhizospheric soils of plants naturally growing at a zinc mine area in India and identified on the genus, respectively the species level. Aspergillus aeneus isolate NJP12 has been shown to have a high zinc metal tolerance ability and a potential for extracellular synthesis of ZnO nanoparticles under ambient conditions. UV–visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction analysis, transmission electron microscopy, and energy dispersive spectroscopy studies further confirmed the crystallinity, morphology, and composition of synthesized ZnO nanoparticles. The results revealed the synthesis of spherical nanoparticles coated with protein molecules which served as stabilizing agents. Investigations on the role of fungal extracellular proteins in the synthesis of nanoparticles indicated that the process is nonenzymatic but involves amino acids present in the protein chains.     

A comprehensive urinary metabolomic approach for identifying kidney cancerr

The diagnosis of cancer by examination of the urine has the potential to improve patient outcomes by means of earlier detection. Due to the fact that the urine contains metabolic signatures of many biochemical pathways, this biofluid is ideally suited for metabolomic analysis, especially involving diseases of the kidney and urinary system. In this pilot study, we test three independent analytical techniques for suitability for detection of renal cell carcinoma (RCC) in urine of affected patients. Hydrophilic interaction chromatography (HILIC-LC-MS), reversed-phase ultra performance liquid chromatography (RP-UPLC-MS), and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) all were used as complementary separation techniques. The combination of these techniques is best suited to cover a very large part of the urine metabolome by enabling the detection of both lipophilic and hydrophilic metabolites present therein. In this study, it is demonstrated that sample pretreatment with urease dramatically alters the metabolome composition apart from removal of urea. Two new freely available peak alignment methods, MZmine and XCMS, are used for peak detection and retention time alignment. The results are analyzed by a feature selection algorithm with subsequent univariate analysis of variance (ANOVA) and a multivariate partial least squares (PLS) approach. From more than 2000 mass spectral features detected in the urine, we identify several significant components that lead to discrimination between RCC patients and controls despite the relatively small sample size. A feature selection process condensed the significant features to less than 30 components in each of the data sets. In future work, these potential biomarkers will be further validated with a larger patient cohort. Such investigation will likely lead to clinically applicable assays for earlier diagnosis of RCC, as well as other malignancies, and thereby improved patient prognosis.     

A chemical and biological approach towards the definition of calcareous soils

Summary Several agricultural problems are associated with the presence of certain levels of CaCO₃ in soils. The level of CaCO₃ at which the phosphate fixation becomes an apparent agricultural problem, is thought to be an appropriate margine at which the soil can be considered calcareous. Thus, a set of soil mixtures, ranging in CaCO₃ content from 1 to 96% was prepared and used in a column study to determine the level at which the CaCO₃ fraction becomes a dominant factor controlling. P³² movement and distribution.Increasing the percentage of oolitic sand, in the soil mixture, from 1 to 10% caused a sharp drop in P³² movement with soil solution and any increase in CaCO₃ content above 10% did not show any further drop in P³² movement. The amount of P³² removed with the soil solution was generally low compared to that retained in soil columns. Studying the distribution of P³² in soil columns, after five displacements, has indicated that the migration of P³² from the top soil increased by increasing CaCO₃ from 1 and 2 to 6%. The amount of P³² removed was however retained in lower sections. A very sharp decrease in P³² migration from the top soil was observed when CaCO₃ content was raised from 8 to 10%.A similar picture was shown when the CaCO₃ material used was in clay size fraction. However the sharp increase in phosphate retention in top soil sections took place at CaCO₃ content of 8% rather than at 10%. A limit of 8 to 10% CaCO₃ was proposed as an appropriate margine for defining calcareous soils.     

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the folding process. Coupled with high computing power and large scale storage, researchers now can computationally simulate the protein folding process in atomistic details at femtosecond temporal resolution. Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. As a result, effectively managing and analyzing such trajectories is becoming increasingly important.