Biohazards of Protein Biotoxins

Biotoxins are toxic substances produced by a living organism that cause diseases in humanbeings, animals, or plants. The agent may be lethal or incapacitating. The new, emerging threatagents are biotoxins produced by animals, plants, fungi, and bacteria. Many types of organismsproduce substances that are toxic to humans. Examples of such biotoxins are botulinum toxin,tetanus toxin, and ricin. Several bioactive molecules produced by the pharmaceutical industrycan be even more toxic than the classical chemical warfare agents. Such new agents, like thebiotoxins and bioregulators, often are called mid-spectrum agents. The threat to human beingsfrom agents developed by modern chemical synthesis and by genetic engineering also must beconsidered, since such agents may be more toxic or more effective in causing death orincapacitation than classical warfare agents. By developing effective medical protection andtreatment against the most likely chemical and mid-spectrum threat agents, the effects of suchagents in a war scenario or following a terrorist attack can be reduced. Toxin-mediated diseaseshave made human beings ill for millennia. The use of biological agents as weapons of terror hasnow been realised, and separating naturally occurring disease from bioterroristic events hasbecome an important public health goal

EnzymeMiner: Exploration of sequence space of enzymes

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Strategies and software tools for engineering protein tunnels and dynamical gates

Improvements in the catalytic activity, substrate specificity or enantioselectivity of enzymes are traditionally achieved by modification of enzymes’ active sites. We have recently proposed that the enzyme engineering endeavors should target both the active sites and the access tunnels/channels [1,2]. Using the model enzymes haloalkane dehalogenases, we have demonstrated that engineering of access tunnels provides enzymes with significantly improved catalytic properties [3] and stability [4]. User-friendly software tools Caver [5], Caver Analyst [6], CaverDock [7] and Caver Web [8], have been developed for the computational design of protein tunnels/channels; FireProt [9] and HotSpot Wizard [10] for automated design of stabilizing mutations and smart libraries. Using these tools we were able to introduce a new tunnel to a protein structure and tweak its conformational dynamics. This engineering strategy has led to improved catalytic efficiency [2], enhanced promiscuity or even a functional switch (unpublished). Our concepts and software tools are widely applicable to various enzymes with known structures and buried active sites. 1. Damborsky, J., et al., 2009: Computational Tools for Designing and Engineering Biocatalysts. Current Opinion in Chemical Biology 13: 26-34. 2. Prokop, Z., et al., 2012: Engineering of Protein Tunnels: Keyhole-lock-key Model for Catalysis by the Enzymes with Buried Active Sites. Protein Engineering Handbook, Wiley-VCH, Weinheim, pp. 421-464. 3. Brezovsky, J., et al., 2016: Engineering a de Novo Transport Tunnel. ACS Catalysis 6: 7597-7610. 4. Koudelakova, T., et al., 2013: Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel. Angewandte Chemie 52: 1959-1963. 5. Chovancova, E., et al., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708. 6. Jurcik, A., et al., 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics 34: 3586-3588. 7. Vavra, O., et al., 2019: CaverDock 1.0: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. Bioinformatics (under review). 8. Stourac, J., et al. 2019: Caver Web 1.0: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport. Nucleic Acids Research (under review). 9. Musil, M., et al., 2017: FireProt: Web Server for Automated Design of Thermostable Proteins. Nucleic Acids Research 45: W393-W399. 10. Sumbalova, L. et al., 2018: HotSpot Wizard 3.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research 46: W356-W362

Advanced database mining integrating sequence and structure bioinformatics with microfluidics challenges enzyme engineering

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Canagliflozin and renal outcomes in type 2 diabetes and nephropathy

BACKGROUND Type 2 diabetes mellitus is the leading cause of kidney failure worldwide, but few effective long-term treatments are available. In cardiovascular trials of inhibitors of sodium–glucose cotransporter 2 (SGLT2), exploratory results have suggested that such drugs may improve renal outcomes in patients with type 2 diabetes. METHODS In this double-blind, randomized trial, we assigned patients with type 2 diabetes and albuminuric chronic kidney disease to receive canagliflozin, an oral SGLT2 inhibitor, at a dose of 100 mg daily or placebo. All the patients had an estimated glomerular filtration rate (GFR) of 30 to <90 ml per minute per 1.73 m2 of body-surface area and albuminuria (ratio of albumin [mg] to creatinine [g], >300 to 5000) and were treated with renin–angiotensin system blockade. The primary outcome was a composite of end-stage kidney disease (dialysis, transplantation, or a sustained estimated GFR of <15 ml per minute per 1.73 m2), a doubling of the serum creatinine level, or death from renal or cardiovascular causes. Prespecified secondary outcomes were tested hierarchically. RESULTS The trial was stopped early after a planned interim analysis on the recommendation of the data and safety monitoring committee. At that time, 4401 patients had undergone randomization, with a median follow-up of 2.62 years. The relative risk of the primary outcome was 30% lower in the canagliflozin group than in the placebo group, with event rates of 43.2 and 61.2 per 1000 patient-years, respectively (hazard ratio, 0.70; 95% confidence interval [CI], 0.59 to 0.82; P=0.00001). The relative risk of the renal-specific composite of end-stage kidney disease, a doubling of the creatinine level, or death from renal causes was lower by 34% (hazard ratio, 0.66; 95% CI, 0.53 to 0.81; P<0.001), and the relative risk of end-stage kidney disease was lower by 32% (hazard ratio, 0.68; 95% CI, 0.54 to 0.86; P=0.002). The canagliflozin group also had a lower risk of cardiovascular death, myocardial infarction, or stroke (hazard ratio, 0.80; 95% CI, 0.67 to 0.95; P=0.01) and hospitalization for heart failure (hazard ratio, 0.61; 95% CI, 0.47 to 0.80; P<0.001). There were no significant differences in rates of amputation or fracture. CONCLUSIONS In patients with type 2 diabetes and kidney disease, the risk of kidney failure and cardiovascular events was lower in the canagliflozin group than in the placebo group at a median follow-up of 2.62 years

Software tools overview : process integration, modelling and optimisation for energy saving and pollution reduction

This paper provides an overview of software tools based on long experience andapplications in the area of process integration, modelling and optimisation. The first part reviews the current design practice and the development of supporting software tools. Those are categorised as: (1) process integration and retrofit analysis tools, (2) general mathematical modelling suites with optimisation libraries, (3) flowsheeting simulation and (4) graph-based process optimisation tools. The second part covers an assessment of tools which enable the generation of new sustainable alternatives to adapt to the future needs. They deal with waste, environment, energy consumption, resources depletion and production cost constrains. The emphasis of the sustainable process design tools is largely on the evaluation of process viability under sustainable economic conditions, synthesis of sustainable process and supply chain process maintenance and life cycle analysis. Major software tools development and the potential of the research-based tools for sustainable process design task are overviewed in theconcluding part

Enhanced cascade table analysis to target and design multi-constraint resource conservation networks

Process Integration tools have served the process industries by identifying resource conservation solutions that minimise process waste, reducing the environmental impacts and costs. For dealing with water and wastewater minimisation, Pinch-based targeting and network design approaches are well established to handle single-quality water conservation problems. The Cascade Table Analysis, which has been an extension of the method used for targeting and designing single-quality material recycling networks, has evolved to handle multiple qualities. Based on previous analysis, multiple cascades with individual contaminant/quality indicators are analysed sequentially. Each contaminant is assigned a cascade table. Each sink is classified into the proper contaminant cascade based on their limiting contaminant, and the sources are prioritised based on the contaminant. This work also proposes a new way of arranging the Cascade Table streams to adapt for the multiple contaminants, which is by determining whether they belong to the high quality (Below the Pinch) region and the probable Pinch-causing source. The overall framework has been first identifying preliminary resource targets for each sink, followed by specific heuristics for additional reduction of the fresh resource. The proposed algorithm could yield an accurate minimum resource target and the associated network design. This work also explores the water-using processes with fixed load and fixed flowrate operations. An illustrative study and a real case study from a Brazilian paper mill are used to demonstrate the approach. The fresh water resource identified for the case study is 2,822 kg/h. The developed approach provides an informative interface to the user for the exact allocation of sources to the sinks. The numerical approach also shows directly the location of the Pinch Point(s), the overall fresh resource intake and the waste generation

Suggests rgl (> = 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer,GenomeGraphs

Description This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D

Advanced Database Mining of Efficient Biocatalysts by Sequence and Structure Bioinformatics and Microfluidics

Next-generation sequencing doubles genomic databases every 2.5 years. The accumulation of sequence data provides a unique opportunity to identify interesting biocatalysts directly in the databases without tedious and time-consuming engineering. Herein, we present a pipeline integrating sequence and structural bioinformatics with microfluidic enzymology for bioprospecting of efficient and robust haloalkane dehalogenases. The bioinformatic part identified 2,905 putative dehalogenases and prioritized a “small-but-smart” set of 45 genes, yielding 40 active enzymes, 24 of which were biochemically characterized by microfluidic enzymology techniques. Combining microfluidics with modern global data analysis provided precious mechanistic insights related to the high catalytic efficiency of selected enzymes. Overall, we have doubled the dehalogenation “toolbox” characterized over three decades, yielding biocatalysts that surpass the efficiency of currently available wild-type and engineered enzymes. This pipeline is generally applicable to other enzyme families and can accelerate the identification of efficient biocatalysts for industrial use