Curr Opin Biotechnol Research Articles

Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or toxin-stressors.

Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.

A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants.

Plant genomes harbor a particularly rich landscape of repetitive sequences. Transposable elements (TEs) represent a major fraction of this diversity and are intimately linked with plasticity and evolution of genomes across the tree of life (Fedoroff, Science 338:758-767, 2012). Amplification of Long Terminal Repeats (LTR) retrotransposons have shaped the genomic landscape by reshuffling genomic regions, altering gene expression, and providing new regulatory sequences, some of which have been instrumental for crop domestication and breeding (Lisch, Nat Rev Genet 14:49-61, 2013; Vitte et al., Brief Funct Genomics 13:276-295, 2014). While many retrotransposon families are still active within plant genomes, the repetitive nature of retrotransposons has hindered accurate annotation and kingdom-wide predictive assessment of their activity and molecular evolution. While it is natural for the first approach towards a genome annotation to characterize all regions of the genome and associate them with known structures such as particular genes, transposable elements, or other types of non-coding regions, such efforts can result in a large proportion of false-positive annotations when seeking for active loci. To overcome this issue, the next round of annotation efforts needs to include functional annotations based on rigorously defined sequence structures and protein domain compositions. In the context of retrotransposons, such a functional annotation can enable efforts to mobilize particular retrotransposon families in species living today and harness their mutagenic potency for crop improvement (Paszkowski, Curr Opin Biotechnol 32:200-206, 2015). For this purpose, we present a predictive analytical approach to infer the activity and natural variation of retrotransposon families in plants. This is achieved by applying a combination of software and molecular biology tools we developed for functional annotation, activity monitoring, and the assessment of the population structure of particular retrotransposon families in multiple plant species.

Benchtop Bioreactors in Mammalian Cell Culture: Overview and Guidelines.

Bioreactors are manufactured apparatuses that allow the generation of a specific environment for the highly controlled cultivation of living cells. Originally used for microbial production systems, they have found widespread applications in fields as diverse as vaccine production, plant cell cultivation, and the growth of human brain organoids and exist in equally diverse designs (Chu and Robinson, Curr Opin Biotechnol 12(2):180-187, 2001; Qian et al., Nat Protoc 13:565-580, 2018). Manufacturing of biologics is currently mostly performed using a stirred tank bioreactor and CHO host cells and represents the most "classical" bioreactor production process. In this chapter, we will therefore use the cultivation of suspension Chinese hamster ovary (CHO) cells for recombinant protein production in a stirred tank bioreactor as an example. However, general guidelines provided in this chapter are transferable to different bioreactor types and host cells (Li et al., MAbs 2(5):466-479, 2010).The preparation and operation of a bioreactor (also referred to as upstream process in a biotechnological/industrial setting) is comprised of three main steps: expansion (generation of biomass), production (batch, fed-batch, or continuous process), and harvest. The expansion of cells can last from few days to weeks depending on the number of cells at the start, the cellular doubling time, and the required biomass to inoculate the production bioreactor. The production phase lasts a few weeks and is a highly sensitive phase as the concentration of different chemicals and physical parameters need to be tightly controlled. Finally, the harvest will allow the separation of the product of interest from large particles and then the desired material (cell culture supernatant or cells) is transferred to the downstream process.The raw materials used during the upstream phase (all three steps) need to be aligned with the final purpose of the manufactured product, as the presence of residual impurities may have an impact on suitability of the final product for a desired purpose.

Comment on “Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production” by Baroukh et al. [Curr Opin Biotechnol. 2015, 33:198–205

Comment on “Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production” by Baroukh et al. [Curr Opin Biotechnol. 2015, 33:198–205

Protective role of glycerol against benzene stress: insights from the Pseudomonas putida proteome

Chemical activities of hydrophobic substances can determine the windows of environmental conditions over which microbial systems function and the metabolic inhibition of microorganisms by benzene and other hydrophobes can, paradoxically, be reduced by compounds that protect against cellular water stress (Bhaganna et al. in Microb Biotechnol 3:701-716, 2010; Cray et al. in Curr Opin Biotechnol 33:228-259, 2015a). We hypothesized that this protective effect operates at the macromolecule structure-function level and is facilitated, in part at least, by genome-mediated adaptations. Based on proteome profiling of the soil bacterium Pseudomonas putida, we present evidence that (1) benzene induces a chaotrope-stress response, whereas (2) cells cultured in media supplemented with benzene plus glycerol were protected against chaotrope stress. Chaotrope-stress response proteins, such as those involved in lipid and compatible-solute metabolism and removal of reactive oxygen species, were increased by up to 15-fold in benzene-stressed cells relative to those of control cultures (no benzene added). By contrast, cells grown in the presence of benzene+glycerol, even though the latter grew more slowly, exhibited only a weak chaotrope-stress response. These findings provide evidence to support the hypothesis that hydrophobic substances induce a chaotropicity-mediated water stress, that cells respond via genome-mediated adaptations, and that glycerol protects the cell's macromolecular systems. We discuss the possibility of using compatible solutes to mitigate hydrocarbon-induced stresses in lignocellulosic biofuel fermentations and for industrial and environmental applications.

Concomitant osmotic and chaotropicity-induced stresses in Aspergillus wentii: compatible solutes determine the biotic window.

Whereas osmotic stress response induced by solutes has been well-characterized in fungi, less is known about the other activities of environmentally ubiquitous substances. The latest methodologies to define, identify and quantify chaotropicity, i.e. substance-induced destabilization of macromolecular systems, now enable new insights into microbial stress biology (Cray et al. in Curr Opin Biotechnol 33:228-259, 2015a, doi: 10.1016/j.copbio.2015.02.010 ; Ball and Hallsworth in Phys Chem Chem Phys 17:8297-8305, 2015, doi: 10.1039/C4CP04564E ; Cray et al. in Environ Microbiol 15:287-296, 2013a, doi: 10.1111/1462-2920.12018 ). We used Aspergillus wentii, a paradigm for extreme solute-tolerant fungal xerophiles, alongside yeast cell and enzyme models (Saccharomyces cerevisiae and glucose-6-phosphate dehydrogenase) and an agar-gelation assay, to determine growth-rate inhibition, intracellular compatible solutes, cell turgor, inhibition of enzyme activity, substrate water activity, and stressor chaotropicity for 12 chemically diverse solutes. These stressors were found to be: (i) osmotically active (and typically macromolecule-stabilizing kosmotropes), including NaCl and sorbitol; (ii) weakly to moderately chaotropic and non-osmotic, these were ethanol, urea, ethylene glycol; (iii) highly chaotropic and osmotically active, i.e. NH4NO3, MgCl2, guanidine hydrochloride, and CaCl2; or (iv) inhibitory due primarily to low water activity, i.e. glycerol. At ≤0.974 water activity, Aspergillus cultured on osmotically active stressors accumulated low-M r polyols to ≥100mgg dry weight(-1). Lower-M r polyols (i.e. glycerol, erythritol and arabitol) were shown to be more effective for osmotic adjustment; for higher-M r polyols such as mannitol, and the disaccharide trehalose, water-activity values for saturated solutions are too high to be effective; i.e. 0.978 and 0.970 (25 ºC). The highly chaotropic, osmotically active substances exhibited a stressful level of chaotropicity at physiologically relevant concentrations (20.0-85.7kJkg(-1)). We hypothesized that the kosmotropicity of compatible solutes can neutralize chaotropicity, and tested this via in-vitro agar-gelation assaysfor the model chaotropes urea, NH4NO3, phenol and MgCl2. Of the kosmotropic compatible solutes, the most-effective protectants were trimethylamine oxide and betaine; but proline, dimethyl sulfoxide, sorbitol, and trehalose were also effective, depending on the chaotrope. Glycerol, by contrast (a chaotropic compatible solute used as a negative control) was relatively ineffective. The kosmotropic activity of compatible solutes is discussed as one mechanism by which these substances can mitigate the activities of chaotropic stressors in vivo. Collectively, these data demonstrate that some substances concomitantly induce chaotropicity-mediated and osmotic stresses, and that compatible solutes ultimately define the biotic window for fungal growth and metabolism. The findings have implications for the validity of ecophysiological classifications such as 'halophile' and 'polyextremophile'; potential contamination of life-support systems used for space exploration; and control of mycotoxigenic fungi in the food-supply chain.

Water Soluble CdTe Quantum Dots for Mercury Detection

Nanomaterials are becoming one of the most important classes of material research [1]. For example, quantum dots (QDs), especially water soluble QDs, have been used in many areas of research [2-3]. QDs are nanosize crystals of inorganic semiconductors with diameter in the range of 1-10 nm [4]. At such small sizes (close to or smaller than the dimensions of the exciton Bohr radius within the corresponding bulk material), these nanostructured materials behave differently from bulk solids, because of quantum-confinement effects [4]. As a result of quantum-confinement, they have unique optical and electronic properties such as broad excitation spectra and narrow, symmetric and tunable emission spectra [4]. Therefore, QDs have been used as novel luminescent sensors for chemical and biological species [5-8].This study fabricated cadmium telluride (CdTe) QDs from aqueous solution containing CdCl2 and Te precursor in presence of thioglycolic acid. The resulted QDs were characterized by using Uv-Vis. spectroscopy, photoluminescence (PL) spectroscopy and transmission electron microscopy (TEM). The results demonstrated that low concentration, in nano-molar range, of Hg(II) ions could effectively quench the CdTe QDs fluorescence because Hg(II) ions form a stable complex with QDs coating (thioglycolic acid) which allow for an effective electron transfer from the QDs to the Hg(II). A linear response to Hg(II) ions in the concentration range from 0.625 to 8.0 n M was observed and the detection limit of this sensor was 0.625 nM and sensitivity was equal to 53.4 /nM. References Rosi NL, Mirkin CA Nanostructures in biodiagnostics. Chem Rev 105:1547–1562 (2005)Goldman ER, Balighian ED, Mattoussi H, Kuno MK, Mauro JM, Tran PT, Anderson GP (2002) Avidin: a natural bridge for quantum dot-antibody conjugates. J Am Chem Soc 124:6378–6382Chen Y, Rosenzweig Z (2002) Luminescent CdS quantum dots as selective ion probes. Anal Chem 74:5132–5138Alivisatos AP (1996) Perspectives on the physical chemistry of semiconductor nanocrystals. J Phys Chem 100:13226–13239Chan WCW, Maxwel DJ, Gao X, Bailey RE, Han M, Nie S (2002) Luminescent quantum dots for multiplexed biological detection and imaging. Curr Opin Biotechnol 13:40–46Zhang L, Ci Xu, Li B (2009) Simple and sensitive detection method for chromium(VI) in water using glutathione—capped CdTe quantum dots as fluorescent probes. Microchim Acta 166: 61–68Landes C, Burda C, Braun M, El-Sayed MA (2001) Photoluminescence of CdSe nanoparticles in the presence of a hole acceptor: n-Butylamine. J Phys Chem B 105:2981–2986Dong F, Hu K, Han H, Liang J (2009) A novel method for methimazole determination using CdSe quantum dots as fluorescence probes. Microchim Acta 165:195–201

Synergism of Wild Grass and Hydrocarbonoclastic Bacteria in Petroleum Biodegradation

Synergism of Wild Grass and Hydrocarbonoclastic Bacteria in Petroleum Biodegradation

Manufacturing of peptides exhibiting biological activity.

Numerous studies have shown that food proteins may be a source of bioactive peptides. Those peptides are encrypted in the protein sequence. They stay inactive within the parental protein until release by proteolytic enzymes (Mine and Kovacs-Nolan in Worlds Poult Sci J 62(1):87–95, 2006; Hartman and Miesel in Curr Opin Biotechnol 18:163–169, 2007). Once released the bioactive peptides exhibit several biofunctionalities and may serve therapeutic roles in body systems. Opioid peptides, peptides lowering high blood pressure, inhibiting platelet aggregation as well as being carriers of metal ions and peptides with immunostimulatory, antimicrobial and antioxidant activities have been described (Hartman and Miesel in Curr Opin Biotechnol 18:163–169, 2007). The biofunctional abilities of the peptides have therefore aroused a lot of scientific, technological and consumer interest with respect to the role of dietary proteins in controlling and influencing health (Möller et al. in Eur J Nutr 47(4):171–182, 2008). Biopeptides may find wide application in food production, the cosmetics industry as well as in the prevention and treatment of various medical conditions. They are manufactured by chemical and biotechnological methods (Marx in Chem Eng News 83(11):17–24. 2005; Hancock and Sahl in Nat Biotechnol 24(12):1551–1557, 2006). Depending on specific needs (food or pharmaceutical industry) different degrees of peptide purifications are required. This paper discusses the practicability of manufacturing bioactive peptides, especially from food proteins.

Targeting Proteases in Cardiovascular Diseases by Mass Spectrometry-Based Proteomics

Proteases hydrolyze peptide bonds, thereby controlling the function of proteins and peptides on the posttranslational level. In the cardiovascular system, proteases play pivotal roles in the regulation of blood pressure, coagulation and other essential physiological processes. Accordingly, proteases are prime targets for therapeutic interventions and diagnostics. Proteases are part of complex proteolytic networks comprised of enzymes, inhibitors, activators, substrates and cleavage products. Analyzing these networks on a system-wide level is essential to understanding cardiovascular function and how dysregulation can lead to pathological conditions. Mass spectrometry-based quantitative and dynamic proteomics approaches are leading the way to enhance our knowledge of proteolytic networks such as the renin-angiotensin-system. Here, we critically review proteomics tools utilized in protease biology and provide an overview on how these methods can be used to characterize and validate protease function.

Editorial: Systems biology for biotech applications

Biotechnology JournalVolume 5, Issue 7 p. 636-637 EditorialFree Access Editorial: Systems biology for biotech applications Nathan D. Price, Nathan D. Price University of Illinois, Urbana-Champaign, IL, USASearch for more papers by this authorSang Yup Lee, Sang Yup Lee KAIST, Daejeon, KoreaSearch for more papers by this author Nathan D. Price, Nathan D. Price University of Illinois, Urbana-Champaign, IL, USASearch for more papers by this authorSang Yup Lee, Sang Yup Lee KAIST, Daejeon, KoreaSearch for more papers by this author First published: 14 July 2010 https://doi.org/10.1002/biot.201000216Citations: 1AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. REFERENCES 1 Barrett, C.L. et al., Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol. 2006, 17, 488– 492. 2 Gibson, D.G. et al., Creation of a bacterial cell controlled by a chemically synthesized genome Science 2010, in press. 3 Milne, C.B. et al., Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol. J. 2009, 4, 1653– 1670. 4 Kim, T.Y. et al., Strategies for systemslevel metabolic engineering. Biotechnol. J. 2008, 3, 612– 623. Citing Literature Volume5, Issue7Special Issue: Systems Biology for Biotech ApplicationsJuly 2010Pages 636-637 ReferencesRelatedInformation

Plant research accelerates along the (bio)informatics superhighway

The Keystone Symposium on Plant Sensing, Response and Adaptation to the Environment took place between 11 and 16 January 2009, at Big Sky, Montana, USA, and was organized by S.A. Kay & J. Chory. ![][1] See Glossary for abbreviations used in this article In spite of the fanfare surrounding the two‐hundredth anniversary of the birth of Charles Darwin, and the one‐hundred and fiftieth anniversary of his most celebrated book ‘ On the Origin of Species ’ (Darwin, 1859), many people would still be surprised to learn that Darwin wrote a nearly 600 page book entitled ‘ The Power of Movement in Plants ’ (Darwin, 1880). As most plants have their location fixed as soon as their roots enter the soil, non‐specialists might wonder how much movement plants can make. However, movement is not limited to locomotion, and many of the movements studied by Darwin probably evolved in response to the unique challenges imposed by the rooted habit. Unable to change location, plants have developed exquisite abilities to sense, respond to and adapt to their local environment. One example that captured Darwin's attention is the navigation of the radicle (root) tip through the complex soil environment to optimize water and nutrient acquisition. He stated, “It is hardly an exaggeration to say that the tip of the radicle thus endowed, and having the power of directing the movements of the adjoining parts, acts like the brain of one of the lower animals[…].” These root‐growth movements were but one of many environmental responses discussed by plant biologists gathered at the recent Keystone Symposium on Plant Sensing, Response and Adaptation to the Environment. Root growth is controlled by gravity, water and nutrient acquisition; whereas growth of the aerial shoot is regulated primarily by the light environment. Various photoreceptors allow plants to judge light intensity, direction … [1]: /embed/graphic-1.gif

Stromal–epithelial interactions in skin homeostasis, wound repair and skin cancer

Stromal–epithelial interactions in skin homeostasis, wound repair and skin cancer

Anthrax Vaccines

SUMMARYAnthrax, an uncommon disease in humans, is caused by a large bacterium, Bacillus anthracis. The risk of inhalation infection is the main indication for anthrax vaccination. Pre-exposure vaccination is provided by an acellular vaccine (anthrax vaccine adsorbed or AVA), which contains anthrax toxin elements and results in protective immunity after 3 to 6 doses. Anthrax vaccine precipitated (AVP) is administered at primovaccination in 3 doses with a booster dose after 6 months. To evoke and maintain protective immunity, it is necessary to administer a booster dose once at 12 months. In Russia, live spore vaccine (STI) has been used in a two-dose schedule. Current anthrax vaccines show considerable local and general reactogenicity (erythema, induration, soreness, fever). Serious adverse reactions occur in about 1% of vaccinations. New second-generation vaccines in current research programs include recombinant live vaccines and recombinant sub-unit vaccines.

360 NFkB expression and disease outcome in prostate cancer

The miniaturization of biological and chemical analytical devices by micro-electro-mechanical-systems (MEMS) technology has posed a vital influence on such fields as medical diagnostics, microbial detection and other bio-analysis. Among many miniaturized analytical devices, the polymerase chain reaction (PCR) microchip/microdevices are studied extensively, and thus great progress has been made on aspects of on-chip micromachining (fabrication, bonding and sealing), choice of substrate materials, surface chemistry and architecture of reaction vessel, handling of necessary sample fluid, controlling of three or two-step temperature thermocycling, detection of amplified nucleic acid products, integration with other analytical functional units such as sample preparation, capillary electrophoresis (CE), DNA microarray hybridization, etc. However, little has been done on the review of above-mentioned facets of the PCR microchips/microdevices including the two formats of flow-through and stationary chamber in spite of several earlier reviews [Zorbas, H. Miniature continuous-flow polymerase chain reaction: a breakthrough? Angew Chem Int Ed 1999; 38 (8):1055–1058; Krishnan, M., Namasivayam, V., Lin, R., Pal, R., Burns, M.A. Microfabricated reaction and separation systems. Curr Opin Biotechnol 2001; 12:92–98; Schneegaβ, I., Köhler, J.M. Flow-through polymerase chain reactions in chip themocyclers. Rev Mol Biotechnol 2001; 82:101–121; deMello, A.J. DNA amplification: does ‘small’ really mean ‘efficient’? Lab Chip 2001; 1: 24N–29N; Mariella, Jr. R. MEMS for bio-assays. Biomed Microdevices 2002; 4 (2):77–87; deMello AJ. Microfluidics: DNA amplification moves on. Nature 2003; 422:28–29; Kricka, L.J., Wilding, P. Microchip PCR. Anal BioAnal Chem 2003; 377:820–825]. In this review, we survey the advances of the above aspects among the PCR microfluidic devices in detail. Finally, we also illuminate the potential and practical applications of PCR microfluidics to some fields such as microbial detection and disease diagnosis, based on the DNA/RNA templates used in PCR microfluidics. It is noted, especially, that this review is to help a novice in the field of on-chip PCR amplification to more easily find the original papers, because this review covers almost all of the papers related to on-chip PCR microfluidics.

Molecular Profiling of Angiogenic Markers: A Step Towards Interpretive Analysis of a Complex Biological Function

Gene expression profiling is now being used routinely to define complex biological events. The profiling of a large array of genes expressed in the progression of a biological response opens the door to our understanding the unique relationships between genes and their functions. Angiogenesis, the process of new blood vessel development, is a necessary component of both normal and pathological physiology. In this issue of The American Journal of Pathology, Shih and colleagues 1 have used quantitative molecular profiling of angiogenic-related factors to define some of the elements required for angiogenic profiling. Although presented as a technical advance, the basic concept of this work is that the use of quantitative molecular profiling of gene expression gives additional insight into functional interrelationships between the genes expressed during the angiogenic process. This approach can be applied in large array format as a diagnostic tool for experimental systems and pathological samples.