Trends in biotechnology

Potential of Arabidopsis systems biology to advance the biofuel field.

Publication Date: 2010 Aug 25 PMID: 20800303
Authors: Vanholme, R. - Van Acker, R. - Boerjan, W.
Journal: Trends Biotechnol

Plant biomass is a renewable and potentially sustainable resource for the production of liquid biofuels and a multitude of bio-based materials. To tailor plants for biofuel production, a powerful gene discovery program targeted to cell wall recalcitrance genes is needed. In parallel, a system is required that reveals the pleiotropic effects of gene modifications and that delivers the fundamental knowledge necessary for successful gene stacking. In our opinion, these objectives can be pioneered through a systems biology approach in Arabidopsis. We develop our ideas with a focus on the lignin biosynthetic pathway, because lignin is among the most important factors determining cell wall recalcitrance.

post to: CiteULike

Platform technologies for tubular organ regeneration.

Publication Date: 2010 Aug 25 PMID: 20800302
Authors: Basu, J. - Ludlow, J. W.
Journal: Trends Biotechnol

As a result of recent successes in regenerative medicine approaches to engineering multiple disparate tubular organs, methodology commonalities are emerging. Principal themes include the importance of a biodegradable scaffold seeded with a population of smooth muscle cells. Such composites trigger a regenerative response following in vivo implantation, resulting in de novo organogenesis. In this review, we examine bladder regeneration as a foundational platform technology to highlight key principles applicable to the regeneration of any tubular organ, and illustrate how these general concepts underlie current strategies to regenerate components of gastrointestinal, vascular, pulmonary and genitourinary systems. We focus on identifying the elements of this platform that have facilitated the transition of tubular organ regeneration from academic proof-of-concept to commercial viability.

post to: CiteULike

Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development.

Publication Date: 2010 Aug 18 PMID: 20727604
Authors: Chen, Z. - Wilmanns, M. - Zeng, A. P.
Journal: Trends Biotechnol

The future of industrial biotechnology requires efficient development of highly productive and robust strains of microorganisms. Present praxis of strain development cannot adequately fulfill this requirement, primarily owing to the inability to control reactions precisely at a molecular level, or to predict reliably the behavior of cells upon perturbation. Recent developments in two areas of biology are changing the situation rapidly: structural biology has revealed details about enzymes and associated bioreactions at an atomic level; and synthetic biology has provided tools to design and assemble precisely controllable modules for re-programming cellular metabolic circuitry. However, because of different emphases, to date, these two areas have developed separately. A linkage between them is desirable to harness their concerted potential. We therefore propose structural synthetic biotechnology as a new field in biotechnology, specifically for application to the development of industrial microbial strains.

post to: CiteULike

DREAMS of metabolism.

Publication Date: 2010 Aug 18 PMID: 20727603
Authors: Soh, K. C. - Hatzimanikatis, V.
Journal: Trends Biotechnol

Metabolic networks have been studied for several decades, and sophisticated computational frameworks are needed to augment experimental approaches to harness these complex networks. BNICE (Biochemical Network Integrated Computational Explorer), a computational approach for the discovery of novel biochemical pathways that is based on biochemical transformations, overcomes many of the current limitations. BNICE and similar frameworks can be used in several different areas: (i) 'Design' of novel pathways for metabolic engineering; (ii) 'Retrosynthesis' of metabolic compounds; (iii) 'Evolution' analysis between metabolic pathways of different organisms; (iv) 'Analysis' of metabolic pathways; (v) 'Mining' of omics data; and (vi) 'Selection' of targets for enzyme engineering. Here, we discuss the issues and challenges in building such frameworks as well as the gamut of applications in biotechnology, metabolic engineering and synthetic biology.

post to: CiteULike

Nanosilver as a new generation of nanoproduct in biomedical applications.

Publication Date: 2010 Aug 17 PMID: 20724010
Authors: Chaloupka, K. - Malam, Y. - Seifalian, A. M.
Journal: Trends Biotechnol

Nanosilver (NS), comprising silver nanoparticles, is attracting interest for a range of biomedical applications owing to its potent antibacterial activity. It has recently been demonstrated that NS has useful anti-inflammatory effects and improves wound healing, which could be exploited in developing better dressings for wounds and burns. The key to its broad-acting and potent antibacterial activity is the multifaceted mechanism by which NS acts on microbes. This is utilized in antibacterial coatings on medical devices to reduce nosocomial infection rates. Many new synthesis methods have emerged and are being evaluated for NS production for medical applications. NS toxicity is also critically discussed to reflect on potential concerns before widespread application in the medical field.

post to: CiteULike

Targeting cancer cells with nucleic acid aptamers.

Publication Date: 2010 Aug 16 PMID: 20719399
Authors: Cerchia, L. - de Franciscis, V.
Journal: Trends Biotechnol

Aptamers are short, structured, single-stranded RNA or DNA ligands that bind with high affinity to their target molecules, which range from small chemicals to large cell-surface and transmembrane proteins. Aptamers are now emerging as promising molecules to target specific cancer epitopes in clinical diagnosis and therapy. Furthermore, because of their high specificity and low toxicity, aptamers might be considered as the compounds-of-choice for in vivo cell recognition. Specific cancer cell recognition could be capitalized upon for delivering therapeutic nanoparticles, small interfering RNA bioconjugates, chemotherapeutic cargos or molecular imaging probes. In this article, we review recent advances in the use of aptamers for in vivo cancer cell recognition, with a particular focus on novel applications of aptamers for targeting the cell surface.

post to: CiteULike

More genomic resources for less-studied crops.

Publication Date: 2010 Sep PMID: 20692061
Authors: Varshney, R. K. - Glaszmann, J. C. - Leung, H. - Ribaut, J. M.
Journal: Trends Biotechnol

Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and diversity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic diversity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries.

post to: CiteULike

Polymer- and colloid-mediated bioassays, sensors and diagnostics.

Publication Date: 2010 Sep PMID: 20691489
Authors: Horgan, A. M. - Moore, J. D. - Noble, J. E. - Worsley, G. J.
Journal: Trends Biotechnol

Synthetic polymers and colloids are increasingly being exploited in bioassays to help measure gene expression, sequence genomes, monitor metabolic disorders and detect the presence of disease. This can be attributed to their potential to reduce reaction scales, improve throughput, lower costs and improve the sensitivity, selectivity, stability and reproducibility of assays. This review highlights the newest application areas, including some of the strategies employed, as well as major technical challenges and future opportunities. The move away from conventional assay approaches is being driven by a desire to improve our basic understanding of human biology, to diagnose diseases earlier, and to manage healthcare resources more efficiently. These endeavors are important owing to a rising world population and an increasing average life span.

post to: CiteULike

Pharmacokinetic, pharmacodynamic and immunogenicity comparability assessment strategies for monoclonal antibodies.

Publication Date: 2010 Aug 4 PMID: 20691488
Authors: Putnam, W. S. - Prabhu, S. - Zheng, Y. - Subramanyam, M. - Wang, Y. M.
Journal: Trends Biotechnol

Regulatory guidance stipulates that comparability assessment is required to support manufacturing process changes during the development of a biological product or post-approval. However, strategies for assessing the comparability of pre- and post-change materials are still evolving. A hierarchical risk-based approach is recommended, starting with analytical testing to ensure quality, followed by biological characterization and, if needed, in vivo pharmacokinetic (PK), PK-pharmacodynamic (PD), safety and/or efficacy studies. The need for an in vivo study and the type of study required depend on the magnitude and the potential impact of the changes and the timing in the development process. This review discusses factors affecting the PK, PD and immunogenicity of monoclonal antibodies, and provides guidance for determining non-clinical and clinical comparability assessment strategies.

post to: CiteULike

Glucose metabolism in mammalian cell culture: new insights for tweaking vintage pathways.

Publication Date: 2010 Sep PMID: 20691487
Authors: Mulukutla, B. C. - Khan, S. - Lange, A. - Hu, W. S.
Journal: Trends Biotechnol

Cultured mammalian cells are major vehicles for producing therapeutic proteins, and energy metabolism in those cells profoundly affects process productivity. The characteristic high glucose consumption and lactate production of industrial cell lines as well as their adverse effects on productivity have been the target of both cell line and process improvement for several decades. Recent research advances have shed new light on regulation of glucose metabolism and its links to cell proliferation. This review highlights our current understanding in this area of crucial importance in bioprocessing and further discusses strategies for harnessing new findings toward process enhancement through the manipulation of cellular energy metabolism.

post to: CiteULike

Recent advances in the photochemical control of protein function.

Publication Date: 2010 Sep PMID: 20667607
Authors: Riggsbee, C. W. - Deiters, A.
Journal: Trends Biotechnol

Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented.

post to: CiteULike

Genome-wide approaches to systematically identify substrates of the ubiquitin-proteasome pathway.

Publication Date: 2010 Sep PMID: 20637515
Authors: Liu, C. - Choe, V. - Rao, H.
Journal: Trends Biotechnol

The ubiquitin-proteasome system handles the majority of controlled proteolysis in eukaryotes. Defects in the ubiquitin-proteasome system have been implicated in diseases ranging from cancers to neurodegenerative disorders. However, the precise role of ubiquitin-proteasome-mediated degradation in health and disease is far from clear. A major challenge is to link specific substrates directly to a particular degradation pathway. Here, we review genome-wide approaches that have been developed in recent years to comprehensively identify ubiquitylated substrates of a particular pathway. Components of the ubiquitin-proteasome system are attractive drug targets, as illustrated by the efficacy of some proteasome inhibitors in the treatment of multiple myeloma. Information that has emerged from these studies could reveal novel drug targets and strategies for treating human diseases.

post to: CiteULike

Site-specific DNA excision via engineered zinc finger nucleases.

Publication Date: 2010 Sep PMID: 20621372
Authors: Lee, H. J. - Kim, E. - Kim, J. S.
Journal: Trends Biotechnol

post to: CiteULike

Role and reality: technology transfer at Canadian universities.

Publication Date: 2010 Sep PMID: 20598388
Authors: Bubela, T. M. - Caulfield, T.
Journal: Trends Biotechnol

Technology transfer offices (TTOs) play a central role in the knowledge translation and commercialization agenda of Canadian universities. Despite this presumed mandate, there is a disconnect between the expectations of government and research institutions (which view TTOs' primary role as the promotion of profitable commercialization activities) and the reality of what TTOs do. Interviews with professionals at Canadian TTOs have revealed that, at their best, TTOs support the social and academic missions of their institutions by facilitating knowledge mobilization and research relationships with other sectors, including industry; however, this does not always produce obvious or traditional commercial outputs. Thus, the existing metrics used to measure the success of TTOs do not capture this reality and, as such, realignment is needed.

post to: CiteULike