Trends in biotechnology

Exploiting cell surface thiols to enhance cellular uptake.

Publication Date: 2012 Jan 17 PMID: 22260747
Authors: Torres, A. G. - Gait, M. J.
Journal: Trends Biotechnol

Efficient cellular delivery is one of the key issues that has hampered the therapeutic development of novel synthetic biomolecules such as oligonucleotides, peptides and nanoparticles. The highly specialized cellular plasma membrane specifically internalizes compounds through tightly regulated mechanisms. It is possible to exploit these natural mechanisms of cellular uptake with rationally designed reagents. Here, we discuss how thiol groups (-SH) naturally present on the cell surface (exofacial thiols) can be used to enhance cellular association and internalization of various materials bearing thiol-reactive groups in their structure. We propose that such thiol modifications should be considered in future design of synthetic biomolecules for optimized cellular delivery.

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Applications and perspectives of multi-parameter flow cytometry to microbial biofuels production processes.

Publication Date: 2012 Jan 16 PMID: 22257766
Authors: Silva, T. L. - Roseiro, J. C. - Reis, A.
Journal: Trends Biotechnol

Conventional microbiology methods used to monitor microbial biofuels production are based on off-line analyses. The analyses are, unfortunately, insufficient for bioprocess optimization. Real time process control strategies, such as flow cytometry (FC), can be used to monitor bioprocess development (at-line) by providing single cell information that improves process model formulation and validation. This paper reviews the current uses and potential applications of FC in biodiesel, bioethanol, biomethane, biohydrogen and fuel cell processes. By highlighting the inherent accuracy and robustness of the technique for a range of biofuel processing parameters, more robust monitoring and control may be implemented to enhance process efficiency.

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Bacterial inclusion bodies: making gold from waste.

Publication Date: 2012 Feb PMID: 22037492
Authors: Garcia-Fruitos, E. - Vazquez, E. - Diez-Gil, C. - Corchero, J. L. - Seras-Franzoso, J. - Ratera, I. - Veciana, J. - Villaverde, A.
Journal: Trends Biotechnol

Many protein species produced in recombinant bacteria aggregate as insoluble protein clusters named inclusion bodies (IBs). IBs are discarded from further processing or are eventually used as a pure protein source for in vitro refolding. Although usually considered as waste byproducts of protein production, recent insights into the physiology of recombinant bacteria and the molecular architecture of IBs have revealed that these protein particles are unexpected functional materials. In this Opinion article, we present the relevant mechanical properties of IBs and discuss the ways in which they can be explored as biocompatible nanostructured materials, mainly, but not exclusively, in biocatalysis and tissue engineering.

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Genetic design automation: engineering fantasy or scientific renewal?

Publication Date: 2012 Feb PMID: 22001068
Authors: Lux, M. W. - Bramlett, B. W. - Ball, D. A. - Peccoud, J.
Journal: Trends Biotechnol

The aim of synthetic biology is to make genetic systems more amenable to engineering, which has naturally led to the development of computer-aided design (CAD) tools. Experimentalists still primarily rely on project-specific ad hoc workflows instead of domain-specific tools, which suggests that CAD tools are lagging behind the front line of the field. Here, we discuss the scientific hurdles that have limited the productivity gains anticipated from existing tools. We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype.

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Activity-based protein profiling of host-virus interactions.

Publication Date: 2012 Feb PMID: 21944551
Authors: Blais, D. R. - Nasheri, N. - McKay, C. S. - Legault, M. C. - Pezacki, J. P.
Journal: Trends Biotechnol

Virologists have benefited from large-scale profiling methods to discover new host-virus interactions and to learn about the mechanisms of pathogenesis. One such technique, referred to as activity-based protein profiling (ABPP), uses active site-directed probes to monitor the functional state of enzymes, taking into account post-translational interactions and modifications. ABPP gives insight into the catalytic activity of enzyme families that does not necessarily correlate with protein abundance. ABPP has been used to investigate several viruses and their interactions with their hosts. Differential enzymatic activity induced by viruses has been monitored using ABPP. In this review, we present recent advances and trends involving the use of ABPP methods in understanding host-virus interactions and in identifying novel targets for diagnostic and therapeutic applications.

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Platforms for enrichment of phosphorylated proteins and peptides in proteomics.

Publication Date: 2012 Feb PMID: 21944550
Authors: Batalha, I. L. - Lowe, C. R. - Roque, A. C.
Journal: Trends Biotechnol

Protein phosphorylation is a complex and highly dynamic process involved in numerous biological events. Abnormal phosphorylation is one of the underlying mechanisms for the development of cancer and metabolic disorders. The identification and absolute quantification of specific phospho-signatures can help elucidate protein functions in signaling pathways and facilitate the development of new and personalized diagnostic and therapeutic tools. This review presents a variety of strategies currently utilized for the enrichment of phosphorylated proteins and peptides before mass spectrometry analysis during proteomic studies. The investigation of specific affinity reagents, allied to the integration of different enrichment processes, is triggering the development of more selective, rapid and cost-effective high-throughput automated platforms.

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Optical imaging techniques for the study of malaria.

Publication Date: 2012 Feb PMID: 21930322
Authors: Cho, S. - Kim, S. - Kim, Y. - Park, Y.
Journal: Trends Biotechnol

Malarial infection needs to be imaged to reveal the mechanisms behind malaria pathophysiology and to provide insights to aid in the diagnosis of the disease. Recent advances in optical imaging methods are now being transferred from physics laboratories to the biological field, revolutionizing how we study malaria. To provide insight into how these imaging techniques can improve the study and treatment of malaria, we summarize recent progress on optical imaging techniques, ranging from in vitro visualization of the disease progression of malaria infected red blood cells (iRBCs) to in vivo imaging of malaria parasites in the liver.

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Engineering new metabolic capabilities in bacteria: lessons from recombinant cellulolytic strategies.

Publication Date: 2012 Feb PMID: 21930321
Authors: Mazzoli, R. - Lamberti, C. - Pessione, E.
Journal: Trends Biotechnol

Cellulose waste biomass is the most attractive substrate for 'biorefinery strategies' producing high-value products (e.g. fuels or plastics) by fermentation. However, traditional biomass bioconversions are economically inefficient multistep processes. Thus far, no microorganisms able to perform single-step fermentation into products (consolidated bioprocessing; CBP) have been isolated. Metabolic engineering is currently employed to develop recombinant microorganisms suitable for CBP. The heterologous expression of extracellular proteins (e.g. cellulases or hemicellulases) is the key feature of recombinant cellulolytic strategies, conferring cellulolytic ability to microorganisms exhibiting high product yields and titers. Although more molecular tools are becoming available, efficient heterologous expression of secreted proteins is still a challenge. The present review summarizes both bottlenecks and solutions of organism engineering for biomass biorefinery strategies.

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Fruit improvement using intragenesis and artificial microRNA.

Publication Date: 2012 Feb PMID: 21871680
Authors: Molesini, B. - Pii, Y. - Pandolfini, T.
Journal: Trends Biotechnol

Genetic engineering methods based on the use of transgenes have been successfully adopted to improve crops. A novel all-native DNA gene technology consists of the creation of intragenic constructs by isolating genetic elements from a crop, rearranging them in vitro, and inserting them back into the plant. The ever-increasing genomic information and the elucidation of the molecular mechanisms that control fruit development could be exploited to confer the desired fruit phenotypes using endogenous DNA. The spatial/temporal regulation of genes can be modified by using appropriate endogenous regulatory elements, such as fruit-specific promoters. In addition, intragenic silencing can be employed to downregulate fruit-related genes. Here, we describe the available tools for intragenic manipulation of early phases of fleshy fruit initiation.

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