New biotech books

The 60th Frankfurt Book Fair takes place in Frankfurt/Main, Germany, from October 15-19, 2008. The Frankfurt Book Fair is the largest of its kind in the world and is also the place to get to know and browse through the newest scientific books and journals published all around the globe. As not all our readers will be able visit the Wiley-Blackwell booth, we would like to seize the occasion to present here new book publications in the field of biotech, most of which are already available or soon to come.     

Biomass to fuels via microbial transformations

The conversion of biomass to fuels is advancing on two fronts: first, to enhance the usability of biomass and second, to generate the best fuel molecule(s). Lignin generally presents a barrier to biomass utilization; this problem may be circumvented by the genetic alteration of lignin-producing plants. Plant cellulosic material will need to be utilized more efficiently, requiring a greater knowledge of the multiprotein complex, the cellulosome. Many biofuel types are being considered: alcohols, esters, ethers, and hydrocarbons. Intrinsic alcohol toxicity to cells may impose limitations on ethanol and n-butanol production. Biodiesel, or fatty acid esters, can now be synthesized via recombinant Escherichia coli and may offer an improvement over alcohol fermentations. Biopetroleum (hydrocarbons) is being considered as an alternative biofuel.     

Kingdom animalia: The zoological malaise from a microbial perspective

Pain and cognitive dissonance abounds amongst biologists: theplant-animal, botany-zoology wound has nearly healed and thenew gash—revealed by department and budget reorganizations—is"molecular" vs. "organismic" biology. Here I contend that resolutionof these tensions within zoology requires that an autopoietic-gaianview replace a mechanical-neodarwinian perspective; in the interestof brevity and since many points have been discussed elsewhere,rather than develop detailed arguments I must make staccatostatements and refer to a burgeoning literature. The first centralconcept is that animals, all organisms developing from blastularembryos, evolved from single protist cells that were unableto reproduce their undulipodia. The second points to the usefulnessof recognizing the analogy between cyclically established symbiosesand meiotic sexuality     

Metabolic shifts: a fitness perspective for microbial cell factories

Performance of industrial microorganisms as cell factories is limited by the capacity to channel nutrients to desired products, of which optimal production usually requires careful manipulation of process conditions, or strain improvement. The focus in process improvement is often on understanding and manipulating the regulation of metabolism. Nonetheless, one encounters situations where organisms are remarkably resilient to further optimization or their properties become unstable. Therefore it is important to understand the origin of these apparent limitations to find whether and how they can be improved. We argue that by considering fitness effects of regulation, a more generic explanation for certain behaviour can be obtained. In this view, apparent process limitations arise from trade-offs that cells faced as they evolved to improve fitness. A deeper understanding of such trade-offs using a systems biology approach can ultimately enhance performance of cell factories.     

Chemometrics applications in biotech processes: a review

Biotech unit operations are often characterized by a large number of inputs (operational parameters) and outputs (performance parameters) along with complex correlations amongst them. A typical biotech process starts with the vial of the cell bank, ends with the final product, and has anywhere from 15 to 30 such unit operations in series. The aforementioned parameters can impact process performance and product quality and also interact amongst each other. Chemometrics presents one effective approach to gather process understanding from such complex data sets. The increasing use of chemometrics is fuelled by the gradual acceptance of quality by design and process analytical technology amongst the regulators and the biotech industry, which require enhanced process and product understanding. In this article, we review the topic of chemometrics applications in biotech processes with a special focus on recent major developments. Case studies have been used to highlight some of the significant applications.     

New biotech applications from evolved D-amino acid oxidases

D-Amino acid oxidase (DAAO) is a well-known flavoenzyme that catalyzes the oxygen-dependent oxidative deamination of amino acid D-isomers with absolute stereospecificity, which results in α-keto acids, ammonia and hydrogen peroxide. Recently, the extraordinary functional plasticity of DAAO has become evident; in turn, boosting research on this flavoprotein. Protein engineering has allowed for a redesign of DAAO substrate specificity, oxygen affinity, cofactor binding, stability, and oligomeric state. We review recent developments in utilizing DAAO, including as a biocatalyst for resolving racemic amino acid mixtures, as a tool for biosensing, and as a new mechanism of herbicide resistance. Perspectives for future biotechnological applications of this oxidative biocatalyst are also outlined.     

Coastal connectivity and spatial subsidy from a microbial perspective

The transfer of organic material from one coastal environment to another can increase production in recipient habitats in a process known as spatial subsidy. Microorganisms drive the generation, transformation, and uptake of organic material in shallow coastal environments, but their significance in connecting coastal habitats through spatial subsidies has received limited attention. We address this by presenting a conceptual model of coastal connectivity that focuses on the flow of microbially mediated organic material in key coastal habitats. Our model suggests that it is not the difference in generation rates of organic material between coastal habitats but the amount of organic material assimilated into microbial biomass and respiration that determines the amount of material that can be exported from one coastal environment to another. Further, the flow of organic material across coastal habitats is sensitive to environmental change as this can alter microbial remineralization and respiration rates. Our model highlights microorganisms as an integral part of coastal connectivity and emphasizes the importance of including a microbial perspective in coastal connectivity studies.     

Role and challenges of proteomics in pharma and biotech: technical, scientific and commercial perspective

Contemporary proteomics, currently in its exponential growth phase, is a bewildering array of tools. Proteomic methods are the result of a convergence of rapidly improving mass spectrometry technologies, protein chemistry and separation sciences, genomics and bioinformatics. Strides in improving proteomics technologies to map and measure proteomes and subproteomes are being made. However, no single proteomic platform appears ideally suited to address all research needs or accomplish ambitious goals satisfactorily. However, proteomics is in a unique position to contribute to protein discovery and to public health in terms of better biomarkers, diagnostics and treatment of disease. While the potential is great, many challenges and issues remain to be solved. Fundamental issues, such as biological variability, pre-analytic factors and analytical reproducibility, remain to be resolved. Neither an all-genetic approach nor an all-proteomic approach will solve biological complexity. Proteomics will be the foundation for constructing and extracting useful knowledge to pharma and biotech depicted in the following path: data --> structured data --> information --> information architecture --> knowledge --> useful knowledge.     

Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system

Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plant and animal ecology, we tailored spatially organized, water-unsaturated model microcosms using hyphae of Pythium ultimum as invasion paths and flagellated soil-bacterium Pseudomonas putida KT2440 as carrier for co-transport of Escherichia virus T4. P. putida KT2440 efficiently dispersed along P. ultimum to new habitats and dispatched T4 phages across air gaps transporting ≈0.6 phages bacteria⁻¹. No T4 displacement along hyphae was observed in the absence of carrier bacteria. If E. coli occupied the new habitat, T4 co-transport fueled the fitness of invading P. putida KT2440, while the absence of phage co-transport led to poor colonization followed by extinction. Our data emphasize the importance of hyphal transport of bacteria and associated phages in regulating fitness and composition of microbial populations in water-unsaturated systems. As such co-transport seems analogous to macroecological invasion processes, hyphosphere systems with motile bacteria and co-transported phages could be useful models for testing hypotheses in invasion ecology.Subject terms: Microbial ecology, Ecosystem ecology, Macroecology, Population dynamics     

微生物气溶胶检测技术的研究进展

生物气溶胶中微生物的种类复杂多样,其采集和鉴定是全面掌握微生物气溶胶生物特性的关键,对防控气溶胶病原体传播十分重要.本文简要综述了微生物气溶胶的生物特性和潜在危害性,介绍了微生物气溶胶的一般采集方法,采集器采集生物气溶胶的基本原理、特点和优缺点.将有助于研究人员根据实验目的在采集低浓度生物气溶胶时选择合适的采样器.本文...     

Editorial: Advances in biotech

As Biotechnology Journal is entering its third volume, its shape and branding become more defined. After the success of last year's “Methods and Advances in Biotech” issue, I would like to quickly glance back at BTJ 2007 content (Table 1), and consider a frame for future directions to take in 2008.