Next issue (April 2008): Novel Approaches to Drug Discovery in Signal Transduction

Edited by Lodewijk Dekker, Nottingham, UK – Computational chemistry approaches – Cell-based assays for G-Protein-coupled Receptors – Cell-based label-free technologies Methods and Advances in Biotech – Application of proteomics in biotechnology – Mining marine biological wastes for bioactive molecules – PCR-based strategy to express endogenous protein levels in yeast – Method for tracking nanogel particles – Gene expression studies on bio-electrosprayed primary cardiac myocytes Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”. http://www.biotechnology-journal.com     

Upcoming articles in BTJ

Next issue: RNA-assisted Protein Folding The July 2008 issue of BTJ is devoted to RNA-assisted Protein Folding, edited by Professor Marc Blondel (Brest, France). BTJ will be featuring articles on: – Role of ribosomes in protein folding – Tools for the study of Ribosome-borne Protein Folding Activity (RPFA) – RNA-driven cyclin-dependent kinase regulation – The presence of rRNA sequences in polyadenylated RNAs and its potential functions – Non-coding RNAs in neurodegeneration and stress response – Folding at the rhythm of the rare codon beat Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”. http://www.biotechnology-journal.com     

Next issue: Mitochondria and ageing

The June 2008 issue of BTJ is devoted to Mitochondria and ageing. Featuring articles on: – Dietary restriction genes involved in energy metabolism – Structural implications of mitochondrial dynamics – Mitochondrial protein quality control: Implications in ageing – Age-related mitochondrial degenerative diseases in humans – The impact of mitochondrial DNA on human life span – Insulin-like growth factor induced signals activate mitochondrial respiration – Senescence factors in Podospora anserina independent of intrinsic senescence – Native-DIGE: A new look at the mitochondrial membrane proteome – Fusion and fission genes and the regulation of mitochondrial dynamics Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”.     

Next issue (January 2008): Methods and Advances in Biotech

Edited by Dr. Barbara Janssens, Managing Editor – Recombinant therapeutic proteins – Technical aspects of biocatalysis – Advances in safe and efficient DNA therapy – SeSaM-Tv: A random mutagenesis method – Bioinformatics: Identifying interacting residues using boolean learning and support vector machines – 3D imaging flow cytometry – Flow cytometry technology responding to HIV-tuberculosis coinfections – Stem cell cultures: Technical aspects Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”.     

BTJ future topical issues

Next issue: Biotech in Korea The May 2008 issue of BTJ is devoted to Biotech in Korea. Featuring articles on: – Recent progress in microbial genome projects of Korea – Bio-Vision 2016: the 2nd Base Plan for biotechnology promotion in Korea – Strategies for systems-level metabolic engineering – Cell engineering strategies for improved therapeutic protein production in CHO cells – Development of bioadhesives from marine mussels – Dynamical analysis of the calcium signaling pathway in cardiac myocytes – Systems biology of heart and calcium signaling networks – Non-labeled detection of waterborne pathogen Cryptosporidium parvum – Injectable and sustained delivery of human growth hormone: A new method – Exploring sequence space: Screening for ω-aminotransferases Many of these exciting articles are already available online under "Early View"! A sneak preview of other content can be found under “News”. http://www.biotechnology-journal.com     

Next issue: Methods and Advances in Biotech

The March 2008 issue of BTJ is again entirely devoted to Methods and Advances; featuring articles on: – BRET technology and application to screening assays – Using a commercial DNA extraction kit to obtain RNA for RT-PCR – Method of tracking nanogel particles in vivo and in vitro – RNA interference: An emerging generation of biologicals – Whole genome amplification using single primer PCR – Enzyme restriction and ligation-independent recombination expression vectors – Protoplast isolation and transient gene expression in switchgrass – Roust macroporous matrixes for cell immobilization – Hepatogenic differentiation of mesenchymal stem cells using microfluidic chips – A transformation procedure for the recalcitrant tomato – Bioreactor scale-up and oxygen transfer rate in microbial processes: An overview – Recent research of the genus Aspergillus for food and biotech applications Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”. http://www.biotechnology-journal.com     

Correction to: How origin,packaging and seasonality determine the environmental impact of apples,magnified by food waste and losses

The International Journal of Life Cycle Assessment - After publishing the abovementioned article in the “Online First Articles” list, an error was discovered.     

What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments

Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a “replication fork trap” – found within a chromosomal region where forks are allowed to enter but not leave – is set by the protein–DNA roadblock Tus–Ter. The exact sequence of events by which Tus–Ter blocks replisomes approaching from one direction but not the other has been the subject of controversy for many decades. Specific protein–protein interactions between the nonpermissive face of Tus and the approaching helicase were challenged by biochemical and structural studies. These studies show that it is the helicase-induced strand separation that triggers the formation of new Tus–Ter interactions at the nonpermissive face – interactions that result in a highly stable “locked” complex. This controversy recently gained renewed attention as three single-molecule-based studies scrutinized this elusive Tus–Ter mechanism – leading to new findings and refinement of existing models, but also generating new questions. Here, we discuss and compare the findings of each of the single-molecule studies to find their common ground, pinpoint the crucial differences that remain, and push the understanding of this bipartite DNA–protein system further.     

Time-Qualified Reference Limits (Chronodesms) for 24-Hour Blood Pressure Values: Classical and Bayesian

Background – This paper is a concrete example of the problems raised by the need of constructing the time-qualified reference limits (chronodesms) for blood pressure (BP), in order to clinically estimate the hemodynamic parameter in its intrinsic nychtohemeral variability. Methods – Assuming that the noninvasive ambulatory BP monitoring (ABPM) is the eligible technique for this need, it must be realized that the BP chronodems may be of two types, depending on the sample being used for their calculation. The first type may be regarded as “ a priori ” because of the fact that they are derived by a sample of normotensive subjects who are unavoidably recruited via “ causal ” sphygmomanometric measurements and reclassified as normotensive by comparing their ABPM to the fixed reference limits (monodesms) given by WHO (monodiagnosis). Therefore, the “ a priori ” BP chonodesms are by principle derived by subjects who could not be correctly classified as normotensive, their ABPM being not tested versus the time-varying physiological limits. The second type may regarded as “ a posteriori ” in virtue of the fact that they may be constructed on a sample which contemplates the previous subjects who result to be true normotensive via the reassessment of their ABPM versus the “ a priori ” BP chronodesms (chronodiagnosis). The “ a posteriori ” chronodesms may be regarded as biometrically reliable, whether the sample for their construction is additionally constituted by those subjects of the local population who have been erroneously monodiagnosed as hypertensive, while they result to be true normotensive via the chronodiagnostic comparison of their ABPM versus the “ a priori ” BP chronodesms. Results – The biometric reliability of the “ a posteriori ” BP chronodems is demonstrated by the fact that their upper limits are statistically significantly less pronounced due to the fact that they are provided by a sample which has been depured by the falsely monodiagnosed normotensives. Conclusions – The “ a posteriori ” BP upper chronodesms are the time-qualified reference limits which should be used in clinical practice for the chronodiagnosis of hypertension.     

Recent advances in exploiting ionic liquids for biomolecules: Solubility,stability and applications

The technological utility of biomolecules (e.g. proteins, enzymes and DNA) can be significantly enhanced by combining them with ionic liquids (ILs) – potentially attractive ”green“ and ”designer“ solvents – rather than using in conventional organic solvents or water. In recent years, ILs have been used as solvents, cosolvents, and reagents for biocatalysis, biotransformation, protein preservation and stabilization, DNA solubilization and stabilization, and other biomolecule‐based applications. Using ILs can dramatically enhance the structural and chemical stability of proteins, DNA, and enzymes. This article reviews the recent technological developments of ILs in protein‐, enzyme‐, and DNA‐based applications. We discuss the different routes to increase biomolecule stability and activity in ILs, and the design of biomolecule‐friendly ILs that can dissolve biomolecules with minimum alteration to their structure. This information will be helpful to design IL‐based processes in biotechnology and the biological sciences that can serve as novel and selective processes for enzymatic reactions, protein and DNA stability, and other biomolecule‐based applications.     

Molecular composition and origin of substrate-attached material from normal and virus-transformed cells

The proteins and polysaccharides which are left adherent to the tissue culture substrate after EGTA-mediated removal of normal, virus-transformed, and revertant mouse cells (so-called SAM, or substrate-attached material), and which have been implicated in the cell-substrate adhesion process, have been characterized by SDS-PAGE and other types of analyses under various conditions of cell growth and attachment. The following components have been identified in SAM: 3 size classes of hyaluronate proteoglycans; glycoprotein C_o (the LETS glycoprotein); protein C_a (a myosin-like protein); protein C_b (MW 85,000); protein C₁ (MW 56,000, which is apparently not tubulin); protein C₂ (actin); proteins C₃–C₅ (histones) which are artifactually bound to the substrate as a result of EGTA-mediated leaching from the cell; and proteins C_c, C_d, C_e, and C_f. The LETS glycoprotein (C_o) and C_d appear in newly-synthesized SAM (which is probably enriched in “footpad” material – “footpads” being focal areas of subsurface membranous contact with the substrate) in greater relative quantities than in the SAM accumulated over a long period of time (which is probably enriched in “footprint” material – remnants of footpads left behind as cells move across the substrate). C_o and C_d turn over very rapidly following short radiolabeling periods during chase analysis. The SAM's deposited during a wide variety of cellular attachment and growth conditions contained the same components in similar relative proportions. This may indicate well-controlled and coordinate deposition of a cell “surface” complex involving the hyaluronate proteoglycans, the LETS glycoprotein, actin-containing microfilaments with associated proteins, and a limited number of additional proteins in the substrate adhesion site. Evidence indicates that SAM is the remnant of “footpad” vesicles by which the cell adheres to the substrate and that EGTA treatment weakens the subsurface cytoskeleton, allowing these footpad vesicles to be pinched off from the rest of the cell. Three different models of cell-substrate adhesion are presented and discussed.     

Race,ethnicity and disciplinary divides: what is the path forward?

We pose several questions that emerged for us from Valdez and Golash-Boza’s “U.S. Racial and Ethnic Relations in the twenty-first Century.” First, we raise questions about their framing of the problem with current scholarship – are immigration/ethnicity and race scholars talking past each other or are they having more fundamental disagreements? Second, we raise questions about their critique of the “the race literature” – do too many of us ignore questions of agency and inclusion? Finally, we raise questions about the stability and utility of the concepts they deploy (“race” and “ethnicity”) and draw on recent scholarship that has argued that we need new language or frameworks to adequately describe the reality on the ground.     

Suitability of Molluscs as Bioindicators for Meadow‐ and Flood‐Channels of the Elbe‐Floodplains

The goals of the subproject “molluscs” within the inter‐disciplinary research project “Indicator systems for the characterisation and prediction of ecological changes in floodplain systems” were: – develop further existing mollusc‐based indicator systems of site quality and to test their transferability, – characterise grassland sites within the recent floodplains of three study areas along the Elbe River, – analyse the relationships between indicator species‐/groups and abiotic parameters, – compile and use selected species traits in the analytical process. The results clearly show several characteristic species groups related to the hydrology of the sites (i.e. inundation and desiccation regime) and on to the degree of agricultural use. These dependencies can be interpreted by the simultaneous analysis of the species traits. “Models” are proposed, that are applicable to nature protection measures at the landscape scale. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The tyrosine corner: A feature of most greek key β-barrel proteins

The Tyr corner is a conformation in which a tyrosine (residue “Y”) near the beginning or end of an antiparallel β-strand makes an H bond from its side-chain OH group to the backbone NH and/or CO of residue Y – 3, Y – 4, or Y – 5 in the nearby connection. The most common “classic” case is a Δ4 Tyr corner (more than 40 examples listed), in which the H bond is to residue Y – 4 and the Tyr x1 is near ?60°. Y – 2 is almost always a glycine, whose left-handed β or very extended β conformation helps the backbone curve around the Tyr ring. Residue Y – 3 is in polyproline II conformation (often Pro), and residue Y – 5 is usually a hydrophobic (often Leu) that packs next to the Tyr ring. The consensus sequence, then, is LxPGxY, where the first x (the H-bonding position) is hydrophilic. Residues Y and Y – 2 both form narrow pairs of β-sheet H-bonds with the neighboring strand, Δ5 Tyr corners have a 1-residue insertion between the Gly and the Tyr, forming a β-bulge. One protein family has a Δ4 corner formed by a His rather than a Tyr, and several examples use Trp in place of Tyr. For almost all these cases, the protein or domain is a Greek key β-barrel structure, the Tyr corner ends a Greek key connection, and it is well-conserved in related proteins. Most low-twist Greek key β-barrels have 1 Tyr corner. “Reverse” Δ4 Tyr corners (H bonded to Y + 4) and other variants are described, all less common and less conserved. It seems likely that the more classic Tyr corners (Δ4, Δ5, and Δ3 Tyr, Trp, or His) contribute to the stability of a Greek key connection over a hairpin connection, and also that they may aid in the process of folding up Greek key structures.     

Racialization: a defense of the concept

This paper defends the concept of racialization against its critics. As the concept has become increasingly popular, questions about its meaning and value have been raised, and a backlash against its use has occurred. I argue that when “racialization” is properly understood, criticisms of the concept are unsuccessful. I defend a definition of racialization and identify its companion concept, “racialized group.” Racialization is often used as a synonym for “racial formation.” I argue that this is a mistake. Racial formation theory is committed to racial ontology, but racialization is best understood as the process through which racialized – rather than racial – groups are formed. “Racialization” plays a unique role in the conceptual landscape, and it is a key concept for race eliminativists and anti-realists about race.     

The ontogenetical and supposed phylogenetical fate of the parietal muscles in the Ctenostomata (Bryozoa)

A new term, “trophon”, has been introduced for the feeding and sexually propagating unit in the stolonate ctenostomes; the “stolon” and the “trophon” represent “sukzooids”, because they are homologous only to parts of the autozooids in the uniserially arranged ctenostomes. – The ontogeny of the muscles, especially the parietal muscles, has been studied in 17 species of ctenostomatous bryozoans belonging to different sub-groups of this order; the main effort was directed toward the details of the differentiations in living animals (14 of the investigated species). In various species of the Ctenostomata two separate sets of parietal muscles develop – probably as a consequence of the elongation of the cystid; the functional parietal muscles in the trophons of the stolonial forms are homologous to the secondary parietal muscles found in several uniserial ctenostomes. Contrary to the supposition by Soule (1954) in the different families of the serially arranged forms the muscles appear in different sequences during the development of the zooid and partly have different ontogenetical fates. Neither the “Carnosa” nor the “Paludicellea” (s. 1.) nor the “Stolonifera” can be maintained as taxa with the argument of a similar ontogeny of the muscles. A detailed comparison regarding the fate of the parietal muscles (and the polypide anlage) showed similarities between certain of the uniserial to either some of the stolonial, the sheet like, or the cystid-fusing forms suggesting a separate evolutionary origin of the advanced forms in those groups of the serially growing forms. – A new family, Pottsiellidae fam. nov., has been introduced and defined.     

Imprecise naming: the anadromous and the sea spawning threespine stickleback should be discriminated by names

Two ecological forms of the threespine stickleback Gasterosteus aculeatus – a strictly marine form and an anadromous form – are often merged in the literature as a single “marine” form. Because we know virtually nothing of the life style of the two oceanic ecotypes in the sea and consequently nothing on reproductive isolation and gene flow I argue for a precise use of the ecological terms “marine” and “anadromous” for these two ecotypes. These terms should be self-describing. The frequent use of terms incorrectly describing intraspecific variation and life style of ecotypes can bias studies on community composition and interactions of populations.     

Sex Cells: Gender and the Language of Bacterial Genetics

Between 1946 and 1960, a new phenomenon emerged in the field of bacteriology. “Bacterial sex,” as it was called, revolutionized the study of genetics, largely by making available a whole new class of cheap, fast-growing, and easily manipulated organisms. But what was “bacterial sex?” How could single-celled organisms have “sex” or even be sexually differentiated? The technical language used in the scientific press – the public and inalienable face of 20th century science – to describe this apparently neuter organism was explicit: the cells “copulated,” had “intimate contract,” “conjugal unions,” and engaged in “ménage ã trois” relationships. And yet, to describe bacteria as sexually reproducing organisms, the definition of sex itself had to change. Despite manifold contradictions and the availability of alternative language, the notion of sexually active (even promiscuous) single-celled organisms has persisted, even into contemporary textbooks on cell biology and genetics. In this paper I examine the ways in which bacteria were brought into the genetic fold, sexualized, and given gender; I also consider the issues underlying the durability of “bacterial sex.”     

Biofuels – challenges & chances: How biofuel development can benefit from advanced process technology

The presented article highlights the process of biofuel production with a special focus on bioethanol. After a short introduction to the “problems” of biofuels – the “first generation” biofuels (in regards to their competition to feed and food production) and the “second generation” biofuels (in regards to the required more complex process technology) − the different steps in the process from natural resources towards the final product are presented and the underlying biotechnological challenges discussed: the pre-treatment of the natural resources followed by the biotechnological processes of hydrolysis and fermentation. Topics such as enzyme screening for efficient or even multi-step hydrolysis as well as microbial strain selection under process conditions and the optimization of the anaerobic fermentative conversion of the saccharides to bioethanol are discussed. Optimizing the production of bioethanol to be competitive with petrochemical fuels is the main challenge for the underlying process development.