A new type of semi-empirical molecular orbital method for large molecules.

A new type of molecular orbital method is proposed. It is applicable to large molecules containing large conjugated substructures. Only π-electrons in the conjugated part, but all-valence electrons in the non-conjugated part of a molecule, are taken into account explicitly. The Fock matrix elements are evaluated from the semi-empirical values employed in the existing all-valence-electron methods. The examples presented here suggest that the new type of MO method predicts electronic structures which are quite similar to those obtained by complete semi-empirical MO calculations. This new method may make it possible to reasonably well describe the electronic structure of, and interaction between, large molecules using considerably less computation time and core storage than the complete calculation analogs.     

Exploitation of biotechnology in a large company

Almost from the outset, most large companies saw the 'new biotechnology' not as a new business but as a set of very powerful techniques that, in time, would radically improve the understanding of biological systems. This new knowledge was generally seen by them as enhancing the process of invention and not as a substitute for tried and tested ways of meeting clearly identified targets. As the knowledge base grows, so the big-company response to biotechnology becomes more positive. Within ICI, biotechnology is now integrated into five bio-businesses (Pharmaceuticals, Agrochemicals, Seeds, Diagnostics and Biological Products). Within the Central Toxicology Laboratory it also contributes to the understanding of the mechanisms of toxic action of chemicals as part of assessing risk. ICI has entered two of these businesses (Seeds and Diagnostics) because it sees biotechnology making a major contribution to the profitability of each.     

Chitin deacetylases: new, versatile tools in biotechnology

Chitin deacetylases have been identified in several fungi and insects. They catalyse the hydrolysis of N-acetamido bonds of chitin, converting it to chitosan. Chitosans, which are produced by a harsh thermochemical procedure, have several applications in areas such as biomedicine, food ingredients, cosmetics and pharmaceuticals. The use of chitin deacetylases for the conversion of chitin to chitosan, in contrast to the presently used chemical procedure, offers the possibility of a controlled, non-degradable process, resulting in the production of novel, well-defined chitosan oligomers and polymers.     

Small molecules as geneticists

Stuart Schreiber and colleagues show how small molecule sensitivities can be used to probe the natural genetic variation present in populations of organisms.     

Small HDL particles containing two apoA-I molecules are precursors in vivo to medium and large HDL particles containing three and four apoA-I molecules in nonhuman primates.

We hypothesized that small HDL particles, containing two apoA-I molecules but no apoA-II (LpAI), may be converted in vivo into medium and large HDL particles, containing three or four apoA-I molecules, respectively, and that more conversion will occur in animals with higher HDL concentrations. To test this possibility, kinetic studies of small LpAI were performed in African green monkeys with either high plasma HDL cholesterol concentrations (120 +/- 36 mg/dl, mean +/- SD, n = 3) or low plasma HDL cholesterol concentrations (40 +/- 13 mg/dl, n = 3). Tracer small LpAI was purified, without ultracentrifugation, by immunoaffinity and gel filtration. After injection, the specific activity of apoA-I in small, medium, and large HDL, consisting of both LpAI and LpAI:AII particles, was followed. A multicompartmental model was developed with the simultaneous analysis of urine and plasma turnover data for the kinetics of apoA-I in small, medium, and large HDL. These analyses indicated that small HDL is converted to either medium or large HDL with little or no interconversion of medium HDL and large HDL. Much of the metabolic conversion of small HDL occurs in a sequestered pool, effectively outside the circulating plasma, in a unidirectional manner before reentering the circulating plasma as medium or large HDL. The mean fractional catabolic rate of apoA-I in small, medium, and large HDL was not different comparing the high and low HDL group. In contrast, the mean production rate of apoA-I was greater in the high HDL group compared with the low HDL group. These data support the hypothesis that the plasma concentration of HDL is primarily a function of the rate of appearance of apoA-I in medium and large HDL.     

Small molecules and chemical tools at the interface

As our understanding of the molecular mechanisms driving complex biological processes grows, the role of chemical biology will continue to expand. The 2008 American Society for Biochemistry and Molecular Biology meeting showcased recent progress in the field of chemical biology while simultaneously pointing toward the future of research at the interface between chemistry and biology.     

The biofreezer,a new contained freezing equipment in biotechnology

Summary The Biofreezer has been designed for freezing biomass or cell-suspensions in the laboratory, pilot and large scale biotechnology under hygienic and biosafe conditions. The principle is based on the freezing of biomass drops on the surface of a liquid nitrogen bath to form small beads, which are harvested automatically. The application is presented as a part of the Roferon-A production (leukocyte interferon -2a Roche), representing a physically contained system extending from 1000 l fermenter through continuous centrifugation to the frozen biomass beads. The freezing process in the Biofreezer is extremely fast and complete and the beads can be thawed instantaneously. Comparisons with other freezing systems are described.     

Small molecules: the lexicon of biodiversity

The extent of microbial diversity in the Biosphere is not known (and probably never will be!). One aspect of this diversity is the production of biologically active small molecules; within the Streptomycetes alone this may be millions of compounds with an extraordinary diversity and complexity of structure. First recognised as pigments and later, in the 1950s, as antibiotics, it is now clear that the small molecules produced by microbes have many different functions in nature. This huge collection of biologically active compounds with various properties has been used as pharmaceuticals and agriculturals. They also interact with proteins and RNA with high specificity and have been shown to be regulators and effectors of diverse biochemical reactions. The use of small molecules (other than as pharmaceuticals) deserves to be explored in order to exploit microbial biotechnology to the full.     

A rhelogical separator for very large DNA molecules.

We present a rheological separation method for DNA molecules in which their deformability is used to advantage. This is the "radial migration method"; here we present experimental verification of the principle, theory having been reported elsewhere. The main conclusions are: (1) the theory is reasonably good; (2) radial migration is highly sensitive to the molecular weight, as predicted, and (3) intact T2 DNA (1.25 X 108 daltons) can be made to migrate about three centimeters in less than three hours.     

Surface charging by large multivalent molecules. Extending the standard Gouy-Chapman treatment.

Traditionally, Gouy-Chapman theory has been used to calculate the distribution of ions in the diffuse layer next to a charged surface. In recent years, the same theory has found application to adsorption (incorporation, partitioning) of charged peptides, hormones, or drugs at the membrane-water interface. Empirically it has been found that an effective charge, smaller than the physical charge, must often be used in the Gouy-Chapman formula. In addition, the large size of these molecules can be expected to influence their adsorption isotherms. To improve evaluation techniques for such experiments, comparatively simple extensions of the standard Gouy-Chapman formalism have been studied which are based on a discrete charge virial expansion. The model allows for the mobility of charged groups at the interface. It accounts for finite size of the adsorbed macromolecules and for discrete charge effects arising from pair interactions in the interface plane. In contrast to previous discrete charge treatments this model nearly coincides with the Gouy-Chapman formalism in the case where the adsorbing molecules are univalent. Large discrepancies are found for multivalent molecules. This could explain the reduced effective charges needed in the standard Gouy-Chapman treatment. The reduction factor can be predicted. The model is mainly limited to low surface coverage, typical for the adsorption studies in question.     

NMR spectroscopy of large molecules and multimolecular assemblies in solution.

New strategies and technical advances in NMR spectroscopy and biochemical methods for isotope labeling have enabled solution NMR studies of biomacromolecular systems of 100 kDa and larger. Recent progress has been made, in particular, with techniques for sequential resonance assignments, novel approaches for the direct observation of hydrogen bonds in nucleic acids and proteins, and segmental isotope labeling.     

小RNA分子与精子发生调控

近来研究发现小RNA(small RNAs)可作为转录后及翻译水平上基因表达调节的重要调节因子,利用小RNA来阐明调节精子发生的分子机制取得了显著进展。这些小RNA主要分为3类,即小干扰RNA(siRNA)、微小RNA(miRNA)以及与piwi蛋白相互作用的RNA(piRNA)。在减数分裂和精子发生过程中,小RNA具有多种生物学功能,如利用siRNA体外转染或体内注射来敲低特定基因从而研究该基因在精子发生过程中的作用;miRNA可能参与精子发生中有丝、减数及后减数分裂阶段的基因表达调节;piRNA主要参与调节雄性生殖细胞减数及后减数分裂的过程,在精子发生中起抑制反转录转座子(retrotransposons)的作用。文章对小RNAs合成、作用机制、功能及展望等最新进展进行了综述。