Microbial production of 1,3-propanediol

1,3-Propanediol (1,3-PD) production by fermentation of glycerol was described in 1881 but little attention was paid to this microbial route for over a century. Glycerol conversion to 1,3-PD can be carried out by Clostridia as well as Enterobacteriaceae. The main intermediate of the oxidative pathway is pyruvate, the further utilization of which produces CO₂, H₂, acetate, butyrate, ethanol, butanol and 2,3-butanediol. In addition, lactate and succinate are generated. The yield of 1,3-PD per glycerol is determined by the availability of NADH₂, which is mainly affected by the product distribution (of the oxidative pathway) and depends first of all on the microorganism used but also on the process conditions (type of fermentation, substrate excess, various inhibitions). In the past decade, research to produce 1,3-PD microbially was considerably expanded as the diol can be used for various polycondensates. In particular, polyesters with useful properties can be manufactured. A prerequisite for making a “green” polyester is a more cost-effective production of 1,3-PD, which, in practical terms, can only be achieved by using an alternative substrate, such as glucose instead of glycerol. Therefore, great efforts are now being made to combine the pathway from glucose to glycerol successfully with the bacterial route from glycerol to 1,3-PD. Thus, 1,3-PD may become the first bulk chemical produced by a genetically engineered microorganism. Received: 12 January 1999 / Received revision: 9 March 1999 / Accepted: 14 March 1999     

Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution.

BACKGROUND: Bacteriorhodopsin (bR) from Halobacterium salinarum is a proton pump that converts the energy of light into a proton gradient that drives ATP synthesis. The protein comprises seven transmembrane helices and in vivo is organized into purple patches, in which bR and lipids form a crystalline two-dimensional array. Upon absorption of a photon, retinal, which is covalently bound to Lys216 via a Schiff base, is isomerized to a 13-cis,15-anti configuration. This initiates a sequence of events - the photocycle - during which a proton is transferred from the Schiff base to Asp85, followed by proton release into the extracellular medium and reprotonation from the cytoplasmic side. RESULTS: The structure of bR in the ground state was solved to 1.9 A resolution from non-twinned crystals grown in a lipidic cubic phase. The structure reveals eight well-ordered water molecules in the extracellular half of the putative proton translocation pathway. The water molecules form a continuous hydrogen-bond network from the Schiff-base nitrogen (Lys216) to Glu194 and Glu204 and includes residues Asp85, Asp212 and Arg82. This network is involved both in proton translocation occurring during the photocycle, as well as in stabilizing the structure of the ground state. Nine lipid phytanyl moieties could be modeled into the electron-density maps. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of single crystals demonstrated the presence of four different charged lipid species. CONCLUSIONS: The structure of protein, lipid and water molecules in the crystals represents the functional entity of bR in the purple membrane of the bacteria at atomic resolution. Proton translocation from the Schiff base to the extracellular medium is mediated by a hydrogen-bond network that involves charged residues and water molecules.     

Arsenic disrupts cellular levels of p53 and mdm2: a potential mechanism of carcinogenesis.

The antitumor protein p53 plays a critical role in DNA repair. Inorganic arsenic exposure is associated with a wide variety of human tumors, particularly of the skin. To investigate how inorganic arsenic might interfere with DNA repair and lead to greater incidence of hyperkeratosis and skin tumors, we exposed human keratinocytes (HaCaT) to environmentally relevant concentrations of arsenite for 14 days. Arsenite reduced p53 levels while concomitantly increasing the p53 regulatory protein mdm2 levels in a dose- and time-dependent manner. We propose the disruption of the p53-mdm2 loop regulating cell cycle arrest as a model for arsenic-related skin carcinogenesis and it may be important in tumors with elevated mdm2 levels.     

Memory dynamics in the honeybee

Reward learning in honeybees initiates a sequence of events which leads to long-lasting memory passing through multiple phases of transient memories. The study of memory dynamics is performed at the behavioral (both natural foraging behavior and appetitive conditioning), neural circuit and molecular levels. The results of these combined efforts lead to a model which assumes five kinds of sequential memories, each characterized by a set of behavioral and mechanistic properties. It is argued that these properties, although reflecting general characteristics of step-wise memory formation, are adapted to the species-specific adaptations in natural behavior, here to foraging at scattered and unreliable food sources. Accepted: 12 May 1999     

I smell where you walked – how chemical cues influence movement decisions in ants

Interactions between animals are not restricted to direct encounters. Frequently, individuals detect the proximity of others through cues unintentionally left by others, such as prey species assessing predation risk based on indirect predator cues. However, while the importance of indirect cues in predator–prey interactions has been intensely studied, their role in interactions among competitors, and their consequences for community structure, are little known to date. Ant communities are usually structured by aggressive interactions between competing species. Responding to cues of others should be useful to avoid competitors or discover food sources. In ants and other insects, such cues include chemical footprints, which they leave while walking. Here, we investigated how different ant species respond to footprints of others. Ant colonies were confronted with footprints of other colonies or species, and the workers chose between cue‐bearing and cue‐free areas. Moreover, we determined the chemical composition of footprints, and compared the absolute quantities of footprint and cuticular hydrocarbons. Ants of the species Lasius niger avoided footprints of non‐nestmate conspecifics, and tended to avoid footprints of two other species. We suggest that they avoided encounters with competitors to reduce costly fights. In contrast, three other ant species approached allospecific footprints, which may represent eavesdropping to find resources discovered by others. Three of the four ant species responded differently to nestmates and non‐nestmate footprints either through footprint‐following or antennation behavior. The chemical composition of footprints was species‐specific and largely congruent to cuticular hydrocarbons. Footprint quantities left by single workers represented 1/170 to 1/64 of the quantity of their cuticular hydrocarbons. We showed that chemical footprints represent an important cue for behavioral decisions in ants. The ability to identify and respond to chemical footprints may represent an important strategy for insects to cope with competing species or colonies in their habitat.     

Temporal nitric oxide dynamics in the paranasal sinuses during humming.

In this study, the temporal shape of voice-induced nitric oxide (NO) signals in exhaled air has been investigated in eight healthy individuals by means of laser magnetic resonance spectroscopy. The results of the experimental part have been compared with calculated signals obtained by using a simple one-compartment model of the paranasal sinuses. In the experimental part, a rapidly increasing NO concentration has been found when the subjects started humming. After reaching a maximum, the emission starts to decrease with the shape of an exponential decay and finally reaches a constant level. The time constant of this decay (NO washout) is 3.0 +/- 1.2 s. The peak height of the NO emission during humming increases when the time between two humming processes increases. When no voice-induced NO emission takes place, the NO concentration in the paranasal sinuses rebuilds again to a maximum concentration. The typical time constant for the NO recovery is 4.5 +/- 3.2 min. A three-compartment model defining exactly the geometry and anatomy of the paranasal sinuses has been developed that is based on three main assumptions of the NO dynamics: 1) constant NO production of the epithelium in the sinuses; 2) the rate of the chemical reaction of NO with the epithelium of the paranasal sinuses is proportional to the NO concentration; and 3) the emission of NO from the sinuses (volume/s) is proportional to the NO concentration. It is shown that the three-compartment model under the experimental conditions can be reduced to a one-compartment model, which describes the complete temporal behavior of the NO exchange.     

A segmental maximum a posteriori approach to genome-wide copy number profiling

MOTIVATION: Copy number profiling methods aim at assigning DNA copy numbers to chromosomal regions using measurements from microarray-based comparative genomic hybridizations. Among the proposed methods to this end, Hidden Markov Model (HMM)-based approaches seem promising since DNA copy number transitions are naturally captured in the model. Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis. RESULTS: We introduce a novel Segmental Maximum A Posteriori approach, SMAP, for DNA copy number profiling. Our method is based on discrete-index Hidden Markov Modeling and incorporates genomic distance and overlap between clones. We exploit a priori information through user-controllable parameterization that enables the identification of copy number deviations of various lengths and amplitudes. The model parameters may be inferred at a genome-wide scale to avoid overfitting of model parameters often resulting from chromosome-wise model inference. We report superior performances of SMAP on synthetic data when compared with two recent methods. When applied on our new experimental data, SMAP readily recognizes already known genetic aberrations including both large-scale regions with aberrant DNA copy number and changes affecting only single features on the array. We highlight the differences between the prediction of SMAP and the compared methods and show that SMAP accurately determines copy number changes and benefits from overlap consideration.     

The genetic structure of the mountain forest butterfly Erebia euryale unravels the late Pleistocene and postglacial history of the mountain coniferous forest biome in Europe

The distribution of the mountain coniferous forest biome in Europe throughout time is not sufficiently understood. One character species of this habitat type is the large ringlet, Erebia euryale well reflecting the extension of this biome today, and the genetic differentiation of this species among and within mountain systems may unravel the late Pleistocene history of this habitat type. We therefore analysed the allozyme pattern of 381 E. euryale individuals from 11 populations in four different European mountain systems (Pyrenees, Alps, Carpathians, Rila). All loci analysed were polymorphic. The mean F(ST) over all samples was high (20%). Furthermore, the mean genetic distance among samples was quite high (0.049). We found four different groups well supported by cluster analyses, bootstraps and hierarchical variance analyses: Pyrenees, western Alps, eastern Alps and southeastern Europe (Carpathians and Rila). The genetic diversity of the populations was highest in the southeastern European group and stepwise decreased westwards. Interestingly, the populations from Bulgaria and Romania were almost identical; therefore, we assume that they were not separated by the Danube Valley, at least during the last ice age. On the contrary, the differentiation among the three western Alps populations was considerable. For all these reasons, we assume that (i) the most important refugial area for the coniferous mountain forest biome in Europe has been located in southeastern Europe including at least parts of the Carpathians and the Bulgarian mountains; (ii) important refugial areas for this biome existed at the southeastern edge of the Alps; (iii) fragments of this habitat types survived along the southwestern Alps, but in a more scattered distribution; and (iv) relatively small relicts have persisted somewhere at the foothills of the Pyrenees.     

Experimental and computational studies of two new mono- and dinuclear iridium complexes containing a Buchwald biphenyl phosphine ligand

The reaction of [(η⁴-1,5-C₈H₁₂)₂Ir₂(μ-Cl)₂] with 2-di-t-butylphosphino-2′-methylbiphenyl (t-Bu₂Pbiph^Me) in the presence of AgBF₄ afforded the dichlorido-bridged Ir–Ag complex [(η⁴-1,5-C₈H₁₂)Ir(μ-Cl)₂Ag(t-Bu₂Pbiph^Me)] (1) which was fully characterized by a single crystal X-ray diffraction study. Sequential treatment of the diiridium precursor first with the silver salt and then with the phosphine yielded cyclometalated [(η⁴-1,5-C₈H₁₂)Ir(t-Bu₂Pbiph^Me–H⁺)] (2). Detailed DFT calculations gave evidence that the phosphine ligand of 2 forms a strained four-membered iridaheterocycle through orthometalation rather than a sterically congested six-membered chelate structure through C–H activation on the remote phenyl ring. The phosphonium salt [t-Bu₂P(H)biph^Me]BF₄ was isolated as a by-product of the preparations of 1 and 2; its crystal structure was determined.