Topological characteristics of helical repeat proteins.

The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem repeats of an alpha-helical structural unit, creating extended superhelical structures that are ideally suited to create a protein recognition interface.     

Comparative seed ecology of the endangered shrub, Pimelea spicata and a threatening weed, Bridal Creeper: Smoke, heat and other fire-related germination cues

Summary Pimelea spicata R. Br. is a nationally listed endangered Australian shrub threatened with extinction by habitat fragmentation and environmental weed invasion. Bridal Creeper (Asparagus asparagoides L. W. Wight) is the primary weed threat to the largest remaining populations of P. spicata in the Cumberland Plain. Fire, as part of an integrated pest management program, offers the potential to stimulate P. spicata populations while controlling Bridal Creeper. It is important, therefore, to understand how the components of fire affect the germination and growth of both species. Using laboratory experiments we investigated the effects of smoke, heat, ash and/or light on the germination of P. spicata and Bridal Creeper. We found a significant promotive effect of smoke and indication of an inhibitory heat shock (90°C for 10 min) effect on the germination of P. spicata seeds. The response of Bridal Creeper seeds to the same factors was complex; while the results of one experiment suggested an inhibitory effect of smoke and a promotive effect of heat, subsequent trials were contradictory, implying that Bridal Creeper, like many weeds, is able to germinate under a wide range of environmental conditions. Other experiments investigated the optimal germination temperature and innate dormancy of P. spicata in the absence of fire‐related germination cues. Of the incubation temperatures investigated, the optimal diurnally fluctuating regime for P. spicata germinations was 10°C and 20°C in the night and day, respectively. The innate dormancy of freshly produced seeds disappeared after 3 months. In contrast to Bridal Creeper, we found a persistent germinable seed bank of about 97 P. spicata seeds/m² located in the top 5 cm of the soil profile. While fire alone is unlikely to kill Bridal Creeper plants, fire may help to manage local infestations of the weed by limiting germination and providing opportunity for herbicide treatment of regrowth.     

Two calcium‐binding chaperones from the fat body of the Colorado potato beetle,Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) involved in diapause

Molecular chaperones are crucial for the correct folding of newly synthesized polypeptides, in particular, under stress conditions. Various studies have revealed the involvement of molecular chaperones, such as heat shock proteins, in diapause maintenance and starvation; however, the role of other chaperones in diapause and starvation relatively is unknown. In the current study, we identified two lectin‐type chaperones with calcium affinity, a calreticulin (LdCrT) and a calnexin (LdCnX), that were present in the fat body of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) during diapause. Both proteins possessed an N‐globular domain, a P‐arm domain, and a highly charged C‐terminal domain, while an additional transmembrane domain was present in LdCnX. Phylogenetic analysis revealed distinction at the order level. Both genes were expressed in multiple tissues in larval and adult stages, and constitutively throughout development, though a starvation response was detected only for LdCrT. In females, diapause‐related expression analysis in the whole body revealed an upregulation of both genes by post‐diapause, but a downregulation by diapause only for LdCrT. By contrast, males revealed no alteration in their diapause‐related expression pattern in the entire body for both genes. Fat body‐specific expression analysis of both genes in relation to diapause revealed the same expression pattern with no alteration in females and downregulation in males by post‐diapause. This study suggests that calcium‐binding chaperones play similar and possibly gender‐specific roles during diapause.     

High cell density induces spontaneous bifurcations of dissolved oxygen controllers during CHO cell fermentations

High cell density cultures of CHO cells growing in a bioreactor under dissolved oxygen control were found to undergo spontaneous bifurcations and a subsequent loss of stability some time into the fermentation. This loss of stability was manifested by sustained and amplified oscillations in the bioreactor dissolved oxygen concentration and in the oxygen gas flow rate to the reactor. To identify potential biological and operational causes for the phenomenon, linear stability analysis was applied in a neighborhood of the experimentally observed bifurcation point. The analysis revealed that two steady state process gains, K(P1) and K(P2), regulated k(l)a and gas phase oxygen concentration inputs, respectively, and the magnitude of K(P1) was found to determine system stability about the bifurcation point. The magnitude of K(P1), and hence the corresponding open-loop steady state gain K(OL1), scaled linearly with the bioreactor cell density, increasing with increasing cell density. These results allowed the generation of a fermentation stability diagram, which partitioned K(C)-N operating space into stable and unstable regions separated by the loci of predicted critically stable controller constants, K(C,critical), as a function of bioreactor cell density. This consistency of this operating diagram with experimentally observed changes in system stability was demonstrated. We conclude that time-dependent increases in cell density are the cause of the observed instabilities and that cell density is the critical bifurcation parameter. The results of this study should be readily applicable to the design of a more robust controller.     

Consequences of a Government-Controlled Agricultural Price Increase on Fishing and the Coral Reef Ecosystem in the Republic of Kiribati

Background

Economic development policies may have important economic and ecological consequences beyond the sector they target. Understanding these consequences is important to improving these policies and finding opportunities to align economic development with natural resource conservation. These issues are of particular interest to governments and non-governmental organizations that have new mandates to pursue multiple benefits. In this case study, we examined the direct and indirect economic and ecological effects of an increase in the government-controlled price for the primary agricultural product in the Republic of Kiribati, Central Pacific.

Methods/Principal Findings

We conducted household surveys and underwater visual surveys of the coral reef to examine how the government increase in the price of copra directly affected copra labor and indirectly affected fishing and the coral reef ecosystem. The islands of Kiribati are coral reef atolls and the majority of households participate in copra agriculture and fishing on the coral reefs. Our household survey data suggest that the 30% increase in the price of copra resulted in a 32% increase in copra labor and a 38% increase in fishing labor. Households with the largest amount of land in coconut production increased copra labor the most and households with the smallest amount of land in coconut production increased fishing the most. Our ecological data suggests that increased fishing labor may result in a 20% decrease in fish stocks and 4% decrease in coral reef-builders.

Conclusions/Significance

We provide empirical evidence to suggest that the government increase in the copra price in Kiribati had unexpected and indirect economic and ecological consequences. In this case, the economic development policy was not in alignment with conservation. These results emphasize the importance of accounting for differences in household capital and taking a systems approach to policy design and evaluation, as advocated by sustainable livelihood and ecosystem-based management frameworks.     

A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr      

Selective hydroxylation of alkanes by an extracellular fungal peroxygenase

Fungal peroxygenases are novel extracellular heme-thiolate biocatalysts that are capable of catalyzing the selective monooxygenation of diverse organic compounds, using only H(2)O(2) as a cosubstrate. Little is known about the physiological role or the catalytic mechanism of these enzymes. We have found that the peroxygenase secreted by Agrocybe aegerita catalyzes the H(2)O(2)-dependent hydroxylation of linear alkanes at the 2-position and 3-position with high efficiency, as well as the regioselective monooxygenation of branched and cyclic alkanes. Experiments with n-heptane and n-octane showed that the hydroxylation proceeded with complete stereoselectivity for the (R)-enantiomer of the corresponding 3-alcohol. Investigations with a number of model substrates provided information about the route of alkane hydroxylation: (a) the hydroxylation of cyclohexane mediated by H(2)(18)(2) resulted in complete incorporation of (18)O into the hydroxyl group of the product cyclohexanol; (b) the hydroxylation of n-hexane-1,1,1,2,2,3,3-D(7) showed a large intramolecular deuterium isotope effect [(k(H)/k(D))(obs)] of 16.0 ± 1.0 for 2-hexanol and 8.9 ± 0.9 for 3-hexanol; and (c) the hydroxylation of the radical clock norcarane led to an estimated radical lifetime of 9.4 ps and an oxygen rebound rate of 1.06 × 10(11) s(-1). These results point to a hydrogen abstraction and oxygen rebound mechanism for alkane hydroxylation. The peroxygenase appeared to lack activity on long-chain alkanes (> C(16)) and highly branched alkanes (e.g. tetramethylpentane), but otherwise exhibited a broad substrate range. It may accordingly have a role in the bioconversion of natural and anthropogenic alkane-containing structures (including alkyl chains of complex biomaterials) in soils, plant litter, and wood.     

Nucleotide sequence and hormonal regulation of mouse glycerophosphate dehydrogenase mRNA during adipocyte and muscle cell differentiation

We have studied the structure and regulation of glycerophosphate dehydrogenase (GPD) mRNA during mouse adipocyte and muscle cell differentiation. This message has a size of 2.8 kilobases that includes a coding segment of 1050 bases and a large untranslated 3' end of about 1700 bases. There is a high degree of amino acid homology (91%) between the mouse adipocyte and rabbit muscle GPD proteins. GPD mRNA is not detected in myoblasts, but, as in adipogenesis, it is expressed upon differentiation into myotubes. The modulation of GPD mRNA by cyclic AMP analogues and tumor necrosis factor has been examined in both adipocytes and myotubes. Dibutyryl cAMP or 8-bromo-cAMP causes a large reduction of GPD mRNA levels in both cell types, with less than 20% remaining after 18 h of treatment. Tumor necrosis factor effects a dramatic and rapid reduction in GPD mRNA in fat cells and a slower but significant decrease in the level of this mRNA in muscle cells. These results indicate that GPD gene expression is linked to cell differentiation in both fat and muscle cells, and suggest certain similarities in hormonal modulation in both cell types.     

“Unblocking” Serum Activity <Emphasis Type="Italic">in vitro</Emphasis> in the Polyoma System may Correlate with Antitumour Effects of Antiserum <Emphasis Type="Italic">in vivo</Emphasis>

In a variety of tumour systems, individuals carrying progressively growing neoplasms have lymphoid cells with a specific cytotoxic effect on cultured tumour cells from the same individual^1–4. Since the sera of tumour-bearing individuals have been shown to prevent tumour cell destruction by immune lymphocytes in vitro^2,5–8 and since this serum blocking activity appears early in primary and transplant tumour development^5,7, it has been suggested that the appearance of this serum blocking activity might be responsible for the progressive growth of tumours in individuals having cytotoxic lymphocytes. Counteraction of this blocking activity would thus be of primary importance in facilitating the function of an already existing or bolstered cell-mediated immunity. The serum blocking activity might be inhibited in various ways, by preventing the formation of blocking antibody or by interfering with its action (“unblocking”), as demonstrated in Moloney sarcoma regressor sera⁹. This type of serum also has a therapeutic effect on Moloney sarcomas in vivo^10,11, which has been tentatively attributed to its unblocking activity^8,9 or, possibly, to a complement-dependent cytotoxicity¹⁰. Tumour growth in the Moloney sarcoma system, however, might be due in part to continuous recruitment of neoplastic cells by virus-induced transformation and so the therapeutic effect could be due to a virus-neutralizing serum activity^9,10.