The effects of 1α,25-dihydroxyvitamin D3 on matrix metalloproteinase and prostaglandin E2 production by cells of the rheumatoid lesion

The biologically active metabolite of vitamin D₃, 1α,25-dihydroxyvitamin D₃ [1α,25(OH)₂D₃], acts through vitamin D receptors, which were found in rheumatoid tissues in the present study. IL-1β-activated rheumatoid synovial fibroblasts and human articular chondrocytes were shown to respond differently to exposure to 1α,25(OH)₂D₃, which has different effects on the regulatory pathways of specific matrix metalloproteinases and prostaglandin E₂.     

Prediction in evolutionary systems

Despite its explanatory clout, the theory of evolution has thus far compiled a modest record with respect to predictive power—that other major hallmark of scientific theories. This is considered by many to be an acceptable limitation of a theory that deals with events and processes that are intrinsically random (and historic). However, whether this is an inherent restriction or simply the sign of an incomplete theory is an open question. In an attempt to help answer that question, we propose a classification scheme for several types of prediction that might occur with regard to evolutionary systems, then explore the nature of these predictions in a system that simulates the evolution of neural architectures. This provides a platform from which to consider the relevance of such observations for real biological systems and illuminates a variety of key issues pertaining to prediction in those environments.     

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

The Statistical Mechanics for an Extended Nonlinear Epigenetic Dynamics. I

An extension of the control equations discussed by Goodwin is proposed which allows for arbitrary strong coupling and for arbitrary parallel coupling of metabolic pools and genetic loci. It is demonstrated that these generalized control equations can be put into canonical form and further that Liouville's theorem applies. In addition, it is demonstrated that after a suitable canonical transformation the resulting partition function can be solved in closed form, and this result, as well as that for the mean energy, is exhibited. Some remarks appropriate to additional extensions are presented.     

Molecular phylogenetics and reproductive incompatibility in a complex of cryptic species of aphid parasitoids

We infer the phylogeny of a complex of cryptic species and populations of parasitic wasps and examine how reproductive incompatibility maps onto the molecular phylogeny. We used four nuclear (28S-D2, ITS1, ITS2, ArgK) and two mitochondrial (COI, COII) gene regions to analyze relationships among populations in the Aphelinus varipes species complex (Hymenoptera: Aphelinidae) from throughout Eurasia (France, Georgia, Israel, China, Korea and Japan) and from three aphid hosts (Aphis glycines, Diuraphis noxia and Rhopalosiphum padi; Hemiptera: Aphididae). A combined analysis of 21 genotypes of Aphelinus resulted in six most-parsimonious trees, and successive approximations character-weighting selected two of these as best supported by the data. All six gene regions were necessary to fully resolve the relationships among taxa. Four clades within the A. varipes complex were distinguished: (1) Aphelinus kurdjumovi, (2) Aphelinus hordei, (3) Aphelinus atriplicis, Aphelinus varipes, and Aphelinus albipodus, and (4) Aphelinus certus (populations from China, Korea, and Japan). Based on rates of nucleotide substitutions, these clades diverged between 78 and 526 thousand years ago during a period of repeated glaciations in Eurasia. In laboratory crosses, A. kurdjumovi, A. hordei, and A. varipes were reproductively incompatible with one another and all other populations. A. atriplicis was incompatible with these three species, but not with A. certus. The populations of A. certus from China, Japan, and Korea were reproductively compatible with one another but not with the other populations. Thus, with one exception, entities that were phylogenetically distinct were also reproductively incompatible with one another. Our evidence on molecular differentiation and reproductive incompatibility supports recognition of at least five cryptic species in the A. varipes complex. We discuss likely reasons for the high rate of speciation in this complex.     

Biosynthesis of the tigloyl esters of Datura: Cis-trans isomerism

Datura innoxia plants were wick fed with angelic acid-[1-¹⁴C] and l-isoleucine-[U-¹⁴C] to act as a positive control. After 7 days the root alkaloids 3α-tigloyloxytropane, 3α,6β-ditigloyloxytropane, and 3α,6β-ditigloyloxytropan-7β-ol were isolated and it was determined that angelic acid is not a precursor for the tigloyl moiety of these alkaloids. Tiglic acid-[1-¹⁴C] which was fed via the roots to hydroponic cultures of Datura innoxia, was incorporated to a considerable degree after 8 days.     

Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein

Photoswitchable distance constraints in the form of photoisomerizable chemical cross-links offer a general approach to the design of reversibly photocontrolled proteins. To apply these effectively, however, one must have guidelines for the choice of cross-linker structure and cross-linker attachment sites. Here we investigate the effects of varying cross-linker structure on the photocontrol of folding of the Fyn SH3 domain, a well-studied model protein. We develop a theoretical framework based on an explicit-chain model of protein folding, modified to include detailed model linkers, that allows prediction of the effect of a given linker on the free energy of folding of a protein. Using this framework, we were able to quantitatively explain the experimental result that a longer, but somewhat flexible, cross-linker is less destabilizing to the folded state than a shorter more rigid cross-linker. The models also suggest how misfolded states may be generated by cross-linking, providing a rationale for altered dynamics seen in nuclear magnetic resonance analyses of these proteins. The theoretical framework is readily portable to any protein of known folded state structure and thus can be used to guide the design of photoswitchable proteins generally.     

Modelling the dynamic spatio-temporal response of predators to transient prey patches in the field

The spatio-temporal dynamics of two aphid species ( Metopolophium dirhodum and Sitobion avenae ) and a generalist predator ( Pterostichus melanarius ) were observed in a field-scale study using a grid of 256 sampling locations with a 12-m spacing. Using Spatial Analysis by Distance Indices we demonstrate that populations show ephemeral spatial pattern at the field scale. We observed a positive, lagged beetle response to this aphid pattern; conversely, the aphids displayed a negative, lagged response to beetle spatial pattern. Examination of the local structure of the spatio-temporal dynamics revealed a strong response by the beetle population to aphid patches. The temporal structure of spatial associations between the species shows a strong correspondence with those from a conceptual model of predator–prey spatial interaction. The spatially coupled dynamics were sufficiently strong for the predator to have a negative effect on the intrinsic rate of increase of their prey.     

Biosynthesis of podophyllotoxin in Linum album cell cultures

Cell cultures of Linum album Kotschy ex Boiss. (Linaceae) showing high accumulation of the lignan podophyllotoxin (PTOX) were established. Enzymological studies revealed highest activities of phenylalanine ammonia-lyase, cinnamyl alcohol dehydrogenase, 4-hydroxycinnamate:CoA ligase and cinnamoyl-CoA:NADP oxidoreductase immediately prior to PTOX accumulation. To investigate PTOX biosynthesis, feeding experiments were performed with [2-¹³C]3′,4′-dimethoxycinnamic acid, [2-¹³C]3′,4′-methylenedioxycinnamic acid (MDCA), [2-¹³C]3′,4′,5′-trimethoxycinnamic acid, [2-¹³C]sinapic acid, [2-¹³C]- and [2,3-¹³C₂]ferulic acid. Analysis of the metabolites by HPLC coupled to tandem mass spectrometry revealed incorporation of label from ferulic acid into PTOX and deoxypodophyllotoxin (DOP). In addition, MDCA was also unambiguously incorporated intact into PTOX. These observations suggest that in L. album both ferulic acid and methylenedioxy-substituted cinnamic acid can be incorporated into lignans. Furthermore, it appears that, in this species, the hydroxylation of DOP is a rate-limiting point in the pathway leading to PTOX. Electronic supplementary material to this article is available at and is accessible for authorized users. Electronic Publication