广西西部二叠纪生物礁中的海绵、水螅动物化石

广西西部田林,凌云、凤山地区二叠纪生物礁的造礁生物－海绵、水螅化石保存完美。文中描述串管海绵7属：Stylothalamia,Lichuanospongia,Tebagathalamia,Imbricatocoelia,Intrasporeocoelia,Rhabdactinia,Lingyunocoelis;纤维海绵3属：Peronidella,Intratubospongia,Cavusonella;水螅1属Radiotrabeculopora以及海托盘类Calathium,其中Lingyunocoelia spherica为新属新种,Lichuanospongia guangxiensis为新种,其它均为中国南方二叠纪生物礁内常见分子。Senowbari-Daryan(1990)提出以Discosiphonella来代替Cystauletes,Ascosymplegma,Lichunospongia3属,但Lichuanospongia的房室形状和中央腔缺失横板（泡沫板）显著不同于Discosiphonella,因此文中仍把Lichuanospongia视作独立属,Lingyuncoelia gen.nov。与Sollasia,Girtyocoelia相似,但房室外壁缺乏任何种类的穿孔,因此明显不同于后两属,作者仍把Radiotrabeculopora视为螅纲内的一属,而没有归于纤维海绵目,因为它最明显的特征是发育分布较规则的放射状支柱（不能视为骨纤构造）,且那些纵向分布的出水管实际上应视为支柱之间的沟道。     

Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: Strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species

Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.     

Properties of ecotones: Evidence from five ecotones objectively determined from a coastal vegetation gradient

Abstract. Several properties have been suggested to be characteristic of ecotones, but their prevalence has rarely been tested. We sampled five ecotones to seek evidence on seven generalizations that are commonly made about ecotones: vegetational sharpness, physiognomic change, occurrence of a spatial community mosaic, many exotic species, ecotonal species, spatial mass effect, and species richness higher or lower than either side of the ecotone. The ecotones were in a sequence from scattered mangroves, through salt marsh, rush‐marsh, scrub, woodland, to pasture. We developed a method to objectively define, by rapid vegetational change, the position and depth of an ecotone, identifying five ecotones. Their positions were consistent across three sampling schemes and two spatial grain sizes. One ecotone is a switch ecotone, produced by positive feedback between community and environment. Another is anthropogenic, due to clearing for agriculture. Two others are probably environmental in cause, and one may be largely a relict environmental ecotone. Sharp changes in species composition occurred. Three ecotones were associated with a change in plant physiognomy. In two, the ecotone was located just outside a woodland canopy, in the zone influenced by the canopy. Community mosaicity was evident at only one ecotone. There were few strictly ecotonal species; many species occurred more frequently within ecotones than in adjacent vegetation, but there were never significantly more ecotonal species than expected at random. There was little evidence for the spatial mass effect reducing ecotonal sharpness, or leading to higher species richness within ecotones. Species richness was higher than in the adjacent habitat in only one ecotone. It seems that supposedly characteristic ecotone features depend on the particular ecological situation, and the ecology of the species present, rather than being intrinsic properties of ecotones.     

Participation of galactosylceramide and sulfatide in glycosynapses between oligodendrocyte or myelin membranes

The two major glycosphingolipids of myelin, galactosylceramide (GalC) and sulfatide (SGC), interact with each other by trans carbohydrate-carbohydrate interactions. They face each other in the apposed extracellular surfaces of the multilayered myelin sheath produced by oligodendrocytes (OLs). Multivalent galactose and sulfated galactose, in the form of GalC/SGC-containing liposomes or silica nanoparticles conjugated to galactose and galactose-3-sulfate, interact with GalC and SGC in the membrane sheets of OLs in culture. This stimulus results in transmembrane signaling, loss of the cytoskeleton and clustering of membrane domains, suggesting that GalC and SGC could participate in glycosynapses between apposed OL membranes or extracellular surfaces of mature myelin. Such glycosynapses may be important for myelination and/or myelin function.     

Formation of molecular species of mitochondrial cardiolipin: 2. A mathematical model of pattern formation by phospholipid transacylation

Formation of the unique molecular species of mitochondrial cardiolipin requires tafazzin, a transacylase that exchanges acyl groups between phospholipid molecular species without strict specificity for acyl groups, head groups, or carbon positions. However, it is not known whether phospholipid transacylations can cause the accumulation of specific fatty acids in cardiolipin. Here, a model is shown in linear algebra representation, in which acyl specificity emerges from the transacylation equilibrium of multiple molecular species, provided that different species have different free energies. The model defines the conditions and energy terms, under which transacylations may generate the characteristic composition of mitochondrial cardiolipin. It is concluded that acyl-specific cardiolipin patterns could arise from phospholipid transacylations in the tafazzin domain, even if tafazzin itself does not have substrate specificity.     

Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism

Previous work used hydrogen exchange (HX) experiments in kinetic and equilibrium modes to study the reversible unfolding and refolding of cytochrome c (Cyt c) under native conditions. Accumulated results now show that Cyt c is composed of five individually cooperative folding units, called foldons, which unfold and refold as concerted units in a stepwise pathway sequence. The first three steps of the folding pathway are linear and sequential. The ordering of the last two steps has been unclear because the fast HX of the amino acid residues in these foldons has made measurement difficult. New HX experiments done under slower exchange conditions show that the final two foldons do not unfold and refold in an obligatory sequence. They unfold separately and neither unfolding obligately contains the other, as indicated by their similar unfolding surface exposure and the specific effects of destabilizing and stabilizing mutations, pH change, and oxidation state. These results taken together support a sequential stabilization mechanism in which folding occurs in the native context with prior native-like structure serving to template the stepwise formation of subsequent native-like foldon units. Where the native structure of Cyt c requires sequential folding, in the first three steps, this is found. Where structural determination is ambiguous, in the final two steps, alternative parallel folding is found.     

Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation

Bovine spongiform encephalopathy (BSE) is a fatal neurodegenerative prion disease affecting cattle that is transmissible to humans, manifesting as a variant of Creutzfeldt-Jakob disease (vCJD) likely following the consumption of meat contaminated with BSE prions. High-affinity antibodies are a prerequisite for the development of simple, highly sensitive and non-invasive diagnostic tests that are able to detect even small amounts of the disease-associated PrP conformer (PrP(Sc)). We describe here the affinity maturation of a single-chain Fv antibody fragment with a binding affinity of 1 pM to a peptide derived from the unstructured region of bovine PrP (BoPrP (90-105)). This is the tightest peptide-binding antibody reported to date and may find useful application in diagnostics, especially when PrP(Sc) is pretreated by denaturation and/or proteolysis for peptide-like presentation. Several rounds of directed evolution and off-rate selection with ribosome display were performed using an antibody library generated from a single PrP binder with error-prone PCR and DNA-shuffling. As the correct determinations of affinities in this range are not straightforward, competition biosensor techniques and KinExA methods were both applied and compared. Structural interpretation of the affinity improvement was performed based on the crystal structure of the original prion binder in complex with the BoPrP (95-104) peptide by modeling the corresponding mutations.     

Deletions in the A(L) region of the h4xb plasma membrane Ca(2+) pump. High apparent affinity for Ca(2+) of a deletion mutant resembling the alternative spliced form h4zb

Mutants of the plasma membrane Ca(2+) pump (human isoform 4xb) with deletions in the linker between domain A and transmembrane segment M3 (A(L) region) were constructed and expressed in Chinese hamster ovary cells. The total or partial removal of the amino acid segment 300-349 did not change the maximal Ca(2+) transport activity, but mutants with deletions involving residues 300-338 exhibited a higher apparent affinity for Ca(2+) than the wild type h4xb enzyme. Deletion of the putative acidic lipid interacting sequence (residues 339-349) had no observable functional consequences. The removal of either residues 300-314 or 313-338 resulted in a similar increase in the apparent Ca(2+) affinity of the pump although the increase was somewhat lower than that obtained by the deletion 300-349 suggesting that both deletions affected the same structural determinant. The results show that alterations in the region of the alternative splicing site A change the sensitivity to Ca(2+) of the human isoform 4 of the PMCA.     

Met-enkephalin binding to opiate receptors is not functionally coupled to biodegradation

Using synaptosomal rat brain membranes, the degradation of Met-enkephalin in both free and receptor-bound form was measured, together with the dissociation of Met-enkephalin from the receptors. The results show that the degradation rate of initially receptor-bound Met-enkephalin is significantly smaller than either the rate of dissociation from the receptors or that of the degradation of free Met-enkephalin. These data suggest that intact Met-enkephalin dissociates from the receptors and then it becomes a target for the same membrane-associated peptidases that split free Met-enkephalin. This view is supported by the good fitness of the measured degradation of initially receptor-bound Met-enkephalin to the predicted degradation curve calculated from the dissociation rate of receptor-bound Met-enkephalin and the degradation rate of free Met-enkephalin.     

The complete mitochondrial genome of Sasakia funebris (Leech) (Lepidoptera: Nymphalidae) and comparison with other Apaturinae insects

Sasakia funebris, a member of the lepidopteran family, Nymphalidae (superfamily Papilionoidea) is a rare species and is found only in some areas of South China. In this study, the 15,233 bp long complete mitochondrial genome of S. funebris was determined, and harbors the gene arrangement identical to all other sequenced lepidopteran insects. The nucleotide composition of the genome is highly A + T biased, accounting for 81.2%. All protein-coding genes (PCGs) start with typical ATN codons, except for COI which begins with the CGA codon. All tRNAs have a typical clover-leaf secondary structure, except for tRNA^Ser(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The S. funebris A + T-rich region of 370 bp contains several features common to the Lepidoptera insects, including the motif ATAGA followed by a 19 bp poly-T stretch, and two tandem repeats consisting of 18 bp repeat units and 14 bp repeat units. The phylogenetic analyses of Apaturinae based on mitogenome sequences showed: (S. funebris + Sasakia charonda) + (Apatura metis + Apatura ilia). This result is consistent with the morphological classification.