Heme methyl 1H chemical shifts as structural parameters in some low-spin ferriheme proteins

 The different paramagnetic shifts of the four methyl groups in ferriheme proteins have been described as being due to the effect of the axial ligand nodal plane orientation. An equation, heuristically found and theoretically explained, describing the relation between contact and pseudocontact shifts and the position of the axial ligand(s) has been derived for bis-histidine ferriheme proteins and for cyanide-histidine ferriheme proteins. The values of the heuristic parameters contained in the equations were found by fitting the shifts of bovine cytochrome b ₅ and several bis-histidine cytochromes c ₃ and histidine-cyanide systems. The agreement between the observed and the calculated shifts was found to be good. Therefore, by taking advantage of this study, information on the position of the axial ligands, that can be used as a constraint for structure determination, can be obtained from the shifts of the methyl protons. Received: 13 April 1999 / Accepted: 4 June 1999     

Local control of peptide conformation: Stabilization of cis proline peptide bonds by aromatic proline interactions

In the native state of proteins there is a marked tendency for an aromatic amino acid to precede a cis proline. There are also significant differences between the three aromatic amino acids with Tyr exhibiting a noticeably higher propensity than Phe or Trp to precede a cis proline residue. In order to study the role that local interactions play in these conformation preferences, a set of tetrapeptides of the general sequence acetyl-Gly-X-Pro-Gly-carboxamide (GXPG), where X = Tyr, Phe, Trp, Ala, or cyclohexyl alanine, were synthesized and studied by nmr. Analysis of the nmr data shows that none of the peptides adopt a specific backbone structure. Ring current shifts, the equilibrium constants, the Van't Hoff enthalpy, and the measured rate of cis-trans isomerization all indicate that the cis proline conformer is stabilized by favorable interactions between the aromatic ring and the proline residue. Analysis of the side chain conformation of the aromatic residue and analysis of the chemical shifts of the pyrrolidine ring protons shows that the aromatic side chain adopts a preferred conformation in the cis form. The distribution of rotamers and the effect of an aromatic residue on the cis-trans equilibrium indicate that the preferred conformation is populated to approximately 62% for the Phe containing peptide, 67% for the Tyr containing peptide, and between 75 and 80% for the Trp containing peptide. The interaction is unaffected by the addition of 8M urea. These local interactions favor an aromatic residue immediately preceding a cis proline, but they cannot explain the relative propensities for Phe-Pro, Tyr-Pro, and Trp-Pro cis peptide bonds observed in the native state of proteins. In the model peptides the percentage of the cis proline conformer is 21% GYPG while it is 17% for GFPG. This difference is considerably smaller than the almost three to one preponderance observed for cis Tyr-Pro peptide bonds vs cis Phe-Pro peptide bonds in the protein database. © 1998 John Wiley & Sons, Inc. Biopoly 45: 381–394, 1998     

Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins

The pseudocontact shifts of NMR signals, which arise from the magnetic susceptibility anisotropy of paramagnetic molecules, have been used as structural constraints under the form of a pseudopotential in the SANDER module of the AMBER 4.1 molecular dynamics software package. With this procedure, restrained energy minimization (REM) and restrained molecular dynamics (RMD) calculations can be performed on structural models by using pseudocontact shifts. The structure of the cyanide adduct of the Met80Ala mutant of the yeast iso-1-cytochrome c has been used for successfully testing the calculations. For this protein, a family of structures is available, which was obtained by using NOE and pseudocontact shifts as constraints in a distance geometry program. The structures obtained by REM and RMD calculations with the inclusion of pseudocontact shifts are analyzed. Proteins 29:68–76, 1997. © 1997 Wiley-Liss, Inc.     

实验增温对藏北高寒草甸植物繁殖物候的影响

全球气候变暖对高寒和极地地区的植物物候产生强烈的影响。该研究主要关注增温条件下藏北高寒草甸不同功能型植物繁殖时间(生殖物候)的改变。实验采用开顶箱式增温方法, 对3个主要功能群浅根-早花、浅根-中花和深根-晚花植物的现蕾、开花、结实时间进行观测。研究结果表明: (1)增温导致了土壤水分胁迫, 显著推迟了浅根-早花植物高山嵩草(Kobresia pygmaea)的繁殖时间; (2)增温显著提前了浅根-中花植物钉柱委陵菜(Potentilla saundersiana)和深根晚花植物紫花针茅(Stipa purpurea)和矮羊茅(Festuca coelestis)的繁殖时间; (3)增温没有显著影响浅根-中花植物楔叶委陵菜(Potentilla cuneata)和深根-晚花植物无茎黄鹌菜(Youngia simulatrix)的繁殖时间; (4)增温缩短了3种类型植物的开花持续时间。这些结果显示增温改变了藏北高寒草甸群落中多数物种的繁殖时间, 这预示着在未来更热更干的生长季, 青藏高原高寒草甸系统的植物物候格局可能会被重塑。     

Bioturbation as Driver of Zooplankton Recruitment,Biodiversity and Community Composition in Aquatic Ecosystems

In an experimental study we assessed if benthic bioturbating invertebrates affect the recruitment (hatching) of zooplankton from the sediment, and if this effect persists as differences in the zooplankton community in the water column, that is, if bioturbation quantitatively stimulates benthic–pelagic coupling. We investigated the effects of four different benthic invertebrates (Asellus aquaticus, Chironomus plumosus, Tubifex tubifex in the presence or absence of the predator Sialis lutaria). In total, 45 zooplankton taxa hatched from the sediment and the hatching success of some of these was dependent on the species identity of the bioturbating invertebrate. The predator Sialis reduced the abundance of all three invertebrate species, but tended to positively influence the zooplankton recruitment rates, possibly through increasing the activity of the bioturbating invertebrates. The most striking effect of bioturbation on the hatching and pelagic zooplankton community properties was that, on average, 11% more species hatched in the Asellus treatment than in any other treatment. This was also mirrored in the zooplankton water column community where, on average, 7% more species established a viable population in treatments with Asellus as bioturbator. In a complementary field survey, Asellus was more common in littoral than in profundal sediments. Because Asellus strongly affected recruitment of zooplankton in our experiment, we argue that bioturbation may partly explain why recruitment of resting stages of both phyto- and zooplankton is generally higher in littoral than in profundal areas.     

Biological control of marine invasive species: cautionary tales and land-based lessons

Biological control (biocontrol) has successfully regulated pest populations in terrestrial agroecosystems, but it has also caused negative unintended consequences for native species. Marine biologists and resource managers have recently published a growing number of proposals to include biocontrol in integrated pest management programs in oceans, seas and estuaries. Here, I review six ecologically and taxonomically diverse case studies of marine biocontrol programs at various stages of planning and implementation. Proposals include viral or microbial control of harmful algal blooms, predatory control of the ctenophore Mnemiopsis leidyi in the Black Sea, parasitic regulation of the European green crab Carcinus maenas, castration by ciliates of the seastar Asterias amurensis in Australia, herbivory of the toxic green alga Caulerpa taxifolia in the Mediterranean by sacoglossan sea slugs, and insect biocontrol by the planthopper Prokelesia marginata to ameliorate ecological impacts of the saltmarsh cordgrass Spartina alterniflora. Where data exist, I evaluate these examples in terms of lessons marine invasion biologists can glean from the rich history of terrestrial biocontrol, and explicitly contrast agroecosystems with invaded marine habitats. Host specificity cannot be guaranteed in the marine biocontrol proposals examined. Feasible alternatives to classical biocontrol in the marine realm should be emphasized, including more investment in invasion prevention tools, early detection and eradication while invasions are small, and increased attention to native natural enemies to control exotic pests. Biocontrol in marine habitats is risky: it poses many more uncertainties and has a much sparser history than its counterpart on land.     

Damage released prey alarm substances or predator odours? Risk assessment by an aquatic oligochaete

Although the abilities of prey to detect and respond to chemical substances associated with a predator have been widely reported, the factors promoting the evolution of responses to prey alarm cues vs. predator odours are still vague. In this article, we combined field research with laboratory experiments to explore which chemical substance associated with predator activity (predator odour, conspecific or heterospecific alarm substances) induces defence responses in the aquatic oligochaete Stylaria lacustris, which is vulnerable to common littoral predators. The field results indicated that predators injure the oligochaetes and a great proportion, up to 45% of individuals in the population, were found to be damaged. The results of the laboratory experiments revealed that chemical odours from damselfly larvae feeding on S. lacustris did not induce the defence response in the oligochaetes. On the contrary, oligochaetes detected and responded to alarm substances from damaged conspecifics alone and substances from damaged cladoceran Daphnia magna. We discussed conditions favouring the responses to damage released prey alarm cues instead of predator odours in Stylaria lacustris. Our data suggest that the selection of responses to alarm cues from damaged prey vs. predator odours may be dependent on three factors: (1) non-species-specific predation, (2) divergence of food niche of the different stages of the predator and (3) complex food web with multiple predators. Handling editor: S. Declerk     

CheckShift improved: fast chemical shift reference correction with high accuracy

The construction of a consistent protein chemical shift database is an important step toward making more extensive use of this data in structural studies. Unfortunately, progress in this direction has been hampered by the quality of the available data, particularly with respect to chemical shift referencing, which is often either inaccurate or inconsistently annotated. Preprocessing of the data is therefore required to detect and correct referencing errors. In an earlier study we developed CheckShift, a program for performing this task automatically. Now we spent substantial effort in improving the running time of the CheckShift algorithm, which resulted in an running time decrease of 90%, thereby achieving equivalent quality to the former version of CheckShift. The reason for the running time decrease is twofold. Firstly we improved the search for the optimal re-referencing offset considerably. Secondly, as CheckShift is based on a secondary structure prediction from the amino acid sequence (formally PsiPred was used), we evaluated a wide range of available secondary structure prediction programs focusing on the special needs of the CheckShift algorithm. The results of this evaluation prove empirically that we can use faster secondary structure prediction programs than PsiPred without sacrificing CheckShift’s accuracy. Very recently Wang and Markley (2009) gave a small list of extreme outliers of the former version of the CheckShift web-server. Those were due to the empirical reduction of the search space implemented in the old version. The new version of CheckShift now gives very similar results to RefDB and LACS for all outliers mentioned in Table 1 of Wang and Markley (2009).     

Multiple glacial refugia and complex postglacial range shifts of the obligatory woodland plant Polygonatum verticillatum (Convallariaceae)

The phylogeography of typical alpine plant species is well understood in Europe. However, the genetic patterns of boreo-montane species are mostly unstudied. Therefore, we analysed the AFLPs of 198 individuals of Polygonatum verticillatum over a major part of its European distribution. We obtained a total of 402 reproducible fragments, of which 96.8% were polymorphic. The average Φ _ST over all samples was high (73.0%). The highest number of private fragments was observed in the Cantabrian Mountains; the highest genetic diversities of the populations were detected in populations from the Alps. BAPS, Principal Coordinates and Cluster analyses revealed a deep split between the Cantabrian population and all other samples. The latter further distinguished two major groups in western and eastern Europe. These results suggest a complex biogeographical history of P. verticillatum . The Cantabrian population was most probably isolated for the longest time. Furthermore, putative glacial survival centres might have existed in the western group around the glaciated Alps and in the eastern group in the foothills of the Carpathian and Balkan mountain systems. The origin of the Scandinavian populations is still unresolved, but an origin from the southeastern Alps or the western Balkans appears the most likely scenario.     

Behavioural environments and niche construction: the evolution of dim-light foraging in bees

Most bees forage for floral resources during the day, but temporal patterns of foraging activity vary extensively, and foraging in dim-light environments has evolved repeatedly. Facultative dim-light foraging behaviour is known in five of nine families of bees, while obligate behaviour is known in four families and evolved independently at least 19 times. The light intensity under which bees forage varies by a factor of 10⁸, and therefore the evolution of dim-light foraging represents the invasion of a new, extreme niche. The repeated evolution of dim-light foraging behaviour in bees allows tests of the hypothesis that behaviour acts as an evolutionary pacemaker. With the exception of one species of Apis , facultative dim-light foragers show no external structural traits that are thought to enable visually mediated flight behaviour in low-light environments. By contrast, most obligate dim-light foragers show a suite of convergent optical traits such as enlarged ocelli and compound eyes. In one intensively studied species ( Megalopta genalis ) these optical changes are associated with neurobiological changes to enhance photon capture. The available ecological evidence suggests that an escape from competition for pollen and nectar resources and avoidance of natural enemies are driving factors in the evolution of obligate dim-light foraging.