Distribution, abundance, behavior and metabolism of Periphylla periphylla, a mesopelagic coronate medusa in a Norwegian fjord

The distribution, behavior and metabolism of the mesopelagic jellyfish, Periphylla periphylla (Péron & Lesueur), were investigated in Lurefjorden, Norway. Field studies, conducted in 1998–1999 with plankton nets and a remotely operated vehicle, indicated that 80-90% of the dense (up to 2.5 m^–3) population migrated 200–400 m vertically each day throughout the year. In situ observations with red light revealed that swimming rates and feeding activity varied with age and time of day. Detection of turbulence and contact with surfaces caused this medusa to conceal one or all of its tentacles in the stomach or to shed nematocyst-laden tissue from the tentacles. Stomachs of medusae collected with nets were often full of prey entangled with the sloughed tissue. Stomachs of medusae captured individually with ROV samplers were empty or contained only a few prey in their stomachs (typically, 1–4 copepods Calanus spp. or chaetognaths Eukrohnia hamata Möbius per medusa). Low rates (0.4–5.6 l O₂ mg C^–1 h^–1) of oxygen consumption of P. periphylla suggested that this species was sustained by relatively few (1–34) prey d^–1.     

A single ancient origin of brood parasitism in African finches: implications for host-parasite coevolution

Robust phylogenies for brood-parasitic birds, their hosts, and nearest nesting relatives provide the framework to address historical questions about host-parasite coevolution and the origins of parasitic behavior. We tested phylogenetic hypotheses for the two genera of African brood-parasitic finches, Anomalospiza and Vidua, using mitochondrial DNA sequence data from 43 passeriform species. Our analyses strongly support a sister relationship between Vidua and Anomalospiza, leading to the conclusion that obligate brood parasitism evolved only once in African finches rather than twice, as has been the conventional view. In addition, the parasitic finches (Viduidae) are not recently derived from either weavers (Ploceidae) or grassfinches (Estrildidae), but represent a third distinct lineage. Among these three groups, the parasitic finches and estrildids, which includes the hosts of all 19 Vidua species, are sister taxa in all analyses of our full dataset. Many characters shared by Vidua and estrildids, including elaborate mouth markings in nestlings, unusual begging behavior, and immaculate white eggs, can therefore be attributed to common ancestry rather than convergent evolution. The host-specificity of mouth mimicry in Vidua species, however, is clearly the product of subsequent host-parasite coevolution. The lineage leading to Anomalospiza switched to parasitizing more distantly related Old World warblers (Sylviidae) and subsequently lost these characteristics. Substantial sequence divergence between Vidua and Anomalospiza indicates that the origin of parasitic behavior in this clade is ancient (approximately 20 million years ago), a striking contrast to the recent radiation of extant Vidua. We suggest that the parasitic finch lineage has experienced repeated cycles of host colonization, speciation, and extinction through their long history as brood parasites and that extant Vidua species represent only the latest iterations of this process. This dynamic process may account for a significantly faster rate of DNA sequence evolution in parasitic finches as compared to estrildids and other passerines. Our study reduces by one the tally of avian lineages in which obligate brood parasitism has evolved and suggests an origin of parasitism that involved relatively closely related species likely to accept and provide appropriate care to parasitic young. Given the ancient origin of parasitism in African finches, ancestral estrildids must have been parasitized well before the diversification of extant Vidua, suggesting a long history of coevolution between these lineages preceding more recent interactions between specific hosts and parasites.     

福建省肖叶甲科物种垂直分布与区域分化的比较研究(鞘翅目:肖叶甲科)

研究福建省肖叶甲科物种的垂直分布和区域分化,通过对闽西北武夷山垂直分布的调查分析,认为肖叶甲科垂直分布呈现３个基本分带;海拔３５０ｍ以下,３５０－１２００ｍ和海拔１２００ｍ以上,其中以中间带种类最丰富,与闽中戴云山对比,发现物种的垂直分布范围（上限和下限）在戴云山比在武夷山高,有明显的上移趋势,主要影响因素是南北不同气流的作用和植被垂直分布变化,综合平面分布与垂直分布结果,福建省肖甲科区系以适应于     

The insect immune protein scolexin is a novel serine proteinase homolog

Scolexin is a coagulation-provoking plasma protein induced in response to bacterial or viral infection of larval Manduca sexta, a large lepidopterous insect. Here we report the isolation and sequencing of two cDNA clones that code for scolexin isoforms sharing 80% sequence identity. The scolexin sequences have low but recognizable sequence similarity to members of the chymotrypsin family and represent a new subfamily of chymotrypsin-like serine proteinases. Comparison with known structures reveals the conservation of key catalytic residues and a possible specificity for small nonpolar residues. Most remarkable is the absence of a canonical activation peptide cleavage site. This suggests that the regulation of scolexin activity will involve a novel activation mechanism.     

Bicelle-based liquid crystals for NMR-measurement of dipolar couplings at acidic and basic pH values

It is demonstrated that mixtures of ditetradecyl- phosphatidylcholine or didodecyl-phoshatidylcholine and dihexyl- phosphatidylcholine in water form lyotropic liquid crystalline phases under similar conditions as previously reported for bicelles consisting of dimyristoyl-phosphatidylcholine (DMPC) and dihexanoyl- phosphatidylcholine (DHPC). The carboxy-ester bonds present in DMPC and DHPC are replaced by ether linkages in their alkyl analogs, which prevents acid- or base-catalyzed hydrolysis of these compounds. 15N-1H dipolar couplings measured for ubiquitin over the 2.3–10.4pH range indicate that this protein retains a backbone conformation which is very similar to its structure at pH 6.5 over this entire range.     

TROSY-based HNCO pulse sequences for the measurement of 1HN-15N, 15N-13CO, 1HN-13CO, 13CO-13Cα and 1HN-13Cα dipolar couplings in 15N, 13C, 2H-labeled proteins

HNCO-based 3D pulse schemes are presented for measuring ¹HN-¹⁵N,¹⁵N-¹³CO, ¹HN-¹³CO,¹³CO-¹³C and ¹HN-¹³C dipolar couplings in ¹⁵N,¹³C,²-labeled proteins. The experiments are based on recently developed TROSY methodology for improving spectral resolution and sensitivity. Data sets recorded on a complex of Val, Leu, Ile (1 only) methyl protonated ¹⁵N,¹³C,²H-labeled maltose binding protein and -cyclodextrin as well as ¹⁵N,¹³C,²H-labeled human carbonic anhydrase II demonstrate that precise dipolar couplings can be obtained on proteins in the 30–40 kDa molecular weight range. These couplings will serve as powerful restraints for obtaining global folds of highly deuterated proteins.     

Reflective properties of different eyespot types in dinoflagellates

The reflective properties of different types of dinoflagellate eyespots were investigated using confocal laser scanning microscopy in the epireflection contrast mode. Although the eyespots studied differed with respect to localization (cytosol or plastid) and organization of the globule layer(s), all types effectively absorbed and reflected blue-green laser light (principal lines of 488/514 nm). The relative orientation of the eyespot surface towards the light source strongly influenced the reflective properties. Maximal reflection occurred when the eyespot surface was approximately perpendicular to the light source and rapidly decreased at increasing angles of light incidence. Horizontal and vertical optical sectioning of live and fixed cells resolved differences in the reflection patterns. Focusing of reflected light on the basal portion of the longitudinal flagellum was observed for the cytosolic eyespot of Glenodinium sp. and the triple membrane-bounded eyespot of Peridinium foliaceum, presumably a vestige of a host plastid. This flagellum is thought to be mainly involved in mediating orientational movement responses. In contrast, the reflection patterns obtained from the eyespot of Woloszynskia pascheri, which represents the third and most commonly observed dinoflagellate eyespot type within a plastid, point to only minor focusing. Reflection signals could be followed a considerable distance into the sulcus in all cases, indicating that in dinoflagellate eyespots, irrespective of the presumed receptor location (plasma membrane overlying the eyespot and/or the basal part of the longitudinal flagellum), back reflection of non-absorbed light can enhance the excitation probability of the photoreceptor(s). Such a combined reflection/absorption screen allows maximal contrast modulation and will, in conjunction with the specialized geometry of the dinoflagellate eyespots, increase the directionality of these eyespot aparatuses considerably.     

Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins

MALECON is a progressive combinatorial procedure for multiple alignments of protein structures. It searches a library of pairwise alignments for all three-protein alignments in which a specified number of residues is consistently aligned. These alignments are progressively expanded to include additional proteins and more spatially equivalent residues, subject to certain criteria. This action involves superimposing the aligned proteins by their hitherto equivalent residues and searching for additional Calpha atoms that lie close in space. The performance of MALECON is illustrated and compared with several extant multiple structure alignment methods by using as test the globin homologous superfamily, the OB and the Jellyrolls folds. MALECON gives better definitions of the common structural features in the structurally more diverse proteins of the OB and Jellyrolls folds, but it yields comparable results for the more similar globins. When no consistent multiple alignments can be derived for all members of a protein group, our procedure is still capable of automatically generating consistent alignments and common core definitions for subgroups of the members. This finding is illustrated for proteins of the OB fold and SH3 domains, believed to share common structural features, and should be very instrumental in homology modeling and investigations of protein evolution.     

Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information

In this paper a systematic attempt has been made to develop a better method for predicting alpha-turns in proteins. Most of the commonly used approaches in the field of protein structure prediction have been tried in this study, which includes statistical approach "Sequence Coupled Model" and machine learning approaches; i) artificial neural network (ANN); ii) Weka (Waikato Environment for Knowledge Analysis) Classifiers and iii) Parallel Exemplar Based Learning (PEBLS). We have also used multiple sequence alignment obtained from PSIBLAST and secondary structure information predicted by PSIPRED. The training and testing of all methods has been performed on a data set of 193 non-homologous protein X-ray structures using five-fold cross-validation. It has been observed that ANN with multiple sequence alignment and predicted secondary structure information outperforms other methods. Based on our observations we have developed an ANN-based method for predicting alpha-turns in proteins. The main components of the method are two feed-forward back-propagation networks with a single hidden layer. The first sequence-structure network is trained with the multiple sequence alignment in the form of PSI-BLAST-generated position specific scoring matrices. The initial predictions obtained from the first network and PSIPRED predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. The final network yields an overall prediction accuracy of 78.0% and MCC of 0.16. A web server AlphaPred (http://www.imtech.res.in/raghava/alphapred/) has been developed based on this approach.