Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories

Motivation: After 10-year investigations, the folding mechanismsof β-hairpins are still under debate. Experiments stronglysupport zip-out pathway, while most simulations prefer the hydrophobiccollapse model (including middle-out and zip-in pathways). Inthis article, we show that all pathways can occur during thefolding of β-hairpins but with different probabilities.The zip-out pathway is the most probable one. This is in agreementwith the experimental results. We came to our conclusions by38 100-ns room-temperature all-atom molecular dynamics simulationsof the β-hairpin trpzip2. Our results may help to clarifythe inconsistencies in the current pictures of β-hairpinfolding mechanisms. Contact: yxiao{at}mail.hust.edu.cn Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Anna Tramontano     

PETALIFERA HABEI, A NEW SPECIES FROM JAPAN ADDENDUM

Since Petalifera habei was described in the Proceedings, 34,1, 12–18, April 1960, I have received from Dr. K. Babaa short account of the same species in Publ. Seto. mar. biol.Lab. 7, 3, 337–338. December, 1959, under the title "Thegenus Petalifera and a new species, P. ramosa, from Japan".I was unaware that Dr. Baba intended to describe it. As hispaper antedates mine, his name, Petalifera ramosa, must replaceP. Habei.     

'ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data'

Smilde et al. Bioinformatics (2005), 21(13); 3043–3048 The above paper by Smilde et al. inappropriately quotes results     

Gut evacuation rates and ingestion rates of Eudiaptomus graciloides measured by means of the gut fluorescence method

Journal of Plankton Research, 8, 973–983, 1986 FIg. 2. Time-dependent changes in the gut content (percentageof initial ng pigment) of E. gro.ciloides at different temperaturesunder simultaneous feeding. Fig. 4. The relationship between instantaneous evacuation rateand temperature of E. graciloides. The regresston equation forfeeding animals: y = 0.0044 e(0.141 ) (r² = 0.90). For comparisonthe results of non-feeding animals are indicated with open circles.     

ERRATUM

The publishers apologize for the following errors, which appearedin Plant Geosensors by L. J. Audus (pp. 1051–1073): Page 1058, line 9: the expression should read P = (L²/D)/(l/q) Page 1068, paragraph (c) line 11: should read ‘reticulum, which was fairly uniformly peripheralin vertical roots, aggregated on the’     

Floral Initiation and Inflorescence Architecture: A Comparative View

Annals of Botany 100: 659–676, 2007 The     

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Motivation: Reliable structural modelling of protein–proteincomplexes has widespread application, from drug design to advancingour knowledge of protein interactions and function. This workaddresses three important issues in protein–protein docking:implementing backbone flexibility, incorporating prior indicationsfrom experiment and bioinformatics, and providing public accessvia a server. 3D-Garden (Global And Restrained Docking ExplorationNexus), our benchmarked and server-ready flexible docking system,allows sophisticated programming of surface patches by the uservia a facet representation of the interactors’ molecularsurfaces (generated with the marching cubes algorithm). Flexibilityis implemented as a weighted exhaustive conformer search foreach clashing pair of molecular branches in a set of 5000 modelsfiltered from around 340 000 initially. Results: In a non-global assessment, carried out strictly accordingto the protocols for number of models considered and model qualityof the Critical Assessment of Protein Interactions (CAPRI) experiment,over the widely-used Benchmark 2.0 of 84 complexes, 3D-Gardenidentifies a set of ten models containing an acceptable or bettermodel in 29/45 test cases, including one with large conformationalchange. In 19/45 cases an acceptable or better model is rankedfirst or second out of 340 000 candidates. Availability: http://www.sbg.bio.ic.ac.uk/3dgarden (server) Contact: v.lesk{at}ic.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Burkhard Rost     

Stem Photosynthesis not Pressurized Ventilation is Responsible for Light-enhanced Oxygen Supply to Submerged Roots of Alder (Alnus glutinosa)

Annals of Botany 96: 591–612, 2005 Unfortunately, the legend     

Tintinnids and other microzooplankton--seasonal distributions and relationships to resources and hydrography in a Maine estuary

Journal of Plankton Research, 9, 65–77, 1987. In Table II on page 70 the number of Tintinnopsis minuta foundat 0 m depth on 15 September 1981 should be 1200.     

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

Bioinformatics (2006) 22(23), 2968–2970 The authors would like     

Total and Component Carbon Fluxes of a Scots Pine Ecosystem from Chamber Measurements and Eddy Covariance

Annals of Botany 99: 345–353, 2007 The authors regret that the     

Hyperforin Accumulates in the Translucent Glands of Hypericum perforatum

Annals of Botany 99: 1097–1100, 2007 Unfortunately in Fig. 1D     

Effect of photoinhibition on algal photosynthesis: a dynamic model

Recent evidence from algal physiology and molecular biologyconfirms that photoinhibition is directly related to D1 proteindamage and recovery, and D1 protein damage leads to a decreasein electron transfer or an increase in turnover time of theelectron transfer chain. In this study, the turnover time ofthe electron transfer chain is defined as a function of therelative concentration of D1 protein in reaction centre II andthe photoinhibition processes due to D1 protein degradationare incorporated into a model of photosynthesis, initiated byDubinsky et al. (Plant Cell Physiol., 27, 1335–1349, 1986)and developed by Sakshaug et al. (Limnol. Oceanogr., 34, 198–205,1989). D1 protein damage is assumed to be both light and D1protein concentration dependent, and to be proportional to thecross-section of PSII (     

Parasitic Wasps Learn and Report Diverse Chemicals with Unique Conditionable Behaviors

Chemical Senses, 28, 545–549 Regrettably, an error occurred in Figure 3 of this     

UMBONIUM VESTIARIUM (L.) (GASTROPODA, TROCHACEA) AS THE FOOD SOURCE FOR NATICID GASTROPODS AND A STARFISH ON A MALAYSIAN SANDY SHORE

Umbonium vestiarium (L.) forms virtually the entire diet of3 (possibly 4) species of naticid snails and the starfish Astropectenvappa Mueller annd Troschel on some north Penang sandy shores.Umbonium comprises about 99% of numbers and tissue of macrofauna.Predation totalled some 1.75 Umbonium (ca. 33 mg dry tissue).m^-2.day^-1 across much of the downshore sand flats rising to 2.3Umbonium (ca. 45 mg). m^-2. day^-1 near MLWS. Natica maculosaLamarck comprised > 80% of the predators and took 77–94%of the Umbonium eaten. Natica antonii Phillippi alone addedto this toll on the upper reaches of the zone while Polinicesspp and Astropecten appear to have taken 12–14% of thetotal toll of Umbonium near MLWS. Total predation is indicatedat 237–327 kJ.m^-2. year^-1 across the shore and this representsalmost the total flow of energy from primary consumers to intertidalbenthic predators on such shores and accounts for some 15.6%(lower shore)—20.5% (upper shore) of total Umbonium production. (Received 10 September 1982;     

A simple shape characteristic of protein protein recognition

Bioinformatics (2007) 23(7), 789–792 The authors wish to apologize for the omission     

Analysis of Concentration-response Relationship for Enhanced Sugar Responses of the Chorda Tympani Nerve in the Diabetic db/db Mouse

Chorda tympani responses to sugars were greater in diabetic(db/db) than in non-diabetic control mice. A kinetic analysissuggested that the greater sugar responses in db/db mice wereunlikely due to the increased number of sugar receptors. Chem.Senses 21: 59–63, 1996.     

Influence of the 3'-UTR-length of mKIAA cDNAs and their Sequence Features to the mRNA Expression Level in the Brain

We have previously described the sequence features of 1500 mouseKIAA (mKIAA) genes in comparison with those of human KIAA genes(Okazaki, N., Kikuno, R., Inamoto, S., Hara, Y., Nagase, T.,Ohara, O., and Koga, H. 2002, DNA Res., 9, 179–188; Okazaki,N., Kikuno, R., Ohara, R., Inamoto, S., Aizawa, H., Yuasa, S.,Nakajima, D., Nagase, T., Ohara, O., and Koga, H. 2003, DNARes., 10, 35–48; Okazaki, N., Kikuno, R., Ohara, R., Inamoto,S., Koseki, H., Hiraoka, S., Saga, Y., Nagase, T., Ohara, O.,and Koga, H. 2003, DNA Res., 10, 167–180; and Okazaki,N., F-Kikuno, R., Ohara, R., Inamoto, S., Koseki, H., Hiraoka,S., Saga, Y., Seino, S., Nishimura, M., Kaisho, T., Hoshino,K., Kitamura, H., Nagase, T., Ohara, O., and Koga, H. 2004,DNA Res., 11, 205–218). To validate the orthologous relationshipbetween mKIAA and KIAA genes in detail, we examined their chromosomalpositions and evolutionary rate of synonymous substitutionsand confirmed that >93% of the mKIAA/KIAA gene pairs areorthologous. During the sequence analysis of mKIAA genes, wefound that 3'-untranslated region (3'-UTR) lengths of mKIAAand KIAA genes are extremely long. In the meanwhile, we havealso examined the tissue-specific expression of 1700 mKIAA genesusing cDNA microarray and verified predominantly their expressionin adult brain (Koga, H., Yuasa, S., Nagase, T., Shimada, K.,Nagano, M., Imai, K., Ohara, R., Nakajima, D., Murakami, M.,Kawai, M., Miki, F., Magae, J., Inamoto, S., Okazaki, N., Ohara,O. 2004, DNA Res., 11, 293–304). To connect these twoevidences, we statistically analysed the relationship betweenthem by using the mKIAA genes. Consequently, a positive correlationwas observed between the 3'-UTR lengths and the relative expressionintensities in adult brain. Furthermore, we searched sequenceelements in the 3'-UTR possibly related with their expressionand found some candidates regarding the brain-specific expression.     

Short Delay in Timing of Emergence Determines Establishment Success in Pinus sylvestris across Microhabitats

Annals of Botany 98: 1233–1240, 2006 Unfortunately the final sentence in the Results section