Left Column Research Articles

Genomic Selection Identifies Vertebrate Transcription Factor Fezf2 Binding Sites and Target Genes

Identification of transcription factor targets is critical to understanding gene regulatory networks. Here, we uncover transcription factor binding sites and target genes employing systematic evolution of ligands by exponential enrichment (SELEX). Instead of selecting randomly synthesized DNA oligonucleotides as in most SELEX studies, we utilized zebrafish genomic DNA to isolate fragments bound by Fezf2, an evolutionarily conserved gene critical for vertebrate forebrain development. This is, to our knowledge, the first time that SELEX is applied to a vertebrate genome. Computational analysis of bound genomic fragments predicted a core consensus binding site, which identified response elements that mediated Fezf2-dependent transcription both in vitro and in vivo. Fezf2-bound fragments were enriched for conserved sequences. Surprisingly, ∼20% of these fragments overlapped well annotated protein-coding exons. Through loss of function, gain of function, and chromatin immunoprecipitation, we further identified and validated eomesa/tbr2 and lhx2b as biologically relevant target genes of Fezf2. Mutations in eomesa/tbr2 cause microcephaly in humans, whereas lhx2b is a critical regulator of cell fate and axonal targeting in the developing forebrain. These results demonstrate the feasibility of employing genomic SELEX to identify vertebrate transcription factor binding sites and target genes and reveal Fezf2 as a transcription activator and a candidate for evaluation in human microcephaly.

Erratum: Computational study of the generation of crystal defects in a bcc metal target irradiated by short laser pulses [Phys. Rev. B77, 214108 (2008)

In two places on page 7 and in the caption of Fig. 7, the plane of the stacking fault (slip plane) is mistakenly identified as (100) instead of (101). The text should be as follows: “. . .the stacking fault is created by dividing the system into two parts by a (101) plane. . .” at the bottom of the left column on page 7; “. . .the atoms are allowed to relax in the direction perpendicular to the (101) slip plane. . .” at the top of the right column of page 7; “Generalized stacking fault energy, γGSF, for the (101) slip plane in bcc EAM Cr. . .” in the caption for Figure 7 on page 8. These are typing errors and they do not affect the results reported in the paper.

Highly Selective Tuning of a Silkworm Olfactory Receptor to a Key Mulberry Leaf Volatile

(Current Biology 19, 881–890; June 9, 2009) In this paper, we miscalculated absolute weight of an odorant based on a dilution factor. Through the entire manuscript, the dilution factor is correct, but the converted absolute amounts were 2-fold smaller than the correct values. On page 887, line 26 in the left column, 3 μl of 10−8 diluted solution should correspond to 30 pg, not 0.3 pg. Accordingly, in the last paragraph of the Results, the 0.3 pg–3 ng range should be 30 pg–300 ng. The fourth sentence of the Summary should read “a threshold of 30 pg from 20 cm distance.” In Figure 1C and the corresponding text, the odorant amounts should range from 30 ng to 30 μg. Although these errors do not affect our conclusions, the authors regret the miscalculation and apologize for any inconvenience that they might have caused. Highly Selective Tuning of a Silkworm Olfactory Receptor to a Key Mulberry Leaf VolatileTanaka et al.Current BiologyMay 7, 2009In BriefThe olfactory system plays an important role in the recognition of leaf volatiles during the search of folivore insects for a suitable plant host. For example, volatiles emitted by mulberry leaves trigger chemotaxis behavior in the silkworms Bombyx mori, and as a consequence, they preferentially reside on and consume mulberry leaves. Here, we aimed to identify natural chemoattractants and their corresponding olfactory receptors (Ors) involved in silkworm behavior to mulberry leaves. Full-Text PDF Open Archive

A Specific Two-pore Domain Potassium Channel Blocker Defines the Structure of the TASK-1 Open Pore

Two-pore domain potassium (K2P) channels play a key role in setting the membrane potential of excitable cells. Despite their role as putative targets for drugs and general anesthetics, little is known about the structure and the drug binding site of K2P channels. We describe A1899 as a potent and highly selective blocker of the K2P channel TASK-1. As A1899 acts as an open-channel blocker and binds to residues forming the wall of the central cavity, the drug was used to further our understanding of the channel pore. Using alanine mutagenesis screens, we have identified residues in both pore loops, the M2 and M4 segments, and the halothane response element to form the drug binding site of TASK-1. Our experimental data were used to validate a K2P open-pore homology model of TASK-1, providing structural insights for future rational design of drugs targeting K2P channels.

Attenuation of host NO production by MAMPs potentiates development of the host in the squid-vibrio symbiosis

Bacterial pathogens typically upregulate the host's production of nitric oxide synthase (NOS) and nitric oxide (NO) as antimicrobial agents, a response that is often mediated by microbe-associated molecular patterns (MAMPs) of the pathogen. In contrast, previous studies of the beneficial Euprymna scolopes/Vibrio fischeri symbiosis demonstrated that symbiont colonization results in attenuation of host NOS/NO, which occurs in high levels in hatchling light organs. Here, we sought to determine whether V. fischeri MAMPs, specifically lipopolysaccharide (LPS) and the peptidoglycan derivative tracheal cytotoxin (TCT), attenuate NOS/NO, and whether this activity mediates the MAMPs-induced light organ morphogenesis. Using confocal microscopy, we characterized levels of NOS with immunocytochemistry and NO with a NO-specific fluorochrome. When added exogenously to seawater containing hatchling animals, V. fischeri LPS and TCT together, but not individually, induced normal NOS/NO attenuation. Further, V. fischeri mutants defective in TCT release did not. Experiments with NOS inhibitors and NO donors provided evidence that NO mediates apoptosis and morphogenesis associated with symbiont colonization. Attenuation of NOS/NO by LPS and TCT in the squid-vibrio symbiosis provides another example of how the host's response to MAMPs depends on the context. These data also provide a mechanism by which symbiont MAMPs regulate host development.

Erratum: “Competition between Backbonding and Electron Correlation in Fe Cyanides”

We have found an error in the program code. Correcting the error, we have slightly readjusted the numerical values for the physical parameters. The calculated results for Case A have slightly been affected, as described below. However, the conclusions are never affected by this error. The error mentioned above was related to the calculation of the C–N molecular orbitals. After correcting the error, we have shifted the numerical values of N and for Case A by 0.5 eV, as listed in Tables I and VI, to reproduce the observed Fe 2pXAS. The shift in N has slightly affected both the energy levels of the molecular orbitals listed in Table I and the hybridization matrix elements listed in Table II. The shifts in N and have affected the energy levels listed in Tables III, IV, and V. The energy gap of the system has also been affected: in the 12-th line from the top of the left column on p. 114722-6, ‘‘1.42’’ should be changed to ‘‘1.15’’. However, we have not updated Figs. 2, 3, and 4, since the influence on them is small.

Erratum: Impact of soil compaction on root architecture, leaf water status, gas exchange and growth of maize and triticale seedlings [Plant Root Vol. 3 (2009) 10-16

The editorial office of Plant Root notes the following correction on behalf of the author. The second author in one of the cited papers was incorrect in the original article. [Page 11, left column, “O′Toole and Cruz 1983”; Page 16, right column, “O′Toole JC, Cruz RT 1983”]

The influence of agenda-based and habitual processes on item selection during study.

Research on study-time allocation has largely focused on agenda-based regulation, such as whether learners select items for study that are in their region of proximal learning. In 4 experiments, the authors evaluated the contribution of habitual responding to study-time allocation (e.g., reading from left to right). In Experiments 1 and 2, participants selected items for study from a 3-item array. In Experiment 1, pairs were ordered by learning ease from left to right or in the reverse order. In Experiment 2, pairs were in a column with the easiest item either in the top or bottom position. Participants more likely chose to study the easiest item first when it was presented in the prominent position of an array, but when the difficult item was in the prominent position, it was more often chosen first for study. In Experiment 3, a 3 × 3 array was used. In 1 group, the 3 easy items were in the left column and the 3 difficult ones were in the right column; in another group, these columns were reversed. Participants largely chose items in a top-down or left-to-right order. In Experiment 4, items were presented sequentially for item selection, with either the difficult items presented first (followed by progressively easier items) or in the reverse order. Participants could choose half the items for restudy, and they were more likely to choose items presented earlier in the list, regardless of presentation order. These and other outcomes indicate that both agenda-based regulation (in terms of using the region of proximal learning) and habitual responding contribute to people's selection of items for study.

Erratum to: “Expanding Genetic Code: Aminoacids 21 and 22, Selenocysteine and Pyrrolysine”

127 P. 899, Abstract, line 1: atypical should read nonstandart P. 904, right column, paragraph 1, last line: inhibits should read stimulates P. 908, right column, section heading: CIDE should read CODE P. 909, left column, paragraph 2: acetylation should read acylation P. 909, right column, paragraph 1: codon should read anticodon P. 910, right column, paragraph 2: atypical aminoacids should read unnatural aminoacids. Erratum: “Expanding Genetic Code: Aminoacids 21 and 22, Selenocysteine and Pyrrolysine” [Russ. J. Genet., 2011, vol. 46, no. 8, pp. 899–916]

View-Based Encoding of Actions in Mirror Neurons of Area F5 in Macaque Premotor Cortex

Converging experimental evidence indicates that mirror neurons in the monkey premotor area F5 encode the goals of observed motor acts [1-3]. However, it is unknown whether they also contribute to encoding the perspective from which the motor acts of others are seen. In order to address this issue, we recorded the visual responses of mirror neurons of monkey area F5 by using a novel experimental paradigm based on the presentation of movies showing grasping motor acts from different visual perspectives. We found that the majority of the tested mirror neurons(74%) exhibited view-dependent activity with responses tuned to specific points of view. A minority of the tested mirror neurons (26%) exhibited view-independent responses. We conclude that view-independent mirror neurons encode action goals irrespective of the details of the observed motor acts, whereas the view-dependent ones might either form an intermediate step in the formation of view independence or contribute to a modulation of view-dependent representations in higher-level visual areas, potentially linking the goals of observed motor acts with their pictorial aspects.

An adaptive matrix embedding based on LSB matching for grey-scale images

In this paper, an adaptive matrix embedding method based on LSB matching is proposed for greyscale images. The adaption mechanism of the method is used to embed less message bits in regions with high local correlation and embed more in regions with low local correlation. The 2 × 4 pixel block is taken as a cover unit. The seven pixels of its neighbour left column and up row are utilised to estimate the local correlation of the block. The estimated local correlation is further used to determine the message bit amount and choose the corresponding matrix embedding strategy. And LSB matching is performed to change the parity of the pixel needing modification determined by the matrix embedding. The experimental results indicate that in the test image database the new method can improve the PSNR value as high as about 3.75 dB as compared with simple LSB matching. And our method also has stronger resistance ability against Ker’s adjacency HCF-COM detector than simple LSB matching.

Classifying chemoreceptors: quantity versus quality

Corrigendum26 November 2010free access Classifying chemoreceptors: quantity versus quality Eric S Underbakke Eric S Underbakke Search for more papers by this author Laura L Kiessling Laura L Kiessling Search for more papers by this author Eric S Underbakke Eric S Underbakke Search for more papers by this author Laura L Kiessling Laura L Kiessling Search for more papers by this author Author Information Eric S Underbakke and Laura L Kiessling The EMBO Journal (2010)29:4237-4237https://doi.org/10.1038/emboj.2010.303 This article corrects the following: Classifying chemoreceptors: quantity versus quality20 October 2010 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Correction to: The EMBO Journal (2010) 29, 3435–3436. doi:10.1038/emboj.2010.246 Since the publication of this paper, the authors have noticed errors in reference citations. On page 3436, left column, rows 24 and 32, the reference citations for ‘Sourjik and Berg, 2004’ should instead refer to ‘Neumann et al, 2010’. The authors apologize for any inconvenience caused. Next ArticlePrevious Article Read MoreAbout the coverClose modalView large imageVolume 29,Issue 24,December 15, 2010Blood coagulation is a highly conserved process in vertebrates and begins instantly after an injury. During controlled blood donation, anticoagulant is added to suppress the process. The author explored coagulation at high magnification in vitro, by using a few millilitres of his own blood in combination with CaCl2, which outweighs the effect of the anticoagulant and finally kicks off the clotting cascade. After 2 minutes, a finely-meshed fibrin network was formed. Copyrights: © Martin Oeggerli / www.Micronaut.ch. Kindly supported by the School of Applied Sciences, FHNW. This amazing SEM image was one of the top-scoring entries in the scientific section of The EMBO Journal Cover Contest 2009. If you have scientific (or indeed non-scientific and/or artistic) images that you would like to share with our readers, visit our new contest website at http://covercontest.embo.org for guidelines on how you can participate. The editors and the jury look forward to your submissions. Volume 29Issue 2415 December 2010In this issue RelatedDetailsLoading ...

Errata

Equine Veterinary JournalVolume 43, Issue 1 p. 122-122 Free Access Errata This article corrects the following: The use of intra-articular corticosteroids in the horse: What is known on a scientific basis? C. W. McILWRAITH, Volume 42Issue 6Equine Veterinary Journal pages: 563-571 First Published online: June 7, 2010 First published: 10 December 2010 https://doi.org/10.1111/j.2042-3306.2010.00345_1.xAboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat The Review Article by C.W. McIlwraith (2010) ‘The use of intra-articular corticosteroids in the horse: What is known on a scientific basis?’ published in the September issue of EVJ contains an error. On page 568, the 3rd sentence of the final paragraph in the left column should read: Synovial fluid concentrations were highest one day after injection (7.5 µg/ml) decreasing to a steady state concentration by Day 4 (10 ng/ml) and became undetectable by Day 15. We apologise for this error and any inconvenience it may have caused. Reference McIlwraith, C.W. (2010) The use of intra-articular corticosteroids in the horse: What is known on a scientific basis? Equine vet. J. 42, 563- 571. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Volume43, Issue1January 2011Pages 122-122 ReferencesRelatedInformation

A 2-year-old Girl With Fever, Abdominal Pain, and Lung Cavities

A 2-year-old Girl With Fever, Abdominal Pain, and Lung Cavities

Erratum: Age at time of corticosteroid administration is a risk factor for osteonecrosis in pediatric patients with systemic lupus erythematosus: A prospective magnetic resonance imaging study

In the article by Nakamura et al in the February 2010 issue of Arthritis & Rheumatism (pages 609–615), the mean ± SD highest daily corticosteroid dose according to body weight in subjects without osteonecrosis was reported incorrectly (line 32 of the left column on page 613). The correct value in this group was 1.2 ± 0.3 mg/kg/day. We regret the error.

Correction to “On Functional Duality in Multiuser Source and Channel Coding Problems Having One-Sided Collaboration” [Jul 06 2986-3002

In the above titled paper (ibid., vol. 52, no. 7, pp. 2986-3002, Jul. 06), there is an error on line 8 in the first paragraph on the left column on page 2992 regarding broadcast channels. The equation is not correct and thus the argument given in the rest of the paragraph is not valid. A correct argument is presented here.

Erratum to “Nested Arrays: A Novel Approach to Array Processing With Enhanced Degrees of Freedom” [Aug 10 4167-4181

In the above titled paper (ibid., vol. 58, no. 8, pp. 4167-4181, Aug. 10), the second unnumbered equation in the left column was incorrect. The correct version is presented here.

Corrigendum

CORRIGENDUMCorrigendumPublished Online:01 Sep 2010https://doi.org/10.1152/ajpendo.zh1-6202-corr.2010Original articleMoreSectionsPDF (53 KB)Download PDF ToolsExport citationAdd to favoritesGet permissionsTrack citations ShareShare onFacebookTwitterLinkedInEmailWeChat Volume 299, August 2010Lauritzen HP, Schertzer JD. Measuring GLUT4 translocation in mature muscle fibers; doi:10.1152/ajpendo.00066.2010 http://ajpendo.physiology.org/cgi/content/full/299/2/E169.In this article, on the left column of p. , there is a sentence with reference number that should not have been cited. The sentence presently reads as follows: “It is possible that these factors keep the T-tubule network fully dilated, since diffusion of a fluorescent dye like sulforhodamine B into T-tubules of isolated fibers (+20 min) occurs 10–20 times slower in isolated mouse muscle fibers in vitro (32, 64) compared with in vivo conditions (1–2 min) (37).” The citation of Ref. 32 in this sentence should have been deleted.This article has no references to display. Download PDF Previous Back to Top FiguresReferencesRelatedInformationRelated ArticlesMeasuring GLUT4 translocation in mature muscle fibers 01 Aug 2010American Journal of Physiology-Endocrinology and Metabolism More from this issue > Volume 299Issue 3September 2010Pages E516-E516 Copyright & PermissionsCopyright © 2010 the American Physiological Societyhttps://doi.org/10.1152/ajpendo.zh1-6202-corr.2010History Published online 1 September 2010 Published in print 1 September 2010 Metrics

Strategies of actin reorganisation in plant cells

There were errors published in the e-press version of J. Cell Sci. 123, 3019-3028.In the Introduction, on page 3019, the second last sentence is incorrect.The correct sentence should read:New filaments can be assembled from shorter free cytoplasmic filaments, from the products of F-actin severing and by polymerisation from the ends of extant filaments.On page 3027, left column, second paragraph, the third sentence incorrectly contains the word ‘after’ immediately before the word ‘separation’.The correct sentence should read:For example, the frequency of rings or acquosomes decreases in an aging tobacco BY-2 cell culture (Hasezawa et al., 1988), increases during heat-stress (Chaidee at al., 2008) and following mechanical separation of Zinnia mesophyll cells (Frost and Roberts, 1996).On page 3027, left column, second paragraph, ninth line from bottom.The number of acquosomes is reduced by 98.9%, and not, as incorrectly stated, by 98%.We apologise for these mistakes.

Corrections to A Medicinal Chemist’s Guide to Molecular Interactions

Page 5063. The first sentence of the second paragraph in the left column should be replaced by the following: “In an impressively comprehensive study on several series of thrombin inhibitors, the Hangauer and Klebe groups have analyzed the sources of cooperativity between a lipophilic interaction and a hydrogen bond”.30,31 Page 5075. Figure 16 caption should read as follows: “Radial distribution of carbon atoms around phenyl rings: (a) CH3 bound to O or N (CSD statistics); (b) CH3 bound to sp3 C (CSD statistics); (c) CH3 bound to O or N (PDB statistics). Darker gray corresponds to higher density; peaks above a numerical value of 90 are colored red”. Page 5083. Reference 159 should be replaced by the following: Manley P. W.; Cowan-Jacob S. W.; Fendrich G.; Mestan J.Molecular interactions between the highly selective pan-Bcr-Abl inhibitor, AMN107, and the tyrosine kinase domain of Abl. Blood 2005, 53, 940a−941a.