ALBERT

Description: Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.

Description: ABSTRACT Laboratory observations and computational results for the response of bedform fields to rapid variations in discharge are compared and discussed. The simple case considered here begins with a relatively low discharge over a flat bed on which bedforms are initiated, followed by a short high-flow period with double the original discharge during which the morphology of the bedforms adjusts, followed in turn by a relatively long period of the original low discharge. For the grain size and hydraulic conditions selected, the Froude number remains subcritical during the experiment, and sediment moves predominantly as bedload. Observations show rapid development of quasi-two-dimensional bedforms during the initial period of low flow with increasing wavelength and height over the initial low-flow period. When the flow increases, the bedforms rapidly increase in wavelength and height, as expected from other empirical results. When the flow decreases back to the original discharge, the height of the bedforms quickly decreases in response, but the wavelength decreases much more slowly. Computational results using an unsteady two-dimensional flow model coupled to a disequilibrium bedload transport model for the same conditions simulate the formation and initial growth of the bedforms fairly accurately and also predict an increase in dimensions during the high-flow period. However, the computational model predicts a much slower rate of wavelength increase, and also performs less accurately during the final low-flow period, where the wavelength remains essentially constant, rather than decreasing. In addition, the numerical results show less variability in bedform wavelength and height than the measured values; the bedform shape is also somewhat different. Based on observations, these discrepancies may result from the simplified model for sediment particle step lengths used in the computational approach. Experiments show that the particle step length varies spatially and temporally over the bedforms during the evolution process. Assuming a constant value for the step length neglects the role of flow alterations in the bedload sediment-transport process, which appears to result in predicted bedform wavelength changes smaller than those observed. However, observations also suggest that three-dimensional effects play at least some role in the decrease of bedform wavelength, so incorporating better models for particle hop lengths alone may not be sufficient to improve model predictions. Copyright © 2011 John Wiley & Sons, Ltd.

Description: A small molecule called PD 153035 inhibited the epidermal growth factor (EGF) receptor tyrosine kinase with a 5-pM inhibition constant. The inhibitor was specific for the EGF receptor tyrosine kinase and inhibited other purified tyrosine kinases only at micromolar or higher concentrations. PD 153035 rapidly suppressed autophosphorylation of the EGF receptor at low nanomolar concentrations in fibroblasts or in human epidermoid carcinoma cells and selectively blocked EGF-mediated cellular processes including mitogenesis, early gene expression, and oncogenic transformation. PD 153035 demonstrates an increase in potency over that of other tyrosine kinase inhibitors of four to five orders of magnitude for inhibition of isolated EGF receptor tyrosine kinase and three to four orders of magnitude for inhibition of cellular phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fry, D W -- Kraker, A J -- McMichael, A -- Ambroso, L A -- Nelson, J M -- Leopold, W R -- Connors, R W -- Bridges, A J -- New York, N.Y. -- Science. 1994 Aug 19;265(5175):1093-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, Ann Arbor, MI 48105.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8066447" target="_blank"〉PubMed〈/a〉

Description: Nuclear collisions recreate conditions in the universe microseconds after the Big Bang. Only a very small fraction of the emitted fragments are light nuclei, but these states are of fundamental interest. We report the observation of antihypertritons--comprising an antiproton, an antineutron, and an antilambda hyperon--produced by colliding gold nuclei at high energy. Our analysis yields 70 +/- 17 antihypertritons ((Lambda)(3)-H) and 157 +/- 30 hypertritons (Lambda3H). The measured yields of Lambda3H ((Lambda)(3)-H) and 3He (3He) are similar, suggesting an equilibrium in coordinate and momentum space populations of up, down, and strange quarks and antiquarks, unlike the pattern observed at lower collision energies. The production and properties of antinuclei, and of nuclei containing strange quarks, have implications spanning nuclear and particle physics, astrophysics, and cosmology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉STAR Collaboration -- Abelev, B I -- Aggarwal, M M -- Ahammed, Z -- Alakhverdyants, A V -- Alekseev, I -- Anderson, B D -- Arkhipkin, D -- Averichev, G S -- Balewski, J -- Barnby, L S -- Baumgart, S -- Beavis, D R -- Bellwied, R -- Betancourt, M J -- Betts, R R -- Bhasin, A -- Bhati, A K -- Bichsel, H -- Bielcik, J -- Bielcikova, J -- Biritz, B -- Bland, L C -- Bonner, B E -- Bouchet, J -- Braidot, E -- Brandin, A V -- Bridgeman, A -- Bruna, E -- Bueltmann, S -- Bunzarov, I -- Burton, T P -- Cai, X Z -- Caines, H -- Calderon, M -- Catu, O -- Cebra, D -- Cendejas, R -- Cervantes, M C -- Chajecki, Z -- Chaloupka, P -- Chattopadhyay, S -- Chen, H F -- Chen, J H -- Chen, J Y -- Cheng, J -- Cherney, M -- Chikanian, A -- Choi, K E -- Christie, W -- Chung, P -- Clarke, R F -- Codrington, M J M -- Corliss, R -- Cramer, J G -- Crawford, H J -- Das, D -- Dash, S -- Davila Leyva, A -- De Silva, L C -- Debbe, R R -- Dedovich, T G -- DePhillips, M -- Derevschikov, A A -- Derradi de Souza, R -- Didenko, L -- Djawotho, P -- Dogra, S M -- Dong, X -- Drachenberg, J L -- Draper, J E -- Dunlop, J C -- Dutta Mazumdar, M R -- Efimov, L G -- Elhalhuli, E -- Elnimr, M -- Engelage, J -- Eppley, G -- Erazmus, B -- Estienne, M -- Eun, L -- Evdokimov, O -- Fachini, P -- Fatemi, R -- Fedorisin, J -- Fersch, R G -- Filip, P -- Finch, E -- Fine, V -- Fisyak, Y -- Gagliardi, C A -- Gangadharan, D R -- Ganti, M S -- Garcia-Solis, E J -- Geromitsos, A -- Geurts, F -- Ghazikhanian, V -- Ghosh, P -- Gorbunov, Y N -- Gordon, A -- Grebenyuk, O -- Grosnick, D -- Grube, B -- Guertin, S M -- Gupta, A -- Gupta, N -- Guryn, W -- Haag, B -- Hamed, A -- Han, L-X -- Harris, J W -- Hays-Wehle, J P -- Heinz, M -- Heppelmann, S -- Hirsch, A -- Hjort, E -- Hoffman, A M -- Hoffmann, G W -- Hofman, D J -- Hollis, R S -- Huang, B -- Huang, H Z -- Humanic, T J -- Huo, L -- Igo, G -- Iordanova, A -- Jacobs, P -- Jacobs, W W -- Jakl, P -- Jena, C -- Jin, F -- Jones, C L -- Jones, P G -- Joseph, J -- Judd, E G -- Kabana, S -- Kajimoto, K -- Kang, K -- Kapitan, J -- Kauder, K -- Keane, D -- Kechechyan, A -- Kettler, D -- Kikola, D P -- Kiryluk, J -- Kisiel, A -- Klein, S R -- Knospe, A G -- Kocoloski, A -- Koetke, D D -- Kollegger, T -- Konzer, J -- Kopytine, M -- Koralt, I -- Koroleva, L -- Korsch, W -- Kotchenda, L -- Kouchpil, V -- Kravtsov, P -- Krueger, K -- Krus, M -- Kumar, L -- Kurnadi, P -- Lamont, M A C -- Landgraf, J M -- LaPointe, S -- Lauret, J -- Lebedev, A -- Lednicky, R -- Lee, C-H -- Lee, J H -- Leight, W -- Levine, M J -- Li, C -- Li, L -- Li, N -- Li, W -- Li, X -- Li, Y -- Li, Z -- Lin, G -- Lindenbaum, S J -- Lisa, M A -- Liu, F -- Liu, H -- Liu, J -- Ljubicic, T -- Llope, W J -- Longacre, R S -- Love, W A -- Lu, Y -- Luo, X -- Ma, G L -- Ma, Y G -- Mahapatra, D P -- Majka, R -- Mal, O I -- Mangotra, L K -- Manweiler, R -- Margetis, S -- Markert, C -- Masui, H -- Matis, H S -- Matulenko, Yu A -- McDonald, D -- McShane, T S -- Meschanin, A -- Milner, R -- Minaev, N G -- Mioduszewski, S -- Mischke, A -- Mitrovski, M K -- Mohanty, B -- Mondal, M M -- Morozov, B -- Morozov, D A -- Munhoz, M G -- Nandi, B K -- Nattrass, C -- Nayak, T K -- Nelson, J M -- Netrakanti, P K -- Ng, M J -- Nogach, L V -- Nurushev, S B -- Odyniec, G -- Ogawa, A -- Okada, H -- Okorokov, V -- Olson, D -- Pachr, M -- Page, B S -- Pal, S K -- Pandit, Y -- Panebratsev, Y -- Pawlak, T -- Peitzmann, T -- Perevoztchikov, V -- Perkins, C -- Peryt, W -- Phatak, S C -- Pile, P -- Planinic, M -- Ploskon, M A -- Pluta, J -- Plyku, D -- Poljak, N -- Poskanzer, A M -- Potukuchi, B V K S -- Powell, C B -- Prindle, D -- Pruneau, C -- Pruthi, N K -- Pujahari, P R -- Putschke, J -- Qiu, H -- Raniwala, R -- Raniwala, S -- Ray, R L -- Redwine, R -- Reed, R -- Ritter, H G -- Roberts, J B -- Rogachevskiy, O V -- Romero, J L -- Rose, A -- Roy, C -- Ruan, L -- Sahoo, R -- Sakai, S -- Sakrejda, I -- Sakuma, T -- Salur, S -- Sandweiss, J -- Sangaline, E -- Schambach, J -- Scharenberg, R P -- Schmitz, N -- Schuster, T R -- Seele, J -- Seger, J -- Selyuzhenkov, I -- Seyboth, P -- Shahaliev, E -- Shao, M -- Sharma, M -- Shi, S S -- Sichtermann, E P -- Simon, F -- Singaraju, R N -- Skoby, M J -- Smirnov, N -- Sorensen, P -- Sowinski, J -- Spinka, H M -- Srivastava, B -- Stanislaus, T D S -- Staszak, D -- Stevens, J R -- Stock, R -- Strikhanov, M -- Stringfellow, B -- Suaide, A A P -- Suarez, M C -- Subba, N L -- Sumbera, M -- Sun, X M -- Sun, Y -- Sun, Z -- Surrow, B -- Svirida, D N -- Symons, T J M -- Szanto de Toledo, A -- Takahashi, J -- Tang, A H -- Tang, Z -- Tarini, L H -- Tarnowsky, T -- Thein, D -- Thomas, J H -- Tian, J -- Timmins, A R -- Timoshenko, S -- Tlusty, D -- Tokarev, M -- Trainor, T A -- Tram, V N -- Trentalange, S -- Tribble, R E -- Tsai, O D -- Ulery, J -- Ullrich, T -- Underwood, D G -- Van Buren, G -- van Leeuwen, M -- van Nieuwenhuizen, G -- Vanfossen, J A Jr -- Varma, R -- Vasconcelos, G M S -- Vasiliev, A N -- Videbaek, F -- Viyogi, Y P -- Vokal, S -- Voloshin, S A -- Wada, M -- Walker, M -- Wang, F -- Wang, G -- Wang, H -- Wang, J S -- Wang, Q -- Wang, X L -- Wang, Y -- Webb, G -- Webb, J C -- Westfall, G D -- Whitten, C Jr -- Wieman, H -- Wingfield, E -- Wissink, S W -- Witt, R -- Wu, Y -- Xie, W -- Xu, H -- Xu, N -- Xu, Q H -- Xu, W -- Xu, Y -- Xu, Z -- Xue, L -- Yang, Y -- Yepes, P -- Yip, K -- Yoo, I-K -- Yue, Q -- Zawisza, M -- Zbroszczyk, H -- Zhan, W -- Zhang, J -- Zhang, S -- Zhang, W M -- Zhang, X P -- Zhang, Y -- Zhang, Z P -- Zhao, J -- Zhong, C -- Zhou, J -- Zhou, W -- Zhu, X -- Zhu, Y H -- Zoulkarneev, R -- Zoulkarneeva, Y -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):58-62. doi: 10.1126/science.1183980. Epub 2010 Mar 4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20203011" target="_blank"〉PubMed〈/a〉

Description: The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

Description: The interactions that lead to the emergence of superconductivity in iron-based materials remain a subject of debate. It has been suggested that electron-electron correlations enhance electron-phonon coupling in iron selenide (FeSe) and related pnictides, but direct experimental verification has been lacking. Here we show that the electron-phonon coupling strength in FeSe can be quantified by combining two time-domain experiments into a "coherent lock-in" measurement in the terahertz regime. X-ray diffraction tracks the light-induced femtosecond coherent lattice motion at a single phonon frequency, and photoemission monitors the subsequent coherent changes in the electronic band structure. Comparison with theory reveals a strong enhancement of the coupling strength in FeSe owing to correlation effects. Given that the electron-phonon coupling affects superconductivity exponentially, this enhancement highlights the importance of the cooperative interplay between electron-electron and electron-phonon interactions.