Sampling Plan Optimization: A Data Review and Sampling Frequency Evaluation Process

Lawrence Livermore National Laboratory (LLNL) uses a cost-effective sampling (CES) methodology to evaluate and review ground water contaminant data and optimize the site's ground water monitoring plan. The CES methodology is part of LLNL's regulatory approved compliance monitoring plan (Lamarre et al., 1996 Lamarre, A. L., Nichols, E. M., Berg, L. L., Dresen, M. D., Gelinas, R. J., Bainer, R. W. and Folsom, E. N. 1996. Compliance monitoring plan for the Lawrence Livermore National Laboratory Livermore Site UCRL-AR-120936 [Google Scholar]). It allows LLNL to adjust the ground water sampling plan every quarter in response to changing conditions at the site. Since the use of the CES methodology has been approved by the appropriate regulatory agencies, such adjustments do not need additional regulatory approval. This permits LLNL to respond more quickly to changing conditions. The CES methodology bases the sampling frequency for each location on trend, variability, and magnitude statistics describing the contaminants at that location, and on the input of the technical staff (hydrologists, chemists, statisticians, and project leaders). After initial setup is complete, each application of CES takes only a few days for as many as 400 wells. Effective use of the CES methodology requires sufficient data, an understanding of contaminant transport at the site, and an adequate number of monitoring wells downgradient of the contamination. The initial implementation of CES at LLNL in 1992 produced a 40% reduction in the required number of annual routine ground water samples at LLNL. This has saved LLNL $390,000 annually in sampling, analysis, and data management costs.     

Buried Tracks: Ichnological Applications of High-Frequency Georadar

Recognition and sampling of traces in unconsolidated sands present a major challenge for ichnologists. This can be partially remedied through the application of high-resolution geophysical techniques, such as ground-penetrating radar (GPR or georadar), which uses electromagnetic impulse for continuous imaging of shallow subsurface. It addition to geological applications, GPR imaging has been used in several studies focused on animal traces as related to conservation of endangered fossorial species (Kinlaw et al., 2007 Kinlaw, A. E., Conyers, L. B. and Zajac, W. 2007. Use of ground penetrating radar to image burrows of the gopher tortoise (Gopherus polyphemus). Herpetological Review, 38: 50–56.  [Google Scholar]; Martin et al., 2011 Martin, A. J., Skaggs, S. A., Vance, R. K. and Greco, V. 2011. Ground-penetrating radar investigation of gopher-tortoise burrows: Refining the characterization of modern vertebrate burrows and associated commensal traces. Geological Society of America Abstracts with Programs, 43: 381 [Google Scholar]), slope and levee stability (Nichol et al., 2003 Nichol, D., Lenham, J. W. and Reynolds, J. M. 2003. Application of ground-penetrating radar to investigate the effects of badger setts on slope stability at St. Asaph Bypass, North Wales. Quarterly Journal of Engineering Geology and Hydrogeology, 36: 143–153.  [Google Scholar]; Di Prinzio et al., 2010 Di Prinzio, M, Bittelli, M., Castellarin, A. and Pisa, P. R. 2010. Application of GPR to the monitoring of river embankments. Journal of Applied Geophysics, 7: 53–61.  [Google Scholar]), and mapping of fossil tracks (Matthews et al., 2006 Matthews, N. A., Noble, T. A. and Breithaupt, B. H. 2006. “The application of photogrammetry, remote sensing and geographic information systems (GIS) to fossil resource management”. In Fossils from Federal Lands, Edited by: Lucas, S. G., Spielmann, J. A., Hester, P. M., Kenworthy, J. P. and Santucci, V. L. Vol. 34, 119–131. New Mexico Museum of Natural History and Science Bulletin.  [Google Scholar]; Aucoin and Hasbargen, 2010 Aucoin, C. D. and Hasbargen, L. 2010. Using GPR, GPS and close-range photography to map and characterize dinosaur tracks in the Connecticut River valley. Geological Society of America Abstracts with Programs, 42: 276 [Google Scholar]) and tracking surfaces (Webb, 2007 Webb, S. 2007. Further research of the Willandra Lakes fossil footprint site, southeastern Australia. Journal of Human Evolution, 52: 711–715. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). Few efforts have been dedicated specifically to characterizing burrow and track characteristics (Stott, 1996 Stott, P. 1996. Ground-penetrating radar: a technique for investigating the burrow structure of fossorial vertebrates. Wildlife Research, 22: 519–530.  [Google Scholar]; Sensors & Software Inc., 2010 [compilation on geophysical projects related to animal burrows]; Buynevich and Hasiotis, 2011; Buynevich et al., 2011; Martin et al., 2011) and most of the above studies are published in journals not routinely accessed by ichnologists.     

Salmonella Typhimurium methionine sulfoxide reductase A (MsrA) prefers TrxA in repairing methionine sulfoxide

Intraphagocytic survival of Salmonella Typhimurium (ST) depends (at least in part) upon its ability to repair oxidant-damaged macromolecules. Met residues either free or in protein bound form are highly susceptible to phagocyte-generated oxidants. Oxidation of Mets leads to Met-SO formation, consequently loss of protein functions that results in cell death. Methionine sulfoxide reductase (Msr) reductively repairs Met-SO to Met in the presence of thioredoxin (trx) and thioredoxin reductase (trxR). Earlier we reported that methionine sulfoxide reductase A (msrA) gene deletion strain of ST suffered oxidative stress.^[1 Trivedi, R.N.; Agarwal, P.; Kumawat, M.; Pesingi, P.K.; Gupta, V.K.; Goswami, T.K.; Mahawar, M. Methionine Sulfoxide Reductase A (MsrA) Contributes to Salmonella Typhimurium Survival Against Oxidative Attack of Neutrophils. Immunobiology 2015, 220(12), 1322–1327.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]^] Thioredoxin system of ST comprises of two thioredoxins (trxA and trxC) and one thioredoxin reductase (trxB). Preferred trx utilized in MsrA-mediated repair of Met-SO is not known. In current study, we cloned, expressed, and purified ST TrxA, TrxB, TrxC, and MsrA in recombinant forms. The migration of TrxA, TrxB, TrxC, and MsrA proteins was approximately 10, 36, 16, and 26?kDa on SDS-gels. The nicotinamide adenine dinucleotide phosphate hydrogen (NADPH)-linked reductase assays interpreted that MsrA utilized two times more NADPH for the reduction of S-methyl p-tolyl sulfoxide when TrxA was included in the assays as compared to TrxC.     

EFFICIENT SYNTHESIS OF FUSED ISOTHIAZOLO C-NUCLEOSIDES. III. SYNTHESIS OF 7-SUBSTITUTED ISOTHIAZOLO[4,5-d]PYRIMIDINE C-NUCLEOSIDES*

The Divakar-Reese procedure has been successfully applied for transforming 7-oxo-isothiazolo[4,5-d]pyrimidine C-nucleosides (4a,b, 5a,b, 6a) via 1,2,4-triazol-1-yl intermediates (7a,b, 8a,b) into various 7-substituted C-nucle- osides 15a,b, 16a,b, 17a, 18a, 19a,b, 20a,b; their subsequent deprotection provides novel types of unusual C-glycosides 22b, 23a, 24a,b, 25b, 26b.

C-Nucleosides, possessing on its heterocyclic base other than naturally occuring oxo- or amino substituents, are important model compounds for biological or medicinal studies [2a] Hanessian, S. and Pernet, A. G. 1976. Adv. Carbohydr. Chem. Biochem., 32: 111–188. cf. [Google Scholar], [2b] Mizuno, Y. 1986. The Organic Chemistry of Nucleic Acids Amsterdam: Elsevier.  [Google Scholar], [2c] Huryn, D. M. and Okabe, M. 1992. Chem. Rev., 92: 1745–1768. [Crossref], [Web of Science ®] , [Google Scholar], [2d] Häbich, D. 1991. Chem. in uns. Zeit, 25: 295–307.  [Google Scholar], [2e] Uhlmann, E. and Peyman, A. 1990. Chem. Rev., 90: 543–584. [Crossref], [Web of Science ®] , [Google Scholar], [2f] Thuong, N. T. and Helene, C. 1993. Angew. Chem., 105: 697–723. [Crossref] , [Google Scholar], [2g] 1993. Angew. Chem. Int. Ed. Engl., 33: 666–690.  [Google Scholar], [2h] Yarchoan, R., Mitsuya, H., Zhomas, R. V., Pluda, J. M., Hartman, N. R., Perno, C. F., Marczyk, K. S., Allain, J. P., Johns, D. G. and Broder, S. 1989. Science, 245: 412–414. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar], [2i] Tanaka, H., Baba, M., Hayakawa, H., Sakamaki, T., Miyasaka, T., Ubasawa, M., Takashima, H., Sekiya, E., Nitta, I., Shigeta, S., Walker, R. T., Balzarini, J. and De Clerq, E. 1991. J. Med. Chem., 34: 349–357. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] [3a] Koyama, G., Maeda, K., Umezawa, H. and Iitaka, Y. 1966. Tetrahedron Lett., : 597–602. Some C-glycosides with antibiotic, antiviral (HIV), and anticancer activities [Google Scholar], [3b] Hori, M., Wakashiro, T., Ito, E., Sawa, T., Takeuchi, T. and Umezawa, H. J. 1968. J. Antibiot., 21A: 264–270. [Chem. Abstr. 1968, 69, 11356j] [Google Scholar], [3c] Farkas, J. and ?orm. 1972. F. Collect. Czech. Chem. Commun., 37: 2798–2803.  [Google Scholar], [3d] Acton, E. M., Ryan, K. J., Henry, D. W. and Goodman, L. 1971. J. Chem. Soc., Chem. Commun., : 986–988.  [Google Scholar], [3e] Nakagawa, Y., Kano, H., Tsukuda, Y. and Koyama, H. 1967. Tetrahedron Lett., : 4105–4109.  [Google Scholar], [3f] Inoue, I. and Kuwaijama, I. 1980. J. Chem. Soc., Chem. Commun., : 251–253.  [Google Scholar], [3g] Buchanan, J. G., Stobie, A. and Wightman, R. H. 1980. ibid., : 916–917. [Crossref] , [Google Scholar], [3h] Hildebrand, S. and Leumann, C. 1996. Angew. Chem., 108: 2100–2102. Angew. Chem. Int. Ed. Engl. 1996, 35, 1968–1970 [Google Scholar]. We want to report on the synthesis of novel 7-substituted isothiazolo = [4,5-d]pyrimidine C-nucleosides. As we could show in previous papers [1] Wamhoff, H., Berressem, R. and Nieger, M. 1994. J. Org. Chem., 59: 1912–1917. Part 2 [Google Scholar], [4] Wamhoff, H., Berressem, R. and Nieger. 1993. M. J. Org. Chem., 58: 5181–5185.  [Google Scholar], there exists a simple approach to the protected C-glycosides 4–6.

     

175 Structure-based engineering to generate high-affinity immunotherapy for the drug of abuse

Methamphetamine (METH) abuse is a major threat in the USA and worldwide without any FDA approved medications. Anti-METH antibody antagonists block or slow the rate of METH entry into the brain and have shown efficacy in preclinical studies (Peterson, Laurenzana, Atchley, Hendrickson, & Owens, 2008 Peterson, E. C., Laurenzana, E. M., Atchley, W. T., Hendrickson, H. P. and Owens, S. M. 2008. Development and preclinical testing of a high-affinity single-chain antibody against (+)-methamphetamine. Journal of Pharmacology and Experimental Therapeutics, 08: 124–133.  [Google Scholar]).?A key determinant of the antibody’s efficacy is its affinity for METH and we attempted to enhance the efficacy by designing mutations to alter the shape or the electrostatic character of the binding pocket. Towards this goal, we developed a single chain anti-METH antibody fragment (scFv6H4) from a parent IgG (1). The crystal structure of scFv-6H4 in complex with METH was determined (Celikel, Peterson, Owens, & Varughese, 2009 Celikel, R., Peterson, E. C., Owens, S. M. and Varughese, K. I. 2009. Crystal structures of a therapeutic single chain antibody in complex with two drugs of abuse-Methamphetamine and 3,4-methylenedioxymethamphetamine. Protein Science, 09: 2336–2345.  [Google Scholar]). Based on its elucidated binding interactions, we designed point mutations in the binding pocket to improve its affinity for METH and amphetamine (AMP), the active metabolite of METH. The mutants, scFv-S93T,-I37?M and -Y34?M were cloned, expressed in yeast and tested for affinity against METH and AMP. Two mutants showed enhanced binding affinity for METH: scFv-I37?M by 1.3-fold and scFv-S93T by 2.6-fold. Additionally, all the mutants showed increase in affinity for AMP: scFv-I37?M by 56-fold, scFv-S93T by 17-fold and scFvY34?M by 5-fold. Crystal structure for one of the high-affinity mutant, scFv-S93T, in complex with METH was determined (Figure 1). Binding pocket of the mutant is more hydrophobic in comparison with the wild type. ScFv-6H4 binds METH in a deep pocket containing two water molecules. The substitution of a serine residue by a threonine leads to the expulsion of a water molecule (Figure 2), relieving some unfavorable contacts between the hydrocarbon atoms of METH and the water molecule and increasing the affinity to sub-nanomolar range. Therefore, the present study shows that efficacy could be enhanced by altering the hydrophobicity or the shape of the binding pocket.     

DNA binding,photocleavage, antimicrobial and cytotoxic properties of Ru(II) polypyridyl complexes containing BOPIP ligand, (BOPIP = {2-(4-(benzyloxy) phenyl)-1H-imidazo [4,5-f] [1,2]phenanthroline})

A novel ligand BOPIP (BOPIP?=?{2-(4-(benzyloxy)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline}) and its mononuclear Ru(II) polypyridyl complexes [Ru(phen)₂ BOPIP]²⁺(1) (phen?=?1,10-Phenanthrolene), [Ru(bpy)₂ BOPIP]²⁺(2) (bpy?=?2,2′ bipyridyl), [Ru(dmb)₂ BOPIP]²⁺(3) (dmb?=?4, 4′ -dimethyl 2, 2′ -bipyridine), [Ru(Hdpa)₂ BOPIP]²⁺(4) (Hdpa?=?2,2′dipyridylamine) have been synthesized successfully and characterized by elemental analysis, UV-vis, IR, ¹H, ¹³ Gill, M. R.; Garcia-Lara, J.; Foster, S. J.; Smythe, C.; Battaglia, G.; Thomas, J. A. A Ruthenium(II) polypyridyl Complex for Direct Imaging of DNA Structure in Living Cells. Nat. Chem. 2009, 1, 662–667.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]C-NMR, and ESI-MS Spectroscopy. The interaction of these complexes with CT-DNA was studied using absorption, emission techniques, viscosity measurements and molecular docking studies. The docking study also supports the binding ability of complexes obtained through the absorption and emission techniques. These studies reveal that the Four Ru(II) polypyridyl complexes bind to DNA predominantly by intercalation. The Antimicrobial activity and cytotoxicity of these complexes are also reported.     

Early Oligocene Mammal Tracks from Southeastern France

Two new sites with mammalian footprints in the early Oligocene of southeastern France are described here. They represent one of the best preserved and more numerous record of tracks and trackways in the world with more than 320 ichnites. Many of those are arranged in trackways and sometimes show pes-manus impressions, a quite rare feature in mammalian ichnology. The ichnotaxonomic study indicates the presence of perissodactyls tracks referred to as Rhinoceripeda voconcense (Demathieu et al., 1984 Demathieu, G., Ginsburg, L., Guérin, C. and Truc, G. 1984. Etude paléontologique, ichnologique et paléoécologique du gisement oligocène de Saignon (bassin d’Apt, Vaucluse). Bulletin du Museum National d’Histoire Naturelle, Paris, 6: 153–183.  [Google Scholar]), artiodactyls footprints referred to as Megapecoripeda velox (Demathieu et al., 1984 Demathieu, G., Ginsburg, L., Guérin, C. and Truc, G. 1984. Etude paléontologique, ichnologique et paléoécologique du gisement oligocène de Saignon (bassin d’Apt, Vaucluse). Bulletin du Museum National d’Histoire Naturelle, Paris, 6: 153–183.  [Google Scholar]) and a carnivore footprint referred to as Bestiopeda sp. Vialov (1966) Vialov, O. S. 1966. Sledy zhiznedeyatelnosti organizmow i ikh paleontologicheskoe znachenie. Naukova Dumka, : 219 (in Russian) [Google Scholar]. They can be attributed to early Rhinocerotids, Lophiomerycids and/or Entelodonts and Mustelid-like carnivore, respectively. This study also aims at homogenizing the ichnotaxonomy used for mammal tracks where several genera were erected without a full review of the literature. All this taken together reveals a rich mammalian ichnofauna at a time period when no other fossils of mammals are known in the area and represents a good opportunity to provide state-of-the-art concerning the worldwide known sites that yielded mammalian footprints.     

Redefinition of the hypotrichous ciliate Uncinata,with descriptions of the morphology and phylogeny of three urostylids (Protista,Ciliophora)

We investigated the morphology, morphogenesis and small subunit rRNA gene-based phylogeny of three marine urostylids, Uncinata gigantea Bullington, 1940 Bullington, W. E. (1940). Some ciliates from Tortugas. Papers from the Tortugas Laboratory, 32, 179–221. [Google Scholar], Holosticha heterofoissneri Hu & Song, 2001 Hu, X., & Song, W. (2001). Morphology and morphogenesis of Holosticha heterofoissneri n. sp. from the Yellow Sea, China (Ciliophora, Hypotrichida). Hydrobiologia, 448, 171–179. doi:10.1023/A:1017553406031.[Crossref], [Web of Science ®] , [Google Scholar], and Holosticha cf. heterofoissneri. The dorsal morphogenesis of Uncinata gigantea shows de novo formation of two groups of anlagen near the marginal rows. Holosticha cf. heterofoissneri demonstrates fragmentation of the first dorsal kinety anlage as in Holosticha heterofoissneri. Our population of H. heterofoissneri corresponds well with previously described populations in terms of its general morphology and ciliary pattern. Uncinata gigantea can be recognized by its large and highly contractile body, yellowish to brownish cell colour, two types of cortical granules, and 20–30 transversely oriented and densely arranged cirri in the left marginal row, which often overlie the buccal vertex. Based on the new data, especially infraciliature, the genus Uncinata is here redefined. Both the morphology and phylogenetic analyses suggest that the genus Uncinata should be classified within the family Urostylidae. In addition, both morphological and morphogenetic data suggest that Holosticha bradburyae Gong et al., 2001 Gong, J., Song, W., Hu, X., Ma, H., & Zhu, M. (2001). Morphology and infraciliature of Holosticha bradburyae n. sp. (Ciliophora, Hypotrichida) from the Yellow Sea, China. Hydrobiologia, 464, 63–69. doi:10.1023/A:1013901621439.[Crossref], [Web of Science ®] , [Google Scholar] should be transferred to Uncinata as U. bradburyae (Gong et al., 2001 Gong, J., Song, W., Hu, X., Ma, H., & Zhu, M. (2001). Morphology and infraciliature of Holosticha bradburyae n. sp. (Ciliophora, Hypotrichida) from the Yellow Sea, China. Hydrobiologia, 464, 63–69. doi:10.1023/A:1013901621439.[Crossref], [Web of Science ®] , [Google Scholar]) comb. nov., due to its possession of a characteristically prominent beak-like, leftwards curved projection and the developmental mode of the dorsal kineties. This assignment is supported by the phylogenetic analyses, which placed Uncinata gigantea in a clade with U. bradburyae (Gong et al., 2001 Gong, J., Song, W., Hu, X., Ma, H., & Zhu, M. (2001). Morphology and infraciliature of Holosticha bradburyae n. sp. (Ciliophora, Hypotrichida) from the Yellow Sea, China. Hydrobiologia, 464, 63–69. doi:10.1023/A:1013901621439.[Crossref], [Web of Science ®] , [Google Scholar]) comb. nov., and revealed only 1.13% (19 bp) difference in their SSU-rDNA gene sequence.     

Teaching Bernoulli's Principle through Demonstrations

ABSTRACT

One proven strategy to help students make sense of abstract concepts is to sequence instruction so students have exploratory opportunities to investigate science before being introduced to new science explanations (Abraham and Renner 1986 Abraham, M. R. and Renner, J. W. 1986. The sequence of learning cycle activities in high school chemistry. Journal of Research in Science Teaching, 23: 121–143. [Crossref], [Web of Science ®] , [Google Scholar]; Renner, Abraham, and Birnie 1988 Renner, J. W., Abraham, M. R. and Birnie, H. H. 1988. The necessity of each phase of the learning cycle in teaching high school physics. Journal of Research in Science Teaching, 25: 39–58. [Crossref], [Web of Science ®] , [Google Scholar]). To help physical science teachers make sense of how to effectively sequence lessons, this article summarizes our experiences using an exploration–explanation sequence of instruction to teach Bernoulli's principle to prospective middle and secondary science teachers in a science methods course. We use demonstrations during our Bernoulli unit to help students go back and forth between their observations of phenomenon and what occurs on the microscopic level with what we have termed molecular talk. Students engage in guiding questions, consider their old and new understandings of science, and use evidence to construct new ideas during all stages of the lesson.     

158 A molecular dynamics simulation-based prediction of deleterious angiogenin mutations causing amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the selective death of motor neurons leading to paralysis and death between 3–5?years of diagnosis. Through whole genome association studies, several single nucleotide polymorphisms (SNPs) encoding missense mutations in angiogenin (ANG) protein have been identified as one of the primary factors causing ALS. Structural studies of ANG show that catalytic triad comprising His13, Lys40, and His114 residues imparts ribonucleolytic activity while nuclear localization signal residues ³¹RRR³³ are responsible for nuclear translocation activity. Loss of either ribonucleolytic activity or nuclear translocation activity or both of these functions due to mutations cause ALS. However, the mechanisms of loss-of-functions of ANG mutants are not completely understood. Here, we present a cohesive and comprehensive picture of functional loss mechanisms of all known ALS-associated ANG mutants by extensive molecular dynamics (MD) simulations (Padhi, Kumar, Vasaikar, Jayaram, & Gomes, 2012 Padhi, A. K., Kumar, H., Vasaikar, S. V., Jayaram, B. and Gomes, J. 2012. Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis. PLoS One, 7(2): e32479[PubMed] , [Google Scholar]; AK, 2013 Padhi, A.K., Jayaram, B., & Gomes, J. (accepted for publication). Prediction of functional loss of human angiogenin mutants associated with ALS by molecular dynamics simulations. Scientific Reports (NPG).  [Google Scholar]). Our studies show that conformational switching of catalytic residue His114 is responsible for the loss of ribonucleolytic activity while reduction in solvent-accessible surface area (SASA) of ³¹RRR³³ as a result of local folding is responsible for the loss of nuclear translocation activity (Padhi et al., 2012 Padhi, A. K., Kumar, H., Vasaikar, S. V., Jayaram, B. and Gomes, J. 2012. Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis. PLoS One, 7(2): e32479[PubMed] , [Google Scholar]; AK, 2013 Padhi, A.K., Jayaram, B., & Gomes, J. (accepted for publication). Prediction of functional loss of human angiogenin mutants associated with ALS by molecular dynamics simulations. Scientific Reports (NPG).  [Google Scholar]). Our prediction of loss-of-functions of 17 ANG mutants correlated positively with the reported experimental results. We have subsequently developed a fast molecular dynamics method based on certain global attributes / dynamic markers that can be used to determine whether a mutation is deleterious or benign. To make our method accessible to researchers and clinicians, we created a web server-based tool, ANGDelMut, freely available at http://bioschool.iitd.ernet.in/research.htm, where a user can submit new mutations to ascertain whether they cause ALS. We hope that our method will benefit the community at large and will pave the way for the development of a successful therapy for patients suffering from ALS.     

Translational control of gurken mRNA in Drosophila development

Localized mRNA translation is a widespread mechanism for targeting protein synthesis, important for cell fate, motility and pathogenesis. In Drosophila, the spatiotemporal control of gurken/TGF-α mRNA translation is required for establishing the embryonic body axes. A number of recent studies have highlighted key aspects of the mechanism of gurken mRNA translational control at the dorsoanterior corner of the mid-stage oocyte. Orb/CPEB and Wispy/GLD-2 are required for polyadenylation of gurken mRNA, but unlocalized gurken mRNA in the oocyte is not fully polyadenylated.¹ Norvell A, Wong J, Randolph K, Thompson L. Wispy and Orb cooperate in the cytoplasmic polyadenylation of localized gurken mRNA. Dev Dyn Off Publ Am Assoc Anat 2015; 244:1276-1285. [Google Scholar] At the dorsoanterior corner, Orb and gurken mRNA have been shown to be enriched at the edge of Processing bodies, where translation occurs.² Weil TT, Parton RM, Herpers B, Soetaert J, Veenendaal T, Xanthakis D, Dobbie IM, Halstead JM, Hayashi R, Rabouille C, et al. Drosophila patterning is established by differential association of mRNAs with P bodies. Nat Cell Biol 2012; 14:1305-1313; PMID:23178881; http://dx.doi.org/10.1038/ncb2627[Crossref], [PubMed], [Web of Science ®] [Google Scholar] Over-expression of Orb in the adjacent nurse cells, where gurken mRNA is transcribed, is sufficient to cause mis-expression of Gurken protein.³ Davidson A, Parton RM, Rabouille C, Weil TT, Davis I. Localized translation of gurken/TGF-α mRNA during axis specification is controlled by access to Orb/CPEB on processing bodies. Cell Rep 2016; 14:2451-2462; PMID:26947065; http://dx.doi.org/10.1016/j.celrep.2016.02.038[Crossref], [PubMed], [Web of Science ®] [Google Scholar] In orb mutant egg chambers, reducing the activity of CK2, a Serine/Threonine protein kinase, enhances the ventralized phenotype, consistent with perturbation of gurken translation.⁴ Wong LC, Costa A, McLeod I, Sarkeshik A, Yates J 3rd, Kyin S, Perlman D, Schedl P, et al. The functioning of the drosophila CPEB protein Orb is regulated by phosphorylation and requires casein kinase 2 activity. PLoS One 2011; 6:e24355; PMID:21949709; http://dx.doi.org/10.1371/journal.pone.0024355[Crossref], [PubMed], [Web of Science ®] [Google Scholar] Here we show that sites phosphorylated by CK2 overlap with active Orb and with Gurken protein expression. Together with our new findings we consolidate the literature into a working model for gurken mRNA translational control and review the role of kinases, cell cycle factors and polyadenylation machinery highlighting a multitude of conserved factors and mechanisms in the Drosophila egg chamber.     

Small Amphibian and Reptile Footprints from the Permian Carapacha Basin,Argentina

This paper contains a taxonomic study of the Permian tetrapod ichnofauna from the Carapacha Basin. Tetrapod traces are analyzed in their environmental context and compared with similar faunas from Europe and North America. This ichnofauna is particularly relevant because of the scarcity of Permian tetrapod tracks from South America and also of Permian tetrapod fossils from Argentina. Ephemeral fluvial and shallow lacustrine deposits compose the sedimentary succession of the basin, which is represented by the Carapacha Formation. Most of the tracks have been collected from the upper member of the formation (Urre-Lauquen Member), mainly from freshwater ephemeral lake deposits as well as from playa-lake mudflats. The deposits of this member have been attributed to the early Late Permian on the basis of a Glossopteris fossil flora. Ichnotaxonomic designations of tetrapod traces are made on the basis of morphologic features that reflect the anatomy of the producer and special attention has been paid to extramorphologic deformations observed in the track assemblage. A total of four footprint ichnotaxa have been recognized, namely Batrachichnus salamandroides (Geinitz, 1861 Geinitz, H. B. 1861. Dyas oder die Zechsteinformation und das Rhotliegende—Die animalischen Überreste der Dyas, 130 ppLeipzig: Wilhelm Engelmann.  [Google Scholar]), Hyloidichnus bifurcatus Gilmore, 1927 Gilmore, C. W. 1927. Fossil footprints from the Grand Canyon: second contribution. Smithsonian Miscellaneous Collection, 80(3): 1–78.  [Google Scholar], cf. Amphisauropus isp. and cf. Varanopus isp. These track taxa are associated with two forms of vertebrate swimming traces (Characichnos isp. and type A swimming trace) and a possible fish trail. Invertebrate trace fossils include abundant arthropod locomotion traces and Scoyenia isp. The ichnofauna is composed of six tetrapod ichnocoenoses that are dominated by tiny amphibian tracks attributed to Temnospondyli (Batrachichnus and type A swimming trace) and Seymouriamorpha (Amphisauropus), and also contain the footprints of small reptiles, mostly Captorhinomorpha and possibly Pelycosauria (Hyloidichnus and Varanopus). Even if the ichnofauna of the Carapacha Basin is slightly younger than typical examples from the literature of the Early Permian “red bed ichnofacies” (Hunt et al., 1995b Hunt, A. P., Lucas, S. G., Lockley, M. G., Haubold, H. and Braddy, S. 1995b. Tetrapod ichnofacies in Early Permian red beds of the American Southwest. Bulletin New Mexico Museum of Natural History and Science, 6: 295–301. Early Permian footprint facies [Google Scholar]), a comparison is made. However, further detailed case studies are needed to formally define this “red bed ichnofacies” and its prospective subdivisions.     

The molecular mechanism of Atg13 function in autophagy induction: What is hidden behind the data?

Atg13 is an essential subunit of the Atg1 autophagy initiation complex in yeast and its mammalian counterpart, ATG13, is indispensable for autophagy induction by the ULK1 complex. The N terminus of the protein folds into a HORMA domain, an architecture that has been revealed by crystallography.^1-4 Jao CC, Ragusa MJ, Stanley RE, Hurley JH. A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. P Natl Acad Sci USA 2013; 110:5486-91; PMID:23509291; http://dx.doi.org/10.1073/pnas.1220306110 Suzuki SW, Yamamoto H, Oikawa Y, Kondo-Kakuta C, Kimura Y, Hirano H, Ohsumi Y. Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation. P Natl Acad Sci USA 2015; 112:3350-5; PMID:25737544; http://dx.doi.org/10.1073/pnas.1421092112 Suzuki H, Kaizuka T, Mizushima NNoda NN. Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation. Nat Struct Mol Biol 2015; 22:572-81; PMID:26030876; http://dx.doi.org/10.1038/nsmb.3036 Qi SQ, Kim DJ, Stjepanovic G, Hurley JH. Structure of the human Atg13-Atg101 HORMA heterodimer: An interaction hub within the Ulk1 complex. Structure 2015; 23:1848-57; PMID:26299944; http://dx.doi.org/10.1016/j.str.2015.07.011  In human cells, the ATG13 HORMA domain interacts directly with ATG14, a subunit of the class III phosphatidylinositol 3-kinase complex.⁵ Park JM, Jung CH, Seo M, Otto NM, Grunwald D, Kim KH, Moriarity B, Kim YM, Starker C, Nho RS, et al. The Ulk1 complex mediates mTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating Atg14. Autophagy 2016; 12:547-64; PMID:27046250; http://dx.doi.org/10.1080/15548627.2016.1140293[Taylor & Francis Online], [Web of Science ®] [Google Scholar] In budding yeast, the HORMA domain of Atg13 recruits Atg14, but a direct interaction remains to be proven.¹ Jao CC, Ragusa MJ, Stanley RE, Hurley JH. A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. P Natl Acad Sci USA 2013; 110:5486-91; PMID:23509291; http://dx.doi.org/10.1073/pnas.1220306110[Crossref], [PubMed], [Web of Science ®] [Google Scholar] The amino acid sequence that follows the HORMA domain does not adopt any 3-dimensional structure on its own; therefore, it is termed an intrinsically disordered region (IDR). Here we discuss the results of 2 recent studies in light of previous reports on Atg13 from yeast. Together, they yield an insight into the molecular mechanism for the function of this intriguing protein, and reveal why Atg13, as well as the mammalian homolog ATG13, cannot have a structurally rigid architecture.     

New Important Iguanodontid and Theropod Trackways of the Tracksite Obernkirchen in the Berriasian of NW Germany and Megatracksite Concept of Central Europe

This article examines the high-resolution track horizon stratigraphy at the outcrop Obernkirchen. Massive sandstones, products of marine sand bar and fluviatile environments are present at the tracksite. Recently two track beds were examined in the outcrop. One new track slab of the lower track bed is described exposing well-preserved quadrupedal iguanodontid tracktypes of Iguanodontipus Sarjeant, Delair, and Lockley, 1998 Sarjeant, W. A. S., Delair, J. B. and Lockley, M. G. 1998. The footprints of Iguanodon: a history and taxonomic study. Ichnos, 6: 183–202. [Taylor & Francis Online] , [Google Scholar], and bipedal theropod tracks Megalosauropus Kaever and Lapparent, 1974 Kaever, M. and Lapparent, A. F. de. 1974. Les traces des pas le Dinosaures du Jurassique des Barkhausen (Basse Saxe, Allemagne). Bulletin de la Societé Geologique Français, 16: 516–525.  [Google Scholar]. The ichnogenus Iguanodontipus is discussed and the diagnosis extended. The tracksite Obernkirchen belongs to a megatracksite of the ancient coastline of the marginal marine Hercynic Basin of the Lower Cretaceous of Europe, including the four well-known sites Obernkirchen, Bad Rehburg, Münchehagen, and Bückeburg of Northwest Germany. Three different tracktypes of huge sauropods, theropods, and ornithopods are abundant at basal Lower Cretaceous siliciclastic coastlines in different regions in Spain, Portugal, England, Germany, and Switzerland. Dinosaur tracks are also present in carbonate platform environments of northern Italy and Istria.     

Teaching music in the flat world: Reflections on the work of Darling-Hammond and Rothman

Authors and scholars published within Arts Education Policy Review have been diligent to investigate various topics surrounding music educator preparation, mentoring, retention, as well as avenues for continued professional development and growth. Linda Darling-Hammond and Robert Rothman, along with various chapter authors, address education reform on an international level within Teaching in the Flat World: Learning from High-Performing Systems (2015 Rothman, R., & Darling-Hammond, L. (2015). Teaching quality initiatives in the United States. In L. Darling-Hammond & R. Rothman (Eds.), Teaching in the flat world: Learning from high-performing systems (pp. 6–27). New York, NY: Teachers College Press. [Google Scholar]). The purpose of this article is to examine the recommendations presented by Darling-Hammond, Rothman, and colleagues through the lens of music education research and policy review. Specific areas of focus include: (a) recruitment and rigor of teacher education programs, (b) alternative routes into the teaching profession, (c) teacher induction and new teacher support, (d) career advancement and professional development support, and (e) teacher evaluation.     

Animal-Facilitated Therapy Revisited

In Disney/Pixar's phenomenally popular animated film Finding Nemo (Stanton, 2003 Stanton, A. Writer/Director. 2003. Finding Nemo [Motion picture], United States: Pixar Animation Studios.  [Google Scholar]), one of the central themes of fish welfare was highlighted when the moorish idol, Gill, commented, “Fish aren't meant to be kept in a box, kid. It does things to you.” The notion that fish might have the capacity to suffer in captivity (Chandroo, Duncan, & Moccia, 2004a Chandroo, K. P., Duncan, I. J. H and Moccia, R. D. 2004a. Can fish suffer?: Perspectives on sentience, pain, fear and stress. Applied Animal Behaviour Science, 86: 225–250. [Crossref], [Web of Science ®] , [Google Scholar], 2004b Chandroo, K. P., Duncan, I. J. H and Moccia, R. D. 2004b. An evaluation of current perspectives on consciousness and pain in fish. Fish and Fisheries, 5: 281–295. [Crossref], [Web of Science ®] , [Google Scholar]) links to the larger question of sentiency, which remains a fundamental tenet when justifying concerns for nonhuman animal welfare (Dawkins, 2006 Dawkins, M. S. 2006. Through animal eyes: What behaviour tells us. Applied Animal Behaviour Science, 100: 4–10. [Crossref], [Web of Science ®] , [Google Scholar]; Huntingford et al., 2006 Huntingford, F. A., Adams, C., Braithwaite, V. A., Kadri, S., Pottinger, T. G.Sandoe, P. 2006. Review paper: Current issues in fish welfare. Journal of Fish Biology, 68: 332–372. [Crossref], [Web of Science ®] , [Google Scholar]). Although terrestrial nonhuman-animal welfare has been discussed and explored for many years, the development of aquatic animal welfare concepts and approaches remains relatively new and beyond public awareness (Braastad, Damsgård, & Juell, 2006; Broom, 2007 Broom, D. M. 2007. Cognitive ability and sentience: Which aquatic animals should be protected?. Disease of Aquatic Organisms, 75: 99–108. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]; Farmed Animal Welfare Council, 1996; Fisheries Society of the British Isles, 2002; Håstein, Scarfe, & Lund, 2005; Iwama, 2007 Iwama, G. K. 2007. The welfare of fish. Diseases of Aquatic Organisms, 75: 155–158. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]; Schreck, 1981 Schreck, C. B. 1981. “Stress and compensation in teleostean fishes: Response to social and physical factors”. In Stress and fish, Edited by: Pickering, A. D. 295–321. London: Academic.  [Google Scholar]).     

Synthesis and Biological Evaluations of Click-Generated Nitrogen Mustards

This paper describes the synthesis of new click-generated nitrogen mustards and their biological evaluation. By using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction, we managed to synthesize eight new nitrogen mustards. This strategy paves the way for the synthesis of a new family of nitrogen mustard, with an important structural variability. Furthermore, we studied the biological activity of synthesized compounds by testing their cytotoxicity on four representative cancer cell lines A431, JURKAT, K562, and U266. One structure, 1-benzyl-4-(N,N-di-2-chloroethylaminomethyl)-1H-[1 Noll, D.M.; McG.Mason, T.; Miller, P.S. Formation and repair of interstrand cross-links in DNA. Chem. Rev. 2006, 106, 277–301.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar],2 Rink, S.M.; Hopkins, P.B. Direct evidence for DNA intrastrand cross-linking by the nitrogen mustard mechlorethamine in synthetic oligonucleotides. Bioorg. Med. Chem. Lett. 1995, 5(23), 2845–2850.[Crossref], [Web of Science ®] , [Google Scholar],3 Chabner, B.A.; Collins, J.M. Cancer Chemotherapy: Principles and Practices, PA, J.B. Lippincott Company, Philadelphia, 1990, pp. 276–313. [Google Scholar]]triazole, showed an interesting cytotoxic effect.     

An Efficient Alternative Route To 3,6-Disubstituted-Furo[2,3-d]Pyrimidin-2-One Analogues

Copper(I)-catalyzed 5-endo-dig cyclizations of 5-(alkyn-1-yl)uracil derivatives had given poor yields of substituted furo[2 Robins, M. J. and Barr, P. J. 1983. Nucleic acid related compounds. 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides. J. Org. Chem, 48: 1854–1862. [CSA][CROSSREF][Crossref], [Web of Science ®] , [Google Scholar], 3 De Clercq, E., Descamps, J., Balzarini, J., Giziewicz, J., Barr, P. J. and Robins, M. J. 1983. Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides. J. Med. Chem, 26: 661–666. [PUBMED][INFOTRIEVE][CSA][CROSSREF][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]pyrimidin-2-ones unless the uracil ring was substituted at N1 with alkyl or glycosyl groups. This limited flexibility for the synthesis of analogues with varied substituents at N3 and/or C6 of the furo[2 Robins, M. J. and Barr, P. J. 1983. Nucleic acid related compounds. 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides. J. Org. Chem, 48: 1854–1862. [CSA][CROSSREF][Crossref], [Web of Science ®] , [Google Scholar], 3 De Clercq, E., Descamps, J., Balzarini, J., Giziewicz, J., Barr, P. J. and Robins, M. J. 1983. Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides. J. Med. Chem, 26: 661–666. [PUBMED][INFOTRIEVE][CSA][CROSSREF][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]pyrimidin-2-one core has been overcome with 5-(3-hydroxyalkyn-1-yl)uracil compounds with no substituent at N1. Manipulation of the side-chain hydroxyl group gives access to additional furo[2,3-d]pyrimidin-2-one analogues.