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.     

Integrative taxonomy of the cave-dwelling mysids of the genus Hemimysis

The genus Hemimysis (Malacostraca: Mysida: Mysidae) encompasses near-bottom, demersal and cave-dwelling mysids living in the marine, brackish and freshwater habitats around the European coast, from the Caspian Sea to the Scandinavian Peninsula. We conducted cladistic analysis of 52 morphological characters of all nine species and three subspecies of the genus Hemimysis. We also completed a molecular analysis based on three molecular markers of Hemimysis lamornae (Couch, 1856) found in the English Channel, the Mediterranean Sea, and the Black Sea. Both analyses did not support monophyly of Hemimysis lamornae. We thus consider the former subspecies H. lamornae pontica (Czerniavsky, 1882 Chevaldonné, P., &; Lejeusne, C. (2003). Regional warming‐induced species shift in north‐west Mediterranean marine caves. Ecology Letters, 6, 371–379. doi:10.1046/j.1461-0248.2003.00439.x.[Crossref], [Web of Science ®] , [Google Scholar]) and H. lamornae mediterranea Bacescu, 1936 Bacescu, M. (1936). Hemimysis lamornae sbsp. reducta, nov. sbsp. et Hemimysis anomala dans les eaux roumaines de la Mer Noire (avec une etude comparative des forms de Hem. lamornae des autres mers: H. l. typica et H.l. mediterranea, nov. sbsp.). Annales Scientifiques de L’Universite de Jassy, 23, 331–338. [Google Scholar] as valid species. Analysis of mitochondrial cytochrome oxidase subunit I (COI) sequences of H. pontica shows no significant divergence between mysids living in the marine caves of Crimea and Bulgaria. Morphological trends in Hemimysis are discussed, H. pontica Czerniavsky, 1882 Chevaldonné, P., &; Lejeusne, C. (2003). Regional warming‐induced species shift in north‐west Mediterranean marine caves. Ecology Letters, 6, 371–379. doi:10.1046/j.1461-0248.2003.00439.x.[Crossref], [Web of Science ®] , [Google Scholar] is redescribed, and a new key to all 11 species of the genus is given.     

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.     

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.     

Two new harvestmen species (Arachnida: Opiliones) from the Caucasus

Two new harvestmen species of the family Phalangiidae, Rilaena caucasica sp. n. and Rilaena silhavyi sp. n. are diagnosed, illustrated, and described from the Caucasus region. Comparative illustration of the related Rilaena anatolica (Roewer, 1956), R. atrolutea (Roewer, 1915) and R. kelbajarica Snegovaya &; Pkhakadze, 2014 Snegovaya, N. Y., &; Pkhakadze, V. D. (2014): New species of the genus Rilaena (Opiliones, Phalangiidae) from the mount Gyamish, Azerbaijan. Vestnik zoologii, 48, 313–318. doi: 10.2478/vzoo-2014-0037[Crossref] , [Google Scholar] are given.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:7B29FD94-45A2-4E32-A41E-3276E016410B     

On several conjectures from evolution of dispersal

We address several conjectures raised in Cantrell et al. [Evolution of dispersal and ideal free distribution, Math. Biosci. Eng. 7 (2010), pp. 17–36 [9 Cantrell, R. S., Cosner, C. and Lou, Y. 2010. Evolution of dispersal and ideal free distribution. Math. Biosci. Eng., 7: 17–36. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]] concerning the dynamics of a diffusion–advection–competition model for two competing species. A conditional dispersal strategy, which results in the ideal free distribution of a single population at equilibrium, was found in Cantrell et al. [9 Cantrell, R. S., Cosner, C. and Lou, Y. 2010. Evolution of dispersal and ideal free distribution. Math. Biosci. Eng., 7: 17–36. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. It was shown in [9 Cantrell, R. S., Cosner, C. and Lou, Y. 2010. Evolution of dispersal and ideal free distribution. Math. Biosci. Eng., 7: 17–36. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] that this special dispersal strategy is a local evolutionarily stable strategy (ESS) when the random diffusion rates of the two species are equal, and here we show that it is a global ESS for arbitrary random diffusion rates. The conditions in [9 Cantrell, R. S., Cosner, C. and Lou, Y. 2010. Evolution of dispersal and ideal free distribution. Math. Biosci. Eng., 7: 17–36. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] for the coexistence of two species are substantially improved. Finally, we show that this special dispersal strategy is not globally convergent stable for certain resource functions, in contrast with the result from [9 Cantrell, R. S., Cosner, C. and Lou, Y. 2010. Evolution of dispersal and ideal free distribution. Math. Biosci. Eng., 7: 17–36. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], which roughly says that this dispersal strategy is globally convergent stable for any monotone resource function.     

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.     

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]).     

VEGF-A121a binding to Neuropilins – A concept revisited

All known splice isoforms of vascular endothelial growth factor A (VEGF-A) can bind to the receptor tyrosine kinases VEGFR-1 and VEGFR-2. We focus here on VEGF-A121a and VEGF-A165a, two of the most abundant VEGF-A splice isoforms in human tissue^{1 Kut C, Mac Gabhann F, Popel AS. Where is VEGF in the body? A meta-analysis of VEGF distribution in cancer. Br J Cancer. 2007;97:978-85. doi:10.1038/sj.bjc.6603923. PMID:17912242.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]}, and their ability to bind the Neuropilin co-receptors NRP1 and NRP2. The Neuropilins are key vascular, immune, and nervous system receptors on endothelial cells, neuronal axons, and regulatory T cells respectively. They serve as co-receptors for the Plexins in Semaphorin binding on neuronal and vascular endothelial cells, and for the VEGFRs in VEGF binding on vascular and lymphatic endothelial cells, and thus regulate the initiation and coordination of cell signaling by Semaphorins and VEGFs.^{2 Guo HF, Vander Kooi CW. Neuropilin Functions as an Essential Cell Surface Receptor. J Biol Chem. 2015;290:29120-6. doi:10.1074/jbc.R115.687327. PMID:26451046.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]} There is conflicting evidence in the literature as to whether only heparin-binding VEGF-A isoforms – that is, isoforms with domains encoded by exons 6 and/or 7 plus 8a – bind to Neuropilins on endothelial cells. While it is clear that VEGF-A165a binds to both NRP1 and NRP2, published studies do not all agree on the ability of VEGF-A121a to bind NRPs. Here, we review and attempt to reconcile evidence for and against VEGF-A121a binding to Neuropilins. This evidence suggests that, in vitro, VEGF-A121a can bind to both NRP1 and NRP2 via domains encoded by exons 5 and 8a; in the case of NRP1, VEGF-A121a binds with lower affinity than VEGF-A165a. In in vitro cell culture experiments, both NRP1 and NRP2 can enhance VEGF-A121a-induced phosphorylation of VEGFR2 and downstream signaling including proliferation. However, unlike VEGFA-165a, experiments have shown that VEGF-A121a does not ‘bridge’ VEGFR2 and NRP1, i.e. it does not bind both receptors simultaneously at their extracellular domain. Thus, the mechanism by which Neuropilins potentiate VEGF-A121a-mediated VEGFR2 signaling may be different from that for VEGF-A165a. We suggest such an alternate mechanism: interactions between NRP1 and VEGFR2 transmembrane (TM) and intracellular (IC) domains.     

Gobies are deeply divided: phylogenetic evidence from nuclear DNA (Teleostei: Gobioidei: Gobiidae)

Gobies (Gobiidae sensu Gill & Mooi, 2012 Gill, A. and Mooi, R. 2012. Thalasseleotrididae, new family of marine gobioid fishes from New Zealand and temperate Australia, with a revised definition of its sister taxon, the Gobiidae (Teleostei: Acanthomorpha). Zootaxa, 3266: 41–52.  [Google Scholar]) are one of the most diverse families of vertebrates, and comprise over 1700 species of marine, brackish and freshwater fishes. Phylogenetic studies based on morphological characters and mtDNA have suggested that goby diversity is asymmetrically split between a speciose clade of predominantly marine species, and a less rich, but ecologically diverse, clade comprising predominantly freshwater and brackish species. This study is the first to explore this deep divide in gobies and their relationships at the family level using phylogenetic data from nuclear genes (RAG1, rhodopsin). Our results confirm the split within the Gobiidae, and agree with prior molecular studies on the inclusion of the following taxa within the two goby clades: (i) the more diverse of the two clades of gobies (the ‘Gobiidae’ sensu stricto of Thacker 2009 Thacker, C. E. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia, 1: 93–104. doi:10.1643/CI-08-004[Crossref], [Web of Science ®] , [Google Scholar]) comprises the gobiines, microdesmines, ptereleotrines and kraemeriines; (ii) the less diverse of the two gobiid clades (‘Gobionellidae’ sensu Thacker 2009 Thacker, C. E. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia, 1: 93–104. doi:10.1643/CI-08-004[Crossref], [Web of Science ®] , [Google Scholar]) includes the gobionellines, oxudercines, amblyopines, sicydiines, as well as the European sand gobies. Some relationships within the two major gobiid clades remain unclear. Specifically, there remains confusion regarding the monophyly and interrelationships between the northern Pacific gobionellines, the Mugilogobius group gobionellines, and the European sand gobies. Additionally, within Thacker's (2009 Thacker, C. E. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia, 1: 93–104. doi:10.1643/CI-08-004[Crossref], [Web of Science ®] , [Google Scholar]) Gobiidae sensu stricto, there are several well-supported groups (e.g. the wormfishes and dartfishes, the Coral Gobies, the Gobiosomatini), yet relationships among these groups are still poorly resolved despite the use of data from two conserved nuclear genes. Future phylogenetic analyses of gobies will benefit greatly from taxon sampling that includes groups that have been historically under-represented in molecular studies (e.g. European sand gobies, northern Pacific gobionellines, African species), as well as deeper genetic sampling including large numbers of independent loci from throughout the genome (i.e. a phylogenomic approach).     

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.     

Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds

In total 52 samples of Sahiwal (19 Excoffier L, Laval G, Schneider S. Arlequin 3.01: An integrated software package for population genetics data analysis. Evol Bioinform Online 2005; 1:47–50.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), Tharparkar (17 Hayes BJ, Bowman PJ, Chamberlain, AJ, Goddard ME. Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 2009; 92:433–443.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), and Gir (16 Melka HD, Jeon EK, Kim SW, Han JB, Yoon D, Kim KS. Identification of genomic differences between Hanwoo and Holstein breeds using the Illumina Bovine SNP50 BeadChip. Genomics Inform 2011; 9:69–73.[Crossref] , [Google Scholar]) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%?50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248?±?0.006, 0.241?±?0.007, and 0.242?±?0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold’s genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r²?相似文献   

Conformations of cysteine disulfides of peptide toxins: Advantage of differentiating forward and reverse asymmetric disulfide conformers

Conformations of cysteine disulfides were analyzed in X-ray, nuclear magnetic resonance (NMR), and co-crystal structures of peptide toxins retrieved from Protein Data Bank. The parameters side chain torsional angles, disulfide strain energy, interatomic Cα/Cβ distances, and Ramachandran angles were used as probes to derive conformational features of cysteine disulfides. Schmidt, Ho, and Hogg (2006 Schmidt, B., Ho, L., &; Hogg, P. J. (2006). Allosteric disulfide bonds. Biochemistry, 45, 7429–7433.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) Allosteric disulfide bonds. Biochemistry, 45, 7429–7433 scheme was adapted to classify the disulfide conformations of peptide toxins. Anomalies were observed while treating “forward” and “reverse” asymmetric disulfide conformers as same disulfide conformation in peptide toxins. Thus, new scheme was proposed to classify “forward” and “reverse” asymmetric disulfide conformers separately. Total available conformers space for classification of toxins disulfides is 32. Interestingly, all 32 disulfide conformations are observed in peptide toxins. –LHSpiral is predominant disulfide conformation of peptide toxins. Significant variations were observed in population of occurrence of disulfide conformers, disulfide strain energy, and distribution of D_Cα-Cα and D_Cβ-Cβ values between X-ray, NMR, and co-crystal structures of peptide toxins. The observed differences in conformations of disulfides of same peptide toxins between different states were used as platform to demonstrate advantage of differentiating forward and reverse asymmetric disulfide conformers. Newly proposed scheme allows accurate representation of true conformational diversity of disulfides between X-ray and NMR structures of same peptide toxins. Newly proposed scheme also permits to derive additional structural information from nomenclature which was illustrated by comparing conformations of disulfides between unbound and bound form of toxin with channel/receptor. The results will be of interest for growing field of structural venomics and conformational analysis of peptide/protein disulfides.

Communicated by Ramaswamy H. Sarma     

Mercury risks versus nutritional benefits of tribal commercial fish harvests in the Upper Laurentian Great Lakes

The Inter-Tribal Fisheries and Assessment Program (ITFAP) of the Chippewa Ottawa Resource Authority (CORA) in Sault Ste. Marie, Michigan, has been monitoring contaminant concentrations in the fillet portions of lake trout (Salvelinus namaycush) and lake whitefish (Coregonus clupeaformis) from the waters of lakes Superior, Huron, and Michigan since 1991. The primary purpose of this article is to present a risk quantification of methylmercury (MeHg) that is adjusted for nutritional benefit, originally presented by Ginsberg and Toal (2009 Ginsberg GL and Toal BF. 2009. Quantitative approach for incorporating methylmercury risks and omega-3 fatty acid benefits in developing species-specific fish consumption advice. Environ Health Perspect 117:267–75[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 2015) on trends in contaminant concentrations in fillet portions of these commercial fish that we recently reported in Dellinger et al. (2014 Dellinger JA, Moths MD, Dellinger M, et al. 2014. Contaminant trends in freshwater fish from the Great Lakes: A 20 year analysis. Hum Ecol Risk Assess 20:461–78[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]). Both species of fish caught by tribal fishermen showed clear benefits to cardiovascular health and infant neurodevelopment if consumed at a rate of six ounces per week. However, other popularly consumed fish such as cod, tuna, and tilapia are estimated to have only marginal benefit or net negative effects on cardiovascular health and infant neurodevelopment. This dynamic assessment of benefits and risks further demonstrates the importance of traditionally caught fish in tribal health.     

Capillary Effects on Natural Remobilization of Pools of Dense Non-Aqueous Phase Liquid Mixtures in Porous Media

The natural remobilization of an initially static mixed dense non-aqueous phase liquid (DNAPL) pool due to dissolution was demonstrated by (Roy et al. 2002 Roy, J. W., Smith, J. E. and Gillham, R. W. 2002. Natural remobilization of multicomponent DNAPL pools due to dissolution. J. Contam. Hydrol., 59: 163–186. [Crossref], [PubMed], [Web of Science ®] [Google Scholar], 2004 Roy, J. W., Smith, J. E. and Gillham, R. W. 2004. Laboratory evidence of natural remobilization of multicomponent DNAPL pools due to dissolution. J. Contam. Hydrol., 74: 145–161. [Crossref], [PubMed], [Web of Science ®] [Google Scholar]) using a compositional mathematical model and laboratory experiments with open pools over a porous medium. The purposes of this study were to: a) demonstrate natural remobilization for a pool within porous media (as opposed to an open pool); and b) analyze the capillary effects associated with residual formation, a changing saturation profile, hysteresis, and aging, as these processes may reduce the potential for natural remobilization of pools in porous media. DNAPL pools comprised of tetrachloroethene and benzene were created within a zone of larger glass beads overlying smaller glass beads, in a water-saturated 2-D flow cell. In one case, remobilization occurred in the form of a DNAPL finger, after 56 days of flushing. In another case, no remobilization had occurred after 64 days of flushing, though the density increased by 430 kg m ^?3 and remobilization was predicted by the compositional model. Comparison of observations with model predictions suggest that contact angle hysteresis, related to an observed change in wettability, was the most significant contributing factor causing overprediction of the potential for natural remobilization.