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   

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.     

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.     

Spirodesmos milanai n. isp.: A Shallow-Water Spiral Trace Fossil from the Cambrian of the Eastern Cordillera,Northwest Argentina

Abstract

A new ichnofossiliferous locality in Salta Province (northwest Argentina) contains an association with numerous irregular spiral traces assigned to Spirodesmos milanai n. isp., in mature sandstones and quartzites with rippled bedding surfaces, rare wavy lamination and cross-bedded stratification. This record of early spiral behavior is interpreted as a primitive grazing method formed on muddy laminae above sand layers, and is related to a feeding strategy of an annelid-type of organism. Associated traces are Cruziana cf. semiplicata, Diplocraterion isp., Monocraterion isp., Rusophycus isp., Skolithos linearis Haldeman and Skolithos magnus Howell. The ichnoassemblage is similar to a shallow-water ichnoassociation from the Permian Ecca Group of South Africa (Mason et al., 1983 Mason, T. R., Stanistreet, I. G. and Tavener-Smith, R. 1983. Spiral trace fossils from the Permian Ecca Group of Zululand. Lethaia, 16: 241–247. [Crossref], [Web of Science ®] , [Google Scholar]).     

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.     

Revisiting Lepidonella Yosii (Collembola: Paronellidae): character overview,checklist of world species and reassessment of Pseudoparonella doveri Carpenter

Characters used in the taxonomy of the genus Lepidonella Yosii, 1960 (Collembola: Paronellidae) are listed and discussed. Several new ones are introduced. An overview of pseudopore patterns across Collembola is presented, with several new locations of these structures across Entomobryomorpha. Their interest at different taxonomic level is underlined. The genus Lepidonella is redefined. The American species L. marimuti Soto Adames &; Bellini, 2015 Soto-Adames FN, Bellini BC. 2015. Dorsal chaetotaxy of neotropical species supports a basal position for the genus Lepidonella among scaled Paronellidae (Collembola, Entomobryoidea). Florida Entomologist. 98(1):330–341.[Crossref], [Web of Science ®] , [Google Scholar] is placed in incertae sedis among Lepidonella. Lepidonella species of the world are listed with synonymies and combinations. The Malaysian troglobitic species Pseudoparonella doveri Carpenter, 1933 Carpenter GH. 1933. XIX. Fauna of the Batu caves, Selangor. Journal of the Federated Malay States Museum. 17:217–221. [Google Scholar] is redescribed in detail, with emphasis on its pattern of antennal chaetae, and transferred to the genus Lepidonella. Its close similarity with L. lecongkieti Deharveng &; Bedos, 1995 Deharveng L, Bedos A. 1995. Lepidonella lecongkieti n.sp., premier Collembole cavernicole du Vietnam (Collembola, Paronellidae). Bulletin de la Société entomologique de France. 100(1):21–24. [Google Scholar] from southwestern Vietnam caves is underlined. This disjunct distribution is briefly discussed.     

Understanding Kurdish ethno-nationalism in Turkey: socio-economy,religion, and politics

Abstract

In his recent article in Ethnic and Racial Studies, entitled ‘Curbing Kurdish ethno-nationalism in Turkey’, (Sarigil 2010 Sarigil, Zeki. 2010. Curbing Kurdish ethno-nationalism in Turkey: an empirical assessment of pro-Islamic and socio-economic approaches. Ethnic and Racial Studies, 33(3): 533–53. [Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]) tests two rival hypotheses regarding Kurdish ethno-nationalism in Turkey and, using data from the World Values Survey (WVS), finds that socio-economic status (levels of income and education) better explains the individual roots of Kurdish ethno-nationalism in Turkey than does religiousness. In this paper, I offer both a methodological critique of Sarigil's research and a replication of his model with a more appropriate sample. I first argue that Sarigil's research design lacks internal validity because it studies Kurdish nationalism within a sample that predominantly consists of Turks, which invalidates his findings. I then replicate and expand Sarigil's model within a specific sample of Kurdish-speaking people in Turkey. The results show dramatic changes. Religiosity and political satisfaction seem to be better predictors of support for Kurdish ethno-nationalism in Turkey than do socio-economic factors.     

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.     

Creating a human head finite element model using a multi-block approach for predicting skull response and brain pressure

To better understand head injuries, human head finite element (FE) models have been reported in the literature. In scenarios where the head is directly impacted and measurements of head accelerations are not available, a high-quality skull model, as well as a high-quality brain model, is needed to predict the effect of impact on the brain through the skull. Furthermore, predicting cranial bone fractures requires comprehensively validated skull models. Lastly, high-quality meshes for both the skull and brain are needed for accurate strain/stress predictions across the entire head. Hence, we adopted a multi-block approach to develop hexahedral meshes for the brain, skull, and scalp simultaneously, a first approach in its kind. We then validated our model against experimental data of brain pressures (Nahum et al., 1977 Nahum AM, Smith R, Ward CC. 1977. Intracranial pressure dynamics during head impact. Proceedings of the 21st Stapp Car Crash Conference, SAE Paper No. 770922; Warrendale, PA: Society of Automotive Engineers.[Crossref] , [Google Scholar]) and comprehensive skull responses (Yoganandan et al., 1995 Yoganandan N, Pintar FA, Sances A, Jr., Walsh PR, Ewing CL, Thomas DJ, Snyder RG. 1995. Biomechanics of skull fracture. J Neurotrauma. 12(4):659–668.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], Yoganandan et al., 2004 Yoganandan N, Zhang J, Pintar FA. 2004. Force and acceleration corridors from lateral head impact. Traffic Injury Prevention. 5(4):368–373.[Taylor &; Francis Online] , [Google Scholar], and Raymond et al., 2009 Raymond D, Van Ee C, Crawford G, Bir C. 2009. Tolerance of the skull to blunt ballistic temporo-parietal impact. J Biomech. 42(15):2479–2485.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). We concluded that a human head FE model was developed with capabilities to predict blunt- and ballistic-impact-induced skull fractures and pressure-related brain injuries.     

Chironomidae (Insecta: Diptera) from four protected areas in the state of Pernambuco,Brazil

New records and distributional notes of Chironomidae (Insecta, Diptera) are provided for four protected areas in the state of Pernambuco, northeastern Brazil. Additionally, we also present new records and update of distributional ranges from Brazil and the Neotropical Region. In total, 810 specimens belonging to 35 genera within the subfamilies Chironominae (22 taxa), Tanypodinae (11 taxa) and Orthocladiinae (2 taxa) were found. The subfamilies Chironominae and Tanypodinae predominated. Axarus Roback, 1980 Roback, S.S. (1980), ‘New name for Anceus Roback nec Anceus Risso’, Entomological News, 91, 32.[Web of Science ®] , [Google Scholar] and the Tanytarsus ortoni-group were recorded for the first time in the state of Pernambuco, while Nanocladius Kieffer, 1913a Kieffer, J.J. (1913b), ‘Nouvelle étude sur les Chironomides de l'Indian Museum de Calcutta’, Records of the Indian Museum, 9, 119–197. [Google Scholar] was recorded for the first time in the Northeast Region of Brazil. Our results make evident how much and where current knowledge of the northeastern Brazil chironomids remains fragmentary.     

Social influence networks and understanding of citizenship

Abstract

I propose an analytical model to combine macro-sociological aspects of cultural boundary making with socio-psychological research on social influence networks. This model will help me investigate how the understanding of citizenship of Swiss local politicians is influenced by their interactions with their colleagues in the course of naturalization processes. I argue that the decision-making processes, and debates involving criteria for naturalization, have an impact on individuals’ understandings of citizenship. First, I will invoke Wimmer's (2002 Wimmer , Andreas 2002 Nationalist Exclusion and Ethnic Conflict: Shadows of Modernity , Cambridge : Cambridge University Press [Crossref] , [Google Scholar]) theory on cultural negotiation processes and cultural compromise, to lay the basis for a better understanding of how individual national identities converge. I will then extend my analytical model with theories in social psychology that discuss attitude and norm formations, as well as network theories of social influence, in order to understand why even politicians with strong opinions change their attitudes. The empirical part of the article draws on 180 interviews with Swiss local politicians.     

A metabolic energy expenditure model with a continuous first derivative and its application to predictive simulations of gait

Whether humans minimize metabolic energy in gait is unknown. Gradient-based optimization could be used to predict gait without using walking data but requires a twice differentiable metabolic energy model. Therefore, the metabolic energy model of Umberger et al. (2003 Umberger BR, Gerritsen KG, Martin PE. 2003. A model of human muscle energy expenditure. Comput Methods Biomech Biomed Eng. 6(2):99–111.[Taylor &; Francis Online] , [Google Scholar]) was adapted to be twice differentiable. Predictive simulations of a reaching task and gait were solved using this continuous model and by minimizing effort. The reaching task simulation showed that energy minimization predicts unrealistic movements when compared to effort minimization. The predictive gait simulations showed that objectives other than metabolic energy are also important in gait.     

Welfare of Apes in Captive Environments: Comments On,and By,a Specific Group of Apes

Accurately determining the proper captive environment for apes requires adequately assessing the psychological similarities between apes and humans. Scientists currently believe apes lack mental complexity (Millikan, 2006 Millikan, R. G. 2006. “Styles of rationality”. In Rational animals?, Edited by: Hurley, S. and Nudds, M. 117–126. Oxford, , England: Oxford University Press.. [Crossref] , [Google Scholar]), raising questions concerning the evolution of human culture from ape-like societies (Tomasello, 1999 Tomasello, M. 1999. The cultural origins of human cognition, Cambridge, , MA: Harvard University Press..  [Google Scholar]). A long-term cultural study with bonobos suggests less intellectual divergence from humans than currently postulated (Savage-Rumbaugh, 2005 Savage-Rumbaugh, E. S. 2005. “Individual differences in language competencies in apes resulting from unique rearing conditions imposed by different first epistemologies”. In Symbol use and symbolic representation, Edited by: Namy, L. L. 199–219. Mahwah, , NJ: Lawrence Erlbaum Associates, Inc..  [Google Scholar]). Because humans view apes as mentally limited, some current captive environments may appear idyllic while offering only an illusion of appropriate care, derived from a simplistic view of what apes are, rather than what they might be. This perception of apes determines their handling, which determines their mental development, which perpetuates the prevailing perception. Only breaking this cycle will allow the current perception of apes to change. Their usual captive environment limits any demonstration of culture. However, the bonobo study reveals what ape culture can become, which should affect future welfare considerations for at least those species genetically close to humans (bonobos and chimpanzees). Development of a languaged bonobo culture allows these nonhuman animals to provide their own responses regarding adequate ape welfare.