What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background - The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species. Results - A dataset of 566 South-American accessions (encompassing 89 species and subspecies) was analyzed in two steps. First, with the program STRUCTURE 2.2 in an 'unsupervised' procedure, individual accessions were assigned to inferred clusters based on genetic similarity. The results showed that the South American members of section Petota could be arranged in 16 clusters of various size and composition. Next, the accessions within the clusters were grouped by maximizing the partitioning of genetic diversity among subgroups (i.e., maximizing Fst values) for all available individuals of the accessions (2767 genotypes). This two-step approach produced an optimal partitioning into 44 groups. Some of the species clustered as genetically distinct groups, either on their own, or combined with one or more other species. However, accessions of other species were distributed over more than one cluster, and did not form genetically distinct units. Conclusions - We could not find any support for 43 species (almost half of our dataset). For 28 species some level of support could be found varying from good to weak. For 18 species no conclusions could be drawn as the number of accessions included in our dataset was too low. These molecular data should be combined with data from morphological surveys, with geographical distribution data, and with information from crossing experiments to identify natural units at the species level. However, the data do indicate which taxa or combinations of taxa are clearly supported by a distinct set of molecular marker data, leaving other taxa unsupported. Therefore, the approach taken provides a general method to evaluate the taxonomic system in any species complex for which molecular data are available

Determinants of GBP Recruitment to Toxoplasma gondii Vacuoles and the Parasitic Factors That Control It

IFN-γ is a major cytokine that mediates resistance against the intracellular parasite Toxoplasma gondii. The p65 guanylate-binding proteins (GBPs) are strongly induced by IFN-γ. We studied the behavior of murine GBP1 (mGBP1) upon infection with T. gondii in vitro and confirmed that IFN-γ-dependent re-localization of mGBP1 to the parasitophorous vacuole (PV) correlates with the virulence type of the parasite. We identified three parasitic factors, ROP16, ROP18, and GRA15 that determine strain-specific accumulation of mGBP1 on the PV. These highly polymorphic proteins are held responsible for a large part of the strain-specific differences in virulence. Therefore, our data suggest that virulence of T. gondii in animals may rely in part on recognition by GBPs. However, phagosomes or vacuoles containing Trypanosoma cruzi did not recruit mGBP1. Co-immunoprecipitation revealed mGBP2, mGBP4, and mGBP5 as binding partners of mGBP1. Indeed, mGBP2 and mGBP5 co-localize with mGBP1 in T. gondii-infected cells. T. gondii thus elicits a cell-autonomous immune response in mice with GBPs involved. Three parasitic virulence factors and unknown IFN-γ-dependent host factors regulate this complex process. Depending on the virulence of the strains involved, numerous GBPs are brought to the PV as part of a large, multimeric structure to combat T. gondii.National Institutes of Health (U.S.)Massachusetts Life Sciences Center (New Investigator Award)National Institute of General Medical Sciences (U.S.) (Pre-Doctoral Grant in the Biological Sciences (5-T32-GM007287-33))Studienstiftung des deutschen VolkesCancer Research Institute (New York, N.Y.)Cleo and Paul Schimmel FoundationBayer HealthcareHuman Frontier Science Program (Strasbourg, France

The genome landscape of indigenous African cattle

Background: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. Results: We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/ or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds. Conclusions: Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent

Effects of macromolecular crowding on intracellular diffusion from a single particle perspective

Compared to biochemical reactions taking place in relatively well-defined aqueous solutions in vitro, the corresponding reactions happening in vivo occur in extremely complex environments containing only 60–70% water by volume, with the remainder consisting of an undefined array of bio-molecules. In a biological setting, such extremely complex and volume-occupied solution environments are termed ‘crowded’. Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts. In this review, we seek to highlight how the complex background environment of the cell can affect the diffusion of substances within it. Engaging the subject from the perspective of a single particle’s motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments. We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material

Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred

20-Year Risks of Breast-Cancer Recurrence after Stopping Endocrine Therapy at 5 Years

The administration of endocrine therapy for 5 years substantially reduces recurrence rates during and after treatment in women with early-stage, estrogen-receptor (ER)-positive breast cancer. Extending such therapy beyond 5 years offers further protection but has additional side effects. Obtaining data on the absolute risk of subsequent distant recurrence if therapy stops at 5 years could help determine whether to extend treatment

Augmented Reality for the assessment of children's spatial memory in real settings

Short-term memory can be defined as the capacity for holding a small amount of information in mind in an active state for a short period of time. There are no available, specific, and adapted instruments to study the development of memory and spatial orientation in people while they are moving. In this paper, we present the ARSM (Augmented Reality Spatial Memory) task, the first Augmented Reality task that involves a user's movement to assess spatial short-term memory in healthy children. The experimental procedure of the ARSM task was designed to assess the children s skill to retain visuospatial information. They were individually asked to remember the real place where augmented reality objects were located. The children (N=76) were divided into two groups: preschool (5-6 year olds) and primary school (7-8 year olds). We found a significant improvement in ARSM task performance in the older group. The correlations between scores for the ARSM task and traditional procedures were significant. These traditional procedures were the Dot Matrix subtest for the assessment of visuospatial short-term memory of the computerized AWMA-2 battery and a parent s questionnaire about a child s everyday spatial memory. Hence, we suggest that the ARSM task has high verisimilitude with spatial short-term memory skills in real life. In addition, we evaluated the ARSM task s usability and perceived satisfaction. The study revealed that the younger children were more satisfied with the ARSM task. This novel instrument could be useful in detecting visuospatial short-term difficulties that affect school academic achievementFunded by the Spanish Government (MINECO) and European Regional Development Fund (FEDER) in the CHILDMNEMOS project TIN2012-37381-C02-01, Gobierno de Aragon (Dpt. Industria e Innovacion), Fondo Social Europeo, Fundacion Universitaria Antonio Gargallo and Obra Social Ibercaja. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Juan, M.; Mendez Lopez, M.; Pérez Hernández, E.; Albiol Pérez, S. (2014). Augmented Reality for the assessment of children's spatial memory in real settings. PLoS ONE. 9(12):113751-113771. https://doi.org/10.1371/journal.pone.0113751S113751113771912Linn, M. C., & Petersen, A. C. (1985). Emergence and Characterization of Sex Differences in Spatial Ability: A Meta-Analysis. Child Development, 56(6), 1479. doi:10.2307/1130467Simmons, F. R., Willis, C., & Adams, A.-M. (2012). Different components of working memory have different relationships with different mathematical skills. Journal of Experimental Child Psychology, 111(2), 139-155. doi:10.1016/j.jecp.2011.08.011Alloway, T. P., & Alloway, R. G. (2010). Investigating the predictive roles of working memory and IQ in academic attainment. Journal of Experimental Child Psychology, 106(1), 20-29. doi:10.1016/j.jecp.2009.11.003Bavin, E. L., Wilson, P. H., Maruff, P., & Sleeman, F. (2005). Spatio‐visual memory of children with specific language impairment: evidence for generalized processing problems. International Journal of Language & Communication Disorders, 40(3), 319-332. doi:10.1080/13682820400027750Szucs, D., Devine, A., Soltesz, F., Nobes, A., & Gabriel, F. (2013). Developmental dyscalculia is related to visuo-spatial memory and inhibition impairment. Cortex, 49(10), 2674-2688. doi:10.1016/j.cortex.2013.06.007Mammarella, I. C., & Cornoldi, C. (2013). An analysis of the criteria used to diagnose children with Nonverbal Learning Disability (NLD). Child Neuropsychology, 20(3), 255-280. doi:10.1080/09297049.2013.796920Alloway TP (2007) Automated Working Memory Assessment. London: The Psychological Corporation.Oades, R. D., & Isaacson, R. L. (1978). The development of food search behavior by rats: The effects of hippocampal damage and haloperidol. Behavioral Biology, 24(3), 327-337. doi:10.1016/s0091-6773(79)90184-6Morris, R. (1984). Developments of a water-maze procedure for studying spatial learning in the rat. Journal of Neuroscience Methods, 11(1), 47-60. doi:10.1016/0165-0270(84)90007-4Olton, D. S. (1987). The radial arm maze as a tool in behavioral pharmacology. Physiology & Behavior, 40(6), 793-797. doi:10.1016/0031-9384(87)90286-1Méndez-López, M., Méndez, M., López, L., & Arias, J. L. (2009). Sexually dimorphic c-Fos expression following spatial working memory in young and adult rats. Physiology & Behavior, 98(3), 307-317. doi:10.1016/j.physbeh.2009.06.006Munoz M, Morris RGM (2009) Episodic memory in animals. In:Squire LR editor. New Encyclopedia of Neuroscience. Oxford: Academic Press. pp.1173–1182.SHORE, D. I., STANFORD, L., MACINNES, W. J., KLEIN, R. M., & BROWN, R. E. (2001). Of mice and men: Virtual Hebb-Williams mazes permit comparison of spatial learning across species. Cognitive, Affective, & Behavioral Neuroscience, 1(1), 83-89. doi:10.3758/cabn.1.1.83Astur, R. S., Taylor, L. B., Mamelak, A. N., Philpott, L., & Sutherland, R. J. (2002). Humans with hippocampus damage display severe spatial memory impairments in a virtual Morris water task. Behavioural Brain Research, 132(1), 77-84. doi:10.1016/s0166-4328(01)00399-0Astur, R. S., Tropp, J., Sava, S., Constable, R. T., & Markus, E. J. (2004). Sex differences and correlations in a virtual Morris water task, a virtual radial arm maze, and mental rotation☆. Behavioural Brain Research, 151(1-2), 103-115. doi:10.1016/j.bbr.2003.08.024Sturz, B. R., & Bodily, K. D. (2010). Encoding of variability of landmark-based spatial information. Psychological Research, 74(6), 560-567. doi:10.1007/s00426-010-0277-4Cánovas, R., García, R. F., & Cimadevilla, J. M. (2011). Effect of reference frames and number of cues available on the spatial orientation of males and females in a virtual memory task. Behavioural Brain Research, 216(1), 116-121. doi:10.1016/j.bbr.2010.07.026Cimadevilla, J. M., Cánovas, R., Iribarne, L., Soria, A., & López, L. (2011). A virtual-based task to assess place avoidance in humans. Journal of Neuroscience Methods, 196(1), 45-50. doi:10.1016/j.jneumeth.2010.12.026Cheng, K. (1986). A purely geometric module in the rat’s spatial representation. Cognition, 23(2), 149-178. doi:10.1016/0010-0277(86)90041-7Burgess, N., Maguire, E. A., Spiers, H. J., & O’Keefe, J. (2001). A Temporoparietal and Prefrontal Network for Retrieving the Spatial Context of Lifelike Events. NeuroImage, 14(2), 439-453. doi:10.1006/nimg.2001.0806Burgess, N., Maguire, E. A., & O’Keefe, J. (2002). The Human Hippocampus and Spatial and Episodic Memory. Neuron, 35(4), 625-641. doi:10.1016/s0896-6273(02)00830-9Passolunghi, M. C., & Mammarella, I. C. (2011). Selective Spatial Working Memory Impairment in a Group of Children With Mathematics Learning Disabilities and Poor Problem-Solving Skills. Journal of Learning Disabilities, 45(4), 341-350. doi:10.1177/0022219411400746Thomas, E., Reeve, R., Fredrickson, A., & Maruff, P. (2011). Spatial memory and executive functions in children. Child Neuropsychology, 17(6), 599-615. doi:10.1080/09297049.2011.567980SPOONER, D., & PACHANA, N. (2006). Ecological validity in neuropsychological assessment: A case for greater consideration in research with neurologically intact populations. Archives of Clinical Neuropsychology, 21(4), 327-337. doi:10.1016/j.acn.2006.04.004Juan, M. C., Alcaniz, M., Monserrat, C., Botella, C., Banos, R. M., & Guerrero, B. (2005). Using Augmented Reality to Treat Phobias. IEEE Computer Graphics and Applications, 25(6), 31-37. doi:10.1109/mcg.2005.143Furió, D., González-Gancedo, S., Juan, M.-C., Seguí, I., & Costa, M. (2013). The effects of the size and weight of a mobile device on an educational game. Computers & Education, 64, 24-41. doi:10.1016/j.compedu.2012.12.015Juan MC, Furió D, Alem L, Ashworth P, Cano J (2011) ARGreenet and BasicGreenet: Two mobile games for learning how to recycle. Proceedings of the 19th International Conference on Computer Graphics, Visualization and Computer Vision. pp.25–32.Furió, D., González-Gancedo, S., Juan, M.-C., Seguí, I., & Rando, N. (2013). Evaluation of learning outcomes using an educational iPhone game vs. traditional game. Computers & Education, 64, 1-23. doi:10.1016/j.compedu.2012.12.001Albrecht, U.-V., Folta-Schoofs, K., Behrends, M., & von Jan, U. (2013). Effects of Mobile Augmented Reality Learning Compared to Textbook Learning on Medical Students: Randomized Controlled Pilot Study. Journal of Medical Internet Research, 15(8), e182. doi:10.2196/jmir.2497Liu, P.-H. E., & Tsai, M.-K. (2012). Using augmented-reality-based mobile learning material in EFL English composition: An exploratory case study. British Journal of Educational Technology, 44(1), E1-E4. doi:10.1111/j.1467-8535.2012.01302.xBaddeley AD (1986) Working memory. Oxford: Clarendon Press.Alloway TP (2012) Working Memory Assessment. Second Edi. London: Pearson Assessment.Kamphaus KW, Perez-Hernandez E, Sanchez-Sanchez F (2014) Cuestionario de Evaluación Clínica de la Memoria. In press. Madrid: TEA Ediciones.Smith, A. D., Gilchrist, I. D., & Hood, B. M. (2005). Children’s Search Behaviour in Large-Scale Space: Developmental Components of Exploration. Perception, 34(10), 1221-1229. doi:10.1068/p5270Piccardi, L., Palermo, L., Leonzi, M., Risetti, M., Zompanti, L., D’Amico, S., & Guariglia, C. (2014). The Walking Corsi Test (WalCT): A Normative Study of Topographical Working Memory in a Sample of 4- to 11-Year-Olds. The Clinical Neuropsychologist, 28(1), 84-96. doi:10.1080/13854046.2013.863976Gathercole, S. E., Pickering, S. J., Ambridge, B., & Wearing, H. (2004). The Structure of Working Memory From 4 to 15 Years of Age. Developmental Psychology, 40(2), 177-190. doi:10.1037/0012-1649.40.2.177Best, J. R., & Miller, P. H. (2010). A Developmental Perspective on Executive Function. Child Development, 81(6), 1641-1660. doi:10.1111/j.1467-8624.2010.01499.xBianchini, F., Incoccia, C., Palermo, L., Piccardi, L., Zompanti, L., Sabatini, U., … Guariglia, C. (2010). Developmental topographical disorientation in a healthy subject. Neuropsychologia, 48(6), 1563-1573. doi:10.1016/j.neuropsychologia.2010.01.025Iaria, G., & Barton, J. J. S. (2010). Developmental topographical disorientation: a newly discovered cognitive disorder. Experimental Brain Research, 206(2), 189-196. doi:10.1007/s00221-010-2256-9Lowe, P. A., Mayfield, J. W., & Reynolds, C. R. (2003). Gender differences in memory test performance among children and adolescents. Archives of Clinical Neuropsychology, 18(8), 865-878. doi:10.1093/arclin/18.8.865Barnfield, A. M. C. (1999). Development of Sex Differences in Spatial Memory. Perceptual and Motor Skills, 89(1), 339-350. doi:10.2466/pms.1999.89.1.339Alloway, T. P., Gathercole, S. E., Kirkwood, H., & Elliott, J. (2009). The working memory rating scale: A classroom-based behavioral assessment of working memory. Learning and Individual Differences, 19(2), 242-245. doi:10.1016/j.lindif.2008.10.003Injoque-Ricle, I., Calero, A. D., Alloway, T. P., & Burin, D. I. (2011). Assessing working memory in Spanish-speaking children: Automated Working Memory Assessment battery adaptation. Learning and Individual Differences, 21(1), 78-84. doi:10.1016/j.lindif.2010.09.012Jones, A., Scanlon, E., Tosunoglu, C., Morris, E., Ross, S., Butcher, P., & Greenberg, J. (1999). Contexts for evaluating educational software. Interacting with Computers, 11(5), 499-516. doi:10.1016/s0953-5438(98)00064-2Mayes, J. ., & Fowler, C. . (1999). Learning technology and usability: a framework for understanding courseware. Interacting with Computers, 11(5), 485-497. doi:10.1016/s0953-5438(98)00065-4Squires, D., & Preece, J. (1999). Predicting quality in educational software: Interacting with Computers, 11(5), 467-483. doi:10.1016/s0953-5438(98)00063-0Sun, P.-C., Tsai, R. J., Finger, G., Chen, Y.-Y., & Yeh, D. (2008). What drives a successful e-Learning? An empirical investigation of the critical factors influencing learner satisfaction. Computers & Education, 50(4), 1183-1202. doi:10.1016/j.compedu.2006.11.007Lee, S. J., Srinivasan, S., Trail, T., Lewis, D., & Lopez, S. (2011). Examining the relationship among student perception of support, course satisfaction, and learning outcomes in online learning. The Internet and Higher Education, 14(3), 158-163. doi:10.1016/j.iheduc.2011.04.001Lyons KE, Zelazo PD (2011) Monitoring, metacognition, and executive function: elucidating the role of self-reflection in the development of self-regulation. In:Benson Jeditor. Advances in Child Development and Behavior. Burlington: Academic Press. pp.379–412

Locus coeruleus and dopaminergic consolidation of everyday memory

Item does not contain fulltextThe retention of episodic-like memory is enhanced, in humans and animals, when something novel happens shortly before or after encoding. Using an everyday memory task in mice, we sought the neurons mediating this dopamine-dependent novelty effect, previously thought to originate exclusively from the tyrosine-hydroxylase-expressing (TH+) neurons in the ventral tegmental area. Here we report that neuronal firing in the locus coeruleus is especially sensitive to environmental novelty, locus coeruleus TH+ neurons project more profusely than ventral tegmental area TH+ neurons to the hippocampus, optogenetic activation of locus coeruleus TH+ neurons mimics the novelty effect, and this novelty-associated memory enhancement is unaffected by ventral tegmental area inactivation. Surprisingly, two effects of locus coeruleus TH+ photoactivation are sensitive to hippocampal D1/D5 receptor blockade and resistant to adrenoceptor blockade: memory enhancement and long-lasting potentiation of synaptic transmission in CA1 ex vivo. Thus, locus coeruleus TH+ neurons can mediate post-encoding memory enhancement in a manner consistent with possible co-release of dopamine in the hippocampus