Characterization of active miniature inverted-repeat transposable elements in the peanut genome

Miniature inverted-repeat transposable elements (MITEs), some of which are known as active non-autonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), AhMITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four AhMITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives

The Bank of Standardized Stimuli (BOSS), a New Set of 480 Normative Photos of Objects to Be Used as Visual Stimuli in Cognitive Research

There are currently stimuli with published norms available to study several psychological aspects of language and visual cognitions. Norms represent valuable information that can be used as experimental variables or systematically controlled to limit their potential influence on another experimental manipulation. The present work proposes 480 photo stimuli that have been normalized for name, category, familiarity, visual complexity, object agreement, viewpoint agreement, and manipulability. Stimuli are also available in grayscale, blurred, scrambled, and line-drawn version. This set of objects, the Bank Of Standardized Stimuli (BOSS), was created specifically to meet the needs of scientists in cognition, vision and psycholinguistics who work with photo stimuli

Factors affecting the yield of microRNAs from laser microdissectates of formalin-fixed tissue sections

<p>Abstract</p> <p>Background</p> <p>Quantification of microRNAs in specific cell populations microdissected from tissues can be used to define their biological roles, and to develop and deploy biomarker assays. In this study, a number of variables were examined for their effect on the yield of microRNAs in samples obtained from formalin-fixed paraffin-embedded tissues by laser microdissection.</p> <p>Results</p> <p>MicroRNA yield was improved by using cresyl violet instead of hematoxylin-eosin to stain tissue sections in preparation for microdissection, silicon carbide instead of glass fiber as matrix in RNA-binding columns, and overnight digestion of dissected samples with proteinase K. Storage of slides carrying stained tissue sections at room temperature for up to a week before microdissection, and storage of the microdissectates at room temperature for up to a day before RNA extraction did not adversely affect microRNA yield.</p> <p>Conclusions</p> <p>These observations should be of value for the efficient isolation of microRNAs from microdissected formalin-fixed tissues with a flexible workflow.</p

Controlled variations in stimulus similarity during learning determine visual discrimination capacity in freely moving mice

The mouse is receiving growing interest as a model organism for studying visual perception. However, little is known about how discrimination and learning interact to produce visual conditioned responses. Here, we adapted a two-alternative forced-choice visual discrimination task for mice and examined how training with equiprobable stimuli of varying similarity influenced conditioned response and discrimination performance as a function of learning. Our results indicate that the slope of the gradients in similarity during training determined the learning rate, the maximum performance and the threshold for successful discrimination. Moreover, the learning process obeyed an inverse relationship between discrimination performance and discriminative resolution, implying that sensitivity within a similarity range cannot be improved without sacrificing performance in another. Our study demonstrates how the interplay between discrimination and learning controls visual discrimination capacity and introduces a new training protocol with quantitative measures to study perceptual learning and visually-guided behavior in freely moving mice

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

BACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.RESULTS:Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.CONCLUSION:MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Geographic genetic structure of Iberian columbines (gen. Aquilegia)

Southern European columbines (genus Aquilegia)are involved in active processes of diversification, and the Iberian Peninsula offers a privileged observatory to witness the process. Studies on Iberian columbines have provided significant advances on species diversification,but we still lack a complete perspective of the genetic diversification in the Iberian scenario. This work explores how genetic diversity of the genus Aquilegia is geographically structured across the Iberian Peninsula. We used Bayesian clustering methods, principal coordinates analyses, and NJ phenograms to assess the genetic relationships among 285 individuals from 62 locations and detect the main lineages. Genetic diversity of Iberian columbines consists of five geographically structured lineages, corresponding to different Iberian taxa. Differentiation among lineages shows particularly complex admixture patterns at Northeast and highly homogeneous toward Northwest and Southeast. This geographic genetic structure suggests the existence of incomplete lineage sorting and interspecific hybridization as could be expected in recent processes of diversification under the influence of quaternary postglacial migrations. This scenario is consistent with what is proposed by the most recent studies on European and Iberian columbines, which point to geographic isolation and divergent selection by habitat specialization as the main diversification drivers of the Iberian Aquilegia complex

Outcomes of a Comparison Study into a Group-Based Infant Parenting Programme

This paper reports on a quantitative evaluation of a group-based programme designed to promote parent-infant attachment and child development. Whilst group-based parenting programmes are recommended for treating and preventing conduct disorder in older children, there is, as yet, little evidence as to whether they have a positive effect on very young children and their carers’. Recent UK Government initiatives to support families and improve parenting skills in the first 2 years of children’s lives have increased the demand for the delivery and evaluation of community-based programmes. Eighty mother–child dyads were recruited from nine areas to intervention (n = 54) and control condition (n = 26). Baseline measures were collected in the children’s home when the infants were on average 3-months-old, and follow-up measures were collected 6 months post-baseline (N = 63). Mothers’ positive play behaviours were independently coded from video recordings taken in the home. Other measures included self-reported maternal confidence and mental well-being, assessed infant development and home environment. Socio-demographic data was collected once at baseline. After controlling for baseline scores, control mothers were observed to be significantly less sensitive during play with their baby at the 6 months follow-up with a significant increase in confidence. No differences were found between the groups on the other measures. This paper provides limited evidence for the effectiveness of the Incredible Years Parents and Babies group-based programme delivered in the first year of life. Further evaluation, particularly with parents at increased risk of poorer outcomes is needed to confirm and extend these results

Anodal Transcranial Direct Current Stimulation Reduces Psychophysically Measured Surround Suppression in the Human Visual Cortex

Transcranial direct current stimulation (tDCS) is a safe, non-invasive technique for transiently modulating the balance of excitation and inhibition within the human brain. It has been reported that anodal tDCS can reduce both GABA mediated inhibition and GABA concentration within the human motor cortex. As GABA mediated inhibition is thought to be a key modulator of plasticity within the adult brain, these findings have broad implications for the future use of tDCS. It is important, therefore, to establish whether tDCS can exert similar effects within non-motor brain areas. The aim of this study was to assess whether anodal tDCS could reduce inhibitory interactions within the human visual cortex. Psychophysical measures of surround suppression were used as an index of inhibition within V1. Overlay suppression, which is thought to originate within the lateral geniculate nucleus (LGN), was also measured as a control. Anodal stimulation of the occipital poles significantly reduced psychophysical surround suppression, but had no effect on overlay suppression. This effect was specific to anodal stimulation as cathodal stimulation had no effect on either measure. These psychophysical results provide the first evidence for tDCS-induced reductions of intracortical inhibition within the human visual cortex

Synchronous behavioural shifts in reef fishes linked to mass coral bleaching

Mass coral bleaching causes population declines and mortality of coral reef species1 yet its impacts on behaviour are largely unknown. Here, we unite behavioural theory with community ecology to test whether bleaching-induced mass mortality of corals can cause consistent changes in the behaviour of coral-feeding fishes. We documented 5,259 encounters between individuals of 38 Chaetodon (butterflyfish) species on 17 reefs within the central Indo-Pacific, of which 3,828 were repeated on 10 reefs both before and after the global coral bleaching event in 2016. Aggression between butterflyfishes decreased by two-thirds following large-scale coral mortality, despite no significant change in fish abundance or community composition. Pairwise encounters were most likely to be aggressive between obligate corallivores and on reefs with high coral cover. After bleaching, the proportion of preferred Acropora corals in the diet decreased significantly (up to 85% fewer bites), with no increase in overall bite rate to compensate for the loss of these nutritionally rich corals. The observed reduced aggression at low resource levels due to nutritional deficit follows the predictions of the economic theory of aggressive behaviour2,3. Our results reveal synchronous changes in behaviour in response to coral mortality. Such changes could potentially disrupt territories4, leading to reorganization of ecological communities