Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

APPLICATIONS OF FUNCTIONAL DATA ANALYSIS IN SPORT BIOMECHANICS

This paper reconsiders the challenge of analysing coordination in human movement with particular emphasis on the application of Functional Data Analysis and Functional Principal Component Analysis. The process of Functional Data Analysis is outlined using examples from biomechanics of sports injuries and coordination in race-walking, jumping and running. The evolution of the spring mass model used to describe jumping and hopping behaviour is examined and it is proposed that this model represents a coordination structure in human movement which may be appropriately analysed using Functional Data Analysis methods

Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum

Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1 and 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4, 5 and 6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7, 8, 9, 10, 11, 12, 13, 14 and 15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [ 16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful

CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry

Background: Gene editing using CRISPR/Cas9 is a simple and powerful tool for elucidating genetic controls and for crop improvement and its use has been reported in a growing number of important food crops, including recently Fragaria. In order to inform application of the technology in Fragaria, we targeted the visible endogenous marker gene PDS (phytoene desaturase) in diploid Fragaria vesca ssp. vesca ‘Hawaii 4’ and octoploid F. × ananassa ‘Calypso’. Results: Agrobacterium-mediated transformation of leaf and petiole explants was used for efficient stable integration of constructs expressing plant codon-optimised Cas9 and single guide sequences under control of the Arabidopsis U6-26 consensus promoter and terminator or Fragaria vesca U6III regulatory sequences. More than 80% (‘Hawaii 4’) and 50% (‘Calypso’) putative transgenic shoot lines (multiple shoots derived from a single callus) exhibited mutant phenotypes. Of mutant shoot lines selected for molecular analysis, approximately 75% (‘Hawaii 4’) and 55% (‘Calypso’) included albino regenerants with bi-allelic target sequence variants. Our results indicate the PDS gene is functionally diploid in ‘Calypso’. Conclusion: We demonstrate that CRISPR/Cas9 may be used to generate biallelic mutants at high frequency within the genomes of diploid and octoploid strawberry. The methodology, observations and comprehensive data set pre- sented will facilitate routine application of this technology in Fragaria to single and multiple gene copy targets where mutant phenotypes cannot be identified visually

AN INVESTIGATION OF SCHEMA THEORY APPLIED TO THE BIOMECHANICS OF THE SPRINT START IN ATHLETICS

Schmidt’s schema theory (1975) predicts that variable practice (VP) will outperform constant practice (CP). The implications of this for the teaching of skills such as the sprint start are that VP should allow equal or better learning to CP. The aim of this study was to examine the effect on novice subjects of practicing with varying block settings on the learning of the sprint start. A deterministic model of the spint start was derived using the guidelines of Hay and Reid (1982) to identify factor likely to affect performance. Measures of the factors were obtained using video and laser analysis. The affect of VP and CP on these factors was evaluated using a pre, post retention expermental design. Performance of the sprint start was compared between VP (n=6), CP (n=5), and Control (n=5) groups. Results showed no significant difference (

INFLUENCE OF THE RANGE OF MOTION ON JUMPING HEIGHT IN CHILDHOOD

The purpose of this study was to ascertain whether during childhood, the parameters for the range of motion had more influence on jump height than parameters for application of force. Using force platform, an analysis was made of the counter movement jumps performed by 36 girls aged between 5 to 8 years old. Linear regression was used to analyze the data. The parameters for the range of motion accounted for 66% of the variance in maximum height jump, while application of force accounted for 12%. These results could indicate that the children can enhance their vertical jumping performance by increasing the range of motion rather than improving the ground reaction forces or their application

AN INVESTIGATION OF SCHEMA THEORY APPLIED TO THE BIOMECHANICS OF THE SPRINT START IN ATHLETICS

Schmidt’s schema theory (1975) predicts that variable practice (VP) will outperform constant practice (CP). The implications of this for the teaching of skills such as the sprint start are that VP should allow equal or better learning to CP. The aim of this study was to examine the effect on novice subjects of practicing with varying block settings on the learning of the sprint start. A deterministic model of the spint start was derived using the guidelines of Hay and Reid (1982) to identify factor likely to affect performance. Measures of the factors were obtained using video and laser analysis. The affect of VP and CP on these factors was evaluated using a pre, post retention expermental design. Performance of the sprint start was compared between VP (n=6), CP (n=5), and Control (n=5) groups. Results showed no significant difference (

AN ANALYSIS OF THE POSTACTIVATION POTENTIATION EFFECT OF THE PRIMARY GLUTEAL MUSCLES FOLLOWING HABITUALLY PRESCRIBED ACTIVATION AND COMDlT IONlNG EXERCISES

This study examined the effects of a high load gluteal activation protocol on counter movement jump (CMJ) performance and gluteal activation levels. Eight sprinters performed 5 CMJ's prior to and subsequently after a gluteal activation protocol on two separate days. Height jumped (HJ), peak force (Forcewk), modified reactive strength index (RSId) and electromyographic gluteal activation levels were calculated on both days. Paired samples T tests found no significant differences for all reported variables on either day. This suggests that the gluteal activation protocol had no effect on CMJ performance. Future research should incorporate typical error analysis to investigate potentiation effects on an individual basis due to individual nature of the postactivation potentiation response and biological variability

A BIOMECHANICAL ANALYSIS OF THE INSTEP KICK IN SOCCER WITH PREFERRED AND NON-PREFERRED FOOT

This study examined the kinematics of preferred and non-preferred instep kicking action in competitive soccer players. Using two gen-locked cameras, SHVS video data were obtained for seven players completing eight maximal effort instep kicks at a target with both feet. 3D kinematic analysis was carried out using Peak Motus to obtain joint angles of the standing and kicking legs and the frontal plane pelvic tilt angle. The results showed that when kicking with the preferred limb, the players’ standing foot was closer to the ball and they used a larger frontal plane pelvic tilt angle and greater knee extension of the kicking leg at ball impact. There was greater variability in the kicking leg knee angle and this is consistent with Dynamical Systems Theory

THE EFFECTS OF A UNILATERAL GLUTEAL ACTIVATION PROTOCOL ON SINGLE LEG DROP JUMP PERFORMANCE

This study examined the effects of a gluteal activation protocol (GA) on the performance of drop jumps performed on a force sledge apparatus. Fifteen sprinters performed 10 single-leg drop jumps on three days with a unilateral GA performed within the warm up on day 2. Ground contact time (CT), height jumped (HJ), maximum vertical ground reaction force (GRFmax) and vertical leg-spring stiffness (Kvert) were calculated on all three days. A repeated measures ANOVA was used to examine mean differences on all variables across days. The results show significant differences on all variables between days 1 and 2 and on HJ and Kvert between days 1 and 3 but no differences in any varables between days 2 and 3. This suggests that the improvements in day 2 were due to a practice/learning effect rather than the GA protocol