The use of multiplexed simple sequence repeat (SSR) markers for analysis of genetic diversity in African rice genotypes

Rice is an emerging food and cash crop in Eastern Africa. Thousands of germplasm accessions have been introduced from major rice breeding centers, such as the International Rice Research Institute (IRRI), and Africa Rice but the genetic variability among the introduced rice germplasm is unknown. Knowledge on genetic diversity would be useful in designing measures for comprehensive breeding and conservation. To address this knowledge gap, 10 highly polymorphic rice simple sequence repeat (SSR) markers were used to characterize 99 rice genotypes to determine their diversity and place them in their different population groups. The SSR markers were multiplexed in 3 panels to increase their throughput. An average of 15.9 alleles was detected, ranging from 6 alleles detected by marker RM7 to 30 by marker RM333. The UPGMA dendogram based on Nei’s genetic distance cluster analysis, revealed 5 genetic groups among the genotypes tested. Analysis of molecular variance indicated that 97% of the diversity observed was explained by differences in the genotypes themselves, and only 3% was due to the sources from which the genotypes were obtained. This study sets the stage for further diversity analysis of all the available germplasm lines using SSR markers to ensure effective utilization and conservation of the germplasm.Keywords: Genetic diversity, simple sequences repeat (SSR) markers, multiplexing, rice genotypes, structure. Abbreviation: IRRI, International Rice Research Institute; SSR, simple sequence repeat; NaCRRI, national crops resources research institute; RAPD, random amplified polymorphic DNA; AFLP, amplified fragment length polymorphisms; RFLP, restriction fragment length polymorphisms; SNP, single nucleotide polymorphisms; BAC, bacterial artificial chromosome; PAC, P1-derived artificial chromosome; PCR, polymerase chain reaction; Ho, heterozygosity; He, heterozygosity

Playground social interaction analysis using bespoke wearable sensors for tracking and motion capture

Unstructured play is considered important for the social, physical and cognitive development of children. Traditional observational research examining play behaviour at playtime (recess) has been hampered by challenges in obtaining reliable data and in processing sufficient quantities of that data to permit credible inferences to be drawn. The emergence of wearable wireless sensor technology makes it possible to study individual differences in childhood social behaviour based on collective movement patterns during playtime. In this work, we introduce a new method to enable simultaneous collection of GNSS/IMU data from a group of children interacting on a playground. We present a detailed description of system development and implementation before going on to explore methods of characterising social groups based on collective movement recording and analysis. A case study was carried out for a class of 7-8 year old children in their school playground during 10 episodes of unstructured play. A further 10 play episodes were monitored in the same space following the introduction of large, loose play materials. This study design allowed us to observe the effect of an environmental intervention on social movement patterns. Sociometric analysis was conducted for comparison and validation. This successful case study demonstrates that sensor based movement data can be used to explore children’s social behaviour during naturalistic play.LEGO Foundatio

Mutational spectrum of the succinate semialdehyde dehydrogenase (ALDH5A1) gene and functional analysis of 27 novel disease-causing mutations in patients with SSADH deficiency

Succinate semialdehyde dehydrogenase (SSADH; ALlDH5A1) deficiency, a rare metabolic disorder that disrupts the normal degradation of GABA, gives rise to a highly heterogeneous neurological phenotype ranging from mild to very severe. The nature of the mutation has so far been reported in patients from six families world wide and eight different mutations were described. Here we report the mutational spectrum in 48 additional unrelated families of different geographic origin. We detected 27 novel mutations at the cDNA level, of which 26 could be attributed to changes at the genomic level. Furthermore, six mutations were detected that did not strongly affect SSADH activity when expressed in HEK 293 cells and are considered nonpathogenic allelic variants. Twenty of the mutations were only found in one family. The spectrum of disease-causing mutations from all patients sequenced thus far consists of 25 point mutations, four small insertions, and five small deletions. Seven of these mutations affect splice junctions, seven are nonsense mutations, and 12 are missense mutations. Although there were no mutational hotspots or prevalent mutations responsible for a significant number of cases, 14 out of 37 (38%) of the missense alleles were present in exon 4 or 5. With one exception, the missense mutations we consider to be causative of SSADH deficiency reduced the SSADH activity to less than 5% of the normal activity in our in vitro expression system. This indicates that residual expression is not likely to be an important factor contributing to the large phenotypic differences observed among different families and even among siblings, suggesting that other modifying factors are of great importance in disease pathology. (C) 2003 Wiley,Liss, Inc

Transcutaneous electrical nerve stimulation (TENS) for chronic pain - an overview of Cochrane Reviews

Background Chronic pain, considered to be pain lasting more than three months, is a common and often difficult to treat condition that can significantly impact upon function and quality of life. Treatment typically includes pharmacological and non-pharmacological approaches. Transcutaneous electrical nerve stimulation (TENS)is an adjunct non-pharmacological treatment commonly recommended by clinicians and often used by people with pain.ObjectivesTo provide an overview of evidence from Cochrane Reviews of theeffectiveness of TENS to reduce pain in adults with chronic pain(excluding headache or migraine).To provide an overview of evidence from Cochrane Reviews of the safety of TENS when used to reduce pain in adults with chronic pain (excluding headache or migraine).To identify possible sources of inconsistency in the approaches taken to evaluating the evidence related to TENS for chronic pain (excluding headache or migraine) in the Cochrane Library with a view to recommending strategies to improve consistency in methodology and reporting.To highlight areas of remaining uncertainty regarding the effectiveness of TENS for chronic pain (excluding headache or migraine)with a view to recommending strategies to reduce any uncertainty. Methods Search methods We searched the Cochrane Database of Systematic Reviews(CDSR), in the Cochrane Library, across all years up to Issue 11 of12, 2018. Selection of reviewsTwo authors independently screened the results of the electronic search by title and abstract against inclusion/exclusion criteria. Weincluded all Cochrane Reviews of randomised controlled trials(RCTs) assessing the effectiveness of TENS in people with chronic pain.We included reviews if they investigated the following: TENSversus sham; TENS versus usual care or no treatment/waiting list control;TENS plus active intervention versus active intervention alone; comparisons between different types of TENS; or TENS deliveredusing different stimulation parameters.Data extraction and analysisTwo authors independently extracted relevant data, assessed review quality using the AMSTAR checklist and applied GRADE judge-ments where required to individual reviews. Our primary outcomes included pain intensity and nature/incidence of adverse effects;our secondary outcomes included disability, health-related quality of life, analgesic medication use and participant global impressionof change.Main results We included nine reviews investigating TENS use in people with defined chronic pain or in people with chronic conditions associated with ongoing pain. One review investigating TENS for phantom or stump-associated pain in people following amputation did not have any included studies. We therefore extracted data from eight reviews which represented 51 TENS-related RCTs representing 2895 TENS-comparison participants entered into the studies.The included reviews followed consistent methods and achievedoverall high scores on the AMSTAR checklist. The evidence reportedwithin each review was consistently rated as very low quality.Using review authors’ assessment of risk of bias, there were significant methodological limitations in included studies; and for all reviews, sample sizes were consistently small (the majority of studies included fewer than 50 participants per group).Six of the eight reviews presented a narrative synthesis of included studies. Two reviews reported a pooled analysis.Primary and secondary outcomes One review reported a beneficial effect of TENS versus sham therapy at reducing pain intensity on a 0 to 10 scale (MD−1.58, 95%CI−2.08 to−1.09, P < 0.001, I² = 29%, P = 0.22, 5 studies, 207 participants).However the quality of the evidence was very low due to significant methodological limitations and imprecision. A second review investigating pain intensity performed a pooled analysis by combining studies that compared TENS to sham with studies that compared TENS to no intervention (SMD−0.85, 95% CI−1.36 to−0.34, P = 0.001, I² = 83%, P < 0.001). This pooled analysis was judged as offering very low quality evidence due to significant methodological limitations, large between-trial heterogeneity and imprecision. We considered the approach of combining sham andno intervention data to be problematic since we would predict these different comparisons may be estimating different trueeffects. All remaining reviews also reported pain intensity as an outcome measure; however the data were presented in narrative review form only.Due to methodological limitation and lack of useable data, we were unable to offer any meaningful report on the remaining primary outcome regarding nature/incidence of adverse effects, nor for the remaining secondary outcomes: disability, health-related quality of life, analgesic medication use and participant global impression of change for any comparisons.We found the included reviews had a number of inconsistencies when evaluating the evidence from TENS studies. Approaches to assessing risk of bias around the participant, personnel and outcome-assessor blinding were perhaps the most obvious area of difference across included reviews. We also found wide variability in terms of primary and secondary outcome measures, and inclusion/exclusion criteria for studies varied with respect to including studies which assessed immediate effects of single interventions.Authors’ conclusions We found the methodological quality of the reviews was good, but quality of the evidence within them was very low. We were the reforeunable to conclude with any confidence that, in people with chronic pain, TENS is harmful, or beneficial for pain control, disability,health-related quality of life, use of pain relieving medicines, or global impression of change. We make recommendations with respect to future TENS study designs which may meaningfully reduce the uncertainty relating to the effectiveness of this treatment in people with chronic painNational Institute for Health Research,via Cochrane Infrastructure funding to the Cochrane Pain, Palliative and Supportive Care Review Group (PaPaS

Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data

Combining datasets with a model of the underlying physics prior to mapping of tissue provides a novel approach improving the estimation of parameters. We demonstrate this approach by merging near infrared diffuse optical signal data with diffusion NMR data to inform a model describing the microstructure of a sample. The study is conducted on a homogeneous emulsion of oil in a dispersion medium of water and proteins. The use of a protein based background, rich in collagen, introduces a similarity to real tissues compared to other models such as intralipids. The sample is investigated with the two modalities separately. Then, the two datasets are used to inform a combined model, and to estimate the size of the microstructural elements and the volume fraction. The combined model fits the microstructural properties by minimizing the difference between experimental and modelled data. The experimental results are validated with confocal laser scanning microscopy. The final results demonstrate that the combined model provides improved estimates of microstructural parameters compared to either individual model alone

Stable Panoramic Views Facilitate Snap-Shot Like Memories for Spatial Reorientation in Homing Pigeons

Following spatial disorientation, animals can reorient themselves by relying on geometric cues (metric and sense) specified both by the macroscopic surface layout of an enclosed space and prominent visual landmarks in arrays. Whether spatial reorientation in arrays of landmarks is based on explicit representation of the geometric cues is a matter of debate. Here we trained homing pigeons (Columba livia) to locate a food-reward in a rectangular array of four identical or differently coloured pipes provided with four openings, only one of which allowed the birds to have access to the reward. Pigeons were trained either with a stable or a variable position of the opening on pipes, so that they could view the array either from the same or a variable perspective. Explicit mapping of configural geometry would predict successful reorientation irrespective of access condition. In contrast, we found that a stable view of the array facilitated spatial learning in homing pigeons, likely through the formation of snapshot-like memories

Prebiotic potential of a maize-based soluble fibre and impact of dose on the human gut microbiota

Dietary management of the human gut microbiota towards a more beneficial composition is one approach that may improve host health. To date, a large number of human intervention studies have demonstrated that dietary consumption of certain food products can result in significant changes in the composition of the gut microbiota i.e. the prebiotic concept. Thus the prebiotic effect is now established as a dietary approach to increase beneficial gut bacteria and it has been associated with modulation of health biomarkers and modulation of the immune system. Promitor™ Soluble Corn Fibre (SCF) is a well-known maize-derived source of dietary fibre with potential selective fermentation properties. Our aim was to determine the optimum prebiotic dose of tolerance, desired changes to microbiota and fermentation of SCF in healthy adult subjects. A double-blind, randomised, parallel study was completed where volunteers (n = 8/treatment group) consumed 8, 14 or 21 g from SCF (6, 12 and 18 g/fibre delivered respectively) over 14-d. Over the range of doses studied, SCF was well tolerated Numbers of bifidobacteria were significantly higher for the 6 g/fibre/day compared to 12g and 18g/fibre delivered/day (mean 9.25 and 9.73 Log10 cells/g fresh faeces in the pre-treatment and treatment periods respectively). Such a numerical change of 0.5 Log10 bifidobacteria/g fresh faeces is consistent with those changes observed for inulin-type fructans, which are recognised prebiotics. A possible prebiotic effect of SCF was therefore demonstrated by its stimulation of bifidobacteria numbers in the overall gut microbiota during a short-term intervention