Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset

Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics.

Synergistic effects of geographical strain, temperature and larval food on insecticide tolerance in Callosobruchus maculatus (F.)

This study investigated the multifactorial interaction of various environmental factors including 17 geographical strain (Brazil, Cameroon and Yemen strains), temperature, dose and larval food 18 (cowpea and mungbean) on the response of Callosobruchus maculatus adult to insecticide. All 19 the main factors, their two-way interactions and the four-way interaction had significant effects 20 on C. maculatus response to malathion (an organophosphate insecticide). However, the three-21 way interactions were not statistically significant (except strain x food x dose, P = 0.002). The 22 2 Brazil strain was the most responsive to temperature irrespective of the larval food type. The 23 impact of food type differs from one strain to the other, for instance, the food that imparts higher 24 tolerance in a strain might reduce the tolerance in another. Likewise, the hierarchy of tolerance 25 among the cowpea-reared strains (Brazil > Cameroon > Yemen) was totally different from the 26 mungbean-reared strains (Cameroon > Yemen > Brazil). The reasons for these differences were 27 discussed in the light of their impact on C. maculatus management. The management of both C. 28 maculatus and development of resistance could be complex, hence, the states of a variety of 29 environmental factors need to be considered. This is necessary in order to maximize management 30 success of this bruchid especially in tropical/subtropical developing countries.

Parkinson’s Disease tremor classification – a comparison between Support Vector Machines and neural networks

Deep Brain Stimulation has been used in the study of and for treating Parkinson’s Disease (PD) tremor symptoms since the 1980s. In the research reported here we have carried out a comparative analysis to classify tremor onset based on intraoperative microelectrode recordings of a PD patient’s brain Local Field Potential (LFP) signals. In particular, we compared the performance of a Support Vector Machine (SVM) with two well known artificial neural network classifiers, namely a Multiple Layer Perceptron (MLP) and a Radial Basis Function Network (RBN). The results show that in this study, using specifically PD data, the SVM provided an overall better classification rate achieving an accuracy of 81% recognition.

Variation in the sensitivity of Callosobruchus (Coleoptera: Bruchidae) acetylcholinesterase to the organophosphate insecticide malaoxon: effect of species, geographical strain and food type

BACKGROUND: Bruchid beetles, Callosobruchus species, are serious pests of economically important grain legumes; their activity in stores is often controlled by use of synthetic insecticides. Esterases are known to be involved in insecticide resistance in insects. However, there is dearth of information on esterase activity in the genus Callosobruchus. In this study we investigated the effect of species, geographical strain and food type on the variation of acetylcholinesterase (AChE) activity and its inhibition by malaoxon (malathion metabolite) using an in vitro spectrophotometric method. RESULT: AChE activity varied significantly among species and strains and also among legume type used for rearing them. Generally irrespective of species, strain or food type, the higher the AChE activity of a population, the higher its inhibition by malaoxon. C. chinensis had the highest AChE activity of the species studied and in the presence of malaoxon it had the lowest remaining AChE activity, while C. rhodesianus retained the highest activity. CONCLUSION: A firsthand knowledge of AChE activity in regional Callosobruchus in line with the prevailing food types should be of utmost importance to grain legume breeders, researchers on plant materials for bruchid control and pesticide manufacturer/applicators for a robust integrated management of these bruchids.

Obesity and body fat classification in the metabolic syndrome: impact on cardiometabolic risk metabotype

Obesity is a key factor in the development of the metabolic syndrome (MetS), which is associated with increased cardiometabolic risk. We investigated whether obesity classification by body mass index (BMI) and body fat percentage (BF%) influences cardiometabolic profile and dietary responsiveness in 486 MetS subjects (LIPGENE dietary intervention study). Anthropometric measures, markers of inflammation and glucose metabolism, lipid profiles, adhesion molecules and haemostatic factors were determined at baseline and after 12 weeks of 4 dietary interventions (high saturated fat (SFA), high monounsaturated fat (MUFA) and 2 low fat high complex carbohydrate (LFHCC) diets, 1 supplemented with long chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs)). 39% and 87% of subjects classified as normal and overweight by BMI were obese according to their BF%. Individuals classified as obese by BMI (± 30 kg/m2) and BF% (± 25% (men) and ± 35% (women)) (OO, n = 284) had larger waist and hip measurements, higher BMI and were heavier (P < 0.001) than those classified as non-obese by BMI but obese by BF% (NOO, n = 92). OO individuals displayed a more pro-inflammatory (higher C reactive protein (CRP) and leptin), pro-thrombotic (higher plasminogen activator inhibitor-1 (PAI-1)), pro-atherogenic (higher leptin/adiponectin ratio) and more insulin resistant (higher HOMA-IR) metabolic profile relative to the NOO group (P < 0.001). Interestingly, tumour necrosis factor alpha (TNF-α) concentrations were lower post-intervention in NOO individuals compared to OO subjects (P < 0.001). In conclusion, assessing BF% and BMI as part of a metabotype may help identify individuals at greater cardiometabolic risk than BMI alone.

The monitoring of ecological quality and the classification of standing waters in temperate regions: a review and proposal based on a worked scheme for British waters

This paper reviews the ways that quality can be assessed in standing waters, a subject that has hitherto attracted little attention but which is now a legal requirement in Europe. It describes a scheme for the assessment and monitoring of water and ecological quality in standing waters greater than about I ha in area in England & Wales although it is generally relevant to North-west Europe. Thirteen hydrological, chemical and biological variables are used to characterise the standing water body in any current sampling. These are lake volume, maximum depth, onductivity, Secchi disc transparency, pH, total alkalinity, calcium ion concentration, total N concentration,winter total oxidised inorganic nitrogen (effectively nitrate) concentration, total P concentration, potential maximum chlorophyll a concentration, a score based on the nature of the submerged and emergent plant community, and the presence or absence of a fish community. Inter alia these variables are key indicators of the state of eutrophication, acidification, salinisation and infilling of a water body.

Influence of geographical origin, host animal and stx gene on the virulence characteristics of Escherichia coli O26 strains

The influence of geographical origin, host animal and presence of the stx gene on the virulence of Escherichia coli O26 strains from ruminants was determined in this study. A clear association was found between the virulence profile and geographical origin of Shiga-toxigenic E. coli (STEC) O26 strains, with UK STEC O26 strains harbouring virtually identical profiles, whilst central European strains showed considerable heterogeneity in plasmid-encoded genes. The former group were also more likely to be non-motile and katP gene positive. Comparison of UK STEC and atypical enteropathogenic E. coli (aEPEC O26 strains showed that the presence of the stx1 gene was positively correlated with the presence of espP and katP genes and negatively associated with the presence of the yagP-yagT region and with rhamnose fermentation. In contrast to the uniform profiles of STEC O26 strains from ruminants in the UK, aEPEC O26 strains of bovine and ovine origin showed diverse profiles both within and between groups, and could not be separated into discrete groups. These results indicate that the characteristics of UK O26 strains from ruminants are distinct from those of O26 strains from ruminants and humans in other regions in central Europe. Such differences are expected to influence the zoonotic potential of this pathogen and the subsequent incidence of O26-associated human disease.