Bioethics and culture: an African perspective

The project of Bioethics seems to me to require paying attention to the cultural realities and assumptive frame of reference of different peoples. I assume that this must be one of the views of the organizers of this conference too and that this is why the idea of country reports is taken seriously. If I am right about this, then it makes sense for me to start my discussion with a very brief discussion of some aspects of the cultural realities of Africa with particular reference to the Yoruba of Nigeria. Then I will discuss how this world view raises issues for bioethics. Two aspects of people's worldview relevant to bioethical issues are their conception of the human person and their conception of cause. What they consider themselves to be, and what they consider to be the principles of causation will normally influence their attitudes to health and illness and their choices regarding health care. I will briefly discuss these issues with regard to the Yoruba worldview.     

Moringa oleifera leaf fractions attenuated Naje haje venom-induced cellular dysfunctions via modulation of Nrf2 and inflammatory signalling pathways in rats

Naja haje envenoming could activate multiple pathways linked to haematotoxic, neurological, and antioxidant systems dysfunctions. Moringa oleifera has been used in the management of different snake venom-induced toxicities, but there is no scientific information on its antivenom effects against Naja haje. This study thus, investigated the antivenom activities of different extract partitions of M. oleifera leaves against N. haje envenoming. Forty five male rats were divided into nine groups (n = 5). Groups 2 to 9 were envenomed with 0.025 mg/kg (LD₅₀) of N. haje venom while group 1 was given saline. Group 2 was left untreated, while group 3 was treated with polyvalent antivenom, groups 4, 6 and 8 were treated with 300 mg/kg^?1 of N-hexane, ethylacetate and ethanol partitions of M. oleifera, respectively. Groups 5, 7 and 9 were also treated with 600 mgkg^?1of the partitions, respectively. Ethanol extract and ethyl acetate partition of M. oleifera significantly improved haematological indices following acute anaemia induced by the venom. Likewise, haemorrhagic, haemolytic and anti-coagulant activities of N. haje venom were best inhibited by ethanol partition. Envenoming significantly down-regulated Nuclear factor erythroid 2-related factor 2 (Nrf2) with the consequent elevation of antioxidant enzymes activities in the serum and brain. Treatment with extract partitions however, elevated Nrf2 levels while normalising antioxidant enzyme activities. Furthermore, there were reduction in levels of pro-inflammatory cytokines (TNF-α and interleukin-1β) in tissues of treated envenomed rats. This study concludes that ethanol partition of M. oleifera was most effective against N. haje venom and could be considered as a potential source for antivenom metabolites.     

A time course study on dose-response relationship between alcohol exposure and its effects on lipid profile and biomarkers of tissue damage

This present research investigated variations in lipid profiles and important biomarkers of tissue damage in response to graded concentrations of alcohol administration in male Wistar rats. Group A (control) received distilled water while group B, C and D received 30%, 40% and 50% (v/v) alcohol respectively. Five rats each from groups A-D were sacrificed after day(s) 1, 7, 14, 21 and 28 of administration. A significant increase was observed at day 28 for serum cholesterol by 79% (group B), 78% (group C) and 47% (group D) together with serum phospholipid 58% (group B), 50% (group C) and 92% (group D). Serum triacylglycerol increased by 71% (group B), 43% (group C) and 16% (group D) at day 21, while concentration of serum albumin decreased at day 28 by 40.9% (group B), 50.2% (group C), 53.3% (group D) respectively when compared with control (group A). Serum aminotransferases and alkaline phosphatase specific activities, as well as creatinine and uric acid concentration increased in a concentration-dependent manner, following alcohol administration. Though most of these effects induced by alcohol were time- and concentration-dependent, 40% alcohol appear to be more stable, giving results consistent with alcohol-induced damages, with minimal mortality. This study therefore further validated dyslipidemia and imbalance in clinical biomarkers as hallmarks of tissue damage induced by excessive alcohol consumption with an insight on the time- and concentration-response relationship between alcohol consumption and its toxicity.     

Contribution of direct electron transfer mechanisms to overall electron transfer in microbial fuel cells utilising <Emphasis Type="Italic">Shewanella oneidensis</Emphasis> as biocatalyst

Objectives

To investigate the contribution of direct electron transfer mechanisms to electricity production in microbial fuel cells by physically retaining Shewanella oneidensis cells close to or away from the anode electrode.

Results

A maximum power output of 114 ± 6 mWm^?2 was obtained when cells were retained close to the anode using a dialysis membrane. This was 3.5 times more than when the cells were separated away from the anode. Without the membrane the maximum power output was 129 ± 6 mWm^?2. The direct mechanisms of electron transfer contributed significantly to overall electron transfer from S. oneidensis to electrodes, a result that was corroborated by another experiment where S. oneidensis cells were entrapped in alginate gels.

Conclusion

S. oneidensis transfers electrons primarily by direct electron transfer as opposed to mediated electron transfer.

     

Learning from positive examples when the negative class is undetermined- microRNA gene identification

Background

The application of machine learning to classification problems that depend only on positive examples is gaining attention in the computational biology community. We and others have described the use of two-class machine learning to identify novel miRNAs. These methods require the generation of an artificial negative class. However, designation of the negative class can be problematic and if it is not properly done can affect the performance of the classifier dramatically and/or yield a biased estimate of performance. We present a study using one-class machine learning for microRNA (miRNA) discovery and compare one-class to two-class approaches using naïve Bayes and Support Vector Machines. These results are compared to published two-class miRNA prediction approaches. We also examine the ability of the one-class and two-class techniques to identify miRNAs in newly sequenced species.

Results

Of all methods tested, we found that 2-class naive Bayes and Support Vector Machines gave the best accuracy using our selected features and optimally chosen negative examples. One class methods showed average accuracies of 70–80% versus 90% for the two 2-class methods on the same feature sets. However, some one-class methods outperform some recently published two-class approaches with different selected features. Using the EBV genome as and external validation of the method we found one-class machine learning to work as well as or better than a two-class approach in identifying true miRNAs as well as predicting new miRNAs.

Conclusion

One and two class methods can both give useful classification accuracies when the negative class is well characterized. The advantage of one class methods is that it eliminates guessing at the optimal features for the negative class when they are not well defined. In these cases one-class methods can be superior to two-class methods when the features which are chosen as representative of that positive class are well defined.

Availability

The OneClassmiRNA program is available at: [1]

     

Spectral and Structural Measures of Northwest Forest Vegetation at Leaf to Landscape Scales

We report a multiscale study in the Wind River Valley in southwestern Washington, where we quantified leaf to stand scale variation in spectral reflectance for dominant species. Four remotely sensed structural measures, the normalized difference vegetation index (NDVI), cover fractions from spectral mixture analysis (SMA), equivalent water thickness (EWT), and albedo were investigated using Airborne Visible Infrared Imaging Spectrometer (AVIRIS) data. Discrimination of plant species varied with wavelength and scale, with deciduous species showing greater separability than conifers. Contrary to expectations, plant species were most distinct at the branch scale and least distinct at the stand scale. At the stand scale, broadleaf and conifer species were spectrally distinct, as were most conifer age classes. Intermediate separability occurred at the leaf scale. Reflectance decreased from leaf to stand scales except in the broadleaf species, which peaked in near-infrared reflectance at the branch scale. Important biochemical signatures became more pronounced spectrally progressing from leaf to stand scales. Recent regenerated clear-cuts (less than 10 years old) had the highest albedo and nonphotosynthetic vegetation (NPV). After 50 years, the stands showed significant decreases in albedo, NPV, and EWT and increases in shade. Albedo was lowest in old-growth forests. Peak EWT, a proxy measure for leaf area index (LAI), was observed in 11- to 30-year-old stands. When compared to LAI, EWT and NDVI showed exponentially decreasing, but distinctly different, relationships with increasing LAI. This difference is biologically important: at 95% of the maximum predicted NDVI and EWT, LAI was 5.17 and 9.08, respectively. Although these results confirm the stand structural variation expected with forest succession, remote-sensing images also provide a spatial context and establish a basis to evaluate variance within and between age classes. Landscape heterogeneity can thus be characterized over large areas—a critical and important step in scaling fluxes from stand-based towers to larger scales.     

Numerical study of entrainment of the human circadian system and recovery by light treatment

Background

While the effects of light as a zeitgeber are well known, the way the effects are modulated by features of the sleep-wake system still remains to be studied in detail.

Methods

A mathematical model for disturbance and recovery of the human circadian system is presented. The model combines a circadian oscillator and a sleep-wake switch that includes the effects of orexin. By means of simulations, we characterize the period-locking zone of the model, where a stable 24-hour circadian rhythm exists, and the occurrence of circadian disruption due to both insufficient light and imbalance in orexin. We also investigate how daily bright light treatments of short duration can recover the normal circadian rhythm.

Results

It is found that the system exhibits continuous phase advance/delay at lower/higher orexin levels. Bright light treatment simulations disclose two optimal time windows, corresponding to morning and evening light treatments. Among the two, the morning light treatment is found effective in a wider range of parameter values, with shorter recovery time.

Conclusions

This approach offers a systematic way to determine the conditions under which circadian disruption occurs, and to evaluate the effects of light treatment. In particular, it could potentially offer a way to optimize light treatments for patients with circadian disruption, e.g., sleep and mood disorders, in clinical settings.

     

DNA barcoding of economically important freshwater fish species from north‐central Nigeria uncovers cryptic diversity

This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north‐central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity‐based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor‐joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well‐supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub‐Saharan Africa. Thus, cryptic lineage diversity may illustrate species’ adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.