A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches

Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC) values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54). In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch

Ethnopharmacological survey of Samburu district, Kenya

<p>Abstract</p> <p>Background</p> <p>Ethnobotanical pharmacopoeia is confidently used in disease intervention and there is need for documentation and preservation of traditional medical knowledge to bolster the discovery of novel drugs. The objective of the present study was to document the indigenous medicinal plant utilization, management and their extinction threats in Samburu District, Kenya.</p> <p>Methods</p> <p>Field research was conducted in six divisions of Samburu District in Kenya. We randomly sampled 100 consented interviewees stratified by age, gender, occupation and level of education. We collected plant use data through semi-structured questionnaires; transect walks, oral interviews and focus groups discussions. Voucher specimens of all cited botanic species were collected and deposited at University of Nairobi's botany herbarium.</p> <p>Results</p> <p>Data on plant use from the informants yielded 990 citations on 56 medicinal plant species, which are used to treat 54 different animal and human diseases including; malaria, digestive disorders, respiratory syndromes and ectoparasites.</p> <p>Conclusion</p> <p>The ethnomedicinal use of plant species was documented in the study area for treatment of both human and veterinary diseases. The local population has high ethnobotanical knowledge and has adopted sound management conservation practices. The major threatening factors reported were anthropogenic and natural. Ethnomedical documentation and sustainable plant utilization can support drug discovery efforts in developing countries.</p

Children with Moderate Acute Malnutrition with No Access to Supplementary Feeding Programmes Experience High Rates of Deterioration and No Improvement: Results from a Prospective Cohort Study in Rural Ethiopia

Background: Children with moderate acute malnutrition (MAM) have an increased risk of mortality, infections and impaired physical and cognitive development compared to well-nourished children. In parts of Ethiopia not considered chronically food insecure there are no supplementary feeding programmes (SFPs) for treating MAM. The short-term outcomes of children who have MAM in such areas are not currently described, and there remains an urgent need for evidence-based policy recommendations. Methods: We defined MAM as mid-upper arm circumference (MUAC) of ≥11.0cm and <12.5cm with no bilateral pitting oedema to include Ethiopian government and World Health Organisation cut-offs. We prospectively surveyed 884 children aged 6–59 months living with MAM in a rural area of Ethiopia not eligible for a supplementary feeding programme. Weekly home visits were made for seven months (28 weeks), covering the end of peak malnutrition through to the post-harvest period (the most food secure window), collecting anthropometric, socio-demographic and food security data. Results: By the end of the study follow up, 32.5% (287/884) remained with MAM, 9.3% (82/884) experienced at least one episode of SAM (MUAC <11cm and/or bilateral pitting oedema), and 0.9% (8/884) died. Only 54.2% of the children recovered with no episode of SAM by the end of the study. Of those who developed SAM half still had MAM at the end of the follow up period. The median (interquartile range) time to recovery was 9 (4–15) weeks. Children with the lowest MUAC at enrolment had a significantly higher risk of remaining with MAM and a lower chance of recovering. Conclusions: Children with MAM during the post-harvest season in an area not eligible for SFP experience an extremely high incidence of SAM and a low recovery rate. Not having a targeted nutrition-specific intervention to address MAM in this context places children with MAM at excessive risk of adverse outcomes. Further preventive and curative approaches should urgently be considered

The genetic basis and evolution of red blood cell sickling in deer

Crescent-shaped red blood cells, the hallmark of sickle-cell disease, present a striking departure from the biconcave disc shape normally found in mammals. Characterized by increased mechanical fragility, sickled cells promote haemolytic anaemia and vaso-occlusions and contribute directly to disease in humans. Remarkably, a similar sickle-shaped morphology has been observed in erythrocytes from several deer species, without obvious pathological consequences. The genetic basis of erythrocyte sickling in deer, however, remains unknown. Here, we determine the sequences of human β-globin orthologues in 15 deer species and use protein structural modelling to identify a sickling mechanism distinct from the human disease, coordinated by a derived valine (E22V) that is unique to sickling deer. Evidence for long-term maintenance of a trans-species sickling/non-sickling polymorphism suggests that sickling in deer is adaptive. Our results have implications for understanding the ecological regimes and molecular architectures that have promoted convergent evolution of sickling erythrocytes across vertebrates

Transverse tubule remodelling: a cellular pathology driven by both sides of the plasmalemma?

Transverse (t)-tubules are invaginations of the plasma membrane that form a complex network of ducts, 200–400 nm in diameter depending on the animal species, that penetrates deep within the cardiac myocyte, where they facilitate a fast and synchronous contraction across the entire cell volume. There is now a large body of evidence in animal models and humans demonstrating that pathological distortion of the t-tubule structure has a causative role in the loss of myocyte contractility that underpins many forms of heart failure. Investigations into the molecular mechanisms of pathological t-tubule remodelling to date have focused on proteins residing in the intracellular aspect of t-tubule membrane that form linkages between the membrane and myocyte cytoskeleton. In this review, we shed light on the mechanisms of t-tubule remodelling which are not limited to the intracellular side. Our recent data have demonstrated that collagen is an integral part of the t-tubule network and that it increases within the tubules in heart failure, suggesting that a fibrotic mechanism could drive cardiac junctional remodelling. We examine the evidence that the linkages between the extracellular matrix, t-tubule membrane and cellular cytoskeleton should be considered as a whole when investigating the mechanisms of t-tubule pathology in the failing heart

Magnetostriction Measurement of Amorphous Wires by Means of Small-Angle Magnetization Rotation

The small-angle magnetization rotation method has been shown to be applicable for measuring the saturation magnetostriction of amorphous wires by using the circumferential field generated by an ac current through the wire. The method was used to measure compositional variation of magnetostriction of Fe-Co based amorphous wires. A saturation magnetostriction s of 32.9×10−6 and −2.6×10−6 was found for Fe and Co based wires, respectively. The compositional variation of the saturation magnetostriction, s, for (Fe1−xCox)75Si10B15 amorphous wires (X=0–0.8) decreases with increasing cobalt content and crosses zero around X=0.95 as in amorphous ribbons. The maximum experimental error of measurement was estimated to be about 5%

Effect of stress on the bamboo domains and magnetization process of CoSiB amorphous wire

In this work we have studied the behavior of the bamboo domains under stress (sigma), tension (+ sigma) as well as compression (- sigma), with the aim of making the domain model of the negatively magnetostrictive (- lambda(5)) CoSiB wire clear. It is observed that the growth of the surface bamboo domains due to a has directivity depending on the orientation of the underlying core domain. In one orientation the black bamboo domain grows, while in the opposite orientation the white domain grows. From the stress behavior of the bamboo domains we have concluded that the domain model of - lambda(5) wire consists of two spiral domains of opposite rotation and proposed a new model