LINE-1 preTa elements in the human genome

The preTa subfamily of long interspersed elements (LINEs) is characterized by a three base-pair "ACG" sequence in the 3' untranslated region, contains approximately 400 members in the human genome, and has low level of nucleotide divergence with an estimated average age of 2.34 million years old suggesting that expansion of the L1 preTa subfamily occurred just after the divergence of humans and African apes. We have identified 362 preTa L1 elements from the draft human genomic sequence, investigated the genomic characteristics of preTa L1 insertions, and screened individual elements across diverse human populations and various non-human primate species using polymerase chain reaction (PCR) assays to determine the phylogenetic origin and levels of human genomic diversity associated with the L1 elements. All of the preTa L1 elements analyzed by PCR were absent from the orthologous positions in non-human primate genomes with 33 (14%) of the L1 elements being polymorphic with respect to insertion presence or absence in the human genome. The newly identified L1 insertion polymorphisms will prove useful as identical by descent genetic markers for the study of human population genetics. We provide evidence that preTa L1 elements show an integration site preference for genomic regions with low GC content. Computational analysis of the preTa L1 elements revealed that 29% of the elements amenable to complete sequence analysis have apparently escaped 5' truncation and are essentially full-length (approximately 6kb). In all, 29 have two intact open reading frames and may be capable of retrotransposition.     

Analysis of the human Alu Ya-lineage

The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and focused our analyses on the 2318 human autosomal Ya Alu elements. A total of 1470 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual Ya-lineage Alu elements. About 22% (313/1452) of the Ya-lineage Alu elements were polymorphic for the insertion presence on human autosomes. Less than 0.01% (5/1452) of the Ya-lineage loci analyzed displayed insertions in orthologous loci in non-human primate genomes. DNA sequence analysis of the orthologous inserts showed that the orthologous loci contained older pre-existing Y, Sc or Sq Alu subfamily elements that were the result of parallel forward insertions or involved in gene conversion events in the human lineage. This study is the largest analysis of a group of "young", evolutionarily related human subfamilies. The size, evolutionary age and variable allele insertion frequencies of several of these subfamilies makes members of the Ya-lineage useful tools for human population studies and primate phylogenetics.     

Decorticate, decerebrate and opisthotonic posturing and seizures in Kenyan children with cerebral malaria

Background

Intermittent preventive treatment of malaria during pregnancy (IPTp) is a key intervention in the national strategy for malaria control in Tanzania. SP, the current drug of choice, is recommended to be administered in the second and third trimesters of pregnancy during antenatal care (ANC) visits. To allow for a proper design of planned scaling up of IPT services in Tanzania it is useful to understand the IPTp strategy's acceptability to health managers, ANC service providers and pregnant women. This study assesses the knowledge, attitudes and practices of these groups in relation to malaria control with emphasis on IPTp services.

Methods

The study was conducted in February 2004, in Korogwe District, Tanzania. It involved in-depth interviews with the district medical officer (DMO), district hospital medical officer in charge and relevant health service staff at two peripheral dispensaries, and separate focus group discussions (FGDs) with district Council Health Management Team members at district level and pregnant women at dispensary and community levels.

Results

Knowledge of malaria risks during pregnancy was high among pregnant women although some women did not associate coma and convulsions with malaria. Contacting traditional healers and self-medication with local herbs for malaria management was reported to be common. Pregnant women and ANC staff were generally aware of SP as the drug recommended for IPTp, albeit some nurses and the majority of pregnant women expressed concern about the use of SP during pregnancy. Some pregnant women testified that sometimes ANC staff allow the women to swallow SP tablets at home which gives a room for some women to throw away SP tablets after leaving the clinic. The DMO was sceptical about health workers' compliance with the direct observed therapy in administering SP for IPTp due to a shortage of clean water and cups at ANC clinics. Intensified sensitization of pregnant women about the benefits of IPTp was suggested by the study participants as an important approach for improving IPTp compliance.

Conclusion

The successful implementation of the IPTp strategy in Tanzania depends on the proper planning of, and support to, the training of health staff and sustained sensitization of pregnant women at health facility and community levels about the benefits of IPTp for the women and their unborn babies.     

Acceptability and Use of Portable Drinking Water and Hand Washing Stations in Health Care Facilities and Their Impact on Patient Hygiene Practices,Western Kenya

Many health care facilities (HCF) in developing countries lack access to reliable hand washing stations and safe drinking water. To address this problem, we installed portable, low-cost hand washing stations (HWS) and drinking water stations (DWS), and trained healthcare workers (HCW) on hand hygiene, safe drinking water, and patient education techniques at 200 rural HCFs lacking a reliable water supply in western Kenya. We performed a survey at baseline and a follow-up evaluation at 15 months to assess the impact of the intervention at a random sample of 40 HCFs and 391 households nearest to these HCFs. From baseline to follow-up, there was a statistically significant increase in the percentage of dispensaries with access to HWSs with soap (42% vs. 77%, p<0.01) and access to safe drinking water (6% vs. 55%, p<0.01). Female heads of household in the HCF catchment area exhibited statistically significant increases from baseline to follow-up in the ability to state target times for hand washing (10% vs. 35%, p<0.01), perform all four hand washing steps correctly (32% vs. 43%, p = 0.01), and report treatment of stored drinking water using any method (73% vs. 92%, p<0.01); the percentage of households with detectable free residual chlorine in stored drinking water did not change (6%, vs. 8%, p = 0.14). The installation of low-cost, low-maintenance, locally-available, portable hand washing and drinking water stations in rural HCFs without access to 24-hour piped water helped assure that health workers had a place to wash their hands and provide safe drinking water. This HCF intervention may have also contributed to the improvement of hand hygiene and reported safe drinking water behaviors among households nearest to HCFs.     

Malnutrition and Childhood Disability in Turkana,Kenya: Results from a Case-Control Study

Background

Children with disabilities may be particularly vulnerable to malnutrition, as a result of exclusions and feeding difficulties. However, there is limited evidence currently available on this subject.

Methods

A population-based case-control study was conducted in Turkana County, Kenya, between July and August 2013. Key informants in the community identified children aged 6 months to 10 years who they believed may have a disability. These children were screened by a questionnaire (UNICEF-Washington Group) and assessed by a paediatrician to confirm whether they had a disability and the type. Two controls without disabilities were selected per case: A sibling control (sibling nearest in age) and a neighbourhood control (nearest neighbour within one year of age). The caregiver completed a questionnaire on behalf of the child (e.g. information on feeding, poverty, illness, education), and anthropometric measures were taken. We undertook multivariable logistic and linear regression analyses to estimate the relationship between disability and malnutrition.

Results

The study included 311 cases with disabilities, 196 sibling controls and 300 neighbour controls. Children with disabilities were more likely to report a range of feeding difficulties. They were 1.6–2.9 times more likely to have malnutrition in comparison to neighbour controls or family controls, including general malnutrition (low weight for age), stunting (low height for age), low body mass index (BMI) or low mid upper arm circumference (MUAC) for age. Children with disabilities were almost twice as likely to have wasting (low weight for height) in comparison to neighbour controls (OR = 1.9, 95% CI 1.1–3.2), but this difference was not apparent compared with siblings (OR = 1.5, 95% CI 0.8–2.7). Children with disabilities also faced other exclusions. For instance those aged 5+ were much more likely not to attend school than neighbour controls (OR = 8.5, 95% CI 4.3–16.9).

Conclusions

Children with disabilities were particularly vulnerable to malnutrition, even within this area of food insecurity and widespread malnutrition. Efforts need to be made to include children with disabilities within food supplementation programmes, and school based programmes alone may be inadequate to meet this need. Exclusion of children with disabilities from education is also a priority area to be addressed.     

The management effectiveness of protected areas in Kenya

Merely designating new and/or expanding existing protected areas (PAs) does not guarantee the protection of critical ecosystems and species. The management of PAs must be effective to sustain meaningful conservational outcomes. We inferred the management effectiveness of PAs in Kenya based on the representation of ranges and distribution of multiple diversity dimensions of terrestrial mammals and their association with governance and designation types. We hypothesized that different governance types underlie variable management efficacies, such that stricter-managed PAs have better habitats that attract more wildlife, translating to higher species diversity compared to less strictly-managed PAs, especially for focal species groups (large carnivores, large herbivores, and endangered species). The results showed nearly all terrestrial mammals in Kenya represented in at least one PA. However, the relative proportion of represented ranges were low, and analysis of spatial conservation prioritization showed significant expansion beyond current PAs needed to achieve a one third coverage of focal species’ ranges in a best-solution reserve system. Differences in PA governance and designation types were not systematically associated with diversity variances, and while there were more unique species in state-managed PAs than in privately-managed ones, averaged diversity coefficients were comparable between categories. Diversity variances explained by PA size and status year were low in a combined species pool but increased in focal species groups. These findings suggest that success in terrestrial mammal conservation in PAs in Kenya require clearly and formally streamlined definition, performance feedback, and collaboration terms between state-managed and privately-managed PAs.

     

Spatial heterogeneity in ecosystem structure and productivity in a moist Kenyan savanna

Topographic variations and disturbances are key sources of spatial heterogeneity in the ecosystem and may influence its functioning, productivity, and carbon (C) storage. In water controlled ecosystems, structural and functional heterogeneity become distinct during drought when the ecosystem processes are operating at their limits. We examined spatial heterogeneity arising from grazing, abandoned cropland, presence of Acacia trees, and termite mounds (termitaria). Soil water content (SWC) was significantly (P < 0.05) higher in termitaria and fenced (un-grazed) plots. Higher soil nitrogen (N) content occurred in the Acacia, termitaria, and fenced plots while total biomass was highest in the fenced plot. The termitaria plots showed the highest net ecosystem CO₂ exchange (NEE), ecosystem respiration (R _eco), and gross primary production (GPP) and were the only plots that were net CO₂ sinks. Except in fenced plots, maximum GPP was positively correlated with SWC and green biomass in all the other plots. Green biomass and R _eco were positively correlated with SWC. Shifting cultivation (abandoned farmlands) negatively affected soil quality, ecosystem CO₂ assimilation, and productivity. Removal of grazing (cattle) from the ecosystem negatively influenced GPP, while the presence of termitaria and Acacia trees facilitated soil water and N availability and ecosystem productivity. We concluded that soil water availability was responsible for most of the localized differences in the savanna and has a strong influence on ecosystem C capture and storage. We recommend that future studies on savanna productivity and ecosystem CO₂ fluxes should consider heterogeneity in the ecosystem in order to avoid bias and increase the accuracy of any estimates made.     

The role of the LH subdomain in the function of the Cip/Kip cyclin-dependent kinase regulators

The Cip/Kip protein family, which includes p27, p21, and p57, modulates the activity of cyclin-dependent kinases (Cdks). A domain within these proteins, termed the kinase inhibitory domain (KID), is necessary and sufficient for Cdk inhibition. The KID consists of a cyclin-binding subdomain (termed D1) and a Cdk-binding subdomain (termed D2) joined by a 22-residue linker subdomain (termed LH). Before binding the Cdks, D1 and D2 are largely unstructured and the LH subdomain exhibits nascent helical characteristics. Curiously, although the sequence of the linker subdomain is not highly conserved within the family, its nascent helical structure is conserved. In this study, we explored the role of this structural conservation in interactions with cyclin-dependent kinase 2 (Cdk2) and cyclin A. We constructed chimeric p27-KID molecules in which the p27 LH subdomain was replaced with the corresponding segments of either p21 or p57. The chimeric molecules bind and inhibit Cdk2 in a manner similar to wild-type p27-KID. However, the extent of enthalpy/entropy compensation associated with these interactions was dramatically different, indicating different extents of LH subdomain folding upon binding. Our results indicate that the different LH subdomains, despite their sequence and thermodynamic differences, play similar roles in binding and inhibiting Cdk2/cyclin A.     

Effects of News Frames on Perceived Risk,Emotions, and Learning

The media play a key role in forming opinions by influencing people´s understanding and perception of a topic. People gather information about topics of interest from the internet and print media, which employ various news frames to attract attention. One example of a common news frame is the human-interest frame, which emotionalizes and dramatizes information and often accentuates individual affectedness. Our study investigated effects of human-interest frames compared to a neutral-text condition with respect to perceived risk, emotions, and knowledge acquisition, and tested whether these effects can be "generalized" to common variants of the human-interest frame. Ninety-one participants read either one variant of the human-interest frame or a neutrally formulated version of a newspaper article describing the effects of invasive species in general and the Asian ladybug (an invasive species) in particular. The framing was achieved by varying the opening and concluding paragraphs (about invasive species), as well as the headline. The core text (about the Asian ladybug) was the same across all conditions. All outcome variables on framing effects referred to this common core text. We found that all versions of the human-interest frame increased perceived risk and the strength of negative emotions compared to the neutral text. Furthermore, participants in the human-interest frame condition displayed better (quantitative) learning outcomes but also biased knowledge, highlighting a potential dilemma: Human-interest frames may increase learning, but they also lead to a rather unbalanced view of the given topic on a “deeper level”.