A graphical method for detecting recombination in phylogenetic data sets

Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.      

bilbo, a non-LTR retrotransposon of Drosophila subobscura: a clue to the evolution of LINE-like elements in Drosophila

We used the repetitive character of transposable elements to isolate a non-LTR retrotransposon in Drosophila subobscura. bilbo, as we have called it, has homology to TRIM and LOA elements. Sequence analysis showed a 5' untranslated region (UTR), an open reading frame (ORF) with no RNA-binding domains, a downstream ORF that had structural homology to that of the I factor, and, finally, a 3' UTR which ended in several 5-nt repeats. The results of our phylogenetic and structural analyses shed light on the evolution of Drosophila non-LTR retrotransposons and support the hypothesis that an ancestor of these elements was structurally complex.      

Variation of physico-chemical parameters along a river transect through the Okavango Delta,Botswana

The Okavango Delta depends on water quantity and quality to sustain its ecosystem services. Whereas many studies have been carried out on its hydrology, few have been done on water quality in the delta. Water pH, electrical conductivity (EC), dissolved oxygen (DO), turbidity, total suspended solids (TSS) and dissolved organic carbon (DOC) were monitored at 10 sites along the Okavango–Boro–Thamalakane–Lake Ngami system almost fortnightly from June 2008 to June 2010. Water quality in the delta was generally good, despite high evapotranspiration rates which would normally produce very saline waters. Electrical conductivity and water temperature increased with distance from Mohembo to Lake Ngami, the former most likely due to evapoconcentration. In contrast, pH, DO, turbidity and TSS decreased with distance from Mohembo to Boro at the lower end of the seasonal floodplain, before increasing again to Lake Ngami. Dissolved oxygen and TSS most likely declined due to biological uptake and particle sedimentation, respectively. Strong and significant relationships were observed between TSS and turbidity and between DOC and EC, indicating that turbidity and EC could be useful proxies for routine estimations of TSS and DOC, respectively, in the delta.     

Macroinvertebrates as bioindicators of water quality in the Mkondoa River,Tanzania, in an agricultural area

The suitability of using macroinvertebrates as bioindicators of stream water quality was tested in the Mkondoa River in an agricultural area at Kilosa, using the rapid bioassessment protocol. The family biotic index (FBI) showed marked variation in water quality along the stream from values ranging from 4.1 to 5.0 in the upstream reaches, indicating good water quality, 5.3 to 5.5 in the mid-reaches and 6.0 to 6.5 in the lower reaches. The water quality index (WQI) indicated that water quality was fair (77 ± 0.98) in the upstream reach of the Mkondoa, marginal (55 ± 0.86) in the midstream reach and poor (33 ± 0.45) in the downstream reach. There were significant relationships between biological oxygen demand and dissolved oxygen and the occurrence of specific taxa, mainly Chironomus and Caenis. Significant changes in macroinvertebrate abundance were mostly related to changes in water quality. As in other parts of the world, macroinvertebrate communities proved to be good biological indicators of water quality and they should be used as bioindicators in long-term monitoring of this river.     

Costing Alternative Birth Settings for Women at Low Risk of Complications: A Systematic Review

Background

There is demand from women for alternatives to giving birth in a standard hospital setting however access to these services is limited. This systematic review examines the literature relating to the economic evaluations of birth setting for women at low risk of complications.

Methods

Searches of the literature to identify economic evaluations of different birth settings of the following electronic databases: MEDLINE, CINAHL, EconLit, Business Source Complete and Maternity and Infant care. Relevant English language publications were chosen using keywords and MeSH terms between 1995 and 2015. Inclusion criteria included studies focussing on the comparison of birth setting. Data were extracted with respect to study design, perspective, PICO principles, and resource use and cost data.

Results

Eleven studies were included from Australia, Canada, the Netherlands, Norway, the USA, and the UK. Four studies compared costs between homebirth and the hospital setting and the remaining seven focussed on the cost of birth centre care and the hospital setting. Six studies used a cost-effectiveness analysis and the remaining five studies used cost analysis and cost comparison methods. Eight of the 11 studies found a cost saving in the alternative settings. Two found no difference in the cost of the alternative settings and one found an increase in birth centre care.

Conclusions

There are few studies that compare the cost of birth setting. The variation in the results may be attributable to the cost data collection processes, difference in health systems and differences in which costs were included. A better understanding of the cost of birth setting is needed to inform policy makers and service providers.     

Proteolytic activity of oral streptococci

Streptococcus mutans and Streptococcus sobrinus were the least proteolytic of 8 species of oral streptococci while Streptococcus oralis and Streptococcus sanguis were the most proteolytic. Degradation of FITC-BSA was significantly correlated with the hydrolysis of synthetic endopeptidase substrates. As S. oralis strains proliferate in dental plaque in the absence of dietary food their success, in vivo, might be due partially to their greater proteolytic activity compared to other oral streptococci.     

Passage ofCorynebacterium aquaticum through membrane filters

Summary Cellulose ester and polycarbonate membrane filters were tested for sterilizing capability with a contaminant,Corynebacterium aquaticum, isolated from cell culture medium. This contaminant, often found in water supplies, routinely passes filters of the polycarbonate type, but not of the cellulose ester type.C. aquaticum grows slowly requiring 7 to 10 days incubation in BME at 37°C before turbidity develops. Cryptic contamination is potentially a serious problem with this organism. This work was supported in part by USPHS Grant 5 F32 CA05635-02 from the National Cancer Institute.     

Bubble-induced dysfunction in acute spinal cord decompression sickness

Five anesthetized dogs undertook a chamber dive, on air, to 300 feet of seawater for 15 min. After the dive, spinal cord decompression sickness was detected by recording a reduced amplitude of the somatosensory evoked potential compared with predive base-line values. After the diagnosis of decompression sickness and rapid perfusion fixation of the animal, the spinal cord was removed and examined histologically. Numerous space-occupying lesions (SOL) that disrupted the tissue architecture were found in each cord, mainly in the white matter. The size and distribution of the SOL were determined using computerized morphometry. Although SOL occupied less than 0.5% of the white matter volume, we tested a number of algorithms to assess whether the SOL may have been directly involved in the loss of spinal cord function that followed the dive. We determined that the loss of somatosensory evoked potential amplitude may be attributed to the SOL if 30-100% of the spinal cord fibers that they displaced were rendered nonconducting. A number of possible mechanisms by which SOL may interfere with spinal nerve conduction are discussed.