Selection Affects Genes Involved in Replication during Long-Term Evolution in Experimental Populations of the Bacteriophage φX174

Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying adaptation. Although dissecting these molecular mechanisms is expensive and time-consuming, general patterns can be detected from repeated experiments, illuminating the biological processes involved in evolutionary adaptation. The bacteriophage φX174 was grown for 50 days in replicate chemostats under two culture conditions: Escherichia coli C as host growing at 37°C and Salmonella typhimurium as host growing at 43.5°C. After 50 days, greater than 20 substitutions per chemostat had risen to detectable levels. Of the 97 substitutions, four occurred in all four chemostats, five arose in both culture conditions, eight arose in only the high temperature S. typhimurium chemostats, and seven arose only in the E. coli chemostats. The remaining substitutions were detected only in a single chemostat, however, almost half of these have been seen in other similar experiments. Our findings support previous studies that host recognition and capsid stability are two biological processes that are modified during adaptation to novel hosts and high temperature. Based upon the substitutions shared across both environments, it is apparent that genome replication and packaging are also affected during adaptation to the chemostat environment, rather than to temperature or host per se. This environment is characterized by a large number of phage and very few hosts, leading to competition among phage within the host. We conclude from these results that adaptation to a high density environment selects for changes in genome replication at both protein and DNA sequence levels.     

Visualisation of Respiratory Tumour Motion and Co-Moving Isodose Lines in the Context of Respiratory Gating,IMRT and Flattening-Filter-Free Beams

Respiratory motion during percutaneous radiotherapy can be considered based on respiration-correlated computed tomography (4DCT). However, most treatment planning systems perform the dose calculation based on a single primary CT data set, even though cine mode displays may allow for a visualisation of the complete breathing cycle. This might create the mistaken impression that the dose distribution were independent of tumour motion. We present a movie visualisation technique with the aim to direct attention to the fact that the dose distribution migrates to some degree with the tumour and discuss consequences for gated treatment, IMRT plans and flattening-filter-free beams. This is a feasibility test for a visualisation of tumour and isodose motion. Ten respiratory phases are distinguished on the CT, and the dose distribution from a stationary IMRT plan is calculated on each phase, to be integrated into a movie of tumour and dose motion during breathing. For one example patient out of the sample of five lesions, the plan is compared with a gated treatment plan with respect to tumour coverage and lung sparing. The interplay-effect for small segments in the IMRT plan is estimated. While the high dose rate, together with the cone-shaped beam profile, makes the use of flattening-filter-free beams more problematic for conformal and IMRT treatment, it can be the option of choice if gated treatment is preferred. The different effects of respiratory motion, dose build-up and beam properties (segments and flatness) for gated vs. un-gated treatment can best be considered if planning is performed on the full 4DCT data set, which may be an incentive for future developments of treatment planning systems.     

Routine Paediatric Sickle Cell Disease (SCD) Outpatient Care in a Rural Kenyan Hospital: Utilization and Costs

Background

More than 70% of children with sickle cell disease (SCD) are born in sub-Saharan Africa where the prevalence at birth of this disease reaches 2% or higher in some selected areas. There is a dearth of knowledge on comprehensive care received by children with SCD in sub-Saharan Africa and its associated cost. Such knowledge is important for setting prevention and treatment priorities at national and international levels. This study focuses on routine care for children with SCD in an outpatient clinic of the Kilifi District Hospital, located in a rural area on the coast of Kenya.

Objective

To estimate the per-patient costs for routine SCD outpatient care at a rural Kenyan hospital.

Methods

We collected routine administrative and primary cost data from the SCD outpatient clinic and supporting departments at Kilifi District Hospital, Kenya. Costs were estimated by evaluating inputs - equipment, medication, supplies, building use, utility, and personnel - to reflect the cost of offering this service within an existing healthcare facility. Annual economic costs were similarly calculated based on input costs, prorated lifetime of equipment and appropriate discount rate. Sensitivity analyses evaluated these costs under different pay scales and different discount rate.

Results

We estimated that the annual economic cost per patient attending the SCD clinic was USD 138 in 2010 with a range of USD 94 to USD 229.

Conclusion

This study supplies the first published estimate of the cost of routine outpatient care for children born with SCD in sub-Saharan Africa. Our study provides policy makers with an indication of the potential future costs of maintaining specialist outpatient clinics for children living with SCD in similar contexts.     

Ezrin and HNRNP expression correlate with increased virus release rate and early onset of virus‐induced apoptosis of MDCK suspension cells

With the aim to adapt high‐yield adherent cell lines to suspension growth, Madin Darby canine kidney (MDCK) suspension cells were developed recently that achieved comparable influenza virus yields despite an early induction of apoptosis compared to the parental adherent cell line. For both cell lines, a comprehensive study under comparable infection conditions is performed comprising information on: time course of viral infection, antiviral state of cells, virus‐induced apoptosis, and virus‐induced cellular protein expression for early and late infection with influenza A/PuertoRico/8/34 H1N1. The proteomic analysis is performed with 2D differential gel electrophoreses followed by mass spectrometry. Based on flow cytometric data and on the differential expression of various stress and apoptosis‐related proteins, the earlier onset of virus‐induced apoptosis is confirmed for suspension cells. Surprisingly, the data indicated an increased virus release rate for suspension cells. These observations correlate with an increased expression of the apical marker protein ezrin, known to play a role in influenza‐induced cytoskeletal rearrangement, and the differential expression of heterogeneous nuclear ribonucleoproteins, known to bind actively influenza viral proteins and play a central role in regulating gene expression. Based on these findings, additional studies towards the design of MDCK suspension cells with further increase in influenza virus yields will be performed.     

Aberrant DNA Methylation: Implications in Racial Health Disparity

BackgroundIncidence and mortality rates of colorectal carcinoma (CRC) are higher in African Americans (AAs) than in Caucasian Americans (CAs). Deficient micronutrient intake due to dietary restrictions in racial/ethnic populations can alter genetic and molecular profiles leading to dysregulated methylation patterns and the inheritance of somatic to germline mutations.ResultsDNA from the tumor of AA CRC patients, compared to adjacent normal tissues, contained 1,588 hypermethylated and 100 hypomethylated differentially methylated regions (DMRs). Whereas, 109 hypermethylated and 4 hypomethylated DMRs were observed in DNA from the tumor of CA CRC patients; representing a 14.6-fold and 25-fold change, respectively. Specifically; CHL1, 4 anti-inflammatory genes (i.e., NELL1, GDF1, ARHGEF4, and ITGA4), and 7 miRNAs (of which miR-9-3p and miR-124-3p have been implicated in CRC) were hypermethylated in DNA samples from AA patients with CRC. From the same sample set, RNAseq analysis revealed 108 downregulated genes (including 14 ribosomal proteins) and 34 upregulated genes (including POLR2B and CYP1B1 [targets of miR-124-3p]) in AA patients with CRC versus CA patients.ConclusionDNA methylation profile and/or products of its downstream targets could serve as biomarker(s) addressing racial health disparity.     

A Minimal Intervention to Promote Smoke-Free Homes among 2-1-1 Callers: North Carolina Randomized Effectiveness Trial

This study examined the extent to which delivery of the minimal Smoke-Free Homes intervention by trained 2-1-1 information and referral specialists had an effect on the adoption of home smoking bans in low-income households. A randomized controlled trial was conducted among 2-1-1 callers (n = 500) assigned to control or intervention conditions. 2-1-1 information and referral specialists collected baseline data and delivered the intervention consisting of 3 mailings and 1 coaching call; university-based data collectors conducted follow-up interviews at 3 and 6 months post-baseline. Data were collected from June 2013 through July 2014. Participants were mostly female (87.2%), African American (61.4%), and smokers (76.6%). Participants assigned to the intervention condition were more likely than controls to report a full ban on smoking in the home at both 3- (38.1% vs 19.3%, p = < .001) and 6-month follow-up (43.2% vs 33.2%, p = .02). The longitudinal intent-to-treat analysis showed a significant intervention effect over time (OR = 1.31, p = .001), i.e. OR = 1.72 at 6 months. This study replicates prior findings showing the effectiveness of the minimal intervention to promote smoke-free homes in low-income households, and extends those findings by demonstrating they can be achieved when 2-1-1 information and referral specialists deliver the intervention. Findings offer support for this intervention as a generalizable and scalable model for reducing secondhand smoke exposure in homes.