Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA

Wolbachia endosymbionts are widespread in arthropods and are generally considered reproductive parasites, inducing various phenotypes including cytoplasmic incompatibility, parthenogenesis, feminization and male killing, which serve to promote their spread through populations. In contrast, Wolbachia infecting filarial nematodes that cause human diseases, including elephantiasis and river blindness, are obligate mutualists. DNA purification methods for efficient genomic sequencing of these unculturable bacteria have proven difficult using a variety of techniques. To efficiently capture endosymbiont DNA for studies that examine the biology of symbiosis, we devised a parallel strategy to an earlier array-based method by creating a set of SureSelect? (Agilent) 120-mer target enrichment RNA oligonucleotides (“baits”) for solution hybrid selection. These were designed from Wolbachia complete and partial genome sequences in GenBank and were tiled across each genomic sequence with 60 bp overlap. Baits were filtered for homology against host genomes containing Wolbachia using BLAT and sequences with significant host homology were removed from the bait pool. Filarial parasite Brugia malayi DNA was used as a test case, as the complete sequence of both Wolbachia and its host are known. DNA eluted from capture was size selected and sequencing samples were prepared using the NEBNext® Sample Preparation Kit. One-third of a 50 nt paired-end sequencing lane on the HiSeq? 2000 (Illumina) yielded 53 million reads and the entirety of the Wolbachia genome was captured. We then used the baits to isolate more than 97.1 % of the genome of a distantly related Wolbachia strain from the crustacean Armadillidium vulgare, demonstrating that the method can be used to enrich target DNA from unculturable microbes over large evolutionary distances.     

Steps Toward Developing an EEG Biofeedback Treatment for Chronic Pain

Chronic pain, usually refractory to analgesics, is a significant problem for many individuals with spinal cord injury (SCI). Preliminary studies suggest that electroencephalography (EEG) biofeedback (also known as neurofeedback, NF) has the potential to help patients with otherwise refractory chronic pain. However, there remain many unanswered questions about the effects and mechanisms of this treatment. We studied 13 individuals with SCI and chronic pain with NF. Ten of the 13 individuals completed 4 sessions each of three different neurofeedback protocols assigned in random order for a total of 12 NF sessions. All three protocols had similar immediate effects on pain intensity. In addition, the participants reported modest pre- to post-treatment decreases in worst pain and pain unpleasantness following completion of the 12 NF sessions. These improvements were maintained at 3-month follow-up. The majority of the participants felt they benefited from and were satisfied with the treatment. No significant effects on measures of other outcome domains (sleep quality, pain interference and fatigue) were observed, although there was a non-significant trend for an increase in fatigue. Finally, pre- to post-treatment changes in EEG bandwidth activity, consistent with the training protocols, were observed in θ and α but not β frequencies. The findings provide preliminary support for the potential efficacy of NF for the treatment of SCI-related pain, and suggest that further clinical studies are warranted.     

Beauvericin and divalent cations: crystal structure of the barium complex.

The molecular structure of the 2:2 complex of the cyclohexadepsipeptide antibiotic beauvericin with barium picrate has been determined by X-ray crystallography. The structure serves to confirm previous observations on the bimolecular behavior of beauvericin and of the ions transported by beauvercin. The intimate involvement of the anions in the coordination of the barium also explains observations that the cation specificity of beauvericin in membrane transport depends on the species of anions present.     

Discovery and SAR of benzyl phenyl ethers as inhibitors of bacterial phenylalanyl-tRNA synthetase

A series of benzyl phenyl ethers (BPEs) is described that displays potent inhibition of bacterial phenylalanyl-tRNA synthetase. The synthesis, SAR, and select ADMET data are provided.     

Access to health care among status Aboriginal people with chronic kidney disease

Background

Ethnic disparities in access to health care and health outcomes are well documented. It is unclear whether similar differences exist between Aboriginal and non-Aboriginal people with chronic kidney disease in Canada. We determined whether access to care differed between status Aboriginal people (Aboriginal people registered under the federal Indian Act) and non-Aboriginal people with chronic kidney disease.

Methods

We identified 106 511 non-Aboriginal and 1182 Aboriginal patients with chronic kidney disease (estimated glomerular filtration rate less than 60 mL/min/1.73 m²). We compared outcomes, including hospital admissions, that may have been preventable with appropriate outpatient care (ambulatory-care–sensitive conditions) as well as use of specialist services, including visits to nephrologists and general internists.

Results

Aboriginal people were almost twice as likely as non-Aboriginal people to be admitted to hospital for an ambulatory-care–sensitive condition (rate ratio 1.77, 95% confidence interval [CI] 1.46–2.13). Aboriginal people with severe chronic kidney disease (estimated glomerular filtration rate < 30 mL/min/1.73 m²) were 43% less likely than non-Aboriginal people with severe chronic kidney disease to visit a nephrologist (hazard ratio 0.57, 95% CI 0.39–0.83). There was no difference in the likelihood of visiting a general internist (hazard ratio 1.00, 95% CI 0.83–1.21).

Interpretation

Increased rates of hospital admissions for ambulatory-care–sensitive conditions and a reduced likelihood of nephrology visits suggest potential inequities in care among status Aboriginal people with chronic kidney disease. The extent to which this may contribute to the higher rate of kidney failure in this population requires further exploration.Ethnic disparities in access to health care are well documented;^1,2 however, the majority of studies include black and Hispanic populations in the United States. The poorer health status and increased mortality among Aboriginal populations than among non-Aboriginal populations,^3,4 particularly among those with chronic medical conditions,^5,6 raise the question as to whether there is differential access to health care and management of chronic medical conditions in this population.The prevalence of end-stage renal disease, which commonly results from chronic kidney disease, is about twice as common among Aboriginal people as it is among non-Aboriginal people.^7,8 Given that the progression of chronic kidney disease can be delayed by appropriate therapeutic interventions^9,10 and that delayed referral to specialist care is associated with increased mortality,^11,12 issues such as access to health care may be particularly important in the Aboriginal population. Although previous studies have suggested that there is decreased access to primary and specialist care in the Aboriginal population,^13–15 these studies are limited by the inclusion of patients from a single geographically isolated region,¹³ the use of survey data,¹⁴ and the inability to differentiate between different types of specialists and reasons for the visit.¹⁵In addition to physician visits, admission to hospital for ambulatory-care–sensitive conditions (conditions that, if managed effectively in an outpatient setting, do not typically result in admission to hospital) has been used as a measure of access to appropriate outpatient care.^16,17 Thus, admission to hospital for an ambulatory-care–sensitive condition reflects a potentially preventable complication resulting from inadequate access to care. Our objective was to determine whether access to health care differs between status Aboriginal (Aboriginal people registered under the federal Indian Act) and non-Aboriginal people with chronic kidney disease. We assess differences in care by 2 measures: admission to hospital for an ambulatory-care–sensitive condition related to chronic kidney disease; and receipt of nephrology care for severe chronic kidney disease as recommended by clinical practice guidelines.¹⁸     

DNA Methylation Is Linked to Deacetylation of Histone H3, but Not H4, on the Imprinted Genes Snrpn and U2af1-rs1

The relationship between DNA methylation and histone acetylation at the imprinted mouse genes U2af1-rs1 and Snrpn is explored by chromatin immunoprecipitation (ChIP) and resolution of parental alleles using single-strand conformational polymorphisms. The U2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5' DMR (DMR1) with sequences homologous to the imprinting control center of the Prader-Willi/Angelman region. For both DMR1 of Snrpn and the 5' untranslated region (5'-UTR) and 3'-UTR of U2af1-rs1, the methylated and nonexpressed maternal allele was underacetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allele was exclusively (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cells, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mice that were dipaternal or dimaternal for U2af1-rs1. In contrast, in a region within Snrpn that has biallelic methylation in the cells and tissues analyzed, the paternal (expressed) allele showed relatively increased acetylation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP2 was found, by ChIP, to be associated exclusively with the maternal U2af1-rs1 allele. To ask whether DNA methylation is associated with histone deacetylation, we produced mice with transgene-induced methylation at the paternal allele of U2af1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collectively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that involves selective binding of MBD proteins.     

Quantification of meniscal volume by segmentation of 3T magnetic resonance images

Meniscal injuries place the knee at risk for early osteoarthritis (OA) because they disrupt their load-bearing capabilities. Partial resection is routinely performed to alleviate symptomatic meniscal tears. While the removal of meniscal tissue may not be the only factor associated with partial meniscectomy outcome, the amount removed certainly contributes to functional loss. It is unknown, however, whether there is a critical amount of meniscal tissue that can be removed without diminishing the structure's chondroprotective role. In order to examine the existence of such a threshold, it is necessary to accurately quantify meniscal volume both before and after partial meniscectomy to determine the amount of meniscal tissue removed. Therefore, our goal was to develop and validate an MR-based method for assessing meniscal volume. The specific aims were: (1) to evaluate the feasibility of the MR-based segmentation method; (2) to determine the method's reliability for repeated measurements; and (3) to validate its accuracy in situ. MR images were obtained on a 3T magnet, and each scan was segmented using a biplanar approach. The MR-based volumes for each specimen were compared to those measured by water displacement. The results indicate that the biplanar approach of measuring meniscal volumes is accurate and reliable. The calculated volumes of the menisci were within 5% of the true values, the coefficients of variation were 4%, and the intraclass correlation coefficients were greater than 0.96. These data demonstrate that this method could be used to measure the amount of meniscal tissue excised during partial meniscectomy to within 125.7 mm(3).     

Accuracy of circular contact area measurements with thin-film pressure sensors

Contact area is often used to characterize the biomechanical properties of joints, especially in testing of injury and joint replacement. Several methods have been developed to measure contact area, including piezo-resistive thin-film arrays. The purpose of this study was to determine the accuracy with which one of these systems (Tekscan, Inc., South Boston, MA) could measure the contact area of flat-ended circular indenters of varying known sizes. Static loads ranging from 1000 to 7000 N were applied to four flat, circular indenters (1140, 2027, 3167, and 4560 mm(2)) and the contact areas were recorded with Tekscan 5076 sensor. Similar testing was carried out on a 4000 sensor. I-scan software (Tekscan Inc., South Boston, MA) was used to analyze the Tekscan-recorded area measurements. The Tekscan data were also post-processed to filter out sensel signal intensity values that were at least two standard deviations from the average sensel signal intensity values of the sensor matrix. Unprocessed Tekscan measurements with the 5076 sensor had area percent errors ranging from 5% to 27%. The filtering algorithm reduced most errors to less than 1%. Similar trends of improved accuracy with post-filtering were found with the 4000 sensor. While this method of thresholding out the sensels with the lowest signal intensity values may not work for all surfaces and indenter shapes, it provides a new approach to improve the accuracy of contact area measurements collected with the Tekscan system.