In Vitro Chromatin Assembly: Strategies and Quality Control

Chromatin accessibility is modulated by structural transitions that provide timely access to the genetic and epigenetic information during many essential nuclear processes. These transitions are orchestrated by regulatory proteins that coordinate intricate structural modifications and signaling pathways. In vitro reconstituted chromatin samples from defined components are instrumental in defining the mechanistic details of such processes. The bottleneck to appropriate in vitro analysis is the production of high quality, and quality-controlled, chromatin substrates. In this chapter, we describe methods for in vitro chromatin reconstitution and quality control. We highlight the strengths and weaknesses of various approaches and emphasize quality control steps that ensure reconstitution of a bona fide homogenous chromatin preparation. This is essential for optimal reproducibility and reliability of ensuing experiments using chromatin substrates.

Emergence of pan-resistance in KPC-2 carbapenemase-producing Klebsiella pneumoniae in Crete, Greece: a close call

OBJECTIVES

KPC-2-producing Klebsiella pneumoniae (KPC-KP) ST258 has been rapidly expanding and is often associated with serious nosocomial infections. Last-line antibiotics such as colistin and tigecycline often remain the only treatment option. We describe here the evolving genetic background of KPC-KP isolates in Crete, Greece.

METHODS

We tested the antibiotic susceptibility of 34 clinical isolates from patients hospitalized in 2010 and 2013-14. Whole-genome sequences of these isolates were analysed for acquired resistance genes and gene mutations.

RESULTS

All KPC-KP isolates belonged to ST258 with the exception of one ST147 isolate. From 2014, 26% of isolates were non-susceptible to all antibiotics, compared with 0 of 11 isolates from 2010. Colistin resistance was associated with mutations in mgrB, which was present in 61% of isolates from 2014. Core-genome MLST analysis showed that pan-resistant isolates were closely related and appeared in two separate clusters.

CONCLUSIONS

KPC-KP is rapidly evolving to pan-resistance in Crete. We identified molecular resistance markers for pan-resistant isolates and showed that core-genome MLST is a promising tool for molecular fingerprinting of KPC-KP ST258.

A genome-wide association study suggests an association of Chr8p21.3 (GFRA2) with diabetic neuropathic pain

Background

Neuropathic pain, caused by a lesion or a disease affecting the somatosensory system, is one of the most common complications in diabetic patients. The purpose of this study is to identify genetic factors contributing to this type of pain in a general diabetic population.

Method

We accessed the Genetics of Diabetes Audit and Research Tayside (GoDARTS) datasets that contain prescription information and monofilament test results for 9439 diabetic patients, among which 6927 diabetic individuals were genotyped by Affymetrix SNP6.0 or Illumina OmniExpress chips. Cases of neuropathic pain were defined as diabetic patients with a prescription history of at least one of five drugs specifically indicated for the treatment of neuropathic pain and in whom monofilament test result was positive for sensory neuropathy in at least one foot. Controls were individuals who did not have a record of receiving any opioid analgesics. Imputation of non‐genotyped SNPs was performed by IMPUTE2, with reference files from 1000 Genomes Phase I datasets.

Results

After data cleaning and relevant exclusions, imputed genotypes of 572 diabetic neuropathic pain cases and 2491 diabetic controls were used in the Fisher's exact test. We identified a cluster in the Chr8p21.3, next to GFRA2 with a lowest p‐value of 1.77 × 10⁻⁷ at rs17428041. The narrow‐sense heritability of this phenotype was 11.00%.

Conclusion

This genome‐wide association study on diabetic neuropathic pain suggests new evidence for the involvement of variants near GFRA2 with the disorder, which needs to be verified in an independent cohort and at the molecular level.

Neurodevelopmental delay with critical congenital heart disease is mainly from prenatal injury not infant cardiac surgery: current evidence based on a meta-analysis of functional magnetic resonance imaging

OBJECTIVE

No consensus has been reached regarding whether brain injury related to congenital heart disease (CHD) is caused by infant cardiac surgery and/or prenatal injury resulting from the CHD. We performed this meta-analysis to identify the likely cause of neurodevelopmental delay in CHD patients.

METHODS

We carried out a literature search without language restriction in December 2013, retrieving records from PubMed, EMBASE, the Cochrane Library and the World Health Organization trials center, to identify studies applying functional magnetic resonance imaging (fMRI) evaluation of brain function before surgery and, in some cases, after surgery (both immediate term and short term postoperatively). The preoperative and postoperative fMRI results were extracted, and meta-analysis was performed using Revman 5.1.1 and STATA 11.0, according to the guidelines from the Cochrane review and MOOSE groups.

RESULTS

The electronic search yielded 937 citations. Full text was retrieved for 15 articles and eight articles (nine studies) were eligible for inclusion: six studies (n = 312 cases) with fMRI analysis before surgery and three (n = 36 cases) with complete perioperative fMRI analysis. The overall average diffusivity of CHD cases was significantly higher than that of controls, with a summarized standard (std) mean difference of 1.39 (95% CI, 0.70-2.08), and the fractional anisotropy was lower in CHD cases, with a summarized mean difference of -1.43 (95% CI, -1.95 to -0.91). N-acetylaspartate (NAA)/choline (Cho) for the whole brain was significantly lower in CHD cases compared with healthy ones, while lactate/Cho was significantly higher in CHD cases. Immediate term postoperatively, significant changes in NAA/creatine and NAA/Cho, relative to preoperative values, were found. However, the difference did not persist at the short-term follow-up.

CONCLUSION

This meta-analysis suggests that the delay in neurological development in newborns with CHD is due mainly to prenatal injury, and cardiac surgery might lead to mild brain injuries postoperatively, but fMRI shows recovery within a short period.

The synthesis and structure of chiral enamine N-oxides

Chiral enamine N-oxides have been synthesised by a diastereoselective intermolecular reverse-Cope cycloaddition reaction between chiral hydroxylamines and activated acetylenes. Their structures have been investigated by NMR, X-ray crystallography and computational methods.

Coronary artery fistula in adults: evaluation with dual-source CT coronary angiography

OBJECTIVE

To evaluate the clinical value of dual-source CT (DSCT) coronary angiography in the diagnosis of coronary artery fistula (CAF) in adults.

METHODS

A large cohort of 17,548 patients, who underwent DSCT coronary angiography in our hospital between January 2008 and October 2013, were retrospectively reviewed for CAF. The origin, course and drainage site of CAF and coexisting abnormalities were analysed. The conventional angiography results, treatments and follow-up DSCT images were also evaluated.

RESULTS

A total of 33 CAFs from 17,548 patients were detected. The incidence of CAF was 0.19% by DSCT. CAF originating from the left coronary artery (LCA) was found in 14 (42.4%) patients, from right coronary artery (RCA) in 4 (12.1%) cases and from both LCA and RCA in 15 (45.5%) patients. The pulmonary artery was the most common site of drainage (28/33, 84.8%). 8 of the 33 (24.2%) cases were associated with aneurysms. Six cases were associated with coronary artery atherosclerosis. Four patients underwent conventional angiography.

CONCLUSION

Coronary-pulmonary artery fistula in adults was found more often than in previous studies. CAF commonly originates from LCA or both LCA and RCA in adults. DSCT is a robust tool for investigating the origin, course and drainage site of CAF and coexistent abnormalities.

ADVANCES IN KNOWLEDGE

A large adult patient cohort who underwent DSCT angiography was reviewed to assess CAFs. Coronary-pulmonary artery fistula in adults was found more often than in previous studies. CAF was observed to originate from the LCA or both coronary arteries in adults. DSCT could clearly depict the fistula origin, course, drainage site and coexisting abnormalities. Conventional angiography results, treatments and follow-up DSCT images were analysed.

Simulation of Soot Size Distribution in a Counterflow Flame

Soot formed during the rich combustion of fossil fuels is an undesirable pollutant and health hazard. A newly developed Monte Carlo method is used to simulate the soot formation in a counterflow diffusion flame of ethylene. The simulation uses a new reaction mechanism available in literature, which focuses on modeling the formation of large polycyclic aromatic hydrocarbons (PAHs) up to coronene (C24H12). Nascent soot particles are assumed to form from the collision of eight different PAH molecules. Soot surface growth includes the hydrogen-abstraction-C2H2-addition mechanism and the condensation of the PAHs. Soot coagulation is in the free-molecular regime because particles are small (not more than a hundred nanometer). The coupling between vapor consumption and soot formation is handled by an interpolative moment method. Soot particle diffusion is found negligible throughout the counterflow flame, except for a very narrow region right around the stagnation plane. The soot particle size distribution (PSD) generally exhibits a bimodal shape. The first peak corresponds to a large number of nascent particles, while the second peak results from the competition between nucleation and coagulation. Surface growth affects the PSD quantitatively, but does not change the modality. A comparison with experimental data is also provided.

The mosaic genome structure and phylogeny of Shiga toxin-producing Escherichia coli O104:H4 is driven by short-term adaptation

Shiga toxin-producing Escherichia coli (STEC) O104:H4 emerged as an important pathogen when it caused a large outbreak in Germany in 2011. Little is known about the evolutionary history and genomic diversity of the bacterium. The current communication describes a comprehensive analysis of STEC O104:H4 genomes from the 2011 outbreak and other non-outbreak-related isolates. Outbreak-related isolates formed a tight cluster that shared a monophyletic relation with two non-outbreak clusters, suggesting that all three clusters originated from a common ancestor. Eight single nucleotide polymorphisms, seven of which were non-synonymous, distinguished outbreak from non-outbreak isolates. Lineage-specific markers indicated that recent partitions were driven by selective pressures associated with niche adaptation. Based on the results, an evolutionary model for STEC O104:H4 is proposed. Our analysis provides the evolutionary context at population level and describes the emergence of clones with novel properties, which is necessary for developing comprehensive approaches to early warning and control.

High-intensity focused ultrasound ablation: an effective and safe treatment for secondary hypersplenism

OBJECTIVE

Hypersplenism is a common disease. The conventional treatment is splenectomy and partial splenic embolization; however, both of them have high complication rates and technical defects. Therefore, safer and more effective techniques should be considered for the treatment of hypersplenism. High-intensity focused ultrasound (HIFU) may provide an effective and safe way for treatment of hypersplenism. Therefore, we conducted this study to assess the safety and efficacy of HIFU in treatment of secondary hypersplenism.

METHODS

A total of 28 patients who suffered from secondary hypersplenism were treated with HIFU ablation. All patients who underwent HIFU were closely followed-up over a year. MRI scan was performed, and the spleens were observed. Blood counts and liver function tests were also carried out.

RESULTS

In the follow-up process, the levels of white blood cells and platelets in the blood after HIFU were significantly higher than those before HIFU, liver function also improved after HIFU treatment. In addition, the symptoms were ameliorated significantly or even disappeared. The MRI showed that the ablation area had turned into a non-perfused volume, and after 12 months of HIFU ablation, the ablated area shrank evidently; the sunken spleen formed a lobulated shape and the splenic volume decreased.

CONCLUSION

HIFU ablation is a safe, effective and non-invasive approach for secondary hypersplenism.

ADVANCES IN KNOWLEDGE

For the first time we used HIFU ablation to treat secondary hypersplenism. It not only expands indications of HIFU but also provides better choice for the treatment of secondary hypersplenism.

Selective trioxolane based bifunctional molecular linkers for covalent heme surface functionalisation

A bifunctional molecular linker containing both aryl diazonium and trioxolane groups was synthesised and its ability to sequentially functionalise glassy carbon and covalently immobilise heme investigated. Functionalisation was demonstrated by electrochemical techniques.

Fabrication of PDMS micro through-holes using micromolding in open capillaries

Micromolding in open capillaries, a simpler method for PDMS through-holes fabrication, whose procedures are easy to handle and observe.