Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data.

BACKGROUND: Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount. METHODS: The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team. FINDINGS: Around 80,000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation. INTERPRETATION: Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene-phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial. FUNDING: Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health.

The synthesis and analysis of lignin-bound Hibbert ketone structures in technical lignins.

Understanding the structure of technical lignins resulting from acid-catalysed treatment of lignocellulosic biomass is important for their future applications. Here we report an investigation into the fate of lignin under acidic aqueous organosolv conditions. In particular we examine in detail the formation and reactivity of non-native Hibbert ketone structures found in isolated organosolv lignins from both Douglas fir and beech woods. Through the use of model compounds combined with HSQC, HMBC and HSQC-TOCSY NMR experiments we demonstrate that, depending on the lignin source, both S and G lignin-bound Hibbert ketone units can be present. We also show that these units can serve as a source of novel mono-aromatic compounds following an additional lignin depolymerisation reaction.

Benign peripheral nerve tumors: treatment algorithm and reconstructive options.

Peripheral nerve tumors are mostly benign; however, their excision can result in profound deficits. Nerve reconstruction strategies offer techniques to minimize morbidity. In this prospective study, 20 consecutive patients with benign peripheral nerve tumors were treated using a single-stage surgical paradigm between 2003 and 2007. Nerve fascicles were microdissected off of the tumor; any fascicle that gave origin to the tumor (was inseparable from tumor) was reconstructed using nerve conduits. Patients were followed from 6 to 24 months. All patients had neuropathic pain before tumor excision; only 1 patient had pain persist postoperatively. Seventeen patients had complete functional recovery after nerve reconstruction. No perioperative complications occurred. Benign peripheral nerve tumors require highly specialized surgical care. Tumor excision with immediate nerve reconstruction, for fascicles inseparable from the tumor, optimizes outcomes. Nerve reconstruction with available conduits or allografts should be attempted to restore anatomic integrity to any killed fascicles, thereby minimizing possible deficits.

Preparation and Reactivity of Biomass-Derived Dihydro-Dioxins.

The depolymerization of the biopolymer lignin can give pure aromatic monomers but selective catalytic approaches remain scarce. Here, an approach was rerouted to deliver an unusual phenolic monomer. This monomer's instability proved challenging, but a degradation study identified strategies to overcome this. Heterocycles and a useful synthetic intermediate were prepared. The range of aromatics available from the ß-O-4 unit in lignin was extended.

Unravelling the enigma of ligninOX: can the oxidation of lignin be controlled?

As societal challenges go, the development of efficient biorefineries as a means of reducing our dependence on petroleum refineries is high on the list. One of the core strengths of the petroleum refinery is its ability to produce a huge range of different products using all of the components of the starting material. In contrast, the target of using all the biopolymers present in lignocellulosic biomass is far from realised. Even though our ability to use the carbohydrate-based components has advanced, our plans for lignin lag behind (with the notable exception of vanillin production). One approach to lignin usage is its controlled depolymerisation. This study focuses on an increasingly popular approach to this challenge which involves highly selective lignin oxidation to give a material often referred to as ligninOX. But what do we mean by ligninOX? In this study we show that it is possible to form many different types of ligninOX depending on the oxidation conditions that are used. We show that variations in the levels of processing of the ß-O-4, the ß-ß and a third linkage occur. Through use of this information, we can form a well-defined ligninOX from six different hardwood lignins. This process is reproducible and can be carried out on a large scale. With a source of well-defined ligninOX in hand, we show that it can be converted to simple aromatic monomers and that any remaining ligninOX is sufficiently soluble for further processing to be carried out.

Fractionation and DOSY NMR as Analytical Tools: From Model Polymers to a Technical Lignin.

One key challenge hindering the valorization of lignin is its structural complexity. Artificial lignin-like materials provide a stepping stone between the simplicity of model compounds and the complexity of lignin. Here, we report an optimized synthesis of an all-G ß-O-4 polymer 1 designed to model softwood lignin. After acetylation, the polymer Ac-1(V) was fractionated using a protocol that involved only volatile organic solvents, which left no insoluble residue. Using diffusion ordered spectroscopy NMR in combination with gel permeation chromatography, it was revealed that this fractionated material behaved like a flexible linear polymer in solution (average α > 0.5). Acetylated kraft lignin was subsequently processed using the same fractionation protocol. By comparison with the model polymer, we propose that the acetylated kraft lignin is composed of two classes of materials that exhibit contrasting physical properties. One is comparable to the acetylated all-G ß-O-4 polymer Ac-1, and the second has a significantly different macromolecular structure.

Inhibition of protein-tyrosine phosphatases by mild oxidative stresses is dependent on S-nitrosylation.

Previous studies have shown that a Ca(2+)-dependent nitric-oxide synthase (NOS) is activated as part of a cellular response to low doses of ionizing radiation. Genetic and pharmacological inhibitor studies linked this NO signaling to the radiation-induced activation of ERK1/2. Herein, a mechanism for the radiation-induced activation of Tyr phosphorylation-dependent pathways (e.g. ERK1/2) involving the inhibition of protein-Tyr phosphatases (PTPs) by S-nitrosylation is tested. The basis for this mechanism resides in the redox-sensitive active site Cys in PTPs. These studies also examined oxidative stress induced by low concentrations of H(2)O(2). S-Nitrosylation of total cellular PTP and immunopurified SHP-1 and SHP-2 was detected as protection of PTP enzymatic activity from alkylation by N-ethylmaleimide and reversal by ascorbate. Both radiation and H(2)O(2) protected PTP activity from alkylation by a mechanism reversible by ascorbate and inhibited by NOS inhibitors or expression of a dominant negative mutant of NOS-1. Radiation and H(2)O(2) stimulated a transient increase in cytoplasmic free [Ca(2+)]. Radiation, H(2)O(2), and the Ca(2+) ionophore, ionomycin, also stimulated NOS activity, and this was associated with an enhanced S-nitrosylation of the active site Cys(453) determined by isolation of S-nitrosylated wild type but not active site Cys(453) --> Ser SHP-1 mutant by the "biotin-switch" method. Thus, one consequence of oxidative stimulation of NO generation is S-nitrosylation and inhibition of PTPs critical in cellular signal transduction pathways. These results support the conclusion that a mild oxidative signal is converted to a nitrosative one due to the better redox signaling properties of NO.