Seeing it my way: living with childhood onset visual disability

Background: Although the significant impact of visual disability in childhood has been widely recognized, children's own perspectives of living with a visual impairment have not been considered. We report the experiences of visually impaired (VI) children and young people aged 10–15 years about growing up with impaired sight. Methods: The participants were 32 VI children and young people, aged 10–15 years [visual acuity logarithm of minimum angle of resolution (LogMAR) worse than 0.51] recruited through National Health Service (NHS) paediatric ophthalmology and developmental vision clinics and 11 VI pupils aged 12–17 attending a specialist school for pupils with disabilities. Individual semi‐structured interviews with participants captured their experiences of living with a visual impairment. A child‐centred interview topic guide was developed from a literature review, observations at ophthalmology clinics, consultation with health and education professionals working with VI children and young people, and interviews and a focus group with VI pupils from the specialist school. Collaborative qualitative thematic analysis by three researchers identified emergent themes. NVivo software was used for coding the data. Results: Analysis identified six themes concerning living with a visual impairment: (i) social relationships, participation and acceptance; (ii) independence and autonomy; (iii) psychological and emotional well‐being; (iv) aspirations and concerns about the future; (v) functioning – home, school and leisure; and (vi) treatment of eye condition. Key issues included: the importance of family and peer support; balancing independence, support and safety; the emotional burden and adjustment of living with a disability; concerns about education and job prospects in the future; functional restrictions and limitations; and ongoing management of the eye condition. Conclusions: The findings offer insights into the complex realities of living with visual impairment. They provide the basis for development of patient‐reported outcome measures. They can also serve to help enrich the understanding of health professionals working with VI children and young people, potentially enabling them to better support them

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3′ end modification.

C16orf57 encodes a human protein of unknown function, and mutations in the gene occur in poikiloderma with neutropenia (PN), which is a rare, autosomal recessive disease. Interestingly, mutations in C16orf57 were also observed among patients diagnosed with Rothmund-Thomson syndrome (RTS) and dyskeratosis congenita (DC), which are caused by mutations in genes involved in DNA repair and telomere maintenance. A genetic screen in Saccharomyces cerevisiae revealed that the yeast ortholog of C16orf57, USB1 (YLR132C), is essential for U6 small nuclear RNA (snRNA) biogenesis and cell viability. Usb1 depletion destabilized U6 snRNA, leading to splicing defects and cell growth defects, which was suppressed by the presence of multiple copies of the U6 snRNA gene SNR6. Moreover, Usb1 is essential for the generation of a unique feature of U6 snRNA; namely, the 3'-terminal phosphate. RNAi experiments in human cells followed by biochemical and functional analyses confirmed that, similar to yeast, C16orf57 encodes a protein involved in the 2',3'-cyclic phosphate formation at the 3' end of U6 snRNA. Advanced bioinformatics predicted that C16orf57 encodes a phosphodiesterase whose putative catalytic activity is essential for its function in vivo. Our results predict an unexpected molecular basis for PN, DC, and RTS and provide insight into U6 snRNA 3' end formation

Probabilistic approach to predicting substrate specificity of methyltransferases.

We present a general probabilistic framework for predicting the substrate specificity of enzymes. We designed this approach to be easily applicable to different organisms and enzymes. Therefore, our predictive models do not rely on species-specific properties and use mostly sequence-derived data. Maximum Likelihood optimization is used to fine-tune model parameters and the Akaike Information Criterion is employed to overcome the issue of correlated variables. As a proof-of-principle, we apply our approach to predicting general substrate specificity of yeast methyltransferases (MTases). As input, we use several physico-chemical and biological properties of MTases: structural fold, isoelectric point, expression pattern and cellular localization. Our method accurately predicts whether a yeast MTase methylates a protein, RNA or another molecule. Among our experimentally tested predictions, 89% were confirmed, including the surprising prediction that YOR021C is the first known MTase with a SPOUT fold that methylates a substrate other than RNA (protein). Our approach not only allows for highly accurate prediction of functional specificity of MTases, but also provides insight into general rules governing MTase substrate specificity

Expanding Access to Optically Active Non-Steroidal Anti-Inflammatory Drugs via Lipase-Catalyzed KR of Racemic Acids Using Trialkyl Orthoesters as Irreversible Alkoxy Group Donors

Studies into the enzymatic kinetic resolution (EKR) of 2-arylpropanoic acids (‘profens’), as the active pharmaceutical ingredients (APIs) of blockbuster non-steroidal anti-inflammatory drugs (NSAIDs), by using various trialkyl orthoesters as irreversible alkoxy group donors in organic media, were performed. The enzymatic reactions of target substrates were optimized using several different immobilized preparations of lipase type B from the yeast Candida antarctica (CAL-B). The influence of crucial parameters, including the type of enzyme and alkoxy agent, as well as the nature of the organic co-solvent and time of the process on the conversion and enantioselectivity of the enzymatic kinetic resolution, is described. The optimal EKR procedure for the racemic profens consisted of a Novozym 435-STREM lipase preparation suspended in a mixture of 3 equiv of trimethyl or triethyl orthoacetate as alkoxy donor and toluene or n-hexane as co-solvent, depending on the employed racemic NSAIDs. The reported biocatalytic system provided optically active products with moderate-to-good enantioselectivity upon esterification lasting for 7–48 h, with most promising results in terms of enantiomeric purity of the pharmacologically active enantiomers of title APIs obtained on the analytical scale for: (S)-flurbiprofen (97% ee), (S)-ibuprofen (91% ee), (S)-ketoprofen (69% ee), and (S)-naproxen (63% ee), respectively. In turn, the employment of optimal conditions on a preparative-scale enabled us to obtain the (S)-enantiomers of: flurbiprofen in 28% yield and 97% ee, ibuprofen in 45% yield and 56% ee, (S)-ketoprofen in 23% yield and 69% ee, and naproxen in 42% yield and 57% ee, respectively. The devised method turned out to be inefficient toward racemic etodolac regardless of the lipase and alkoxy group donor used, proving that it is unsuitable for carboxylic acids possessing tertiary chiral centers

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

Abstract Background The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. Results We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. Conclusions The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications

Workflow of the prediction model.

<p>Workflow of the prediction model.</p

General substrate prediction for MTases with unknown substrate specificity.

<p>General substrate prediction for MTases with unknown substrate specificity.</p

Domain architecture of <i>S. cerevisiae</i> MTases.

<p>The MTases were grouped according to their common substrate specificities (e.g., protein, RNA, small molecule or lipid) and the fold of catalytic domain. Known MTases with experimentally determined substrate specificity are shown in a regular font, putative MTases in italics, and newly detected MTase in bold. Non-periodic MTases are underlined. The new domains identified in this study are marked with a red asterisk. Sandwich, beta sandwich; Xyl TIM, TIM beta/alpha-barrel belonging to the Xylose isomerase-like superfamily; Alpha, α-helical domain; Ankyrin, Ankyrin repeats; ZnF, zinc finger; Spb1C, Spb1 C-terminal domain; Defensin, defensin-like fold; iSET, SET-inserted domain; Rubisco, Rubisco LSMT C-terminal-like domain; SRI, SET2 Rpb1 interacting domain; PHD, PHD zinc finger; DNA/RNA, DNA/RNA-binding 3-helical bundle; RNase H, RNase H-like domain; ARM, ARM repeat; RNA_rb, RNA ribose binding domain; SirohemeN, Siroheme synthase N-terminal domain-like; SirohemeM, Siroheme synthase middle domain-like; Cobal_N, Cobalamin-independent synthase N-terminal domain; CoCoA_N, Calcium binding and coiled-coil domain-like (N-terminal); OB, OB-fold domain; RNAb, RNA binding domain.</p