Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids

Plasmids are ubiquitous in biology, where they are used to study gene-function relationships and intricate molecular networks, and hold potential as therapeutic devices. Developing methods to control their function will advance their application in research and may also expedite their translation to clinical settings. Light is an attractive stimulus to conditionally regulate plasmid expression as it is non-invasive, and its properties such as wavelength, intensity, and duration can be adjusted to minimise cellular toxicity and increase penetration. Herein, we have developed a method to site-specifically introduce photocages into plasmids, by resynthesising one strand in a manner similar to Kunkel mutagenesis. Unlike alternative approaches to chemically modify plasmids, this method is sequence-independent at the site of modification and uses commercially available phosphoramidites. To generate our light-activated (LA) plasmids, photocleavable biotinylated nucleobases were introduced at specific sites across the T7 and CMV promoters on plasmids and bound to streptavidin to sterically block access. These LA-plasmids were then successfully used to control expression in both cell-free systems (T7 promoter) and mammalian cells (CMV promoter). These light-activated plasmids might be used to remotely control cellular activity and reduce off-target toxicity for future medical use. Our simple approach to plasmid modification might also be used to introduce novel chemical moieties for advanced function.

Engineering cellular communication between light-activated synthetic cells and bacteria

Gene-expressing compartments assembled from simple, modular parts, are a versatile platform for creating minimal synthetic cells with life-like functions. By incorporating gene regulatory motifs into their encapsulated DNA templates, in situ gene expression and, thereby, synthetic cell function can be controlled according to specific stimuli. In this work, cell-free protein synthesis within synthetic cells was controlled using light by encoding genes of interest on light-activated DNA templates. Light-activated DNA contained a photocleavable blockade within the T7 promoter region that tightly repressed transcription until the blocking groups were removed with ultraviolet light. In this way, synthetic cells were activated remotely, in a spatiotemporally controlled manner. By applying this strategy to the expression of an acyl homoserine lactone synthase, BjaI, quorum-sensing-based communication between synthetic cells and bacteria was controlled with light. This work provides a framework for the remote-controlled production and delivery of small molecules from nonliving matter to living matter, with applications in biology and medicine.

Orthogonal Light-Activated DNA for Patterned Biocomputing within Synthetic Cells

Cell-free gene expression is a vital research tool to study biological systems in defined minimal environments and has promising applications in biotechnology. Developing methods to control DNA templates for cell-free expression will be important for precise regulation of complex biological pathways and use with synthetic cells, particularly using remote, nondamaging stimuli such as visible light. Here, we have synthesized blue light-activatable DNA parts that tightly regulate cell-free RNA and protein synthesis. We found that this blue light-activated DNA could initiate expression orthogonally to our previously generated ultraviolet (UV) light-activated DNA, which we used to generate a dual-wavelength light-controlled cell-free AND-gate. By encapsulating these orthogonal light-activated DNAs into synthetic cells, we used two overlapping patterns of blue and UV light to provide precise spatiotemporal control over the logic gate. Our blue and UV orthogonal light-activated DNAs will open the door for precise control of cell-free systems in biology and medicine.

Precise, Orthogonal Remote-Control of Cell-Free Systems Using Photocaged Nucleic Acids

Cell-free expression of a gene to protein has become a vital tool in nanotechnology and synthetic biology. Remote-control of cell-free systems with multiple, orthogonal wavelengths of light would enable precise, noninvasive modulation, opening many new applications in biology and medicine. While there has been success in developing ON switches, the development of OFF switches has been lacking. Here, we have developed orthogonally light-controlled cell-free expression OFF switches by attaching nitrobenzyl and coumarin photocages to antisense oligonucleotides. These light-controlled OFF switches can be made from commercially available oligonucleotides and show a tight control of cell-free expression. Using this technology, we have demonstrated orthogonal degradation of two different mRNAs, depending on the wavelength used. By combining with our previously generated blue-light-activated DNA template ON switch, we were able to start transcription with one wavelength of light and then halt the translation of the corresponding mRNA to protein with a different wavelength, at multiple timepoints. This precise, orthogonal ON and OFF remote-control of cell-free expression will be an important tool for the future of cell-free biology, especially for use with biological logic gates and synthetic cells.

Handcuffed antisense oligonucleotides for light-controlled cell-free expression

Developing simple methods to silence antisense oligonucleotides (ASOs) using photocages opens up the possibility of precise regulation of biological systems. Here, we have developed a photocaging strategy based on 'handcuffing' two ASOs to a protein. Silencing was achieved by divalent binding of two terminally photocleavable biotin-modified ASOs to a single streptavidin. These 'handcuffed' oligonucleotides showed a drastic reduction in gene knockdown activity in cell-free protein synthesis and were unlocked through illumination, regaining full activity.

Accessible light-controlled knockdown of cell-free protein synthesis using phosphorothioate-caged antisense oligonucleotides

Controlling cell-free expression of a gene to protein with non-invasive stimuli is vital to the future application of DNA nanodevices and synthetic cells. However, little emphasis has been placed on developing light-controlled 'off' switches for cell-free expression. Light-activated antisense oligonucleotides have been developed to induce gene knockdown in living cells; however, they are complicated to synthesise and have not been tested in cell-free systems. Developing simple, accessible methods to produce light-activated antisense oligonucleotides will be crucial for allowing their application in cell-free biology and biotechnology. Here, we report a mild, one-step method for selectively attaching commercially-available photoremovable protecting groups, photocages, onto phosphorothioate linkages of antisense oligonucleotides. Using this photocaging method, upon illumination, the original phosphorothioate antisense oligonucleotide is reformed. Photocaged antisense oligonucleotides, containing mixed phosphorothioate and phosphate backbones, showed a drastic reduction in duplex formation and RNase H activity, which was recovered upon illumination. We then demonstrated that these photocaged antisense oligonucleotides can be used to knock down cell-free protein synthesis using light. This simple and accessible technology will have future applications in light-controlled biological logic gates and regulating the activity of synthetic cells.

Reaction–Diffusion Patterning of DNA-Based Artificial Cells

Biological cells display complex internal architectures with distinct micro environments that establish the chemical heterogeneity needed to sustain cellular functions. The continued efforts to create advanced cell mimics, namely, artificial cells, demands strategies for constructing similarly heterogeneous structures with localized functionalities. Here, we introduce a platform for constructing membraneless artificial cells from the self-assembly of synthetic DNA nanostructures in which internal domains can be established thanks to prescribed reaction–diffusion waves. The method, rationalized through numerical modeling, enables the formation of up to five distinct concentric environments in which functional moieties can be localized. As a proof-of-concept, we apply this platform to build DNA-based artificial cells in which a prototypical nucleus synthesizes fluorescent RNA aptamers that then accumulate in a surrounding storage shell, thus demonstrating the spatial segregation of functionalities reminiscent of that observed in biological cells.

Controlling Synthetic Cell-Cell Communication

Synthetic cells, which mimic cellular function within a minimal compartment, are finding wide application, for instance in studying cellular communication and as delivery devices to living cells. However, to fully realise the potential of synthetic cells, control of their function is vital. An array of tools has already been developed to control the communication of synthetic cells to neighbouring synthetic cells or living cells. These tools use either chemical inputs, such as small molecules, or physical inputs, such as light. Here, we examine these current methods of controlling synthetic cell communication and consider alternative mechanisms for future use.

A Lipid-Based Droplet Processor for Parallel Chemical Signals

A key goal of bottom-up synthetic biology is to construct cell- and tissue-like structures. Underpinning cellular life is the ability to process several external chemical signals, often in parallel. Until now, cell- and tissue-like structures have been constructed with no more than one signaling pathway. Many pathways rely on signal transport across membranes using protein nanopores. However, such systems currently suffer from the slow transport of molecules. We have optimized the application of these nanopores to permit fast molecular transport, which has allowed us to construct a processor for parallel chemical signals from the bottom up in a modular fashion. The processor comprises three aqueous droplet compartments connected by lipid bilayers and operates in an aqueous environment. It can receive two chemical signals from the external environment, process them orthogonally, and then produce a distinct output for each signal. It is suitable for both sensing and enzymatic processing of environmental signals, with fluorescence and molecular outputs. In the future, such processors could serve as smart drug delivery vehicles or as modules within synthetic tissues to control their behavior in response to external chemical signals.

No increased risk of Alzheimer's disease among people with immune-mediated inflammatory diseases: findings from a longitudinal cohort study of U.S. older adults

OBJECTIVE

Immune-mediated inflammatory diseases (IMID) are characterized by systemic inflammation affecting the joints and bodily organs. Studies examining the association between individual IMIDs and the risk of Alzheimer's disease (AD) have yielded inconsistent findings. This study examines AD risk across a group of IMIDs in a large population-based sample of older adults.

METHODS

Data on a national sample of US adults over age 50 was drawn from the Health and Retirement Study (HRS) and linked Medicare claims from 2006 to 2014. IMIDs include rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn's disease, ulcerative colitis, and related conditions. We identified IMIDs from 2006 to 2009 Medicare claims using International Classification of Diseases (ICD9-CM) codes. The date of incident AD was derived from Chronic Conditions Warehouse (CCW) identifiers. We examined the risk of AD from 2009 to 2014 using Cox proportional hazards models, both unadjusted and adjusted for age, gender, education, race, and the genetic risk factor APOE-e4.

RESULTS

One hundred seventy-one (6.02%) of the 2842 total HRS respondents with Medicare coverage and genetic data were classified with IMIDs. Over the subsequent 6 years, 9.36% of IMID patients developed AD compared to 8.57% of controls (unadjusted hazard ratio (HR): 1.09, 95% CI .66-1.81, p = 0.74). Adjusted HR 1.27 (95% CI 0.76-2.12, p = 0.35). Age (HR for 10-year increment 3.56, p < .001), less than high school education (HR 1.70, p = .007), and APOE-e4 (HR 2.61, p < .001 for one or two copies), were also statistically significant predictors of AD.

CONCLUSION

HRS respondents with common IMIDs do not have increased risk of Alzheimer's disease over a 6-year period.

No association between rheumatoid arthritis and cognitive impairment in a cross-sectional national sample of older U.S. adults

BACKGROUND

Studies suggest an increased prevalence of cognitive impairment (CI) among people with rheumatoid arthritis (RA). However, most prior studies have used convenience samples which are subject to selection biases or have failed to adjust for key confounding variables. We thus examined the association between CI and RA in a large national probability sample of older US adults.

METHODS

Data were from interviews with 4462 participants in the 2016 wave of the nationally representative U.S. Health and Retirement Study with linked Medicare claims. RA diagnoses were identified via a minimum of two ICD-9CM or ICD-10 codes in Medicare billing records during the prior 2 years. The Langa-Weir Classification was used to classify cognitive status as normal, cognitively impaired non-dementia (CIND), or dementia based on a brief neuropsychological battery for self-respondents and informant reports for proxy respondents. We compared the odds of CI between older adults with and without RA using logistic regression, adjusted for age, education, gender, and race.

RESULTS

Medicare records identified a 3.36% prevalence of RA (150/4462). While age, gender, education, and race independently predicted CI status, controlling for these covariates we found no difference in CI prevalence according to RA status (prevalent CI in 36.7% of older adults with RA vs. 34.0% without RA; adjusted OR = 1.08, 95% CI 0.74-1.59, p = .69).

CONCLUSION

There was no association between RA and CI in this national sample of older U.S. adults.

Validation of Self-Reported Rheumatoid Arthritis Using Medicare Claims: A Nationally Representative Longitudinal Study of Older Adults

Objective

To determine the validity of self‐reported physician diagnosis of rheumatoid arthritis (RA) using multiple gold‐standard measures based on Medicare claims in a nationally representative sample of older adults and to verify whether additional questions about taking medication and having seen a physician in the past two years for arthritis can improve the positive predictive value (PPV) and other measures of the validity of self‐reported RA.

Methods

A total of 3768 Medicare‐eligible respondents with and without incident self‐reported RA were identified from the 2004, 2008, and 2012 waves of the United States Health and Retirement Study. Self‐reported RA was validated using the following three claims‐based algorithms: 1) a single International Classification of Diseases, ninth edition, Clinical Modification claim for RA, 2) two or more claims no greater than 2 years apart, and 3) two or more claims with at least one diagnosis by a rheumatologist. Additional self‐report questions of medication use and having seen a doctor for arthritis in the past two years were validated against the same criteria.

Results

A total of 345 respondents self‐reported a physician diagnosis of RA. Across all three RA algorithms, the PPV of self‐report ranged from 0.05 to 0.16., the sensitivity ranged from 0.23 to 0.55., and the κ statistic ranged from 0.07 to 0.15. Additional self‐report data regarding arthritis care improved the PPV and other validity measures of self‐report; however, the values remained low.

Conclusion

Most older adults who self‐report RA do not have a Medicare claims history consistent with that diagnosis. Revisions to current self‐reported RA questions may yield more valid identification of RA in national health surveys.

Controlling gene expression with light: a multidisciplinary endeavour

The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.

Multi-responsive hydrogel structures from patterned droplet networks

Responsive hydrogels that undergo controlled shape changes in response to a range of stimuli are of interest for microscale soft robotic and biomedical devices. However, these applications require fabrication methods capable of preparing complex, heterogeneous materials. Here we report a new approach for making patterned, multi-material and multi-responsive hydrogels, on a micrometre to millimetre scale. Nanolitre aqueous pre-gel droplets were connected through lipid bilayers in predetermined architectures and photopolymerized to yield continuous hydrogel structures. By using this droplet network technology to pattern domains containing temperature-responsive or non-responsive hydrogels, structures that undergo reversible curling were produced. Through patterning of gold nanoparticle-containing domains into the hydrogels, light-activated shape change was achieved, while domains bearing magnetic particles allowed movement of the structures in a magnetic field. To highlight our technique, we generated a multi-responsive hydrogel that, at one temperature, could be moved through a constriction under a magnetic field and, at a second temperature, could grip and transport a cargo.

Functional aqueous droplet networks

Droplet interface bilayers (DIBs), comprising individual lipid bilayers between pairs of aqueous droplets in an oil, are proving to be a useful tool for studying membrane proteins. Recently, attention has turned to the elaboration of networks of aqueous droplets, connected through functionalized interface bilayers, with collective properties unachievable in droplet pairs. Small 2D collections of droplets have been formed into soft biodevices, which can act as electronic components, light-sensors and batteries. A substantial breakthrough has been the development of a droplet printer, which can create patterned 3D droplet networks of hundreds to thousands of connected droplets. The 3D networks can change shape, or carry electrical signals through defined pathways, or express proteins in response to patterned illumination. We envisage using functional 3D droplet networks as autonomous synthetic tissues or coupling them with cells to repair or enhance the properties of living tissues.

Femtosecond laser inscription of Bragg grating waveguides in bulk diamond

Femtosecond laser writing is applied to form Bragg grating waveguides in the diamond bulk. Type II waveguides are integrated with a single pulse point-by-point periodic laser modification positioned toward the edge of the waveguide core. These photonic devices, operating in the telecommunications band, allow for simultaneous optical waveguiding and narrowband reflection from a fourth-order grating. This fabrication technology opens the way toward advanced 3D photonic networks in diamond for a range of applications.

Light-patterning of synthetic tissues with single droplet resolution

Synthetic tissues can be generated by forming networks of aqueous droplets in lipid-containing oil. Each droplet contains a cell-free expression system and is connected to its neighbor through a lipid bilayer. In the present work, we have demonstrated precise external control of such networks by activating protein expression within single droplets, by using light-activated DNA to encode either a fluorescent or a pore-forming protein. By controlling the extent of activation, synthetic tissues were generated with graded levels of protein expression in patterns of single droplets. Further, we have demonstrated reversible activation within individual compartments in synthetic tissues by turning a fluorescent protein on-and-off. This is the first example of the high-resolution patterning of droplet networks, following their formation. Single-droplet control will be essential to power subsets of compartments within synthetic tissues or to stimulate subsets of cells when synthetic tissues are interfaced with living tissues.

Aberration correction for direct laser written waveguides in a transverse geometry

The depth dependent spherical aberration is investigated for ultrafast laser written waveguides fabricated in a transverse writing geometry using the slit beam shaping technique in the low pulse repetition rate regime. The axial elongation of the focus caused by the aberration leads to a distortion of the refractive index change, and waveguides designed as single mode become multimode. We theoretically estimate a depth range over which the aberration effects can be compensated simply by adjusting the incident laser power. If deeper fabrication is required, it is demonstrated experimentally that the aberration can be successfully removed using adaptive optics to fabricate single mode optical waveguides over a depth range > 1 mm.

Light-activated communication in synthetic tissues

We have previously used three-dimensional (3D) printing to prepare tissue-like materials in which picoliter aqueous compartments are separated by lipid bilayers. These printed droplets are elaborated into synthetic cells by using a tightly regulated in vitro transcription/translation system. A light-activated DNA promoter has been developed that can be used to turn on the expression of any gene within the synthetic cells. We used light activation to express protein pores in 3D-printed patterns within synthetic tissues. The pores are incorporated into specific bilayer interfaces and thereby mediate rapid, directional electrical communication between subsets of cells. Accordingly, we have developed a functional mimic of neuronal transmission that can be controlled in a precise way.

Combining the Optimized Yeast Cytosine Deaminase Protein Fragment Complementation Assay and an In Vitro Cdk1 Targeting Assay to Study the Regulation of the γ-Tubulin Complex

Cdk1 is the essential cyclin-dependent kinase in the budding yeast Saccharomyces cerevisiae. Cdk1 orchestrates cell cycle control by phosphorylating target proteins with extraordinary temporal and spatial specificity by complexing with one of the nine cyclin regulatory subunits. The identification of the cyclin required for targeting Cdk1 to a substrate can help to place the regulation of that protein at a specific time point during the cell cycle and reveal information needed to elucidate the biological significance of the regulation. Here, we describe a combination of strategies to identify interaction partners of Cdk1, and associate these complexes to the appropriate cyclins using a cell-based protein-fragment complementation assay. Validation of the specific reliance of the OyCD interaction between Cdk1 and budding yeast γ-tubulin on the Clb3 cyclin, relative to the mitotic Clb2 cyclin, was performed by an in vitro kinase assay using the γ-tubulin complex as a substrate.

Exploring the depth range for three-dimensional laser machining with aberration correction

The spherical aberration generated when focusing from air into another medium limits the depth at which ultrafast laser machining can be accurately maintained. We investigate how the depth range may be extended using aberration correction via a liquid crystal spatial light modulator (SLM), in both single point and parallel multi-point fabrication in fused silica. At a moderate numerical aperture (NA = 0.5), high fidelity fabrication with a significant level of parallelisation is demonstrated at the working distance of the objective lens, corresponding to a depth in the glass of 2.4 mm. With a higher numerical aperture (NA = 0.75) objective lens, single point fabrication is demonstrated to a depth of 1 mm utilising the full NA, and deeper with reduced NA, while maintaining high repeatability. We present a complementary theoretical model that enables prediction of the effectiveness of SLM based correction for different aberration magnitudes.

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

Recently, the cytosine modifications 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) were found to exist in the genomic deoxyribonucleic acid (DNA) of a wide range of mammalian cell types. It is now important to understand their role in normal biological function and disease. Here we introduce reduced bisulfite sequencing (redBS-Seq), a quantitative method to decode 5fC in DNA at single-base resolution, based on a selective chemical reduction of 5fC to 5hmC followed by bisulfite treatment. After extensive validation on synthetic and genomic DNA, we combined redBS-Seq and oxidative bisulfite sequencing (oxBS-Seq) to generate the first combined genomic map of 5-methylcytosine, 5hmC and 5fC in mouse embryonic stem cells. Our experiments revealed that in certain genomic locations 5fC is present at comparable levels to 5hmC and 5mC. The combination of these chemical methods can quantify and precisely map these three cytosine derivatives in the genome and will help provide insights into their function.

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

BACKGROUND

DNA methylation (5mC) plays important roles in epigenetic regulation of genome function. Recently, TET hydroxylases have been found to oxidise 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DNA but in addition may have epigenetic signaling functions in their own right. A recent study identified proteins which showed preferential binding to 5-methylcytosine (5mC) and its oxidised forms, where readers for 5mC and 5hmC showed little overlap, and proteins bound to further oxidation forms were enriched for repair proteins and transcription regulators. We extend this study by using promoter sequences as baits and compare protein binding patterns to unmodified or modified cytosine using DNA from mouse embryonic stem cell extracts.

RESULTS

We compared protein enrichments from two DNA probes with different CpG composition and show that, whereas some of the enriched proteins show specificity to cytosine modifications, others are selective for both modification and target sequences. Only a few proteins were identified with a preference for 5hmC (such as RPL26, PRP8 and the DNA mismatch repair protein MHS6), but proteins with a strong preference for 5fC were more numerous, including transcriptional regulators (FOXK1, FOXK2, FOXP1, FOXP4 and FOXI3), DNA repair factors (TDG and MPG) and chromatin regulators (EHMT1, L3MBTL2 and all components of the NuRD complex).

CONCLUSIONS

Our screen has identified novel proteins that bind to 5fC in genomic sequences with different CpG composition and suggests they regulate transcription and chromatin, hence opening up functional investigations of 5fC readers.

Focussing over the edge: adaptive subsurface laser fabrication up to the sample face

Direct laser writing is widely used for fabrication of subsurface, three dimensional structures in transparent media. However, the accessible volume is limited by distortion of the focussed beam at the sample edge. We determine the aberrated focal intensity distribution for light focused close to the edge of the substrate. Aberrations are modelled by dividing the pupil into two regions, each corresponding to light passing through the top and side facets. Aberration correction is demonstrated experimentally using a liquid crystal spatial light modulator for femtosecond microfabrication in fused silica. This technique allows controlled subsurface fabrication right up to the edge of the substrate. This can benefit a wide range of applications using direct laser writing, including the manufacture of waveguides and photonic crystals.

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

Background

Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the methylation landscape is dynamically reprogrammed in part through active demethylation. Recent advances have identified key players involved in active demethylation pathways, including oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) by the TET enzymes, and excision of 5fC by the base excision repair enzyme thymine DNA glycosylase (TDG). Here, we provide the first genome-wide map of 5fC in mouse embryonic stem (ES) cells and evaluate potential roles for 5fC in differentiation.

Results

Our method exploits the unique reactivity of 5fC for pulldown and high-throughput sequencing. Genome-wide mapping revealed 5fC enrichment in CpG islands (CGIs) of promoters and exons. CGI promoters in which 5fC was relatively more enriched than 5mC or 5hmC corresponded to transcriptionally active genes. Accordingly, 5fC-rich promoters had elevated H3K4me3 levels, associated with active transcription, and were frequently bound by RNA polymerase II. TDG down-regulation led to 5fC accumulation in CGIs in ES cells, which correlates with increased methylation in these genomic regions during differentiation of ES cells in wild-type and TDG knockout contexts.

Conclusions

Collectively, our data suggest that 5fC plays a role in epigenetic reprogramming within specific genomic regions, which is controlled in part by TDG-mediated excision. Notably, 5fC excision in ES cells is necessary for the correct establishment of CGI methylation patterns during differentiation and hence for appropriate patterns of gene expression during development.

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. We introduce oxidative bisulfite sequencing (oxBS-Seq), the first method for quantitative mapping of 5hmC in genomic DNA at single-nucleotide resolution. Selective chemical oxidation of 5hmC to 5-formylcytosine (5fC) enables bisulfite conversion of 5fC to uracil. We demonstrate the utility of oxBS-Seq to map and quantify 5hmC at CpG islands (CGIs) in mouse embryonic stem (ES) cells and identify 800 5hmC-containing CGIs that have on average 3.3% hydroxymethylation. High levels of 5hmC were found in CGIs associated with transcriptional regulators and in long interspersed nuclear elements, suggesting that these regions might undergo epigenetic reprogramming in ES cells. Our results open new questions on 5hmC dynamics and sequence-specific targeting by TETs.

Adaptive slit beam shaping for direct laser written waveguides

We demonstrate an improved method for fabricating optical waveguides in bulk materials by means of femtosecond laser writing. We use an LC spatial light modulator (SLM) to shape the beam focus by generating adaptive slit illumination in the pupil of the objective lens. A diffraction grating is applied in a strip across the SLM to simulate a slit, with the first diffracted order mapped onto the pupil plane of the objective lens while the zeroth order is blocked. This technique enables real-time control of the beam-shaping parameters during writing, facilitating the fabrication of more complicated structures than is possible using nonadaptive methods. Waveguides are demonstrated in fused silica with a coupling loss to single-mode fibers in the range of 0.2 to 0.5 dB and propagation loss <0.4 dB/cm.

Specimen-induced distortions in light microscopy

Specimen-induced aberrations affect the imaging properties in optical 3D microscopy, especially when high numerical aperture lenses are used. Studies on aberrations are often properly concerned with the degradation of image quality such as compromised resolution or reduced signal intensity. Apart from these, aberration effects can also introduce geometric image distortions. The effects, discussed here are particularly strong when thick biological specimens are investigated. Using a high numerical aperture interferometer, we measured wavefront aberrations in transmission mode and quantified geometric distortions associated with specimen-induced aberrations. This assessment for a range of biological specimens allows estimation of the accuracy of spatial measurements. The results show that high-resolution spatial measurements can be significantly compromised by specimen-induced aberrations.

Simple optimization procedure for objective lens correction collar setting

We present a new method for setting a coverglass correction collar on an objective lens. Axial scans across the interface between the specimen volume and the slide are used together with a quantitative function of merit to determine the optimum setting of the correction collar. The method, which simplifies the adjustment for the user and reduces photobleaching, was implemented within the software environment of a scanning microscope system.

Simulation of specimen-induced aberrations for objects with spherical and cylindrical symmetry

Wavefront aberrations caused by the refractive index structure of the specimen are known to compromise signal intensity and three-dimensional resolution in confocal and multiphoton microscopy. However, adaptive optics can measure and correct specimen-induced aberrations. For the design of an adaptive optics system, information on the type and amount of the aberration is required. We have previously described an interferometric set-up capable of measuring specimen-induced aberrations and a method for the extraction of the Zernike mode content. In this paper we have modelled specimen-induced aberrations caused by spherical and cylindrical objects using a ray tracing method. The Zernike mode content of the wavefronts was then extracted from the simulated wavefronts and compared with experimental results. Aberrations for a simple model of an oocyte cell consisting of two spherical regions and for a model of a well-characterized optical fibre are calculated. This simple model gave Zernike mode data that are in good agreement with experimental results.

Transfection-free and scalable recombinant AAV vector production using HSV/AAV hybrids

Adeno-associated virus (AAV) vectors are highly efficient tools for use in gene therapy. Current production methods rely on plasmid transfection and are not generally considered amenable to scale-up. To improve recombinant AAV (rAAV) vector production in terms of both final titre and simplicity, we constructed recombinant herpes simplex virus (HSV) vectors, either disabled (ICP27 deleted) or nondisabled, encoding the AAV rep and cap genes. We also integrated an rAAVGFP construct into the nondisabled vector and also into a second pair of HSV vectors (disabled and nondisabled) not expressing rep and cap. Transgene incorporation and expression was confirmed by Southern and Western blot, respectively. Optimal double-infection ratios were established for disabled and nondisabled pairs of rep/cap-expressing and rAAVGFP-containing vectors, resulting in up to 1.55 x 10(12) rAAV capsids and 4 x 10(8) expression units from approximately 1 x 10(7) BHK producer cells. Functionality of the prepared vector was confirmed by the detection of abundant green fluorescent protein (GFP) expression following injections of rAAV preparations into the rat brain. This paper therefore describes a simple, efficient, and transfection-free rAAV production process based on the use of HSV and not relying on a proviral cell line that, with appropriate scale-up, could yield quantities of rAAV sufficient for routine clinical use.

Low-cost, frequency-domain, fluorescence lifetime confocal microscopy

We describe the theory and implementation of a frequency-domain fluorescence lifetime confocal microscope using switched diode laser illumination. Standard, communications-type, radio-frequency electronics are used to provide inexpensive modulation references and to perform phase-sensitive detection. This allows the rapid acquisition of fluorescence intensity and lifetime images and their display in real time. We show fluorescence lifetime images of bead objects and fluorescence lifetime images of biological specimens from a single confocal scan.

Measurement of specimen-induced aberrations of biological samples using phase stepping interferometry

Confocal or multiphoton microscopes, which deliver optical sections and three-dimensional (3D) images of thick specimens, are widely used in biology. These techniques, however, are sensitive to aberrations that may originate from the refractive index structure of the specimen itself. The aberrations cause reduced signal intensity and the 3D resolution of the instrument is compromised. It has been suggested to correct for aberrations in confocal microscopes using adaptive optics. In order to define the design specifications for such adaptive optics systems, one has to know the amount of aberrations present for typical applications such as with biological samples. We have built a phase stepping interferometer microscope that directly measures the aberration of the wavefront. The modal content of the wavefront is extracted by employing Zernike mode decomposition. Results for typical biological specimens are presented. It was found for all samples investigated that higher order Zernike modes give only a small contribution to the overall aberration. Therefore, these higher order modes can be neglected in future adaptive optics sensing and correction schemes implemented into confocal or multiphoton microscopes, leading to more efficient designs.

Survey of Anesthetic Coverage of Electroconvulsive Therapy in the State of Pennsylvania, 1988

To ascertain the current status of anesthesia care for electroconvulsive therapy (ECT) on a statewide basis, 54 facilities identified as providing ECT in the State of Pennsylvania were sent a specially designed 127-item questionnaire. Of 27 (50%) respondents, 25 (93%) included anesthesia personnel (anesthesiologists, nurse anesthetists, and anesthesia residents) on the treatment team and 2 (7%) did not. The questionnaire included items concerning pretreatment evaluation, preparation of patients, anesthesia administration, postanesthetic considerations, treatment locale, and patient profile. The items were derived from the American Psychiatric Association (APA) Task Force Report on Electroconvulsive Therapy, the Guidelines for Patient Care in Anesthesiology of the American Society of Anesthesiologists (ASA), the Standards for Nurse Anesthesia Practice of the American Association of Nurse Anesthetists (AANA), and items that reflected guidelines of the ASA and AANA. The responses of each profession were compared to its own organizational guidelines and to the other guidelines. The professions did not adhere to their own guidelines; the lowest compliance was for psychiatrists to items derived from the APA. Items derived from the APA generally received lower responses from all professions in the study. The study documents the present-day anesthetic coverage of ECT in the State of Pennsylvania, and reflects an almost complete change over a 10-year period (1978-1988) to a two-member team for ECT: a psychiatrist for electroconvulsive treatment and an anesthetist or anesthesiologist for the anesthesia management.

Refractive-index-mismatch induced aberrations in single-photon and two-photon microscopy and the use of aberration correction

We examine the effects of aberrations induced by a refractive index mismatch on the signal level and resolution of single-photon (1-p) and two-photon (2-p), conventional and confocal scanning microscopes. In particular, we consider the aberrations introduced by an interface between oil/glass and water. Resolution is defined in terms of enclosed fluorescence, rather than full-width half-maximum, revealing more useful information for heavily aberrated point spread functions (PSFs). It is shown that, at large focusing depths, the resolution of 2-p conventional and 1-p confocal microscopes are almost identical. The benefits of aberration correction are examined by removing Zernike aberration modes. With aberration correction, the best resolution is found for 1-p confocal and 2-p confocal modes. An approximation based upon geometrical optics is also introduced which shows that the axial resolution of heavily aberrated PSFs is roughly proportional to focusing depth.

Temporary remission of disseminated paecilomycosis in a German shepherd dog treated with ketoconazole

Disseminated mycosis caused by Paecilomyces varioti in a female German shepherd dog presented with chronic forelimb lameness is described. Radiographs of the swollen carpal joint revealed geographic lysis of the radial epiphysis. Diagnosis was based on cytological demonstration of fungal hyphae and chlamydiospores, as well as fungal culture of fluid obtained by arthrocentesis. Temporary remission was characterised by markedly improved clinical signs and laboratory parameters, following treatment with ketoconazole. The dog was euthanased 9 months after the initial diagnosis, following the diagnosis of multifocal discospondylitis. This appears to be the longest described period of temporary remission obtained with treatment in dogs with paecilomycosis. Clinical, clinicopathological and necropsy findings of this disease in another German shepherd dog are briefly described.

Adaptive aberration correction in a two-photon microscope

We demonstrate aberration correction in two-photon microscopy. Specimen-induced aberrations were measured with a modal wavefront sensor, implemented using a ferro-electric liquid crystal spatial light modulator (FLCSLM). Wavefront correction was performed using the same FLCSLM. Axial scanned (xz) images of fluorescently labelled polystyrene beads using an oil immersion lens show restored sectioning ability at a depth of 28 &mgr;m in an aqueous specimen.

Strategies for the compensation of specimen-induced spherical aberration in confocal microscopy of skin

We consider various strategies for confocal imaging of human skin which seek to reduce the effects of the specimen-induced aberrations. We calculate the spherical aberration introduced by the stratified structure of skin and show how the confocal signal is affected when attempting to image at various depths within the dermis. Using simple methods it is shown how images might be improved by compensating for the induced aberration. The methods include the use of an iris to reduce the pupil area, changing the refractive index of the immersion medium and using a lens with variable coverglass correction.

Closed-loop aberration correction by use of a modal Zernike wave-front sensor

We describe the practical implementation of a closed-loop adaptive-optics system incorporating a novel modal wave-front sensor. The sensor consists of a static binary-phase computer-generated holographic element, which generates a pattern of spots in a detector plane. Intensity differences between symmetric pairs of these spots give a direct measure of the Zernike mode amplitudes that are present in the input wave front. We use a ferroelectric liquid-crystal spatial light modulator in conjunction with a 4-f system and a spatial filter as a wave-front correction element. We present results showing a rapid increase in Strehl ratio and focal spot quality as the system corrects for deliberately introduced aberrations.

New modal wave-front sensor: a theoretical analysis

We present a new design of a modal wave-front sensor capable of measuring directly the Zernike components of an aberrated wave front. The sensor shows good linearity for small aberration amplitudes and is particularly suitable for integration in a closed-loop adaptive system. We introduce a sensitivity matrix and show that it is sparse, and we derive conditions specifying which elements are necessarily zero. The sensor may be temporally or spatially multiplexed, the former using a reconfigurable optical element, the latter using a numerically optimized binary optical element. Different optimization schemes are discussed, and their performance is compared.

Malignant fibrous histiocytoma of the deep peri-articular tissue of the stifle in a dog

A Belgian shepherd dog aged 4 years and 9 months was presented with acute onset of non-weight bearing lameness and stifle effusion of the left hind limb, caused by the deep form of a malignant fibrous histiocytoma originating in the deep musculature and fascia surrounding the stifle joint. The tumour progressed rapidly in the tissues along the femoral diaphysis with marked periosteal new bone formation. Cytology of a stifle joint aspirate revealed numerous large polygonal neoplastic cells with considerable anisocytosis and anisokaryosis. These cells were present in clusters, with cytoplasmic projections between the cells, but occasionally also occurred singly. Several cells contained multiple cytoplasmic vacuoles and occasional giant cells were also encountered. Adequate tumour-free margins were not possible with radical limb amputation and the dog was euthanased. Macroscopically the tumour appeared as an extensive pale tan, firm mass with scattered small haemorrhages and foci of yellow discolouration. Histologically the tumour consisted of dense neoplastic expanses or multiple nodules, composed of spindle-shaped fibroblastic cells, polygonal histiocytic cells or cell clusters and scattered giant cells with 2-3 nuclei. The polygonal neoplastic cells were frequently present around and invading lymphatics and blood vessels, causing neoplastic emboli. This is the 1st report of the clinical behaviour, radiography and cytology of the deep form of malignant fibrous histiocytoma in the dog.

Dynamic wave-front generation for the characterization and testing of optical systems

We describe a simple method for generating known optical aberrations dynamically, using a ferroelectric liquid-crystal spatial light modulator. Aberrations inherent in the optical system are measured and corrected, and as an example Kolmogorov turbulence is simulated for aperture sizes D/r(0) from 0 to 30, varying at frame rates up to 2.5 kHz. A measure of wave-front generation efficiency is introduced and is shown to be better than 86% for Kolmogorov phase screens with D/r(0) in the range from 0 to 30.

Nurse anesthetist reaction to the unexpected or untimely death of patients in the operating room

Certified registered nurse anesthetists (CRNAs) experience the unexpected death of the their patients much differently than other nurses. Unlike all other nurses, they are held directly responsible for maintaining their patients' physiologic parameters in the face of surgical and pharmacologic insults and not only for selecting the types of anesthetic and adjuvant drugs but also for manipulating their doses on a minute-to-minute basis. Four factors significantly enhance their stress: the presence of an unrescinded advance medical directive and/or do not resuscitate order; the harvesting of vital organs; psychologic factors, including distractions, errors in clinical judgment, fatigue, boredom, or lack of vigilance; and legal threats. Unless CRNAs have significant coping skills firmly in place, any of these stresses may cause them to deteriorate physically, emotionally, or professionally.

Atypical dermoid sinus in a chow chow dog

A case of multiple dermoid sinuses in the dorsal cervical and craniothoracic regions in an adult chow chow dog is described. One sinus did not open on the skin surface. This is the first reported case of the condition in this breed and the first time absence of the sinus opening on the skin is described. The use of the term pilonidal sinus to describe this condition is challenged.

Continuous wave excitation two-photon fluorescence microscopy exemplified with the 647-nm ArKr laser line

We report on efficient two-photon fluorescence imaging in beam scanning microscopy by exciting UV dyes at the 647-nm line of a continuous wave ArKr mixed gas laser. For a numerical aperture of 1.4 (oil), we used an illumination power of up to 210 mW at the sample. High-resolution images were obtained for DAPI-labelled cell nuclei within 4-60 s. Our method is a simple two-photon alternative to UV confocal imaging with the potential of becoming a very useful feature of laser scanning microscopy.

Identification of serine/threonine protein kinases secreted by Trichinella spiralis infective larvae

Serine/threonine protein kinase activity was identified in excretory/secretory (ES) products of Trichinella spiralis infective larvae, via phosphorylation of exogenous and endogenous substrates. Protein kinase activity was identified as an authentic secretory product via blockade of release into culture medium by brefeldin A. Enzyme activity was reductant-dependent, and the relative resistance to a panel of inhibitors suggested that it could not be readily assigned to any of the major documented subfamilies of serine/threonine protein kinases. There was no evidence for protein tyrosine kinase activity in ES products. The major phosphorylated proteins in this compartment resolved at 50 and 55 kDa by SDS-PAGE, and are therefore designated pp50/55. These proteins contained mainly phosphoserine, and appear to represent differentially glycosylated variants of a 35 kDa polypeptide, modified via the addition of three and four N-linked oligosaccharides, respectively. An autophosphorylation assay following separation by SDS-PAGE identified two protein kinases of 70 and 135 kDa in ES products.

Single-Strand Conformation Polymorphism Mutation Analysis of the p53 Gene

Single-strand conformation polymorphism (SSCP) is a rapid and convenient procedure by which differences in the base composition of short DNA strands may be detected (1, 2). A useful application of this is in the comparison of polymerase chain reaction (PCR) generated products from gene coding sequences of unknown or patient material with a known wild-type standard; where any deviation of the banding pattern produced by the former from that produced by the latter indicates a possible mutation within the sequence of that product.