Reversion to wildtype of a mutated and nonfunctional coxsackievirus B3CRE(2C)

The cis-acting replication element (CRE) in the 2C protein coding region [CRE(2C)] of enteroviruses (EV) facilitates the addition of two uridine residues (uridylylation) onto the virus-encoded protein VPg inorder for it to serve as the RNA replication primer. We demonstrated that coxsackievirus B3 (CVB3) is replication competent in the absence of a native (uridylylating) CRE(2C) and also demonstrated that lackof a functional CRE(2C) led to generation of 5’ terminal genomic deletions in the CVB3 CRE-knock-out (CVB3-CKO) population. We asked whether reversion of the mutated CRE(2C) occurred, thus permitting sustained replication, and when were 5’ terminal deletions generated during replication. Virions were isolated from HeLa cells previously electroporated with infectious CVB3-CKO T7 transcribed RNA or from hearts and spleens of mice after transfection with CVB3-CKO RNA. Viral RNA was isolated in order to amplify the CRE(2C) coding region and the genomic 5’terminal sequences. Sequence analysis revealed reversion of the CVB3-CKO sequence to wildtype occurs by 8 days post-electroporation of HeLa cells and by 20 days post-transfection in mice. However, 5’terminal deletions evolve prior to these times.Reversion of the CRE(2C) mutations to wildtype despite loss of the genomic 5’ termini is consistent with the hypothesis that an intact CRE(2C) is inherently vital to EV replication even when it is not enabling efficient positive strand initiation

Ultracompact fluorescence smartphone attachment using built-in optics for protoporphyrin-IX quantification in skin

Smartphone-based fluorescence imaging systems have the potential to provide convenient quantitative image guidance at the point of care. However, common approaches have required the addition of complex optical attachments, which reduce translation potential. In this study, a simple clip-on attachment appropriate for fluorescence imaging of protoporphyrin-IX (PpIX) in skin was designed using the built-in light source and ultrawide camera sensor of a smartphone. Software control for image acquisition and quantitative analysis was developed using the 10-bit video capability of the phone. Optical performance was characterized using PpIX in liquid tissue phantoms and endogenously produced PpIX in mice and human skin. The proposed system achieves a very compact form factor (\u3c30 cm3) and can be readily fabricated using widely available low-cost materials. The limit of detection of PpIX in optical phantoms was \u3c10 nM, with good signal linearity from 10 to 1000 nM (R2 \u3e0.99). Both murine and human skin imaging verified that in vivo PpIX fluorescence was detected within 1 hour of applying aminolevulinic acid (ALA) gel. This ultracompact handheld system for quantification of PpIX in skin is well-suited for dermatology clinical workflows. Due to its simplicity and form factor, the proposed system can be readily adapted for use with other smartphone devices and fluorescence imaging applications. Hardware design and software for the system is made freely available on GitHub (https://github.com/optmed/CompactFluorescenceCam)

Dual-Channel Red/Blue Fluorescence Dosimetry with Broadband Reflectance Spectroscopic Correction Measures Protoporphyrin IX Production during Photodynamic Therapy of Actinic Keratosis

Dosimetry for aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) photodynamic therapy of actinic keratosis was examined with an optimized fluorescence dosimeter to measure PpIX during treatment. While insufficient PpIX generation may be an indicator of incomplete response, there exists no standardized method to quantitate PpIX production at depths in the skin during clinical treatments. In this study, a spectrometer-based point probe dosimeter system was used to sample PpIX fluorescence from superficial (blue wavelength excitation) and deeper (red wavelength excitation) tissue layers. Broadband white light spectroscopy (WLS) was used to monitor aspects of vascular physiology and inform a correction of fluorescence for the background optical properties. Measurements in tissue phantoms showed accurate recovery of blood volume fraction and reduced scattering coefficient from WLS, and a linear response of PpIX fluorescence versus concentration down to 1.95 and 250 nM for blue and red excitations, respectively. A pilot clinical study of 19 patients receiving 1-h ALA incubation before treatment showed high intrinsic variance in PpIX fluorescence with a standard deviation/mean ratio of \u3c0.9 . PpIX fluorescence was significantly higher in patients reporting higher pain levels on a visual analog scale. These pilot data suggest that patient-specific PpIX quantitation may predict outcome response

Assessing Daylight & Low-Dose Rate Photodynamic Therapy Efficacy, Using Biomarkers of Photophysical, Biochemical and Biological Damage Metrics in Situ.

Background Sunlight can activate photodynamic therapy (PDT), and this is a proven strategy to reduce pain caused by conventional PDT treatment, but assessment of this and other alternative low dose rate light sources, and their efficacy, has not been studied in an objective, controlled pre-clinical setting. This study used three objective assays to assess the efficacy of different PDT treatment regimens, using PpIX fluorescence as a photophysical measure, STAT3 cross-linking as a photochemical measure, and keratinocyte damage as a photobiological measure. Methods Nude mouse skin was used along with in vivo measures of photosensitizer fluorescence, keratinocyte nucleus damage from pathology, and STAT3 cross-linking from Western blot analysis. Light sources compared included a low fluence rate red LED panel, compact fluorescent bulbs, halogen bulbs and direct sunlight, as compared to traditional PDT delivery with conventional and fractionated high fluence rate red LED light delivery. Results Of the three biomarkers, two had strong correlation to the PpIX-weighted light dose, which is calculated as the product of the treatment light dose (J/cm2) and the normalized PpIX absorption spectra. Comparison of STAT3 cross-linking to PpIX-weighted light dose had an R = 0.74, and comparison of keratinocyte nuclear damage R = 0.70. There was little correlation to PpIX fluorescence. These assays indicate most of the low fluence rate treatment modalities were as effective as conventional PDT, while fractionated PDT showed the most damage. Conclusions Daylight or artificial light PDT provides an alternative schedule for delivery of drug-light treatment, and this pre-clinical assay demonstrated that in vivo assays of damage could be used to objectively predict a clinical outcome in this altered delivery process. Graphical abstract Low-fluence daylight photodynamic therapy (PDT) has been shown to reduce pain with similar efficacy of conventional treatments. Three objective assays were performed to assess efficacy of different light treatment strategies: PpIX photobleaching, STAT3 crosslinking, and keratinocyte damage. Of these metrics, STAT3 crosslinking and keratinocyte damage showed a strong correlation to the PpIX-weighted light dose

Effects of Nitrogen and Planting Seed Size on Cotton Growth, Development, and Yield

A standardized experiment was conducted during 2009 and 2010 at 20 location-years across U.S. cotton (Gossypium hirsutum L.)-producing states to compare the N use requirement of contemporary cotton cultivars based on their planting seed size. Treatments consisted of three cotton varieties with planting seed of different numbers of seed per kg and N rates of 0, 45, 90, and 134 kg ha⁻¹. Soil at each trial location was sampled and tested for nitrate presence. High levels of soil nitrate (>91 N-NO₃⁻kg ha⁻¹) were found in Arizona and western Texas, and soil nitrate in the range of 45 to 73 kg N-NO₃⁻ ha⁻¹ was found at locations in the central United States. Cotton lint yield responded to applied N at 11 of 20 locations. Considering only sites that responded to applied N, highest lint yields were achieved with 112 to 224 kg ha⁻¹of applied plus pre-plant residual soil NO₃—translating to an optimal N requirement of 23 kg ha⁻¹ per 218 kg bale of lint produced. Among the varieties tested those with medium-sized seed produced higher yields in response to N than did larger and smaller seeded varieties. Varieties with larger seed had longer and stronger fibers, higher fiber length uniformity than small seeded varieties and decreased micronaire. Seed protein and oil increased and decreased slightly in response to increasing amounts of soil nitrate plus applied N, respectively

Submillimeter Follow-up of WISE-Selected Hyperluminous Galaxies

We have used the Caltech Submillimeter Observatory (CSO) to follow-up a sample of WISE-selected, hyperluminous galaxies, so called W1W2-dropout galaxies. This is a rare (~ 1000 all-sky) population of galaxies at high redshift (peaks at z=2-3), that are faint or undetected by WISE at 3.4 and 4.6 um, yet are clearly detected at 12 and 22 um. The optical spectra of most of these galaxies show significant AGN activity. We observed 14 high-redshift (z > 1.7) W1W2-dropout galaxies with SHARC-II at 350 to 850 um, with 9 detections; and observed 18 with Bolocam at 1.1 mm, with five detections. Warm Spitzer follow-up of 25 targets at 3.6 and 4.5 um, as well as optical spectra of 12 targets are also presented in the paper. Combining WISE data with observations from warm Spitzer and CSO, we constructed their mid-IR to millimeter spectral energy distributions (SEDs). These SEDs have a consistent shape, showing significantly higher mid-IR to submm ratios than other galaxy templates, suggesting a hotter dust temperature. We estimate their dust temperatures to be 60-120 K using a single-temperature model. Their infrared luminosities are well over 10^{13} Lsun. These SEDs are not well fitted with existing galaxy templates, suggesting they are a new population with very high luminosity and hot dust. They are likely among the most luminous galaxies in the Universe. We argue that they are extreme cases of luminous, hot dust-obscured galaxies (DOGs), possibly representing a short evolutionary phase during galaxy merging and evolution. A better understanding of their long-wavelength properties needs ALMA as well as Herschel data.Comment: Will be Published on Sep 1, 2012 by Ap

Dinosaur peptides suggest mechanisms of protein survival

Eleven collagen peptide sequences recovered from chemical extracts of dinosaur bones were mapped onto molecular models of the vertebrate collagen fibril derived from extant taxa. The dinosaur peptides localized to fibril regions protected by the close packing of collagen molecules, and contained few acidic amino acids. Four peptides mapped to collagen regions crucial for cell-collagen interactions and tissue development. Dinosaur peptides were not represented in more exposed parts of the collagen fibril or regions mediating intermolecular cross-linking. Thus functionally significant regions of collagen fibrils that are physically shielded within the fibril may be preferentially preserved in fossils. These results show empirically that structure-function relationships at the molecular level could contribute to selective preservation in fossilized vertebrate remains across geological time, suggest a ‘preservation motif’, and bolster current concepts linking collagen structure to biological function. This non-random distribution supports the hypothesis that the peptides are produced by the extinct organisms and suggests a chemical mechanism for survival

Multi-wavelength lens construction of a Planck and Herschel-detected star-bursting galaxy

We present a source-plane reconstruction of a Herschel and Planck-detected gravitationally lensed dusty star-forming galaxy (DSFG) at z = 1.68 using Hubble, Submillimeter Array (SMA), and Keck observations. The background submillimeter galaxy (SMG) is strongly lensed by a foreground galaxy cluster at z = 0.997 and appears as an arc with a length of ∼15″ in the optical images. The continuum dust emission, as seen by SMA, is limited to a single knot within this arc. We present a lens model with source-plane reconstructions at several wavelengths to show the difference in magnification between the stars and dust, and highlight the importance of multi-wavelength lens models for studies involving lensed DSFGs. We estimate the physical properties of the galaxy by fitting the flux densities to model spectral energy distributions leading to a magnification-corrected starformation rate (SFR) of 390 ± 60 M yr−1 and a stellar mass of 1.1 ± 0.4 10 x 11 M. These values are consistent with high-redshift massive galaxies that have formed most of their stars already. The estimated gas-to-baryon fraction, molecular gas surface density, and SFR surface density have values of 0.43 ± 0.13, 350 ± 200 M pc−2, and ~ 12 7 M yr−1 kpc−2, respectively. The ratio of SFR surface density to molecular gas surface density puts this among the most star-forming systems, similar to other measured SMGs and local ULIRGs

Everyday episodic memory in amnestic mild cognitive impairment: a preliminary investigation

<p>Abstract</p> <p>Background</p> <p>Decline in episodic memory is one of the hallmark features of Alzheimer's disease (AD) and is also a defining feature of amnestic Mild Cognitive Impairment (MCI), which is posited as a potential prodrome of AD. While deficits in episodic memory are well documented in MCI, the nature of this impairment remains relatively under-researched, particularly for those domains with direct relevance and meaning for the patient's daily life. In order to fully explore the impact of disruption to the episodic memory system on everyday memory in MCI, we examined participants' episodic memory capacity using a battery of experimental tasks with real-world relevance. We investigated episodic acquisition and delayed recall (story-memory), associative memory (face-name pairings), spatial memory (route learning and recall), and memory for everyday mundane events in 16 amnestic MCI and 18 control participants. Furthermore, we followed MCI participants longitudinally to gain preliminary evidence regarding the possible predictive efficacy of these real-world episodic memory tasks for subsequent conversion to AD.</p> <p>Results</p> <p>The most discriminating tests at baseline were measures of acquisition, delayed recall, and associative memory, followed by everyday memory, and spatial memory tasks, with MCI patients scoring significantly lower than controls. At follow-up (mean time elapsed: 22.4 months), 6 MCI cases had progressed to clinically probable AD. Exploratory logistic regression analyses revealed that delayed associative memory performance at baseline was a potential predictor of subsequent conversion to AD.</p> <p>Conclusions</p> <p>As a preliminary study, our findings suggest that simple associative memory paradigms with real-world relevance represent an important line of enquiry in future longitudinal studies charting MCI progression over time.</p