Correction to 'ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation'.

[This corrects the article DOI: 10.1093/nargab/lqaa104.].

Detection of flap tissue ischemia in a rat model: Real-time monitoring of changes in oxygenation and perfusion through injectable biosensors.

BACKGROUND: The success of surgical flaps is improved by timely correction of vascular compromise. Current monitoring methods are labor or cost intensive or have limited clinical benefit. We hypothesize that injectable oxygen sensors can identify acute vascular compromise. The purpose of this study was to use a long-term, real-time method of tissue oxygenation detection in a rat flap model with vascular manipulation. METHODS: Sensors incorporated benzo-porphyrin dye into a microporous hydrogel and were injected intradermally 1 day before flap elevation. Inspired oxygen was modulated between 100% and 12% to confirm sensor O2 sensitivity. Eight random flaps (4 cm wide, 8 cm long) were elevated. Sensor and clinical observation to temporary clamping of the flap vascular pedicle was recorded. Sodium fluorescein in saline was injected intraperitoneally on postoperative days 0, 3, and 7 with subsequent perfusion area analysis. RESULTS: Tissue oxygen tension measurements reflected the changes in inspired oxygen levels. Clinical observation of the flaps did not show any significant change in color or temperature with pedicle clamping. However, clamping of the pedicle resulted in a significant decrease in sensor tissue oxygen tension within 70 seconds. CONCLUSION: Oxygen monitoring of myocutaneous flaps is sensitive and can detect acute vascular occlusion. This technique is faster than current methods and offers a cost-effective and accurate means of monitoring surgical tissues.

ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation.

ConsHMM is a method recently introduced to annotate genomes into conservation states, which are defined based on the combinatorial and spatial patterns of which species align to and match a reference genome in a multi-species DNA sequence alignment. Previously, ConsHMM was only applied to a single genome for one multi-species sequence alignment. Here, we apply ConsHMM to produce 22 additional genome annotations covering human and seven other organisms for a variety of multi-species alignments. Additionally, we extend ConsHMM to generate allele-specific annotations, which we use to produce conservation state annotations for every possible single-nucleotide mutation in the human genome. Finally, we provide a web interface to interactively visualize parameters and annotation enrichments for ConsHMM models. These annotations and visualizations comprise the ConsHMM Atlas, which we expect will be a valuable resource for analyzing a variety of major genomes and genetic variation.

Injectable Phosphorescence-based Oxygen Biosensors Identify Post Ischemic Reactive Hyperoxia.

Novel injectable biosensors were used to measure interstitial oxygenation before, during, and after transient ischemia. It is well known that reactive hyperemia occurs following a period of ischemia. However, increased blood flow does not necessarily mean increased oxygen tension in the tissue. Therefore, the purpose of this study was to test the hypothesis that tissue reactive hyperoxia occurs following release of hind-limb tourniquet occlusions. Rats were injected with bilateral hind-limb biosensors and were simultaneously subjected to a unilateral femoral vessel ligation. After approximately one and three months, the rats underwent a series of oxygenation challenges, including transient hind-limb tourniquet occlusion. Along with the biosensors, near infrared spectroscopy was used to measure percent oxyhemoglobin in capillaries and laser Doppler flowmetry was used to measure blood flow. Post-occlusion reactive hyperemia was observed. It was accompanied by tissue reactive hyperoxia, affirming that the post-occlusion oxygen supply must have exceeded the expected increased oxygen consumption. The measurement of the physiologic phenomenon of reactive hyperoxia could prove clinically beneficial for both diagnosis and optimizing therapy.

Deep imaging of absorption and scattering features by multispectral multiple scattering low coherence interferometry.

We have developed frequency domain multispectral multiple scattering low coherence interferometry (ms2/LCI) for deep imaging of absorption and scattering contrast. Using tissue-mimicking phantoms that match the full scattering phase function of human dermal tissue, we demonstrate that ms2/LCI can provide a signal/noise ratio (SNR) improvement of 15.4 dB over conventional OCT at an imaging depth of 1 mm. The enhanced SNR and penetration depth provided by ms2/LCI could be leveraged for a variety of clinical applications including the assessment of burn injuries where current clinical classification of severity only provides limited accuracy. The utility of the approach was demonstrated by imaging a tissue phantom simulating a partial-thickness burn revealing good spectroscopic contrast between healthy and injured tissue regions deep below the sample surface. Finally, healthy rat skin was imaged in vivo with both a commercial OCT instrument and our custom ms2/LCI system. The results demonstrate that ms2/LCI is capable of obtaining spectroscopic information far beyond the penetration depth provided by conventional OCT.

Tracking mesenchymal stromal cells using an ultra-bright TAT-functionalized plasmonic-active nanoplatform.

High-resolution tracking of stem cells remains a challenging task. An ultra-bright contrast agent with extended intracellular retention is suitable for in vivo high-resolution tracking of stem cells following the implantation. Here, a plasmonic-active nanoplatform was developed for tracking mesenchymal stromal cells (MSCs) in mice. The nanoplatform consisted of TAT peptide-functionalized gold nanostars (TAT-GNS) that emit ultra-bright two-photon photoluminescence capable of tracking MSCs under high-resolution optical imaging. In vitro experiment showed TAT-GNS-labeled MSCs retained a similar differentiability to that of non-labeled MSCs controls. Due to their star shape, TAT-GNS exhibited greater intracellular retention than that of commercial Q-Tracker. In vivo imaging of TAT-GNS-labeled MSCs five days following intra-arterial injections in mice kidneys showed possible MSCs implantation in juxta-glomerular (JG) regions, but non-specifically in glomeruli and afferent arterioles as well. With future design to optimize GNS labeling specificity and clearance, plasmonic-active nanoplatforms may be a useful intracellular tracking tool for stem cell research. An ultra-bright intracellular contrast agent is developed using TAT peptide-functionalized gold nanostars (TAT-GNS). It poses minimal influence on the stem cell differentiability. It exhibits stronger two-photon photoluminescence and superior labeling efficiency than commercial Q-Tracker. Following renal implantation, some TAT-GNS-labeled MSCs permeate blood vessels and migrate to the juxta-glomerular region.

Characterization of an atypical gamma-secretase complex from hematopoietic origin.

Gamma-secretase is a widely expressed multisubunit enzyme complex which is involved in the pathogenesis of Alzheimer disease and hematopoietic malignancies through its aberrant processing of the amyloid precursor protein (APP) and Notch1, respectively. While gamma-secretase has been extensively studied, there is a dearth of information surrounding the activity, composition, and function of gamma-secretase expressed in distinct cellular populations. Here we show that endogenous gamma-secretase complexes of hematopoietic origin are distinct from epithelial derived gamma-secretase complexes. Hematopoietic gamma-secretase has reduced activity for APP and Notch1 processing compared to epithelial gamma-secretase. Characterization of the active complexes with small molecule affinity probes reveals that hematopoietic gamma-secretase has an atypical subunit composition with significantly altered subunit stoichiometry. Furthermore, we demonstrate that these discrete complexes exhibit cell-line specific substrate selectivity suggesting a possible mechanism of substrate regulation. These data underscore the need for studying endogenous gamma-secretase to fully understand of the biology of gamma-secretase and its complexity as a molecular target for the development of disease therapeutics.

Identification of candidate disease genes by EST alignments, synteny, and expression and verification of Ensembl genes on rat chromosome 1q43-54.

We aligned Incyte ESTs and publicly available sequences to the rat genome and analyzed rat chromosome 1q43-54, a region in which several quantitative trait loci (QTLs) have been identified, including renal disease, diabetes, hypertension, body weight, and encephalomyelitis. Within this region, which contains 255 Ensembl gene predictions, the aligned sequences clustered into 568 Incyte genes and gene fragments. Of the Incyte genes, 261 (46%) overlapped 184 (72%) of the Ensembl gene predictions, whereas 307 were unique to Incyte. The rat-to-human syntenic map displays rearrangement of this region on rat chr. 1 onto human chromosomes 9 and 10. The mapping of corresponding human disease phenotypes to either one of these chromosomes has allowed us to focus in on genes associated with disease phenotypes. As an example, we have used the syntenic information for the rat Rf-1 disease region and the orthologous human ESRD disease region to reduce the size of the original rat QTL to only 11.5 Mb. Using the syntenic information in combination with expression data from ESTs and microarrays, we have selected a set of 66 candidate disease genes for Rf-1. The combination of the results from these different analyses represents a powerful approach for narrowing the number of genes that could play a role in the development of complex diseases.