Discovery of small molecules that target a tertiary-structured RNA.

There is growing interest in therapeutic intervention that targets disease-relevant RNAs using small molecules. While there have been some successes in RNA-targeted small-molecule discovery, a deeper understanding of structure-activity relationships in pursuing these targets has remained elusive. One of the best-studied tertiary-structured RNAs is the theophylline aptamer, which binds theophylline with high affinity and selectivity. Although not a drug target, this aptamer has had many applications, especially pertaining to genetic control circuits. Heretofore, no compound has been shown to bind the theophylline aptamer with greater affinity than theophylline itself. However, by carrying out a high-throughput screen of low-molecular-weight compounds, several unique hits were identified that are chemically distinct from theophylline and bind with up to 340-fold greater affinity. Multiple atomic-resolution X-ray crystal structures were determined to investigate the binding mode of theophylline and four of the best hits. These structures reveal both the rigidity of the theophylline aptamer binding pocket and the opportunity for other ligands to bind more tightly in this pocket by forming additional hydrogen-bonding interactions. These results give encouragement that the same approaches to drug discovery that have been applied so successfully to proteins can also be applied to RNAs.

Virtual reality cognitive intervention for heart failure: CORE study protocol.

Introduction: Heart failure (HF) is a prevalent, serious chronic illness that affects 6.5 million adults in the United States. Among patients with HF, the prevalence of attention impairment is reported to range from 15% to 27%. Although attention is fundamental to human activities including HF self-care, cognitive interventions for patients with HF that target improvement in attention are scarce. The COgnitive intervention to Restore attention using nature Environment (CORE) study aims to test the preliminary efficacy of the newly developed Nature-VR, a virtual reality-based cognitive intervention that is based on the restorative effects of nature. Nature-VR development was guided by Attention Restoration Theory. The target outcomes are attention, HF self-care, and health-related quality of life (HRQoL). Our exploratory aims examine the associations between attention and several putative/established HF biomarkers (eg, oxygen saturation, brain-derived neurotrophic factor, apolipoprotein E, dopamine receptor, and dopamine transporter genes) as well as the effect of Nature-VR on cognitive performance in other domains (ie, global cognition, memory, visuospatial, executive function, and language), cardiac and neurological events, and mortality. Methods: This single-blinded, two-group randomized-controlled pilot study will enroll 74 participants with HF. The Nature-VR intervention group will view three-dimensional nature pictures using a virtual reality headset for 10 minutes per day, 5 days per week for 4 weeks (a total of 200 minutes). The active comparison group, Urban-VR, will view three-dimensional urban pictures using a virtual reality headset to match the Nature-VR intervention in intervention dose and delivery mode, but not in content. After baseline interviews, four follow-up interviews will be conducted to assess sustained effects of Nature-VR at 4, 8, 26, and 52 weeks. Discussion: The importance and novelty of this study consists of using a first-of-its kind, immersive virtual reality technology to target attention and in investigating the health outcomes of the Nature-VR cognitive intervention among patients with HF.

Development of a Smart Sleep Mask with Multiple Sensors.

In this work, we demonstrated a Smart Sleep Mask with several integrated physiological sensors such as 3-axis accelerometers, respiratory acoustic sensor, and an eye movement sensor. In particular, using infrared optical sensors, eye movement frequency, direction, and amplitude can be directly monitored and recorded during sleep sessions. We also developed a mobile app for data storage, signal processing and data analytics. Aggregation of these signals from a single wearable device may offer ease of use and more insights for sleep monitoring and REM sleep assessment. The user-friendly mask design can enable at-home use applications in the studies of digital biomarkers for sleep disorder related neurodegenerative diseases. Examples include REM Sleep Behavior Disorder, epilepsy event detection and stroke induced facial and eye movement disorder.Clinical Relevance-Many diseases such as stroke, epilepsy, and Parkinson's disease can cause significant abnormal events during sleep or are associated with sleep disorder. A smart sleep mask may serve as a simple platform to provide various physiological signals and generate clinical meaningful insights by revealing the neurological activities during various sleep stages.

Turning the Finger into a Writing Tool.

A novel writing platform composed of a wearable sensor on the fingernail and classification algorithms is described. Findings from using this platform to translate fingertip writing into shapes, letters, and numbers on a range of surfaces are reported. The new wearable platform leverages an architecture with miniaturized electronic circuitry to precisely measure a set of forces in the longitudinal and transverse directions using multiple strain gauges. We find that the directional pressure patterns are translated from the fingertip to the fingernail. Deformation of fingernails in the longitudinal and transverse directions are detected by the fingernail sensor which sends the data wirelessly to a portable electronic system. Fingernail pressure patterns are categorized through signal processing to recognize a range of shapes, numbers, and letters, enabling fingertip writing recognition. Use of the writing platform following a short training session, shows human fingertip writing on multiple surfaces were automatically transcribed to a computer.

Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons.

Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for unusually long distances, is not readily documented by direct field observation. In this pilot study, we investigate the possibility of retrieving baboon population structure in yellow (Papio cynocephalus) and kinda (Papio kindae) baboons from the distribution of variation in a genome-wide set of 494 Alu insertion polymorphisms, made available via the recently completed Baboon Genome Analysis Consortium. Alu insertion variation in a mixed population derived from yellow and olive (Papio anubis) baboons identified each individual's proportion of heritage from either parental species. In an unmixed yellow baboon population, our analysis showed greater similarity between neighboring than between more distantly situated groups, suggesting structuring of the population by male dispersal distance. Finally (and very provisionally), an unexpectedly sharp difference in Alu insertion frequencies between members of neighboring social groups of kinda baboons suggests that intergroup migration may be more rare than predicted in this little known species.

Development and validation of a method for profiling post-translational modification activities using protein microarrays.

BACKGROUND: Post-translational modifications (PTMs) impact on the stability, cellular location, and function of a protein thereby achieving a greater functional diversity of the proteome. To fully appreciate how PTMs modulate signaling networks, proteome-wide studies are necessary. However, the evaluation of PTMs on a proteome-wide scale has proven to be technically difficult. To facilitate these analyses we have developed a protein microarray-based assay that is capable of profiling PTM activities in complex biological mixtures such as whole-cell extracts and pathological specimens. METHODOLOGY/PRINCIPAL FINDINGS: In our assay, protein microarrays serve as a substrate platform for in vitro enzymatic reactions in which a recombinant ligase, or extracts prepared from whole cells or a pathological specimen is overlaid. The reactions include labeled modifiers (e.g., ubiquitin, SUMO1, or NEDD8), ATP regenerating system, and other required components (depending on the assay) that support the conjugation of the modifier. In this report, we apply this methodology to profile three molecularly complex PTMs (ubiquitylation, SUMOylation, and NEDDylation) using purified ligase enzymes and extracts prepared from cultured cell lines and pathological specimens. We further validate this approach by confirming the in vivo modification of several novel PTM substrates identified by our assay. CONCLUSIONS/SIGNIFICANCE: This methodology offers several advantages over currently used PTM detection methods including ease of use, rapidity, scale, and sample source diversity. Furthermore, by allowing for the intrinsic enzymatic activities of cell populations or pathological states to be directly compared, this methodology could have widespread applications for the study of PTMs in human diseases and has the potential to be directly applied to most, if not all, basic PTM research.

A genomewide linkage scan for quantitative trait loci influencing the craniofacial complex in baboons (Papio hamadryas spp.).

Numerous studies have detected significant contributions of genes to variation in development, size, and shape of craniofacial traits in a number of vertebrate taxa. This study examines 43 quantitative traits derived from lateral cephalographs of 830 baboons (Papio hamadryas) from the pedigreed population housed at the Southwest National Primate Research Center. Quantitative genetic analyses were conducted using the SOLAR analytic platform, a maximum-likelihood variance components method that incorporates all familial information for parameter estimation. Heritability estimates were significant and of moderate to high magnitude for all craniofacial traits. Additionally, 14 significant quantitative trait loci (QTL) were identified for 12 traits from the three developmental components (basicranium, splanchnocranium, and neurocranium) of the craniofacial complex. These QTL were found on baboon chromosomes (and human orthologs) PHA1 (HSA1), PHA 2 (HSA3), PHA4 (HSA6), PHA11 (HSA12), PHA13 (HSA2), PHA16 (HSA17), and PHA17 (HSA13) (PHA, P. hamadryas; HSA, Homo sapiens). This study of the genetic architecture of the craniofacial complex in baboons provides the groundwork needed to establish the baboon as an animal model for the study of genetic and nongenetic influences on craniofacial variation.

A randomized trial of alemtuzumab vs. anti-thymocyte globulin induction in renal and pancreas transplantation.

The role of alemtuzumab as an immunosuppressive agent is evolving. We conducted a prospective randomized trial comparing alemtuzumab and rabbit anti-thymocyte globulin (rATG) induction in adult kidney and pancreas transplantation using similar maintenance immunosuppression. Between February 1, 2005 and June 15, 2006 (median follow-up six months), 98 patients were randomized either to alemtuzumab (n = 48) or to rATG (n = 50) induction; 77 (79%) underwent kidney alone (KA) transplant, 17 (17%) pancreas-kidney transplant, and four (4%) pancreas after kidney transplant. Of 77 KA transplants, 66 (86%) were from deceased donors and 31 (40%) from expanded criteria donors (ECD). Re-transplantation, HLA-match, antibody titer, ECD, race, cytomegalovirus status, steroid use, delayed graft function, preservation time, and immunological risk were similar between the two induction groups. Patient, kidney, and pancreas graft survival rates were 100%, 96%, and 95%, respectively. Survival, initial length of stay, delayed graft function, and overall acute rejection rates were similar between alemtuzumab and rATG groups, but acute rejection occurred in nine (20%) rATG patients compared with zero (0%) alemtuzumab patients who received KA transplants (p = 0.007). Mean induction costs differed in the alemtuzumab ($1474) and rATG ($4996, p < 0.001) groups. In the short term after kidney and pancreas transplantation, alemtuzumab and rATG induction therapies are similarly safe and effective.

Optimization of the antibody C(H)3 domain by residue frequency analysis of IgG sequences.

In an attempt to enhance the overall assembly, yield and half-life of recombinant antibody proteins, we have cloned and expressed several IgG1 C(H)3 domains and examined their folding/refolding characteristics. We utilized a cytoplasmic bacterial expression system with a thioredoxin reductase knock-out strain of BL21(DE3) to produce bovine, murine and human C(H)3. Under identical conditions, expression of bovine C(H)3 resulted consistently in the highest yields of properly folded/oxidized protein. Circular dichroism and fluorescence experiments demonstrate that oxidized bovine and murine C(H)3 have surprisingly similar structures and stabilities, considering the marginal sequence conservation between the two molecules. Residue frequency analysis using a limited data set of 36 unique Fc sequences originating from 19 different mammalian species targeted five specific sites for optimization within bovine C(H)3. Combination of three of these mutants increased the thermal stability of the molecule to 86 degrees C. Comparison of this approach to similar studies using larger sequence databases and/or different selection criteria suggests sequence database design can increase the success rate for identifying residue sites worth optimizing. This optimized C(H)3 domain can be used as a particularly stable platform for functional design and can be grafted into full-length antibody sequences to enhance their thermodynamic parameters and shelf-life.