Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries.

Proteolysis is a major posttranslational regulator of biology inside and outside of cells. Broad identification of optimal cleavage sites and natural substrates of proteases is critical for drug discovery and to understand protease biology. Here, we present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical six- to eight-residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases, and the ectodomains of the sheddases, ADAMs 10 and 17. The first library (Lib 10AA) allowed us to identify 104 to 105 unique cleavage sites over a 1,000-fold dynamic range of NGS counts and produced consensus and optimal cleavage motifs based position-specific scoring matrices. A second SPD-NGS library (Lib hP), which displayed virtually the entire human proteome tiled in contiguous 49 amino acid sequences with 25 amino acid overlaps, enabled us to identify candidate human proteome sequences. We identified up to 104 natural linear cut sites, depending on the protease, and captured most of the examples previously identified by proteomics and predicted 10- to 100-fold more. Structural bioinformatics was used to facilitate the identification of candidate natural protein substrates. SPD-NGS is rapid, reproducible, simple to perform and analyze, inexpensive, and renewable, with unprecedented depth of coverage for substrate sequences, and is an important tool for protease biologists interested in protease specificity for specific assays and inhibitors and to facilitate identification of natural protein substrates.

Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis.

A 37-year-old man with a history of seminoma presented with vertigo, ataxia, and diplopia. An autoantibody specific for kelch-like protein 11 (KLHL11) was identified with the use of programmable phage display. Immunoassays were used to identify KLHL11 IgG in 12 other men with similar neurologic features and testicular disease. Immunostaining of the patient's IgG on mouse brain tissue showed sparse but distinctive points of staining in multiple brain regions, with enrichment in perivascular and perimeningeal tissues. The onset of the neurologic syndrome preceded the diagnosis of seminoma in 9 of the 13 patients. An age-adjusted estimate of the prevalence of autoimmune KLHL11 encephalitis in Olmsted County, Minnesota, was 2.79 cases per 100,000 men. (Funded by the Rochester Epidemiology Project and others.).

Photoacoustic monitoring of angiogenesis predicts response to therapy in healing wounds.

Chronic wounds are a major health problem that cause the medical infrastructure billions of dollars every year. Chronic wounds are often difficult to heal and cause significant discomfort. Although wound specialists have numerous therapeutic modalities at their disposal, tools that could three dimensional-map wound bed physiology and guide therapy do not exist. Visual cues are the current standard but are limited to surface assessment; clinicians rely on experience to predict response to therapy. Photoacoustic (PA) ultrasound (US) is a non-invasive, hybrid imaging modality that can solve these major limitations. PA relies on the contrast generated by haemoglobin in blood which allows it to map local angiogenesis, tissue perfusion and oxygen saturation-all critical parameters for wound healing. This work evaluates the use of PA-US to monitor angiogenesis and stratify patients responding versus not-responding to therapy. We imaged 19 patients with 22 wounds once a week for at least 3 weeks. Our findings suggest that PA imaging directly visualises angiogenesis. Patients responding to therapy showed clear signs of angiogenesis and an increased rate of PA increase (p = 0.002). These responders had a significant and negative correlation between PA intensity and wound size. Hypertension was correlated to impaired angiogenesis in non-responsive patients. The rate of PA increase and hence the rate of angiogenesis was able to predict healing times within 30 days from the start of monitoring (power = 88%, alpha = 0.05). This early response detection system could help inform management and treatment strategies while improving outcomes and reducing costs.

Theoretical Paradigm for Thermal Rectification via Phonon Filtering and Spectral Confinement.

Significant thermal rectification has the potential to revolutionize approaches to controlled heat flow and enable breakthrough technologies such as phononic computing. We demonstrate a framework based on phonon population confinement and filtering that has potential to reach rectifications that are an order of magnitude larger than previous literature. With the use of a straightforward modification of the phonon gas model, we illustrate theoretical thermal rectification in a thin film of diamond (1-10 nm) graded to dimensions >1 µm of between 25% and 250%. Utilizing this mechanism for thermal rectification sets the stage for significant development in thermal devices.

Localizing genesis in polydomain liquid crystal elastomers.

Programming the local orientation of liquid crystal elastomers (LCEs) is a differentiated approach to prepare monolithic material compositions with localized deformation. Our prior efforts prepared LCEs with surface-enforced spatial variations in orientation to localize deformation when the LCEs were subjected to directional load. However, because these surface alignment methods included regions of planar orientation, the deformation of these programmed LCEs is inherently directional. The absence of macroscopic orientation in polydomain LCEs results in uniform, nonlinear deformation in all axes (omnidirectional soft elasticity). Here, we exploit the distinct mechanical response of polydomain LCEs prepared with isotropic or nematic genesis. By localizing the polydomain genesis via masked photopolymerizations conducted at different temperatures, we detail the preparation of main-chain, polydomain LCEs that are homogeneous in composition but exhibit spatially localized programmability in their mechanical response that is uniform in all directions.

Nanoscale Wetting and Energy Transmission at Solid/Liquid Interfaces.

Understanding the effects and limitations of solid/liquid interfaces on energy transport is crucial to applications ranging from nanoscale thermal engineering to chemical synthesis. Until now, the majority of experimental evidence regarding solid/liquid interactions has been limited to macroscale observations and experiments. The lack of experimental works exploring nanoscale solid/liquid interactions has been accentuated as the body of knowledge from theory and simulations at these scales has exploded in recent years. In this study, we expand on current nanoscale thermal measurement techniques in order to more fully understand solid/liquid interfacial energy transport. We use thermal ablation threshold measurements on thick Au films in various liquids as a metric to describe thermal transport at the Au/liquid interface. Furthermore, using ultrafast pump-probe experiments, we gain insight into this transport through picosecond ultrasonic coupling at solid/liquid interfaces with known macroscopic observations. We find significant variations in both the ablation threshold and the damping of the acoustic modes within the Au films depending on nanoscopic interactions at the solid/liquid interface rather than typical macroscale metrics such as acoustic mismatch, measured contact angle, and work of adhesion.

Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.

A series of DNA gyrase inhibitors were designed based on the X-ray structure of a parent thiophene scaffold with the objective to improve biochemical and whole-cell antibacterial activity, while reducing cardiac ion channel activity. The binding mode and overall design hypothesis of one series was confirmed with a co-crystal structure with DNA gyrase. Although some analogs retained both biochemical activity and whole-cell antibacterial activity, we were unable to significantly improve the activity of the series and analogs retained activity against the cardiac ion channels, therefore we stopped optimization efforts.

Mechanotropic Elastomers.

Liquid crystal elastomers (LCEs) are anisotropic polymeric materials. When subjected to an applied stress, liquid crystalline (LC) mesogens within the elastomeric polymer network (re)orient to the loading direction. The (re)orientation during deformation results in nonlinear stress-strain dependence (referred to as soft elasticity). Here, we uniquely explore mechanotropic phase transitions in elastomers with appreciable mesogenic content and compare these responses to LCEs in the polydomain orientation. The isotropic (amorphous) elastomers undergo significant directional orientation upon loading, evident in strong birefringence and x-ray diffraction. Functionally, the mechanotropic displacement of the elastomers to load is also nonlinear. However, unlike the analogous polydomain LCE compositions examined here, the isotropic elastomers rapidly recover after deformation. The mechanotropic orientation of the mesogens in these materials increase the toughness of these thiol-ene photopolymers by nearly 1300 % relative to a chemically similar elastomer prepared from wholly isotropic precursors.

Novel KV7 ion channel openers for the treatment of epilepsy and implications for detrusor tissue contraction.

Neuronal voltage-gated potassium channels, KV7s, are the molecular mediators of the M current and regulate membrane excitability in the central and peripheral neuronal systems. Herein, we report novel small molecule KV7 openers that demonstrate anti-seizure activities in electroshock and pentylenetetrazol-induced seizure models without influencing Rotarod readouts in mice. The anti-seizure activity was determined to be proportional to the unbound concentration in the brain. KV7 channels are also expressed in the bladder smooth muscle (detrusor) and activation of these channels may cause localized undesired effects. Therefore, the impact of individual KV7 isoforms was investigated in human detrusor tissue using a panel of KV7 openers with distinct activity profiles among KV7 isoforms. KCNQ4 and KCNQ5 mRNA were highly expressed in detrusor tissue, yet a compound that has significantly reduced activity on homomeric KV7.4 did not reduce detrusor contraction. This may suggest that the homomeric KV7.4 channel plays a less significant role in bladder contraction and further investigation is needed.

Revising the economic imperative for US STEM education.

Over the last decade macroeconomic studies have established a clear link between student achievement on science and math tests and per capita gross domestic product (GDP) growth, supporting the widely held belief that science, technology, engineering, and math(STEM) education are important factors in the production of economic prosperity. We critique studies that use science and math tests to predict GDP growth, arguing that estimates of the future economic value of STEM education involve substantial speculation because they ignore the impacts of economic growth on biodiversity and ecosystem functionality, which, in the long-term, limit the potential for future economic growth. Furthermore, we argue that such ecological impacts can be enabled by STEM education. Therefore, we contend that the real economic imperative for the STEM pipeline is not just raising standardized test scores, but also empowering students to assess, preserve, and restore ecosystems in order to reduce ecological degradation and increase economic welfare.

Dysprosium-doped cadmium oxide as a gateway material for mid-infrared plasmonics.

The interest in plasmonic technologies surrounds many emergent optoelectronic applications, such as plasmon lasers, transistors, sensors and information storage. Although plasmonic materials for ultraviolet-visible and near-infrared wavelengths have been found, the mid-infrared range remains a challenge to address: few known systems can achieve subwavelength optical confinement with low loss in this range. With a combination of experiments and ab initio modelling, here we demonstrate an extreme peak of electron mobility in Dy-doped CdO that is achieved through accurate 'defect equilibrium engineering'. In so doing, we create a tunable plasmon host that satisfies the criteria for mid-infrared spectrum plasmonics, and overcomes the losses seen in conventional plasmonic materials. In particular, extrinsic doping pins the CdO Fermi level above the conduction band minimum and it increases the formation energy of native oxygen vacancies, thus reducing their populations by several orders of magnitude. The substitutional lattice strain induced by Dy doping is sufficiently small, allowing mobility values around 500 cm(2) V(-1) s(-1) for carrier densities above 10(20) cm(-3). Our work shows that CdO:Dy is a model system for intrinsic and extrinsic manipulation of defects affecting electrical, optical and thermal properties, that oxide conductors are ideal candidates for plasmonic devices and that the defect engineering approach for property optimization is generally applicable to other conducting metal oxides.

Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing.

OBJECTIVE: Identification of a particular cause of meningoencephalitis can be challenging owing to the myriad bacteria, viruses, fungi, and parasites that can produce overlapping clinical phenotypes, frequently delaying diagnosis and therapy. Metagenomic deep sequencing (MDS) approaches to infectious disease diagnostics are known for their ability to identify unusual or novel viruses and thus are well suited for investigating possible etiologies of meningoencephalitis. METHODS: We present the case of a 74-year-old woman with endophthalmitis followed by meningoencephalitis. MDS of her cerebrospinal fluid (CSF) was performed to identify an infectious agent. RESULTS: Sequences aligning to Balamuthia mandrillaris ribosomal RNA genes were identified in the CSF by MDS. Polymerase chain reaction subsequently confirmed the presence of B. mandrillaris in CSF, brain tissue, and vitreous fluid from the patient's infected eye. B. mandrillaris serology and immunohistochemistry for free-living amoebas on the brain biopsy tissue were positive. INTERPRETATION: The diagnosis was made using MDS after the patient had been hospitalized for several weeks and subjected to costly and invasive testing. MDS is a powerful diagnostic tool with the potential for rapid and unbiased pathogen identification leading to early therapeutic targeting.

Humane genomics education can reduce racism.

Moving instruction "beyond Mendel" can counter inaccurate, essentialist views.

Sex and gender essentialism in textbooks.

Several widely used high school biology texts depart from established science.

Unveiling the proteome-wide autoreactome enables enhanced evaluation of emerging CAR T cell therapies in autoimmunity.

Given the global surge in autoimmune diseases, it is critical to evaluate emerging therapeutic interventions. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leveraged advances in programmable-phage immunoprecipitation methodology to explore the modulation, or lack thereof, of autoantibody profiles, proteome-wide, in both health and disease. Using a custom set of over 730,000 human-derived peptides, we demonstrated that each individual, regardless of disease state, possesses a distinct and complex constellation of autoreactive antibodies. For each individual, the set of resulting autoreactivites constituted a unique immunological fingerprint, or "autoreactome," that was remarkably stable over years. Using the autoreactome as a primary output, we evaluated the relative effectiveness of various immunomodulatory therapies in altering autoantibody repertoires. We found that therapies targeting B cell maturation antigen (BCMA) profoundly altered an individual's autoreactome, while anti-CD19 and anti-CD20 therapies had minimal effects. These data both confirm that the autoreactome comprises autoantibodies secreted by plasma cells and strongly suggest that BCMA or other plasma cell-targeting therapies may be highly effective in treating currently refractory autoantibody-mediated diseases.

Motor Competence Among Irish Adolescents: An Investigation of Sex Differences and Relatedness Between Fundamental Movement Skills and Functional Movement.

In prior research, Irish youth displayed poor motor competence across fundamental movement skills (FMS) and functional movements (FM). Our purpose in this study was to compare FMS and FM across male and female Irish adolescents and to determine whether there are associations between these movement domains. We collected data on 373 adolescents (178 females; M age = 14.38, SD = 0.87 years) from six Irish secondary schools, including motor competence testing of 10 FMS, and 7 FM. Overall levels of motor competence of both FMS and FM were low, and certain levels of dysfunctional movement were high. We observed significant sex-based differences in both FMS and FM, and there was a moderate association between FMS and FM that warrants further investigation. There is a need for societal intervention and policy changes to address low levels of motor competence among adolescent youth.

Identification of a small molecule for enhancing lentiviral transduction of T cells.

Genetic modification of cells using viral vectors has shown huge therapeutic benefit in multiple diseases. However, inefficient transduction contributes to the high cost of these therapies. Several transduction-enhancing small molecules have previously been identified; however, some may be toxic to the cells or patient, otherwise alter cellular characteristics, or further increase manufacturing complexity. In this study, we aimed to identify molecules capable of enhancing lentiviral transduction of T cells from available small-molecule libraries. We conducted a high-throughput flow-cytometry-based screen of 27,892 compounds, which subsequently was narrowed down to six transduction-enhancing small molecules for further testing with two therapeutic lentiviral vectors used to manufacture GSK's clinical T cell therapy products. We demonstrate enhanced transduction without a negative impact on other product attributes. Furthermore, we present results of transcriptomic analysis, suggesting alteration of ribosome biogenesis, resulting in reduced interferon response, as a potential mechanism of action for the transduction-enhancing activity of the lead compound. Finally, we demonstrate the ability of the lead transduction enhancer to produce a comparable T cell product using a 3-fold reduction in vector volume in our clinical manufacturing process, resulting in a predicted 15% reduction in the overall cost of goods.

Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy.

The prevalence and burden of autoimmune and autoantibody mediated disease is increasing worldwide, yet most disease etiologies remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in programmable-phage immunoprecipitation (PhIP-Seq) methodology to explore the modulation, or lack thereof, of proteome-wide autoantibody profiles in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or "autoreactome", that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual's autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.