Sequence-Directed Covalent Protein-RNA Linkages in a Single Step Using Engineered HUH-Tags.

Replication-initiating HUH-endonucleases (Reps) are enzymes that form covalent bonds with single-stranded DNA (ssDNA) in a sequence specific manner to initiate rolling circle replication. These nucleases have been co-opted for use in biotechnology as sequence specific protein-ssDNA bioconjugation fusion partners dubbed 'HUH-tags'. Here, we describe the engineering and in vitro characterization of a series of laboratory evolved HUH-tags capable of forming robust sequence-directed covalent bonds with unmodified RNA substrates. We show that promiscuous Rep-RNA interaction can be enhanced through directed evolution from nearly undetectable levels in wildtype enzymes to robust reactivity in final engineered iterations. Taken together, these engineered HUH-tags represent a promising platform for enabling site-specific protein-RNA covalent bioconjugation in vitro, potentially mediating a host of new applications and offering a valuable addition to the HUH-tag repertoire.

ReCorDE: a framework for identifying drug classes targeting shared vulnerabilities with applications to synergistic drug discovery.

Cancer is typically treated with combinatorial therapy, and such combinations may be synergistic. However, discovery of these combinations has proven difficult as brute force combinatorial screening approaches are both logistically complex and resource-intensive. Therefore, computational approaches to augment synergistic drug discovery are of interest, but current approaches are limited by their dependencies on combinatorial drug screening training data or molecular profiling data. These dataset dependencies can limit the number and diversity of drugs for which these approaches can make inferences. Herein, we describe a novel computational framework, ReCorDE (Recurrent Correlation of Drugs with Enrichment), that uses publicly-available cell line-derived monotherapy cytotoxicity datasets to identify drug classes targeting shared vulnerabilities across multiple cancer lineages; and we show how these inferences can be used to augment synergistic drug combination discovery. Additionally, we demonstrate in preclinical models that a drug class combination predicted by ReCorDE to target shared vulnerabilities (PARP inhibitors and Aurora kinase inhibitors) exhibits class-class synergy across lineages. ReCorDE functions independently of combinatorial drug screening and molecular profiling data, using only extensive monotherapy cytotoxicity datasets as its input. This allows ReCorDE to make robust inferences for a large, diverse array of drugs. In conclusion, we have described a novel framework for the identification of drug classes targeting shared vulnerabilities using monotherapy cytotoxicity datasets, and we showed how these inferences can be used to aid discovery of novel synergistic drug combinations.

Lestaurtinib's antineoplastic activity converges on JAK/STAT signaling to inhibit advanced forms of therapy resistant ovarian cancer.

Ovarian cancer is the deadliest gynecological malignancy, owing to its late-stage diagnosis and high rates of recurrence and resistance following standard-of-care treatment, highlighting the need for novel treatment approaches. Through an unbiased drug screen, we identified the kinase inhibitor, lestaurtinib, as a potent antineoplastic agent for chemotherapy- and PARP-inhibitor (PARPi)-sensitive and -resistant ovarian cancer cells and patient derived xenografts (PDXs). RNA-sequencing revealed that lestaurtinib potently suppressed JAK/STAT signaling and lestaurtinib efficacy was shown to be directly related to JAK/STAT pathway activity in cell lines and PDX models. Most ovarian cancer cells exhibited constitutive JAK/STAT pathway activation and genetic loss of STAT1 and STAT3 resulted in growth inhibition. Lestaurtinib also displayed synergy when combined with cisplatin and olaparib, including in a model of PARPi resistance. In contrast, the most well-known JAK/STAT inhibitor, ruxolitinib, lacked antineoplastic activity against all ovarian cancer cell lines and PDX models tested. This divergent behavior was reflected in the ability of lestaurtinib to block both Y701/705 and S727 phosphorylation of STAT1 and STAT3, whereas ruxolitinib failed to block S727. Consistent with these findings, lestaurtinib additionally inhibited JNK and ERK activity, leading to more complete suppression of STAT phosphorylation. Concordantly, combinatorial treatment with ruxolitinib and a JNK or ERK inhibitor resulted in synergistic antineoplastic effects at dose levels where single agents were ineffective. Taken together, these findings indicate that lestaurtinib, and other treatments that converge on JAK/STAT signaling, are worthy of further pre-clinical and clinical exploration for the treatment of highly aggressive and advanced forms of ovarian cancer. Statement of significance: Lestaurtinib is a novel inhibitor of ovarian cancer, including chemotherapy- and PARPi-resistant models, that acts through robust inhibition of the JAK/STAT pathway and synergizes with standard-of-care agents at clinically relevant concentrations.

Hydrogen Sulfide Delivery to Enhance Bone Tissue Engineering Cell Survival.

Though crucial for natural bone healing, local calcium ion (Ca2+) and phosphate ion (Pi) concentrations can exceed the cytotoxic limit leading to mitochondrial overload, oxidative stress, and cell death. For bone tissue engineering applications, H2S can be employed as a cytoprotective molecule to enhance mesenchymal stem cell (MSC) tolerance to cytotoxic Ca2+/Pi concentrations. Varied concentrations of sodium hydrogen sulfide (NaSH), a fast-releasing H2S donor, were applied to assess the influence of H2S on MSC proliferation. The results suggested a toxicity limit of 4 mM for NaSH and that 1 mM of NaSH could improve cell proliferation and differentiation in the presence of cytotoxic levels of Ca2+ (32 mM) and/or Pi (16 mM). To controllably deliver H2S over time, a novel donor molecule (thioglutamic acid-GluSH) was synthesized and evaluated for its H2S release profile. Excitingly, GluSH successfully maintained cytoprotective level of H2S over 7 days. Furthermore, MSCs exposed to cytotoxic Ca2+/Pi concentrations in the presence of GluSH were able to thrive and differentiate into osteoblasts. These findings suggest that the incorporation of a sustained H2S donor such as GluSH into CaP-based bone graft substitutes can facilitate considerable cytoprotection, making it an attractive option for complex bone regenerative engineering applications.

Unification of Road Scene Segmentation Strategies Using Multistream Data and Latent Space Attention.

Road scene understanding, as a field of research, has attracted increasing attention in recent years. The development of road scene understanding capabilities that are applicable to real-world road scenarios has seen numerous complications. This has largely been due to the cost and complexity of achieving human-level scene understanding, at which successful segmentation of road scene elements can be achieved with a mean intersection over union score close to 1.0. There is a need for more of a unified approach to road scene segmentation for use in self-driving systems. Previous works have demonstrated how deep learning methods can be combined to improve the segmentation and perception performance of road scene understanding systems. This paper proposes a novel segmentation system that uses fully connected networks, attention mechanisms, and multiple-input data stream fusion to improve segmentation performance. Results show comparable performance compared to previous works, with a mean intersection over union of 87.4% on the Cityscapes dataset.

Substituent Effects on Torsional Strain in Cyclopentene Derivatives: A Computational Study.

Density functional theory calculations were used to create a library of ring strain energies (RSEs) for 73 cyclopentene derivatives with potential use as monomers for ring-opening metathesis polymerization (ROMP). An overarching goal was to probe how substituent choice may influence torsional strain, which is the driving force for ROMP and one of the most understudied types of RSEs. Potential trends investigated include substituent location, size, electronegativity, hybridization, and steric bulk. Using traditional and recently developed homodesmotic equations, our results show that the size and substitution (bulk) of the atom directly bonded to the ring have the greatest influence on torsional RSE. A complex interplay between bond length, bond angle, and dihedral angle dictates the relative eclipsed conformations between the substituent and its neighboring hydrogens and was found to be responsible for the notable differences in RSEs. Furthermore, substituents placed on the homoallylic position resulted in higher RSEs than the same substituent placed on the allylic position due to increased eclipsing interactions. Different levels of theory were also assessed, and it was determined that consideration of electron correlation in calculations increased RSEs by ∼2-5 kcal mol-1. Further increasing the level of theory did not significantly change RSEs, indicating that the increased computational cost and time may not be necessary for improved accuracy.

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases.

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair's identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps. IMPORTANCE Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses are a ubiquitous group of viruses that infect organisms across all domains of life. These viruses negatively impact both agriculture and human health. All members of this viral family employ a multifunctional nuclease (Rep) to initiate replication. Reps are structurally similar throughout this family, making them targets of interest for viral inhibition strategies. Here, we investigate the functional dependencies of the Rep protein from Muscovy duck circovirus for ssDNA interaction. We demonstrate that this Rep requires an intramolecular Watson-Crick base pairing for origin of replication (Ori) recognition and interaction. We show that noncognate base pair swaps are well tolerated, highlighting a local structural specificity over sequence specificity. Bioinformatic analysis found that the vast majority of CRESS-DNA Oris form base pairs in conserved positions, suggesting this pairing is a universal requirement for replication initiation in the CRESS-DNA virus family.

Expanded [23]-Helicene with Exceptional Chiroptical Properties via an Iterative Ring-Fusion Strategy.

Expanded helicenes are an emerging class of helical nanocarbons composed of alternating linear and angularly fused rings, which give rise to an internal cavity and a large diameter. The latter is expected to impart exceptional chiroptical properties, but low enantiomerization free energy barriers (ΔG‡e) have largely precluded experimental interrogation of this prediction. Here, we report the syntheses of expanded helicenes containing 15, 19, and 23 rings on the inner helical circuit, using two iterations of an Ir-catalyzed, site-selective [2 + 2 + 2] reaction. This series of compounds displays a linear relationship between the number of rings and ΔG‡e. The expanded [23]-helicene, which is 7 rings longer than any known single carbohelicene and among the longest known all-carbon ladder oligomers, exhibits a ΔG‡e that is high enough (29.2 ± 0.1 kcal/mol at 100 °C in o-DCB) to halt enantiomerization at ambient temperature. This enabled the isolation of enantiopure samples displaying circular dichroism dissymmetry factors of ±0.056 at 428 nm, which are ≥1.7× larger than values for previously reported classical and expanded helicenes. Computational investigations suggest that this improved performance is the result of both the increased diameter and length of the [23]-helicene, providing guiding design principles for high dissymmetry molecular materials.

Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology.

BACKGROUND: Cellular immune memory responses post coronavirus disease 2019 (COVID-19) have been difficult to assess due to the risks of contaminating the immune response readout with memory responses stemming from previous exposure to endemic coronaviruses. The work herein presents a large-scale long-term follow-up study investigating the correlation between symptomology and cellular immune responses four to five months post seroconversion based on a unique severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific peptide pool that contains no overlapping peptides with endemic human coronaviruses. METHODS: Peptide stimulated memory T cell responses were assessed with dual interferon-gamma (IFNγ) and interleukin (IL)-2 Fluorospot. Serological analyses were performed using a multiplex antigen bead array. RESULTS: Our work demonstrates that long-term SARS-CoV-2-specific memory T cell responses feature dual IFNγ and IL-2 responses, whereas cross-reactive memory T cell responses primarily generate IFNγ in response to SARS-CoV-2 peptide stimulation. T cell responses correlated to long-term humoral immune responses. Disease severity as well as specific COVID-19 symptoms correlated with the magnitude of the SARS-CoV-2-specific memory T cell response four to five months post seroconversion. CONCLUSION: Using a large cohort and a SARS-CoV-2-specific peptide pool we were able to substantiate that initial disease severity and symptoms correlate with the magnitude of the SARS-CoV-2-specific memory T cell responses.

Zwitterions Raise the Dielectric Constant of Soft Materials.

Materials exhibiting high dielectric constants (ϵ_{s}) are critical for energy storage and actuators. A successful approach to increase ϵ_{s} is to incorporate polar additives (with high ϵ_{s}) but controlling the resulting dispersion state is difficult. Here, we show that significant ϵ_{s} increases are realized by adding zwitterions, which are small molecules with a cation and an anion separated by covalent bonds. The increase in ϵ_{s} with zwitterion addition is attributed to the large molecular dipole of zwitterions, ranging from 35 to 41 D, as experimentally quantified and confirmed using density functional theory. At elevated zwitterion concentration in an ethylene glycol medium, there is a nonlinear increase of ϵ_{s} that eventually saturates due to the strong Coulombic interactions between zwitterions. The presented work provides a fundamental molecular understanding of why zwitterions are effective additives in boosting ϵ_{s} in soft materials.

Operationalising the "One Health" approach in India: facilitators of and barriers to effective cross-sector convergence for zoonoses prevention and control.

BACKGROUND: There is a strong policy impetus for the One Health cross-sectoral approach to address the complex challenge of zoonotic diseases, particularly in low/lower middle income countries (LMICs). Yet the implementation of this approach in LMIC contexts such as India has proven challenging, due partly to the relatively limited practical guidance and understanding on how to foster and sustain cross-sector collaborations. This study addresses this gap by exploring the facilitators of and barriers to successful convergence between the human, animal and environmental health sectors in India. METHODS: A mixed methods study was conducted using a detailed content review of national policy documents and in-depth semi-structured interview data on zoonotic disease management in India. In total, 29 policy documents were reviewed and 15 key informant interviews were undertaken with national and state level policymakers, disease managers and experts operating within the human-animal-environment interface of zoonotic disease control. RESULTS: Our findings suggest that there is limited policy visibility of zoonotic diseases, although global zoonoses, especially those identified to be of pandemic potential by international organisations (e.g. CDC, WHO and OIE) rather than local, high burden endemic diseases, have high recognition in the existing policy agenda setting. Despite the widespread acknowledgement of the importance of cross-sectoral collaboration, a myriad of factors operated to either constrain or facilitate the success of cross-sectoral convergence at different stages (i.e. information-sharing, undertaking common activities and merging resources and infrastructure) of cross-sectoral action. Importantly, participants identified the lack of supportive policies, conflicting departmental priorities and limited institutional capacities as major barriers that hamper effective cross-sectoral collaboration on zoonotic disease control. Building on existing informal inter-personal relationships and collaboration platforms were suggested by participants as the way forward. CONCLUSION: Our findings point to the importance of strengthening existing national policy frameworks as a first step for leveraging cross-sectoral capacity for improved disease surveillance and interventions. This requires the contextual adaptation of the One Health approach in a manner that is sensitive to the underlying socio-political, institutional and cultural context that determines and shapes outcomes of cross-sector collaborative arrangements.

The technologically-mediated self: reflections on the container and field of telecommunications.

This paper contains reflections on the use of the imagination in technologically-mediated therapy and analysis. As part of the individuation process the psyche is seen as needing to adapt to new technological ways of communicating. The notion of a technologically-mediated self is posited describing a self which can only be apprehended through, and by, the use of telecommunications. This self is seen as identical to the in-person self, a subset, or superset of it. There is a revisioning of our notions of the container and the field in this work performed through technological-mediation. The need to engage the imagination in approaching this kind of work is emphasized in order to create an imaginal play-space in which the body will be deeply affected. Some thoughts on how the process of individuation might look through such analytic work is presented.

Cet article contient des réflexions sur l'utilisation de l'imagination dans la thérapie et l'analyse pratiquées par la médiation de la technologie. En tant que partie intégrante du processus d'individuation, la psyché est considérée comme devant s'adapter à de nouvelles façons de communiquer, basées sur la technologie. La notion d'un soi atteint par la médiation de la technologie est postulée, un soi qui ne peut être appréhendé que par le biais de l'utilisation des télécommunications. Ce soi est considéré comme étant identique au soi dans la personne; un sous-ensemble, ou un sur-ensemble. L'article présente une révision de nos notions de contenant et de champ quand on travaille avec la médiation de la technologie. Il souligne le besoin de mobiliser l'imagination quand on aborde ce genre de travail afin de créer un espace imaginal de jeu dans lequel le corps sera profondément affecté. Il propose quelques pensées sur comment le processus d'individuation pourrait se présenter au travers d'un tel travail analytique.

El presente trabajo contiene reflexiones sobre el uso de la imaginación en terapia y análisis mediado por la tecnología. Como parte del proceso de individuación, la psique necesita adaptarse a nuevos modos tecnológicos de comunicación. Se propone la noción de un self mediado-tecnológicamente, al describir a un self que solamente puede ser aprehendido a través y por el uso de las telecomunicaciones. Este self es considerado como idéntico al self presencial, una parte o una versión mayor del mismo. Se presenta una revisión de nuestras nociones acerca del campo y del espacio de contención en este trabajo realizado a través de la mediación tecnológica. Se enfatiza la necesidad de comprometer a la imaginación al abordar esta forma de trabajo, para crear un espacio de juego-imaginal, en el cual el cuerpo estará profundamente afectado. Se presentan algunas reflexiones acerca de cómo podría mirarse el proceso de individuación a través de dicho trabajo.

Resistance to venetoclax and hypomethylating agents in acute myeloid leukemia.

Despite the success of the combination of venetoclax with the hypomethylating agents (HMA) decitabine or azacitidine in inducing remission in older, previously untreated patients with acute myeloid leukemia (AML), resistance - primary or secondary - still constitutes a significant roadblock in the quest to prolong the duration of response. Here we review the proposed and proven mechanisms of resistance to venetoclax monotherapy, HMA monotherapy, and the doublet of venetoclax and HMA for the treatment of AML. We approach the mechanisms of resistance to HMAs and venetoclax in the light of the agents' mechanisms of action. We briefly describe potential therapeutic strategies to circumvent resistance to this promising combination, including alternative scheduling or the addition of other agents to the HMA and venetoclax backbone. Understanding the mechanisms of action and evolving resistance in AML remains a priority in order to maximize the benefit from novel drugs and combinations, identify new therapeutic targets, define potential prognostic markers, and avoid treatment failure.

A 62-year-old man with new-onset bullae.

Cutaneous blisters and/or bullae can occur in autoimmune disorders, infections, genetic diseases, and drug hypersensitivity. We present the case of a 62-year-old man with two autoimmune conditions who was admitted for antibiotic treatment of a lower extremity infection and suddenly developed a bullous rash. His physical examination was significant for tense, bullous lesions that involved his chin, palms, and inner thighs. Narrowing the differential diagnosis for patients with blistering skin lesions is imperative for timely and appropriate management.

What is a Jungian analyst dreaming when myth comes to mind? Thirdness as an aspect of the anima media natura.

Listening analytically is not listening just to what is said but listening to what is just below the surface waiting to be said. This paper looks at Jung's insight into a 'third thing' being created intra-psychically and within the analytic encounter. Ogden's concept of an 'analytic third' is used to describe the clinical aspects of this thirdness. This paper explores: how the state of thirdness is created and accessed through use of reverie and associative dreaming; how the material emerging from it is used in a from or about manner; and the eventual fate of the third in a successful analysis by a reexamination of plates four and ten of the Rosarium. The focus is particularly on the awareness and possible meanings of mythological motifs appearing in the mind of the analyst while in session. Thirdness can be viewed as the interpersonal aspect of the anima media natura and functions in a way that informs us of permeability in and between individuals, while the operation of the anima mundi means that there is always an inseparability of the individual with the world.

An in situ toxicity identification and evaluation water analysis system: Laboratory validation.

It is difficult to assess the toxicity of a single stressor and establish a strong stressor-causality link when multiple stressors coexist. Toxicity identification evaluation (TIE) methodology uses a series of chemical and physical manipulations to fractionate compounds within a matrix and systematically identify potential toxicants. The current US Environmental Protection Agency application of TIE can provide valuable information but often lacks ecological realism and is subject to laboratory-related artifacts. An in situ TIE device (iTIED) was designed to assess the sources of toxicity in aquatic ecosystems. For this laboratory validation, each unit was equipped with a sorbent resin chamber, an organism exposure chamber, a water collection container, and a peristaltic pump. Chemical analyses of water processed by each iTIED unit were compared with both lethal and sublethal molecular responses of the organisms. The compound removal effectiveness of different sorbent resins was also compared. In addition to successfully fractionating diverse chemical mixtures, the iTIED demonstrated a potential for early detection of molecular biomarkers, which could identify chronic toxicity that may go unnoticed in traditional TIE assays. Utilizing this novel in situ system will reduce the uncertainty associated with laboratory-based simulations and aid management efforts in targeting compounds that pose the greatest threat. Environ Toxicol Chem 2017;36:1636-1643. © 2016 SETAC.

Analysis of viral diversity for vaccine target discovery.

BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis. CONCLUSION: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

g-FLUA2H: a web-based application to study the dynamics of animal-to-human mutation transmission for influenza viruses.

g-FLUA2H is a web-based application focused on the analysis of the dynamics of influenza virus animal-to-human (A2H) mutation transmissions. The application only requires the viral protein sequences from both the animal and human host populations as input datasets. The comparative analyses between the co-aligned sequences of the two viral populations is based on a sliding window approach of size nine for statistical significance and data application to the major histocompatibility complex (MHC) and T-cell receptor (TCR) immune response mechanisms. The sequences at each of the aligned overlapping nonamer positions for the respective virus hosts are classified as four patterns of characteristic diversity motifs, as a basis for quantitative analyses: (i) "index", the most prevalent sequence; (ii) "major" variant, the second most common sequence and the single most prevalent variant of the index, with at least one amino acid mutation; (iii) "minor" variants, multiple different sequences, each with an incidence (percent occurrence) less than that of the major variant; and (iv) "unique" variants, each with only one occurrence in the alignment. The diversity motifs and their incidences at each of the nonamer positions allow evaluation of the mutation transmission dynamics and selectivity of the viral sequences in relation to the animal and the human hosts. g-FLUA2H is facilitated by a grid back-end for parallel processing of large sequence datasets. The web-application is publicly available at http://bioinfo.perdanauniversity.edu.my/g-FLUA2H. It can be used for a detailed characterization of the composition and incidence of mutations present in the proteomes of influenza viruses from animal and human host populations, for a better understanding of host tropism.