Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci.

Current approaches for inserting autonomous transgenes into the genome, such as CRISPR-Cas9 or virus-based strategies, have limitations including low efficiency and high risk of untargeted genome mutagenesis. Here, we describe precise RNA-mediated insertion of transgenes (PRINT), an approach for site-specifically primed reverse transcription that directs transgene synthesis directly into the genome at a multicopy safe-harbor locus. PRINT uses delivery of two in vitro transcribed RNAs: messenger RNA encoding avian R2 retroelement-protein and template RNA encoding a transgene of length validated up to 4 kb. The R2 protein coordinately recognizes the target site, nicks one strand at a precise location and primes complementary DNA synthesis for stable transgene insertion. With a cultured human primary cell line, over 50% of cells can gain several 2 kb transgenes, of which more than 50% are full-length. PRINT advantages include no extragenomic DNA, limiting risk of deleterious mutagenesis and innate immune responses, and the relatively low cost, rapid production and scalability of RNA-only delivery.

Detecting residents at risk of attrition - A Singapore pathology residency's experience.

The SingHealth Pathology Residency Program (SHPRP) is a 5-year postgraduate training program in Singapore. We face the problem of resident attrition, which has a significant impact on the individual, program and healthcare providers. Our residents are regularly evaluated, using in-house evaluations as well as assessments required in our partnership with the Accreditation Council for Graduate Medical Education International (ACGME-I). We hence sought to determine if these assessments were able to distinguish residents who would attrite from residents who would graduate successfully. Retrospective analysis of existing residency assessments was performed on all residents who have separated from SHPRP and compared with residents currently in senior residency or graduated from the program. Statistical analysis was performed on quantitative assessment methods of Resident In-Service Examination (RISE), 360-degree feedback, faculty assessment, Milestones and our own annual departmental mock examination. Word frequency analysis of narrative feedback from faculty assessment was used to generate themes. Since 2011, 10 out of 34 residents have separated from the program. RISE, Milestone data and the departmental mock examination showed statistical significance in discriminating residents at risk of attrition for specialty-related reasons from successful residents. Analysis of narrative feedback showed that successful residents performed better in areas of organization, preparation with clinical history, application of knowledge, interpersonal communication and achieving sustained progress. Existing assessment methods used in our pathology residency program are effective in detecting residents at risk of attrition. This also suggests applications in the way that we select, assess and teach residents.

The Lateral Epidermis Actively Counteracts Pulling by the Amnioserosa During Dorsal Closure.

Dorsal closure is a prominent morphogenetic process during Drosophila embryogenesis, which involves two epithelial tissues, that is, the squamous amnioserosa and the columnar lateral epidermis. Non-muscle myosin II-driven constriction in the amnioserosa leads to a decrease in the apical surface area and pulls on the adjacent lateral epidermis, which subsequently moves dorsally. The pull by the amnioserosa becomes obvious in an elongation of the epidermal cells, especially of those in the first row. The contribution of the epidermal cell elongation has remained unclear to dorsal closure. Cell elongation may be a mere passive consequence or an active response to the pulling by the amnioserosa. Here, we found that the lateral epidermis actively responds. We analyzed tensions within tissues and cell junctions by laser ablation before and during dorsal closure, the elliptical and dorsal closure stages, respectively. Furthermore, we genetically and optochemically induced chronic and acute cell contraction, respectively. In this way, we found that tension in the epidermis increased during dorsal closure. A correspondingly increased tension was not observed at individual junctions, however. Junctional tension even decreased during dorsal closure in the epidermis. We strikingly observed a strong increase of the microtubule amount in the epidermis, while non-muscle myosin II increased in both tissues. Our data suggest that the epidermis actively antagonizes the pull from the amnioserosa during dorsal closure and the increased microtubules might help the epidermis bear part of the mechanical force.

Absence of pure voltage instabilities in the third-order model of power grid dynamics.

Secure operation of electric power grids fundamentally relies on their dynamical stability properties. For the third-order model, a paradigmatic model that captures voltage dynamics, three routes to instability are established in the literature: a pure rotor angle instability, a pure voltage instability, and one instability induced by the interplay of both. Here, we demonstrate that one of these routes, the pure voltage instability, requires infinite voltage amplitudes and is, thus, nonphysical. We show that voltage collapse dynamics nevertheless exist in the absence of any voltage instabilities.

Observational study on wearable biosensors and machine learning-based remote monitoring of COVID-19 patients.

Patients infected with SARS-CoV-2 may deteriorate rapidly and therefore continuous monitoring is necessary. We conducted an observational study involving patients with mild COVID-19 to explore the potentials of wearable biosensors and machine learning-based analysis of physiology parameters to detect clinical deterioration. Thirty-four patients (median age: 32 years; male: 52.9%) with mild COVID-19 from Queen Mary Hospital were recruited. The mean National Early Warning Score 2 (NEWS2) were 0.59 ± 0.7. 1231 manual measurement of physiology parameters were performed during hospital stay (median 15 days). Physiology parameters obtained from wearable biosensors correlated well with manual measurement including pulse rate (r = 0.96, p < 0.0001) and oxygen saturation (r = 0.87, p < 0.0001). A machine learning-derived index reflecting overall health status, Biovitals Index (BI), was generated by autonomous analysis of physiology parameters, symptoms, and other medical data. Daily BI was linearly associated with respiratory tract viral load (p < 0.0001) and NEWS2 (r = 0.75, p < 0.001). BI was superior to NEWS2 in predicting clinical worsening events (sensitivity 94.1% and specificity 88.9%) and prolonged hospitalization (sensitivity 66.7% and specificity 72.7%). Wearable biosensors coupled with machine learning-derived health index allowed automated detection of clinical deterioration.

Topological Determinants of Perturbation Spreading in Networks.

Spreading phenomena essentially underlie the dynamics of various natural and technological networked systems, yet how spatiotemporal propagation patterns emerge from such networks remains largely unknown. Here we propose a novel approach that reveals universal features determining the spreading dynamics in diffusively coupled networks and disentangles them from factors that are system specific. In particular, we first analytically identify a purely topological factor encoding the interaction structure and strength, and second, numerically estimate a master function characterizing the universal scaling of the perturbation arrival times across topologically different networks. The proposed approach thereby provides intuitive insights into complex propagation patterns as well as accurate predictions for the perturbation arrival times. The approach readily generalizes to a wide range of networked systems with diffusive couplings and may contribute to assess the risks of transient influences of ubiquitous perturbations in real-world systems.

Telomere length set point regulation in human pluripotent stem cells critically depends on the shelterin protein TPP1.

Telomere maintenance is essential for the long-term proliferation of human pluripotent stem cells, while their telomere length set point determines the proliferative capacity of their differentiated progeny. The shelterin protein TPP1 is required for telomere stability and elongation, but its role in establishing a telomere length set point remains elusive. Here, we characterize the contribution of the shorter isoform of TPP1 (TPP1S) and the amino acid L104 outside the TEL patch, TPP1's telomerase interaction domain, to telomere length control. We demonstrate that cells deficient for TPP1S (TPP1S knockout [KO]), as well as the complete TPP1 KO cell lines, undergo telomere shortening. However, TPP1S KO cells are able to stabilize short telomeres, while TPP1 KO cells die. We compare these phenotypes with those of TPP1L104A/L104A mutant cells, which have short and stable telomeres similar to the TPP1S KO. In contrast to TPP1S KO cells, TPP1L104A/L104A cells respond to increased telomerase levels and maintain protected telomeres. However, TPP1L104A/L104A shows altered sensitivity to expression changes of shelterin proteins suggesting the mutation causes a defect in telomere length feedback regulation. Together this highlights TPP1L104A/L104A as the first shelterin mutant engineered at the endogenous locus of human stem cells with an altered telomere length set point.

Vulnerability in dynamically driven oscillatory networks and power grids.

Vulnerability of networks has so far been quantified mainly for structural properties. In driven systems, however, vulnerability intrinsically relies on the collective response dynamics. As shown recently, dynamic response patterns emerging in driven oscillator networks and AC power grid models are highly heterogeneous and nontrivial, depending jointly on the driving frequency, the interaction topology of the network, and the node or nodes driven. Identifying which nodes are most susceptible to dynamic driving and may thus make the system as a whole vulnerable to external input signals, however, remains a challenge. Here, we propose an easy-to-compute Dynamic Vulnerability Index (DVI) for identifying those nodes that exhibit largest amplitude responses to dynamic driving signals with given power spectra and thus are most vulnerable. The DVI is based on linear response theory, as such generic, and enables robust predictions. It thus shows potential for a wide range of applications across dynamically driven networks, for instance, for identifying the vulnerable nodes in power grids driven by fluctuating inputs from renewable energy sources and fluctuating power output to consumers.

The Emergent Yo-yo Movement of Nuclei Driven by Cytoskeletal Remodeling in Pseudo-synchronous Mitotic Cycles.

Many aspects in tissue morphogenesis are attributed to a collective behavior of the participating cells. Yet, the mechanism for emergence of dynamic tissue behavior is not well understood. Here, we report that the "yo-yo"-like nuclear movement in the Drosophila syncytial embryo displays emergent features indicative of collective behavior. Following mitosis, the array of nuclei moves away from the wave front by several nuclear diameters only to return to its starting position about 5 min later. Based on experimental manipulations and numerical simulations, we find that the ensemble of elongating and isotropically oriented spindles, rather than individual spindles, is the main driving force for anisotropic nuclear movement. ELMO-dependent F-actin restricts the time for the forward movement and ELMO- and dia-dependent F-actin is essential for the return movement. Our study provides insights into how the interactions among the cytoskeleton as individual elements lead to collective movement of the nuclear array on a macroscopic scale.

Fluctuation-induced distributed resonances in oscillatory networks.

Across physics, biology, and engineering, the collective dynamics of oscillatory networks often evolve into self-organized operating states. How such networks respond to external fluctuating signals fundamentally underlies their function, yet is not well understood. Here, we present a theory of dynamic network response patterns and reveal how distributed resonance patterns emerge in oscillatory networks once the dynamics of the oscillatory units become more than one-dimensional. The network resonances are topology specific and emerge at an intermediate frequency content of the input signals, between global yet homogeneous responses at low frequencies and localized responses at high frequencies. Our analysis reveals why these patterns arise and where in the network they are most prominent. These results may thus provide general theoretical insights into how fluctuating signals induce response patterns in networked systems and simultaneously help to develop practical guiding principles for real-world network design and control.

Quantifying transient spreading dynamics on networks.

Spreading phenomena on networks are essential for the collective dynamics of various natural and technological systems, from information spreading in gene regulatory networks to neural circuits and from epidemics to supply networks experiencing perturbations. Still, how local disturbances spread across networks is not yet quantitatively understood. Here, we analyze generic spreading dynamics in deterministic network dynamical systems close to a given operating point. Standard dynamical systems' theory does not explicitly provide measures for arrival times and amplitudes of a transient spreading signal because it focuses on invariant sets, invariant measures, and other quantities less relevant for transient behavior. We here change the perspective and introduce formal expectation values for deterministic dynamics to work out a theory explicitly quantifying when and how strongly a perturbation initiated at one unit of a network impacts any other. The theory provides explicit timing and amplitude information as a function of the relative position of initially perturbed and responding unit as well as depending on the entire network topology.

Escape routes, weak links, and desynchronization in fluctuation-driven networks.

Shifting our electricity generation from fossil fuel to renewable energy sources introduces large fluctuations to the power system. Here, we demonstrate how increased fluctuations, reduced damping, and reduced intertia may undermine the dynamical robustness of power grid networks. Focusing on fundamental noise models, we derive analytic insights into which factors limit the dynamic robustness and how fluctuations may induce a system escape from an operating state. Moreover, we identify weak links in the grid that make it particularly vulnerable to fluctuations. These results thereby not only contribute to a theoretical understanding of how fluctuations act on distributed network dynamics, they may also help designing future renewable energy systems to be more robust.

Network susceptibilities: Theory and applications.

We introduce the concept of network susceptibilities quantifying the response of the collective dynamics of a network to small parameter changes. We distinguish two types of susceptibilities: vertex susceptibilities and edge susceptibilities, measuring the responses due to changes in the properties of units and their interactions, respectively. We derive explicit forms of network susceptibilities for oscillator networks close to steady states and offer example applications for Kuramoto-type phase-oscillator models, power grid models, and generic flow models. Focusing on the role of the network topology implies that these ideas can be easily generalized to other types of networks, in particular those characterizing flow, transport, or spreading phenomena. The concept of network susceptibilities is broadly applicable and may straightforwardly be transferred to all settings where networks responses of the collective dynamics to topological changes are essential.

Endogenous Telomerase Reverse Transcriptase N-Terminal Tagging Affects Human Telomerase Function at Telomeres In Vivo.

Telomerase action at telomeres is essential for the immortal phenotype of stem cells and the aberrant proliferative potential of cancer cells. Insufficient telomere maintenance can cause stem cell and tissue failure syndromes, while increased telomerase levels are associated with tumorigenesis. Both pathologies can arise from only small perturbation of telomerase function. To analyze telomerase at its low endogenous expression level, we genetically engineered human pluripotent stem cells (hPSCs) to express various N-terminal fusion proteins of the telomerase reverse transcriptase from its endogenous locus. Using this approach, we found that these modifications can perturb telomerase function in hPSCs and cancer cells, resulting in telomere length defects. Biochemical analysis suggests that this defect is multileveled, including changes in expression and activity. These findings highlight the unknown complexity of telomerase structural requirements for expression and function in vivo.

Minimized human telomerase maintains telomeres and resolves endogenous roles of H/ACA proteins, TCAB1, and Cajal bodies.

We dissected the importance of human telomerase biogenesis and trafficking pathways for telomere maintenance. Biological stability of human telomerase RNA (hTR) relies on H/ACA proteins, but other eukaryotes use other RNP assembly pathways. To investigate additional rationale for human telomerase assembly as H/ACA RNP, we developed a minimized cellular hTR. Remarkably, with only binding sites for telomerase reverse transcriptase (TERT), minimized hTR assembled biologically active enzyme. TERT overexpression was required for cellular interaction with minimized hTR, indicating that H/ACA RNP assembly enhances endogenous hTR-TERT interaction. Telomere maintenance by minimized telomerase was unaffected by the elimination of the telomerase holoenzyme Cajal body chaperone TCAB1 or the Cajal body scaffold protein Coilin. Surprisingly, wild-type hTR also maintained and elongated telomeres in TCAB1 or Coilin knockout cells, with distinct changes in telomerase action. Overall, we elucidate trafficking requirements for telomerase biogenesis and function and expand mechanisms by which altered telomere maintenance engenders human disease.

Critical Links and Nonlocal Rerouting in Complex Supply Networks.

Link failures repeatedly induce large-scale outages in power grids and other supply networks. Yet, it is still not well understood which links are particularly prone to inducing such outages. Here we analyze how the nature and location of each link impact the network's capability to maintain a stable supply. We propose two criteria to identify critical links on the basis of the topology and the load distribution of the network prior to link failure. They are determined via a link's redundant capacity and a renormalized linear response theory we derive. These criteria outperform the critical link prediction based on local measures such as loads. The results not only further our understanding of the physics of supply networks in general. As both criteria are available before any outage from the state of normal operation, they may also help real-time monitoring of grid operation, employing countermeasures and support network planning and design.

Flexible and free-standing ternary Cd2GeO4 nanowire/graphene oxide/CNT nanocomposite film with improved lithium-ion battery performance.

To realize flexible lithium-ion batteries (LIBs), the design of flexible electrode/current collector materials with high mechanical flexibility, superior conductivity and excellent electrochemical performance and electrical stability are highly desirable. In this work, we developed a new ternary Cd2GeO4 nanowire/graphene oxide/carbon nanotube nanocomposite (Cd2GeO4 NW/GO/CNT) film electrode. Benefiting from the efficient combination of GO and Cd2GeO4 NWs, our Cd2GeO4 NW/GO/CNT composite film exhibits a capacity of 784 mA h g(-1) after 30 cycles at 200 mA g(-1), which is 2.7 times higher than that of Cd2GeO4 NW/CNT film (290 mA h g(-1)). At a higher rate of 400 mA g(-1) and 1 A g(-1), the Cd2GeO4 NW/GO/CNT film delivers a stable capacity of 617 and 397 mA h g(-1), respectively. Even at 2.5 A g(-1), it still exhibits a high rate capacity of 180 mA h g(-1). The flexible Cd2GeO4 NW/GO/CNT film clearly demonstrates good cycling stability and rate performance for anode materials in LIBs. This route may be extended to design other flexible free-standing metal germanate nanocomposite anode materials.