Conformations of Linear DNA

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spatial configurations of the molecule in the infinite- length limit were obtained. A unique configuraion minimizes the energy for a given set of physical conditions. An elastic model incorporating thermal fluctuations provides excellent agreement with experimental results on the plectonemic transition.Comment: 5 pages, RevTeX; 6 postscript figure

Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery

Therapies based on biologics involving delivery of proteins, DNA, and RNA are currently among the most promising approaches. However, although large combinatorial libraries of biologics and delivery vehicles can be readily synthesized, there are currently no means to rapidly characterize them in vivo using animal models. Here, we demonstrate high-throughput in vivo screening of biologics and delivery vehicles by automated delivery into target tissues of small vertebrates with developed organs. Individual zebrafish larvae are automatically oriented and immobilized within hydrogel droplets in an array format using a microfluidic system, and delivery vehicles are automatically microinjected to target organs with high repeatability and precision. We screened a library of lipid-like delivery vehicles for their ability to facilitate the expression of protein-encoding RNAs in the central nervous system. We discovered delivery vehicles that are effective in both larval zebrafish and rats. Our results showed that the in vivo zebrafish model can be significantly more predictive of both false positives and false negatives in mammals than in vitro mammalian cell culture assays. Our screening results also suggest certain structure–activity relationships, which can potentially be applied to design novel delivery vehicles.National Institutes of Health (U.S.) (Transformative Research Award R01 NS073127)National Institutes of Health (U.S.) (Director's Innovator Award DP2 OD002989)David & Lucile Packard Foundation (Award in Science and Engineering)Sanofi Aventis (Firm)Foxconn International Holdings Ltd.Hertz Foundation (Fellowship)University Grants Committee (Hong Kong, China) (Early Career Award 125012)National Natural Science Foundation (China) (81201164)ITC (ITS/376/13)Chinese University of Hong Kong (Grant 9610215)Chinese University of Hong Kong (Grant 7200269

Tops and Writhing DNA

The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.Comment: 17 pages two figure

Proceedings, Pot Chrysanthemum School, 1971

Space management / Robert W. Langhans -- Soils / D. C. Kiplinger -- Nutrition / George L. Staby -- Temperature and photoperiod / Joseph W. Love -- Automated short day control -- R. A. Aldrich -- Growth regulators / James B. Shanks -- Programming for insect-free pot mums / Richard K. Lindquist -- Programming for disease-free pot mums / Lester P. Nichols and Paul E. Nelson -- Where you go wrong / Harry K. Tayam

Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery

Therapies based on biologics involving delivery of proteins, DNA, and RNA are currently among the most promising approaches. However, although large combinatorial libraries of biologics and delivery vehicles can be readily synthesized, there are currently no means to rapidly characterize them in vivo using animal models. Here, we demonstrate high-throughput in vivo screening of biologics and delivery vehicles by automated delivery into target tissues of small vertebrates with developed organs. Individual zebrafish larvae are automatically oriented and immobilized within hydrogel droplets in an array format using a microfluidic system, and delivery vehicles are automatically microinjected to target organs with high repeatability and precision. We screened a library of lipid-like delivery vehicles for their ability to facilitate the expression of protein-encoding RNAs in the central nervous system. We discovered delivery vehicles that are effective in both larval zebrafish and rats. Our results showed that the in vivo zebrafish model can be significantly more predictive of both false positives and false negatives in mammals than in vitro mammalian cell culture assays. Our screening results also suggest certain structure–activity relationships, which can potentially be applied to design novel delivery vehicles.National Institutes of Health (U.S.) (Transformative Research Award R01 NS073127)National Institutes of Health (U.S.) (Director's Innovator Award DP2 OD002989)David & Lucile Packard Foundation (Award in Science and Engineering)Sanofi Aventis (Firm)Foxconn International Holdings Ltd.Hertz Foundation (Fellowship)University Grants Committee (Hong Kong, China) (Early Career Award 125012)National Natural Science Foundation (China) (81201164)ITC (ITS/376/13)Chinese University of Hong Kong (Grant 9610215)Chinese University of Hong Kong (Grant 7200269

Intensive Care Unit Mortality and Length of Stay Among Critically Ill Patients With Sepsis Treated With Corticosteroids: A Retrospective Cohort Study

Objectives: Sepsis is a major cause of morbidity and mortality in critically ill patients worldwide, and corticosteroids are commonly used to treat it. However, the evidence supporting the use of corticosteroids in sepsis patients admitted to the intensive care unit (ICU) is of low certainty, with conflicting results reported in previous studies. Thus, we aimed to investigate the potential association between corticosteroid treatment and various outcomes, including 30-day ICU mortality, ICU length of stay (LOS), mechanical ventilation use, new onset of infection, and hyperglycemia in patients diagnosed with sepsis and admitted to the ICU. Materials and Methods: We conducted a cohort study utilizing data from the Medical Information Mart for Intensive Care-IV (MIMIC-IV) database from 2008 to 2019. The study compared users of corticosteroids following admission to the ICU with non-users. Outcomes assessed included 30-day ICU mortality, ICU length of stay (LOS), mechanical ventilation use, new onset of infection, and hyperglycemia. Doubly robust, augmented inverse propensity weighted models were employed to control for confounders and determine the average treatment effect (ATE) of corticosteroids on study outcomes. Results: A total of 10,098 patients with a first diagnosis of sepsis were identified, of which 1,235 (12.2%) received corticosteroid treatment, and 8,863 (87.8%) did not. Corticosteroid use was associated with increased 30-day ICU mortality (ATE, 0.127; 95% CI, 0.083 to 0.171), ICU LOS (ATE, 1.773; 95% CI, 1.036 to 2.510), mechanical ventilation use (ATE, 0.181; 95% CI, 0.130 to 0.233), new onset of infection (ATE, 0.063; 95% CI, 0.032 to 0.094), and hyperglycemia (ATE, 0.024; 95% CI, 0.013 to 0.035) compared to non-use. Conclusion: The safety profile of corticosteroid therapy in sepsis patients admitted to the ICU remains a concern. Clinicians should carefully consider all available evidence and patient preferences when deciding to prescribe corticosteroids. Given the low certainty of evidence supporting the current treatment guidelines, further research is warranted to provide a more conclusive understanding of the risks and benefits associated with corticosteroid use in this patient population

Short-term caloric restriction, resveratrol, or combined treatment regimens initiated in late-life alter mitochondrial protein expression profiles in a fiber-type specific manner in aged animals

AbstractAging is associated with a loss in muscle known as sarcopenia that is partially attributed to apoptosis. In aging rodents, caloric restriction (CR) increases health and longevity by improving mitochondrial function and the polyphenol resveratrol (RSV) has been reported to have similar benefits. In the present study, we investigated the potential efficacy of using short-term (6weeks) CR (20%), RSV (50mg/kg/day), or combined CR+RSV (20% CR and 50mg/kg/day RSV), initiated at late-life (27months) to protect muscle against sarcopenia by altering mitochondrial function, biogenesis, content, and apoptotic signaling in both glycolytic white and oxidative red gastrocnemius muscle (WG and RG, respectively) of male Fischer 344×Brown Norway rats. CR but not RSV attenuated the age-associated loss of muscle mass in both mixed gastrocnemius and soleus muscle, while combined treatment (CR+RSV) paradigms showed a protective effect in the soleus and plantaris muscle (P<0.05). Sirt1 protein content was increased by 2.6-fold (P<0.05) in WG but not RG muscle with RSV treatment, while CR or CR+RSV had no effect. PGC-1α levels were higher (2-fold) in the WG from CR-treated animals (P<0.05) when compared to ad-libitum (AL) animals but no differences were observed in the RG with any treatment. Levels of the anti-apoptotic protein Bcl-2 were significantly higher (1.6-fold) in the WG muscle of RSV and CR+RSV groups compared to AL (P<0.05) but tended to occur coincident with elevations in the pro-apoptotic protein Bax so that the apoptotic susceptibility as indicated by the Bax to Bcl-2 ratio was unchanged. There were no alterations in DNA fragmentation with any treatment in muscle from older animals. Additionally, mitochondrial respiration measured in permeabilized muscle fibers was unchanged in any treatment group and this paralleled the lack of change in cytochrome c oxidase (COX) activity. These data suggest that short-term moderate CR, RSV, or CR+RSV tended to modestly alter key mitochondrial regulatory and apoptotic signaling pathways in glycolytic muscle and this might contribute to the moderate protective effects against aging-induced muscle loss observed in this study

Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus

Background Vaccines comprising recombinant subunit proteins are well-suited to low-cost and high-volume production for global use. The design of manufacturing processes to produce subunit vaccines depends, however, on the inherent biophysical traits presented by an individual antigen of interest. New candidate antigens typically require developing custom processes for each one and may require unique steps to ensure sufficient yields without product-related variants. Results We describe a holistic approach for the molecular design of recombinant protein antigens—considering both their manufacturability and antigenicity—informed by bioinformatic analyses such as RNA-seq, ribosome profiling, and sequence-based prediction tools. We demonstrate this approach by engineering the product sequences of a trivalent non-replicating rotavirus vaccine (NRRV) candidate to improve titers and mitigate product variants caused by N-terminal truncation, hypermannosylation, and aggregation. The three engineered NRRV antigens retained their original antigenicity and immunogenicity, while their improved manufacturability enabled concomitant production and purification of all three serotypes in a single, end-to-end perfusion-based process using the biotechnical yeast Komagataella phaffii. Conclusions This study demonstrates that molecular engineering of subunit antigens using advanced genomic methods can facilitate their manufacturing in continuous production. Such capabilities have potential to lower the cost and volumetric requirements in manufacturing vaccines based on recombinant protein subunits

Dependence of Aspen Stands on a Subsurface Water Subsidy: Implications for Climate Change Impacts

The reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait‐ and process‐based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and maximize photosynthetic potential. Subsidy dependence increased with stand hydraulic conductance. Four of the six “subsidized” stands were predicted to be stressed during the survey year owing to a subsidy shortfall. Since winter snowpack is closely related to groundwater recharge in the region, we compared winter precipitation with tree‐ring chronologies. Consistent with model predictions, chronologies were more sensitive to snowpack in subsidized stands than in nonsubsidized ones. The results imply that aspen stand health in the region is more coupled to winter snowpack than to growing season water supply. Winters are predicted to have less precipitation as snow, indicating a stressful future for the region\u27s aspen forests

Classical Ising model test for quantum circuits

We exploit a recently constructed mapping between quantum circuits and graphs in order to prove that circuits corresponding to certain planar graphs can be efficiently simulated classically. The proof uses an expression for the Ising model partition function in terms of quadratically signed weight enumerators (QWGTs), which are polynomials that arise naturally in an expansion of quantum circuits in terms of rotations involving Pauli matrices. We combine this expression with a known efficient classical algorithm for the Ising partition function of any planar graph in the absence of an external magnetic field, and the Robertson-Seymour theorem from graph theory. We give as an example a set of quantum circuits with a small number of non-nearest neighbor gates which admit an efficient classical simulation.Comment: 17 pages, 2 figures. v2: main result strengthened by removing oracular settin