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Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by the Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables the optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for the fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20-200 aM sensitivity. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies.

Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20 - 200 aM sensitivity without any specialized equipment. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies., Competing Interests: CONFLICT OF INTEREST DISCLOSURE K.K.A. M. C. J. & J.B.L. are founders and have financial interest in Stemloop, Inc, and these interests are reviewed and managed by Northwestern University and Stanford University in accordance with their conflict-of-interest policies. All other authors declare no conflicts of interest.

Functional design of ribosomes with mutant ribosomal RNA (rRNA) can expand opportunities for understanding molecular translation, building cells from the bottom-up, and engineering ribosomes with altered capabilities. However, such efforts are hampered by cell viability constraints, an enormous combinatorial sequence space, and limitations on large-scale, 3D design of RNA structures and functions. To address these challenges, we develop an integrated community science and experimental screening approach for rational design of ribosomes. This approach couples Eterna, an online video game that crowdsources RNA sequence design to community scientists in the form of puzzles, with in vitro ribosome synthesis, assembly, and translation in multiple design-build-test-learn cycles. We apply our framework to discover mutant rRNA sequences that improve protein synthesis in vitro and cell growth in vivo, relative to wild type ribosomes, under diverse environmental conditions. This work provides insights into rRNA sequence-function relationships and has implications for synthetic biology., (© 2023. The Author(s).)

Ribosome engineering is a powerful approach for expanding the catalytic potential of the protein synthesis apparatus. Due to the potential detriment the properties of the engineered ribosome may have on the cell, the designer ribosome needs to be functionally isolated from the translation machinery synthesizing cellular proteins. One solution to this problem was offered by Ribo-T, an engineered ribosome with tethered subunits which, while producing a desired protein, could be excluded from general translation. Here, we provide a conceptually different design of a cell with two orthogonal protein synthesis systems, where Ribo-T produces the proteome, while the dissociable ribosome is committed to the translation of a specific mRNA. The utility of this system is illustrated by generating a comprehensive collection of mutants with alterations at every rRNA nucleotide of the peptidyl transferase center and isolating gain-of-function variants that enable the ribosome to overcome the translation termination blockage imposed by an arrest peptide.

The synthetic capability of the Escherichia coli ribosome has attracted efforts to repurpose it for novel functions, such as the synthesis of polymers containing non-natural building blocks. However, efforts to repurpose ribosomes are limited by the lack of complete peptidyl transferase center (PTC) active site mutational analyses to inform design. To address this limitation, we leverage an in vitro ribosome synthesis platform to build and test every possible single nucleotide mutation within the PTC-ring, A-loop and P-loop, 180 total point mutations. These mutant ribosomes were characterized by assessing bulk protein synthesis kinetics, readthrough, assembly, and structure mapping. Despite the highly-conserved nature of the PTC, we found that >85% of the PTC nucleotides possess mutational flexibility. Our work represents a comprehensive single-point mutant characterization and mapping of the 70S ribosome's active site. We anticipate that it will facilitate structure-function relationships within the ribosome and make possible new synthetic biology applications., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Coagulation factor VIII represents one of the oldest protein-based therapeutics, serving as an effective hemophilia A treatment for half a century. Optimal treatment consists of repeated intravenous infusions of blood coagulation factor VIII (FVIII) per week for life. Despite overall treatment success, significant limitations remain, including treatment invasiveness, duration, immunogenicity, and cost. These issues have inspired research into the development of bioengineered FVIII products and gene therapies., Objectives: To structurally characterize a bioengineered construct of FVIII, termed ET3i, which is a human/porcine chimeric B domain-deleted heterodimer with improved expression and slower A2 domain dissociation following proteolytic activation by thrombin., Methods: The structure of ET3i was characterized with X-ray crystallography and tandem mass spectrometry-based glycoproteomics., Results: Here, we report the 3.2 Å crystal structure of ET3i and characterize the distribution of N-linked glycans with LC-MS/MS glycoproteomics. This structure shows remarkable conservation with the human FVIII protein and provides a detailed view of the interface between the A2 domain and the remaining FVIII structure. With two FVIII molecules in the crystal, we observe two conformations of the C2 domain relative to the remaining FVIII structure. The improved model and stereochemistry of ET3i served as a scaffold to generate an improved, refined structure of human FVIII. With the original datasets at 3.7 Å and 4.0 Å resolution, this new structure resulted in improved refinement statistics., Conclusions: These improved structures yield a more confident model for next-generation engineering efforts to develop FVIII therapeutics with longer half-lives, higher expression levels, and lower immunogenicity., (© 2019 International Society on Thrombosis and Haemostasis.)

Ribo-T is a ribosome with covalently tethered subunits where core 16S and 23S ribosomal RNAs form a single chimeric molecule. Ribo-T makes possible a functionally orthogonal ribosome-mRNA system in cells. Unfortunately, use of Ribo-T has been limited because of low activity of its original version. Here, to overcome this limitation, we use an evolutionary approach to select new tether designs that are capable of supporting faster cell growth and increased protein expression. Further, we evolve new orthogonal Ribo-T/mRNA pairs that function in parallel with, but independent of, natural ribosomes and mRNAs, increasing the efficiency of orthogonal protein expression. The Ribo-T with optimized designs is able to synthesize a diverse set of proteins, and can also incorporate multiple non-canonical amino acids into synthesized polypeptides. The enhanced Ribo-T designs should be useful for exploring poorly understood functions of the ribosome and engineering ribosomes with altered catalytic properties.

RNA nanotechnology seeks to create nanoscale machines by repurposing natural RNA modules. The field is slowed by the current need for human intuition during three-dimensional structural design. Here, we demonstrate that three distinct problems in RNA nanotechnology can be reduced to a pathfinding problem and automatically solved through an algorithm called RNAMake. First, RNAMake discovers highly stable single-chain solutions to the classic problem of aligning a tetraloop and its sequence-distal receptor, with experimental validation from chemical mapping, gel electrophoresis, solution X-ray scattering and crystallography with 2.55 Å resolution. Second, RNAMake automatically generates structured tethers that integrate 16S and 23S ribosomal RNAs into single-chain ribosomal RNAs that remain uncleaved by ribonucleases and assemble onto messenger RNA. Third, RNAMake enables the automated stabilization of small-molecule binding RNAs, with designed tertiary contacts that improve the binding affinity of the ATP aptamer and improve the fluorescence and stability of the Spinach RNA in cell extracts and in living Escherichia coli cells.

Building variant ribosomes offers opportunities to reveal fundamental principles underlying ribosome biogenesis and to make ribosomes with altered properties. However, cell viability limits mutations that can be made to the ribosome. To address this limitation, the in vitro integrated synthesis, assembly and translation (iSAT) method for ribosome construction from the bottom up was recently developed. Unfortunately, iSAT is complex, costly, and laborious to researchers, partially due to the high cost of reaction buffer containing over 20 components. In this study, we develop iSAT in Escherichia coli BL21Rosetta2 cell lysates, a commonly used bacterial strain, with a cost-effective poly sugar and nucleotide monophosphate-based metabolic scheme. We achieved a 10-fold increase in protein yield over our base case with an evolutionary design of experiments approach, screening 490 reaction conditions to optimize the reaction buffer. The computationally guided, cell-free, high-throughput technology presented here augments the way we approach multicomponent synthetic biology projects and efforts to repurpose ribosomes.

Investigations suggest the benefits of low-level laser therapy (LLLT) to improve noninvasive body contouring treatments, inflammation, insulin resistance and to reduce body fat. However, the mechanism for such potential effects in association with exercise training (ET) and possible implications in browning adiposity processes remains unclear. Forty-nine obese women were involved, aged between 20 and 40 years with a body mass index (BMI) of 30-40 kg/m 2 . The volunteers were divided into Phototherapy (808 nm) and SHAM groups. Interventions consisted of exercise training and phototherapy applications post exercise for 4 months, with three sessions/week. Body composition, lipid profile, insulin resistance, atrial natriuretic peptide (ANP), WNT5 signaling, interleukin-6 (IL-6), and fibroblast growth factor-21 (FGF-21) were measured. Improvements in body mass, BMI, body fat mass, lean mass, visceral fat, waist circumference, insulin, HOMA-IR, total cholesterol, LDL-cholesterol, triglycerides, and ANP in both groups were demonstrated. Only the Phototherapy group showed a reduction in interleukin-6 and an increase in WNT5 signaling. In addition, it was possible to observe a higher magnitude change for the fat mass, insulin, HOMA-IR, and FGF-21 variables in the Phototherapy group. In the present investigation, it was demonstrated that exercise training associated with LLLT promotes an improvement in body composition and inflammatory processes as previously demonstrated. The Phototherapy group especially presented positive modifications of WNT5 signaling, FGF-21, and ANP, possible biomarkers associated with browning adiposity processes. This suggests that this kind of intervention promotes results applicable in clinical practice to control obesity and related comorbidities.

The ribosome is the cell's factory for protein synthesis. With protein synthesis rates of up to 20 amino acids per second and at an accuracy of 99.99%, the extraordinary catalytic capacity of the bacterial translation machinery has attracted extensive efforts to engineer, reconstruct, and repurpose it for biochemical studies and novel functions. Despite these efforts, the potential for harnessing the translation apparatus to manufacture bio-based products beyond natural limits remains underexploited, and fundamental constraints on the chemistry that the ribosome's RNA-based active site can carry out are unknown. This review aims to cover the past and present advances in ribosome design and engineering to understand the fundamental biology of the ribosome to facilitate the construction of synthetic manufacturing machines. The prospects for the development of engineered, or designer, ribosomes for novel polymer synthesis are reviewed, future challenges are considered, and promising advances in a variety of applications are discussed.

In this report, we report a case study on a 50-year-old male patient with different chronic wounds, such as venous ulcer and arterial ulcer in both legs. These wounds have persisted for more than 10 years, despite the different treatments applied, including, different dressings, hyperbaric camera, as well as the used of several medicines of oral and topical application. The case is addressed with the aim to evaluate if treatment that uses combined techniques such as low level laser therapy (LLLT), photodynamic therapy and cellulose membrane is able to improve healing and reduction of time of treatment in those types of chronic wounds. The results show the clinical protocol is effective for the healing of arterial and venous ulcers and can be considered as a promising possibility., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Oxyropsis ephippia, a new species of loricariid catfish in the subfamily Hypoptopomatinae, is described from the Essequibo and Branco basins, Guyana. Based on the presence of a keel-like row of relatively enlarged odontodes on trunk median plates immediately above the lateral line canal, the new species is assigned to the genus Oxyropsis Eigenmann & Eigenmann 1889. It can be distinguished from its congeners by having the keel-like row on each median plate dominated by a single odontode (one closest to the posterior margin of the plate) conspicuously larger than preceding ones, and by having the sides of the trunk below the median series (approximately between median plates 7 to 12) shielded only by plates of the midventral series, with the exclusion of plates from the ventral series. The report of O. ephippia from the Essequibo is the first record of the genus in a river system that drains the north-central portion of the Guiana Shield into the Atlantic Ocean.

Obesity affects approximately 20% of the world population, and exercise is the primary non-pharmacological therapy. The combined use of exercise and low-level laser therapy (LLLT) may potentiate the effects promoted by exercise. The objective of this study was to investigate the effects of exercise in combination with phototherapy on adipocyte area, activity of the enzyme citrate synthase and muscle morphological analysis. We used 64 Wistar rats, which were divided into eight groups with 8 rats each: sedentary chow-diet (SC); sedentary chow-diet plus laser therapy (SCL), exercised chow-diet (EC); exercised chow-diet plus laser therapy (ECL); sedentary high-fat diet (SH); sedentary high-fat diet plus laser therapy (SHL); exercised high-fat diet (EH); exercised high-fat diet, laser therapy (EHL). The animals were submitted to a program of swimming training for 90min/5 times per week for 8weeks and LLLT (GA-Al-AS, 830nm) at a dose of 4.7J/point and a total energy of 9.4J/animal, with duration of 47s, which was applied to both gastrocnemius muscles after exercise. We conclude that the combined use of exercise and phototherapy increases the activity of the enzyme citrate synthase and decreases the white adipocyte area epididymal, retroperitoneal and visceral in obese rats, enhancing the effects of exercise., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Recently, investigations suggest the benefits of low-level laser (light) therapy (LLLT) in noninvasive treatment of cellulite, improvement of body countering, and control of lipid profile. However, the underlying key mechanism for such potential effects associated to aerobic plus resistance training to reduce body fat and inflammatory process, related to obesity in women still unclear. The purpose of the present investigation was to evaluate the effects of combined therapy of LLLT and aerobic plus resistance training in inflammatory profile and body composition of obese women. For this study, it involved 40 obese women with age of 20-40 years. Inclusion criteria were primary obesity and body mass index (BMI) greater than 30 kg/m(2) and less than 40 kg/m(2). The voluntaries were allocated in two different groups: phototherapy group and SHAM group. The interventions consisted on physical exercise training and application of phototherapy (808 nm), immediately after the physical exercise, with special designed device. Proinflammatory/anti-inflammatory adipokines were measured. It was showed that LLLT associated to physical exercise is more effective than physical exercise alone to increase adiponectin concentration, an anti-inflammatory adipokine. Also, it showed reduced values of neck circumference (cm), insulin concentration (μU/ml), and interleukin-6 (pg/ml) in LLLT group. In conclusion, phototherapy can be an important tool in the obesity, mostly considering its potential effects associated to exercise training in attenuating inflammation in women, being these results applicable in the clinical practices to control related risk associated to obesity.

Obesity and associated dyslipidemia is the fastest growing health problem throughout the world. The combination of exercise and low-level laser therapy (LLLT) could be a new approach to the treatment of obesity and associated disease. In this work, the effects of LLLT associated with exercises on the lipid metabolism in regular and high-fat diet rats were verified. We used 64 rats divided in eight groups with eight rats each, designed: SC, sedentary chow diet; SCL, sedentary chow diet laser, TC, trained chow diet; TCL, trained chow diet laser; SH, sedentary high-fat diet; SHL, sedentary high-fat diet laser; TH, trained high-fat diet; and THL, trained high-fat diet laser. The exercise used was swimming during 8 weeks/90 min daily and LLLT (GA-Al-As, 830 nm) dose of 4.7 J/point and total energy 9.4 J per animal, applied to both gastrocnemius muscles after exercise. We analyzed biochemical parameters, percentage of fat, hepatic and muscular glycogen and relative mass of tissue, and weight percentage gain. The statistical test used was ANOVA, with post hoc Tukey-Kramer for multiple analysis between groups, and the significant level was p < 0.001, p < 0.01, and p < 0.05. LLLT decreased the total cholesterol (p < 0.05), triglycerides (p < 0.01), low-density lipoprotein cholesterol (p < 0.05), and relative mass of fat tissue (p < 0.05), suggesting increased metabolic activity and altered lipid pathways. The combination of exercise and LLLT increased the benefits of exercise alone. However, LLLT without exercise tended to increase body weight and fat content. LLLT may be a valuable addition to a regimen of diet and exercise for weight reduction and dyslipidemic control.

The aim of this study was to determine the effects of successive cycles of a moderately restrictive diet and refeeding with a high-fat diet on the metabolism of the adipose and hepatic tissues of obese rats. Rats were assigned to the following groups: a chow diet; a high-fat diet; a moderate caloric restriction; or a moderate caloric restriction plus refeeding. Some animals in each group were given [1-(14)C]triolein intragastrically, while others received an intraperitoneal injection of 3 mCi (3)H(2)O. All animals were killed by decapitation. The retroperitoneal, visceral epididymal and omental white adipose tissues, brown adipose tissue, liver and blood were immediately removed. The lipid uptake from the diet, in vivo rate of lipogenesis, percentage of fat, lipid profile and leptin concentration were analysed. The high-fat diet promoted an increase in fatty liver (P ≤ 0.05), adiposity mass (P ≤ 0.05) and the plasma concentration of leptin (P ≤ 0.05) and a decreased lipid uptake in white adipose tissue depots (P ≤ 0.05) in relation to the chow diet. The moderate caloric restriction did not reverse the changes promoted by the high-fat diet but induced a small decrease in adiposity, which was reversed after refeeding, and the animals maintained a dyslipidaemic profile and high fat deposition in the liver. We can conclude that the high-fat diet and subsequent moderate caloric restriction plus refeeding increased the risks of developing visceral obesity, dyslipidaemia and non-alcoholic fatty liver disease, which suggests that this type of experimental protocol can be used to study mechanisms related to the metabolic syndrome.

Morphology of the postotic laterosensory canal was surveyed across loricarioid and outgroup catfishes in order to resolve conflicting statements regarding homology and phylogenetic significance of intrinsic character variation. A pterotic branch is widespread among catfishes and has been identified as a synapomorphy for siluriforms, but its presence in loricarioid catfishes has been disputed. In contrast to previous statements that absence of a pterotic branch is synapomorphic for loricarioids, we confirm the presence of a pterotic branch in Nematogenys inermis and other trichomycterids, callichthyids, and loricariids. The pterotic branch is secondarily absent in scoloplacids and astroblepids. We present criteria for establishing homology of the pterotic branch and review character state optimization schemes on the currently accepted phylogeny. The postotic region of loricariids is further specialized in having an expanded swimbladder capsule that incorporates the trunk lateral line canal and has a lateral opening covered by a greatly expanded pterotic complex. The trunk lateral line enters the swimbladder capsule mesial to the pterotic lateral wall and passes anteromedially as a fleshy tube before forming the postotic canal in the pterotic, a morphology reported previously for a single loricariid representative. Variation in the relative extent and topographic position of postotic canal branches and other morphologies is diagnostic of certain loricariid taxa, suggesting a rich character complex of potential utility in phylogeny reconstruction.