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This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

In literature, various mathematical models have been developed to have a better insight into the transmission dynamics and control the spread of infectious diseases. Aiming to explore more about various aspects of infectious diseases, in this work, we propose conceptual mathematical model through a SEIQR (Susceptible-Exposed-Infected-Quarantined-Recovered) mathematical model and its control measurement. We establish the positivity and boundedness of the solutions. We also compute the basic reproduction number and investigate the stability of equilibria for its epidemiological relevance. To validate the model and estimate the parameters to predict the disease spread, we consider the special case for COVID-19 to study the real cases of infected cases from [2] for Russia and India. For better insight, in addition to mathematical model, a history based LSTM model is trained to learn temporal patterns in COVID-19 time series and predict future trends. In the end, the future predictions from mathematical model and the LSTM based model are compared to generate reliable results.

The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.

Various studies have shown that the microbial proteins are often more stable than belongs to other sources like plant and animal origin. Hence, the interest in microbial enzymes has gained much attention due to many potential applications like bioenergy, biofuel production, biobleaching, bioconversion and so on. Additionally, recent trends revealed that the interest in isolating novel microbes from harsh environments have been the main focus of many scientists for various applications. Basically, industrially important enzymes can be categorized into mainly three groups: carbohydrases, proteases, and lipases. Among those, the enzymes especially carbohydrases involved in production of sugars. Carbohydrases include amylases, xylanases, pectinases, cellulases, chitinases, mannases, laccases, ligninases, lactase, glucanase, and glucose oxidase. Thus, here, an approach has been made to highlight five enzymes namely amylase, cellulase, laccase, pectinase, and xylanase from different sources with special emphasis on their properties, mechanism, applications, production optimization, purification, molecular approaches for its enhanced and stable production, and also biotechnological perspectives of its future development. Also, green and sustainable catalytic conversion strategies using nanoparticles of these enzymes have also been discussed. This review will provide insight into the carbohydrases importance and their usefulness that will help to the researchers working in this field. [ABSTRACT FROM AUTHOR]

Polymers have been used in various industries over the past few decades due to their tremendous applications. Among these, polyhydroxyalkanoates and poly(lactic acid) are easily biodegradable biopolymers derived from bacteria, including recombinant Escherichia coli, Alcaligenes eutrophus, Alcaligenes latus, Azotobacter vinelandii, methylotrophs and Pseudomonas. Conventional petroleum‐derived polymers have become potentially harmful to the environment due to their complex degradation process. The nonbiodegradability of synthetic polymers has become a global issue of concern. There is an urgent need for a substitute to tackle the increasing environmental stress. Microorganisms are small factories for producing different types of polymers during their growth cycle. Various features like biodegradability, biocompatibility, nontoxicity and wide substrate spectrum make such microbial polymers highly reliable. Biopolymers such as alginate, cellulose, cyanophycin, levan, polyhydroxyalkanoates, xanthan, poly(lactic acid) and poly(γ‐glutamic acid) can be obtained from different microorganisms like Aureobasdium pullulans, Acetobacter xylinum, Bacillus thermoamylovorans and Cupriavidusnecator. These are extensively used in various fields like food, medicine, wastewater treatment, biofuel production, packaging and cosmetics. Despite being advantageous in several ways, the biopolymer market still faces several hurdles. This review mainly emphasizes the different types of biopolymers, production by microorganisms and various applications of these biopolymers in different fields. The main drawback limiting the development of these polymers is the high production cost and low efficiency of the microbial strains. Genetic recombination is an efficient technique to enhance the microbial yield and to expand the biopolymer market size. © 2023 Society of Chemical Industry (SCI). [ABSTRACT FROM AUTHOR]

In this paper, we study a predator-prey model with prey refuge and delay. We investigate the combined role of prey refuge and delay on the dynamical behaviour of the delayed system by incorporating discrete type gestation delay of predator. It is found that Hopf bifurcation occurs when the delay parameter τ crosses some critical value. In particular, it is shown that the conditions obtained for the Hopf bifurcation behaviour are sufficient but not necessary and the prey reserve is unable to stabilize the unstable interior equilibrium due to Hopf bifurcation. In particular, the direction and stability of bifurcating periodic solutions are determined by applying normal form theory and center manifold theorem for functional differential equations. Mathematically, we analyze the effect of increase or decrease of prey reserve on the equilibrium states of prey and predator species. At the end, we perform some numerical simulations to substantiate our analytical findings.

This paper discusses a predator-prey model with prey refuge. We investigate the role of prey refuge on the existence and stability of the positive equilibrium. The global asymptotic stability of positive interior equilibrium solution is established using suitable Lyapunov functional, which shows that the prey refuge has no influence on the permanence property of the system. Mathematically, we analyze the effect of increase or decrease of prey reserve on the equilibrium states of prey and predator species. To access the usability of proposed predator-prey model in practical scenarios, we also suggest, the use of Levenberg-Marquardt (LM) method for associated parameter estimation problem. Numerical results demonstrate faithful reconstruction of system dynamics by estimated parameter by LM method. The analytical results found in this paper are illustrated with the help of suitable numerical examples