Novel insights into construct toxicity, strain optimization, and primary sequence design for producing recombinant silk fibroin and elastin-like peptide in E. coli.

Spider silk proteins (spidroins) are a remarkable class of biomaterials that exhibit a unique combination of high-value attributes and can be processed into numerous morphologies for targeted applications in diverse fields. Recombinant production of spidroins represents the most promising route towards establishing the industrial production of the material, however, recombinant spider silk production suffers from fundamental difficulties that includes low titers, plasmid instability, and translational inefficiencies. In this work, we sought to gain a deeper understanding of upstream bottlenecks that exist in the field through the production of a panel of systematically varied spidroin sequences in multiple E. coli strains. A restriction on basal expression and specific genetic mutations related to stress responses were identified as primary factors that facilitated higher titers of the recombinant silk constructs. Using these findings, a novel strain of E. coli was created that produces recombinant silk constructs at levels 4-33 times higher than standard BL21(DE3). However, these findings did not extend to a similar recombinant protein, an elastin-like peptide. It was found that the recombinant silk proteins, but not the elastin-like peptide, exert toxicity on the E. coli host system, possibly through their high degree of intrinsic disorder. Along with strain engineering, a bioprocess design that utilizes longer culturing times and attenuated induction was found to raise recombinant silk titers by seven-fold and mitigate toxicity. Targeted alteration to the primary sequence of the recombinant silk constructs was also found to mitigate toxicity. These findings identify multiple points of focus for future work seeking to further optimize the recombinant production of silk proteins and is the first work to identify the intrinsic disorder and subsequent toxicity of certain spidroin constructs as a primary factor related to the difficulties of production.

Genome-Wide Analysis of Translation in Replicatively Aged Yeast.

Protein synthesis is an essential process that affects major cellular functions including growth, energy production, cell signaling, and enzymatic reactions. However, how it is impacted by aging and how the translation of specific proteins is changed during the aging process remain understudied. Although yeast is a widely used model for studying eukaryotic aging, analysis of age-related translational changes using ribosome profiling in this organism has been challenging due to the need for isolating large quantities of old cells. Here, we provide a detailed protocol for genome-wide analysis of protein synthesis using ribosome profiling in replicatively aged yeast. By combining genetic enrichment of old cells with the biotin affinity purification step, this method allows large-scale isolation of aged cells sufficient for generating ribosome profiling libraries. We also describe a strategy for normalization of samples using a spike-in with worm lysates that permits quantitative comparison of absolute translation levels between young and old cells.

Inkjet-printed paper-based colorimetric sensor coupled with smartphone for determination of mercury (Hg2+).

We report an inkjet-printed paper based colorimetric sensor with silver nanoparticles (AgNPs) using smartphone and color detector App for on-site determination of mercuric ion (Hg2+) from environmental water samples. The AgNPs printed on Whatman filter paper (No. 1) is employed for detection of Hg2+ which is reliant on the color change of NPs from yellow to discoloration depending on the concentration of target analyte in sample solution. The quantitative determination was performed by calculating the signal intensity of AgNPs on printed paper substrate after the introduction of Hg2+ using smartphone and RGB color detector. The mechanism for detection of Hg2+ on paper substrate is verified using UV-Vis spectrophotometry (UV-Vis), transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS), dynamic light scattering (DLS) and basic chemical assays. The linear range acquired for paper based colorimetric detection in the range of 40-1200 µgL-1 with limit of detection of 10 µgL-1. The results obtained using an inkjet-printed paper-based chemical sensor combined with a smartphone is validated with data of inductively coupled plasma-atomic emission spectroscopy (ICP-AES) measurement. The advantages of paper based detection are simple, rapid, economic and can be applied at the sample sources for determination of Hg2+.

Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis.

Metabolic changes alter the cellular milieu; can this also change intracellular protein folding? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change protein folding, arguably, it should also alter mutational buffering. Here we find that altered cellular metabolic states in E. coli buffer distinct mutations on model proteins. Buffered-mutants have folding problems in vivo and are differently chaperoned in different metabolic states. Notably, this assistance is dependent upon the metabolites and not on the increase in canonical chaperone machineries. Being able to reconstitute the folding assistance afforded by metabolites in vitro, we propose that changes in metabolite concentrations have the potential to alter protein folding capacity. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in cellular proteostasis.

A direct DRS-FTIR probe for rapid detection and quantification of fluoroquinolone antibiotics in poultry egg-yolk.

We report a novel diffuse reflectance-Fourier transforms infrared (DRS-FTIR) spectral monitoring of fluoroquinolone antibiotics such as ciprofloxacin (CIP) and norfloxacin (NOR) for their quantification in poultry egg-yolks. To the best of our knowledge, this is the first report to describe the rapid quantitative determination of fluoroquinolone antibiotics in poultry egg samples using DRS-FTIR. The characteristic absorption peaks obtained at 1627 and 1026 cm-1 were used for optimization and determination of CIP and NOR, respectively. The linearity range obtained for the determination of CIP and NOR in egg samples was 0.05-0.50 ng mL-1 with limit of detection and limit of quantification of 0.032 and 1.551 ng mL-1 and 0.028 and 0.194 ng mL-1, respectively. Good recoveries were obtained in the range of 83.1-102.3% from poultry eggs samples using DRS-FTIR method. The advantages of the DRS-FTIR method are its simplicity, sensitivity and suitability for high-throughput analysis towards the food samples.

Differential strengths of molecular determinants guide environment specific mutational fates.

Organisms maintain competitive fitness in the face of environmental challenges through molecular evolution. However, it remains largely unknown how different biophysical factors constrain molecular evolution in a given environment. Here, using deep mutational scanning, we quantified empirical fitness of >2000 single site mutants of the Gentamicin-resistant gene (GmR) in Escherichia coli, in a representative set of physical (non-native temperatures) and chemical (small molecule supplements) environments. From this, we could infer how different biophysical parameters of the mutations constrain molecular function in different environments. We find ligand binding, and protein stability to be the best predictors of mutants' fitness, but their relative predictive power differs across environments. While protein folding emerges as the strongest predictor at minimal antibiotic concentration, ligand binding becomes a stronger predictor of mutant fitness at higher concentration. Remarkably, strengths of environment-specific selection pressures were largely predictable from the degree of mutational perturbation of protein folding and ligand binding. By identifying structural constraints that act as determinants of fitness, our study thus provides coarse mechanistic insights into the environment specific accessibility of mutational fates.

A G-quadruplex motif at the 3' end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency.

Originating as a component of prokaryotic adaptive immunity, the type II CRISPR/Cas9 system has been repurposed for targeted genome editing in various organisms. Although Cas9 can bind and cleave DNA efficiently under in vitro conditions, its activity inside a cell can vary dramatically between targets owing to the differences between genomic loci and the availability of enough Cas9/sgRNA (single guide RNA) complex molecules for cleavage. Most methods have so far relied on Cas9 protein engineering or base modifications in the sgRNA sequence to improve CRISPR/Cas9 activity. Here we demonstrate that a structure based rational design of sgRNAs can enhance the efficiency of Cas9 cleavage in vivo. By appending a naturally forming RNA G-quadruplex motif to the 3' end of sgRNAs we can improve its stability and target cleavage efficiency in zebrafish embryos without inducing off-target activity, thereby underscoring its value in the design of better and optimized genome editing triggers.

Selective inhibition of miR-21 by phage display screened peptide.

miRNAs are nodal regulators of gene expression and deregulation of miRNAs is causally associated with different diseases, including cancer. Modulation of miRNA expression is thus of therapeutic importance. Small molecules are currently being explored for their potential to downregulate miRNAs. Peptides have shown to have better potency and selectivity toward their targets but their potential in targeting and modulating miRNAs remain unexplored. Herein, using phage display we found a very selective peptide against pre-miR-21. Interestingly, the peptide has the potential to downregulate miR-21, by binding to pre-miR-21 and hindering Dicer processing. It is selective towards miR-21 inside the cell. By antagonising miR-21 function, the peptide is able to increase the expression of its target proteins and thereby increase apoptosis and suppress cell proliferation, invasion and migration. This peptide can further be explored for its anti-cancer activity in vivo and may be even extended to clinical studies.

A simple and sensitive analytical method for the determination of antimony in environmental and biological samples.

The results of a study and application of leucocrystal violet for the determination of antimony in parts per million levels is described here. The proposed method is based on the reaction of antimony(III) with acidified potassium iodate to liberate iodine. The liberated iodine selectively oxidizes leucocrystal violet to crystal violet dye. The formed dye shows maximum absorbance at 590 nm. The color system obeys Beer's law in the concentration range from 0.4 - 3.6 microg antimony per 25 ml of final solution. The molar absorptivity and Sandell's sensitivity were found to be 7.32 x 10(5) l mol(-1) cm(-1) and 0.0016 microg cm(-2), respectively. All variables were studied in order to optimize the reaction. The proposed method is satisfactorily applicable for the analysis of antimony in various environmental and biological samples. The method is simple, highly sensitive, accurate and reliable.