DULIP: A dual luminescence-based co-immunoprecipitation assay for interactome mapping in mammalian cells

Mapping of protein-protein interactions (PPIs) is critical for understanding protein function and complex biological processes. Here, we present DULIP, a dual luminescence-based co-immunoprecipitation assay, for systematic PPI mapping in mammalian cells. DULIP is a second-generation luminescence-based PPI screening method for the systematic and quantitative analysis of co-immunoprecipitations using two different luciferase tags. Benchmarking studies with positive and negative PPI reference sets revealed that DULIP allows the detection of interactions with high sensitivity and specificity. Furthermore, the analysis of a PPI reference set with known binding affinities demonstrated that both low- and high-affinity interactions can be detected with DULIP assays. Finally, using the well-characterized interaction between Syntaxin-1 and Munc18, we found that DULIP is capable of detecting the effects of point mutations on interaction strength. Taken together, our studies demonstrate that DULIP is a sensitive and reliable method of great utility for systematic interactome research. It can be applied for interaction screening as well as for the validation of PPIs in mammalian cells. Moreover, DULIP permits the specific analysis of mutation-dependent binding patterns

Robust superhydrophobic cellulose nanofiber aerogel for multifunctional environmental applications

The fabrication of superadsorbent for dye adsorption is a hot research area at present. However, the development of low-cost and highly efficient superadsorbents against toxic textile dyes is still a big challenge. Here, we fabricated hydrophobic cellulose nanofiber aerogels from cellulose nanofibers through an eco-friendly silanization reaction in liquid phase, which is an extremely efficient, rapid, cheap, and environmentally friendly procedure. Moreover, the demonstrated eco-friendly silanization technique is easy to commercialize at the industrial level. Most of the works that have reported on the hydrophobic cellulose nanofiber aerogels explored their use for the elimination of oil from water. The key novelty of the present work is that the demonstrated hydrophobic cellulose nanofibers aerogels could serve as superadsorbents against toxic textile dyes such as crystal violet dye from water and insulating materials for building applications. Here, we make use of the possible hydrophobic interactions between silane-modified cellulose nanofiber aerogel and crystal violet dye for the removal of the crystal violet dye from water. With a 10 mg/L of crystal violet (CV) aqueous solution, the silane-modified cellulose nanofiber aerogel showed a high adsorption capacity value of 150 mg/g of the aerogel. The reason for this adsorption value was due to the short-range hydrophobic interaction between the silane-modified cellulose nanofiber aerogel and the hydrophobic domains in crystal violet dye molecules. Additionally, the fabricated silane-modified cellulose nanofiber hydrophobic aerogels exhibited a lower thermal conductivity value of 0.037 W\ub7m -1 K -1 , which was comparable to and lower than the commercial insulators such as mineral wools (0.040 W\ub7m -1 K -1 ) and polystyrene foams (0.035 W\ub7m -1 K -1 ). We firmly believe that the demonstrated silane-modified cellulose nanofiber aerogel could yield an eco-friendly adsorbent that is agreeable to adsorbing toxic crystal violet dyes from water as well as active building thermal insulators

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. Alpha-rods are flexible and expose a large surface, which makes them suitable for protein interaction. Although most likely originating by tandem duplication of a two-helix unit, their detection using sequence similarity between repeats is poor. Here, we show that alpha-rod repeats can be detected using a neural network. The network detects more repeats than are identified by domain databases using multiple profiles, with a low level of false positives (<10%). We identify alpha-rod repeats in approximately 0.4% of proteins in eukaryotic genomes. We then investigate the results for all human proteins, identifying alpha-rod repeats for the first time in six protein families, including proteins STAG1-3, SERAC1, and PSMD1-2 & 5. We also characterize a short version of these repeats in eight protein families of Archaeal, Bacterial, and Fungal species. Finally, we demonstrate the utility of these predictions in directing experimental work to demarcate three alpha-rods in huntingtin, a protein mutated in Huntington's disease. Using yeast two hybrid analysis and an immunoprecipitation technique, we show that the huntingtin fragments containing alpha-rods associate with each other. This is the first definition of domains in huntingtin and the first validation of predicted interactions between fragments of huntingtin, which sets up directions toward functional characterization of this protein. An implementation of the repeat detection algorithm is available as a Web server with a simple graphical output: http://www.ogic.ca/projects/ard. This can be further visualized using BiasViz, a graphic tool for representation of multiple sequence alignments

Mechanically Robust Antibacterial Nanopapers Through Mixed Dimensional Assembly for Anionic Dye Removal

There is a piqued interest in development of biobased sorbents for water treatment. Here in we reported, the fabrication of mechanically strong nanopapers by mixed dimensional assembly of 1D Cellulose nanofibers and 2D amino functionalized graphene oxide for water treatment. The fabricated amino functionalized GO/ cellulose nanofiber (AMGO-CNF) nanopaper showed superior antibacterial resistance towards Escherichia coli MTCC 1610 and Klebsiella due to the enhanced surface roughness which was confirmed from SEM and AFM studies. The amino group present in the AMGO enhanced the adsorption efficiency of the nanopaper towards methyl orange dye. The fabricated nanopaper showed an adsorption of 11.05 mg/gm 30 mg/L concentration at pH 2. Maximum adsorption was observed at pH 2 which was due to protonation of amine group. Moreover, the fabricated membrane showed excellent hydrolytic stability which can be corroborated to the surface roughness and reduced hydrophilicity. The investigation into the surface chemistries of cellulose nanofibers beyond the adoption of toxic solvents can enhance the economic usefulness of the process and yield a new eco-friendly adsorbent material that is agreeable to adsorbing various toxic pollutants

Common Mode of Remodeling AAA ATPases p97 CDC48 by Their Disassembling Cofactors ASPL PUX1

The hexameric ring structure of the type II AAA+ ATPases is considered as stable and permanent. Recently, the UBX domain-containing cofactors Arabidopsis thaliana PUX1 and human alveolar soft part sarcoma locus (ASPL) were reported to bind and disassemble the cognate AAA+ ATPases AtCDC48 and human p97. Here, we present two crystal structures related to these complexes: a truncated AtCDC48 (AtCDC48-ND1) and a hybrid complex containing human p97-ND1 and the UBX domain of plant PUX1 (p97-ND1:PUX1-UBX). These structures reveal close similarity between the human and plant AAA+ ATPases, but also highlight differences between disassembling and non-disassembling AAA+ ATPase cofactors. Based on an AtCDC48 disassembly assay with PUX1 and known crystal structures of the p97-bound human cofactor ASPL, we propose a general ATPase disassembly model. Thus, our structural and biophysical investigations provide detailed insight into the mechanism of AAA+ ATPase disassembly by UBX domain cofactors and suggest a general mode of regulating the cellular activity of these molecular machines

Nanocellulose-Based Membranes for Water Purification

Scarcity and contamination of worldwide drinking water demand advanced, effective water purification methodologies. Eliminating numerous contaminants, such as heavy metals, toxic textile dyes, pesticides, oil, and other industrial, as well as agricultural, wastes, from water has become a serious concern because of their adverse effects on human health and the ecosystem. Recently, developments in nanoscience and nanotechnology propose that several of the present problems relating to water quality could be greatly reduced by using nanomaterials because of their good adsorption efficiency, higher surface area, and greater active sites for interaction with contaminants in water. In this context, nanocellulose is the most abundant and renewable polymer available globally and consists of repeating β-d-glucopyranose units covalently linked through acetal functions between the hydroxyl groups of C4 and C1 carbon atoms that provide it chirality and reactivity properties. Nanocellulose is a fascinating material for practical applications because it is cost-effective, is renewable, and can be handled at huge scale using conventional wood industry techniques. Nanocellulose is a valuable filtration material because it is affordable, sustainable, inert, and stable at a broad range of pH/ionic strength. Moreover, the abundant availability of the surface hydroxyl groups on the nanocellulose facilitates various surface chemistries that can be explored for targeting various contaminants in water. This chapter covers the recent developments and literature of nanocellulose in the field of water purification

Robust Superhydrophobic Cellulose Nanofiber Aerogel for Multifunctional Environmental Applications

The fabrication of superadsorbent for dye adsorption is a hot research area at present. However, the development of low-cost and highly efficient superadsorbents against toxic textile dyes is still a big challenge. Here, we fabricated hydrophobic cellulose nanofiber aerogels from cellulose nanofibers through an eco-friendly silanization reaction in liquid phase, which is an extremely efficient, rapid, cheap, and environmentally friendly procedure. Moreover, the demonstrated eco-friendly silanization technique is easy to commercialize at the industrial level. Most of the works that have reported on the hydrophobic cellulose nanofiber aerogels explored their use for the elimination of oil from water. The key novelty of the present work is that the demonstrated hydrophobic cellulose nanofibers aerogels could serve as superadsorbents against toxic textile dyes such as crystal violet dye from water and insulating materials for building applications. Here, we make use of the possible hydrophobic interactions between silane-modified cellulose nanofiber aerogel and crystal violet dye for the removal of the crystal violet dye from water. With a 10 mg/L of crystal violet (CV) aqueous solution, the silane-modified cellulose nanofiber aerogel showed a high adsorption capacity value of 150 mg/g of the aerogel. The reason for this adsorption value was due to the short-range hydrophobic interaction between the silane-modified cellulose nanofiber aerogel and the hydrophobic domains in crystal violet dye molecules. Additionally, the fabricated silane-modified cellulose nanofiber hydrophobic aerogels exhibited a lower thermal conductivity value of 0.037 W&middot;m&minus;1 K&minus;1, which was comparable to and lower than the commercial insulators such as mineral wools (0.040 W&middot;m&minus;1 K&minus;1) and polystyrene foams (0.035 W&middot;m&minus;1 K&minus;1). We firmly believe that the demonstrated silane-modified cellulose nanofiber aerogel could yield an eco-friendly adsorbent that is agreeable to adsorbing toxic crystal violet dyes from water as well as active building thermal insulators

Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers

Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity