Female Gametophyte Development in Higher Plants - Meiosis and Mitosis Break the Cellular Barrier

Abstract: Meiotic products in higher plants should undergo a determined number of mitotic cycles before differentiating gametes. This creates a unique meiosis-mitosis interface, traverse of which is an absolute requirement for gametophyte development. In the absence of cytokinesis during megasporogenesis - as seen in the bisporic and tetrasporic types - the haploid nuclei produced by meiosis are driven to undergo mitotic cycles within the same cell. Similarly, the last of the mitotic cycles leads to a unique type of cell wall formation resulting in cellularization of the coenocytic female gametophyte, creating a mitosis-cellularization interface. Cell cycle regulation in terms of the molecules that interface with these two key spatio-temporal developmental settings should be of interest to both cell and developmental biologists. High throughput techniques of functional genomics are required for both interpretation of female gametophyte evolution and success of the biotechnological initiatives of transferring apomixis-related genes to crop plants.     

Tertiary motifs as building blocks for the design of protein‐binding peptides

Despite advances in protein engineering, the de novo design of small proteins or peptides that bind to a desired target remains a difficult task. Most computational methods search for binder structures in a library of candidate scaffolds, which can lead to designs with poor target complementarity and low success rates. Instead of choosing from pre‐defined scaffolds, we propose that custom peptide structures can be constructed to complement a target surface. Our method mines tertiary motifs (TERMs) from known structures to identify surface‐complementing fragments or “seeds.” We combine seeds that satisfy geometric overlap criteria to generate peptide backbones and score the backbones to identify the most likely binding structures. We found that TERM‐based seeds can describe known binding structures with high resolution: the vast majority of peptide binders from 486 peptide‐protein complexes can be covered by seeds generated from single‐chain structures. Furthermore, we demonstrate that known peptide structures can be reconstructed with high accuracy from peptide‐covering seeds. As a proof of concept, we used our method to design 100 peptide binders of TRAF6, seven of which were predicted by Rosetta to form higher‐quality interfaces than a native binder. The designed peptides interact with distinct sites on TRAF6, including the native peptide‐binding site. These results demonstrate that known peptide‐binding structures can be constructed from TERMs in single‐chain structures and suggest that TERM information can be applied to efficiently design novel target‐complementing binders.     

Interface Engineering of Hierarchical Branched Mo‐Doped Ni3S2/NixPy Hollow Heterostructure Nanorods for Efficient Overall Water Splitting

Rational design and construction of bifunctional electrocatalysts with excellent activity and durability is imperative for water splitting. Herein, a novel top‐down strategy to realize a hierarchical branched Mo‐doped sulfide/phosphide heterostructure (Mo‐Ni₃S₂/Ni_xP_y hollow nanorods), by partially phosphating Mo‐Ni₃S₂/NF flower clusters, is proposed. Benefitting from the optimized electronic structure configuration, hierarchical branched hollow nanorod structure, and abundant heterogeneous interfaces, the as‐obtained multisite Mo‐Ni₃S₂/Ni_xP_y/NF electrode has remarkable stability and bifunctional electrocatalytic activity in the hydrogen evolution reaction (HER)/oxygen evolution reaction (OER) in 1 m KOH solutions. It possesses an extremely low overpotential of 238 mV at the current density of 50 mA cm^?2 for OER. Importantly, when assembled as anode and cathode simultaneously, it merely requires an ultralow cell voltage of 1.46 V to achieve the current density of 10 mA cm^?2, with excellent durability for over 72 h, outperforming most of the reported Ni‐based bifunctional materials. Density functional theory results further confirm that the doped heterostructure can synergistically optimize Gibbs free energies of H and O‐containing intermediates (OH*, O*, and OOH*) during HER and OER processes, thus accelerating the catalytic kinetics of electrochemical water splitting. This work demonstrates the importance of the rational combination of metal doping and interface engineering for advanced catalytic materials.     

A novel electroconductive interface based on Fe3O4 magnetic nanoparticle and cysteamine functionalized AuNPs: Preparation and application as signal amplification element to minoring of antigen‐antibody immunocomplex and biosensing of prostate cancer

In this study, a novel electroconductive interface was prepared based on Fe₃O₄ magnetic nanoparticle and cysteamine functionalized gold nanoparticle. The engineered interface was used as signal amplification substrate in the electrochemical analysis of antibody‐antigen binding. For this purpose, biotinilated‐anti‐prostate‐specific antigen (PSA) antibody was bioconjugated with iron oxide magnetic nanoparticles (Fe₃O₄) and drop‐casted on the surface of glassy carbon electrode (GCE). Also, secondary antibody (HRP‐Ab2) encapsulated on gold nanoparticles caped by cysteamine was immobilized on the surface of GCE modified electrode. A transmission electron microscopy images shows that a sandwich immunoreaction was done and binding of Ab1 and Ab2 performed successfully. Various parameters of immunoassay, including the loading of magnetic nanoparticles, the amount of gold nanoparticle conjugate, and the immunoreaction time, were optimized. The detection limit of 0.001 μg. L^?1 of PSA was obtained under optimum experimental conditions. It is found that such magneto‐bioassay could be readily used for simultaneous parallel detection of multiple proteins by using multiple inorganic metal nanoparticle tracers and are expected to open new opportunities for early stage diagnosis of cancer in near future.     

Finite Element Analysis of Tibial Implants — Effect of Fixation Design and Friction Model

Abstract

A three dimensional nonlinear finite element model was developed to investigate tibial fixation designs and friction models (Coulomb's vs nonlinear) in total knee arthroplasty in the immediate postoperative period with no biological attachment. Bi-directional measurement-based nonlinear friction constitutive equations were used for the bone-porous coated implant interface. Friction properties between the polyethylene and femoral components were measured for this study. Linear elastic isotropic but heterogeneous mechanical properties taken from literature were considered for the bone. The Tensile behaviour of polyethylene was measured and subsequently modeled by an elasto-plastic model. Based on the earlier finite element and experimental pull-out studies, pegs and screws were also realistically modeled. The geometry of every component was obtained through measurement. The PCA tibial baseplate with three different configurations was considered; one with three screws, one with one screw and two short inclined porous-coated pegs, and a third one with no fixation for the sake of comparison. The axial load of 2000N was applied through the femoral component on the medial plateau of articular insert. It was found that Coulomb's friction significantly underestimates the relative micromotion at the bone-implant interface. The lowest micromotion and lift-off were found for the design with screws. Relative micromotion and stress transfer at the bone-implant interface depended significantly on the friction model and on the baseplate anchorage configuration. Cortical and cancellous bones carried, respectively, 10–13% and 65–86% of the axial load depending on the fixation configuration used. The remaining portion was transmitted as shear force by screws and pegs. Normal and Mises stresses as well as contact area in the polyethylene insert were nearly independent of the baseplate fixation design. The Maximum Mises stress in the polyethylene exceeded yield and was found 1–2 mm below the contact surface for all designs.     

Intact Histological Characterization of Brain-implanted Microdevices and Surrounding Tissue

Research into the design and utilization of brain-implanted microdevices, such as microelectrode arrays, aims to produce clinically relevant devices that interface chronically with surrounding brain tissue. Tissue surrounding these implants is thought to react to the presence of the devices over time, which includes the formation of an insulating "glial scar" around the devices. However, histological analysis of these tissue changes is typically performed after explanting the device, in a process that can disrupt the morphology of the tissue of interest.Here we demonstrate a protocol in which cortical-implanted devices are collected intact in surrounding rodent brain tissue. We describe how, once perfused with fixative, brains are removed and sliced in such a way as to avoid explanting devices. We outline fluorescent antibody labeling and optical clearing methods useful for producing an informative, yet thick tissue section. Finally, we demonstrate the mounting and imaging of these tissue sections in order to investigate the biological interface around brain-implanted devices.     

Bottom‐up proteome analysis of E. coli using capillary zone electrophoresis‐tandem mass spectrometry with an electrokinetic sheath‐flow electrospray interface

The Escherichia coli proteome was digested with trypsin and fractionated using SPE on a C18 SPE column. Seven fractions were collected and analyzed by CZE‐ESI‐MS/MS. The separation was performed in a 60‐cm‐long linear polyacrylamide‐coated capillary with a 0.1% v/v formic acid separation buffer. An electrokinetic sheath‐flow electrospray interface was used to couple the separation capillary with an Orbitrap‐Velos operating in higher‐energy collisional dissociation mode. Each CZE‐ESI‐MS/MS run lasted 50 min and total MS time was 350 min. A total of 23 706 peptide spectra matches, 4902 peptide IDs, and 871 protein group IDs were generated using MASCOT with false discovery rate less than 1% on the peptide level. The total mass spectrometer analysis time was less than 6 h, the sample identification rate (145 proteins/h) was more than two times higher than previous studies of the E. coli proteome, and the amount of sample consumed (<1 μg) was roughly fourfold less than previous studies. These results demonstrate that CZE is a useful tool for the bottom‐up analysis of prokaryote proteomes.     

Role of tyrosine hot‐spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study

The endonuclease activity of the bacterial colicin 9 enzyme is controlled by the specific and high‐affinity binding of immunity protein 9 (Im9). Molecular dynamics simulation studies in explicit solvent were used to investigate the free energy change associated with the mutation of two hot‐spot interface residues [tyrosine (Tyr): Tyr54 and Tyr55] of Im9 to Ala. In addition, the effect of several other mutations (Leu33Ala, Leu52Ala, Val34Ala, Val37Ala, Ser48Ala, and Ile53Ala) with smaller influence on binding affinity was also studied. Good qualitative agreement of calculated free energy changes and experimental data on binding affinity of the mutations was observed. The simulation studies can help to elucidate the molecular details on how the mutations influence protein–protein binding affinity. The role of solvent and conformational flexibility of the partner proteins was studied by comparing the results in the presence or absence of solvent and with or without positional restraints. Restriction of the conformational mobility of protein partners resulted in significant changes of the calculated free energies but of similar magnitude for isolated Im9 and for the complex and therefore in only modest changes of binding free energy differences. Although the overall binding free energy change was similar for the two Tyr–Ala mutations, the physical origin appeared to be different with solvation changes contributing significantly to the Tyr55Ala mutation and to a loss of direct protein–protein interactions dominating the free energy change due to the Tyr54Ala mutation. Proteins 2013. © 2012 Wiley Periodicals, Inc.