p62, Ref(2)P and ubiquitinated proteins are conserved markers of neuronal aging,aggregate formation and progressive autophagic defects

Suppression of macroautophagy, due to mutations or through processes linked to aging, results in the accumulation of cytoplasmic substrates that are normally eliminated by the pathway. This is a significant problem in long-lived cells like neurons, where pathway defects can result in the accumulation of aggregates containing ubiquitinated proteins. The p62/Ref(2)P family of proteins is involved in the autophagic clearance of cytoplasmic protein bodies or sequestosomes. These unique structures are closely associated with protein inclusions containing ubiquitin as well as key components of the autophagy pathway. In this study we show that detergent fractionation followed by western blot analysis of insoluble ubiquitinated proteins (IUP), mammalian p62 and its Drosophila homologue, Ref(2)P can be used to quantitatively assess the activity level of aggregate clearance (aggrephagy) in complex tissues. Using this technique we show that genetic or age-dependent changes that modify the long-term enhancement or suppression of aggrephagy can be identified. Moreover, using the Drosophila model system this method can be used to establish autophagy-dependent protein clearance profiles that are occurring under a wide range of physiological conditions including developmental, fasting and altered metabolic pathways. This technique can also be used to examine proteopathies that are associated with human disorders such as frontotemporal dementia, Huntington and Alzheimer disease. Our findings indicate that measuring IUP profiles together with an assessment of p62/Ref(2)P proteins can be used as a screening or diagnostic tool to characterize genetic and age-dependent factors that alter the long-term function of autophagy and the clearance of protein aggregates occurring within complex tissues and cells.     

p62, Ref(2)P and ubiquitinated proteins are conserved markers of neuronal aging, aggregate formation and progressive autophagic defects

Suppression of macroautophagy, due to mutations or through processes linked to aging, results in the accumulation of cytoplasmic substrates that are normally eliminated by the pathway. This is a significant problem in long-lived cells like neurons, where pathway defects can result in the accumulation of aggregates containing ubiquitinated proteins. The p62/Ref(2)P family of proteins is involved in the autophagic clearance of cytoplasmic protein bodies or sequestosomes. These unique structures are closely associated with protein inclusions containing ubiquitin as well as key components of the autophagy pathway. In this study we show that detergent fractionation followed by western blot analysis of insoluble ubiquitinated proteins (IUP), mammalian p62 and its Drosophila homologue, Ref(2)P can be used to quantitatively assess the activity level of aggregate clearance (aggrephagy) in complex tissues. Using this technique we show that genetic or age-dependent changes that modify the long-term enhancement or suppression of aggrephagy can be identified. Moreover, using the Drosophila model system this method can be used to establish autophagy-dependent protein clearance profiles that are occurring under a wide range of physiological conditions including developmental, fasting and altered metabolic pathways. This technique can also be used to examine proteopathies that are associated with human disorders such as frontotemporal dementia, Huntington and Alzheimer disease. Our findings indicate that measuring IUP profiles together with an assessment of p62/Ref(2)P proteins can be used as a screening or diagnostic tool to characterize genetic and age-dependent factors that alter the long-term function of autophagy and the clearance of protein aggregates occurring within complex tissues and cells.     

Automated Cell Enrichment of Cytomegalovirus-specific T cells for Clinical Applications using the Cytokine-capture System

The adoptive transfer of pathogen-specific T cells can be used to prevent and treat opportunistic infections such as cytomegalovirus (CMV) infection occurring after allogeneic hematopoietic stem-cell transplantation. Viral-specific T cells from allogeneic donors, including third party donors, can be propagated ex vivo in compliance with current good manufacturing practice (cGMP), employing repeated rounds of antigen-driven stimulation to selectively propagate desired T cells. The identification and isolation of antigen-specific T cells can also be undertaken based upon the cytokine capture system of T cells that have been activated to secrete gamma-interferon (IFN-γ). However, widespread human application of the cytokine capture system (CCS) to help restore immunity has been limited as the production process is time-consuming and requires a skilled operator. The development of a second-generation cell enrichment device such as CliniMACS Prodigy now enables investigators to generate viral-specific T cells using an automated, less labor-intensive system. This device separates magnetically labeled cells from unlabeled cells using magnetic activated cell sorting technology to generate clinical-grade products, is engineered as a closed system and can be accessed and operated on the benchtop. We demonstrate the operation of this new automated cell enrichment device to manufacture CMV pp65-specific T cells obtained from a steady-state apheresis product obtained from a CMV seropositive donor. These isolated T cells can then be directly infused into a patient under institutional and federal regulatory supervision. All the bio-processing steps including removal of red blood cells, stimulation of T cells, separation of antigen-specific T cells, purification, and washing are fully automated. Devices such as this raise the possibility that T cells for human application can be manufactured outside of dedicated good manufacturing practice (GMP) facilities and instead be produced in blood banking facilities where staff can supervise automated protocols to produce multiple products.     

Continuous measurement of lysis of radioactively marked fibrin clots

Methods for continuous measurement of dissolution of experimentally induced radioactively labelled thrombi were described. They are suited for the use in artificial circulating systems and in animal experiments. The radioactivity can be measured continuously in a circulating system by fitting a flow through cell with a well scintillator. In order to measure thrombotic processes in vivo, we developed a specially adapted single hole collimator. By this device changes in radioactivity over a defined occluded area of the vessel could be detected. The usefulness of the methods was demonstrated by means of a thrombolytic agent.     

铁硫簇的生物合成

铁硫簇在细胞的生物学过程中起着重要的作用,可参与电子传递、代谢控制和基因调节等过程。研究显示铁硫簇具有多样性,它的合成依赖于ISC和SUF系统,固氮酶中还需要NIF系统的参与。ISC系统由iscSUA-hscBA-fdx基因串编码,合成的是一类“管家”蛋白,适于在正常条件下表达。SUF系统由基因串sufABCDSE编码,常在恶劣环境如氧化应激和铁饥饿条件下表达。NIF系统由nifSU基因编码,适于固氮酶(厌氧条件下起作用)铁硫簇的合成。     

High-throughput Gene Tagging in Trypanosoma brucei

Improvements in mass spectrometry, sequencing and bioinformatics have generated large datasets of potentially interesting genes. Tagging these proteins can give insights into their function by determining their localization within the cell and enabling interaction partner identification. We recently published a fast and scalable method to generate Trypanosoma brucei cell lines that express a tagged protein from the endogenous locus. The method was based on a plasmid we generated that, when coupled with long primer PCR, can be used to modify a gene to encode a protein tagged at either terminus. This allows the tagging of dozens of trypanosome proteins in parallel, facilitating the large-scale validation of candidate genes of interest. This system can be used to tag proteins for localization (using a fluorescent protein, epitope tag or electron microscopy tag) or biochemistry (using tags for purification, such as the TAP (tandem affinity purification) tag). Here, we describe a protocol to perform the long primer PCR and the electroporation in 96-well plates, with the recovery and selection of transgenic trypanosomes occurring in 24-well plates. With this workflow, hundreds of proteins can be tagged in parallel; this is an order of magnitude improvement to our previous protocol and genome scale tagging is now possible.     

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells

Many microbial cells have the ability to form sessile microbial communities defined as biofilms that have altered physiological and pathological properties compared to free living microorganisms. Biofilms in nature are often difficult to investigate and reside under poorly defined conditions¹. Using a transparent substratum it is possible to device a system where simple biofilms can be examined in a non-destructive way in real-time: here we demonstrate the assembly and operation of a flow cell model system, for in vitro 3D studies of microbial biofilms generating high reproducibility under well-defined conditions^2,3.The system consists of a flow cell that serves as growth chamber for the biofilm. The flow cell is supplied with nutrients and oxygen from a medium flask via a peristaltic pump and spent medium is collected in a waste container. This construction of the flow system allows a continuous supply of nutrients and administration of e.g. antibiotics with minimal disturbance of the cells grown in the flow chamber. Moreover, the flow conditions within the flow cell allow studies of biofilm exposed to shear stress. A bubble trapping device confines air bubbles from the tubing which otherwise could disrupt the biofilm structure in the flow cell.The flow cell system is compatible with Confocal Laser Scanning Microscopy (CLSM) and can thereby provide highly detailed 3D information about developing microbial biofilms. Cells in the biofilm can be labeled with fluorescent probes or proteins compatible with CLSM analysis. This enables online visualization and allows investigation of niches in the developing biofilm. Microbial interrelationship, investigation of antimicrobial agents or the expression of specific genes, are of the many experimental setups that can be investigated in the flow cell system.     

The Chimpanzee as a Model to Test the Side Effects of Human Interferons

Interferons are naturally occurring proteins that are currently under evaluation as potential antiviral and antitumor agents. Currently all human interferons can in principle be produced in adequate amounts by recombinant DNA technology. Human interferons produce side effects, but because they are species-specific the toxicity cannot be tested in lower mammals. The chimpanzee is the only species in which the side effects of human interferon can be reproduced, and only in this species the toxicity of human interferons can be screened.     

Automatic Classification and Pattern Discovery in High-throughput Protein Crystallization Trials

Conceptually, protein crystallization can be divided into two phases search and optimization. Robotic protein crystallization screening can speed up the search phase, and has a potential to increase process quality. Automated image classification helps to increase throughput and consistently generate objective results. Although the classification accuracy can always be improved, our image analysis system can classify images from 1536-well plates with high classification accuracy (85%) and ROC score (0.87), as evaluated on 127 human-classified protein screens containing 5600 crystal images and 189472 non-crystal images. Data mining can integrate results from high-throughput screens with information about crystallizing conditions, intrinsic protein properties, and results from crystallization optimization. We apply association mining, a data mining approach that identifies frequently occurring patterns among variables and their values. This approach segregates proteins into groups based on how they react in a broad range of conditions, and clusters cocktails to reflect their potential to achieve crystallization. These results may lead to crystallization screen optimization, and reveal associations between protein properties and crystallization conditions. We also postulate that past experience may lead us to the identification of initial conditions favorable to crystallization for novel proteins.     

Detection of proteins and bacteria using an array of feedback capacitance sensors

An integrated array of micron-dimension capacitors, originally developed for biometric applications (fingerprint identification), was engineered for detection of biological agents such as proteins and bacteria. This device consists of an array of 93,184 (256 x 364) individual capacitor-based sensing elements located underneath a thin (0.8 microm) layer of glass. This glass layer can be functionalized with organosilane-based monolayers to provide groups amenable for the immobilization of bioreceptors such as antibodies, enzymes, peptides, aptamers, and nucleotides. Upon functionalization with antibodies and in conjunction with signal amplification schemes that result in perturbation of the dielectric constant around the captured antigens, this system can be used as a detector of biological agents. Two signal amplification schemes were tested in this work: one consisted of 4 microm diameter latex immunobeads and a second one was based on colloidal gold catalyzed reduction of silver. These signal amplification approaches were demonstrated and show that this system is capable of specific detection of bacteria (Escherichia coli) and proteins (ovalbumin). The present work shows proof-of-principle demonstration that a simple fingerprint detector based on feedback capacitance measurements can be implemented as a biosensor. The approach presented could be easily expanded to simultaneously test for a large number of analytes and multiple samples given that this device has a large number of detectors. The device and required instrumentation is highly portable and does not require expensive and bulky instrumentation because it relies purely on electronic detection.     

Learning and evolution in bacterial taxis: an operational amplifier circuit modeling the computational dynamics of the prokaryotic 'two component system' protein network

Adaptive behavior in unicellular organisms (i.e., bacteria) depends on highly organized networks of proteins governing purposefully the myriad of molecular processes occurring within the cellular system. For instance, bacteria are able to explore the environment within which they develop by utilizing the motility of their flagellar system as well as a sophisticated biochemical navigation system that samples the environmental conditions surrounding the cell, searching for nutrients or moving away from toxic substances or dangerous physical conditions. In this paper we discuss how proteins of the intervening signal transduction network could be modeled as artificial neurons, simulating the dynamical aspects of the bacterial taxis. The model is based on the assumption that, in some important aspects, proteins can be considered as processing elements or McCulloch-Pitts artificial neurons that transfer and process information from the bacterium's membrane surface to the flagellar motor. This simulation of bacterial taxis has been carried out on a hardware realization of a McCulloch-Pitts artificial neuron using an operational amplifier. Based on the behavior of the operational amplifier we produce a model of the interaction between CheY and FliM, elements of the prokaryotic two component system controlling chemotaxis, as well as a simulation of learning and evolution processes in bacterial taxis. On the one side, our simulation results indicate that, computationally, these protein 'switches' are similar to McCulloch-Pitts artificial neurons, suggesting a bridge between evolution and learning in dynamical systems at cellular and molecular levels and the evolutive hardware approach. On the other side, important protein 'tactilizing' properties are not tapped by the model, and this suggests further complexity steps to explore in the approach to biological molecular computing.     

Adaptive filter mechanisms in human vision

As a result of our experiments we find that the absolute visibility of simple edge and bar patterns is determined by a cooperation between the maximum amplitude and the difference between the maximum gradients occurring in the patterns. Proceeding from the assumption that the second spatial derivative represents a basic mechanism in our visual system (Mach-bands, effects of masking between narrow lines and sharp edges, existence of even-symmetrical receptive fields in the retina and the LGN), we suggest a nonlinear summation device which produces the difference between gradients as a sum over the second derivative. Expressed in a slightly different manner we assume that the sum over the excitation embodied in a Mach-band acts as criterion during the absolute visibility of edge and bar patterns.     

An assessment of the Sartorius MD8 microbiological air sampler

Tests described in this paper show that gelatine membrane filters used in the MD8 microbiological air sampling system collected monodispersed aerosols between 0·7 and 1·0 μm containing viable Bacillus subtilis var. niger spores, with an efficiency of 99·9995%. Gelatine membrane filters linked to the MD8 control pump system were as effective as the well established Casella slit-to-agar device for collecting some viable bacteria, nebulized under controlled experimental conditions and naturally occurring airborne micro-organisms in a pharmaceutical plant. By using a long flexible hose connection to the control pump, the head could be positioned where sampling was required in locations remote from the pump exhaust, making it suitable for microbiological monitoring in critical locations such as laminar flow stations and isolators.     

Statistical process control for electron beam monitoring

PurposeTo assess the electron beam monitoring statistical process control (SPC) in linear accelerator (linac) daily quality control. We present a long-term record of our measurements and evaluate which SPC-led conditions are feasible for maintaining control.MethodsWe retrieved our linac beam calibration, symmetry, and flatness daily records for all electron beam energies from January 2008 to December 2013, and retrospectively studied how SPC could have been applied and which of its features could be used in the future. A set of adjustment interventions designed to maintain these parameters under control was also simulated.ResultsAll phase I data was under control. The dose plots were characterized by rising trends followed by steep drops caused by our attempts to re-center the linac beam calibration. Where flatness and symmetry trends were detected they were less-well defined. The process capability ratios ranged from 1.6 to 9.3 at a 2% specification level. Simulated interventions ranged from 2% to 34% of the total number of measurement sessions. We also noted that if prospective SPC had been applied it would have met quality control specifications.ConclusionsSPC can be used to assess the inherent variability of our electron beam monitoring system. It can also indicate whether a process is capable of maintaining electron parameters under control with respect to established specifications by using a daily checking device, but this is not practical unless a method to establish direct feedback from the device to the linac can be devised.     

Proteomics unravels the exportability of mitochondrial respiratory chains

Expression of F1Fo-ATP synthase, which generates the majority of cellular ATP and is believed to be strictly confined to mitochondria, has recently been identified in ectopic locations, together with the four complexes of oxidative phosphorylation (OXPHOS) or enzymes from the Krebs cycle. Identification of these proteins has mostly been accomplished by proteomic methods and mass spectrometry - techniques that hold great promise in increasing our understanding of the proteome. The ectopic presence of ATP synthase has variably been attributed to contamination of the sample or to its action as a cell-surface receptor for apparently unrelated ligands, but OXPHOS proteins have sometimes been found to be catalytically active in oxidative phosphorylation, as they were true components of the system under investigation. The present article focuses on how mass spectrometry can increase our understanding of the proteome of subcellular membranes. We review the recent evidence for an extra-mitochondrial expression of OXPHOS by proteomics studies, highlighting what we can learn by combining these data.     

Coupled plasmon-waveguide resonance spectroscopy studies of the cytochrome b6f/plastocyanin system in supported lipid bilayer membranes.

The incorporation of cytochrome (cyt) b6f into a solid-supported planar egg phosphatidylcholine (PC) bilayer membrane and complex formation with plastocyanin have been studied by a variant of surface plasmon resonance called coupled plasmon-waveguide resonance (CPWR) spectroscopy, developed in our laboratory. CPWR combines greatly enhanced sensitivity and spectral resolution with direct measurement of anisotropies in refractive index and optical extinction coefficient, and can therefore probe structural properties of lipid-protein and protein-protein interactions. Cyt b6f incorporation into the membrane proceeds in two stages. The first occurs at low protein concentration and is characterized by an increase in total proteolipid mass without significant changes in the molecular order of the system, as demonstrated by shifts of the resonance position to larger incident angles without changing the refractive index anisotropy. The second stage, occurring at higher protein concentrations, results in a decrease in both the mass density and the molecular order of the system, evidenced by shifts of the resonance position to smaller incident angles and a large decrease in the membrane refractive index anisotropy. Plastocyanin can bind to such a proteolipid system in three different ways. First, the addition of plastocyanin before the second stage of b6f incorporation begins results in complex formation between the two proteins with a KD of approximately 10 microM and induces structural changes in the membrane that are similar to those occurring during the second stage of complex incorporation. The addition of larger amounts of plastocyanin under these conditions leads to nonspecific binding to the lipid phase with a KD of approximately 180 microM. Finally, the addition of plastocyanin after the completion of the second phase of b6f incorporation results in tighter binding between the two proteins (KD approximately 1 microM). Quantitation of the binding stoichiometry indicates that two plastocyanin molecules bind tightly to the dimeric form of the cyt b6f complex, assuming random insertion of the cytochrome into the bilayer. The structural basis for these results and formation of the proteolipid membrane are discussed.     

Chemically methylated DNA repair in Escherichia coli--the role of alkB protein

Methylating agents belong to mutagens occurring most frequently in our environment. They methylate mainly the nitrogen bases in DNA and RNA, affecting their functions. In E. coli the alkylated bases are repaired by proteins and enzymes either permanently present in the cells (Ogt, Ada) or produced transiently (Ada, AlkB, AlkA, Aid), after induction of the Ada defence system. Alkylating agents induce also the SOS system, which enhances the synthesis of about 40 proteins, including those participating in recombination, replication and mutagenesis of DNA. All DNA interactions, modifications and repairs constitute an amazing and highly efficiently functioning cellular system. Among the repair proteins there are some which affect the alkylated bases in a non-conventional way, very rarely occurring in nature. Especially amazing is the mechanism of action of dioxogenase AlkB, which combines the repair of methyl-, ethyl- and etheno-base derivatives with oxidation and dissociation of the modified groups, leading to direct recovery of natural bases. This review attempts to elucidate the role of the individual proteins involved in the repair processes.     

Proteomics unravels the exportability of mitochondrial respiratory chains

Expression of F1Fo-ATP synthase, which generates the majority of cellular ATP and is believed to be strictly confined to mitochondria, has recently been identified in ectopic locations, together with the four complexes of oxidative phosphorylation (OXPHOS) or enzymes from the Krebs cycle. Identification of these proteins has mostly been accomplished by proteomic methods and mass spectrometry – techniques that hold great promise in increasing our understanding of the proteome. The ectopic presence of ATP synthase has variably been attributed to contamination of the sample or to its action as a cell-surface receptor for apparently unrelated ligands, but OXPHOS proteins have sometimes been found to be catalytically active in oxidative phosphorylation, as they were true components of the system under investigation. The present article focuses on how mass spectrometry can increase our understanding of the proteome of subcellular membranes. We review the recent evidence for an extra-mitochondrial expression of OXPHOS by proteomics studies, highlighting what we can learn by combining these data.     

Application of the "codon-shuffling" method. Synthesis and selection of de novo proteins as antibacterials

Library-based methods of non-rational and part-rational designed de novo peptides are worthy beacons in the search for bioactive peptides and proteins of medicinal importance. In this report, we have used a recently developed directed evolution method called "codon shuffling" for the synthesis and selection of bioactive proteins. The selection of such proteins was based on the creation of an inducible library of "codon-shuffled" genes that are constructed from the ligation-based assembly of judiciously designed hexamer DNA duplexes called dicodons. Upon induction with isopropyl 1-thio-beta-D-galactopyranoside, some library members were found to express dicodon-incorporated proteins. Because of this, the host cells, in our case Escherichia coli, were unable to grow any further. The bactereostatic/lytic nature of the dicodon proteins was monitored by growth curves as well as by zone clearance studies. Transmission electron microscopy of the affected cells illustrated the extent of cell damage. The proteins themselves were overexpressed as fusion partners and subsequently purified to homogeneity. One such purified protein was found to strongly bind heparin, an indication that the interaction of the de novo proteins may be with the nucleic acids of the host cell, much like many of the naturally occurring antibacterial peptides, e.g. Buforin. Therefore, our approach may help in generating a multitude of finely tuned antibacterial proteins that can potentially be regarded as lead compounds once the method is extended to pathogenic hosts, such as Mycobacteria, for example.