A multifunctional system for automating physiological experiments

The methodical problems of automatization of physiological investigations on the basis of modern computer complexes "micro-CAMAC-lab" are discussed. The considered conceptions are illustrated by example of CAMEX-program-system ensuring the measurement, storing, visual control, editing and analysis of physiological experimental data.     

A model for streamlining and automating path exchange hybrid life cycle assessment

The International Journal of Life Cycle Assessment - Life cycle assessment (LCA) is inherently complex and time consuming. The compilation of life cycle inventories (LCI) using a traditional...     

Flagellar regeneration in Chlamydomonas: a model system for studying organelle assembly

How do the many different components of an organelle assemble into a functional structure at an appropriate place and time? Flagellar regeneration by the biflagellate green alga Chlamydomonas is one experimental system in which genetics, biochemistry and ultrastructural analysis are being combined to investigate the assembly of a microtubule-containing organelle. Recent advances in the molecular biology of this 'green yeast' have made possible several new approaches to the problem of flagellar assembly; insights from these new approaches are the focus of this review.     

A model two-component system for studying the architecture of elastin assembly in vitro

Tropoelastin is encoded by a single human gene that spans 36 exons and is oxidized in vivo by mammalian lysyl oxidase at the epsilon amino group of available lysines to give the adipic semialdehyde, which then facilitates covalent cross-link formation in an enzyme-free process involving tropoelastin association. We demonstrate here that this process is effectively modeled by a two protein component system using purified lysyl oxidase from the yeast Pichia pastoris to facilitate the oxidation and subsequent cross-linking of recombinant human tropoelastin. The oxidized human tropoelastin forms an elastin-like polymer (EL) that is elastic, shows hydrogel behavior and contains typical elastin cross-links including lysinonorleucine, allysine aldol, and desmosine. Protease digestion and subsequent mass-spectrometry analysis of multiple ELs allowed for the identification of specific intra- and inter-molecular cross-links, leading to a model of the molecular architecture of elastin assembly in vitro. Specific intra-molecular cross-links were confined to the region of tropoelastin encoded by exons 6-15. Inter-molecular cross-links were prevalent between the regions encoded by exons 19-25. We find that assembly of tropoelastin molecules in ELs are highly enriched for a defined subset of cross-links.     

A model chromatin assembly system. Factors affecting nucleosome spacing

Poly[d(A-T)].poly[d(A-T)], when reconstituted with chicken erythrocyte core histones and subsequently incubated with sufficient histone H5 in a solution containing polyglutamic acid, forms structures resembling chromatin. H5 induces nucleosome alignment in about two hours at physiological ionic strength and 37 degrees C. The nucleosome spacing and apparent linker heterogeneity in the assembled nucleoprotein are very similar to those in chicken erythrocyte chromatin. Also, condensed chromatin-like fibers on the polynucleotide can be visualized. The binding of one mole of H5 per mole of core octamer is necessary to generate the physiological nucleosome spacing, which remains constant with the addition of more H5. The nucleosome repeat length is not a function of the core histone to poly[d(A-T)] ratio for values lower than the physiological ratio. With increasing ratios, in excess of the physiological value, nucleosome spacing first becomes non-uniform, and then takes on the close packing limit of approximately 165 base-pairs. In addition to eliminating possible base sequence effects on nucleosome positioning, poly[d(A-T)] allows nucleosomes to slide more readily than does DNA, thereby facilitating alignment. Evidence is presented that polyglutamic acid facilitates the nucleosome spacing activity of histone H5, primarily by keeping the nucleoprotein soluble. This model system should be useful for understanding how different repeat lengths arise in chromatin.     

A scheduling model for multirobot assembly cells

We propose a mixed 0–1 linear programming model for repetitive scheduling of multirobot assembly and machining cells. The approach adopted is monolithic as opposed to hierarchical to avoid system suboptimization. The model permits any number of alternative ways (or modes) to perform each operation. A mode of an operation is determined by the required resources (facilities) and the duration of their use. The model incorporates facility changeover times. Robot collisions are avoided. Several objective functions are formulated to support different purposes. The scheduling problem of a multirobot assembly cell is formulated and solved by using commercially available mathematical programming software. Solutions under four different objective functions are reported. Acknowledging the complexity and considerable size of the formulation required, we prescribe and illustrate specific methods to achieve size reduction. Finally, for successful use of our model, an information processing schema is offered as a general guidance to help data management needed by the model.     

Clathrin assembly proteins: affinity purification and a model for coat assembly

Assembly protein (AP) preparations from bovine brain coated vesicles have been fractionated by clathrin-Sepharose affinity chromatography. Two distinct fractions that possess coat assembly activity were obtained and are termed AP-1 and AP-2. The AP-1, not retained on the resin, has principal components with molecular weights of 108,000, 100,000, 47,000, and 19,000. The AP-2, bound to the resin and eluted by Tris-HCl at a concentration that parallels the latter's effect on coat disassembly, corresponds to the active complex described previously (Zaremba, S., and J. H. Keen, 1983, J. Cell Biol., 97:1339-1347). Its composition is similar to that of the AP-1 in that it contains 100,000-, 50,000-, and 16,000-mol-wt polypeptides in equimolar amounts; minor amounts of 112,000- and 115,000-mol-wt polypeptides are also present. Both are distinct from a recently described assembly protein of larger subunit molecular weight that we term AP-3. These results indicate the existence of a family of assembly proteins within cells. On incubation with clathrin both AP-1 and AP-2 induce the formation of coat structures, those containing AP-1 slightly smaller (mean diameter = 72 nm) than those formed in the presence of AP-2 (mean diameter = 79 nm); both structures have been detected previously in coated vesicle preparations from brain. Coats formed in the presence of AP-2 consistently contain approximately one molecule each of the 100,000-, 50,000-, and 16,000-mol-wt polypeptides per clathrin trimer. By low angle laser light scattering the molecular weight of native AP-2 was determined to be approximately 343,000, indicating that it is a dimer of each of the three subunits, and implying that it is functionally bivalent in clathrin binding. A model for AP-mediated coat assembly is proposed in which a bivalent AP-2 molecule bridges the distal legs or terminal domains of two clathrin trimers that are destined to occupy adjacent vertices in the assembled coat. Binding of a second AP-2 molecule locks these two trimers in register for assembly and further addition of AP-2 to free trimer legs promotes completion of the clathrin lattice. Effects of AP binding on the angle and flexibility of the legs at the hub of the trimer (the "pucker") are suggested to account for the characteristic size distributions of coats formed under varied conditions and, more speculatively, to contribute to the transformation of flat clathrin lattices to curved coated vesicles that are thought to occur during endocytosis.     

AutoFAIR-A portal for automating FAIR assessments for bioinformatics resources

BackgroundResearch in Bioinformatics generates tools and datasets in Bioinformatics at a very fast rate. Meanwhile, a lot of effort is going into making these resources findable and reusable to improve resource discovery by researchers in the course of their work.PurposeThis paper proposes a semi-automated tool to assess a resource according to the Findability, Accessibility, Interoperability and Reusability (FAIR) criteria. The aim is to create a portal that presents the assessment score together with a report that researchers can use to gauge a resource.MethodOur system uses internet searches to automate the process of generating FAIR scores. The process is semi-automated in that if a particular property of the FAIR scores has not been captured by AutoFAIR, a user is able to amend and supply the information to complete the assessment.ResultsWe compare our results against FAIRshake that was used as the benchmark tool for comparing the assessments. The results show that AutoFAIR was able to match the FAIR criteria in FAIRshake with minimal intervention from the user.ConclusionsWe show that AutoFAIR can be a good repository for storing metadata about tools and datasets, together with comprehensive reports detailing the assessments of the resources. Moreover, AutoFAIR is also able to score workflows, giving an overall indication of the FAIRness of the resources used in a scientific study.     

Reconstitution of Flock House provirions: a model system for studying structure and assembly.

Assembly of Flock House virus in infected Drosophila cells proceeds through an intermediate, the provirion, which lacks infectivity until the coat precursor protein, alpha, undergoes a spontaneous "maturation" cleavage (A. Schneemann, W. Zhong, T. M. Gallagher, and R. R. Rueckert, J. Virol 6:6728, 1992). We describe here methods for purifying provirions in a state which permitted dissociation and reassembly. Dissociation, to monomeric alpha protein and free RNA, was accomplished by freezing at pH 9.0 in the presence of 0.5 M salt and 0.1 M urea. When dialyzed at low ionic strength and pH 6.5, the dissociation products reassembled spontaneously to form homogeneous provirions with a normal complement of RNA as judged by cosedimentation with authentic virions and by ability to undergo maturation cleavage with acquisition of substantial, though subnormal, infectivity. Reconstitution experiments, i.e., remixing components after separating RNA from capsid protein, generated abnormal particles, suggesting the presence in the unfractionated dissociation products of an unidentified "nucleating" component.     

Design of single assembly line for the delayed differentiation of product variants

Delayed Product Differentiation (DPD) can reduce the manufacturing complexities arising due to the proliferation of products variety. A new optimization model constructs the optimum layout of delayed differentiation assembly lines for a mix of products to be manufactured by the same system and optimizes the position of the differentiation points. This model employs a classification tool (Cladistics) used in biological analysis and modifies it for use in planning DPD assembly lines configurations in order to incorporate the assembly precedence constraints, required production rates of different product variants and existing production capacity of work stations. The optimum layout configuration ensures that the quantities required of different products are produced on the same line; while achieving balance, minimizing duplication of stations and maximizing the overall system utilization. The developed model has been applied to a group of automobile engine accessories normally assembled on different lines. The use of Cladistics to analyze product variants that are candidates for delayed assembly is an original approach for designing the assembly line layout and identifying the best differentiation points. It also helps rationalize the design of product variants and their features to further delay their assembly differentiation and achieve economy of scale without affecting their functionality.     

Two-phase bioreactor system for cell-laden hydrogel assembly

Bottom-up approach is a potentially useful tool for hydrogel assembly of cell-laden individual building blocks. In this article, we assembled individual building blocks of photocrosslinkable microgels in a rapid and controlled manner. Individual building blocks of poly(ethylene glycol) (PEG) microgels with square and hexagonal shapes were fabricated by using a photolithography technique. Individual building blocks of PEG microgels were assembled on a hydrophobic mineral oil phase in a bioreactor with a magnetic stirrer. The hydrophobic mineral oil minimized the surface free energy to assemble hydrophilic PEG microgels on a two-phase oil-aqueous solution interface. We used the hydrophobic effect as a driving force for the hydrogel assembly. Various types of the hydrogel assembly were generated by controlling the stirring rate. As stirring speed increased, the percentage of linear, branched, and closely packed hydrogel assembly was increased. However, the percentage of random assembly was reduced by increasing stirring rate. The stirring time also played an important role in controlling the types of hydrogel assembly. The percentage of linear, branched, and closely packed hydrogel assembly was improved by increasing stirring time. Therefore, we performed directed cell-laden hydrogel assembly using a two-phase bioreactor system and optimized the stirring rate and time to regulate the desired types of hydrogel assembly. Furthermore, we analyzed cell viability of hydrogel linear assembly with square shapes, showing highly viable even after secondary photocrosslinking reaction. This bioreactor system-based hydrogel assembly could be a potentially powerful approach for creating tissue microarchitectures in a three-dimensional manner.     

A two-step scaffolding model for mitotic chromosome assembly

Topoisomerase IIalpha (topoIIalpha) and 13S condensin are both required for mitotic chromosome assembly. Here we show that they constitute the two main components of the chromosomal scaffold on histone-depleted chromosomes. The structural stability and chromosomal shape of the scaffolding toward harsh extraction procedures are shown to be mediated by ATP or its nonhydrolyzable analogs, but not ADP. TopoIIalpha and 13S condensin components immunolocalize to a radially restricted, longitudinal scaffolding in native-like chromosomes. Double staining for topoIIalpha and condensin generates a barber pole appearance of the scaffolding, where topoIIalpha- and condensin-enriched "beads" alternate; this structure appears to be generated by two juxtaposed, or coiled, chains. Cell cycle studies establish that 13S condensin appears not to be involved in the assembly of prophase chromatids; they lack this complex but contain a topoIIalpha-defined (-mediated?) scaffolding. Condensin associates only during the pro- to metaphase transition. This two-step assembly process is proposed to generate the barber pole appearance of the native-like scaffolding.     

A model for fd phage penetration and assembly

Below 15 degrees C, chloroform causes fd phage to contract to I-forms, which are compact structures about 1/3 as long as the original phage. Above 15 degrees C, chloroform causes I-forms to contract to even more compact spheroidal S-forms. Here we show that the coat protein structure in I-forms is the same as the protein structure in the phage and the protein structure in S-forms is the same as the protein structure in bilayers. The conversions from fd----I-forms----S-forms are therefore suggested to mimic steps in fd penetration. The same conversions, in reverse order, are suggested to mimic steps in fd assembly.     

Isolated rabbit enterocytes as a model cell system for investigations of chylomicron assembly and secretion.

A method is described for the isolation of viable enterocytes from rabbit small intestine. The procedure can also be used to isolate populations of epithelial cells from the crypt/villus gradient. The isolated enterocytes synthesized and secreted apoB-48 and triacylglycerol in particles of the density of chylomicrons. Secretion was stimulated by addition of bile salt/lipid micelles. Pulse-chase experiments demonstrated that newly synthesized apoB-48 is degraded intracellularly and that degradation is inhibited by provision of lipid micelles, suggesting that regulation of chylomicron assembly and secretion is broadly similar to that of very low density lipoprotein assembly in hepatocytes. This procedure for preparation of isolated enterocytes will provide a useful model system for investigation of the molecular details of chylomicron assembly.     

A recursion model for cellular production/assembly systems

This article presents an efficient algorithm for applying the recursion modeling approach to describe the transient operation of cellular production/assembly systems that incorporate features such as finite buffers, job-shop routing, lot sequencing, and material handling. Tests evaluate the approximation method relative to number of machines at a station, capacity of input/output buffers, degree of balance among station processing times, and sequencing rule. Furthermore, the method is demonstrated in application to a hypothetical industrial setting that involves the assembly of electronic circuit cards in a facility composed of several cells. All tests indicate that the method gives accurate estimates of transient performance within reasonable runtime. In comparison with earlier recursion models, this research incorporates a number of new features (see list above), improves the accuracy of approximation, and facilitates implementation with a new, more efficient algorithm.