The molecular manipulation of milk composition

The introduction of cloned genes into the mouse germ line is now routine. Although more difficult technically, gene transfer has been accomplished in farm animals and offers the potential for genetic improvement. In this regard, we have been investigating the use of transgenic animals as production vehicles for high value proteins in milk. We have shown that DNA sequences derived from the gene encoding sheep beta-lactoglobulin mediate efficient and specific expression in the mammary gland. A fusion gene comprising beta-lactoglobulin sequences and those encoding antihemophilic human factor IX has been constructed. This construct has been introduced into sheep; it is expressed in the mammary gland, and the corresponding protein is secreted into milk.     

The chemical composition of interstellar molecular clouds

Relative abundances for molecules observed by radio astronomical techniques have been determined for several interstellar regions with differing physical properties.     

The chemical composition of interstellar molecular clouds

Relative abundances for molecules observed by radio astronomical techniques have been determined for several interstellar regions with differing physical properties.     

Single molecular functional assay of ferritin arrays

In situ functional assay of each ferritin molecule in single-layer 2D arrays for horse spleen apoferritin and recombinant horse L- and human H-apoferritins was conducted by observing the iron-cores formed in the arrays by TEM. The study of the time-course, pH-dependence, and temperature-dependence of the function confirmed the iron-core formation to be due to the native function of apoferritins in array. Dark-field TEM imaging revealed that there was crystallinity in the cores in the array of recombinant human H-apoferritin. This iron-core formation was perfectly preserved in the array even after 3 months of storage at room temperature and low humidity. Moreover, about 50% of the function was found to remain in the array after it was exposed to 150 ° C in vacuum for 1 hr.     

The molecular composition of the volutin granule of yeast.

The effects of insulin on glucose uptake and lactate release in the perfused working rat heart have been investigated in three types of preparation: (i) a control low-workload preparation; (ii) an increased-pressure-workload preparation, simulating conditions of aortic pressure encountered in vivo; (iii) an increased-volume-workload preparation, where pumping work done is approximately the same as (ii) but coronary flow is restricted because of the decreased aortic pressure. Insulin stimulated glucose uptake and lactate release in preparations (i) and (ii), but failed to do so in preparation (iii). It was considered possible that preparation (iii) was hypoxic, thus necessitating a maximal stimulation of glucose uptake. This was confirmed by improving cardiac oxygenation by addition of stroma-free haemoglobin to the perfusate in preparation (iii). Under these conditions in the absence of insulin, glucose uptake and lactate release were decreased compared with perfusions in the absence of haemoglobin. Insulin stimulation of both processes was restored. We conclude that the failure of other workers to observe insulin effects on glucose uptake and lactate release under physiological workloads [preparation (ii)] may be a consequence of intracellular hypoxia in their preparations.     

High-throughput protein arrays: prospects for molecular diagnostics

High-throughput protein arrays allow the miniaturized and parallel analysis of large numbers of diagnostic markers in complex samples. Using automated colony picking and gridding, cDNA or antibody libraries can be expressed and screened as clone arrays. Protein microarrays are constructed from recombinantly expressed, purified, and yet functional proteins, entailing a range of optimized expression systems. Antibody microarrays are becoming a robust format for expression profiling of whole genomes. Alternative systems, such as aptamer, PROfusion, nano- and microfluidic arrays are all at proof-of-concept stage. Differential protein profiles have been used as molecular diagnostics for cancer and autoimmune diseases and might ultimately be applied to screening of high-risk and general populations.     

Protein arrays for gene expression and molecular interaction screening

The array format has revolutionised biomedical experimentation and diagnostics, enabling ordered high-throughput analysis. During the past decade, classic solid phase substrates, such as microtitre plates, membrane filters and microscopic slides, were turned into high-density, chip-like structures. The concept of the arrayed library was central to this development which now extends from DNA to protein. The new and versatile protein array technology allows high-throughput screening for gene expression and molecular interactions. As a major platform for functional genomics, it is already on its way into medical diagnostics.     

The reversible action of alpha-amanitin on nuclear structure and molecular composition

The effects of brief trypsin treatment on cell shape, surface topography, cytoskeletal components and the freeze-fracture distribution of plasma membrane intramembranous particles (PMP) are examined in contact-inhibited 3T3 cells. Untreated 3T3 cells are flat without many surface modifications, have highly organized microfilaments and microtubules and have clusters of PMP. Within seconds of trypsin treatment using a concentration of trypsin used for routine passage numerous zeiotic blebs appear on the cell surface which appear to “cap” or coalesce on the central superior aspect of the cell. In later stages retraction fibers are observed and the cells then round up and detach from the substrate. Using thin section transmission electron microscopy (TEM) the zeiotic blebs are observed and various constituents of the cytosol, including lysosomes, ribosomes, etc. pinch off and are surrounded by plasma membrane. In general there is a profound disruption of microfilaments and cortical microtubules. There is, however, a focal coalescence of microfilaments subjacent to the zones of the “capped” zeiotic blebs and some relative resistance of centriolar associated microtubules to tryptic degradation. Trypsin also causes profound changes in the nucleus which transforms from the normal round shape to a very convoluted and irregular shape. In addition to the zeiotic bleb formation which can be visualized by freeze-fracture the distribution of PMP goes from the normally clustered state to a more uniform distribution following treatment with trypsin. These studies suggest that there may be some coordinated control of the changes in cell surface topography, cytoskeletal components and intramembranous particle distribution.     

Self-organized density patterns of molecular motors in arrays of cytoskeletal filaments

The stationary states of systems with many molecular motors are studied theoretically for uniaxial and centered (asterlike) arrangements of cytoskeletal filaments using Monte Carlo simulations and a two-state model. Mutual exclusion of motors from binding sites of the filaments is taken into account. For small overall motor concentration, the density profiles are exponential and algebraic in uniaxial and centered filament systems, respectively. For uniaxial systems, exclusion leads to the coexistence of regions of high and low densities of bound motors corresponding to motor traffic jams, which grow upon increasing the overall motor concentration. These jams are insensitive to the motor behavior at the end of the filament. In centered systems, traffic jams remain small and an increase in the motor concentration leads to a flattening of the profile if the motors move inwards, and to the buildup of a concentration maximum in the center of the aster if motors move outwards. In addition to motor density patterns, we also determine the corresponding patterns of the motor current.     

Amino acid composition of zein molecular components

Zein extracted from maize endosperm has been fractionated into four polypeptide chains, having the following MWs 23 000, 21 000, 13 500 and 9600. By amino acid analysis the two smaller MW chains (representing 30% of total zeins) have been found to be zein-type molecules. These two chains are thought to be responsible for zein granule formation via -S-S- bridges. Zein is also highly heterogeneous in charge, and is resolved into at least 15 components, with pI's in the pH range 5–9. As demonstrated by amino acid analysis, part of this heterogeneity is due to spot mutations in some of the genes responsible for zein synthesis.     

The molecular composition of the sarcomeric M-band correlates with muscle fiber type

The M-band is the transverse structure that cross-links the thick filaments in the center and provides a perfect alignment of the A-band in the activated sarcomere. The molecular composition of the M-bands in adult mouse skeletal muscle is fiber-type dependent. All M-bands in fast fibers contain M-protein while M-bands in slow fibers contain a significant proportion of the EH-myomesin isoform, previously detected only in embryonic heart muscle. This fiber-type specificity develops during the first postnatal weeks. However, the ratio between the amounts of myosin and of myomesin, taken as sum of both isoforms, remains nearly constant in all studied muscles. Ultrastructural analysis demonstrates that some of the soleus fibers show a diffuse appearance of the M-band, resembling the situation in the embryonic heart. A model is proposed to explain the functional consequence of differential M-band composition for the physiological and morphological properties of sarcomeres in different muscle types.     

Direct observation of molecular arrays in the organized smooth endoplasmic reticulum

Background  

Tubules and sheets of endoplasmic reticulum perform different functions and undergo inter-conversion during different stages of the cell cycle. Tubules are stabilized by curvature inducing resident proteins, but little is known about the mechanisms of endoplasmic reticulum sheet stabilization. Tethering of endoplasmic reticulum membranes to the cytoskeleton or to each other has been proposed as a plausible way of sheet stabilization.     

High-throughput molecular identification of fish eggs using multiplex suspension bead arrays

The location and abundance of fish eggs provide information concerning the timing and location of spawning activities and can provide fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species' eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g. via 'DNA barcoding'). By taking advantage of a DNA barcode database, we have developed oligonucleotide probes for 23 marine fish species that produce pelagic eggs commonly found in California waters. Probes were coupled to fluorescent microspheres to create a suspension bead array. Biotin-labelled primers were used to amplify the mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from individual fish eggs. The amplicons were then hybridized to the bead array, and after the addition of a reporter fluorophore, samples were analysed by flow cytometry with Luminex 100 instrumentation. Probes specifically targeted eggs that are abundant and/or from morphologically indistinguishable species pairs. Results showed that the 33 different probes designed for this study accurately identified all samples when PCR was successful. Suspension bead arrays have a number of benefits over other methods of molecular identification; these arrays permit high multiplexing, simple addition of new probes, high throughput and lower cost than DNA sequencing. The increasing availability of DNA barcode data for numerous fish faunas worldwide suggests that bead arrays could be developed and widely used for fish egg, larval and tissue identifications.     

Characterizing molecular flexibility by combining least root mean square deviation measures

The root mean square deviation (RMSD) and the least RMSD are two widely used similarity measures in structural bioinformatics. Yet, they stem from global comparisons, possibly obliterating locally conserved motifs. We correct these limitations with the so-called combined RMSD, which mixes independent lRMSD measures, each computed with its own rigid motion. The combined RMSD is relevant in two main scenarios, namely to compare (quaternary) structures based on motifs defined from the sequence (domains and SSE) and to compare structures based on structural motifs yielded by local structural alignment methods. We illustrate the benefits of combined RMSD over the usual RMSD on three problems, namely (a) the assignment of quaternary structures for hemoglobin (scenario #1), (b) the calculation of structural phylogenies (case study: class II fusion proteins; scenario #1), and (c) the analysis of conformational changes based on combined RMSD of rigid structural motifs (case study: one class II fusion protein; scenario #2). Based on these illustrations, we argue that the combined RMSD is a tool of choice to perform positive and negative discrimination of degree of freedom, with applications to the design of move sets and collective coordinates. Executables to compute combined RMSD are available within the Structural Bioinformatics Library ( http://sbl.inria.fr ).     

The thermotropic behavior and major molecular species composition of the phospholipids of echinoderms

This study examines the molecular species composition and heat-induced crystalline-liquid crystalline phase transitions of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) from the muscle tissues of six species of echinoderms that were collected during the summer: the starfishes Distolasterias nipon and Asterias amurensis, the sea urchin Strongylocentrotus intermedius, and the holothurians Eupentacta fraudatrix, Cucumaria frondosa japonica, and Apostichopus japonicus. Phospholipids (PLs) were in the liquid crystalline state, which is optimal for the functioning of the cell membranes. The use of data on the molecular species composition of PLs for the interpretation of their thermotropic behavior indicated that homeoviscous adaptation is achieved by various rearrangements in the composition of the aliphatic groups of PLs. The phase transitions of PC and PE of echinoderms (except holothurians) were symbatic. The presence of a high-temperature peak on the PC thermograms of C. frondosa japonica and A. japonicus is attributable to the melting of the phospholipid domain, which is composed of molecular species with saturated aliphatic groups. Such domains are responsible for a significant shift in the temperature ranges of the phase transitions of phospholipids of holothurians and sea urchin towards temperatures above 0°C.     

Controlling composition of coexisting phases via molecular transitions

Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely unexplored how the behavior of phase-separating systems with molecular transitions differs between thermodynamic equilibrium and cases in which the detailed balance of the molecular transition rates is broken because of the presence of fuel. Here, we present a model of a phase-separating ternary mixture in which two components can convert into each other. At thermodynamic equilibrium, we find that molecular transitions can give rise to a lower dissolution temperature and thus reentrant phase behavior. Moreover, we find a discontinuous thermodynamic phase transition in the composition of the droplet phase if both converting molecules attract themselves with similar interaction strength. Breaking the detailed balance of the molecular transition leads to quasi-discontinuous changes in droplet composition by varying the fuel amount for a larger range of intermolecular interactions. Our findings showcase that phase separation with molecular transitions provides a versatile mechanism to control properties of intracellular and synthetic condensates via discontinuous switches in droplet composition.     

The molecular architecture of the extracellular hemoglobin of Ophelia bicornis: Analysis of two-dimensional crystalline arrays

The double-layered hexagonal disks of the extracellular hemoglobin of the annelid worm Ophelia bicornis form two types of two-dimensional crystalline arrays. The hexagonal type exhibited a typical honeycomb pattern of top views with a center-to-center distance of 26.2 nm. Laterally oriented molecules formed rectangular crystals with lattice constants a = 26.7 run and b = 19.8 nm. The three-dimensional structure was determined from both crystal forms by reconstruction from images of tilt series. At the resolutions obtained, 1.8 nm for the hexagonal form and 2.5 nm for the rectangular form, flattening of the hemoglobin molecules against the support was observed. Nevertheless the two independent reconstructions provided information about the mass distribution within the main subunit and the connectivity between different parts of the molecule.