Structural and functional properties of chromatophores and membrane vesicles from Rhodepseudomonas sphaeroides

Membrane vesicles have been isolated by a modified procedure from Rhodopseudomonas sphaeroides, grown phototrophically under high light intensity. In addition,chromatophores have been isolated from this organism grown phototrophically with low light intensities.Structural, chemical and functional properties of both preparations have been investigated and compared. The orientation of the membrane preparations has been studied by freeze-etch electron microscopy, the localization of cytochrome c₂, and light-driven active transport of amino acids and Ca²⁺. The results demonstrate that the orientation of the vesicle membrane is the same as the cytoplasmic membrane of intact cells; the membranes in chromatophores, however, have an inverted orientation.On a dry weight basis, the membrane vesicles contain less protein, carotenoids and bacteriochlorophyll and more lipids than do chromatophores. Qualitatively, however, the composition of both preparations is similar.It is concluded that the intracytoplasmic structures from which the chromatophores are derived are structurally and functionally similar to (and most likely continuous with) the cytoplasmic membranes from which the vesicles are derived.     

Pediatric autoimmune liver diseases: the molecular basis of humoral and cellular immunity

Pediatric autoimmune liver disease is mainly represented by two similar liver disorders: autoimmune hepatitis (AIH) and autoimmune sclerosing cholangitis (ASC), both characterized by hypergammalobulinemia, interface hepatitis and the presence of a wide range of circulating autoantibodies. Although similar features are seen in AIH and inflammatory bowel disease, histological biliary changes are more common in ASC. In addition to their role as diagnostic markers, autoantibodies, such as anti-extractable nuclear antigen (ENA) antibodies and liver kidney microsomal antibody type 1 (LKM1) may be involved directly in inducing aggressive liver diseases. Although the cellular immune response in pediatric autoimmune liver disease has been less intensively investigated than humoral immunity, the importance of antigen specific T cells has been explored. Both alphabeta and gammadelta T cells derived from either peripheral blood and liver biopsies have highly heterogeneous TCR gene usage and cytolytic activity has been demonstrated. There have been attempts to seek triggers of liver autoimmunity and several sequences shared in common between autoantigens and hepatotropic viruses, namely hepatitis B, C and cytomegalovirus have been identified. The presence of cross-reactivity between homologous sequences, especially between HCV and cytochromes, supports the possibility that molecular mimicry plays a role in the induction of autoantibodies and autoreactive cytotoxic T cells.     

Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions

A molecular dynamics simulation of the operator binding domain of the lambda repressor protein has been carried out. The protein was embedded in explicit waters, Na(+) and CL(-) ions. The Amber 4.1 computer package and the Cornell et al. Force field were used for energy-minimization and molecular dynamics simulation. We find that the atoms distributions in the environment of waters and Na(+) ions are in excellent agreement with those derived from the analysis of water molecules in crystal structures and ion-binding proteins. We also find that, on the whole, both distributions are similar to each other.     

Morphological and immunological comparison of caprine arthritis encephalitis and ovine progressive pneumonia viruses.

Caprine arthritis encephalitis virus (CAEV) causes a variety of pathological conditions ranging from mild to very severe and from acute to chronic, depending upon the age of initial infection and other variables. Although the virus has been reported to have properties of characteristic of retroviruses and to be related to maedi-visna virus (also called progressive pneumonia virus [PPV]), relatively little information about its morphological and immunological characteristics has been reported. We describe the morphological features of CAEV replicating in cultured caprine cells. Although the virus replicates slowly and very little virus is released from productively infected cells, it is apparent that the morphogenesis of CAEV is strikingly similar to that of maedi-visna. After the transmission of CAEV to a more permissive permanent cell line derived from Himalayan tahr ovary, it was possible to grow and purify enough virus to initiate biochemical characterization. The structural proteins of CAEV are generally very similar to those of PPV, suggesting that the two viruses are closely related but not identical. This was substantiated by showing that serum from a CAEV-infected goat immunoprecipitated both CAEV and PPV virion structural antigens from extracts of radiolabeled virus and also precipitated putative nonstructural viral antigens from extracts of both CAEV- and PPV-infected cells.     

Epigenetic reprogramming of embryos derived from sperm frozen at −20°C

Cryopreservation of spermatozoa is a strategy that has been used to conserve the sperm of animal species and animal strains that are valuable for biomedical research. A simple method for preserving spermatozoa after application of intracytoplasmic sperm injection (ICSI) is much needed. It has been shown previously that spermatozoa frozen at 20°C can activate oocytes and support full-term embryo development. However, epigenetic reprogramming could be affected by the environment and by the in vitro manipulation of gametes. Here, we investigated embryo epigenetic reprogramming including DNA methylation and histone modification, in embryos derived from sperm preserved at 20°C without cryoprotectants. The results showed that although both fertilization and embryo developmental competence were decreased, the dynamic epigenetic reprogramming of embryos derived from frozen sperm was similar to the reprogramming of embryos derived from fresh sperm. The results reported in this study indicate that sperm frozen without cryoprotectant is epigenetically safe for ICSI.     

Segmented and "equivalent" representation of the cable equation

The linear cable theory has been applied to a modular structure consisting of n repeating units each composed of two subunits with different values of resistance and capacitance. For n going to infinity, i.e., for infinite cables, we have derived analytically the Laplace transform of the solution by making use of a difference method and we have inverted it by means of a numerical procedure. The results have been compared with those obtained by the direct application of the cable equation to a simplified nonmodular model with "equivalent" electrical parameters. The implication of our work in the analysis of the time and space course of the potential of real fibers has been discussed. In particular, we have shown that the simplified ("equivalent") model is a very good representation of the segmented model for the nodal regions of myelinated fibers in a steady situation and in every condition for muscle fibers. An approximate solution for the steady potential of myelinated fibers has been derived for both nodal and internodal regions. The applications of our work to other cases dealing with repeating structures, such as earthworm giant fibers, have been discussed and our results have been compared with other attempts to solve similar problems.     

Growth coordination and the shoot epidermis

Cell-cell communication is essential for growth and development of multicellular organisms. In higher plants, the shoot organs are derived from three clonally distinct cell layers present in the meristem. The role of the outermost L1 cell layer and its derived epidermis in coordinating growth of the inner-cell layers has long been debated. This question has been revisited recently using molecular tools to manipulate cell cycle progression or cell expansion, specifically in the epidermis. These studies conclude that cells in the epidermis both promote and restrict growth of the entire shoot by sending growth signals - either physical or chemical - to the inner layers.     

SNP and mutation data on the web - hidden treasures for uncovering

SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant.     

Secondary structure of the RNA component of a nuclear/mitochondrial ribonucleoprotein.

RNase mitochondrial RNA processing (MRP) is a site-specific endoribonuclease located in both the nucleus and mitochondria of vertebrate cells. The enzyme is a ribonucleoprotein whose RNA component has been shown to be encoded by a nuclear gene. Because RNase MRP is particular in its substrate requirement, RNA-RNA interaction has been proposed as important for the cleavage reaction. A secondary structure of this RNA from mouse cells has been derived by chemical modification of in vivo MRP RNA in ribonucleoprotein form, as isolated free RNA, and as RNA synthesized in vitro. Full-length MRP RNA appears to adopt a conformation containing a significant number of single-stranded residues and may form a pseudoknot. The data are consistent with both the RNA within the ribonucleoprotein and the free RNA possessing comparable secondary structures and suggest a possible site of interaction between enzyme and substrate. The human MRP RNA can be folded into a conformation very similar to that predicted for the mouse MRP RNA. A more limited analysis of human MRP RNA is consistent with the structure proposed for the mouse species.     

Cre reporter mouse expressing a nuclear localized fusion of GFP and beta-galactosidase reveals new derivatives of Pax3-expressing precursors

A new Cre-reporter strain of mouse has been developed that expresses a fusion protein derived from the lacZ gene fused to GFP with a nuclear localization signal. This construct is expressed from the ROSA26 locus upon Cre-mediated recombination that removes a loxP-flanked PGK-neo cassette, thus allowing for detection of Cre activity in all tissues. This reporter strain, which is similar to prior R26R and R26EGFP strains, has certain advantages related to the nuclear expression and the combined expression of both beta-galactosidase and GFP activities. We show that the use of this newly developed reporter line allows for enhanced resolution, detection and co-localization. Thus, we report a previously unrecognized subset of venous endothelial cells derived from Pax3 expressing precursors.     

The uptake and subsequent loss of beryllium by rat liver parenchymal and non-parenchymal cells after the intravenous administration of particulate and soluble forms

A cell isolation technique has been used to study the uptake and subsequent loss of beryllium (Be) by rat liver after intravenous administration of non-lethal doses of either particulate beryllium phosphate or the more hepatotoxic soluble BeSO₄. It has been shown that beryllium phosphate is removed from the blood predominantly by the non-parenchymal (sinusoidal) cells of the liver and to a lesser extent more slowly by the parenchymal cells. After 24 h when the parenchymal cells have reached maximal Be content there has been a 50% loss of Be from the non-parenchymal cells and a similar loss from whole liver which is reflected in an increased level of Be in the blood. The Be count of non-parenchymal cells subsequently decreases much more slowly in a manner similar to that of the parenchymal cells, both being only halved during the following week. Within 24–48 h some redistribution of Be to the spleen occurs and it is suggested that this in part may be the result of Kupffer cell death. In splenectomized animals a high proportion of this redistributed Be appears to be retaken up by the liver mainly by the parenchymal cell population. After administration of BeSO₄, which is known to form beryllium phosphate in plasma, a greater proportion of the Be is taken up slowly by the parenchymal cells and no redistribution of Be to the spleen is observed. It is suggested that this behaviour is related primarily to the smaller size and nature of the beryllium phosphate particles formed in plasma under these conditions. The rate of loss of Be from both the parenchymal and non-parenchymal cells is similar to that measured in beryllium phosphate treated animals. It has been estimated that liver cell death is produced when the cell content exceeds 2–3 nmol Be/10⁶ cells although parenchymal cells appear to be more sensitive to Be derived from BeSO₄ than preformed beryllium phosphate.     

Macrophages: sentinels and regulators of the immune system

The important role of macrophages in host defense against a variety of pathogens has long been recognized and has been documented and reviewed in numerous publications. Recently, it has become clear that tissue macrophages are not entirely derived from monocytes, as has been assumed for a long time, but rather show an ontogenetic dichotomy in most tissues: while part of the tissue macrophages are derived from monocytes, a major subset is prenatally seeded from the yolk sac. The latter subset shows a remarkable longevity and is maintained by self‐renewal in the adult animal. This paradigm shift poses interesting questions: are these two macrophage subsets functionally equivalent cells that are recruited into the tissue at different development stages, or are both macrophage subsets discrete cell types with distinct functions, which have to exist side by side? Is the functional specialization that can be observed in most macrophages due to their lineage or due to their anatomical niche? This review will give an overview about what we know of macrophage ontogeny and will discuss the influence of the macrophage lineage and location on their functional specialization.     

Similarity between 5'- and 3'-terminal nucleotide sequences and double-stranded RNA-derived sequences of eukaryotic mRNA

It has been reported recently that parts of the nucleotide sequences present in the 5′- and 3′-terminal regions of cytoplasmic mRNA are derived from double-stranded hairpin structures of heterogeneous nuclear RNA—a putative mRNA precursor (Naora, 1979). In order to explore the nature of double-stranded hairpin structures, using the sequencing data of human and rabbit globin mRNA and hen ovalbumin mRNA, we examined the following possibility: that certain regions of both the 5′- and 3′-terminal nucleotide sequences of mature mRNA were present in double-stranded hairpin structures covalently linked to both sides of the message sequence in the precursor mRNA molecule and that these double-stranded hairpin structures are similar to each other. The results support the above possibility by showing substantial similarity of nucleotide sequences between the 5′- and 3′-terminal regions of these mRNAs in terms of the formation of similar double-stranded hairpin structures.     

Analysis of mfbA alleles of the eubasidiomycete Lentinus edodes

A fruiting-body-specific mfbA cDNA derived from Lentinus edodes FMC2 has been shown to encode a high-molecular-weight protein, MFBA, containing the cell-adhesion-promoting Arg-Gly-Asp (RGD) sequence. Southern-blot analysis showed that all L. edodes strains tested have the mfbA gene (homologue). Nucleotide sequence analysis of the 1-kb mfbA fragments containing the RGD-coding sequence showed that each L. edodes strain has two types of mfbA homologues. It was found in FMC2 that two mfbA homologues are derived from different nuclei and these mfbA alleles are transcribed with similar frequencies in the fruiting bodies.     

Patterns of natural selection at the Alcohol dehydrogenase gene of Drosophila americana

Similar outcomes are often observed in species exposed to similar selective regimes, but it is unclear how often the same mechanism of adaptive evolution is followed. Here we present an analysis of selection affecting sequence variation in the Alcohol dehydrogenase (Adh) gene of Drosophila americana, a species endemic to a large climate range that has been colonized by D. melanogaster. Unlike D. melanogaster, there is no evidence of selection on allozymes of ADH across the sampled range. This indicates that if there has been a similar adaptive response to climate in D. americana, it is not within the coding region of Adh. Instead, analyses of a combined dataset containing 86 alleles of Adh reveal purifying selection on the Adh gene, especially within its intron sequences. Frequency spectra of derived unpreferred variants at synonymous sites indicate that these sites are affected by weak purifying selection, but the deviation from neutrality is less drastic than observed for derived variants in noncoding introns. This contrast further supports the notion that noncoding sites in Drosophila are often subject to stronger selection pressures than synonymous sites.     

Simple sequences are rare in the Protein Data Bank

A simple sequence is abundant in the proteins that have been sequenced to date. But unusual protein features, such as a simple sequence, are not present in the same high frequency within structural databases. A subset of these simple sequences, a group with a highly repetitive nature has been shown to be abundant in eukaryotes but not in prokaryotes. In this study, an examination of the eukaryotic proteins in the Protein Data Bank (PDB) has revealed a large deficiency of low complexity, highly repetitive protein repeats. Through simulated databases of similar samples of eukaryotic proteins taken from the National Center for Biotechnology Information (NCBI) database, it is shown that the PDB contains a significantly less highly repetitive, simple sequence than artificial databases of similar composition randomly derived from NCBI. When the structural data for those few PDB sequences that did contain a highly repetitive simple sequence is examined in detail, it is found that in most cases the tertiary structure is unknown for the regions consisting of a simple sequence. This lack of a simple sequence both in the PDB database and in the structural information suggests that this type of simple sequence may produce disordered structures that make structural characterization difficult.     

Multiple synaptonemal complexes (polycomplexes): origin, structure and function

Multiple synaptonemal complexes (polycomplexes) (PC) are similar in structure to synaptonemal complexes (SC) and are also highly conserved through evolution. They have been described in over 70 organisms throughout all life forms. The appearance of PCs are restricted to meiotic and germ-line derived tissues and are most commonly present after SC formation. However, in a number of animals and plants, both extra- and intranuclear PCs are present during premeiotic and pre-pachytene stages. The structure and biochemical composition of PCs is similar to SCs that the basic unit is tripartite, consisting of two lateral elements and a central region (in which transverse elements are located), and the dimensions of such structures are equivalent. Stacking of SC subunits, while still maintaining equivalent SC dimensions, creates a problem since the lateral elements (LE) would then be twice as thick in the PC as compared to the SC. Recently, it has been shown that the LE of the SC is actually multistranded, thus the LE of each subunit of the PC is half as thick as its counterpart in the SC.     

Conformation of the common purine (beta) ribosides in solution: further evidence for a correlation between N-S state of the ribose moiety and syn-anti equilibrium.

The solution conformations of adenosine, guanosine and inosine in liquid ND3 have been determined by NMR. Comparison of the Karplus analysis of the proton HR spectra of the ribose moiety obtained in this solvent with the data from aqueous solutions of A and I proves that the conformations of the nucleosides are very similar in both liquids. From the analysis of the vicinal coupling constants of the ring protons it has been deduced that the S state C(2')-endo is slightly preferred. The mole fraction in S approximates 0.6 for all three nucleosides. C-13 relaxation measurements have been applied in the determination of the correlation times for rotational diffusion. Only at temperatures below - 40 degrees C is the pseudo-rotation of the furanoside ring slowed down sufficiently for it not to contribute to the measured relaxation rates. From NOE studies and T1 measurements on the individual protons it is derived that the N, C(3')-endo, form of the ribose is correlated with an anti conformation of the base (Y approximately 210 degrees to 220 degrees) and the S, C(2')-endo, form of the ribose with a syn conformation of the base (Y approximately 30 degrees to 50 degrees). The glycosyl torsion angles derived for the two conformations of A, G, and I are equal within the limits of accuracy.     

Characterization of baroreflex gain in the domestic pigeon (Columba livia)

Birds have a remarkable capacity to regulate circulation yet little is known about the avian baroreflex. Although both linear regression and curve-fitting techniques are frequently used to assess baroreflex function in mammals, only the former technique has been used in birds. We characterized baroreflex gain in domestic pigeons (Columba livia) and compared gain values derived from applying linear regression to ramp changes in mean arterial pressure (MAP) to values derived from fitting a four-parameter sigmoidal function to steady-state alterations in MAP. We found that, unlike mammals, pigeons do not display circadian patterns in MAP, HR or gain derived from bolus injections of vasoactive drugs. The pressor, but not depressor response, was attenuated by administration of the NMDA-antagonist ketamine, suggesting that central processing of the baroreflex may be similar in birds and mammals despite anatomical differences in arterial baroreceptive zones. Because graded infusions of vasoactive drugs could not consistently produce a plateau in the HR response, fitting data to a sigmoidal curve was difficult. Thus, we propose that variations of the Oxford method and linear regression analysis are superior method to assess baroreflex gain in pigeons than curve fitting.