Conserved organization of an avian histone gene cluster with inverted duplications of H3 and H4 genes

Summary The organization of histone gene clusters of the duckCairina moschata was studied in the DNA inserts of two recombinant phage that overlap and feature identical histone gene arrangements but differ in sequence details and in the extent of repetition of an AT-rich motif in one of the nontranscribed spacer regions. These few but substantial differences between otherwise nearly identical histone gene groups suggest that we have independently isolated alleles of the same site of the duck genome or that this gene arrangement occurs (with slight variations) more than once per haploid genome. Within the histone gene cluster described, H3 and H4 genes are duplicated (with inverted orientation), whereas one H1 gene is flanked by single H2A and H2B genes. The arrangement of duck histone genes described here is identical to a subsection of the chicken genome but differs from any other published histone gene cluster.     

A further definition of characteristics of DNA-excision repair in xeroderma pigmentosum complementation group A strains

The location in the genome of excision repair following exposure to UV (254 nm) of two XP complementation group A strains, XP12BE and XP8LO, that differ considerably in their excision-repair rates, have been determined. Capacity for repair in XP8LO has also been determined. Sites repaired in DNA in a 24-h post-UV period were located relative to the remaining pyrimidine dimers using the M. luteus UV-endonuclease to nick partially repaired DNA and sedimentation in alkaline sucrose to size the resulting DNA. Repair in group A occurs randomly throughout the genome in a manner similar to that observed for normal cells but in contrast to domain-limited repair in group C strains. This observation defines a further similarity of the excision repair detected in group A compared to normal cells that is in addition to the previously reported related characteristics of the respective excision rate curves. A reduced repair capacity in XP8LO relative to normal cells was detected. This strain, which repairs DNA at an initial rate identical to that of normal strains when irradiated with doses of 5 J/m2 or less, repairs DNA at a slower than normal but constant rate at higher doses. This leads to the suggestion that XP8LO is defective in the number of repair enzyme complexes compared to normal cells.     

Kinetic distinction between rapid-equilibrium random and abortive ordered enzymatic mechanisms using alternative substrates or kinetic isotope effects

Alternative substrates, such as those isotopically-labeled, which differ in their rate constants of catalysis but not in their rate constants of binding, generate identical values of V/Ka in ordered kinetic mechanisms of bireactant enzymes. This is shown to be true even for the rapid-equilibrium ordered mechanism in which an abortive complex between free enzyme and the second substrate is formed. In contrast, rapid-equilibrium random mechanisms have non-identical values for V/Ka. Consequently, the effect of alternative substrates or isotope effects on V/Ka provides a means to distinguish between these nearly identical kinetic mechanisms.     

Analysis of the major histocompatibility complex in Syrian hamsters. III. Cellular and humoral immunity to alloantigens.

Among the genetic loci incorporated into the major histocompatibility complex in every species studied to date have been prominent genes encoding for strong histocompatibility determinants that elicit detectable alloantibody responses and which are the chief antigenic targets of cell-mediated cytotoxicity reactions. The K and D regions of the H-2 complex in the mouse and the A, B, and C regions of the HLA complex in man are representative examples. Syrian hamsters, as described in this report, do not make alloantibodies to antigens of this type and only very poorly do they carry out in vitro cell-mediated cytotoxicity to target cells putatively bearing these antigens. Since hamsters are quite capable of discriminating analogous antigenic differences in xenogeneic species, and xenogeneic sources cannot distinguish immunologically between the antigens encoded by the two hamster major histocompatibility alleles. Hm-1a and Hm-1b, we conclude that the hamster strains we work with are serologically indistinguishable by the methods used here. However, they obviously differ for determinants which elicit T cell-mediated responses, as evidenced by their ability to express acute skin graft rejection, mixed lymphocyte reactivity, graft-vs-host reactions, and cell-mediated cytotoxicity reactions. Such alloreactivity may reflect a mutation at an SD locus, affecting antigenic sites recognized only by T cells, or that the available hamster strains are SD identical, but differ at loci similar to the I region loci in mice. Alternatively, we cannot exclude the possibility that Syrian hamsters somehow fail to express properly the genes coding for SD determinants.     

Linear plasmids in plant mitochondria: Peaceful coexistences or malicious invasions?

Plant mitochondria contain small extrachromosomal DNAs in addition to a large and complex main mitochondrial genome. These molecules can be regarded as extrachromosomal replicons or plasmids, of which there are two forms, circular and linear. Linear mitochondrial plasmids are present in many fungi and in some plants, but they seem to be absent from most animal cells. They usually have a common structural feature, called an invertron, that is characterized by the presence of terminal inverted repeats and proteins covalently attached to their 5 termini. Linear mitochondrial plasmids possess one to six ORFs that can encode unknown proteins but often code for the DNA and RNA polymerases. Although the functions of most linear plasmids in plant mitochondria are unknown, some plasmids may be associated with mitochondrial genome rearrangements and may have phenotypic effects due to their integration into mitochondrial genome. The Brassica 11.6-kb plasmid, one of the linear mitochondrial plasmids in plants, shows a non-maternal inheritance, in contrast to mitochondrial genomes. The origin of these plasmids is still a mystery, but indirect evidence indicates the possibility of horizontal transfer from fungal mitochondria. In this review, the main features of these unique DNAs present in plant mitochondria are described.     

Lysogeny and conversion characteristics of microbes in the genus Bordetella

The genomes of B. pertussis bacteriophages 134 and 41405 and B. bronchiseptica bacteriophage 214 have been studied. As revealed by the methods of heteroduplex and restriction analyses, the populations of these bacteriophages are heterogeneous and their DNAs differ in size and location of inserts. The study carried out with the use of blot hybridization techniques has shown that in lysogenic cells the genome is not integrated into the chromosome, but exists as an autonomous plasmid replicon. Only partial incorporation of the phage genome into the recipient chromosome takes place in the process of conversion, the phage genome continuing its existence as an autonomous replicon.     

The Embryonics Project: a machine made of artificial cells.

It is possible to trace the origins of biological inspiration in the design of electronic circuits to the very dawn of the field of computer engineering, with the work of John von Neumann in the 1940s. To his brilliance we owe not only the first methodical attempts to define the electronic equivalents of many fundamental biological process, but also the development of the first self-replicating computing machines. Unfortunately, the electronic technology of the time would not allow a physical realization of von Neumann's machines, and it was not until the introduction of new programmable circuits in the 1980s that the field of bio-inspired machines gained new momentum. In this article, we describe the Embryonics (embryonic electronics) Project, an attempt to draw inspiration from the ontogenetic processes that determine the growth of multicellular organisms in the design of new, massively parallel arrays of processors (the artificial cells). Our cells are simple processors, all based on an identical hardware structure and all containing the same program (our artificial genome), but executing different parts of the genome depending on their spatial coordinates within the array. As in living beings, the presence of the genome in every cell allows the introduction of features such as self-replication and self-repair (cicatrization). In addition, the cells are implemented using an array of programmable elements (the artificial molecules), which allows their structure to be adapted to a given application. Through the parallel operation of many of these simple processors, we hope to realize highly complex systems, the equivalent of multicellular organisms in the natural world.     

Tumor induction by simian virus 40 in mice is controlled by long-term persistence of the viral genome and the immune response of the host.

Simian virus 40 (SV40), which transforms mouse cells in vitro, has not been previously observed to cause tumors when injected in immunocompetent mice. We have investigated both the fate of the injected virion in mice and several immunological parameters as potential factors controlling tumorigenicity. We find that although SV40 does not replicate in mouse cells, the viral DNA can persist for many months postinjection; the majority of the viral DNA is found in the cytoplasm, but a small amount of the viral DNA is integrated at multiple sites in the host nuclear DNA. The persistence of the viral genome is independent of the ability of the mouse to mount an SV40 TSTA specific cytotoxic T-cell response and may be attributed to the cytoplasmic location of the majority of the viral genome. However, in long-term studies of SV40-injected mice, genetically identical except for the major histocompatibility complex, we find that tumors were induced in some mice of the H-2d (low cytotoxic T-lymphocyte responder to SV40 TSTA) but not of the H-2k (high responder to SV40 TSTA) haplotype. Thus, a combination of inefficient disposal of the injected virion and inefficient immunological surveillance and elimination of cells containing nuclear SV40 DNA can eventually result in SV40-induced tumors at multiple sites in mice.     

The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae)

Polyploidy, an important factor in eukaryotic evolution, is especially abundant in angiosperms, where it often acts in concert with hybridization to produce allopolyploids. The application of molecular phylogenetic techniques has identified the origins of numerous allopolyploids, but little is known on genomic and chromosomal consequences of allopolyploidization, despite their important role in conferring divergence of allopolyploids from their parental species. Here, using several plastid and nuclear sequence markers, we clarify the origin of tetra- and hexaploids in a group of American daisies, allowing characterization of genome dynamics in polyploids compared to their diploid ancestors. All polyploid species are allopolyploids. Among the four diploid gene pools, the propensity for allopolyploidization is unevenly distributed phylogenetically with a few species apparently more prone to participate, but the underlying causes remain unclear. Polyploid genomes are characterized by differential loss of ribosomal DNA loci (5S and 35S rDNA), known hotspots of chromosomal evolution, but show genome size additivity, suggesting limited changes beyond those affecting rDNA loci or the presence of processes counterbalancing genome reduction. Patterns of rDNA sequence conversion and provenance of the lost loci are highly idiosyncratic and differ even between allopolyploids of identical parentage, indicating that allopolyploids deriving from the same lower-ploid parental species can follow different evolutionary trajectories.     

Spontaneous Curvature,Differential Stress,and Bending Modulus of Asymmetric Lipid Membranes

Lipid bilayers can exhibit asymmetric states, in which the physical characteristics of one leaflet differ from those of the other. This most visibly manifests in a different lipid composition, but it can also involve opposing lateral stresses in each leaflet that combine to an overall vanishing membrane tension. Here, we use theoretical modeling and coarse-grained simulation to explore the interplay between a compositional asymmetry and a nonvanishing differential stress. Minimizing the total elastic energy leads to a preferred spontaneous curvature that balances torques due to both bending moments and differential stress, with sometimes unexpected consequences. For instance, asymmetric flat bilayers, whose specific areas in each leaflet are matched to those of corresponding tensionless symmetric flat membranes, still exhibit a residual differential stress because the conditions of vanishing area strain and vanishing bending moment differ. We also measure the curvature rigidity of asymmetric bilayers and find that a sufficiently strong differential stress, but not compositional asymmetry alone, can increase the bending modulus. The likely cause is a stiffening of the compressed leaflet, which appears to be related to its gel transition but not identical with it. We finally show that the impact of cholesterol on differential stress depends on the relative strength of elastic and thermodynamic driving forces: if cholesterol solvates equally well in both leaflets, it will redistribute to cancel both leaflet tensions almost completely, but if its partitioning free energy prefers one leaflet over the other, the resulting distribution bias may even create differential stress. Because cells keep most of their lipid bilayers in an asymmetric nonequilibrium steady state, our findings suggest that biomembranes are elastically more complex than previously thought: besides a spontaneous curvature, they might also exhibit significant differential stress, which could strongly affect their curvature energetics.     

Leaf thionins, a novel class of putative defence factors

Leaf thionins of barley have been identified as a novel class of highly abundant polypeptides with antifungal activity, which are present in walls and vacuoles of barley leaf cells. Similar thionins occur not only in monocotyledonous but also in various dicotyledonous plants. The leaf thionins of barley are encoded by a complex multigene family, which consists of at least 50–100 members per haploid genome. The toxicity of these thionins for plant pathogenic fungi and the fact that their synthesis can also be triggered by pathogens strongly suggest that leaf thionins are involved in the mechanism of plant defence against microbiol infection.     

What does it mean to identify a protein in proteomics?

The annotation of the human genome indicates the surprisingly low number of approximately 40,000 genes. However, the estimated number of proteins encoded by these genes is two to three orders of magnitude higher. The ability to unambiguously identify the proteins is a prerequisite for their functional investigation. As proteins derived from the same gene can be largely identical, and might differ only in small but functionally relevant details, protein identification tools must not only identify a large number of proteins but also be able to differentiate between close relatives. This information can be generated by mass spectrometry, an approach that identifies proteins by partial analysis of their digestion-derived peptides. Information gleaned from databases fills in the missing sequence information. Because both sequence databases and experimental data are limited, a certain ambiguity often remains concerning which sequence variant(s) and modification(s) are present. As the common denominator of all the isoforms is a gene, in our opinion, it would be more accurate to state that a product of this particular gene rather than a certain protein has been identified by mass spectrometry.     

Genome structure and differential expression of two isoforms of a novel PDZ-containing myosin (MysPDZ) (Myo18A)

We previously cloned a gene for a novel myosin (called MysPDZ) containing a PDZ-domain from bone marrow stromal cells. This new myosin is found in humans and classified as one of the class XVIII myosins (Myo18A). Here, we report the hematopoietic cell-specific splicing isoform (MysPDZbeta) in addition to the previously reported isoform (MysPDZalpha). Combined with mouse genome sequence data, the overall genome structure and generation of the two spliced isoforms are deduced. The MysPDZbeta protein lacks a PDZ-domain in the N-terminal region. Studies of the subcellular localization of the two spliced isoforms indicated that MysPDZalpha containing the PDZ domain co-localizes with the ER-Golgi complex, while MysPDZbeta, which lacks the PDZ domain, localizes diffusely in the cytoplasm. These results suggest that the isoforms differ in their subcellular localization and may have different functions in membrane ruffling and membrane traffic pathways. The PDZ-containing spliced isoform (MysPDZalpha) is not expressed in bone marrow hematopoietic cells, whereas MysPDZbeta lacking the PDZ is specifically expressed in most hematopoietic cells. It is noted that neither isoform is expressed in red blood cells. Interestingly, MysPDZalpha was detected in mature but not in immature macrophages, and its level increased after the induction of differentiation of M1 cells, suggesting a functional role of PDZ-containing myosin in macrophages.     

Wanderings of Hobo: A Transposon in Drosophila Melanogaster and its Close Relatives

The transposon hobo is present in the genomes of Drosophila melanogaster and Drosophila simulans (and D. mauritiana and probably D. sechellia, based on Southern blots) as full-size elements and internally deleted copies. The full-size melanogaster, simulans and mauritiana hobo elements are 99.9% identical at the DNA sequence level, and internally deleted copies in these species essentially differ only in having deletions. In addition to these, hobo-related sequences are present and detectable with a hobo probe in all these species. Those in D. melanogaster are 86-94% identical to the canonical hobo, but with many indels. We have sequenced one that appears to be inserted in heterochromatin (GenBank Acc. No. AF520587). It is 87.6% identical to the canonical hobo, but quite fragmented by indels, with remnants of other transposons inserted in and near it, and clearly is defunct. Numerous similar elements are found in the sequenced D. melanogaster genome. It has recently been shown that some are fixed in the euchromatic genome, but it is probable that still more reside in heterochromatic regions not included in the D. melanogaster genome database. They are probably all relics of an earlier introduction of hobo into the ancestral species. There appear to have been a minimum of two introductions of hobo into the melanogaster subgroup, and more likely three, two ancient and one quite recent. The recent introduction of hobo was probably followed by transfers between the extant species (whether 'horizontally' or by infrequent interspecific hybridization).     

Condensin and cohesin: more than chromosome compactor and glue

Two related protein complexes, cohesin and condensin, are essential for separating identical copies of the genome into daughter cells during cell division. Cohesin glues replicated sister chromatids together until they split at anaphase, whereas condensin reorganizes chromosomes into their highly compact mitotic structure. Unexpectedly, mutations in the subunits of these complexes have been uncovered in genetic screens that target completely different processes. Exciting new evidence is emerging that cohesin and condensin influence crucial processes during interphase, and unforeseen aspects of mitosis. Each complex can perform several roles, and individual subunits can associate with different sets of proteins to achieve diverse functions, including the regulation of gene expression, DNA repair, cell-cycle checkpoints and centromere organization.