Evidence for type III restriction and modification systems in Mycoplasma pulmonis

Mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type III restriction and modification (R-M) enzymes. Transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of R-M activity. Genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element.     

Harnessing Type I and Type III CRISPR-Cas systems for genome editing

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini-CRISPR array and a donor DNA containing a non-target sequence. Transformation of a pGE plasmid would yield two alternative fates to transformed cells: wild-type cells are to be targeted for chromosomal DNA degradation, leading to cell death, whereas those carrying the mutant gene would survive the cell killing and selectively retained as transformants. Using this strategy, different types of mutation were generated, including deletion, insertion and point mutations. We envision this method is readily applicable to different bacteria and archaea that carry an active CRISPR-Cas system of DNA interference provided the protospacer adjacent motif (PAM) of an uncharacterized PAM-dependent CRISPR-Cas system can be predicted by bioinformatic analysis.     

Evidence for dissociation between the perceptual and visuomotor systems in humans

When a visual stimulus is continuously moved behind a small stationary window, the window appears displaced in the direction of motion of the stimulus. In this study we showed that the magnitude of this illusion is dependent on (i) whether a perceptual or visuomotor task is used for judging the location of the window (ii) the directional signature of the stimulus, and (iii) whether or not there is a significant delay between the end of the visual presentation and the initiation of the localization measure. Our stimulus was a drifting sinusoidal grating windowed in space by a stationary, two-dimensional, Gaussian envelope (sigma=1 cycle of sinusoid). Localization measures were made following either a short (200 ms) or long (4.2 s) post-stimulus delay. The visuomotor localization error was up to three times greater than the perceptual error for a short delay. However, the visuomotor and perceptual localization measures were similar for a long delay. Our results provide evidence in support of the hypothesis that separate cortical pathways exist for visual perception and visually guided action and that delayed actions rely on stored perceptual information.     

Genetic variation inLycopersicon pimpinellifolium: Evidence of evolutionary change in mating systems

L. pimpinellifolium is a highly heterogeneous species, exhibiting pronounced trends from one end of its linear distribution to the other in nearly every studied genetic locus. Drastic differences between populations were also detected in genetic variability and rates of outcrossing. Highly significant positive correlations exist in every possible comparison between flower size, degree of stigma exsertion, heterozygosity, and allelic polymorphism. The hypothesis most compatible with observations proposes that the very uniform, highly self-pollinated biotypes originated from the more primitive, more variable, facultatively allogamous forms.Dedicated with affection, gratitude and respect to the memory ofTheodosius Dobzhansky.     

Evidence for an Adenovirus Type 2-Coded Early Glycoprotein

We have identified an adenovirus type 2 (Ad2)-induced early glycopolypeptide with an apparent molecular weight of 20,000 to 21,000 (20/21K), as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The 20/21K polypeptide could be labeled in vivo with [(3)H]glucosamine. [(35)S]methionine- and [(3)H]-glucosamine-labeled 20/21K polypeptides bound to concanavalin A-Sepharose columns and were eluted with 0.2 M methyl-alpha-d-mannoside. The pulse-labeled polypeptide appeared as a sharp band with an apparent molecular weight of 21K, but after a chase it converted to multiple bands with an average molecular weight of 20K. This variability in electrophoretic mobility is consistent with glycosylation or deglycosylation of the 20/21K polypeptide. Analysis of the pulse and pulse-chase-labeled forms by using partial proteolysis indicated that the polypeptides were highly related chemically, but not identical. Most of the 20/21K polypeptide is localized in the cytoplasm fraction of infected cells lysed by Nonidet P-40. The 20/21K polypeptide and a 44K polypeptide, labeled with [(35)S]methionine or [(3)H]glucosamine in Ad2-infected human cells, were precipitated by a rat antiserum against an Ad2-transformed rat cell line (T2C4), but not by antisera against three other Ad2-transformed rat cell lines, or by serum from nonimmune rats. The partial proteolysis patterns of the 20/21K and the 44K polypeptides were indistinguishable, indicating that the two polypeptides are highly related, and suggesting that the 44K polypeptide might be a dimer of the 20/21K polypeptide. The 20/21K polypeptide was also induced in Ad2-early infected monkey and hamster cells. These results imply that the 20/21K polypeptide is synthesized in Ad2-infected human, monkey, and hamster cells, and in one but not all Ad2-transformed rat cells. Thus, the 20/21K polypeptide is probably viral coded rather than cell coded and viral induced.     

A framework for evolutionary systems biology

Background  

Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.     

Type III 5-methylcytosine modification of DNA in Neisseria gonorrhoeae.

We present here the first report of a type III methyltransferase that modifies a cytosine. Neisseria gonorrhoeae 82409/55 (pJD1) modifies the first cytosine on only one strand from the 5' end of the nonpalindromic sequence: (Formula; see text). We have called this modifying activity M X NgoVIII.     

Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone

Background  

Type III secretion systems are a common virulence mechanism in many Gram-negative bacterial pathogens. These systems use a nanomachine resembling a molecular needle and syringe to provide an energized conduit for the translocation of effector proteins from the bacterial cytoplasm to the host cell cytoplasm for the benefit of the pathogen. Prior to translocation specialized chaperones maintain proper effector protein conformation. The class II chaperone, Invasion plasmid gene (Ipg) C, stabilizes two pore forming translocator proteins. IpgC exists as a functional dimer to facilitate the mutually exclusive binding of both translocators.     

Niche modification and stability of competitive systems. III. Simulation model analysis

Simulation model for niche shift in ecological time scale was constructed on the basis of the optimal foraging theory. In accordance with the previous experimental study (Shimada andFujii , 1985), the model competitive system consisted of 2 parasitoid wasp species utilizing 4 host stages. Wasps were assumed to choose host stages in the manner that they realized the maximal gain/cost values, where gain was represented by body weight of a wasp progeny emerging from each host stage and cost was expressed by time required to search for and detect an unparasitized host. The number of parasitized hosts in each host stage was calculated numerically by usingArditt 's (1983) model for avoidance of superparasitism. The model simulated well the experimental results ofShimada andFujii (1985) andShimada (1985). Sensitivity analysis of the model showed that the experimentally derived criterion for competitive coexistence (different second-best host stages between competing species even with the common best) was not necessarily the indispensable condition for niche shift and separation, but that if the criterion was not satisfied, stable competitive coexistence occurred only in the narrow range of the parametric values. Further, niche shift in ecological time scale made the competitive coexistence more stable than fixed niche on which the current niche theory stands.     

The mating systems of ratites and tinamous: an evolutionary perspective

The breeding behaviour of ratites and tinamous is reviewed. This group includes many of the homeothermic animals which habitually show prominent or exclusive paternal care of eggs and offspring. This unusual parental care pattern is associated with a diverse array of mating systems, ranging from monogamy to mixed polygyny/polyandry. This latter system, typical of the rhcas, is unknown among higher vertebrates outside the taxa considered herein. This diversity of mating systems, together with their great geographical and ecological range, makes ratites and tinamous a group of great potential importance in the investigation of the adaptive significance of social organization, mating systems and parental care patterns. Inadequately described features of their reproductive biology have become incorporated into various considerations of the evolution of reproductive behaviour patterns, and are in danger of assuming the status of fact through repetition. We show that these birds are very little known, in the main, and urge that caution be exercised in the use of what information is available. Directions for new research in ratite breeding biology are suggested, and an interpretation of parental care and pair-bond patterns in these birds is offered.     

Comparisons of canid and felid social systems from an evolutionary perspective

Canids and felids are compared regarding evolutionary history, distribution, habitat preferences, morphology and behaviour. Factors permitting and promoting sociality in both families are discussed, and communication mechanisms within each sensory modality compared. A solitary existence is compatible with felid specializations, the mother and young being the basic social unit. Canid specializations have permitted the development of a pair bond and male provisioning of young. As an adaptation to hunting large herbivorous prey, an increase in size occurred in the felids, but canids developed sophisticated pack-hunting techniques. Group structure in canids is based on long-term affiliations between a pair and matured offspring, while in the lion, the only truly social felid, it is based on a mother and maturing daughters.     

Evidence for an in vivo modification of mitochondrial proteins by coenzyme A.

Following denaturation of mitochondrial proteins by sodium dodecyl sulfate, a [1-14C]pantothenic acid-derived radioactivity proved to be acid precipitable in the outer membrane, the intermembrane space, the inner membrane and in the matrix of rat liver mitochondria, where it had the highest specific radioactivity of 541 +/- 29 cpm/100 micrograms protein. This tightly and/or covalently bound protein radioactivity could be released by incubation in the presence of dithioerythreitol; it was identified as [14C]coenzyme A by its HPLC retention time, its absorption spectrum and its radioactivity. This acid-stable and thiol-labile coenzyme A-binding apparently refers to specific protein binding sites. With the purified, homogeneous mitochondrial matrix enzymes acetyl-CoA acetyltransferase (acetoacetyl-CoA thiolase) (EC 2.3.1.9, acetyl-CoA:acetyl-CoA C-acetyltransferase) and 3-oxoacyl-CoA thiolase (EC 2.3.1.16) coenzyme A was found exclusively, e.g., in the modified, partially-active forms A1 und A2 of acetyl-CoA acetyltransferase and not in the unmodified fully-active enzyme. Thus it is evident that this coenzyme A modification is transient. We suggest that coenzyme A-modification is a signal involved in the assembly or the degradation process of distinct mitochondrial matrix proteins.     

Evolve III: A discrete events model of an evolutionary ecosystem

Evolve III is a discrete events model of an evolutionary ecosystem. The model includes three levels of organization: population, organism and genetic structure. Each of these components was modeled independently, so that selective replacement of subsystems can be used to create families of models capable of testing alternative hypotheses about the real system. To demonstrate the use of the model we describe an experiment on the relationship between adaptability of populations and the variability of the environment. Populations cultured in a constant environment usually dominated those cultured in a variable environment when both were placed in a variable environment at an early stage of development, whereas the opposite is the case at later stages of development. This agrees with experiments on laboratory microcosms and lends credence to the potential predictive value of the model.     

Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance.

The Thy-1 membrane glycoprotein from rat brain is shown to have structural and sequence homologies with immunoglobulin (Ig) domains on the basis of the following evidence. 1. The two disulphide bonds of Thy-1 are both consistent with the Ig-fold. 2. The molecule contains extensive beta-structure as shown by the c.d. spectrum. 3. Secondary structure prediction locates beta-strands along the sequence in a manner consistent with the Ig-fold. 4. On the basis of rules derived from known beta-sheet structures, a three-dimensional structure with the Ig-fold is predicted as favourable for Thy-1. 5. Sequences in the proposed beta-strands of Thy-1 and known beta-strands of Ig domains show significant sequence homology. This homology is statistically more significant than for the comparison of proposed beta-strand sequences of beta 2-microglobulin with Ig domains. An hypothesis is presented for the possible functional significance of an evolutionary relationship between Thy-1 and Ig. It is suggested that both Thy-1 and Ig evolved from primitive molecules, with an Ig fold, which mediated cell--cell interactions. The present-day role of Thy-1 may be similar to that of the primitive domain.