Integrons: Novel DNA elements which capture genes by site-specific recombination

Integrons are unusual DNA elements which include a gene encoding a site-specific DNA recombinase, a DNA integrase, and an adjacent site at which a wide variety of antibiotic resistance and other genes are found as inserts. One or more genes can be found in the insert region, but each gene is part of an independent gene cassette. The inserted genes are expressed from a promoter in the conserved sequences located 5 to the genes, and integrons are thus natural expression vectors. A model for gene insertion in which circular gene cassettes are inserted individually via a single site-specific recombination event has been proposed and verified experimentally. The gene cassettes include a gene coding region and, at the 3 end of the gene an imperfect inverted repeat, a 59-base element. The 59-base elements are a diverse family of elements which function as sites recognized by the DNA integrase. Site-specific insertion of individual genes thus represents a further mechanism which contributes to the evolution of the genomes of Gram-negative bacteria and their plasmids and transposons.Members of the most studied class of integrons, which include thesulI gene in the conserved sequences, are believed to be mobile DNA elements on the basis that they are found in many independent locations, and a discrete boundary is found at the outer end of the 5-conserved segment. However, the length of the 3-conserved segment is variable in the integrons examined to date, and it is likely that this variability has arisen as the result of insertion and deletion events. Though the true extent of the 3-conserved segment remains to be determined, it seems likely that these integrons are mobile DNA elements. The second known class of integrons comprises members of the Tn7 transposon family.     

Integrons found in different locations have identical 5' ends but variable 3' ends.

The positions of the outer boundaries of the 5'- and 3'-conserved segment sequences of integrons found at several different locations have been determined. The position of the 5' end of the 5'-conserved segment is the same for six independently located integrons, In1 (R46), In2 (Tn21), In3 (R388), In4 (Tn1696), In5 (pSCH884), and In0 (pVS1). However, the extent of the 3'-conserved segment differs in each integron. The sequences of In2 and In0 diverge first from the conserved sequence, and their divergence point corresponds to the 3'-conserved segment endpoint defined previously (H.W. Stokes and R.M. Hall, Mol. Microbiol. 3:1669-1683, 1989), which now represents the endpoint of a 359-base deletion in In0 and In2. The sequence identity in In3, In1, In4, and In5 extends beyond this point, but each sequence diverges from the conserved sequence at a different point within a short region. Insertions of IS6100 were identified adjacent to the end of the conserved region in In1 and 123 bases beyond the divergence point of In4. These 123 bases are identical to the sequence found at the mer end of the 11.2-kb insertion in Tn21 but are inverted. In5 and In0 are bounded by the same 25-base inverted repeat that bounds the 11.2-kb insert in Tn21, and this insert now corresponds to In2. However, while In0, In2, and In5 have features characteristic of transposable elements, differences in the structures of these three integrons and the absence of evidence of mobility currently preclude the identification of all of the sequences associated with a functional transposon of this type.     

(Not) Keeping the stem straight: a proteomic analysis of maritime pine seedlings undergoing phototropism and gravitropism

Background  

Plants are subjected to continuous stimuli from the environment and have evolved an ability to respond through various growth and development processes. Phototropism and gravitropism responses enable the plant to reorient with regard to light and gravity.     

Direct measurement of intervertebral disc maximum shear strain in six degrees of freedom: motions that place disc tissue at risk of injury

Human intervertebral disc specimens were tested to determine the regions of largest maximum shear strain (MSS) experienced by disc tissues in each of three principal displacements and three rotations, and to identify the physiological rotations and displacements that may place the disc at greatest risk for large tissue strains and injury. Tearing of disc annulus may be initiated by large interlamellar shear strains. Nine human lumbar discs were tagged with radiographic markers on the endplates, disc periphery and with a grid of wires in the mid-transverse plane and subjected to each of the six principal displacements and rotations. Stereo-radiographs were taken in each position and digitized for reconstruction of the three-dimensional position of each marker. Maximum tissue shear strains were calculated from relative marker displacements and normalized by the input displacement or rotation. Lateral shear, compression, and lateral bending were the motions that produced the mean (95% confidence interval) largest mean MSS of 9.6 (0.7)%/mm, 9.0 (0.5)%/mm, and 5.8 (1.6)%/ degrees , respectively, and which occurred in the posterior, posterolateral and lateral peripheral regions of the disc. After taking into account the reported maximum physiological range of motion for each degree of freedom, motions producing the highest physiological MSS were lateral bending (57.8 (16.2)%) and flexion (38.3 (3.3)%), followed by lateral shear (14.4 (1.1)%) and compression (12.6 (0.7)%).     

Things We Like: Human Preferences among Similar Organisms and Implications for Conservation

Human preferences will increasingly determine many species’ prospects for survival. However, aside from a small number of survey-based studies of preference among disparate taxa, human species preferences have received little attention. I determined human aesthetic preferences among a relatively homogenous group, the penguins, from representation in all recently published, comprehensive, popular books of photographs of penguins (n = 4 books; 304 photographs). Representation of visually distinguishable types of penguins, measured by total photograph area, was highly skewed and rankings were highly concordant across books, suggesting large and commonly held differences in aesthetic appeal. Multiple regression analysis indicated that amount of warm color was the only significant determinant of representation, and warm color was highly correlated (r ² = 0.96) with mean representation of the penguin types. Body size and neotenic form, traits found to influence human preferences among other animals, were not significant, suggesting that the bases of human species preferences differ by species type. The results of this study indicate that human aesthetic preferences discriminate finely among species and may be based on minor features. Conservationists must be vigilant to the potential for aesthetic responses to influence conservation efforts.     

Plant biomechanical strategies in response to frequent disturbance: uprooting of Phyllostachys nidularia (Poaceae) growing on landslide-prone slopes in Sichuan, China

Bamboo is considered useful for controlling landslides, but we observed numerous shallow-slope failures in forests of big node bamboo (Phyllostachys nidularia) in Sichuan, China. Therefore, we inventoried landslide occurrence and vegetation type along one valley. To quantify bamboo root anchorage, we performed uprooting tests and measured plant morphological characteristics. Landslide occurrence was greatest at sites with bamboo and young trees. Culm failure was common because of the high length to diameter ratio (242 ± 6). Uprooting tests showed that the maximal force to cause failure was small (1615 ± 195 N). Uprooting force was strongly and positively regressed with a combination of the predictors lateral root number and volume (R(2) = 0.92), and root systems were highly superficial (depth = 0.15 ± 0.12 m), contributing little to slope stability. In P. nidularia, which grows on landslide-prone slopes, surprisingly few resources have been allocated to anchorage. We suggest that this strategy puts this pioneer at an advantage on steep slopes, where it contributes little to slope stability and colonizes frequently formed gaps through vegetative regeneration. Fewer disturbances would result in subsequent secondary succession and dying back of this shade intolerant species.     

A high-throughput strategy to screen 2D crystallization trials of membrane proteins

Electron microscopy of two-dimensional (2D) crystals has demonstrated potential for structure determination of membrane proteins. Technical limitations in large-scale crystallization screens have, however, prevented a major breakthrough in the routine application of this technology. Dialysis is generally used for detergent removal and reconstitution of the protein into a lipid bilayer, and devices for testing numerous conditions in parallel are not readily available. Furthermore, the small size of resulting 2D crystals requires electron microscopy to evaluate the results and automation of the necessary steps is essential to achieve a reasonable throughput. We have designed a crystallization block, using standard microplate dimensions, by which 96 unique samples can be dialyzed simultaneously against 96 different buffers and have demonstrated that the rate of detergent dialysis is comparable to those obtained with conventional dialysis devices. A liquid-handling robot was employed to set up 2D crystallization trials with the membrane proteins CopA from Archaeoglobus fulgidus and light-harvesting complex II (LH2) from Rhodobacter sphaeroides. For CopA, 1 week of dialysis yielded tubular crystals and, for LH2, large and well-ordered vesicular 2D crystals were obtained after 24 h, illustrating the feasibility of this approach. Combined with a high-throughput procedure for preparation of EM-grids and automation of the subsequent negative staining step, the crystallization block offers a novel pipeline that promises to speed up large-scale screening of 2D crystallization and to increase the likelihood of producing well-ordered crystals for analysis by electron crystallography.     

Modelling and predicting the spatial distribution of tree root density in heterogeneous forest ecosystems

Background and Aims In mountain ecosystems, predicting root density in three dimensions (3-D) is highly challenging due to the spatial heterogeneity of forest communities. This study presents a simple and semi-mechanistic model, named ChaMRoots, that predicts root interception density (RID, number of roots m^–2). ChaMRoots hypothesizes that RID at a given point is affected by the presence of roots from surrounding trees forming a polygon shape.Methods The model comprises three sub-models for predicting: (1) the spatial heterogeneity – RID of the finest roots in the top soil layer as a function of tree basal area at breast height, and the distance between the tree and a given point; (2) the diameter spectrum – the distribution of RID as a function of root diameter up to 50 mm thick; and (3) the vertical profile – the distribution of RID as a function of soil depth. The RID data used for fitting in the model were measured in two uneven-aged mountain forest ecosystems in the French Alps. These sites differ in tree density and species composition.Key Results In general, the validation of each sub-model indicated that all sub-models of ChaMRoots had good fits. The model achieved a highly satisfactory compromise between the number of aerial input parameters and the fit to the observed data.Conclusions The semi-mechanistic ChaMRoots model focuses on the spatial distribution of root density at the tree cluster scale, in contrast to the majority of published root models, which function at the level of the individual. Based on easy-to-measure characteristics, simple forest inventory protocols and three sub-models, it achieves a good compromise between the complexity of the case study area and that of the global model structure. ChaMRoots can be easily coupled with spatially explicit individual-based forest dynamics models and thus provides a highly transferable approach for modelling 3-D root spatial distribution in complex forest ecosystems.     

Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification

The requirement for large amounts of good quality DNA for whole-genome applications prohibits their use for small, laser capture micro-dissected (LCM), and/or rare clinical samples, which are also often formalin-fixed and paraffin-embedded (FFPE). Whole-genome amplification of DNA from these samples could, potentially, overcome these limitations. However, little is known about the artefacts introduced by amplification of FFPE-derived DNA with regard to genotyping, and subsequent copy number and loss of heterozygosity (LOH) analyses. Using a ligation adaptor amplification method, we present data from a total of 22 Affymetrix SNP 6.0 experiments, using matched paired amplified and non-amplified DNA from 10 LCM FFPE normal and dysplastic oral epithelial tissues, and an internal method control. An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples, and concordance was a promising 82.4%. Paired analysis for copy number, LOH, and both combined, showed that copy number changes were reduced in amplified DNA, but were 99.5% concordant when detected, amplifications were the changes most likely to be 'missed', only 30% of non-amplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined ～50% of gene changes detected in the unamplified DNA were also detected in the amplified DNA and within these changes, 86.5% were concordant for both copy number and LOH status. However, there are also changes introduced as ～20% of changes in the amplified DNA are not detected in the non-amplified DNA. An integrative network biology approach revealed that changes in amplified DNA of dysplastic oral epithelium localize to topologically critical regions of the human protein-protein interaction network, suggesting their functional implication in the pathobiology of this disease. Taken together, our results support the use of amplification of FFPE-derived DNA, provided sufficient samples are used to increase power and compensate for increased error rates.