Construction of Double-helical DNA Structures Based on Dinucleotide Building Blocks

Abstract

We present a new method for building full 3-D structures of DNA sequences. A database of the conformational properties of dinucleotide steps has been compiled using X-ray crystal structures of oligonucleotides. The protocol uses these dinucleotides as building blocks to generate three dimensional structures of any required sequence in any required conformation.     

A Novel Method to Analyze the Similarity of Biological Sequences

Abstract

In this paper, we propose a new method based on the 2-D graphical representation to analyze the similarity of biological sequences and classify the protein secondary structure sequences. Instead of computing some characteristics from the distance matrix, the average area surrounded by the curve and X axis is computed as a new invariant. The new method is tested on two sets: the coding sequences of 30 mitochondrial genes from NCBI and 12 protein secondary structure sequences. The similarity/disimilarity and phylogenetic tree (dendrogram) of these sequences verify the validity of our method.     

Invasion of breast cancer cells into collagen matrix requires TGF-α and Cdc42 signaling

Invasion of MDA-MB-231 breast cancer cells into three-dimensional (3-D) type I-collagen matrices depends on TGF-α. We characterized the steps of invasion mediated by TGF-α. Cell migration, as observed by videomicroscopy, was effectively stimulated by collagen, suggesting that TGF-α may specifically participate in the invasion of a 3-D collagen matrix. We assessed the role of small GTPases of the Rho family in the invasion. Cdc42 was found to be necessary for invasion but dispensable for cell migration. These results suggest that TGF-α mediates invasion into 3-D collagen matrices by initiating the formation of protrusions into collagen, likely through activation of Cdc42.

Structured summary

PAKphysically interacts with Rac1 by pull down (View interaction)PAKphysically interacts with CDC42 by pull down (View interaction)     

Understanding crown shyness from a 3-D perspective

Background and AimsCrown shyness describes the phenomenon whereby tree crowns avoid growing into each other, producing a puzzle-like pattern of complementary tree crowns in the canopy. Previous studies found that tree slenderness plays a role in the development of crown shyness. Attempts to quantify crown shyness have largely been confined to 2-D approaches. This study aimed to expand the current set of metrics for crown shyness by quantifying the characteristic of 3-D surface complementarity between trees displaying crown shyness, using LiDAR-derived tree point clouds. Subsequently, the relationship between crown surface complementarity and slenderness of trees was assessed.MethodsFourteen trees were scanned using a laser scanning device. Individual tree points clouds were extracted semi-automatically and manually corrected where needed. A metric that quantifies the surface complementarity (S_c) of a pair of protein molecules is applied to point clouds of pairs of adjacent trees. Then 3-D tree crown surfaces were generated from point clouds by computing their α shapes.Key ResultsTree pairs that were visually determined to have overlapping crowns scored significantly lower S_c values than pairs that did not overlap (n = 14, P < 0.01). Furthermore, average slenderness of pairs of trees correlated positively with their S_c score (R² = 0.484, P < 0.01), showing agreement with previous studies on crown shyness.ConclusionsThe characteristic of crown surface complementarity present in trees displaying crown shyness was succesfully quantified using a 3-D surface complementarity metric adopted from molecular biology. Crown surface complementarity showed a positive relationship to tree slenderness, similar to other metrics used for measuring crown shyness. The 3-D metric developed in this study revealed how trees adapt the shape of their crowns to those of adjacent trees and how this is linked to the slenderness of the trees.     

Natural selection for 2,4,5-trichlorophenoxyacetic acid mineralizing bacteria in agent orange contaminated soil

Agent Orange contaminated soils were utilized in direct enrichment culture studies to isolate 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) and 2,4-dichlorophenoxyacetic acid (2,4-D) mineralizing bacteria. Two bacterial cultures able to grow at the expense of 2,4,5-T and/or 2,4-D were isolated. The 2,4,5-T degrading culture was a mixed culture containing two bacteria, Burkholderia species strain JR7B2 and Burkholderia species strain JR7B3. JR7B3 was able to metabolize 2,4,5-T as the sole source of carbon and energy, and demonstrated the ability to affect metabolism of 2,4-D to a lesser degree. Strain JR7B3 was able to mineralize 2,4,5-T in pure culture and utilized 2,4,5-T in the presence of 0.01 yeast extract. Subsequent characterization of the 2,4-D degrading culture showed that one bacterium, Burkholderiaspecies strain JRB1, was able to utilize 2,4-D as a sole carbon and energy source in pure culture. Polymerase chain reaction (PCR) experiments utilizing known genetic sequences from other 2,4-D and 2,4,5-T degrading bacteria demonstrated that these organisms contain gene sequences similar to tfdA, B, C, E, and R (Strain JRB1) and the tftA, C, and E genes (Strain JR7B3). Expression analysis confirmed that tftA, C, and E and tfdA, B, and C were transcribed during 2,4,5-T and 2,4-D dependent growth, respectively. The results indicate a strong selective pressure for 2,4,5-T utilizing strains under field condition.     

Phylogenetic Analysis of Ruminant Theileria spp. from China Based on 28S Ribosomal RNA Gene

Species identification using DNA sequences is the basis for DNA taxonomy. In this study, we sequenced the ribosomal large-subunit RNA gene sequences (3,037-3,061 bp) in length of 13 Chinese Theileria stocks that were infective to cattle and sheep. The complete 28S rRNA gene is relatively difficult to amplify and its conserved region is not important for phylogenetic study. Therefore, we selected the D2-D3 region from the complete 28S rRNA sequences for phylogenetic analysis. Our analyses of 28S rRNA gene sequences showed that the 28S rRNA was useful as a phylogenetic marker for analyzing the relationships among Theileria spp. in ruminants. In addition, the D2-D3 region was a short segment that could be used instead of the whole 28S rRNA sequence during the phylogenetic analysis of Theileria, and it may be an ideal DNA barcode.     

Assessing eco-toxicological effects of industrial 2,4-D acid iso-octylester herbicide on rat pancreas and liver

Abstract

We studied the eco-toxic and carcinogenic effects of a commonly used 2,4-D acid iso-octylester herbicide on rat liver and pancreas. The rats in Group 1 were fed a standard feed and the rats in Group 2 were fed with standard feed to which was added 200 mg/kg/day 2,4-D acid iso-octylester for 16 weeks. Azaserine, 30 mg/kg/body weight, was injected into rats of Groups 3 and 4 to investigate the effects of 2,4-D acid iso-octylester on the development of neoplasms. After feeding the rats with neoplasms in Group 4 with food including 200 mg/kg/day 2,4-D acid iso-octylester for 16 weeks, an autopsy was carried out on all animals. We found that 2,4-D acid iso-octylester caused the formation of atypical cell foci (ACF) in the pancreata and livers of rats. ACF that were formed experimentally by exposure to azaserine had increased diameter, volume and number of atypical cell foci/mm² and mm³ after exposure to 2,4-D acid iso-octylester. Our observations indicated that this herbicide potentially is a cancer initiator.     

Monte Carlo study of the influence of energy spectra,mesh size,high Z element on dose and PVDR based on 1-D and 3-D heterogeneous mouse head phantom for Microbeam Radiation Therapy

PurposeTo evaluate the influence of energy spectra, mesh sizes, high Z element on dose and PVDR in Microbeam Radiation Therapy (MRT) based on 1-D analogy-mouse-head-model (1-D MHM) and 3-D voxel-mouse-head-phantom (3-D VMHP) by Monte Carlo simulation.MethodsA Microbeam-Array-Source-Model was implemented into EGSnrc/DOSXYZnrc. The microbeam size is assumed to be 25 μm, 50 μm or 75 μm in thickness and fixed 1 mm in height with 200 μm c-t-c. The influence of the energy spectra of ID17@ESRF and BMIT@CLS were investigated. The mesh size was optimized. PVDR in 1-D MHM and 3-D VMHP was compared with the homogeneous water phantom. The arc influence of 3-D VMHP filled with water (3-D VMHWP) was compared with the rectangle phantom.ResultsPVDR of the lower BMIT@CLS spectrum is 2.4 times that of ID17@ESRF for lower valley dose. The optimized mesh is 5 µm for 25 µm, and 10 µm for 50 µm and 75 µm microbeams with 200 µm c-t-c. A 500 μm skull layer could make PVDR difference up to 62.5% for 1-D MHM. However this influence is limited (<5%) for the farther homogeneous media (e.g. 600 µm). The peak dose uniformity of 3-D VMHP at the same depth could be up to 8% for 1.85 mm × 1 mm irradiation field, whereas that of 3-D VMHWP is <1%. The high Z element makes the dose uniformity enhance in target. The surface arc could affect the superficial PVDR (from 44% to 21% in 0.2 mm depth), whereas this influence is limited for the more depth (<1%).ConclusionAn accurate MRT dose calculation algorithm should include the influence of 3-D heterogeneous media.     

The liquid overlay technique is the key to formation of co-culture spheroids consisting of primary osteoblasts, fibroblasts and endothelial cells

Background aimsThe 3-dimensional (3-D) culture of various cell types reflects the in vivo situation more precisely than 2-dimensional (2-D) cell culture techniques. Spheroids as 3-D cell constructs have been used in tumor research for a long time. They have also been used to study angiogenic mechanisms, which are essential for the success of many tissue-engineering approaches. Several methods of forming spheroids are known, but there is a lack of systematic studies evaluating the performance of these techniques.MethodsWe evaluated the performance of the hanging drop technique, carboxymethyl cellulose technique and liquid overlay technique to form both mono- and co-culture spheroids consisting of primary osteoblasts, fibroblasts and endothelial cells. The performance of the three techniques was evaluated in terms of rate of yield and reproducibility. The size of the generated spheroids was determined systematically.ResultsThe liquid overlay technique was the most suitable for generating spheroids reproducibly. The rate of yield for this technique was between 60% and 100% for monoculture spheroids and 100% for co-culture spheroids. The size of the spheroids could be adjusted easily and precisely by varying the number of seeded cells organized in one spheroid. The formation of co-culture spheroids consisting of three different cell types was possible.ConclusionsOur results show that the most suitable technique for forming spheroids can vary from the chosen cell type, especially if primary cells are used. Co-culture spheroids consisting of three different cell types will be used to study angiogenic phenomena in further studies.     

Aminopyrimidines and Derivatives. 19 1. Reaction of 1, 6-Dihydro-4-Beta; D (2, 3, 4, 6-Tetra-0-Acetyl)Glucopyranosylamino-1-Methyl-Z-Methoxy-6-Oxo Pyrimidine with Choracetyl Chloride

Abstract

Reaction between 1, 6-dihydro-4-β-D(2, 3, 4, 6-tetra-O-acetyl) glucopyranosylamino-l-methyl-2-methoxy-6-oxo pyrimidine and chloracetyl chloride yields the corresponding 5-α-chloracetyl derivative and 2,6-di oxo-4-β -D (2,3,4,6-tetra-0-acetyl) glucopyranosylamino-l-methyl-1,2,3,6 tetrahdro pyrimidine. The first compund has been cyclized to the corresponding 7-β-D-glucopyranosyl-pyrrolo 2, 3-d pyrimidine and the second one to 3-βD-glucopyranosyl-vic-triazolo 4,5-d pyrimidine.     

Protein surface representation and analysis by dimension reduction

Background

Protein structures are better conserved than protein sequences, and consequently more functional information is available in structures than in sequences. However, proteins generally interact with other proteins and molecules via their surface regions and a backbone-only analysis of protein structures may miss many of the functional and evolutionary features. Surface information can help better elucidate proteins' functions and their interactions with other proteins. Computational analysis and comparison of protein surfaces is an important challenge to overcome to enable efficient and accurate functional characterization of proteins.

Methods

In this study we present a new method for representation and comparison of protein surface features. Our method is based on mapping the 3-D protein surfaces onto 2-D maps using various dimension reduction methods. We have proposed area and neighbor based metrics in order to evaluate the accuracy of this surface representation. In order to capture functionally relevant information, we encode geometric and biochemical features of the protein, such as hydrophobicity, electrostatic potential, and curvature, into separate color channels in the 2-D map. The resulting images can then be compared using efficient 2-D image registration methods to identify surface regions and features shared by proteins.

Results

We demonstrate the utility of our method and characterize its performance using both synthetic and real data. Among the dimension reduction methods investigated, SNE, LandmarkIsomap, Isomap, and Sammon's mapping provide the best performance in preserving the area and neighborhood properties of the original 3-D surface. The enriched 2-D representation is shown to be useful in characterizing the functional site of chymotrypsin and able to detect structural similarities in heat shock proteins. A texture mapping using the 2-D representation is also proposed as an interesting application to structure visualization.

     

Effect of patient positioning on carbon-ion therapy planned dose distribution to pancreatic tumors and organs at risk

PurposePancreatic tumor treatment dose distribution variations associated with supine and prone patient positioning were evaluated.MethodsA total of 33 patients with pancreatic tumors who underwent CT in the supine and prone positions were analyzed retrospectively. Gross tumor volume (GTV), planning target volume (PTV), and organs at risk (OARs) (duodenum and stomach) were contoured. The prescribed dose of 55.2 Gy (RBE) was planned from four beam angles (0°, 90°, 180°, and 270°). Patient collimator and compensating boli were designed for each field. Dose distributions were calculated for each field in the supine and prone positions. To improve dose distribution, patient positioning was selected from supine or prone for each beam field.ResultsCompared with conventional beam angle and patient positioning, D2cc of 1st-2nd portion of duodenum (D1-D2), 3rd-4th portion of duodenum (D3-D4), and stomach could be reduced to a maximum of 6.4 Gy (RBE), 3.5 Gy (RBE), and 4.5 Gy (RBE) by selection of patient positioning. V10 of D1-D2, D3-D4, and stomach could be reduced to a maximum of 7.2 cc, 11.3 cc, and 11.5 cc, respectively. D95 of GTV and PTV were improved to a maximum of 6.9% and 3.7% of the prescribed dose, respectively.ConclusionsOptimization of patient positioning for each beam angle in treatment planning has the potential to reduce OARs dose maintaining tumor dose in pancreatic treatment.     

Improvement of regeneration ability in Phleum pratense L. in vitro culture by dicamba

Calli were induced from mature caryopses of timothy grass (Phleum pratense L.) on MS medium (Murashige and Skoog 1962) supplemented with 500 mg·dm⁻³ casein hydrolysate and 5 mg·dm⁻³ 2,4-D (2,4-dicholorophenoxyacetic acid) or 2 mg·dm⁻³ dicamba (3,6-dichloro-o-anisic acid). Twelve-week-old calli were passaged on media with reduced levels of auxins (2 mg·dm⁻³ 2,4-D or 1 mg·dm⁻³ dicamba). Tissues induced on medium with 2,4-D were transferred on medium with 2,4-D and on medium with dicamba; parallely calli initiated on medium with dicamba were passaged on medium with 2,4-D or dicamba. Calli from various media sequences were used to establish cell suspension cultures in media containing 2 mg·dm⁻³ 2,4-D or 1 mg·dm⁻³ dicamba. An assessment of regeneration ability of calli was made on MS medium containing 0.2 mg·dm⁻³ kinetin. Callus tissue induced and/or subcultured on any of the media with 2,4-D did not regenerate plants while dicamba added to the media was the effective stimulator of regenerability. In the presence of 2,4-D calli and suspensions produced a jelly-like extracellular matrix. In cell suspension this phenomenon was observed 4–5 days after each passage. The measurements of electric potential of calli, growing on MS medium with kinetin were performed. Non-regenerating callus areas had an electric potential close to 0 mV while parts of tissue with meristematic centres were characterized by lower values of electric potential.     

Characterization of a commercial scintillation detector for 2-D dosimetry in scanned proton and carbon ion beams

IntroductionPencil beam scanning technique used at CNAO requires beam characteristics to be carefully assessed and periodically checked to guarantee patient safety. This study aimed at characterizing the Lynx® detector (IBA Dosimetry) for commissioning and periodic quality assurance (QA) for proton and carbon ion beams, as compared to EBT3 films, currently used for QA checks.Methods and materialsThe Lynx® is a 2-D high-resolution dosimetry system consisting of a scintillating screen coupled with a CCD camera, in a compact light-tight box. The scintillator was preliminarily characterized in terms of short-term stability, linearity with number of particles, image quality and response dependence on iris setting and beam current; Lynx® was then systematically tested against EBT3 films. The detector response dependence on radiation LET was also assessed.ResultsPreliminary results have shown that Lynx is suitable to be used for commissioning and QA checks for proton and carbon ion scanning beams; the cross-check with EBT3 films showed a good agreement between the two detectors, for both single spot and scanned field measurements. The strong LET dependence of the scintillator due to quenching effect makes Lynx® suitable only for relative 2-D dosimetry measurements.ConclusionLynx® appears as a promising tool for commissioning and periodic QA checks for both protons and carbon ion beams. This detector can be used as an alternative of EBT3 films, allowing real-time measurements and analysis, with a significant time sparing.     

Characterization and Sequence Variation in the rDNA Region of Six Nematode Species of the Genus Longidorus (Nematoda)

Total DNA was isolated from individual nematodes of the species Longidorus helveticus, L. macrosoma, L. arthensis, L. profundorum, L. elongatus, and L. raskii collected in Switzerland. The ITS region and D1-D2 expansion segments of the 26S rDNA were amplified and cloned. The sequences obtained were aligned in order to investigate sequence diversity and to infer the phylogenetic relationships among the six Longidorus species. D1-D2 sequences were more conserved than the ITS sequences that varied widely in primary structure and length, and no consensus was observed. Phylogenetic analyses using the neighbor-joining, maximum parsimony and maximum likelihood methods were performed with three different sequence data sets: ITS1-ITS2, 5.8S-D1-D2, and combining ITS1-ITS2+5.8S-D1-D2 sequences. All multiple alignments yielded similar basic trees supporting the existence of the six species established using morphological characters. These sequence data also provided evidence that the different regions of the rDNA are characterized by different evolution rates and by different factors associated with the generation of extreme size variation.     

Iranian Strawberry crinkle cytorhabdovirus variation assessed using its movement protein (P3) gene

Background

Strawberry crinkle virus (SCV) is a member of the genus Cytorhabdovirus, family Rhabdovirida, and order Mononegavirales. SCV affects the production of various strawberry cultivars. In this study we investigated the genetic diversity of SCV in strawberry fields based on P3 (movement protein) gene.

Methods and results

The samples were collected from strawberry fields in the Kurdistan Province, Iran. P3 gene from 20 SCV isolates, representing 18 nucleic acid haplotypes, is composed of 729 nucleotides, encoding a protein with 243 amino acids. SCV-P3 sequences shared 98.77%–99.86% nucleotide and 97.5%–100% amino acid sequence identity. Phylogenetic analyses of the new P3 sequences with two previously published SCV-P3 sequences from the Czech Republic showed that there are two major phylogroups (I and II) and three minor phylogroups in the body of the phylogeny, I-1, I-2, II-1. Comparisons of P3 gene sequences revealed a mutational bias, with more differences being transitions than transversions. The ratio of non-synonymous/synonymous nucleotide changes was?<?1, indicating that SCV-P3 gene is under predominantly negative selection.

Conclusions

Phylogenetic and sequence identity analyses showed that SCV isolates from Iran are closely related and have not diverged more than 2% based on P3 gene despite geographical separation and strawberry cultivar. This is the first report of the genetic diversity of SCV worldwide.

     

Automatic extraction and measurement of individual trees from mobile laser scanning point clouds of forests

Background and AimsIn addition to terrestrial laser scanning (TLS), mobile laser scanning (MLS) is increasingly arousing interest as a technique which provides valuable 3-D data for various applications in forest research. Using mobile platforms, the 3-D recording of large forest areas is carried out within a short space of time. Vegetation structure is described by millions of 3-D points which show an accuracy in the millimetre range and offer a powerful basis for automated vegetation modelling. The successful extraction of single trees from the point cloud is essential for further evaluations and modelling at the individual-tree level, such as volume determination, quantitative structure modelling or local neighbourhood analyses. However, high-precision automated tree segmentation is challenging, and has so far mostly been performed using elaborate interactive segmentation methods.MethodsHere, we present a novel segmentation algorithm to automatically segment trees in MLS point clouds, applying distance adaptivity as a function of trajectory. In addition, tree parameters are determined simultaneously. In our validation study, we used a total of 825 trees from ten sample plots to compare the data of trees segmented from MLS data with manual inventory parameters and parameters derived from semi-automatic TLS segmentation.Key ResultsThe tree detection rate reached 96 % on average for trees with distances up to 45 m from the trajectory. Trees were almost completely segmented up to a distance of about 30 m from the MLS trajectory. The accuracy of tree parameters was similar for MLS-segmented and TLS-segmented trees.ConclusionsBesides plot characteristics, the detection rate of trees in MLS data strongly depends on the distance to the travelled track. The algorithm presented here facilitates the acquisition of important tree parameters from MLS data, as an area-wide automated derivation can be accomplished in a very short time.     

On A Six-Dimensional Representation of RNA Secondary Structures

Abstract

In this paper, we proposed a 6-D representation of RNA secondary structures. The use of the 6-D representation is illustrated by constructing structure invariants. Comparisons with the similarity/dissimilarity results based on 6-D representation for a set of RNA secondary structures, are considered to illustrate the use of our structure invariants based on the entries in derived sequence matrices restricted to a selected width of a band along the main diagonal.     

Phylogenetic Utility of Histone H3 Intron Sequences in the Perennial Relatives of Soybean (Glycine:Leguminosae)

Histone H3 loci form a large multigene family in most plant species. InGlycine,some of these loci possess introns, whose sequences can provide characters for assessing phylogenetic relationships among species of the genus. Phylogenetic analyses of two closely related H3-B loci revealed a complex evolutionary pattern, producing trees from which species relationships could not be inferred readily. The single H3-D locus, in contrast, provided data suitable for the construction of gene trees whose topologies were sufficiently similar to other hypotheses of relationships within the subgenusGlycineto give confidence that evolution at this locus is tracking species phylogenies. H3-D topologies identified several of the same groupings found in previous phylogenetic studies using the chloroplast genome. However, histone H3-D and chloroplast genome data sets were in other respects incongruent, as revealed by both topological differences and numerical measures of congruence. The principal difference involvedGlycine falcata,whose chloroplast genome belongs to one of the three strongly supported clades in the subgenus, but whose histone H3-D allele was sister to those of the remaining members of the subgenus. The H3-D topology is more in keeping with the morphologically, ecologically, and genetically divergent nature of this species. The H3-D locus appears to be a useful source of phylogenetic characters for interspecific studies inGlycine,providing resolution among taxa whose relationships were unresolved in previous studies.     

Comparison of 16S rRNA gene phylogeny and functional tfdA gene distribution in thirty-one different 2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic acid degraders

31 different bacterial strains isolated using the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole source of carbon, were investigated for their ability to mineralize 2,4-D and the related herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA). Most of the strains mineralize 2,4-D considerably faster than MCPA. Three novel primer sets were developed enabling amplification of full-length coding sequences (CDS) of the three known tfdA gene classes known to be involved in phenoxy acid degradation. 16S rRNA genes were also sequenced; and in order to investigate possible linkage between tfdA gene classes and bacterial species, tfdA and 16S rRNA gene phylogeny was compared. Three distinctly different classes of tfdA genes were observed, with class I tfdA sequences further partitioned into the two sub-classes I-a and I-b based on more subtle differences. Comparison of phylogenies derived from 16S rRNA gene sequences and tfdA gene sequences revealed that most class II tfdA genes were encoded by Burkholderia sp., while class I-a, I-b and III genes were found in a more diverse array of bacteria.