A standalone version of IsoFinder for the computational prediction of isochores in genome sequences

Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a researcher may want to perform batch processing of many sequences simultaneously in its local machine, instead of analyzing them on one by one basis through the web. To this end, standalone versions are required. We report here the implementation of two standalone programs, able to predict isochores at the sequence level: 1) a command-line version (IsoFinder) for Windows and Linux systems; and 2) a user-friendly version (IsoFinderWin) running under Windows.Comment: 7 pages, 3 figure

Deposition and transport of functionalized carbon nanotubes in water-saturated sand columns

Knowledge of the fate and transport of functionalized carbon nanotubes (CNTs) in porous media is crucial to understand their environmental impacts. In this study, laboratory column and modeling experiments were conducted to mechanistically compare the retention and transport of two types of functionalized CNTs (i.e., single-walled nanotubes and multi-walled nanotubes) in acid-cleaned, baked, and natural sand under unfavorable conditions. The CNTs were highly mobile in the acid-cleaned sand columns but showed little transport in the both natural and baked sand columns. In addition, the retention of the CNTs in the both baked and natural sand was strong and almost irreversible even after reverse, high-velocity, or surfactant flow flushing. Both experimental and modeling results showed that pH is one of the factors dominating CNT retention and transport in natural and baked sand. Retention of the functionalized CNTs in the natural and baked sand columns reduced dramatically when the system pH increased. Our results suggest that the retention and transport of the functionalized CNTs in natural sand porous media were mainly controlled by strong surface deposition through the electrostatic and/or hydrogen-bonding attractions between surface function groups of the CNTs and metal oxyhydroxide impurities on the sand surfaces

lntrogression of Bacterial Leaf Blight Resistance Gene from Oryza Minuta J.B. Presl. Ex C. B. Presl. into New Rice Type (Oryza sativa L.)

F1 Hybrids, backcross progenies, advanced introgression lines (2n=24) and monosomic alien addition lines or MAALs (2n=25) were successfully produced following embryo rescue between an elite new plant type (NPT) breeding line of Oryza sativa (2n=24, AA) and a wild species, O. minuta (2n=48, BBCC). F1 hybrids performance were intermediate between the parents. The F1 hybrids had 36 chromosomes indicating having 12 chromosome A from O. sativa and 12 B and 12 C from O. minuta. THE BACK CROSS progenies had different chromosome number indicating abnormal meiosis of the hybrids and back cross progenies. Plant with 2n=24 and 25 chromosomes were obtained in BC4FI. The hybrids and backcross progenies were susceptible to bacterial leaf blight (BB). However, several of the 2n=24 plants derived resistant plant to bacterial leaf blight race 1 of the Philippines races. The gene is different from introgressed gene intio rice from O. longistaminata ( Xa21) and from O. Minuta Acc. 101141   I Key words: Oryza minuta, MAALS, Bacterial leaf bligh

Numerical Classification of the Genus Cynodon

Agronom

Methods of using carbon nanotubes as filter media to remove aqueous heavy metals

Although carbon nanotubes (CNTs) are well known to have a strong affinity to various heavy metals in aqueous solution, little research has been dedicated to exploit their use in fixed-bed water treatment systems (e.g., trickling filters). In this work, batch sorption and fixed-bed experiments were conducted to examine the ability of functionalized multi-walled CNTs as filter media to remove two heavy metal ions (Pb2+ and Cu2+) from infiltrating water. Batch sorption experiments confirmed the strong sorption affinity of the CNTs for Pb2+ and Cu2+ in both single and dual metal solution systems. In addition, sonication-promoted dispersion of the CNT particles enhanced their heavy metal sorption capacity by 23.9–32.2%. For column experiments, laboratory-scale fixed-bed columns were packed with CNTs and natural quartz sand by three different packing: layered, mixed, and deposited. While all the three packing methods enhanced the fixed-bed filtering efficiency of Pb2+ and Cu2+ from single and dual metal systems, the CNT-deposited packing method was superior. Although the amount of the CNTs added into the fixed-bed columns was only 0.006% (w/w) of the sand, they significantly improved the fixed-bed’s filtering efficiency of Pb2+ and Cu2+ by 55–75% and 31–57%, respectively. Findings from this study demonstrate that functionalized multi-walled CNTs, together with natural sand, can be used to effectively and safely remove heavy metals from water

Phylogenetic distribution of large-scale genome patchiness

[Background] The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level. [Results] The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. [Conclusion] Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.This work was supported by the Spanish Government (BIO2005-09116-C03-01) and Plan Andaluz de Investigación (CVI-162, P06-FQM-01858, P07-FQM-03163 and TIC-640)

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands

Evaluation of Oryza sativa x O. glaberrima derived progenies for resistance to rootknot nematode and identification of introgressed alien chromosome segments using SSR markers

The genus Oryza has two cultivated species, Asian rice (Oryza sativa L.) and African rice (Oryza glaberrima Steud.) and 22 wild species. O. glaberrima is low yielding but has useful genes for resistance to biotic and abiotic stresses. Introgression lines derived from backcrossing of O. sativa x O. glaberrima, using O. sativa as recurrent parent, were evaluated for tolerance to root-knot nematode (Meloidogyne graminicola). Testing in sick plots infested with nematodes showed reduction in plant height, shoot and root biomass and leaf area index compared to the control. Based on gall rating and the ratio of the final population to the initial population of nematodes (Pf/Pi ratio), three introgression lines were found to be resistant to nematodes (IR80311-9-B-B-1-2 and IR80311-2-B-B-1-2 under screenhouse and IR80311-48-BB- 1 under phytotron conditions). Gall rating and the Pf/Pi ratio showed positive correlation (r = 0.61). Analysis of 122 introgression lines using simple sequence repeat (SSR) markers detected introgression of O. glaberrima segments into O. sativa