A new <Emphasis Type="Italic">Dactylella</Emphasis> species from <Emphasis Type="Italic">Orbilia alba</Emphasis>

A new Dactylella species, Dactylella alba was isolated from the ascospores of Orbilia alba collected in Wenshan County, Yunnan Province, China. Conidiophores were either not branched or occasionally branched, bearing divergent sterigmata on the tip with single conidium on each. Conidia were elongated ellipsoids, 1–2 septate, mostly 1 septate. By combining the ITS sequence with morphological characteristics, a new anamorphic species is described and illustrated together with its teleomorph.     

The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts

The Registry of Standard Biological Parts only accepts genetic parts compatible with the RFC 10 BioBrick format. This combined assembly and submission standard requires that four unique restriction enzyme sites must not occur in the DNA sequence encoding a part. We present evidence that this requirement places a nontrivial burden on iGEM teams developing large and novel parts. We further argue that the emergence of inexpensive DNA synthesis and versatile assembly methods reduces the utility of coupling submission and assembly standards and propose a submission standard that is compatible with current quality control strategies while nearly eliminating sequence constraints on submitted parts.     

Functional markers based molecular characterization and cloning of resistance gene analogs encoding NBS-LRR disease resistance proteins in finger millet (<Emphasis Type="Italic">Eleusine coracana)</Emphasis>

Magnaporthe grisea, the blast fungus is one of the main pathological threats to finger millet crop worldwide. A systematic search for the blast resistance gene analogs was carried out, using functional molecular markers. Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encodes nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from Eleusine coracana. Genomic DNA sequences sharing homology with NBS region of resistance gene analogs were isolated and characterized from resistant genotypes of finger millet using PCR based approach with primers designed from conserved regions of NBS domain. Attempts were made to identify molecular markers linked to the resistance gene and to differentiate the resistant bulk from the susceptible bulk. A total of 9 NBS-LRR and 11 EST-SSR markers generated 75.6 and 73.5% polymorphism respectively amongst 73 finger millet genotypes. NBS-5, NBS-9, NBS-3 and EST-SSR-04 markers showed a clear polymorphism which differentiated resistant genotypes from susceptible genotypes. By comparing the banding pattern of different resistant and susceptible genotypes, five DNA amplifications of NBS and EST-SSR primers (NBS-05_504, NBS-09₇₁₁, NBS-07₆₈₈, NBS-03₅₀₉ and EST-SSR-04₂₄₁) were identified as markers for the blast resistance in resistant genotypes. Principal coordinate plot and UPGMA analysis formed similar groups of the genotypes and placed most of the resistant genotypes together showing a high level of genetic relatedness and the susceptible genotypes were placed in different groups on the basis of differential disease score. Our results provided a clue for the cloning of finger millet blast resistance gene analogs which not only facilitate the process of plant breeding but also molecular characterization of blast resistance gene analogs from Eleusine coracana.     

Microbial characterization and hydrocarbon biodegradation potential of natural bilge waste microflora

Shipping operations produce oily wastes that must be managed properly to avoid environmental pollution. The aim of this study was to characterize microorganisms occurring in ship bilge wastes placed in open lagoons and, particularly, to assess their potential to degrade polycyclic aromatic hydrocarbons (PAHs). A first-order kinetic was suitable for describing hydrocarbon biodegradation after 17 days of treatment. The calculated rate constants were 0.0668 and 0.0513 day^–1 with a corresponding half-life of 10.3 and 13.5 days for the aliphatic and aromatic hydrocarbon fractions, respectively. At day 17, PAH removal percentages were: acenaphtylene 100, fluorene 95.2, phenanthrene 93.6, anthracene 70.3, and pyrene 71.5. Methyl phenanthrene removals were lower than that of their parent compound (3-methyl phenanthrene 83.6, 2-methyl phenanthrene 80.8, 1-methyl phenanthrene 77.3, 9-methyl phenanthrene 75.1, and 2,7-dimethyl phenanthrene 76.6). Neither pure cultures nor the microbial community from these wastes showed extracellular biosurfactant production suggesting that the addition of an exogenously produced biosurfactant may be important in enhancing hydrocarbon bioavailability and biodegradation. DNA analysis of bilge waste samples revealed a ubiquitous distribution of the nahAc genotype in the dump pools. Although almost all of the isolates grew on naphthalene as sole carbon source, only some of them yielded nahAc amplification under the experimental conditions used. The variety of PAHs in bilge wastes could support bacteria with multiple degradation pathways and a diversity of catabolic genes divergent from the classical nah-like type.     

The inhibition of polyamine biosynthesis weakens the drought tolerance in white clover (<Emphasis Type="Italic">Trifolium repens</Emphasis>) associated with the alteration of extensive proteins

Changes of endogenous polyamine (PA) levels could be a key adaptive response to drought in plants. White clover pretreated with or without dicyclohexylamine (DCHA), an inhibitor of PA biosynthesis, was subjected to drought stress induced by 18% polyethylene glycol 6000 for 8 days in controlled growth chambers. Results showed that drought stress significantly increased endogenous PA content, whereas DCHA significantly decreased PA accumulation under drought stress. The attenuate PA biosynthesis was unfavorable for plant growth and drought tolerance, as reflected by significantly lower relative water content, relative growth rate, instantaneous water use efficiency, and cell membrane stability in leaves in response to drought. On the basis of proteomic analysis, the inhibition of PA synthesis decreased the accumulation of many key differentially expressed proteins including (1) ribosomal structure and biogenesis: elongation factor, ribosomal protein S10E, and 30S ribosomal protein; (2) amino acid transport and metabolism: cysteine synthase, delta-1-pyrroline-5-carboxylate synthetase, and glutamate decarboxylase; (3) carbohydrate metabolism and energy production: photosystem apoprotein, sucrose-phosphate synthase, phosphogluconate dehydrogenase, sucrose-phosphatase, NADH oxidoreductase, and ATP synthase; (4) antioxidant metabolism: catalase, peroxidase I, ascorbate peroxidase, and glutathione S-transferase; and (5) other biological processes: heat shock protein 70, heat shock protein 90, and calcium-dependent protein kinase associated with the decreased drought tolerance in white clover. These findings indicate that PAs play a critical role in the regulation of growth, ribosome, amino acid and energy metabolism, and antioxidant reactions in white clover under drought stress. Drought-induced increases in endogenous PAs could be one of key adaptive responses against drought stress in white clover.     

A Model of Holocene Mangrove Development and Relative Sea-level Changes on the Bragança Peninsula (Northern Brazil)

Based on the integration of geological information, the pollen record, radiocarbon data, and modern mangrove distribution, this paper proposes a model of evolutionary development for mangroves on the Brazilian Bragança Peninsula driven by relative sea-level changes from the middle to late Holocene. After a postglacial relative sea-level rise (RSL), the mangrove habitats on the Bragança Peninsula began to develop at about 5100 years BP close to the current RSL, originating in the middle of the peninsula. Between 1800 and 1400 years BP, this littoral area underwent a maximum RSL fall of 1 m below the current one, followed by a gradual RSL rise until 1000 years BP, when the modern RSL was reached. Between 5100 and 1000 years BP, the RSL of the Bragança coastline was probably never higher than 0.6 m above the present level. The first Holocene mangrove forest (5100 years BP) in this region disappeared from the plains due to RSL fall and was replaced by herbaceous vegetation (Cyperaceae and Poaceae).     

Use of a herbicide or lysine plus threonine for non-antibiotic selection of transgenic chickpea

A desensitized aspartate kinase (AK) gene has been developed as a non-antibiotic selection marker for use in the production of transgenic chickpea (Cicer arietinum L.). Transgenic shoots regenerated from embryo explants bombarded with the desensitized AK gene were selected on media containing two amino acids, lysine and threonine (LT). Approximately 15% of the putative transgenic shoots of vars. P-362 and P-1042 survived after 4 weeks of growth on MSB5 medium (MS mineral salts and B5 vitamins) containing 2 µM thidiazuron (TDZ) and 2 mM lysine and 2 mM threonine. These shoots were subsequently grown on MSB5 medium supplemented with 2 µM TDZ and 5 mM lysine and 5 mM threonine, and nearly 1% continued to grow after 16 weeks of selection. A phosphinothricin (PPT) selection system for Agrobacterium-mediated chickpea transformation was also developed. Three varieties of chickpea, P-362, P-1042 and P-1043, were successfully used for Agrobacterium transformation. Following Agrobacterium infection, 3-8% of the regenerated shoots remained green and continued to grow on MSB5 medium supplemented with 2.5 mg l^-1 PPT. Increasing the concentrations of PPT to 15 mg l^-1 reduced transgenic shoot production in P-362, P-1042 and P-1043 to 0.7%, 1.2% and 1.1%, respectively. Selected putatively transformed shoots of all three varieties were rooted and grown to maturity. Southern hybridization analysis revealed single as well as multiple integration of genes in selected transgenic lines. The level of AK activity detected in LT-selected plants was higher than that detected in the non-transformed control.Abbreviations AK: Aspartate kinase - CP: Chlorophenol red - GUS: -Glucuronidase - IBA: Indole-3-butyric acid - Kn: Kinetin (6-furfuryl aminopurine) - LT: Lysine plus threonine - MSB5: Murashige and Skoog salts with B5 vitamins - nptII: Neomycin phosphotransferase II - pat: Phosphinothricin-acetyltransferase - PPT: Phosphinothricin - TDZ: Thidiazuron [1-phenyl-3-(1,2,3-thiadiazol-5-YL) urea]Communicated by P. LakshmananJ. Sen and N. Tewari-Singh have contributed equally to this article.     

Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes — a comparative study of group-I intron structures

In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.     

Corrected western Atlantic sea-level curve for the last 11,000 years based on calibrated <Superscript>14</Superscript>C dates from<Emphasis Type="Italic"> Acropora palmata</Emphasis> framework and intertidal mangrove peat

A corrected western Atlantic Holocene sea-level curve was constructed from 145 calibrated ¹⁴C and TIMS U-Th dates from shallow Acropora palmata framework and intertidal Rhizopora mangle peat from the Florida Keys, Belize, and the wider Caribbean. Data include both previously published and newly reported coral and peat dates. With the elevations of corals restricted to positions below sea level and those of peats to intertidal and higher levels, a curve bracketed by corals below and peat above effectively delineates the positions of a rising Holocene sea. From 3–11 ka, the corrected curve shifts progressively to older calibrated ages, reaching an ~1-kyr increase at –21 m MSL (mean sea level). Elevations and calibrated ages of samples from each locality in the wider Caribbean region constitute an important database for future refinement with glacio-hydro-isostatic elevation corrections from 3-D Earth models. In future studies of the history of western Atlantic coral reefs, scientists will be able to relate calibrated radiocarbon dates to this sea-level curve to determine paleo water depths and rates of sea-level rise.