Pseudouridine modification in <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> spliceosomal snRNAs: unique modifications are found in regions involved in snRNA-snRNA interactions

Background  

Pseudouridine (Ψ) is an abundant modified nucleoside in RNA and a number of studies have shown that the presence of Ψ affects RNA structure and function. The positions of Ψ in spliceosomal small nuclear RNAs (snRNAs) have been determined for a number of species but not for the snRNAs from Caenorhabditis elegans (C. elegans), a popular experimental model system of development.     

Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase <Emphasis Type="Italic">Bacillus subtilis</Emphasis> levansucrase

Background  

Fructans – β-D-fructofuranosyl polymers with a sucrose starter unit – constitute a carbohydrate reservoir synthesised by a considerable number of bacteria and plant species. Biosynthesis of levan (αGlc(1–2)βFru [(2–6)βFru]_n), an abundant form of bacterial fructan, is catalysed by levansucrase (sucrose:2,6-β-D-fructan-6-β-D-fructosyl transferase), utilizing sucrose as the sole substrate. Previously, we described the tertiary structure of Bacillus subtilis levansucrase in the ligand-free and sucrose-bound forms, establishing the mechanistic roles of three invariant carboxylate side chains, Asp86, Asp247 and Glu342, which are central to the double displacement reaction mechanism of fructosyl transfer. Still, the structural determinants of the fructosyl transfer reaction thus far have been only partially defined.     

Climate change and recent genetic flux in populations of <Emphasis Type="Italic">Drosophila robusta</Emphasis>

Background  

Studied since the early 1940's, chromosomal polymorphisms in the deciduous woods species Drosophila robusta have been characterized by well-defined latitudinal, longitudinal, and elevational clines, but – until at least ten years ago – stable, local population frequencies. Recent biogeographical analyses indicate that D. robusta invaded North America from southeast Asia and has persisted in eastern temperate forests for at least 20–25 my without speciating. The abundant chromosome polymorphisms found across the range of D. robusta are thus likely to be relatively ancient, having accumulated over many well known climatic cycles in North America. Sufficient long-term data are now available such that we can now gauge the rate of these evolutionary changes in natural populations due to environmental change.     

Germination responses of <Emphasis Type="Italic">Erica andevalensis</Emphasis> to different chemical and physical treatments

Erica andevalensis Cabezudo & Rivera is a threatened edaphic endemic species of Andalusia (SW Spain). Under natural conditions, the plants produce a very large number of small seeds (0.3–0.4 mm) but very few seedlings survive. Different treatments (high temperature, cold pre-treatment, nitrogen salts, and gibberellic acid applications) were tested to assess germination patterns in different populations and to determinate the most favorable conditions for germination. Gibberellic acid was provided in five different concentrations from 0 to 400 ppm GA₃, while nitrogen was applied as 10 mM of either KNO₃ or NH₄NO₃. The effect of pH on germination was also tested. The species always showed a low germination rate (6.50–22%) that was not stimulated either by 1 or 4 months in dry cold pre-treatment, nitrogen application, acid pH medium, or by high temperature (80°C for 10 min); although gibberellic acid application (100–400 ppm) significantly enhanced germination. The highest percentage of germination (41.6%) was achieved with a mean germination time to start germination (t ₀) of 7.6 ± 0.54 days when the seeds were subjected to 400 ppm gibberellic acid treatment. The population origin did not have a significant effect on germination percentage.     

Reconstructing the history of an invasion: the toxic phytoplankton species <Emphasis Type="Italic">Gymnodinium catenatum</Emphasis> in the Northeast Atlantic

The phytoplankton species Gymnodinium catenatum is responsible for major worldwide losses in aquaculture due to shellfish toxicity. On the West coast of the Iberian Peninsula, toxic blooms have been reported since the mid-1970s. While the recent geographical spread of this species into Australasia has been attributed to human-mediated introduction, its origin in the Northeast Atlantic is still under debate. Gymnodinium catenatum forms a highly resistant resting stage (cyst) that can be preserved in coastal sediments, building-up an historical record of the species. Similar cyst types (termed microreticulate) are produced by other non-toxic Gymnodinium species that often co-occur with G. catenatum. We analysed the cyst record of microreticulate species in dated sediment cores from the West Iberian shelf covering the past ca. 150 years. Three distinct morphotypes were identified on the basis of cyst diameter and paracingulum reticulation. These were attributed to G. catenatum (35.6–53.3 μm), G. nolleri (23.1–36.4 μm), and G. microreticulatum (20.5–34.3 μm). Our results indicate that G. catenatum is new to the NE Atlantic, where it appeared by 1,889 ± 10, expanding northwards along the West Iberian coast. The earliest record is from the southernmost sample, while in the central Portuguese shelf the species appears in sediments dated to 1,933 ± 3, and in the North, off Oporto, in 1,951 ± 4. On the basis of the cyst record and toxic bloom reports, we reconstruct the invasive pathway of G. catenatum in the NE Atlantic. Although human-mediated introduction cannot be discarded, the available evidence points towards natural range expansion, possibly from NW Africa.     

<Emphasis Type="Italic">Glyptothorax dikrongensis</Emphasis>, a new species of catfish (Teleostei: Sisoridae) from Arunachal Pradesh,northeastern India

Glyptothorax dikrongensis, a new species of sisorid catfish from the Dikrong River in northeastern India, is described. Glyptothorax dikrongensis can be differentiated from all congeners, except G. indicus, G. rugimentum and G. obliquimaculatus, by the presence of an unculiferous patch on the posterior region of the lower lip, in between the inner mandibular-barbel bases, and unculiferous striae of the thoracic adhesive apparatus extending anteriorly onto the gular region. Glyptothorax dikrongensis is distinguished from G. indicus by the following combination of characters: equal distance between the posterior end of the pectoral-fin base and the pelvic-fin origin and between the pelvic-fin and the anal-fin origin (vs. distance between posterior end of pectoral-fin base and pelvic-fin origin greater than between pelvic-fin origin and anal-fin origin), and the pelvic-fin origin anterior to or almost at a vertical through the posterior end of the dorsal-fin base (vs. posterior to the dorsal-fin base). Glyptothorax dikrongensis is distinguished from G. rugimentum in lacking vertical bars on the body and caudal peduncle, and having a deeper caudal peduncle (8.4–9.2 vs. 6.1–7.6% SL) and a shorter dorsal-fin spine (10.1–11.1 vs. 15.2–18.6% SL). It is distinguished from G. obliquimaculatus in lacking dark, oblique blotches on the body, and in having a shorter dorsal-fin spine (10.1–11.1 vs. 13.4–16.4% SL).     

<Emphasis Type="Italic">Dolichopteryx pseudolongipes</Emphasis>, a new species of spookfish (Argentinoidei: Opisthoproctidae) from the eastern Pacific Ocean

A new species of opisthoproctid, Dolichopteryx pseudolongipes, is described on the basis of three specimens (48.7–79.9 mm in standard length: SL) collected from the eastern Pacific Ocean. This species is characterized by small tubular eyes (diameter 2.7–3.9% SL), presence of an adipose fin, anal fin base originating under the dorsal fin base, relatively short predorsal (73.3–73.8% SL), prepelvic (64.3–67.9% SL), preanal (77.4–80.1% SL), and preanus (71.5–75.7% SL) lengths; 31–33 (=9–10 + 22–24) gill rakers and 43–45 vertebrae. Although D. pseudolongipes had previously been confused with Dolichopteryx longipes, many differences between the species are apparent [e.g., adipose fin absent, anal fin base origin just behind dorsal fin base, greater prepelvic length (70.3–72.7% SL), 25 gill rakers, and 46–47 vertebrae in D. longipes].     

Rapid acid treatment of <Emphasis Type="Italic">Escherichia coli</Emphasis>: transcriptomic response and recovery

Background  

Many E. coli genes show pH-dependent expression during logarithmic growth in acid (pH 5–6) or in base (pH 8–9). The effect of rapid pH change, however, has rarely been tested. Rapid acid treatment could distinguish between genes responding to external pH, and genes responding to cytoplasmic acidification, which occurs transiently following rapid external acidification. It could reveal previously unknown acid-stress genes whose effects are transient, as well as show which acid-stress genes have a delayed response.     

Regulation of <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> body size and male tail development by the novel gene <Emphasis Type="Italic">lon-8</Emphasis>

Background  

In C. elegans and other nematode species, body size is determined by the composition of the extracellular cuticle as well as by the nuclear DNA content of the underlying hypodermis. Mutants that are defective in these processes can exhibit either a short or a long body size phenotype. Several mutations that give a long body size (Lon) phenotype have been characterized and found to be regulated by the DBL-1/TGF-β pathway, that controls post-embryonic growth and male tail development.     

A new anchovy, <Emphasis Type="Italic">Stolephorus teguhi</Emphasis> (Clupeiformes: Engraulidae), from North Sulawesi,Indonesia

Stolephorus teguhi sp. nov. is described from the holotype and 14 paratypes, 49–77 mm in standard length, collected from North Sulawesi, Indonesia. The species is characterized by having numerous gill rakers (31–35 + 41–46 = 72–82) and a short upper jaw, its posterior tip reaching to or extending slightly beyond the anterior margin of the preopercle. Stolephorus pacificus and S. multibranchus also have relatively numerous gill rakers for species of this genus (21–27 + 29–36 = 53–61 and 21–28 + 30–35 = 54–60, respectively), but counts for S. teguhi exceed those for the two species. Although S. advenus also has a short upper jaw similar to that of S. teguhi, the former has far fewer gill rakers (19 + 24 = 43) than the latter.     

<Emphasis Type="Italic">Geobacillus zalihae</Emphasis> sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

Background  

Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification.     

Introgression potential between safflower (Carthamus tinctorius) and wild relatives of the genus Carthamus

Background  

Safflower, Carthamus tinctorius, is a thistle that is grown commercially for the production of oil and birdseed and recently, as a host for the production of transgenic pharmaceutical proteins. C. tinctorius can cross with a number of its wild relatives, creating the possibility of gene flow from safflower to weedy species. In this study we looked at the introgression potential between different members of the genus Carthamus, measured the fitness of the parents versus the F1 hybrids, followed the segregation of a specific transgene in the progeny and tried to identify traits important for adaptation to different environments.     

Relationships of gag-pol diversity between <Emphasis Type="Italic">Ty3/Gypsy</Emphasis> and <Emphasis Type="Italic">Retroviridae</Emphasis>LTR retroelements and the three kings hypothesis

Background  

The origin of vertebrate retroviruses (Retroviridae) is yet to be thoroughly investigated, but due to their similarity and identical gag-pol (and env) genome structure, it is accepted that they evolve from Ty3/Gypsy LTR retroelements the retrotransposons and retroviruses of plants, fungi and animals. These 2 groups of LTR retroelements code for 3 proteins rarely studied due to the high variability – gag polyprotein, protease and GPY/F module. In relation to 3 previously proposed Retroviridae classes I, II and II, investigation of the above proteins conclusively uncovers important insights regarding the ancient history of Ty3/Gypsy and Retroviridae LTR retroelements.     

Phylogeny of the nematode genus <Emphasis Type="Italic">Pristionchus</Emphasis> and implications for biodiversity,biogeography and the evolution of hermaphroditism

Background  

The nematode Pristionchus pacificus has originally been developed as a satellite organism for comparison to Caenorhabditis elegans. A 10X coverage of the whole genome of P. pacificus is available, making P. pacificus the first non- Caenorhabditis nematode with a fully sequenced genome. The macroevolutionary comparison between P. pacificus and C. elegans has been complemented by microevolutionary studies of closely related strains and species within the genus Pristionchus. In addition, new understanding of the biology of Pristionchus from field studies, demonstrating a close association with various scarab beetles and the Colorado potato beetle, supports consideration of this nematode in studies of ecosystems. In the course of field studies on four continents more than 1,200 isolates were established from 15,000 beetle specimens representing 18 Pristionchus species. Two remarkable features of the Pristionchus – beetle association are the high species specificity of the interaction and the interception of the beetle's sex communication system for host recognition by the nematodes, as suggested by chemotaxis studies. Evolutionary interpretations of differences in developmental, behavioral and ecological patterns require a phylogenetic framework of the genus Pristionchus.     

<Emphasis Type="Italic">Chirita luochengensis</Emphasis> (Gesneriaceae), a new species from limestone areas in northern Guangxi,China

Chirita luochengensis, a new species of Gesneriaceae from Guangxi, China, is described and illustrated. The new species is similar to C. linearifolia in leaf shape, but can be distinguished by the apex of leaf blade obtuse to round, corolla purplish, 3–4.2 cm long, corolla tube 2–2.5 cm long, 10–15 mm diameter at the mouth, staminodes 3, disc ca. 2.5 mm in height, pistil 2.5–3 cm long, stigma obtrapeziform, 4 mm long, and apex shallowly 2-lobed.     

The influence of growth conditions on the cell dry weight per unit biovolume of <Emphasis Type="Italic">Klebsormidium flaccidum</Emphasis> (Charophyta), a typical ubiquitous soil alga

The dry weight per unit biovolume of 810 single, living cells of the ubiquitous soil algae Klebsormidium flaccidum from 80 experiments were determined using a Mach–Zehnder double-beam interference microscope. Different substrates such as agarized nutrient solution, different soils, and slag heap material, different pH values, temperatures and light intensities were used and cells from both growth and stationary phase were measured. The total possible range of dry weight with respect to carbon per unit biovolume (C/ubv) values was 93–226 fg μm⁻³. The mean value of all data was 147 fg μm⁻³, which concurs with the average value as taken from literature data of several planktonic algal species and groups within the respective size range (cell volume 300–1,000 μm³). We could show that C/ubv is suitable to quantify environmental stress conditions: C/ubv values ≤140 fg μm⁻³ are characteristic of cells grown under optimum conditions, and values ≥160 fg μm⁻³ reflect quantitatively graded stress situations. We propose integrating the microscope interferometric method using K. flaccidum as a test organism into a soil test system to determine the prevailing environmental conditions.     

pH tolerance of the biofouling invasive hydrozoan <Emphasis Type="Italic">Cordylophora caspia</Emphasis>

The hydrozoan Cordylophora caspia, with its origin in the Caspian and Black Seas, is considered an invasive biofouling species to power stations and water treatment plants in Brazil, causing economic and ecological impacts. Tolerance of the species to variation in pH was tested to evaluate its resistance to acidic and basic pH levels. Values of pH were tested over a range from 4.0 to 10.0. The colonies were exposed for 6 h to each treatment, using phosphoric acid and NaOH to set water pH to the desired acidic or basic levels, respectively. Colonies of C. caspia displayed 100% mortality only at pH 4 and 10, and showed high survival rates (>50%) within the pH range of 5.0–8.5. The species demonstrated tolerance to a wide range of pH levels, and the results will help in the development of techniques to reduce biofouling by this species. Treatments that keep the pH below 5 or above 8.5 for at least 6 h are suggested to control and eradicate C. caspia where fouling causes significant economic impacts.     

Optimization of <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation conditions in mature embryos of elite wheat

Immature embryos have been used frequently as target tissues in the genetical transformation of wheat. However, obtaining a large number of high quality immature embryos throughout the year is a laborious and delicate process, because of the need to cultivate the plants under controlled conditions. To circumvent this, we have employed mature embryos rather than immature ones as starter explants for Agrobacterium-mediated transformation of an elite wheat (Triticum aestivum L.) cultivar EM12. The neomycin phosphotransferase ІІ (npt ІІ) and β-glucuronidase (gus) genes were used as selectable and screenable marker genes, respectively, to assess and optimize the performance of T-DNA delivery. With the aid of an orthogonal design, the effect of four factors in combination on transfer DNA (T-DNA) delivery was studied. These factors were preculture duration, different kinds of inoculation, length of inoculation and co-culture condition. Optimal conditions for T-DNA delivery were obtained for mature embryos precultured for 14 days, followed by immersing in inoculation suspension with full strength Murashige and Skoog (MS) salts in darkness at 23–25°C for 3 h, and then co-culturing with Agrobacterium under desiccating condition in the dark at 23–24°C for 2–3 days. Complete analysis of transgene insertion demonstrated that the optimized method for Agrobacterium-mediated transformation of mature embryos of wheat was efficient and practicable.     

An EST database from saffron stigmas

Background  

Saffron (Crocus sativus L., Iridaceae) flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part – the stigmas – are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron.