S Elements: A Family of Tc1-like Transposons in the Genome of Drosophila Melanogaster

The S elements form a diverse family of long-inverted-repeat transposons within the genome of Drosophila melanogaster. These elements vary in size and sequence, the longest consisting of 1736 bp with 234-bp inverted terminal repeats. The longest open reading frame in an intact S element could encode a 345-amino acid polypeptide. This polypeptide is homologous to the transposases of the mariner-Tc1 superfamily of transposable elements. S elements are ubiquitous in D. melanogaster populations and also appear to be present in the genomes of two sibling species; however, they seem to be absent from 17 other Drosophila species that were examined. Within D. melanogaster strains, there are, on average, 37.4 cytologically detectable S elements per diploid genome. These elements are scattered throughout the chromosomes, but several sites in both the euchromatin and β heterochromatin are consistently occupied. The discovery of an S-element-insertion mutation and a reversion of this mutation indicates that S elements are at least occasionally mobile in the D. melanogaster genome. These elements seem to insert at an AT dinucleotide within a short palindrome and apparently duplicate that dinucleotide upon insertion.     

In vitro selection of Coffea arabica callus for resistance to partially purified phytotoxic culture filtrates from Colletotrichum kahawae

Calli derived from hypocotyl explants of a susceptible and resistant genotype of Coffea arabica were evaluated for their response to different concentrations of partially purified culture filtrates (PPCFs) produced by Colletotrichum kahawae which are phytotoxic. The size of calli was measured non-destructively by automated image analysis. Differential responses of calli ranged from complete necrosis or reduced growth in the susceptible genotype (N39) to an absence of necrosis and rapid growth in the resistant genotype (cv. Hybrido de Timor). Subsequently, one selection cycle in the presence of PPCF was devised and applied to calli of nine C. arabica genotypes. Normal plants were regenerated through somatic embryogenesis of callus lines that survived the phytotoxin treatment and in vitro and in vivo testing of these plants against the PPCF showed that increased resistance to the toxin had been obtained. These studies suggest that in vitro selection of calli may be a feasible approach to acquiring germplasm with improved resistance to coffee berry disease.     

Cloning and characterization of tomato leaf senescence-related cDNAs

Senescence-related cDNA clones designated SENU1, 4, 5 (senescence up-regulated) and SEND32, 33, 34, 35 and 36 (senescence down-regulated) isolated from a tomato leaf cDNA library [9] were characterized. Southern analysis showed that SEND32 is encoded by a single-copy gene while SEND33, 34, 35, 36 and SENU1 and SENU5 are members of small gene families. DNA and protein database searches revealed that SEND32, SEND35, SENU1 and SENU5 are novel cDNAs of unknown function. SEND33 encodes ferredoxin, SEND34 encodes a photosystem II 10 kDa polypeptide and SEND36 encodes catalase. The SENU4 sequence is identical to the P6 tomato protein previously reported to be pathogenesis-related [46]. The mRNA levels of SENU1, 4 and 5 increased during leaf senescence and SENU1 and SENU5 were also expressed at high levels during leaf development and in other plant organs. The SENU4 mRNA was associated more specifically with leaf senescence, although low expression was also detected in green fruit. The mRNAs for all SEND clones decreased during tomato leaf development and senescence and all except SEND32 were expressed at low levels in other plant organs. The accumulation of mRNA homologous to SENU4 and the decrease in abundance of SEND32 provide good molecular markers for leaf senescence.     

Ratio-imaging of Ca2+i in the self-incompatibility response in pollen tubes of Papaver rhoeas

The data presented here describe ratio-imaging of in intracellular free calcium (Ca²⁺_i) during the self-incompatibility (SI) response in pollen. Use of the ratiometric indicator, fura-2 dextran, in pollen tubes of Papaver rhoeas has provided new, detailed information about the spatial-temporal alterations in Ca²⁺_i, and has permitted calibration of alterations in the concentration of intracellular free calcium ([Ca²⁺]_i) in the SI response. Ratio images demonstrate that, like other pollen tubes, normally growing P. rhoeas pollen tubes exhibit a tip-focused gradient of Ca^2+bf_i, with levels reaching 1–2 μM at the extreme apex of the pollen tube. Non-growing pollen tubes did not exhibit this tip-focused gradient. Basal levels of Ca²⁺_i in the shank of the pollen tube were fairly consistent and had a mean value of 210 nM, with low-level fluctuations +/? 50 nM observed. Challenge with incompatible S proteins resulted in S-specific, rapid and dramatic alterations in [Ca²⁺]_i within a few seconds of challenge. Increases in [Ca²⁺]_i were visualized in the subapical/shank regions of the pollen tube and alterations in [Ca²⁺]_i in this region subsequently increased for several minutes, reaching> 1.5 μM. At the pollen tube tip, a diminution of the tip-focused gradient was observed, which following some fluctuation, was reduced to basal levels within ～1 min. Our data suggest that some of these alterations in [Ca²⁺]_i might be interpreted as a calcium wave, as the changes are not global. Although the increases in [Ca²⁺]_i in the subapical/shank region are very rapid, because tip [Ca²⁺]_i oscillates during normal growth, it is difficult to ascertain whether the increases in the shank of the pollen tube precede the decreases in [Ca²⁺]_i at the pollen tube tip.     

Evaluating a sampling protocol for assessing plant diversity in prairie fens

Prairie fens are globally vulnerable wetlands that are considered a conservation priority due to threats to their high biodiversity and hydrological functions. Establishing a thorough and repeatable plant sampling protocol is critical to evaluating conservation and management initiatives. Our goal was to evaluate a sample methodology designed to assess prairie fen plant diversity and determine if it produced results (1) representative of site diversity, (2) comparable among fens, and (3) efficient to collect. Nineteen fens between 8.5 and 28.4 ha were surveyed twice within one growing season during 2012 and 2013 field seasons using an area-proportional, random design. The turnover in species between spring and summer sampling periods within a site ranged from 8 to 50 %. Sample coverage of total estimated plant species richness ranged from 84.8 to 95.0 % with a mean of 90.1 %. We compared results from our area-proportional, random design to simulated random samples of 10, 15, 20, 25, 30, 35 and 40 quadrats per site. No significant difference was found in sample coverage per fen when using sampling rates of 25, 30, or 35 quadrats per site versus the area-proportional design. Shannon’s diversity index and floristic quality index differed by sample period and number of quadrats sampled per fen. Our sample design produced acceptable levels of coverage and facilitated comparisons across fens. Our methodology could be applied to future research, restoration monitoring, and conservation planning efforts in Midwestern prairie fens.     

Rapid generation of subclones for DNA sequencing using the reverse cloning procedure

A fast and reliable procedure for generating subclones necessary for sequencing long stretches of DNA has been developed. The reverse cloning procedure involves cloning a fragment of DNA into a single-stranded plasmid or phage vector containing a polycloning region; synthesizing variable lengths of double-stranded DNA using a "Universal Primer"; isolating the double-stranded DNA; and force cloning the double-stranded DNA fragments into a complementary vector with the polycloning region in the reverse orientation. The resulting clones can be sequenced, using the same Universal Primer and T7 DNA polymerase, to provide overlapping DNA sequences. The reverse cloning procedure can be used to construct deletion mutations.     

Studies on morphological transformation of BALB/3T3-derived clones by murine leukemia virus.

We have described a cell line, UC1-B, derived spontaneously from BALB/3T3 mouse embryo cells, which, unlike the standard BALB/3T3, are morphologically transformed and produce bizarre viral forms in response to murine leukemia virus. Although UC1-B and BALB/3T3 are morphologically similar, and both form contact-inhibited monolayers at confluence, the UC1-B cells are partially transformed because: they grow to a slightly higher saturation density than 3T3 cells, they grow in medium lacking serum growth factors, and they produce tumors in mice. Another clone, 12A-3, derived from BALB/3T3, also transforms and produces bizarre viral forms after infection with murine leukemia virus. Unlike UC1-B cells, the 12A3-8 cells are identical in growth properties to BALB/3T3; therefore, a partially altered morphology is not required for the induction of transformation by murine leukemia virus.