The morphology of the preimaginal stages of Squamapion elongatum (Germar, 1817) (Coleoptera,Curculionoidea, Apionidae) and notes on its biology

Data on the morphology of the egg, mature larva (L₃) and pupa of Squamapion elongatum (Germar, 1817) are presented. The development cycle of this species lasts 51–54 days: a 12-day egg period, a 30-day larval period, and a 12-day pupal period, on average. The larvae are attacked by parasitic hymenopterans of the superfamily Chalcidoidea.     

Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex

Background

Species from the Paracoccidioides complex are thermally dimorphic fungi and the causative agents of paracoccidioidomycosis, a deep fungal infection that is the most prevalent systemic mycosis in Latin America and represents the most important cause of death in immunocompetent individuals with systemic mycosis in Brazil. We previously described the identification of eight new families of DNA transposons in Paracoccidioides genomes. In this work, we aimed to identify potentially active retrotransposons in Paracoccidioides genomes.

Results

We identified five different retrotransposon families (four LTR-like and one LINE-like element) in the genomes of three Paracoccidioides isolates. Retrotransposons were present in all of the genomes analyzed. P. brasiliensis and P. lutzii species harbored the same retrotransposon lineages but differed in their copy numbers. In the Pb01, Pb03 and Pb18 genomes, the number of LTR retrotransposons was higher than the number of LINE-like elements, and the LINE-like element RtPc5 was transcribed in Paracoccidioides lutzii (Pb01) but could not be detected in P. brasiliensis (Pb03 and Pb18) by semi-quantitative RT-PCR.

Conclusion

Five new potentially active retrotransposons have been identified in the genomic assemblies of the Paracoccidioides species complex using a combined computational and experimental approach. The distribution across the two known species, P. brasiliensis and P. lutzii, and phylogenetics analysis indicate that these elements could have been acquired before speciation occurred. The presence of active retrotransposons in the genome may have implications regarding the evolution and genetic diversification of the Paracoccidioides genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1564-7) contains supplementary material, which is available to authorized users.     

A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data

The measurement of (1)H transverse paramagnetic relaxation enhancement (PRE) has been used in biomolecular systems to determine long-range distance restraints and to visualize sparsely-populated transient states. The intrinsic flexibility of most nitroxide and metal-chelating paramagnetic spin-labels, however, complicates the quantitative interpretation of PREs due to delocalization of the paramagnetic center. Here, we present a novel, disulfide-linked nitroxide spin label, R1p, as an alternative to these flexible labels for PRE studies. When introduced at solvent-exposed α-helical positions in two model proteins, calmodulin (CaM) and T4 lysozyme (T4L), EPR measurements show that the R1p side chain exhibits dramatically reduced internal motion compared to the commonly used R1 spin label (generated by reacting cysteine with the spin labeling compound often referred to as MTSL). Further, only a single nitroxide position is necessary to account for the PREs arising from CaM S17R1p, while an ensemble comprising multiple conformations is necessary for those observed for CaM S17R1. Together, these observations suggest that the nitroxide adopts a single, fixed position when R1p is placed at solvent-exposed α-helical positions, greatly simplifying the interpretation of PRE data by removing the need to account for the intrinsic flexibility of the spin label.     

Plant economy at a late Neolithic lake dwelling site in Slovenia at the time of the Alpine Iceman

We present the results of a plant macroremain study of the late Neolithic lakeshore settlement Stare gmajne (SG) at Ljubljansko barje, Slovenia, with cultural horizons that ended around 3330 and 3110 cal. b.c., as obtained by dendrochronological and radiocarbon dating of the most frequent construction timbers of Quercus sp. (oak) and Fraxinus sp. (ash). Fourteen systematically taken samples were investigated, using standard methods for studying waterlogged plant remains, which had been developed during lake dwelling research north of the Alps. Most of the remains were preserved in a waterlogged state, and we identified a total of 93 taxa. The most important cultivated plants were Triticum dicoccum (emmer), Hordeum vulgare (six-rowed naked barley), T. monococcum (einkorn), Linum usitatissimum (flax) and Papaver somniferum (opium poppy). The numerous possibly gathered plants also included Trapa natans (water chestnut) and Vitis vinifera ssp. sylvestris (wild grapevine). Chenopodium album (goosefoot) and Brassica rapa (turnip) with seeds/fruits rich in oil and starch were probably gathered as well. Comparisons of the Stare gmajne results with contemporary north Alpine sites (NA) showed, among other things, that Triticum durum/turgidum (tetraploid naked wheat), frequent at NA, was not found at SG. Trapa natans (water chestnut) was rare and Vitis (grapevine) was not found at NA. The observed differences in the wild plant spectra may have ecological causes, for example a warmer climate south of the Alps, but differences in cultivar spectra are more likely for cultural-historical reasons.     

Expression of functional recombinant human growth hormone in transgenic soybean seeds

We produced human growth hormone (hGH), a protein that stimulates growth and cell reproduction, in genetically engineered soybean [Glycine max (L.) Merrill] seeds. Utilising the alpha prime (α') subunit of β-conglycinin tissue-specific promoter from soybean and the α-Coixin signal peptide from Coix lacryma-jobi, we obtained transgenic soybean lines that expressed the mature form of hGH in their seeds. Expression levels of bioactive hGH up to 2.9% of the total soluble seed protein content (corresponding to approximately 9?g?kg(-1)) were measured in mature dry soybean seeds. The results of ultrastructural immunocytochemistry assays indicated that the recombinant hGH in seed cotyledonary cells was efficiently directed to protein storage vacuoles. Specific bioassays demonstrated that the hGH expressed in the soybean seeds was fully active. The recombinant hGH protein sequence was confirmed by mass spectrometry characterisation. These results demonstrate that the utilisation of tissue-specific regulatory sequences is an attractive and viable option for achieving high-yield production of recombinant proteins in stable transgenic soybean seeds.     

Differential epithelium DNA damage response to ATM and DNA-PK pathway inhibition in human prostate tissue culture

The ability of cells to respond and repair DNA damage is fundamental for the maintenance of genomic integrity. Ex vivo culturing of surgery-derived human tissues has provided a significant advancement to assess DNA damage response (DDR) in the context of normal cytoarchitecture in a non-proliferating tissue. Here, we assess the dependency of prostate epithelium DDR on ATM and DNA-PKcs, the major kinases responsible for damage detection and repair by nonhomologous end-joining (NHEJ), respectively. DNA damage was caused by ionizing radiation (IR) and cytotoxic drugs, cultured tissues were treated with ATM and DNA-PK inhibitors, and DDR was assessed by phosphorylation of ATM and its targets H2AX and KAP1, a heterochromatin binding protein. Phosphorylation of H2AX and KAP1 was fast, transient and fully dependent on ATM, but these responses were moderate in luminal cells. In contrast, DNA-PKcs was phosphorylated in both luminal and basal cells, suggesting that DNA-PK-dependent repair was also activated in the luminal cells despite the diminished H2AX and KAP1 responses. These results indicate that prostate epithelial cell types have constitutively dissimilar responses to DNA damage. We correlate the altered damage response to the differential chromatin state of the cells. These findings are relevant in understanding how the epithelium senses and responds to DNA damage.Key words: DNA damage, prostate, γH2AX, ATM, DNA-PK     

Estimation of Wheat Grain Tissue Cohesion via Laser Induced Breakdown Spectroscopy

During the wheat milling process, the bran fractionation is related to its mechanical properties, which are measured using tensile tests on hand-isolated tissues. However, the dissection of wheat tissues implies a soaking stage in water that can modify tissue properties. New methodologies are required to evaluate wheat tissue properties directly on native grains. The aim of this work was to estimate wheat grain tissue cohesion by the ionization effectiveness via laser-induced breakdown spectroscopy (LIBS) technique. Isolated bran tissues and wheat grains were submitted to LIBS analysis using a pulsed argon fluoride (193 nm, 15 ns, 1 Hz, 2 J cm⁻²) excimer laser and a compact optic fiber spectrometer (HR2000). The first approach was to correlate the ratios of ionic to atomic emission lines (MgII/MgI and CaII/CaI) of isolated tissues to their mechanical measurements. The energy needed to rupture the tissue was correlated to MgII/MgI (R ² = 0.72). Secondly, native grains were irradiated and chemometrics was applied to discriminate tissue spectra. The aleurone layer isolated after the soaking step presented a higher MgII/MgI than the aleurone layer from native grains, indicating a possible water effect on the tissue cohesion. In conclusion, the LIBS technique may be a potential method for rapid structural analysis of vegetal material allowing wheat population screening of both compositional and mechanical properties.     

Evolution of rDNA FISH patterns in the Fagaceae

The Fagaceae is one of the most important plant families in European forest ecosystems, and it includes several genera distributed in the Northern hemisphere. In this work we studied the genome organization and evolution within the family, by karyotyping and physically mapping rDNA in ten European and Asian species of the genera Fagus, Quercus, and Castanea. All of the species studied had a chromosome number of 2n=2x=24, except for the first report of a single individual of Quercus suber which proved to be triploid (2n=3x=36). The rDNA physical mapping revealed several patterns: the dominant one is present in European and Asian Quercus subgenus Quercus, and in Castanea sativa and Castanea crenata, consisting of two 18S–25S rDNA loci (one subterminal major and one pericentromeric minor) and one 5S rDNA pericentromeric locus. In Fagus sylvatica and in Quercus sessilifolia, different patterns were observed: four terminal 18S–25S rDNA loci and two 5S rDNA pericentromeric loci in the former, and five 18S–25S rDNA loci (three terminal and two intercalary) and one 5S rDNA pericentromeric locus in the latter. In Castanea mollissima a distinct rDNA distribution pattern with two intercalary 18S–25S rDNA loci and two 5S rDNA was found. These findings suggest rDNA loci restructuring during Castanea evolution, and variability of 18S–25S loci between Quercus and Cyclobalanopsis subgenera.     

A New Species of Gall Midge (Diptera: Cecidomyiidae) Infesting Switchgrass in the Northern Great Plains

A new species of gall midge, Chilophaga virgati Gagn?? (Diptera: Cecidomyiidae), collected from tillers of switchgrass at Brookings, South Dakota (44.31134?? N, 96.78374?? W) is described here. Plant morphological symptoms of infestation and frequency of tillers infested are also provided. Full-grown larvae of C. virgati were found inside the sheath of the flag leaf of reproductive tillers of clonally replicated spaced plants of a selected southern upland population of switchgrass during October 2008 and 2009. Infested tillers were shorter and lighter than normal tillers and had panicles that were partially encased in the sheath of the flag leaf due to reduced elongation of the peduncle as a result of the feeding of larvae of C. virgati at the proximal end of the panicle and in the intercalary meristem area of the peduncle. Variation was found among 10 genotypes for percentage of tillers infested by C. virgati, with a range from 7.2% to 21.8%. No difference was found between years for infestation rate (12.7% in 2008 and 14.3% in 2009). The mass of infested tillers was 35% that of normal tillers, and infested tillers produced no appreciable amount of viable seeds. Results of this research revealed that C. virgati had direct negative impacts on biomass and seed production in spaced plant nurseries of switchgrass. C. virgati was also observed in seeded swards of northern upland switchgrass cultivars, but its impact in seeded swards has not yet been determined.     

Three-Dimensional cryoEM Reconstruction of Native LDL Particles to 16? Resolution at Physiological Body Temperature

Background

Low-density lipoprotein (LDL) particles, the major carriers of cholesterol in the human circulation, have a key role in cholesterol physiology and in the development of atherosclerosis. The most prominent structural components in LDL are the core-forming cholesteryl esters (CE) and the particle-encircling single copy of a huge, non-exchangeable protein, the apolipoprotein B-100 (apoB-100). The shape of native LDL particles and the conformation of native apoB-100 on the particles remain incompletely characterized at the physiological human body temperature (37°C).

Methodology/Principal Findings

To study native LDL particles, we applied cryo-electron microscopy to calculate 3D reconstructions of LDL particles in their hydrated state. Images of the particles vitrified at 6°C and 37°C resulted in reconstructions at ∼16 Å resolution at both temperatures. 3D variance map analysis revealed rigid and flexible domains of lipids and apoB-100 at both temperatures. The reconstructions showed less variability at 6°C than at 37°C, which reflected increased order of the core CE molecules, rather than decreased mobility of the apoB-100. Compact molecular packing of the core and order in a lipid-binding domain of apoB-100 were observed at 6°C, but not at 37°C. At 37°C we were able to highlight features in the LDL particles that are not clearly separable in 3D maps at 6°C. Segmentation of apoB-100 density, fitting of lipovitellin X-ray structure, and antibody mapping, jointly revealed the approximate locations of the individual domains of apoB-100 on the surface of native LDL particles.

Conclusions/Significance

Our study provides molecular background for further understanding of the link between structure and function of native LDL particles at physiological body temperature.