The IFT-A complex regulates Shh signaling through cilia structure and membrane protein trafficking

Hectd1 mutant mouse embryos exhibit the neural tube defect exencephaly associated with abnormal cranial mesenchyme. Cellular rearrangements in cranial mesenchyme are essential during neurulation for elevation of the neural folds. Here we investigate the molecular basis of the abnormal behavior of Hectd1 mutant cranial mesenchyme. We demonstrate that Hectd1 is a functional ubiquitin ligase and that one of its substrates is Hsp90, a chaperone protein with both intra- and extracellular clients. Extracellular Hsp90 enhances migration of multiple cell types. In mutant cranial mesenchyme cells, both secretion of Hsp90 and emigration of cells from cranial mesenchyme explants were enhanced. Importantly, we show that this enhanced emigration was highly dependent on the excess Hsp90 secreted from mutant cells. Together, our data set forth a model whereby increased secretion of Hsp90 in the cranial mesenchyme of Hectd1 mutants is responsible, at least in part, for the altered organization and behavior of these cells and provides a potential molecular mechanism underlying the neural tube defect.     

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

Hierarchical shotgun sequencing remains the method of choice for assembling high‐quality reference sequences of complex plant genomes. The efficient exploitation of current high‐throughput technologies and powerful computational facilities for large‐insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole‐genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high‐quality assemblies of a large number of clones to assemble map‐based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.     

Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs

Translational stop codon readthrough provides a regulatory mechanism of gene expression that is extensively utilised by positive-sense ssRNA viruses. The misreading of termination codons is achieved by a variety of naturally occurring suppressor tRNAs whose structure and function is the subject of this survey. All of the nonsense suppressors characterised to date (with the exception of selenocysteine tRNA) are normal cellular tRNAs that are primarily needed for reading their cognate sense codons. As a consequence, recognition of stop codons by natural suppressor tRNAs necessitates unconventional base pairings in anticodon–codon interactions. A number of intrinsic features of the suppressor tRNA contributes to the ability to read non-cognate codons. Apart from anticodon–codon affinity, the extent of base modifications within or 3′ of the anticodon may up- or down-regulate the efficiency of suppression. In order to out-compete the polypeptide chain release factor an absolute prerequisite for the action of natural suppressor tRNAs is a suitable nucleotide context, preferentially at the 3′ side of the suppressed stop codon. Three major types of viral readthrough sites, based on similar sequences neighbouring the leaky stop codon, can be defined. It is discussed that not only RNA viruses, but also the eukaryotic host organism might gain some profit from cellular suppressor tRNAs.     

Intron excision from tRNA precursors by plant splicing endonuclease requires unique features of the mature tRNA domain.

It has been proposed that yeast and Xenopus splicing endonucleases initially recognize features in the mature tRNA domain common to all tRNA species and that the sequence and structure of the intron are only minor determinants of splice-site selection. In accordance with this postulation, we show that yeast endonuclease splices heterologous pre-tRNA(Tyr) species from vertebrates and plants which differ in their mature domains and intron secondary structures. In contrast, wheat germ splicing endonuclease displays a pronounced preference for homologous pre-tRNA species; an extensive study of heterologous substrates revealed that neither yeast pre-tRNA species specific for leucine, serine, phenylalanine and tyrosine nor human and Xenopus pre-tRNA(Tyr) species were spliced. In order to identify the elements essential for pre-tRNA splicing in plants, we constructed chimeric genes coding for tRNA precursors with a plant intron secondary structure and with mature tRNA(Tyr) domains from yeast and Xenopus, respectively. The chimeric pre-tRNA comprising the mature tRNA(Tyr) domain from Xenopus was spliced efficiently in wheat germ extract, whereas the chimeric construct containing the mature tRNA(Tyr) domain from yeast was not spliced at all. These data indicate that intron secondary structure contributes to the specificity of plant splicing endonuclease and that unique features of the mature tRNA domain play a dominant role in enzyme-substrate recognition. We further investigated the influence of specific nucleotides in the mature domain on splicing by generating a number of mutated pre-tRNA species. Our results suggest that nucleotides located in the D stem, i.e. in the center of the pre-tRNA molecule, are recognition points for plant splicing endonuclease.     

Nonintrusive Field Experiments Show Different Plant Responses to Warming and Drought Among Sites,Seasons, and Species in a North–South European Gradient

We used a novel, nonintrusive experimental system to examine plant responses to warming and drought across a climatic and geographical latitudinal gradient of shrubland ecosystems in four sites from northern to southern Europe (UK, Denmark, The Netherlands, and Spain). In the first two years of experimentation reported here, we measured plant cover and biomass by the pinpoint method, plant ¹⁴C uptake, stem and shoot growth, flowering, leaf chemical concentration, litterfall, and herbivory damage in the dominant plant species of each site. The two years of approximately 1°C experimental warming induced a 15% increase in total aboveground plant biomass growth in the UK site. Both direct and indirect effects of warming, such as longer growth season and increased nutrient availability, are likely to be particularly important in this and the other northern sites which tend to be temperature-limited. In the water-stressed southern site, there was no increase in total aboveground plant biomass growth as expected since warming increases water loss, and temperatures in those ecosystems are already close to the optimum for photosynthesis. The southern site presented instead the most negative response to the drought treatment consisting of a soil moisture reduction at the peak of the growing season ranging from 33% in the Spanish site to 82% in The Netherlands site. In the Spanish site there was a 14% decrease in total aboveground plant biomass growth relative to control. Flowering was decreased by drought (up to 24% in the UK and 40% in Spain). Warming and drought decreased litterfall in The Netherlands site (33% and 37%, respectively) but did not affect it in the Spanish site. The tissue P concentrations generally decreased and the N/P ratio increased with warming and drought except in the UK site, indicating a progressive importance of P limitation as a consequence of warming and drought. The magnitude of the response to warming and drought was thus very sensitive to differences among sites (cold-wet northern sites were more sensitive to warming and the warm-dry southern site was more sensitive to drought), seasons (plant processes were more sensitive to warming during the winter than during the summer), and species. As a result of these multiple plant responses, ecosystem and community level consequences may be expected.     

Soil Solution Chemistry and Element Fluxes in Three European Heathlands and Their Responses to Warming and Drought

Soil water chemistry and element budgets were studied at three northwestern European Calluna vulgaris heathland sites in Denmark (DK), The Netherlands (NL), and Wales (UK). Responses to experimental nighttime warming and early summer drought were followed during a two-year period. Soil solution chemistry measured below the organic soil layer and below the rooting zone and water fluxes estimated with hydrological models were combined to calculate element budgets. Remarkably high N leaching was observed at the NL heath with 18 and 6.4 kg N ha^–1 year^–1 of NO₃–N and NH₄–N leached from the control plots, respectively, indicating that this site is nitrogen saturated. Increased soil temperature of +0.5°C in the heated plots almost doubled the concentrations and losses of NO₃–N and DON at this site. Temperature also increased mobilization of N in the O horizon at the UK and DK heaths in the first year, but, because of high retention of N in the vegetation or mineral soil, there were no significant effects of warming on seepage water NO₃–N and NH₄–N. Retention of P was high at all three sites. In several cases, drought increased concentrations of elements momentarily, but element fluxes decreased because of a lower flux of water. Seepage water DOC and DON was highly significantly correlated at the UK site where losses of N were low, whereas losses of C and N were uncoupled at the NL site where atmospheric N input was greatest. Based on N budgets, calculations of the net change in the C sink or source strength in response to warming suggest no change or an increase in the C sink strength during these early years.     

Horse conceptuses secrete insulin-like growth factor-binding protein 3

Insulin-like growth factor-I (IGF-I) promotes early embryonic development in several species. In the rabbit, IGF-I binds to the embryonic coats from Day 3 of development onward by a 38-kDa protein that is probably insulin-like growth factor-binding protein 3 (IGFBP3). In the present study, ligand, Western, and Northern blot analyses were used to demonstrate the presence of IGF-I-binding activity, several immunoreactive IGFBP3 proteins, and IGFBP3 mRNA in horse conceptuses with particularly large amounts of immunoreactive IGFBP3 in the conceptus capsule. In addition, immunoprecipitation of radiolabeled proteins showed that cultured horse conceptuses secreted IGFBP3 into the culture medium. Endometrial samples from mares also contained IGFBP3 mRNA and protein; but there was no evidence of secretion of IGFBP3 into the uterine lumen by ligand blot analysis, and there was evidence of only very small amounts by Western blot analysis. These results indicate that the horse conceptus secretes significant quantities of IGFBP3 toward the conceptus capsule from as early as Day 10 after ovulation. Thus, most of the IGFBP3 contained within the capsule, which binds IGF-I to this special extracellular matrix of the preimplantation horse conceptus, is likely to be embryonic in origin. IGFBP3 in the horse conceptus capsule may enhance or modulate the action of IGFs on the developing conceptus.     

Adipose-Derived Stromal Cells Protect Intervertebral Disc Cells in Compression: Implications for Stem Cell Regenerative Disc Therapy

Introduction: Abnormal biomechanics plays a role in intervertebral disc degeneration. Adipose-derived stromal cells (ADSCs) have been implicated in disc integrity; however, their role in the setting of mechanical stimuli upon the disc''s nucleus pulposus (NP) remains unknown. As such, the present study aimed to evaluate the influence of ADSCs upon NP cells in compressive load culture.Methods: Human NP cells were cultured in compressive load at 3.0MPa for 48 hours with or without ADSCs co-culture (the ratio was 50:50). We used flow cytometry, live/dead staining and scanning electron microscopy (SEM) to evaluate cell death, and determined the expression of specific apoptotic pathways by characterizing the expression of activated caspases-3, -8 and -9. We further used real-time (RT-) PCR and immunostaining to determine the expression of the extracellular matrix (ECM), mediators of matrix degradation (e.g. MMPs, TIMPs and ADAMTSs), pro-inflammatory factors and NP cell phenotype markers.Results: ADSCs inhibited human NP cell apoptosis via suppression of activated caspase-9 and caspase-3. Furthermore, ADSCs protected NP cells from the degradative effects of compressive load by significantly up-regulating the expression of ECM genes (SOX9, COL2A1 and ACAN), tissue inhibitors of metalloproteinases (TIMPs) genes (TIMP-1 and TIMP-2) and cytokeratin 8 (CK8) protein expression. Alternatively, ADSCs showed protective effect by inhibiting compressive load mediated increase of matrix metalloproteinases (MMPs; MMP-3 and MMP-13), disintegrin and metalloproteinase with thrombospondin motifs (ADAMTSs; ADAMTS-1 and 5), and pro-inflammatory factors (IL-1beta, IL-6, TGF-beta1 and TNF-alpha).Conclusions: Our study is the first in vitro study assessing the impact of ADSCs on NP cells in an un-physiological mechanical stimulation culture environment. Our study noted that ADSCs protect compressive load induced NP cell death and degradation by inhibition of activated caspase-9 and -3 activity; regulating ECM and modulator genes, suppressing pro-inflammatory factors and preserving CK8. Consequently, the protective impact of ADSCs found in this study provides an essential understanding and expands our knowledge as to the utility of ADSCs therapy for intervertebral disc regeneration.     

Controlling and sampling adult sand flies with a fumigant containing permethrin and deltamethrin

The efficacy of a new smoke-generating formulation (fumigant, MidMos Solutions Ltd., GB), containing the active ingredients permethrin and deltamethrin, was evaluated against adult sand flies in an apartment (280 m(3)), a semi-open large animal shelter (enclosing an area of 300 m(2)), a closed Bedouin animal tent (104 m(3)), and a garden (141 m(2)) enclosed by a stone wall. In each location, four cages with approx. 100 Phlebotomus papatasi were exposed to the fumigant 0.5 m and 2.0 m above ground for 15 and 60 min. Controls were kept in untreated similar rooms and there were two repetitions. In the apartment and the animal tent, a single cartridge caused 100% mortality within 15 min. In the large animal shelter, one fumigant caused mortality of 86% in the lower cages and 75% in the upper cages after 15 min. After 60 min, mortality was 94 and 87%, respectively. With two fumigants, mortality was 98.5 and 91% after 15 min and after 60 min all sand flies were dead. In the garden, one fumigant caused mortality of 93% in the lower cages and 85.5% in the upper cages after 15 min. After 60 min the mortality was 98 and 92%, respectively. With two fumigants, all flies were dead within 15 min.