Porcine models in spinal research: calibration and comparative finite element analysis of various configurations during flexion-extension

This study was conducted to develop and calibrate a detailed 3-dimensional finite element model of the porcine lumbar spine and to compare this model with various configurations in flexion and extension. Computed tomography scans obtained from the L4-L5 lumbar segment of a Landrace x Large White pig were used to generate a solid volume. The various passive components were characterized by using a step-by-step calibration procedure in which the material properties of the anatomic structures were modified to match the corresponding in vitro data set-points retrieved from the literature. The range of motion of the totally assembled intact model was assessed under a 10-Nm flexion-extension moment and compared with data from a bilateral complete and hemifacetectomy configuration. In addition, the results from our porcine model were compared with published data regarding range of motion in a human finite element model in order to predict the configuration of the porcine model that most closely represented the human spine. Both the intact and hemifacetectomy configurations of the porcine model were comparable to the human spine. However, qualitative analysis of the instantaneous axis of rotation revealed a dissimilarity between the intact porcine model and human spine behavior, indicating the hemifacetectomy configuration of the porcine model as the most appropriate for spinal instrumentation studies. The present 3-dimensional finite element porcine model offers an additional tool to improve understanding of the biomechanics of the porcine spine and to decrease the expense of spinal research.     

Crystal structure of human ERp44 shows a dynamic functional modulation by its carboxy-terminal tail

ERp44 mediates thiol-dependent retention in the early secretory pathway, forming mixed disulphides with substrate proteins through its conserved CRFS motif. Here, we present its crystal structure at a resolution of 2.6 A. Three thioredoxin domains-a, b and b'-are arranged in a clover-like structure. A flexible carboxy-terminal tail turns back to the b' and a domains, shielding a hydrophobic pocket in domain b' and a hydrophobic patch around the CRFS motif in domain a. Mutational and functional studies indicate that the C-terminal tail gates the CRFS area and the adjacent hydrophobic pocket, dynamically regulating protein quality control.     

TILLMore, a resource for the discovery of chemically induced mutants in barley

A sodium azide-mutagenized population of barley (cv. 'Morex') was developed and utilized to identify mutants at target genes using the 'targeting induced local lesions in genomes' (TILLING) procedure. Screening for mutations at four agronomically important genes (HvCO1, Rpg1, eIF4E and NR) identified a total of 22 new mutant alleles, equivalent to the extrapolated rate of one mutation every 374 kb. All mutations except one were G/C to A/T transitions and several (approximately 68%) implied a change in protein amino acid sequence and therefore a possible effect on phenotype. The high rate of mutation detected through TILLING is in keeping with the high frequency (32.7%) of variant phenotypes observed amongst the M(3) families. Our results indicate the feasibility of using this resource for both reverse and forward genetics approaches to investigate gene function in barley and related crops.     

A SNP transferability survey within the genus <Emphasis Type="Italic">Vitis</Emphasis>

Background  

Efforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115) genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus.     

SNP high-throughput screening in grapevine using the SNPlex™ genotyping system

Background

Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods.

Results

Herein we report the first application of the SNPlex? genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay.

Conclusion

Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories.     

Paired comparisons of carbon exchange between undisturbed and regenerating stands in four managed forests in Europe

The effects of harvest on European forest net ecosystem exchange (NEE) of carbon and its photosynthetic and respiratory components (GPP (gross primary production) and TER (total ecosystem respiration)) were examined by comparing four pairs of mature/harvested sites in Europe via a combination of eddy covariance measurements and empirical modeling. Three of the comparisons represented high coniferous forestry (spruce in Britain, and pines in Finland and France), while a coppice‐with‐standard oak plantation was examined in Italy. While every comparison revealed that harvesting converted a mature forest carbon sink into a carbon source of similar magnitude, the mechanisms by which this occurred were very different according to species or management practice. In Britain, Finland, and France the annual sink (source) strength for mature (clear‐cut) stands was estimated at 496 (112), 138 (239), and 222 (225) g C m^?2, respectively, with 381 (427) g C m^?2 for the mature (coppiced) stand in Italy. In all three cases of high forestry in Britain, Finland, and France, clear‐cutting crippled the photosynthetic capacity of the ecosystem – with mature (clear‐cut) GPP of 1970 (988), 1010 (363), and 1600 (602) g C m^?2– and also reduced ecosystem respiration to a lesser degree – TER of 1385 (1100), 839 (603), and 1415 (878) g C m^?2, respectively. By contrast, harvesting of the coppice oak system provoked a burst in respiration – with mature (clear‐cut) TER estimated at 1160 (2220) gC m^?2– which endured for the 3 years sampled postharvest. The harvest disturbance also reduced GPP in the coppice system – with mature (clear‐cut) GPP of 1600 (1420) g C m^?2– but to a lesser extent than in the coniferous forests, and with near‐complete recovery within a few years. Understanding the effects of harvest on the carbon balance of European forest systems is a necessary step towards characterizing carbon exchange for timberlands on large scales.     

The role of lipoic acid in the regulation of the redox status of wheat irrigated with 20% sea water.

The effect of irrigation with 20% sea water was studied in 14 and 21-day-old seedlings of durum wheat (Triticum durum, cv. Ofanto). Comparisons between control (Hoagland's 2 solution) and treated (20% sea water in Hoagland's solution) plants included, besides HPLC determination of reduced (DHLA) and oxidised (LA) forms of lipoic acid, ascorbate and glutathione contents, their redox status, the activity of ascorbate peroxidase (APX, EC 1.11.1.11.) and glutathione reductase (GR, EC 1.6.4.2.). The results indicated a more relevant presence of lipoic acid in the roots in comparison to the shoots. An involvement of its reduced form in the regeneration of the reduced glutathione, at least at 14 days of treatment, suggested, besides its role as dehydrogenase enzyme cofactor, a role in the recycling of the other antioxidants. The amount of LA always increased with growth in shoots and decreased in roots, while DHLA remained constant in control and increased in treated plants. Besides, the oxidised form always decreased with sea water while the reduced form decreased in shoots and increased in roots. The ascorbate pool exerted its positive influence especially in the shoots, while APX and GR activities resulted differently modulated by the salinity level.     

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre

Structural and functional annotation of the large and growing database of genomic sequences is a major problem in modern biology. Protein structure prediction by detecting remote homology to known structures is a well-established and successful annotation technique. However, the broad spectrum of evolutionary change that accompanies the divergence of close homologues to become remote homologues cannot easily be captured with a single algorithm. Recent advances to tackle this problem have involved the use of multiple predictive algorithms available on the Internet. Here we demonstrate how such ensembles of predictors can be designed in-house under controlled conditions and permit significant improvements in recognition by using a concept taken from protein loop energetics and applying it to the general problem of 3D clustering. We have developed a stringent test that simulates the situation where a protein sequence of interest is submitted to multiple different algorithms and not one of these algorithms can make a confident (95%) correct assignment. A method of meta-server prediction (Phyre) that exploits the benefits of a controlled environment for the component methods was implemented. At 95% precision or higher, Phyre identified 64.0% of all correct homologous query-template relationships, and 84.0% of the individual test query proteins could be accurately annotated. In comparison to the improvement that the single best fold recognition algorithm (according to training) has over PSI-Blast, this represents a 29.6% increase in the number of correct homologous query-template relationships, and a 46.2% increase in the number of accurately annotated queries. It has been well recognised in fold prediction, other bioinformatics applications, and in many other areas, that ensemble predictions generally are superior in accuracy to any of the component individual methods. However there is a paucity of information as to why the ensemble methods are superior and indeed this has never been systematically addressed in fold recognition. Here we show that the source of ensemble power stems from noise reduction in filtering out false positive matches. The results indicate greater coverage of sequence space and improved model quality, which can consequently lead to a reduction in the experimental workload of structural genomics initiatives.     

The ATP-binding cassette transporter-encoding gene CgSNQ2 is contributing to the CgPDR1-dependent azole resistance of Candida glabrata

Our previous investigation on Candida glabrata azole-resistant isolates identified two isolates with unaltered expression of CgCDR1 / CgCDR2 , but with upregulation of another ATP-binding cassette transporter, CgSNQ2 , which is a gene highly similar to ScSNQ2 from Saccharomyces cerevisiae. One of the two isolates (BPY55) was used here to elucidate this phenomenon. Disruption of CgSNQ2 in BPY55 decreased azole resistance, whereas reintroduction of the gene in a CgSNQ2 deletion mutant fully reversed this effect. Expression of CgSNQ2 in a S. cerevisiae strain lacking PDR5 mediated not only resistance to azoles but also to 4-nitroquinoline N -oxide, which is a ScSNQ2 -specific substrate. A putative gain-of-function mutation, P822L, was identified in CgPDR1 from BPY55. Disruption of CgPDR1 in BPY55 conferred enhanced azole susceptibility and eliminated CgSNQ2 expression, whereas introduction of the mutated allele in a susceptible strain where CgPDR1 had been disrupted conferred azole resistance and CgSNQ2 upregulation, indicating that CgSNQ2 was controlled by CgPDR1 . Finally, CgSNQ2 was shown to be involved in the in vivo response to fluconazole. Together, our data first demonstrate that CgSNQ2 contributes to the development of CgPDR1 -dependent azole resistance in C. glabrata . The overlapping in function and regulation between CgSNQ2 and ScSNQ2 further highlight the relationship between S. cerevisiae and C. glabrata .     

Bis(sulfonamide) isosters of mycophenolic adenine dinucleotide analogues: inhibition of inosine monophosphate dehydrogenase

Synthesis of novel inhibitors of human IMP dehydrogenase is described. These inhibitors are isosteric methylenebis(sulfonamide) analogues 5-8 of earlier reported mycophenolic adenine methylenebis(phosphonate)s 1-3. The parent bis(phosphonate) 1 and its bis(sulfonamide) analogue 5 showed similar sub-micromolar inhibitory activity against IMPDH2 (K(i) approximately 0.2 microM). However, the bis(sulfonamide) analogues 6 and 8 substituted at the position 2 of adenine were approximately 3- to 10-fold less potent inhibitors of IMPDH2 (K(i)=0.3-0.4 microM) than the corresponding parent bis(phosphonate)s 2 and 3 (K(i)=0.04-0.11 microM), respectively.