Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

PEEK (Polyether-ether-ketone) Based Cervical Total Disc Arthroplasty: Contact Stress and Lubrication Analysis

This paper presents a theoretical analysis of the maximum contact stress and the lubrication regimes for PEEK (Polyether-ether-ketone) based self-mating cervical total disc arthroplasty. The NuNec® cervical disc arthroplasty system was chosen as the study object, which was then analytically modelled as a ball on socket joint. A non-adhesion Hertzian contact model and elastohydrodynamic lubrication theory were used to predict the maximum contact stress and the minimum film thickness, respectively. The peak contact stress and the minimum film thickness between the bearing surfaces were then determined, as the radial clearance or lubricant was varied. The obtained results show that under 150 N loading, the peak contact stress was in the range 5.9 – 32.1 MPa, well below the yield and fatigue strength of PEEK; the calculated minimum film thickness ranged from 0 to 0.042 µm and the corresponding lambda ratio range was from 0 to 0.052. This indicates that the PEEK based cervical disc arthroplasty will operate under a boundary lubrication regime, within the natural angular velocity range of the cervical spine.

PEEK (Polyether-ether-ketone) Based Cervical Total Disc Arthroplasty: Contact Stress and Lubrication Analysis

This paper presents a theoretical analysis of the maximum contact stress and the lubrication regimes for PEEK (Polyether-ether-ketone) based self-mating cervical total disc arthroplasty. The NuNec^® cervical disc arthroplasty system was chosen as the study object, which was then analytically modelled as a ball on socket joint. A non-adhesion Hertzian contact model and elastohydrodynamic lubrication theory were used to predict the maximum contact stress and the minimum film thickness, respectively. The peak contact stress and the minimum film thickness between the bearing surfaces were then determined, as the radial clearance or lubricant was varied. The obtained results show that under 150 N loading, the peak contact stress was in the range 5.9 – 32.1 MPa, well below the yield and fatigue strength of PEEK; the calculated minimum film thickness ranged from 0 to 0.042 µm and the corresponding lambda ratio range was from 0 to 0.052. This indicates that the PEEK based cervical disc arthroplasty will operate under a boundary lubrication regime, within the natural angular velocity range of the cervical spine.

Identification of the abscisic acid receptor VvPYL1 in Vitis vinifera

The phytohormone abscisic acid (ABA) plays a central role in many developmental processes and in responses to several abiotic stresses. Identification of the ABA receptor is a first step towards understanding ABA signalling. In this study, using homology analysis, we cloned three genes, named VvPYL1, VvPYL2 and VvPYL3, from Vitis vinifera. An isothermal titration calorimetry assay suggested that VvPYL1 could bind to ABA. A phosphatase activity assay demonstrated that VvPYL1 inhibits phosphatase activity of ABI1, a negative regulator of ABA signalling, in the presence of ABA. Subcellular localisation demonstrates that VvPYL1 is distributed in both the nucleus and cytosol, which is similar to the subcellular localisation of ABA receptors in Arabidopsis. We therefore conclude that VvPYL1 is an ABA receptor that modulates ABA signalling by inhibiting type 2C protein phosphatases (PP2Cs).

Distribution and function of polycystin-2 in mouse retinal ganglion cells

The polycystin family of transient receptor potential (TRP) channels form Ca(2+) regulated cation channels with distinct subcellullar localizations and functions. As part of heteromultimeric channels and multi-protein complexes, polycystins control intracellular Ca(2+) signals and more generally the translation of extracellular signals and stimuli to intracellular responses. Polycystin-2 channels have been cloned from retina, but their distribution and function in retinal ganglion cells (RGCs) have not yet been established. In the present study, we determined cellular and subcellular localization as well as functional properties of polycystin-2 channels in RGCs. Polycystin-2 expression and distribution in RGCs was assessed by immunohistochemistry on vertical cryostat section of mouse retina as well as primary cultured mouse RGCs, using fluorescence microscopy. Biophysical and pharmacological properties of polycystin-2 channels isolated from primary cultured RGCs were determined using planar lipid bilayer electrophysiology. We detected polycystin-2 immunoreactivity both in the ganglion cell layer as well as in primary cultured RGCs. Subcellular analysis revealed strong cytosolic localization pattern of polycystin-2. Polycystin-2 channel current was Ca(2+) activated, had a maximum slope conductance of 114 pS, and could be blocked in a dose-dependent manner by increasing concentrations of Mg(2+). The cytosolic localization of polycystin-2 in RGCs is in accordance with its function as intracellular Ca(2+) release channel. We conclude that polycystin-2 forms functional channels in RGCs, of which biophysical and pharmacological properties are similar to polycystin-2 channels reported for other tissues and organisms. Our data suggest a potential role for polycystin-2 in RGC Ca(2+) signaling.

Transcription profile analysis reveals that zygotic division results in uneven distribution of specific transcripts in apical/basal cells of tobacco

BACKGROUND

Asymmetric zygotic division in higher plants results in the formation of an apical cell and a basal cell. These two embryonic cells possess distinct morphologies and cell developmental fates. It has been proposed that unevenly distributed cell fate determinants and/or distinct cell transcript profiles may be the underlying reason for their distinct fates. However, neither of these hypotheses has convincing support due to technical limitations.

METHODOLOGY/PRINCIPAL FINDINGS

Using laser-controlled microdissection, we isolated apical and basal cells and constructed cell type-specific cDNA libraries. Transcript profile analysis revealed difference in transcript composition. PCR and qPCR analysis confirmed that transcripts of selected embryogenesis-related genes were cell-type preferentially distributed. Some of the transcripts that existed in zygotes were found distinctly existed in apical or basal cells. The cell type specific de novo transcription was also found after zygotic cell division.

CONCLUSIONS/SIGNIFICANCE

Thus, we found that the transcript diversity occurs between apical and basal cells. Asymmetric zygotic division results in the uneven distribution of some embryogenesis related transcripts in the two-celled proembryos, suggesting that a differential distribution of some specific transcripts in the apical or basal cells may involve in guiding the two cell types to different developmental destinies.

Dynamic changes of transcript profiles after fertilization are associated with de novo transcription and maternal elimination in tobacco zygote, and mark the onset of the maternal-to-zygotic transition

The maternal-to-zygotic transition (MZT) is characterized by the turnover of zygote development from maternal to zygotic control, and has been extensively studied in animals. A majority of studies have suggested that early embryogenesis is maternally controlled and that the zygotic genome remains transcriptionally inactive prior to the MZT. However, little is known about the MZT in higher plants, and its timing and impact remain uncharacterized. Here, we constructed cDNA libraries from tobacco (Nicotiana tabacum) egg cells, zygotes and two-celled embryos for gene expression profiling analysis, followed by RT-PCR confirmation. These analyses, together with experiments using zygote microculture coupled with transcription inhibition, revealed that a marked change in transcript profiles occurs approximately 50 h after fertilization, and that the MZT is initiated prior to zygotic division in tobacco. Although maternal transcripts deposited in egg cells support several early developmental processes, they appear to be insufficient for zygotic polar growth and subsequent cell divisions. Thus, we propose that de novo transcripts are probably required to trigger embryogenesis in later zygotes in tobacco.

Hypoxia and cell cycle regulation of the von Hippel-Lindau tumor suppressor

Inactivation of von Hippel-Lindau tumor suppressor protein (pVHL) is associated with von Hippel-Lindau disease, an inherited cancer syndrome, as well as the majority of patients with sporadic clear cell renal carcinoma (RCC). While the involvement of pVHL in oxygen sensing through targeting HIFα subunits to ubiquitin-dependent proteolysis has been well documented, less is known about pVHL regulation under both normoxic and hypoxic conditions. We found that pVHL levels decreased in hypoxia and that hypoxia-induced cell cycle arrest is associated with pVHL expression in RCC cells. pVHL levels fluctuate during the cell cycle, paralleling cyclin B1 levels, with decreased levels in mitosis and G1. pVHL contains consensus Destruction box sequences, and pVHL associates with Cdh1, an activator of the anaphase promoting complex/cyclosome (APC/C) E3 ubiquitin ligase. We show that pVHL has a decreased half-life in G1, Cdh1 downregulation results in increased pVHL expression, while Cdh1 overexpression results in decreased pVHL expression. Taken together these results suggest that pVHL is a novel substrate of APC/C^Cdh1. Destruction box-independent pVHL degradation was also detected, indicating that other ubiquitin ligases are also activated for pVHL degradation.

Targeting glutamine metabolism sensitizes melanoma cells to TRAIL-induced death

Targeting specific metabolic pathways has emerged for cancer therapeutics. For melanoma, metabolic studies have solely focused on high glucose uptake. By contrast, little is known regarding addiction to glutamine. Using five melanoma lines and two normal cell types, addition of aminooxyacetate (AOA), an inhibitor of glutamate-dependent transaminase regulating glutaminolytic pathway, two lines underwent low levels of apoptosis (>30%), while the other three lines were resistant, as were normal cells to AOA. However, three resistant lines (but not normal cells), became sensitized to undergoing apoptosis when TRAIL was combined with AOA. TRAIL by itself had minimal effects on all cell lines and normal cells, and did not augment AOA-induced killing in the two sensitive melanoma lines. AOA plus TRAIL induced a caspase-dependent apoptotic response. AOA did not influence TRAIL DR4 or DR5 cell surface death receptor levels, but AOA enhanced pro-apoptotic protein levels of Noxa, while reducing pro-survival protein Mcl-1. To verify AOA was targeting glutamine pathway, depletion of glutamine produced similar results, because absence of glutamine sensitized three melanoma lines, but not fibroblasts to killing by TRAIL. Glutamine depletion also led to Noxa induction. These results indicate some lines are addicted to glutamine, and treatment with AOA or glutamine depletion sensitizes melanoma to TRAIL-mediated killing, while sparing normal cells. Future studies are indicated to translate these discoveries to metastatic melanoma as there is currently no treatment available to prolong survival.

3-Bromopyruvate induces necrotic cell death in sensitive melanoma cell lines

Clinicians successfully utilize high uptake of radiolabeled glucose via PET scanning to localize metastases in melanoma patients. To take advantage of this altered metabolome, 3-bromopyruvate (BrPA) was used to overcome the notorious resistance of melanoma to cell death. Using four melanoma cell lines, BrPA triggered caspase independent necrosis in two lines, whilst the other two lines were resistant to killing. Mechanistically, sensitive cells differed from resistant cells by; constitutively lower levels of glutathione, reduction of glutathione by BrPA only in sensitive cells; increased superoxide anion reactive oxygen species, loss of outer mitochondrial membrane permeability, and rapid ATP depletion. Sensitive cell killing was blocked by N-acetylcysteine or glutathione. When glutathione levels were reduced in resistant cell lines, they became sensitive to killing by BrPA. Taken together, these results identify a metabolic-based Achilles' heel in melanoma cells to be exploited by use of BrPA. Future pre-clinical and clinical trials are warranted to translate these results into improved patient care for individuals suffering from metastatic melanoma.