Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato

Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.

Effect of Irradiance and Exposure Duration on Temperature and Degree of Conversion of Dual-Cure Resin Cement for Ceramic Restorations

This study investigated the effects of irradiance and exposure duration on dual-cured resin cements irradiated through ceramic restorative materials. A single light-curing unit was calibrated to three different irradiances (500, 1000, and 1500 mW/cm²) and irradiated to three different attenuating materials (transparent acryl, lithium disilicate, zirconia) with 1-mm thicknesses for 20 or 60 seconds. The changes in irradiance and temperature were measured with a radiometer (or digital thermometer) under the attenuating materials. The degree of conversion (DC) of dual-cure resin cement after irradiation at different irradiances and exposure durations was measured with Fourier transform near infrared spectroscopy. Two-way analysis of variance revealed that irradiance ( p<0.001) and exposure duration ( p<0.001) significantly affected temperature and DC. All groups showed higher DCs with increased exposure times ( p<0.05), but there were no statistically significant differences between the groups irradiated with 1000 mW/cm² and 1500 mW/cm² ( p>0.05). Higher-intensity irradiances yielded higher temperatures ( p<0.05), but exposure time did not affect temperature when materials were irradiated at 500 mW/cm² ( p>0.05).

Preliminary evaluation of the pattern cutting and the ligating loop virtual laparoscopic trainers

INTRODUCTION

The Fundamentals of Laparoscopic Surgery (FLS) trainer is currently the standard for training and evaluating basic laparoscopic skills. However, its manual scoring system is time-consuming and subjective. The Virtual Basic Laparoscopic Skill Trainer (VBLaST©) is the virtual version of the FLS trainer which allows automatic and real time assessment of skill performance, as well as force feedback. In this study, the VBLaST© pattern cutting (VBLaST-PC©) and ligating loop (VBLaST-LL©) tasks were evaluated as part of a validation study. We hypothesized that performance would be similar on the FLS and VBLaST© trainers, and that subjects with more experience would perform better than those with less experience on both trainers.

METHODS

Fifty-five subjects with varying surgical experience were recruited at the Learning Center during the 2013 SAGES annual meeting and were divided into two groups: experts (PGY 5, surgical fellows and surgical attendings) and novices (PGY 1-4). They were asked to perform the PC or the ligating loop task on the FLS and the VBLaST© trainers. Their performance scores for each trainer were calculated and compared.

RESULTS

There were no significant differences between the FLS and VBLaST© scores for either the PC or the ligating loop task. Experts' scores were significantly higher than the scores for novices on both trainers.

CONCLUSION

This study showed that the subjects' performance on the VBLaST© trainer was similar to the FLS performance for both tasks. Both the VBLaST-PC© and the VBLaST-LL© tasks permitted discrimination between the novice and expert groups. Although concurrent and discriminant validity has been established, further studies to establish convergent and predictive validity are needed. Once validated as a training system for laparoscopic skills, the system is expected to overcome the current limitations of the FLS trainer.

A Logarithmic Complexity Floating Frame of Reference Formulation with Interpolating Splines for Articulated Multi-Flexible-Body Dynamics

An interpolating spline-based approach is presented for modeling multi-flexible-body systems in the divide-and-conquer (DCA) scheme. This algorithm uses the floating frame of reference formulation and piecewise spline functions to construct and solve the non-linear equations of motion of the multi-flexible-body system undergoing large rotations and translations. The new approach is compared with the flexible DCA (FDCA) that uses the assumed modes method [1]. The FDCA, in many cases, must resort to sub-structuring to accurately model the deformation of the system. We demonstrate, through numerical examples, that the interpolating spline-based approach is comparable in accuracy and superior in efficiency to the FDCA. The present approach is appropriate for modeling flexible mechanisms with thin 1D bodies undergoing large rotations and translations, including those with irregular shapes. As such, the present approach extends the current capability of the DCA to model deformable systems. The algorithm retains the theoretical logarithmic complexity inherent in the DCA when implemented in parallel.

Comparison of three different methods for the detection of human papillomavirus infected in cervical lesions

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Background: Several techniques are in use for HPV DNA detection: Hybrid Capture IIR(HCIIR) assay, PCR-based DNA microarray and Luminex-based assay. This study was aimed to examine the performances of three validated HPV assays. We compared the concordance between the three methods for detecting HPV in cervical specimen. Methods: Cervical samples of 189 Korean women (21∼77 ages, average 41.2 age) were tested for HPV detection in this study. We examined the performances of three validated HPV assays according to each method's instructions : 1) Hybrid Capture IIR (HCIIR) assay (HCIIR; Digene Corporation, USA) was used to test for detection of 18 types of HPV (high-risk types: HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68 and low-risk types types: HPV 6, 11, 42, 43, 44). 2) HPV DNA Chip, PCR-based DNA microarray system (MyGene Co., Seoul, South Korea) was used to test for genotyping of 24 types of HPV: 15 types of high-risk types (HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68) and 9 types of low-risk types (HPV6, 11, 34, 40, 42, 43, 44, 54, 70). 3) Luminex-based HPV test (YBT, Seoul, Korea) was performed for genotyping 26 types of HPV including 15 high-risk HPV types (HPV-16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68) and 11 low-risk types (HPV-6, 11, 34, 40, 42, 43, 44, 54, 55, 67, 70). Results: We compared HPV detection results obtained by the HC II assay with those from the Luminex assay. 51 cases were discordant: 29 samples were HC II negative/Luminex positive and 22 samples were HCII positive/Luminex negative. We also compared HPV detection results obtained by the DNA chip assay with those from the Luminex assay. 37 cases were discordant: 5 samples were DNA chip negative/Luminex positive and 32 samples were DNA chip positive/Luminex negative. Conclusions: The distribution of the HPV detection results obtained for 91 samples using three different methods suggested that the results of DNA chip assay are more often discordant (17.9% instead of 5.1% for Luminex assay and 5.1% for the HC II assay).

No significant financial relationships to disclose.

Microscale Heat Transfer Transduced by Surface Plasmon Resonant Gold Nanoparticles

Visible radiation at resonant frequencies is transduced to thermal energy by surface plasmons on gold nanoparticles. Temperature in Collapse

Key Words Collapse

MESH Headings Collapse

Grants

• R03 EB004886 NIBIB NIH HHS
• R03 EB004886-01A1 NIBIB NIH HHS
• R03 EB004886-02 NIBIB NIH HHS

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Affiliation(s)

D Keith Roper Department of Chemical Engineering, 3290 MEB, University of Utah, Salt Lake City, Utah 84112
W Ahn
M Hoepfner

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Coordination of pancreatic HCO3- secretion by protein-protein interaction between membrane transporters

Increasing evidence suggests that protein-protein interaction is essential in many biological processes including epithelial transport. In this report, we discuss the significance of protein interactions to HCO(3)(-) secretion in pancreatic duct cells. In pancreatic ducts HCO(3)(-) secretion is mediated by cystic fibrosis transmembrane conductance regulator (CFTR) activated luminal Cl(-)/HCO(3)(-) exchange activity and HCO(3)(-) absorption is achieved by Na(+)-dependent mechanisms including Na(+)/H(+) exchanger 3 (NHE3). We found biochemical and functional association between CFTR and NHE3. In addition, protein binding through PDZ modules is needed for this regulatory interaction. CFTR affected NHE3 activities in two ways. Acutely, CFTR augmented the cAMP-dependent inhibition of NHE3. In a chronic mechanism, CFTR increases the luminal expression of Na(+)/H(+) exchange in pancreatic duct cells. These findings reveal that protein complexes in the plasma membrane of pancreatic duct cells are highly organized for efficient HCO(3)(-) secretion.

Regulatory interaction between the cystic fibrosis transmembrane conductance regulator and HCO3- salvage mechanisms in model systems and the mouse pancreatic duct

The pancreatic duct expresses cystic fibrosis transmembrane conductance regulator (CFTR) and HCO3- secretory and salvage mechanisms in the luminal membrane. Although CFTR plays a prominent role in HCO3- secretion, the role of CFTR in HCO3- salvage is not known. In the present work, we used molecular, biochemical, and functional approaches to study the regulatory interaction between CFTR and the HCO3- salvage mechanism Na+/H+ exchanger isoform 3 (NHE3) in heterologous expression systems and in the native pancreatic duct. We found that CFTR regulates NHE3 activity by both acute and chronic mechanisms. In the pancreatic duct, CFTR increases expression of NHE3 in the luminal membrane. Thus, luminal expression of NHE3 was reduced by 53% in ducts of homozygote DeltaF508 mice. Accordingly, luminal Na+-dependent and HOE694- sensitive recovery from an acid load was reduced by 60% in ducts of DeltaF508 mice. CFTR and NHE3 were co-immunoprecipitated from PS120 cells expressing both proteins and the pancreatic duct of wild type mice but not from PS120 cells lacking CFTR or the pancreas of DeltaF508 mice. The interaction between CFTR and NHE3 required the COOH-terminal PDZ binding motif of CFTR, and mutant CFTR proteins lacking the C terminus were not co-immunoprecipitated with NHE3. Furthermore, when expressed in PS120 cells, wild type CFTR, but not CFTR mutants lacking the C-terminal PDZ binding motif, augmented cAMP-dependent inhibition of NHE3 activity by 31%. These findings reveal that CFTR controls overall HCO3- homeostasis by regulating both pancreatic ductal HCO3- secretory and salvage mechanisms.

HCO3- salvage mechanisms in the submandibular gland acinar and duct cells

In the present work, we characterized H(+) and HCO3- transport mechanisms in the submandibular salivary gland (SMG) ducts of wild type, NHE2-/-, NHE3-/-, and NHE2-/-;NHE3-/- double knock-out mice. The bulk of recovery from an acid load across the luminal membrane (LM) of the duct was mediated by a Na(+)-dependent HOE and ethyl-isopropyl-amiloride (EIPA)-inhibitable and 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS)-insensitive mechanism. HCO3- increased the rate of luminal Na(+)-dependent pH(i) recovery but did not change inhibition by HOE and EIPA or the insensitivity to DIDS. Despite expression of NHE2 and NHE3 in the LM of the duct, the same activity was observed in ducts from wild type and all mutant mice. Measurements of Na(+)-dependent OH(-) and/or HCO3- cotransport (NBC) activities in SMG acinar and duct cells showed separate DIDS-sensitive/EIPA-insensitive and DIDS-insensitive/EIPA-sensitive NBC activities in both cell types. Functional and immunocytochemical localization of these activities in the perfused duct indicated that pNBC1 probably mediates the DIDS-sensitive/EIPA-insensitive transport in the basolateral membrane, and splice variants of NBC3 probably mediate the DIDS-insensitive/EIPA-sensitive NBC activity in the LM of duct and acinar cells. Notably, the acinar cell NBC3 variants transported HCO3- but not OH(-). By contrast, duct cell NBC3 transported both OH(-) and HCO3-. Accordingly, reverse transcription-polymerase chain reaction analysis revealed that both cell types expressed mRNA for pNBC1. However, the acini expressed mRNA for the NBC3 splice variants NBCn1C and NBCn1D, whereas the ducts expressed mRNA for NCBn1B. Based on these findings we propose that the luminal NBCs in the HCO3- secreting SMG acinar and duct cells function as HCO3- salvage mechanisms at the resting state. These studies emphasize the complexity but also begin to clarify the mechanism of HCO3- homeostasis in secretory epithelia.

Intracellular calcium mobilization induces immediate early gene pip92 via Src and mitogen-activated protein kinase in immortalized hippocampal cells

Regulation of intracellular calcium levels plays a central role in cell survival, proliferation, and differentiation. A cell-permeable, tumor-promoting thapsigargin elevates the intracellular calcium levels by inhibiting endoplasmic reticulum Ca(2+)-ATPase. The Src-tyrosine kinase family is involved in a broad range of cellular responses ranging from cell growth and cytoskeletal rearrangement to differentiation. The immediate early gene pip92 is induced in neuronal cell death as well as cell growth and differentiation. To resolve the molecular mechanism of cell growth by intracellular calcium mobilization, we have examined the effect of thapsigargin and subsequent intracellular calcium influx on pip92 expression in immortalized rat hippocampal H19-7 cells. An increase of intracellular calcium ion levels induced by thapsigargin stimulated the expression of pip92 in H19-7 cells. Transient transfection of the cells with kinase-inactive mitogen-activated protein kinase kinase (MEK) and Src kinase or pretreatment with the chemical MEK inhibitor PD98059 significantly inhibited pip92 expression induced by thapsigargin. When constitutively active v-Src or MEK was overexpressed, the transcriptional activity of the pip92 gene was markedly increased. Dominant inhibitory Raf-1 blocked the transcriptional activity of pip92 induced by thapsigargin. The transcription factor Elk1 is activated during thapsigargin-induced pip92 expression. Taken together, these results suggest that an increase of intracellular calcium ion levels by thapsigargin stimulates the pip92 expression via Raf-MEK-extracellular signal-regulated protein kinase- as well as Src kinase-dependent signaling pathways.

Causal status as a determinant of feature centrality

One of the major problems in categorization research is the lack of systematic ways of constraining feature weights. We propose one method of operationalizing feature centrality, a causal status hypothesis which states that a cause feature is judged to be more central than its effect feature in categorization. In Experiment 1, participants learned a novel category with three characteristic features that were causally related into a single causal chain and judged the likelihood that new objects belong to the category. Likelihood ratings for items missing the most fundamental cause were lower than those for items missing the intermediate cause, which in turn were lower than those for items missing the terminal effect. The causal status effect was also obtained in goodness-of-exemplar judgments (Experiment 2) and in free-sorting tasks (Experiment 3), but it was weaker in similarity judgments than in categorization judgments (Experiment 4). Experiment 5 shows that the size of the causal status effect is moderated by plausibility of causal relations, and Experiment 6 shows that effect features can be useful in retrieving information about unknown causes. We discuss the scope of the causal status effect and its implications for categorization research.

Causal status effect in children's categorization

The current study examined the causal status effect (weighing cause features more than effect features in categorization) in children. Adults (Study 1) and 7-9-year-old children (Study 2) learned descriptions of novel animals, in which one feature caused two other features. When asked to determine which transfer item was more likely to be an example of the animal they had learned, both adults and children preferred an animal with a cause feature and an effect feature rather than an animal with two effect features. This study is the first direct demonstration of the causal status effect in children.

Na(+)-dependent transporters mediate HCO(3)(-) salvage across the luminal membrane of the main pancreatic duct

To study the roles of Na(+)-dependent H(+) transporters, we characterized H(+) efflux mechanisms in the pancreatic duct in wild-type, NHE2(-/-), and NHE3(-/-) mice. The pancreatic duct expresses NHE1 in the basolateral membrane, and NHE2 and NHE3 in the luminal membrane, but does not contain NHE4 or NHE5. Basolateral Na(+)-dependent H(+) efflux in the microperfused duct was inhibited by 1.5 microM of the amiloride analogue HOE 694, consistent with expression of NHE1, whereas the luminal activity required 50 microM HOE 694 for effective inhibition, suggesting that the efflux might be mediated by NHE2. However, disruption of NHE2 had no effect on luminal transport, while disruption of the NHE3 gene reduced luminal Na(+)-dependent H(+) efflux by approximately 45%. Notably, the remaining luminal Na(+)-dependent H(+) efflux in ducts from NHE3(-/-) mice was inhibited by 50 microM HOE 694. Hence, approximately 55% of luminal H(+) efflux (or HCO(3)(-) influx) in the pancreatic duct is mediated by a novel, HOE 694-sensitive, Na(+)-dependent mechanism. H(+) transport by NHE3 and the novel transporter is inhibited by cAMP, albeit to different extents. We propose that multiple Na(+)-dependent mechanisms in the luminal membrane of the pancreatic duct absorb Na(+) and HCO(3)(-) to produce a pancreatic juice that is poor in HCO(3)(-) and rich in Cl(-) during basal secretion. Inhibition of the transporters during stimulated secretion aids in producing the HCO(3)(-)-rich pancreatic juice.

A novel effect of rebamipide: generation of [Ca(2+)](i) oscillations through activation of CCK(1) receptors in rat pancreatic acinar cells

The protective effect of 2-(4-chlorobenzoylamino)-3-[2(1H)-quinolinon-4-yl]-propionic acid (rebamipide) on gastric mucosa is well established. Here we demonstrate that rebamipide acts on pancreatic acinar cells to generate oscillations of intracellular Ca(2+) concentration ([Ca(2+)](i)) through the activation of cholecystokinin subtype 1 (CCK(1)) receptors. At concentrations higher than 5 microM, rebamipide induced [Ca(2+)](i) oscillations in individual fura-2-loaded pancreatic acinar cells. The frequency of oscillations increased with increasing concentrations of rebamipide, while the latency between stimulation of cells and initiation of [Ca(2+)](i) oscillations decreased with increasing concentration. The [Ca(2+)](i) oscillations evoked by rebamipide were inhibited by the CCK(1) receptor antagonist L-364,718 but not by atropine or the CCK(2) receptor antagonist L-365,260 indicating that rebamipide is a nonpeptide CCK(1) receptor agonist.

Why are different features central for natural kinds and artifacts?: the role of causal status in determining feature centrality

Ahn and Lassaline [Ahn, W., Lassaline, M.E., 1995. Causal structure in categorization. Proceedings of the Seventeenth Annual Conference of the Cognitive Science Society, Pittsburgh, PA, pp. 521-526] recently proposed a causal status hypothesis which states that features that play a causal role in a relational structure are more central than their effects. This hypothesis can account for previous research demonstrating that compositional features are generally important for natural kinds but functional features are generally important for artifacts. The causal status hypothesis explains this category-feature interaction effect in terms of differences in the causal status of compositional and functional features between natural kinds and artifacts. Experiments 1 and 2 examined real-life categories used in previous studies, and found positive correlations between the causal status of the features and their centrality across natural and artifactual kinds. Experiments 3 and 4 manipulated the causal status of compositional and functional features in artificial categories, and showed that it was causal status rather than the interaction between the type of feature and the type of category per se that accounted for feature centrality. The implications of these results on the distinctions between natural kinds and artifacts are discussed.