Mathematical modeling of the indole-3-butyric acid applications on rooting of northern highbush blueberry (<Emphasis Type="Italic">Vaccinium corymbosum</Emphasis> L.) softwood-cuttings

The objective of the present study is to develop a mathematical model to predict the effect of indole-3-butyric acid (IBA) on mean rooting (%) and mean root growth of northern highbush blueberry cultivars (Vaccinium corymbosum L.). The best estimating equations for the rooting (%) and root growth are formulized as: RG = (5.672183) + [0.002851 × (IBA)] − [2.0E⁻⁶ × (IBA)2] + (−0.27211 × Cv.) and R = (82.00649) + [0.030801 × (IBA)] − [2,4E⁻⁵ × (IBA)2] − [2.36218 × (Cv.)] where RG is root growth, R is rooting, IBA is indole-3-butyric acid (ppm) and Cv. is cultivar. Cultivars are Ivanhoe [1], Jersey [2], Rekord [3], Northland [4], Berkeley [5] and Bluejay [6]. The numbers given in square brackets represent the blueberry cultivars for the equations. Multiple regression analysis was carried out until the least sum of squares (R2) was obtained. R ² value 0.90 for rooting and 0.95 for root growth. Standard errors were found to be significant at the p < 0.001 level. The actual rooting differed to the blueberry cultivars and it was between 57.76 and 83.23% while estimated rooting percentage calculated by the produced mathematical model was between 59.04 and 83.80%.     

Comparison and Optimisation of Transfection of Human Dental Follicle Cells,a Novel Source of Stem Cells,with Different Chemical Methods and Electro-poration

Introduction Human dental follicle cells (HDFCs) derived from human impacted third molars (wisdom teeth) have been shown to be a significant source of adult stem cells. Generation of mesenchymal stem cell-like cells from dental follicles causes minimal surgical stress. In vitro and in vivo reports showed that HDFCs can be utilized in gene and cell therapy applications which make them an attractive alternative source for different gene-cell therapy applications. However, there are currently no systematic comparative studies on transfection potential of HDFC cells using different chemical and electro-poration techniques. Methods Stem cells from impacted third tooth molars were isolated, and analyzed for expression of surface markers. Transfection efficiencies of four commercially available transfection reagents (Transfast, Escort V, Superfect and FuGene HD) and electro-poration on isolated stem cells were compared. Results Isolated HDFCs were stained positive for CD105, CD90, CD73, CD166, and negative for CD34, CD45, and CD133. Among the chemical transfection reagents used in this study, FuGene HD was the most efficient in transfecting HDFCs, even in the presence of 10% serum. Conclusion Electro-poration of HDFCs yield relatively high transfection rates and cell viability when compared to chemical transfection techniques. Our observations might be useful for developing gene and cell therapy applications using dental follicle stem cells.     

Direct electrochemical genosensing for multiple point mutation detection of Mycobacterium tuberculosis during the development of rifampin resistance

We present a robust and simple method for the direct detection of multiple point mutations in the Mycobacterium tuberculosis rpoB gene during the development of rifampin (RIF) resistance using an electrochemical genosensor. The device contained five different capture probes which are designed to hybridize with several sequence segments within the bacterial rpoB gene hotspot region. Point mutations were detected by monitoring the guanine oxidation with differential pulse voltammetry after hybridization between PCR amplicons and inosine modified capture probes at graphite surface. Changes in the peak voltage corresponding to guanine oxidation provide an electrochemical signal for hybridization that can be used to determine the presence of point mutations conferring rifampin resistance. The analytical parameters (sensitivity, selectivity and reproducibility) were evaluated. High selective discrimination against point mutation of bacteria at hot-spot region was observed. Several mutations were detected at several parts of the amplicon from 21 positive samples.     

Laboratory evaluation of Turkish entomopathogenic nematodes for suppression of the chestnut pests,Curculio elephas (Coleoptera: Curculionidae) and Cydia splendana (Lepidoptera: Tortricidae)

The lepidopteran, Cydia splendana, and the coleopteran, Curculio elephas, are the most serious pests of chestnut fruit in Turkey. We evaluated the biological control potential of three Turkish entomopathogenic nematode species, Steinernema feltiae, S. weiseri and Heterorhabditis bacteriophora, against the last instar larvae of C. splendana and C. elephas, both of which occur in the soil from fall (October–November) until mid-summer (August). The optimal temperature for infection, time to death of the hosts, and reproductive potential of the nematodes were determined at 10, 15, 20 and 25°C for both pest species. Cydia splendana was more susceptible to nematode infection than C. elephas. Temperature had a significant effect on the infectivity and development of entomopathogenic nematodes. The cold-adapted S. weiseri and S. feltiae were the most virulent species at 10 and 15°C, whereas the warm-adapted H. bacteriophora was the most effective at 20 and 25°C. In soil pot experiments conducted at 15°C, S. weiseri was the most virulent species against C. elephas and C. splendana. However, our data show that C. elephas larvae had a lower and C. splendana larvae had a higher susceptibility to the nematode species tested. Accordingly, we recommend that future efforts of using entomopathogenic nematodes, especially S. weiseri, be directed against C. splendana and that there be a continued effort to find more virulent nematode isolates against larvae of C. elephas.     

Modeling of polygalacturonase enzyme activity and biomass production by <Emphasis Type="Italic">Aspergillus sojae</Emphasis> ATCC 20235

Aspergillus sojae, which is used in the making of koji, a characteristic Japanese food, is a potential candidate for the production of polygalacturonase (PG) enzyme, which of a major industrial significance. In this study, fermentation data of an A. sojae system were modeled by multiple linear regression (MLR) and artificial neural network (ANN) approaches to estimate PG activity and biomass. Nutrient concentrations, agitation speed, inoculum ratio and final pH of the fermentation medium were used as the inputs of the system. In addition to nutrient conditions, the final pH of the fermentation medium was also shown to be an effective parameter in the estimation of biomass concentration. The ANN parameters, such as number of hidden neurons, epochs and learning rate, were determined using a statistical approach. In the determination of network architecture, a cross-validation technique was used to test the ANN models. Goodness-of-fit of the regression and ANN models was measured by the R ² of cross-validated data and squared error of prediction. The PG activity and biomass were modeled with a 5-2-1 and 5-9-1 network topology, respectively. The models predicted enzyme activity with an R ² of 0.84 and biomass with an R ² value of 0.83, whereas the regression models predicted enzyme activity with an R ² of 0.84 and biomass with an R ² of 0.69.     

Mutation and association analysis of the PVR and PVRL2 genes in patients with non-syndromic cleft lip and palate

Orofacial clefts (OFC; MIM 119530) are among the most common major birth defects. Here, we carried out mutation screening of the PVR and PVRL2 genes, which are both located at an OFC linkage region at 19q13 (OFC3) and are closely related to PVRL1, which has been associated with both syndromic and non-syndromic cleft lip and palate (nsCLP). We screened a total of 73 nsCLP patients and 105 non-cleft controls from the USA for variants in PVR and PVRL2, including all exons and encompassing all isoforms. We identified four variants in PVR and five in PVRL2. One non-synonymous PVR variant, A67T, was more frequent among nsCLP patients than among normal controls, but this difference did not achieve statistical significance.     

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

Background

Discovering the functions of all genes is a central goal of contemporary biomedical research. Despite considerable effort, we are still far from achieving this goal in any metazoan organism. Collectively, the growing body of high-throughput functional genomics data provides evidence of gene function, but remains difficult to interpret.

Results

We constructed the first network of functional relationships for Drosophila melanogaster by integrating most of the available, comprehensive sets of genetic interaction, protein-protein interaction, and microarray expression data. The complete integrated network covers 85% of the currently known genes, which we refined to a high confidence network that includes 20,000 functional relationships among 5,021 genes. An analysis of the network revealed a remarkable concordance with prior knowledge. Using the network, we were able to infer a set of high-confidence Gene Ontology biological process annotations on 483 of the roughly 5,000 previously unannotated genes. We also show that this approach is a means of inferring annotations on a class of genes that cannot be annotated based solely on sequence similarity. Lastly, we demonstrate the utility of the network through reanalyzing gene expression data to both discover clusters of coregulated genes and compile a list of candidate genes related to specific biological processes.

Conclusions

Here we present the the first genome-wide functional gene network in D. melanogaster. The network enables the exploration, mining, and reanalysis of experimental data, as well as the interpretation of new data. The inferred annotations provide testable hypotheses of previously uncharacterized genes.     

High-throughput single cell arrays as a novel tool in biopreservation

Microwell array cytometry is a novel high-throughput experimental technique that makes it possible to correlate pre-stress cell phenotypes and post-stress outcomes with single cell resolution. Because the cells are seeded in a high density grid of cell-sized microwells, thousands of individual cells can be tracked and imaged through manipulations as extreme as freezing or drying. Unlike flow cytometry, measurements can be made at multiple time points for the same set of cells. Unlike conventional image cytometry, image analysis is greatly simplified by arranging the cells in a spatially defined pattern and physically separating them from one another. To demonstrate the utility of microwell array cytometry in the field of biopreservation, we have used it to investigate the role of mitochondrial membrane potential in the cryopreservation of primary hepatocytes.Even with optimized cryopreservation protocols, the stress of freezing almost always leads to dysfunction or death in part of the cell population. To a large extent, cell fate is dominated by the stochastic nature of ice crystal nucleation, membrane rupture, and other biophysical processes, but natural variation in the initial cell population almost certainly plays an important and under-studied role. Understanding why some cells in a population are more likely to survive preservation will be invaluable for the development of new approaches to improve preservation yields.For this paper, primary hepatocytes were seeded in microwell array devices, imaged using the mitochondrial dyes Rh123 or JC-1, cryopreserved for up to a week, rapidly thawed, and checked for viability after a short recovery period. Cells with a high mitochondrial membrane potential before freezing were significantly less likely to survive the freezing process, though the difference in short term viability was fairly small. The results demonstrate that intrinsic cell factors do play an important role in cryopreservation survival, even in the short term where extrinsic biophysical factors would be expected to dominate. We believe that microwell array cytometry will be an important tool for a wide range of studies in biopreservation and stress biology.