Aptamer Selection Express: A Novel Method for Rapid Single-Step Selection and Sensing of Aptamers

Here we describe a new DNA capture element (DCE) sensing system, based on the quenching and dequenching of a double-stranded aptamer. This system shows very good sensitivity and thermal stability. While quenching, dequenching, and separating the DCE systems made from different aptamers (all selected by SELEX), an alternative method to rapidly select aptamers was developed—the Aptamer Selection Express (ASExp). This process has been used to select aptamers against different types of targets (Bacillus anthracis spores, Bacillus thuringiensis spores, MS-2 bacteriophage, ovalbumin, and botulinum neurotoxin). The DCE systems made from botulinum neurotoxin aptamers selected by ASExp have been investigated. The results of this investigation indicate that ASExp can be used to rapidly select aptamers for the DCE sensing system.     

Somatic Embryogenesis and Plant Regeneration in Kinnow Mandarin

Somatic embryogenesis and plant regeneration from stem explants of kinnow mandarin, a hybrid of king and willow mandarins, are reported. It is an economically important cash crop of India with great deal of production and export. This is for the first time that callus induction and internodal regeneration has been successfully achieved in this citrus cultivar. Callus was induced from nodal segment (1-2 cm) of kinnow mandarin on Murashige and Skoog (MS) medium supplemented with α-naphthaleneacetic acid (NAA) and benzyl amino purine (BAP). Cotyledonary stage somatic embryos with regenerated shoots were induced on BAPenriched medium. Roots developed when regenerated shoots were excised and cultured on half strength MS medium supplemented with NAA only.     

Safety assessment of leaf curl virus resistant tomato developed using viral derived sequences

Genetic engineering of food crops has significantly influenced the agricultural productivity over the past two decades. It has proved a valuable tool, offering crops with higher yields, improved nutritional quality, resistance against pesticides, herbicides and tolerance against abiotic stresses. However, the safety assessment of genetically engineered (GE) crops is prerequisite before introduction into human food chain. The present study was aimed to assess the toxicity and allergenicity of leaf curl virus resistant GE tomato compared to its wild-type species. Balb/c mice fed with genetically engineered or wild-type tomato did not show significant differences in growth, body weight (P > 0.05) and food consumption when compared with control mice. Values for serum glutamic oxaloacetic transaminase and serum glutamic pyruvic transaminase, urea and cholesterol were comparable in GE and wild-type tomato fed mice. Mice immunized with GE or wild-type tomato extract showed low IgE response. Lung histology of ovalbumin fed mice showed bronchoconstriction with eosinophilic infiltration whereas GE or wild-type tomato showed no cellular infiltration with normal airways. Genetically engineered and wild-type tomato sensitized mice demonstrated similar IL-4 release in splenic cell culture supernatant. GE and wild tomato extract on ELISA showed comparable IgE binding (P > 0.05) with food allergic patients’ sera. In conclusion, genetically engineered tomato showed no toxicity in mice and allergenicity is similar to the wild-type tomato.     

Identification of Critical Regions and Candidate Genes for Cardiovascular Malformations and Cardiomyopathy Associated with Deletions of Chromosome 1p36

Cardiovascular malformations and cardiomyopathy are among the most common phenotypes caused by deletions of chromosome 1p36 which affect approximately 1 in 5000 newborns. Although these cardiac-related abnormalities are a significant source of morbidity and mortality associated with 1p36 deletions, most of the individual genes that contribute to these conditions have yet to be identified. In this paper, we use a combination of clinical and molecular cytogenetic data to define five critical regions for cardiovascular malformations and two critical regions for cardiomyopathy on chromosome 1p36. Positional candidate genes which may contribute to the development of cardiovascular malformations associated with 1p36 deletions include DVL1, SKI, RERE, PDPN, SPEN, CLCNKA, ECE1, HSPG2, LUZP1, and WASF2. Similarly, haploinsufficiency of PRDM16–a gene which was recently shown to be sufficient to cause the left ventricular noncompaction–SKI, PRKCZ, RERE, UBE4B and MASP2 may contribute to the development of cardiomyopathy. When treating individuals with 1p36 deletions, or providing prognostic information to their families, physicians should take into account that 1p36 deletions which overlie these cardiac critical regions may portend to cardiovascular complications. Since several of these cardiac critical regions contain more than one positional candidate gene–and large terminal and interstitial 1p36 deletions often overlap more than one cardiac critical region–it is likely that haploinsufficiency of two or more genes contributes to the cardiac phenotypes associated with many 1p36 deletions.     

Direct Comparisons of 2D and 3D Dental Microwear Proxies in Extant Herbivorous and Carnivorous Mammals

The analysis of dental microwear is commonly used by paleontologists and anthropologists to clarify the diets of extinct species, including herbivorous and carnivorous mammals. Currently, there are numerous methods employed to quantify dental microwear, varying in the types of microscopes used, magnifications, and the characterization of wear in both two dimensions and three dimensions. Results from dental microwear studies utilizing different methods are not directly comparable and human quantification of wear features (e.g., pits and scratches) introduces interobserver error, with higher error being produced by less experienced individuals. Dental microwear texture analysis (DMTA), which analyzes microwear features in three dimensions, alleviates some of the problems surrounding two-dimensional microwear methods by reducing observer bias. Here, we assess the accuracy and comparability within and between 2D and 3D dental microwear analyses in herbivorous and carnivorous mammals at the same magnification. Specifically, we compare observer-generated 2D microwear data from photosimulations of the identical scanned areas of DMTA in extant African bovids and carnivorans using a scanning white light confocal microscope at 100x magnification. Using this magnification, dental microwear features quantified in 2D were able to separate grazing and frugivorous bovids using scratch frequency; however, DMTA variables were better able to discriminate between disparate dietary niches in both carnivorous and herbivorous mammals. Further, results demonstrate significant interobserver differences in 2D microwear data, with the microwear index remaining the least variable between experienced observers, consistent with prior research. Overall, our results highlight the importance of reducing observer error and analyzing dental microwear in three dimensions in order to consistently interpret diets accurately.     

Engineering tomato for resistance to tomato leaf curl disease using viral <Emphasis Type="Italic">rep</Emphasis> gene sequences

Transgenic tomato resistant to tomato leaf curl disease (ToLCD) using replicase (rep) gene sequences of Tomato leaf curl virus in antisense orientation were developed via Agrobacterium-mediated transformation. A binary vector carrying the antisense rep gene (untranslatable full length sequence, 1086 bp) along with the npt II gene was used for transformation. High level of resistance and inheritability of the transgene was observed up to T₂ stage following challenge inoculation with the virus. The mechanism of resistance appears RNA-mediated, since the plants carried the untranslatable antisense rep gene. Progeny analysis of these plants showed classical Mendelian pattern of inheritance in two of the six transgenic lines having single transgene insertion.     

Biomanufacturing process analytical technology (PAT) application for downstream processing: Using dissolved oxygen as an indicator of product quality for a protein refolding reaction

Process analytical technology (PAT) is an initiative from the US FDA combining analytical and statistical tools to improve manufacturing operations and ensure regulatory compliance. This work describes the use of a continuous monitoring system for a protein refolding reaction to provide consistency in product quality and process performance across batches. A small‐scale bioreactor (3 L) is used to understand the impact of aeration for refolding recombinant human vascular endothelial growth factor (rhVEGF) in a reducing environment. A reverse‐phase HPLC assay is used to assess product quality. The goal in understanding the oxygen needs of the reaction and its impact to quality, is to make a product that is efficiently refolded to its native and active form with minimum oxidative degradation from batch to batch. Because this refolding process is heavily dependent on oxygen, the % dissolved oxygen (DO) profile is explored as a PAT tool to regulate process performance at commercial manufacturing scale. A dynamic gassing out approach using constant mass transfer (k_La) is used for scale‐up of the aeration parameters to manufacturing scale tanks (2,000 L, 15,000 L). The resulting DO profiles of the refolding reaction show similar trends across scales and these are analyzed using rpHPLC. The desired product quality attributes are then achieved through alternating air and nitrogen sparging triggered by changes in the monitored DO profile. This approach mitigates the impact of differences in equipment or feedstock components between runs, and is directly inline with the key goal of PAT to “actively manage process variability using a knowledge‐based approach.” Biotechnol. Bioeng. 2009; 104: 340–351 © 2009 Wiley Periodicals, Inc.