ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

<p>Abstract</p> <p>Background</p> <p>The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis.</p> <p>Results</p> <p>We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at <url>http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/</url>.</p> <p>Conclusions</p> <p>ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.</p

How to create environmentalists: the best motivators

Purpose: The purpose of this paper is to identify how five factors (environmental involvement, environmental concern, financial motivations, social motivations and energy concern motivations) motivate individuals to engage in pro-environmental behaviors (curtailment, capital investment behaviors and food-related behaviors). Design/methodology/approach: A survey approach is used to collect data, and regression analysis is used to answer the research question. Findings: Results show that social motivations are positively associated with all three behaviors such as environmental involvement, Environmental Concern and Energy Concern Motivations are positively associated with some behaviors; and Financial Motivations are not associated with any behaviors examined in this study. Research limitations/implications: These results highlight the widespread impact of social motivations, the more specific impact of environmental involvement, environmental concern and energy concern motivations, and the lack of impact of financial motivations on these three distinct pro-environmental behaviors. Practical implications: Given that social motivation is so strong and pervasive across all three categories of pro-environmental behaviors, leadership in encouraging a dialogue/debate around these issues is needed from all stakeholders, including government, industry leaders, think tanks and environmental organizations. Originality/value: This study incorporates multiple factors that have differing impact on three distinct pro-environmental behaviors

From thinking green to buying green: consumer motivation makes the difference

Purpose: The purpose of this paper is to discuss the need for appropriate green marketing communication strategies to close the gap between consumers’ strong environmental concerns and weak engagement in sustainable behaviors. In doing so, our overarching goal is to provide new direction for creating targeted marketing communication strategies that will more effectively motivate consumer purchasing of green products and services. Design/methodology/approach: The authors use a survey approach to collect data and regression analysis to test our hypotheses. Findings: The findings suggest that demographic variables (gender, ethnicity and age) as well as concern for waste, concern for health and concern for environmental technology influence five different categories of sustainable behaviors. Research limitations/implications: The results suggest that future studies should consider multiple dimensions of environmental concern because each dimension has a different impact on sustainable behaviors. Practical implications: The findings contribute to the continued development of a green consumer profile and highlight the need for marketers to carefully select appropriate dimensions of environmental concern to emphasize in their communication strategies. Results also reinforce the need to consider demographics in targeted communications. Originality/value: This study considers the impact of different dimensions of environmental concern and demographic variables on different types of sustainable behaviors

From thinking green to buying green: consumer motivation makes the difference

Purpose: The purpose of this paper is to discuss the need for appropriate green marketing communication strategies to close the gap between consumers’ strong environmental concerns and weak engagement in sustainable behaviors. In doing so, our overarching goal is to provide new direction for creating targeted marketing communication strategies that will more effectively motivate consumer purchasing of green products and services. Design/methodology/approach: The authors use a survey approach to collect data and regression analysis to test our hypotheses. Findings: The findings suggest that demographic variables (gender, ethnicity and age) as well as concern for waste, concern for health and concern for environmental technology influence five different categories of sustainable behaviors. Research limitations/implications: The results suggest that future studies should consider multiple dimensions of environmental concern because each dimension has a different impact on sustainable behaviors. Practical implications: The findings contribute to the continued development of a green consumer profile and highlight the need for marketers to carefully select appropriate dimensions of environmental concern to emphasize in their communication strategies. Results also reinforce the need to consider demographics in targeted communications. Originality/value: This study considers the impact of different dimensions of environmental concern and demographic variables on different types of sustainable behaviors

Factors affecting the relationship between environmental concern and behaviors

Purpose – The purpose of this paper is to understand the mediating factors affecting the relationship between environmental concerns and sustainable behaviors. Design/methodology/approach – The authors survey 467 respondents and use a structural equation modeling approach to assess environmental involvement and willingness to pay more for green products as mediating variables between a multi-dimensional measure of environmental concern and sustainable behaviors. Findings – The findings suggest that environmental involvement and willingness to pay more for green products mediate the relationship between environmental concern and sustainable behaviors. But of the three dimensions of environmental concern, only concern for energy is statistically significant in the model. Research limitations/implications – The results empirically validate the multi-dimensionality of the environmental concern construct and its relationship with consumers’ sustainable behaviors. Both involvement and willingness to pay more for an environmentally friendly product play an important role in linking environmental concern to actionable behaviors. Practical implications – To reach green consumers who are willing to pay more for environmentally friendly products and ultimately engage in sustainable behaviors, marketers should target those consumers who are most concerned with energy and more involved with the environment. Originality/value – This paper is the first to study the gap between environmental concern and sustainable behaviors by utilizing involvement and willingness to pay more for an environmentally friendly product as mediators. Results provide critical insight into this often elusive gap. The authors also fill an important gap in the literature by including psychological factors driving consumers’ willingness to pay more for green products

Factors affecting the relationship between environmental concern and behaviors

Purpose – The purpose of this paper is to understand the mediating factors affecting the relationship between environmental concerns and sustainable behaviors. Design/methodology/approach – The authors survey 467 respondents and use a structural equation modeling approach to assess environmental involvement and willingness to pay more for green products as mediating variables between a multi-dimensional measure of environmental concern and sustainable behaviors. Findings – The findings suggest that environmental involvement and willingness to pay more for green products mediate the relationship between environmental concern and sustainable behaviors. But of the three dimensions of environmental concern, only concern for energy is statistically significant in the model. Research limitations/implications – The results empirically validate the multi-dimensionality of the environmental concern construct and its relationship with consumers’ sustainable behaviors. Both involvement and willingness to pay more for an environmentally friendly product play an important role in linking environmental concern to actionable behaviors. Practical implications – To reach green consumers who are willing to pay more for environmentally friendly products and ultimately engage in sustainable behaviors, marketers should target those consumers who are most concerned with energy and more involved with the environment. Originality/value – This paper is the first to study the gap between environmental concern and sustainable behaviors by utilizing involvement and willingness to pay more for an environmentally friendly product as mediators. Results provide critical insight into this often elusive gap. The authors also fill an important gap in the literature by including psychological factors driving consumers’ willingness to pay more for green products

Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes

The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of > or =99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of > or =4 C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing

N-glycans of recombinant human acid α-glucosidase expressed in the milk of transgenic rabbits

Pompe disease is a lysosomal glycogen storage disorder characterized by acid α-glucosidase (GAA) deficiency. More than 110 different pathogenic mutations in the gene encoding GAA have been observed. Patients with this disease are being treated by intravenous injection of recombinant forms of the enzyme. Focusing on recombinant approaches to produce the enzyme means that specific attention has to be paid to the generated glycosylation patterns. Here, human GAA was expressed in the mammary gland of transgenic rabbits. The N-linked glycans of recombinant human GAA (rhAGLU), isolated from the rabbit milk, were released by peptide-N4-(N-acetyl-β-glucosaminyl)asparagine amidase F. The N-glycan pool was fractionated and purified into individual components by a combination of anion-exchange, normal-phase, and Sambucus nigra agglutinin-affinity chromatography. The structures of the components were analyzed by 500 MHz one-dimensional and 600 MHz cryo two-dimensional (total correlation spectroscopy [TOCSY] nuclear Overhauser enhancement spectroscopy)1H nuclear magnetic resonance spectroscopy, combined with two-dimensional31P-filtered1H-1H TOCSY spectroscopy, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, and high-performance liquid chromatography (HPLC)-profiling of 2-aminobenzamide-labeled glycans combined with exoglycosidase digestions. The recombinant rabbit glycoprotein contained a broad array of different N-glycans, comprising oligomannose-, hybrid-, and complex-type structures. Part of the oligomannose-type glycans showed the presence of phospho-diester-bridged N-acetylglucosamine. For the complex-type glycans (partially) (α2-6)-sialylated (nearly only N-acetylneuraminic acid) diantennary structures were found; part of the structures were (α1-6)-core-fucosylated or (α1-3)-fucosylated in the upper antenna (Lewis x). Using HPLC-mass spectrometry of glycopeptides, information was generated with respect to the site-specific location of the various glycans