An Evaluation of “Diabetes Day” using Implementation Science to Improve Support for Families of Children with Type 1 Diabetes Mellitus

Background: Type 1 diabetes (T1D) is one of the most common life-long endocrine disorders in children and adolescents. Attending to the psychosocial and emotional needs of children with T1D and their families is fundamental in attaining optimal clinical health outcomes. Diabetes Day is a collaborative effort that is offered at a pediatric endocrinology clinic in Western Massachusetts. The Diabetes Day team spends multiple hours planning, recruiting and implementing Diabetes Day as a way to provide this requested support; however, participation rates of families continues to decrease.Purpose: The purpose of this DNP project was to evaluate the process of planning, implementation and evaluation of Diabetes Day to improve family participation and attendance. Methods: The plan, do, study, act (PDSA) model was used to implement this QI project consisting of qualitative questionnaires from Diabetes Day family participants as well as the Diabetes Day staff. Results: Barriers to participation included a fear of missing work/school or the time of the day. Suggestions for improving the implementation process include updating recruitment methods, sharing the burden of recruitment, and providing more education to families describing Diabetes Day. Conclusion: Successful implementation of Diabetes Day can provide improved diabetes management and patient outcomes. The results of this project will continue to be used to guide the Diabetes Day team to uncover additional barriers to participation that can be overcome using a different approach to recruitment resulting in an increase in family participation

Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus

<p>Abstract</p> <p>Background</p> <p>An available whole genome sequence for <it>Aspergillus flavus </it>provides the opportunity to characterize factors involved in pathogenicity and to elucidate the regulatory networks involved in aflatoxin biosynthesis. Functional analysis of genes within the genome is greatly facilitated by the ability to disrupt or mis-express target genes and then evaluate their result on the phenotype of the fungus. Large-scale functional analysis requires an efficient genetic transformation system and the ability to readily select transformants with altered expression, and usually requires generation of double (or multi) gene deletion strains or the use of prototrophic strains. However, dominant selectable markers, an efficient transformation system and an efficient screening system for transformants in <it>A. flavus </it>are absent.</p> <p>Results</p> <p>The efficiency of the genetic transformation system for <it>A. flavus </it>based on uracil auxotrophy was improved. In addition, <it>A. flavus </it>was shown to be sensitive to the antibiotic, phleomycin. Transformation of <it>A. flavus </it>with the <it>ble </it>gene for resistance to phleomycin resulted in stable transformants when selected on 100 μg/ml phleomycin. We also compared the phleomycin system with one based on complementation for uracil auxotrophy which was confirmed by uracil and 5-fluoroorotic acid selection and via transformation with the <it>pyr4 </it>gene from <it>Neurospora crassa </it>and <it>pyrG </it>gene from <it>A. nidulans </it>in <it>A. flavus </it>NRRL 3357. A transformation protocol using <it>pyr4 </it>as a selectable marker resulted in site specific disruption of a target gene. A rapid and convenient colony PCR method for screening genetically altered transformants was also developed in this study.</p> <p>Conclusion</p> <p>We employed phleomycin resistance as a new positive selectable marker for genetic transformation of <it>A. flavus</it>. The experiments outlined herein constitute the first report of the use of the antibiotic phleomycin for transformation of <it>A. flavus</it>. Further, we demonstrated that this transformation protocol could be used for directed gene disruption in <it>A. flavus</it>. The significance of this is twofold. First, it allows strains to be transformed without having to generate an auxotrophic mutation, which is time consuming and may result in undesirable mutations. Second, this protocol allows for double gene knockouts when used in conjunction with existing strains with auxotrophic mutations.</p> <p>To further facilitate functional analysis in this strain we developed a colony PCR-based method that is a rapid and convenient method for screening genetically altered transformants. This work will be of interest to those working on molecular biology of aflatoxin metabolism in <it>A. flavus</it>, especially for functional analysis using gene deletion and gene expression.</p

Long-term Effects of Weed Management on Earthworm Abundance in a Banana Plantation in Davao City, Southern Mindanao, Philippines

Earthworm densities have been regarded as reliable indicators of soil health. A long-term field experiment was conducted in two sites (15% and 25% slope) to compare the effects of manual and chemical weeding (using paraquat and glyphosate) and determine other factors that may affect earthworm populations in a banana plantation. Based on four years of field observation, no significant difference in earthworm count between manual and chemical plots (15% slope: F-ratio: 0.96, p = 0.43; 25% slope: F-ratio: 14.18, p = 0.06) were observed. The earthworm species composition was found to differ between the two sites. The 15% site tends to have a higher earthworm population compared to the 25%-slope site, likely because of the former’s higher soil organic matter content. Earthworm populations were on a declining trend in both treatments for both sites, but regression analyses show these trends to be insignificant. Rainfall, organic mulch, and weed cover were not significantly correlated with the earthworm counts. However, the declining pH in both sites could help explain the decline in earthworm populations. Pontocolex corethrurus showed significant avoidance response to normal glyphosate concentrations (8.055 × 10–3 mL per 350 g soil) (p = 0.03), but not to paraquat (1.5 × 10–3 g per 350 g soil) (p = 0.55). Experiments suggest that both weed management treatments do not pose a significant threat to earthworms under the conditions studied. The negative effect of declining pH needs further study

Impacts of Long-term Weed Management on the Diversity and Abundance of Grasses in Banana Plantation Slopes in Davao City, Philippines

Banana is one of the main export products in the Philippines. The growing demand for banana products generates a need for plantation expansion even in erosion-prone areas like slopes. Effective farming practices in slopes are therefore needed to conserve the soil and establish a sustainable production. One of these systems is weed management, which is a critical component of farming practice in sloping lands. A 3-year study was conducted to compare manual and chemical (paraquat and glyphosate) weed management on the abundance and diversity of grasses in a banana plantation. Counts, biomasses, seed bank, and diversity indices of grasses were compared in identical experiments in 15% and 25% slopes. From the seed banks, 7 grass species were observed: Cyperus brevifolius, Cynodon dactylon, Eleusine indica, Imperata cylindrica, Paspalum conjugatum, Digitaria ciliaris, and Digitaria longiflora. Generally, there was a decreasing trend in the seed bank counts in both manual and chemical plots of 15% and 25% slope. However, the differences between treatments were not significant. Chemical treatments reduced the general counts and biomass of monocot weeds, but this effect was generally not significant. Chemical treatments significantly reduced the counts of P. conjugatum in 15% slope and the biomass of E. indica in 25% slope in the field. C. dactylon was found to be the dominant species in the field because of its early establishment in the slopes, its spreading growth and its allelopathic properties, which suppressed other species. There was a significant increase in diversity in both treatments on two slopes, but chemical plots had a significantly higher diversity compared to the manual plots. Chemical weeding was also less expensive and less laborious than manual weeding

Grounding knowledge and normative valuation in agent-based action and scientific commitment

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations

College student sleep quality and mental and physical health are associated with food insecurity in a multi-campus study

Objective: To assess the relationship between food insecurity, sleep quality, and days with mental and physical health issues among college students. Design: An online survey was administered. Food insecurity was assessed using the ten-item Adult Food Security Survey Module. Sleep was measured using the nineteen-item Pittsburgh Sleep Quality Index (PSQI). Mental health and physical health were measured using three items from the Healthy Days Core Module. Multivariate logistic regression was conducted to assess the relationship between food insecurity, sleep quality, and days with poor mental and physical health. Setting: Twenty-two higher education institutions. Participants: College students (n 17 686) enrolled at one of twenty-two participating universities. Results: Compared with food-secure students, those classified as food insecure (43·4 %) had higher PSQI scores indicating poorer sleep quality (P \u3c 0·0001) and reported more days with poor mental (P \u3c 0·0001) and physical (P \u3c 0·0001) health as well as days when mental and physical health prevented them from completing daily activities (P \u3c 0·0001). Food-insecure students had higher adjusted odds of having poor sleep quality (adjusted OR (AOR): 1·13; 95 % CI 1·12, 1·14), days with poor physical health (AOR: 1·01; 95 % CI 1·01, 1·02), days with poor mental health (AOR: 1·03; 95 % CI 1·02, 1·03) and days when poor mental or physical health prevented them from completing daily activities (AOR: 1·03; 95 % CI 1·02, 1·04). Conclusions: College students report high food insecurity which is associated with poor mental and physical health, and sleep quality. Multi-level policy changes and campus wellness programmes are needed to prevent food insecurity and improve student health-related outcomes

Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation

Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species

Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms

<p>Abstract</p> <p>Background</p> <p>Database searching is the most frequently used approach for automated peptide assignment and protein inference of tandem mass spectra. The results, however, depend on the sequences in target databases and on search algorithms. Recently by using an alternative splicing database, we identified more proteins than with the annotated proteins in <it>Aspergillus flavus</it>. In this study, we aimed at finding a greater number of eligible splice variants based on newly available transcript sequences and the latest genome annotation. The improved database was then used to compare four search algorithms: Mascot, OMSSA, X! Tandem, and InsPecT.</p> <p>Results</p> <p>The updated alternative splicing database predicted 15833 putative protein variants, 61% more than the previous results. There was transcript evidence for 50% of the updated genes compared to the previous 35% coverage. Database searches were conducted using the same set of spectral data, search parameters, and protein database but with different algorithms. The false discovery rates of the peptide-spectrum matches were estimated < 2%. The numbers of the total identified proteins varied from 765 to 867 between algorithms. Whereas 42% (1651/3891) of peptide assignments were unanimous, the comparison showed that 51% (568/1114) of the RefSeq proteins and 15% (11/72) of the putative splice variants were inferred by all algorithms. 12 plausible isoforms were discovered by focusing on the consensus peptides which were detected by at least three different algorithms. The analysis found different conserved domains in two putative isoforms of UDP-galactose 4-epimerase.</p> <p>Conclusions</p> <p>We were able to detect dozens of new peptides using the improved alternative splicing database with the recently updated annotation of the <it>A. flavus </it>genome. Unlike the identifications of the peptides and the RefSeq proteins, large variations existed between the putative splice variants identified by different algorithms. 12 candidates of putative isoforms were reported based on the consensus peptide-spectrum matches. This suggests that applications of multiple search engines effectively reduced the possible false positive results and validated the protein identifications from tandem mass spectra using an alternative splicing database.</p

What can comparative genomics tell us about species concepts in the genus Aspergillus?

Understanding the nature of species” boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species

The Effect of Diel Temperature and Light Cycles on the Growth of Nannochloropsis oculata in a Photobioreactor Matrix

A matrix of photobioreactors integrated with metabolic sensors was used to examine the combined impact of light and temperature variations on the growth and physiology of the biofuel candidate microalgal species Nannochloropsis oculata. The experiments were performed with algal cultures maintained at a constant 20u C versus a 15°C to 25°C diel temperature cycle, where light intensity also followed a diel cycle with a maximum irradiance of 1920 μmol photons m-2 s-1. No differences in algal growth (Chlorophyll a) were found between the two environmental regimes; however, the metabolic processes responded differently throughout the day to the change in environmental conditions. The variable temperature treatment resulted in greater damage to photosystem II due to the combined effect of strong light and high temperature. Cellular functions responded differently to conditions before midday as opposed to the afternoon, leading to strong hysteresis in dissolved oxygen concentration, quantum yield of photosystem II and net photosynthesis. Overnight metabolism performed differently, probably as a result of the temperature impact on respiration. Our photobioreactor matrix has produced novel insights into the physiological response of Nannochloropsis oculata to simulated environmental conditions. This information can be used to predict the effectiveness of deploying Nannochloropsis oculata in similar field conditions for commercial biofuel production. © 2014 Tamburic et al