Sharing Feedback, Sharing Screens: Videoconferencing as a Tool for Stakeholder-Driven Web Design

Videoconferencing is a low-cost, high-reward tool for engaging stakeholders in participatory design and usability testing for online Extension products. This article details how we used the videoconference program BlueJeans to facilitate the redesign of the Great Lakes Aquatic Nonindigenous Species Information System database and highlights the benefits of this technique along with the methods we used for stakeholder interviews in the project

Proteomic Analysis of the Secretory Response of Aspergillus niger to D-Maltose and D-Xylose

Fungi utilize polysaccharide substrates through extracellular digestion catalyzed by secreted enzymes. Thus far, protein secretion by the filamentous fungus Aspergillus niger has mainly been studied at the level of individual proteins and by genome and transcriptome analyses. To extend these studies, a complementary proteomics approach was applied with the aim to investigate the changes in secretome and microsomal protein composition resulting from a shift to a high level secretion condition. During growth of A. niger on d-sorbitol, small amounts of d-maltose or d-xylose were used as inducers of the extracellular amylolytic and xylanolytic enzymes. Upon induction, protein compositions in the extracellular broth as well as in enriched secretory organelle (microsomal) fractions were analyzed using a shotgun proteomics approach. In total 102 secreted proteins and 1,126 microsomal proteins were identified in this study. Induction by d-maltose or d-xylose resulted in the increase in specific extracellular enzymes, such as glucoamylase A on d-maltose and β-xylosidase D on d-xylose, as well as of microsomal proteins. This reflects the differential expression of selected genes coding for dedicated extracellular enzymes. As expected, the addition of extra d-sorbitol had no effect on the expression of carbohydrate-active enzymes, compared to addition of d-xylose or d-maltose. Furthermore, d-maltose induction caused an increase in microsomal proteins related to translation (e.g., Rpl15) and vesicular transport (e.g., the endosomal-cargo receptor Erv14). Millimolar amounts of the inducers d-maltose and d-xylose are sufficient to cause a direct response in specific protein expression levels. Also, after induction by d-maltose or d-xylose, the induced enzymes were found in microsomes and extracellular. In agreement with our previous findings for d-xylose induction, d-maltose induction leads to recruitment of proteins involved in proteasome-mediated degradation

Mitochondrial Associated Ubiquitin Fold Modifier-1 Mediated Protein Conjugation in Leishmania donovani

In this report, we demonstrate the existence of the ubiquitin fold modifier-1 (Ufm1) and its conjugation pathway in trypanosomatid parasite Leishmania donovani. LdUfm1 is activated by E1-like enzyme LdUba5. LdUfc1 (E2) specifically interacted with LdUfm1 and LdUba5 to conjugate LdUfm1 to proteinaceous targets. Mass spectrometry analysis revealed that LdUfm1 is conjugated to Leishmania protein targets that are associated with mitochondria. Immunofluorescence experiments showed that Leishmania Ufm1, Uba5 and Ufc1 are associated with the mitochondria. The demonstration that all the components of this system as well as the substrates are associated with mitochondrion suggests it may have physiological roles not yet described in any other organism. Overexpression of a non-conjugatable form of LdUfm1 and an active site mutant of LdUba5 resulted in reduced survival of Leishmania in the macrophage. Since mitochondrial activities are developmentally regulated in the life cycle of trypanosomatids, Ufm1 mediated modifications of mitochondrial proteins may be important in such regulation. Thus, Ufm1 conjugation pathway in Leishmania could be explored as a potential drug target in the control of Leishmaniasis

Plasmodium falciparum metacaspase PfMCA-1 triggers a z-VAD-fmk inhibitable protease to promote cell death.

Activation of proteolytic cell death pathways may circumvent drug resistance in deadly protozoan parasites such as Plasmodium falciparum and Leishmania. To this end, it is important to define the cell death pathway(s) in parasites and thus characterize proteases such as metacaspases (MCA), which have been reported to induce cell death in plants and Leishmania parasites. We, therefore, investigated whether the cell death function of MCA is conserved in different protozoan parasite species such as Plasmodium falciparum and Leishmania major, focusing on the substrate specificity and functional role in cell survival as compared to Saccharomyces cerevisae. Our results show that, similarly to Leishmania, Plasmodium MCA exhibits a calcium-dependent, arginine-specific protease activity and its expression in yeast induced growth inhibition as well as an 82% increase in cell death under oxidative stress, a situation encountered by parasites during the host or when exposed to drugs such as artemisins. Furthermore, we show that MCA cell death pathways in both Plasmodium and Leishmania, involve a z-VAD-fmk inhibitable protease. Our data provide evidence that MCA from both Leishmania and Plasmodium falciparum is able to induce cell death in stress conditions, where it specifically activates a downstream enzyme as part of a cell death pathway. This enzymatic activity is also induced by the antimalarial drug chloroquine in erythrocytic stages of Plasmodium falciparum. Interestingly, we found that blocking parasite cell death influences their drug sensitivity, a result which could be used to create therapeutic strategies that by-pass drug resistance mechanisms by acting directly on the innate pathways of protozoan cell death

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition

Multifaceted value profiles of forest owner categories in South Sweden: The river helge å catchment as a case study

Forest landscapes provide benefits from a wide range of goods, function and intangible values. But what are different forest owner categories\u27 profiles of economic use and non-use values? This study focuses on the complex forest ownership pattern of the River Helge å catchment including the Kristianstad Vattenrike Biosphere Reserve in southern Sweden. We made 89 telephone interviews with informants representing the four main forest owner categories. Our mapping included consumptive and non-consumptive direct use values, indirect use values, and non-use values such as natural and cultural heritage. While the value profiles of non-industrial forest land owners and municipalities included all value categories, the forest companies focused on wood production, and the Swedish Environmental Protection Agency on nature protection. We discuss the challenges of communicating different forest owners\u27 economic value profiles among stakeholders, the need for a broader suite of forest management systems, and fora for collaborative planning. © 2013 The Author(s)

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

Forest biodiversity, ecosystem functioning and the provision of ecosystem services

Forests are critical habitats for biodiversity and they are also essential for the provision of a wide range of ecosystem services that are important to human well-being. There is increasing evidence that biodiversity contributes to forest ecosystem functioning and the provision of ecosystem services. Here we provide a review of forest ecosystem services including biomass production, habitat provisioning services, pollination, seed dispersal, resistance to wind storms, fire regulation and mitigation, pest regulation of native and invading insects, carbon sequestration, and cultural ecosystem services, in relation to forest type, structure and diversity. We also consider relationships between forest biodiversity and multifunctionality, and trade-offs among ecosystem services. We compare the concepts of ecosystem processes, functions and services to clarify their definitions. Our review of published studies indicates a lack of empirical studies that establish quantitative and causal relationships between forest biodiversity and many important ecosystem services. The literature is highly skewed; studies on provisioning of nutrition and energy, and on cultural services, delivered by mixed-species forests are under-represented. Planted forests offer ample opportunity for optimising their composition and diversity because replanting after harvesting is a recurring process. Planting mixed-species forests should be given more consideration as they are likely to provide a wider range of ecosystem services within the forest and for adjacent land uses. This review also serves as the introduction to this special issue of Biodiversity and Conservation on various aspects of forest biodiversity and ecosystem services

Impact of different eddy covariance sensors, site set-up, and maintenance on the annual balance of CO2 and CH4 in the harsh Arctic environment

Improving year-round data coverage for CO2 and CH4 fluxes in the Arctic is critical for refining the global C budget but continuous measurements are very sparse due to the remote location limiting instrument maintenance, to low power availability, and to extreme weather conditions. The need for tailoring instrumentation, site set up, and maintenance at different sites can add uncertainty to estimates of annual C budgets from different ecosystems. In this study, we investigated the influence of different sensor combinations on fluxes of sensible heat, CO2, latent heat (LE), and CH4, and assessed the differences in annual CO2 and CH4 fluxes estimated with different instrumentation at the same sites. Using data from four sites across the North Slope of Alaska, we found that annual CO2 fluxes estimated with heated (7.5 ± 1.4 gC m−2 yr−1) and non-heated (7.9 ± 1.3 gC m−2 yr−1) anemometers were within uncertainty bounds. Similarly, despite elevated noise in 30-min flux data, we found that summer CO2 fluxes from open (−17.0 ± 1.1 gC m−2 yr−1) and close-path (−14.2 ± 1.7 gC m−2 yr−1) gas analyzers were not significantly different. Annual CH4 fluxes were also within uncertainty bounds when comparing both open (4.5 ± 0.31 gC m−2 yr−1) and closed-path (4.9 ± 0.27 gC m−2 yr−1) gas analyzers as well as heated (3.7 ± 0.26 gC m−2 yr−1) and non-heated (3.7 ± 0.28 gC m−2 yr−1) anemometers. A continuously heated anemometer increased data coverage (64%) relative to non-heated anemometers (47–52%). However, sensible heat fluxes were over-estimated by 12%, on average, with the heated anemometer, contributing to the overestimation of CO2, CH4, and LE fluxes (mean biases of −0.03 μmol m−2 s−1, −0.05 mgC m−2 h−1, and −3.77 W m−2, respectively). To circumvent this potential bias and reduce power consumption, we implemented an intermittent heating strategy whereby activation only occurred when ice or snow blockage of the transducers was detected. This resulted in comparable coverage (50%) during winter to the continuously heated anemometer (46%), while avoiding flux over-estimation. Closed and open-path analyzers showed good agreement, but data coverage was generally greater when using closed-path, especially during winter. Winter data coverage of 26–32% was obtained with closed-path devices, vs 10–14% for the open-path devices with unheated anemometers or up to 46% and 35% using closed and open-path analyzers, respectively with heated anemometers. Accurate estimation of LE remains difficult in the Arctic due to strong attenuation in closed-path systems, even when intake tubes are heated, and due to poor data coverage from open-path sensors in such a harsh environment