Human dimensions of global environmental change: A review of frameworks and research gaps.

This review of current knowledge in, and development of, priorities for research into the human dimensions of global environmental change has been conducted to assist the Foundation for Research Science and Technology to formulate their research needs agenda. An overview of the emergence of the human dimension of the global environmental change research field is used as a prelude to a review of the international literature on frameworks for conducting human dimensions research. The terminology used in the human dimension field is diverse. An attempt is therefore made to consolidate the myriad of definitions for key concepts, in order to form a basis for human dimensions research in New Zealand and build a platform for the remainder of this report. Three disciplinary areas of academic inquiry were explored in the context of human dimensions of global environmental change research: economics, law and biological sciences. These disciplinary perspectives are reviewed through the international literature and in a New Zealand context. A conceptual framework for research into the human dimensions of global environmental change is provided based on the knowledge-base developed from the both international and New Zealand research. Core concepts, such as found in multidisciplinary and transdisciplinary research are reviewed in historical context to form the basis for a specific research framework for New Zealand. Some general needs for research are derived from the New Zealand framework. The remainder of this report details the methods used for drawing out expert opinion on the priorities for research on the human dimensions of global environmental change in the context of information, knowledge and method. Thirty-eight interviews and two hui were conducted and 254 research needs defined by questions were obtained. A modified Delphi technique was applied to the questions and prioritised lists of responses are provided. The final list Provides European/Pakeha and Māori perspectives. Divergence and convergence between the European/Pakeha and Māori responses is provided, as well as justification for the prioritisation stance that is taken. This research had four outputs: A conceptual framework for considering the human dimensions of global environmental changes and research contributions; A description of the gaps in knowledge that impede effective response to global change and provisional research needs: one for New Zealand generally, and one on Māori in particular; A network of end-users and research providers that are cognisant of, and contributors to, the human dimensions research assessment; A set of priority research needs pertaining to the human dimensions of global environmental change, in a form suitable for use by FRST

Lifestyle and Horizontal Gene Transfer- Mediated Evolution of \u3ci\u3eMucispirillum schaedleri\u3c/i\u3e, a Core Member of the Murine Gut Microbiota

Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem

Lifestyle and Horizontal Gene Transfer- Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota

Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem

Intrinsic response time of graphene photodetectors

Graphene-based photodetectors are promising new devices for high-speed optoelectronic applications. However, despite recent efforts, it is not clear what determines the ultimate speed limit of these devices. Here, we present measurements of the intrinsic response time of metal-graphene-metal photodetectors with monolayer graphene using an optical correlation technique with ultrashort laser pulses. We obtain a response time of 2.1 ps that is mainly given by the short lifetime of the photogenerated carriers. This time translates into a bandwidth of ~262 GHz. Moreover, we investigate the dependence of the response time on gate voltage and illumination laser power

Microcavity-integrated graphene photodetector

The monolithic integration of novel nanomaterials with mature and established technologies has considerably widened the scope and potential of nanophotonics. For example, the integration of single semiconductor quantum dots into photonic crystals has enabled highly efficient single-photon sources. Recently, there has also been an increasing interest in using graphene - a single atomic layer of carbon - for optoelectronic devices. However, being an inherently weak optical absorber (only 2.3 % absorption), graphene has to be incorporated into a high-performance optical resonator or waveguide to increase the absorption and take full advantage of its unique optical properties. Here, we demonstrate that by monolithically integrating graphene with a Fabry-Perot microcavity, the optical absorption is 26-fold enhanced, reaching values >60 %. We present a graphene-based microcavity photodetector with record responsivity of 21 mA/W. Our approach can be applied to a variety of other graphene devices, such as electro-absorption modulators, variable optical attenuators, or light emitters, and provides a new route to graphene photonics with the potential for applications in communications, security, sensing and spectroscopy.Comment: 19 pages, 4 figure

Methods for comparative metagenomics

<p>Abstract</p> <p>Background</p> <p>Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans. The recent development of ultra-high throughput sequencing technologies, which do not require cloning or PCR amplification, and can produce huge numbers of DNA reads at an affordable cost, has boosted the number and scope of metagenomic sequencing projects. Increasingly, there is a need for new ways of comparing multiple metagenomics datasets, and for fast and user-friendly implementations of such approaches.</p> <p>Results</p> <p>This paper introduces a number of new methods for interactively exploring, analyzing and comparing multiple metagenomic datasets, which will be made freely available in a new, comparative version 2.0 of the stand-alone metagenome analysis tool MEGAN.</p> <p>Conclusion</p> <p>There is a great need for powerful and user-friendly tools for comparative analysis of metagenomic data and MEGAN 2.0 will help to fill this gap.</p

Lifestyle and Horizontal Gene Transfer- Mediated Evolution of \u3ci\u3eMucispirillum schaedleri\u3c/i\u3e, a Core Member of the Murine Gut Microbiota

Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem

Metatranscriptomic Analysis of Arctic Peat Soil Microbiota

Recent advances in meta-omics and particularly metatranscriptomic approaches have enabled detailed studies of the structure and function of microbial communities in many ecosystems. Molecular analyses of peat soils, ecosystems important to the global carbon balance, are still challenging due to the presence of coextracted substances that inhibit enzymes used in downstream applications. We sampled layers at different depths from two high-Arctic peat soils in Svalbard for metatranscriptome preparation. Here we show that enzyme inhibition in the preparation of metatranscriptomic libraries can be circumvented by linear amplification of diluted template RNA. A comparative analysis of mRNA-enriched and nonenriched metatranscriptomes showed that mRNA enrichment resulted in a 2-fold increase in the relative abundance of mRNA but biased the relative distribution of mRNA. The relative abundance of transcripts for cellulose degradation decreased with depth, while the transcripts for hemicellulose debranching increased, indicating that the polysaccharide composition of the peat was different in the deeper and older layers. Taxonomic annotation revealed that Actinobacteria and Bacteroidetes were the dominating polysaccharide decomposers. The relative abundances of 16S rRNA and mRNA transcripts of methanogenic Archaea increased substantially with depth. Acetoclastic methanogenesis was the dominating pathway, followed by methanogenesis from formate. The relative abundances of 16S rRNA and mRNA assigned to the methanotrophic Methylococcaceae, primarily Methylobacter, increased with depth. In conclusion, linear amplification of total RNA and deep sequencing constituted the preferred method for metatranscriptomic preparation to enable high-resolution functional and taxonomic analyses of the active microbiota in Arctic peat soil

Gene expression of lactobacilli in murine forestomach biofilms

Lactobacilli populate the gastro‐intestinal tract of vertebrates, and are used in food fermentations and as probiotics. Lactobacilli are also major constituents of stable biofilms in the forestomach of rodents. In order to investigate the lifestyle of these biofilm lactobacilli in C57BL/6 mice, we applied metatranscriptomics to analyse gene expression (assessed by mRNA) and community composition (assessed by rRNA). Lactobacillales were the major biofilm inhabitants (62–82% of rRNA reads), followed by Clostridiales (8–31% of rRNA reads). To identify mRNA transcripts specific for the forestomach, we compared forestomach and hindgut metatranscriptomes. Gene expression of the biofilm microbiota was characterized by high abundance of transcripts related to glucose and maltose utilization, peptide degradation, and amino acid transport, indicating their major catabolic and anabolic pathways. The microbiota transcribed genes encoding pathways enhancing oxidative stress (glutathione synthesis) and acid tolerance. Various pathways, including metabolite formation (urea degradation, arginine pathway, γ‐aminobutyrate) and cell wall modification (DltA, cyclopropane‐fatty‐acyl‐phospholipid synthase), contributed to acid tolerance, as judged from the transcript profile. In addition, the biofilm microbiota expressed numerous genes encoding extracellular proteins involved in adhesion and/or biofilm formation (e.g. MucBP, glycosyl hydrolase families 68 and 70). This study shed light on the lifestyle and specific adaptations of lactobacilli in the murine forestomach that might also be relevant for lactobacilli biofilms in other vertebrates, including humans.ISSN:1751-7915ISSN:1751-790