SOS : save our swamps for peat's sake

The Malaysian government's scheme for the agricultural intensification of oil palm production is putting increasing pressure on lowland areas dominated by peat swamp forests.This paper focuses on the peat swamp forests of Sarawak, home to 64 per cent of the peat swamp forests in Malaysia and earmarked under the Malaysian government's Third National Agriculture Policy (1998-2010) for the development and intensification of the oil palm industry.Sarawak's tropical peat swamp forests form a unique ecosystem, where rare plant and animal species, such as the alan tree and the red-banded langur, can be found.They also play a vital role in maintaining the carbon balance, storing up to 10 times more carbon per hectare than other tropical forests. Draining these forests for agricultural purposes endangers the unique species of flora and fauna that live in them and increases the likelihood of uncontrollable peat fires, which emit lethal smoke that can pose a huge environmental risk to the health of humans and wildlife.This paper calls for a radical reassessment of current agricultural policies by the Malaysian government and highlights the need for concerted effort to protect the fragile ecosystems of Sarawak's endangered peat swamp forests

Hierarchical dynamics of individual RNA helix base pair formation and disruption

This thesis explores the RNA folding problem using single-molecule field effect transistors (smFETs) to measure the lifetimes of individual RNA base-pairing rearrangements. In the course of this research, considerable computational, chemical, and engineering contributions were developed so that the single-molecule measurements could be conducted and quantified. These advancements have allowed, on the basis of the smFET data collected herein, the quantification of a kinetic model for RNA stem-loop structures which has been generalized to quantitatively explore the phenomenological observation that an RNA found in the bacillus subtilis strain acts as a metabolite-sensing switch, allowing RNA polymerase to transcribe the messenger RNA when the metabolite is present and preventing transcription when the metabolite is absent. Together, the data presented quantify a simple model for the base pairing rearrangements that underlie RNA folding

A Review on Land Use in the Malaysian State of Sarawak, Borneo and Recommendations for Wildlife Conservation Inside Production Forest Environment

The Malaysian state of Sarawak, which lies in the island of Borneo, is rich in plant and animal diversity, andforms one of the global biodiversity hotspots. The major land uses include logging, agriculture and forestplantations. Deforestation and degradation of forests are occurring at a rate of 0.64% annually, largely due toexpansion of oil palm plantations which increases at an average rate of 10.2% annually. More areas are beingconverted into forest plantations, which accounts for 3.25% of the total forested area. On the other hand,protected areas remain small, representing only 6.64% of total forested area or 4.23% of the total land area, andare located far apart. The bulk of forests are subjected to logging and many areas may be converted in thefuture to other land use such as agriculture. Furthermore, logging has been a major economic activity, and willcontinue to be so in the future. Hence, the network of production forests become crucial for wildlife andworking with logging companies in this aspect is a realistic approach towards wildlife conservation. Somemeasures proposed include encouraging collaborative research in production forests; making sustainable forestmanagement practices mandatory; creating buffer zones in areas adjacent to protected areas; and maintainingmaximum connectivity of habitat for wildlife

Whistleblower Law 101: Facing Food Industry Retaliation

This Article is an annotated transcript of a panel that occurred on February 11, 2011 at the American University Washington College of Law. The podcast of the event can be found on the American University website at http://media.wcl.american.edu/mediasite/SilverlightPlayer/ Default.aspx?peid=f68cdf9c-6bab-4202-b009-26b50bf563bf. The event was co-sponsored by the Washington College of Law and the Government Accountability Project

Whistleblower Law 101: Facing Food Industry Retaliation

This Article is an annotated transcript of a panel that occurred on February 11, 2011 at the American University Washington College of Law. The podcast of the event can be found on the American University website at http://media.wcl.american.edu/mediasite/SilverlightPlayer/ Default.aspx?peid=f68cdf9c-6bab-4202-b009-26b50bf563bf. The event was co-sponsored by the Washington College of Law and the Government Accountability Project

Robotic Minimally Invasive Tools for Restricted Access Confined Spaces

A study has been performed in the design and fabrication of deployable borehole robots into confined spaces. Three robot systems have been developed to perform a visual survey of a subterranean space where for any reason humans could not enter. A 12mm diameter snake arm was designed with a focus on the cable tensions and the failure modes for the components that make the snake arm. An iterative solver was developed to model the snake arm and algorithmically calculate the snake arms optimal length with consideration of the failure modes. A robot was developed to extend the range capabilities of borehole robots using reconfigurable borehole robots based around established actuation and manufacturing techniques. The expected distance and weight requirements of the robot are calculated alongside the forces the robot is required to generate in order to achieve them. The whegged design incorporated into the tracks is also analysed to measure the capability of the robot over rough terrain. Finally, the experiments to find the actual driving forces of the tracks are performed and used to calculate the actual range of the robot in comparison to the target range. The potential of reconfigurable mobile robots for deployment through boreholes is limited by the requirement for conventional gears, motors, and joints. This chapter explores the use of smart materials and innovative manufacturing techniques to form a novel concept of a self-folding robotic joint for a self-assembling robotic system. The design uses shape memory alloys fabricated in laminate structures with heaters to create folding structures

Discovery and characterization of chromatin states for systematic annotation of the human genome

A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal 'chromatin states' in human T cells, based on recurrent and spatially coherent combinations of chromatin marks. We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, large-scale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function.National Science Foundation (U.S.). (Award 0905968)National Human Genome Research Institute (U.S.) (Award U54-HG004570)National Human Genome Research Institute (U.S.) (Award RC1-HG005334

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease