Revisiting Michael Bonell's work on humid tropical rainforest catchments: Isotope tracers reveal seasonal shifts in catchment hydrology

It has been almost 50 years since the foundational work at the Babinda catchments in North Queensland kickstarted the field of tropical hydrology globally. To expand upon this work and build a more generalized hydrological understanding of steep rainforest catchments, we studied the seasonal evolution of hydrological response from two catchments with broadly similar characteristics to the Babinda catchments. Both hydrometric and water stable isotope data were collected at relatively high frequencies during one wet season (Thompson Creek) and a 3-year period (Atika Creek). The longer dataset spans a wide range of environmental conditions experienced in the humid tropics, including events that cover the wetting-up transitional period of the wet season and tropical cyclones (TC). Both catchments displayed a fast streamflow response to rainfall with the shallow upper soil profile responding quickly to rainfall at Atika Creek. New findings from this study include the importance of pre-event water (>50% using the two component hydrograph separation technique) for overall event flows, especially when the catchment was wet. Rainfall, surface runoff and groundwater isotope and specific electrical conductivity (SEC) compositions varied between rainfall events with the most complex bivariate mixing plots observed for multi-peak events that occurred at the start of the wet season and after a dry period within the wet season. Two-tracer, 3 component hydrograph separations did not provide satisfactory results in identifying source water contributions to streamflow. These results highlighted the time-variant and non-conservative behaviour of the rainfall, surface runoff and shallow groundwater source waters over the seasonal timescale, with soil water being an important unidentified source contributor. Our findings highlight the need for high frequency multi-source sampling to accurately interpret catchment behaviour and the importance of soil water contributions to streamflow. We propose a framework to describe the seasonal evolution of streamflow response in steep tropical rainforest catchments experiencing seasonal rainfall activity

Modelling environmental impacts of agriculture, focusing on oil palm

Cultivation of crops affects the environment via flows of energy and materials. Impacts are felt in the atmosphere, hydrosphere, surrounding terrestrial ecosystems and the field itself. Models are useful tools for improving our understanding of the processes and predicting how they might be affected by changes in management. Current models range from simple indicators of risk or impact, based on empirical relationships, to dynamic process-based models. Increasingly complex and comprehensive models with increasing spatial and temporal resolution and extent are being developed, mostly by coupling diverse sub-models. This chapter reviews the range of models developed for oil palm systems, and discusses how other existing models might be adapted for oil palm

Performance Auditing to Assess the Implementation of the Sustainable Development Goals (SDGs) in Indonesia

Regular assessment of progress on the implementation of Sustainable Development Goals (SDGs) is crucial for achieving the goals by 2030 yet such assessments often require extensive resources and data. Here, we describe a method using performance auditing as a novel approach for assessing the implementation of SDGs that would be useful for countries with limited resources and data availability but might also provide an alternative to choosing particular goals and implementing them one at a time, for all countries. We argue that, instead of monitoring all 169 targets and 242 indicators, a country could assess the effectiveness of its governance arrangement as a way of ensuring that progress on implementing SDGs is on track, and hence improve the likelihood of achieving the SDGs by 2030. Indonesia is an archipelagic upper-middle-income country facing challenges in data availability and reliability, which limits accurate assessments of SDG implementation. We applied a standardized performance audit to assess the effectiveness of current governance arrangements for the implementation of SDGs. We used the Gephi 0.9.2 software (Open sourced program by The Gephi Concortium, Compiègne, France) to illustrate the regulatory coordination among public institutions. We found that Indonesia’s governance arrangements are not yet effective. They might be improved if Indonesia: (1) synchronize its SDG regulations; (2) redesigns its governance structure to be more fit for purpose; and (3) involves audit institutions in the SDG governance arrangements. These findings would likely apply to many other countries striving to implement the SDGs

Denitrification bioreactor trial in the Russell River catchment of the Wet Tropics: final report

Dissolved inorganic nitrogen (DIN) in runoff from agricultural land is considered to have a significant detrimental impact on the Great Barrier Reef (GBR). Losses of DIN to runoff can be reduced by good agricultural practices, but they cannot be eliminated entirely in the Wet Tropics due to the need for adequate nitrogen supply to crops, the high solubility of DIN, particularly nitrate, and high rainfall. Thus, it is inevitable that DIN concentrations are higher in runoff from agricultural land than from forested areas. Some of this DIN is removed from the water as it moves through aquifers, creeks, rivers, and wetlands on its way to the sea, through the process of microbial denitrification. Denitrification involves the conversion of nitrate and nitrite (NOx-N) to dinitrogen (N2) gas, which is lost to the atmosphere. Denitrification requires NOx-N, organic matter, and low oxygen concentration. Wetlands provide these conditions, so DIN concentrations decline in water moving through them. Similarly, denitrifying bioreactors are designed to treat water by passing it through a porous organic material, typically woodchips. The woodchips provide organic matter for the microorganisms, which in turn lower the oxygen concentration, providing ideal conditions for denitrification. Denitrifying bioreactors are now widely used to remove the NOx-N component of DIN from agricultural runoff water elsewhere, but they have not yet been evaluated in the Wet Tropics. The Wet Tropics pose a challenge for efficacy due to the large volumes of water moving through the landscape. The objective of this project was “to establish the effectiveness of denitrifying bioreactors as a remediation technology for excess DIN in agricultural runoff within the Babinda Swamp Drainage Area (BSDA) of the Russell catchment”. The Russell River exports a disproportionate amount of DIN to the GBR lagoon because of the high rainfall and high proportion of agriculture, mostly sugarcane, in its catchment

Laser Feedback Interferometry as a Tool for Analysis of Granular Materials at Terahertz Frequencies: Towards Imaging and Identification of Plastic Explosives

We propose a self-consistent method for the analysis of granular materials at terahertz (THz) frequencies using a quantum cascade laser. The method is designed for signals acquired from a laser feedback interferometer, and applied to non-contact reflection-mode sensing. Our technique is demonstrated using three plastic explosives, achieving good agreement with reference measurements obtained by THz time-domain spectroscopy in transmission geometry. The technique described in this study is readily scalable: replacing a single laser with a small laser array, with individual lasers operating at different frequencies will enable unambiguous identification of select materials. This paves the way towards non-contact, reflection-mode analysis and identification of granular materials at THz frequencies using quantum cascade lasers

Optical feedback effects on terahertz quantum cascade lasers: modelling and applications

Terahertz (THz) quantum cascade lasers (QCLs) are compact sources of radiation in the 1–5 THz range with significant potential for applications in sensing and imaging. Laser feedback interferometry (LFI) with THz QCLs is a technique utilizing the sensitivity of the QCL to the radiation reflected back into the laser cavity from an external target. We will discuss modelling techniques and explore the applications of LFI in biological tissue imaging and will show that the confocal nature of the QCL in LFI systems, with their innate capacity for depth sectioning, makes them suitable for skin diagnostics with the well-known advantages of more conventional confocal microscopes. A demonstration of discrimination of neoplasia from healthy tissue using a THz, LFI-based system in the context of melanoma is presented using a transgenic mouse model. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Ribosomal S6 Kinase 2 (RSK2) Maintains Genomic Stability by Activating the Atm/p53-Dependent DNA Damage Pathway

10.1371/journal.pone.0074334PLoS ONE89-POLN

A Companion Cell–Dominant and Developmentally Regulated H3K4 Demethylase Controls Flowering Time in Arabidopsis via the Repression of FLC Expression

Flowering time relies on the integration of intrinsic developmental cues and environmental signals. FLC and its downstream target FT are key players in the floral transition in Arabidopsis. Here, we characterized the expression pattern and function of JMJ18, a novel JmjC domain-containing histone H3K4 demethylase gene in Arabidopsis. JMJ18 was dominantly expressed in companion cells; its temporal expression pattern was negatively and positively correlated with that of FLC and FT, respectively, during vegetative development. Mutations in JMJ18 resulted in a weak late-flowering phenotype, while JMJ18 overexpressors exhibited an obvious early-flowering phenotype. JMJ18 displayed demethylase activity toward H3K4me3 and H3K4me2, and bound FLC chromatin directly. The levels of H3K4me3 and H3K4me2 in chromatins of FLC clade genes and the expression of FLC clade genes were reduced, whereas FT expression was induced and the protein expression of FT increased in JMJ18 overexpressor lines. The early-flowering phenotype caused by the overexpression of JMJ18 was mainly dependent on the functional FT. Our findings suggest that the companion cell–dominant and developmentally regulated JMJ18 binds directly to the FLC locus, reducing the level of H3K4 methylation in FLC chromatin and repressing the expression of FLC, thereby promoting the expression of FT in companion cells to stimulate flowering

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field