Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

More than an offender location tool: Geographic profiling and body deposition

In homicide cases, it is difficult to provide resolution for the bereaved or to obtain a successful criminal conviction of the guilty party when no body is found. Since the mid-nineteenth century, geographic and environmental patterns have been used to better understand the relationship between crime and its environment. Now known as geographic profiling, practitioners in this field amalgamate criminological, psychological, and geographical knowledge, as well as aspects of mathematics, statistics, and physics to identify spatial patterns associated with criminal behaviour as a means of locating anchor points of an offender (where they live, or work). The same techniques can also be used to locate the covert body deposition sites of their victims. This paper aims to (1) provide a brief summary of criminal behaviour and the environment and how understanding their relationship can be helpful to geographic profiling, (2) amalgamate the available literature on the application of geographic profiling in locating clandestine graves (as most documented uses are to locate offender residences), and (3) include a geographic profile of Ivan Milat, an Australian serial killer (officially) active from 1989 to 1992, demonstrating how geographic profiling techniques can help to identify additional victims and potential body deposition sites. The information in this review will be helpful to law enforcement and practitioners to improve missing persons investigations and searches for clandestine graves.

Assessing Vehicle Profiling Accuracy of Handheld LiDAR Compared to Terrestrial Laser Scanning for Crash Scene Reconstruction

Forensic crash investigation often requires developing detailed profiles showing the location and extent of vehicle damage to identify impact areas, impact direction, deformation, and estimated vehicle speeds at impact. Traditional damage profiling techniques require extended and comprehensive setups for mapping and measurement that are quite labor- and time-intensive. Due to the time involved, this damage profiling is usually done in a remote holding area after the crash scene is cleared. Light detection and ranging (LiDAR) scanning technology in consumer handheld electronic devices, such as smartphones and tablets, holds significant potential for conducting this damage profile mapping in just a few minutes, allowing the mapping to be conducted at the scene before the vehicle(s) are moved. However, there is limited research and even scarcer published literature on field procedures and/or accuracy for these emerging smartphones and tablets with LiDAR. This paper proposes a methodology and subsequent measurement accuracy comparisons for survey-grade terrestrial laser scanning (TLS) and handheld alternatives. The maximum root mean square error (RMSE) obtained for profile distance between handheld (iPad) and survey-grade TLS LiDAR scans for a damaged vehicle was observed to be 3 cm, a level of accuracy that is likely sufficient and acceptable for most forensic studies.

Thermal Stress and Bleaching in the Cnidarian-Dinoflagellate Symbiosis: The Application of Metabolomics

<p>Reef-building corals form critical ecosystems, which provide a diverse range of goods and services. Their success is based on a complex symbiosis between cnidarian host, dinoflagellate algae (genus Symbiodinium) and associated microorganisms (together termed the holobiont). Under functional conditions nutrients are efficiently recycled within the holobiont; however, under conditions of thermal stress, this dynamic relationship can dysfunction, resulting in the loss of symbionts (bleaching). Mass coral bleaching associated with elevated temperatures is a major threat to the long-term persistence of coral reefs. Further study is therefore necessary in order to elucidate the cellular and metabolic networks associated with function in the symbiosis and to determine change elicited by exposure to thermal stress. Metabolomics is the study of small compounds (metabolites) in a cell, tissue or whole organism. The metabolome comprises thousands of components, which will respond rapidly to change, reflecting a combination of genotype, phenotype and the environment. As a result, the study of these metabolic networks serves as a sensitive tool for the detection and elucidation of cellular responses to abiotic stress in complex systems. This thesis presents outputs of gas chromatography-mass spectrometry-based metabolite profiling techniques, which have been applied to the study of thermal stress and bleaching in the cnidarian-dinoflagellate symbiosis. In Chapter 2 these techniques were developed and applied to the model symbiotic cnidarian Aiptasia sp., and its homologous symbiont (Symbiodinium ITS 2 type B1), to characterise both ambient and thermally-induced metabolite profiles (amino and non-amino organic acids) in both partners. Thermal stress, symbiont photodamage and associated bleaching, resulted in characteristic modifications to the free metabolite pools of both partners. These changes differed between partners and were associated with modifications to central metabolism, biosynthesis, catabolism of stores and homeostatic responses to thermal and oxidative stress. In Chapter 3 metabolite profiling techniques (focussing this time on carbohydrate pools) were once again applied to the study of thermally-induced changes to the free pools of the coral Acropora aspera and its symbionts (dominant Symbiodinium ITS 2 type C3) at differing stages of symbiont photodamage and thermal stress. Additionally, targeted analysis was employed to quantify these changes in terms of absolute amounts. Once again exposure to elevated temperatures resulted in symbiont photodamage, bleaching and characteristic modifications to the free metabolite pools of symbiont and host, which differed between partners and with the duration of thermal stress. These changes were associated with increased turnover of a number of networks including: energy-generating pathways, antioxidant networks, ROS-associated damage and damage signalling, and were also indicative of potential alterations to the composition of the associated microbial holobiont. Finally in Chapter 4, metabolite profiling techniques optimized in Chapter 2 and 3 were coupled to 13C labelling in both Aiptasia sp. and A. aspera, in order to further investigate the questions raised in these preceding studies. Once again changes were observed to central metabolism, biosynthesis and alternative energy-generation modes in symbiont and host, in both symbioses. Interestingly however, in all cases there was continued fixation of carbon, production- and translocation of mobile products by the remaining symbionts in hospite. This suggests that even during the later stages of bleaching, symbionts are, at least in part, metabolically functional in terms of photosynthate provision. This study therefore serves as an important first step in developing the application of metabolomics-based techniques to the study of thermal stress in the cnidarian-dinoflagellate symbiosis. The power of these techniques lies in the capacity to simultaneously assess rapid and often post-translational change in a highly repeatable and quantitative manner. With the use of these methods, this study has shown how metabolic, homeostatic and acclimatory networks interact to elicit change in each partner of the symbiosis during thermal stress and how these responses vary between symbiotic partners. Further understanding of these networks, individual sensitivities- and enhanced resistance to thermal stress are essential if we are to better understand the capacity of coral reefs to acclimate and persist in the face of climate change.</p>

Thermal Stress and Bleaching in the Cnidarian-Dinoflagellate Symbiosis: The Application of Metabolomics

<p>Reef-building corals form critical ecosystems, which provide a diverse range of goods and services. Their success is based on a complex symbiosis between cnidarian host, dinoflagellate algae (genus Symbiodinium) and associated microorganisms (together termed the holobiont). Under functional conditions nutrients are efficiently recycled within the holobiont; however, under conditions of thermal stress, this dynamic relationship can dysfunction, resulting in the loss of symbionts (bleaching). Mass coral bleaching associated with elevated temperatures is a major threat to the long-term persistence of coral reefs. Further study is therefore necessary in order to elucidate the cellular and metabolic networks associated with function in the symbiosis and to determine change elicited by exposure to thermal stress. Metabolomics is the study of small compounds (metabolites) in a cell, tissue or whole organism. The metabolome comprises thousands of components, which will respond rapidly to change, reflecting a combination of genotype, phenotype and the environment. As a result, the study of these metabolic networks serves as a sensitive tool for the detection and elucidation of cellular responses to abiotic stress in complex systems. This thesis presents outputs of gas chromatography-mass spectrometry-based metabolite profiling techniques, which have been applied to the study of thermal stress and bleaching in the cnidarian-dinoflagellate symbiosis. In Chapter 2 these techniques were developed and applied to the model symbiotic cnidarian Aiptasia sp., and its homologous symbiont (Symbiodinium ITS 2 type B1), to characterise both ambient and thermally-induced metabolite profiles (amino and non-amino organic acids) in both partners. Thermal stress, symbiont photodamage and associated bleaching, resulted in characteristic modifications to the free metabolite pools of both partners. These changes differed between partners and were associated with modifications to central metabolism, biosynthesis, catabolism of stores and homeostatic responses to thermal and oxidative stress. In Chapter 3 metabolite profiling techniques (focussing this time on carbohydrate pools) were once again applied to the study of thermally-induced changes to the free pools of the coral Acropora aspera and its symbionts (dominant Symbiodinium ITS 2 type C3) at differing stages of symbiont photodamage and thermal stress. Additionally, targeted analysis was employed to quantify these changes in terms of absolute amounts. Once again exposure to elevated temperatures resulted in symbiont photodamage, bleaching and characteristic modifications to the free metabolite pools of symbiont and host, which differed between partners and with the duration of thermal stress. These changes were associated with increased turnover of a number of networks including: energy-generating pathways, antioxidant networks, ROS-associated damage and damage signalling, and were also indicative of potential alterations to the composition of the associated microbial holobiont. Finally in Chapter 4, metabolite profiling techniques optimized in Chapter 2 and 3 were coupled to 13C labelling in both Aiptasia sp. and A. aspera, in order to further investigate the questions raised in these preceding studies. Once again changes were observed to central metabolism, biosynthesis and alternative energy-generation modes in symbiont and host, in both symbioses. Interestingly however, in all cases there was continued fixation of carbon, production- and translocation of mobile products by the remaining symbionts in hospite. This suggests that even during the later stages of bleaching, symbionts are, at least in part, metabolically functional in terms of photosynthate provision. This study therefore serves as an important first step in developing the application of metabolomics-based techniques to the study of thermal stress in the cnidarian-dinoflagellate symbiosis. The power of these techniques lies in the capacity to simultaneously assess rapid and often post-translational change in a highly repeatable and quantitative manner. With the use of these methods, this study has shown how metabolic, homeostatic and acclimatory networks interact to elicit change in each partner of the symbiosis during thermal stress and how these responses vary between symbiotic partners. Further understanding of these networks, individual sensitivities- and enhanced resistance to thermal stress are essential if we are to better understand the capacity of coral reefs to acclimate and persist in the face of climate change.</p>

A Magnetic Survey of the Southwest Pacific Ocean

<p>The design and construction of a free precession proton magnetometer which give a reading of the field directly in gamma is described. This instrument has been used to obtain magnetic profiles across the Southwest Pacific Ocean during the 1963-65 summer Antarctic supply cruises of H.M.N.Z.S. Endeavour. The magnetic and bathymetric profiler obtained on these cruises have been analysed to determine the nature and structure of the oceanic crust in this region. The region is divided into four divisions. (l) The New Zealand Plateau, with an almost continental crustal thickness. (2) The Southwest Pacific Basin, at a depth of 3,000 fathoms. (3) The Pacific-Antarctic Ridge, pert of the world encircling mind-ocean ridge system. (4) The Ross Sea, an epicontinental sea across the Antarctic continental shelf. Subtraction of the regional field form the magnetic results has enabled a regional field map of the area to be drawn. Comparison with earlier results indicates a westward drift of the earth's field of approximately 0.25 degrees /yr. Some discussion of regional anomalies (~ 100 miles period) has been given. Because of the excellent correlation of magnetic anomalies from track to track across the basin it has been possible to draw an anomaly contour map of this part. This map illustrates the predominantly east-west trend of features over the basin. To the north the features parallel the edge of the New Zealand Plateau. To the south the features swing more towards the Pacific-Antarctic Ridge. A major discontinuity is indicated along a direction 9 degrees E of S meeting the Plateau just southwest of Antipodes Islands. If this discontinuity is extrapolated south to the ridge it meets it at approximately 180 degrees E, where the ridge turns N-E towards Easter Island. Across the ridge the magnetic pattern shows three distinct regions. Over the northern flanks large anomalies are evident but the correlation of anomalies from track to track is very poor. Further south, across the upper flanks, the magnetic records are very much subdued. The extent of this region varies appreciably from track to track. Over the axis of the ridge large, steep-sided anomalies are obtained. These correlate well over part of the region studied. The southern flanks of the ridge are hidden by the Balleny Plateau which seems to form a link between Antarctica and the ridge in this region. The bathymetry records obtained indicate a step-type formation over the ridge. A narrow median valley appears to exist along the axis of the ridge. Some preliminary experimentation has been carried out with continual seismic profiling techniques over the region. The equipment that has been developed and the preliminary results obtained with it are discussed.</p>

A Magnetic Survey of the Southwest Pacific Ocean

<p>The design and construction of a free precession proton magnetometer which give a reading of the field directly in gamma is described. This instrument has been used to obtain magnetic profiles across the Southwest Pacific Ocean during the 1963-65 summer Antarctic supply cruises of H.M.N.Z.S. Endeavour. The magnetic and bathymetric profiler obtained on these cruises have been analysed to determine the nature and structure of the oceanic crust in this region. The region is divided into four divisions. (l) The New Zealand Plateau, with an almost continental crustal thickness. (2) The Southwest Pacific Basin, at a depth of 3,000 fathoms. (3) The Pacific-Antarctic Ridge, pert of the world encircling mind-ocean ridge system. (4) The Ross Sea, an epicontinental sea across the Antarctic continental shelf. Subtraction of the regional field form the magnetic results has enabled a regional field map of the area to be drawn. Comparison with earlier results indicates a westward drift of the earth's field of approximately 0.25 degrees /yr. Some discussion of regional anomalies (~ 100 miles period) has been given. Because of the excellent correlation of magnetic anomalies from track to track across the basin it has been possible to draw an anomaly contour map of this part. This map illustrates the predominantly east-west trend of features over the basin. To the north the features parallel the edge of the New Zealand Plateau. To the south the features swing more towards the Pacific-Antarctic Ridge. A major discontinuity is indicated along a direction 9 degrees E of S meeting the Plateau just southwest of Antipodes Islands. If this discontinuity is extrapolated south to the ridge it meets it at approximately 180 degrees E, where the ridge turns N-E towards Easter Island. Across the ridge the magnetic pattern shows three distinct regions. Over the northern flanks large anomalies are evident but the correlation of anomalies from track to track is very poor. Further south, across the upper flanks, the magnetic records are very much subdued. The extent of this region varies appreciably from track to track. Over the axis of the ridge large, steep-sided anomalies are obtained. These correlate well over part of the region studied. The southern flanks of the ridge are hidden by the Balleny Plateau which seems to form a link between Antarctica and the ridge in this region. The bathymetry records obtained indicate a step-type formation over the ridge. A narrow median valley appears to exist along the axis of the ridge. Some preliminary experimentation has been carried out with continual seismic profiling techniques over the region. The equipment that has been developed and the preliminary results obtained with it are discussed.</p>

How to use Fibonacci numbers to teach recursive programming

There are too many examples and programming guides (which, e.g., an internet search for "recursive procedure Fibonacci" will turn up) to count that use Fibonacci numbers as an example to illustrate recursive programming. The motivation for this article is to show why the naive way of doing this is a bad idea, as it is horrendously inefficient. We will exhibit much more efficient ways of computing Fibonacci numbers, both iterative and recursive, and analyze and compare worst case running times and memory usages. Using some mathematical properties of Fibonacci numbers leads to the most efficient method for their computation. For illustration and benchmarking, we will use Maple and its programming language, however, similar behaviour can be demonstrated in almost any other programming language. This exposition combines and explores the mathematical properties of Fibonacci numbers, notions of algorithmic complexity, and efficient Maple programming and profiling techniques, and may be used as an introduction to any of these three subjects. The techniques described can be readily generalized to more general types of linear recurrences with constant coefficients.

Who Am I?

To enable targeted ads, companies profile Internet users, automatically inferring potential interests and demographics. While current profiling centers on users' web browsing data, smartphones and other devices with rich sensing capabilities portend profiling techniques that draw on methods from ubiquitous computing. Unfortunately, even existing profiling and ad-targeting practices remain opaque to users, engendering distrust, resignation, and privacy concerns. We hypothesized that making profiling visible at the time and place it occurs might help users better understand and engage with automatically constructed profiles. To this end, we built a technology probe that surfaces the incremental construction of user profiles from both web browsing and activities in the physical world. The probe explores transparency and control of profile construction in real time. We conducted a two-week field deployment of this probe with 25 participants. We found that increasing the visibility of profiling helped participants anticipate how certain actions can trigger specific ads. Participants' desired engagement with their profile differed in part based on their overall attitudes toward ads. Furthermore, participants expected algorithms would automatically determine when an inference was inaccurate, no longer relevant, or off-limits. Current techniques typically do not do this. Overall, our findings suggest that leveraging opportunistic moments within pervasive computing to engage users with their own inferred profiles can create more trustworthy and positive experiences with targeted ads.