A sweet deal? Sugarcane, water and agricultural transformation in Sub-Saharan Africa

Globally, the area of sugarcane is rising rapidly in response to growing demands for bioethanol and increased sugar demand for human consumption. Despite considerable diversity in production systems and contexts, sugarcane is a particularly “high impact” crop with significant positive and negative environmental and socio-economic impacts. Our analysis is focused on Sub-Saharan Africa (SSA), which is a critical region for continued expansion, due to its high production potential, low cost of production and proximity, and access, to European markets. Drawing on a systematic review of scientific evidence, combined with information from key informants, stakeholders and a research-industry workshop, we critically assess the impacts of sugarcane development on water, soil and air quality, employment, food security and human health. Our analysis shows that sugarcane production is, in general, neither explicitly good nor bad, sustainable nor unsustainable. The impacts of expansion of sugarcane production on the environment and society depend on the global political economy of sugar, local context, quality of scheme, nature of the production system and farm management. Despite threats from climate change and forthcoming changes in the trade relationship with the European Union, agricultural development policies are driving national and international interest and investment in sugarcane in SSA, with expansion likely to play an important role in sustainable development in the region. Our findings will help guide researchers and policy makers with new insights in understanding the situated environmental and social impacts associated with alternative sugar economy models, production technologies and qualities of management

Promotion of testa rupture during garden cress germination involves seed compartment-specific expression and activity of pectin methylesterases

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination

Empirical validation of the InVEST water yield ecosystem service model at a national scale

A variety of tools have emerged with the goal of mapping the current delivery of ecosystem services and quantifying the impact of environmental changes. An important and often overlooked question is how accurate the outputs of these models are in relation to empirical observations. In this paper we validate a hydrological ecosystem service model (InVEST Water Yield Model) using widely available data. We modelled annual water yield in 22 UK catchments with widely varying land cover, population and geology, and compared model outputs with gauged river flow data from the UK National River Flow Archive. Values for input parameters were selected from existing literature to reflect conditions in the UK and were subjected to sensitivity analyses. We also compared model performance between precipitation and potential evapotranspiration data sourced from global- and UK-scale datasets. We then tested the transferability of the results within the UK by additional validation in a further 20 catchments. Whilst the model performed only moderately with global-scale data (linear regression of modelled total water yield against empirical data; slope = 0.763, intercept = 54.45, R2 = 0.963) with wide variation in performance between catchments, the model performed much better when using UK-scale input data, with closer fit to the observed data (slope = 1.07, intercept = 3.07, R2 = 0.990). With UK data the majority of catchments showed less than 10% difference between measured and modelled water yield but there was a minor but consistent overestimate per hectare (86 m3/ha/year). Additional validation on a further 20 UK catchments was similarly robust, indicating that these results are transferable within the UK. These results suggest that relatively simple models can give accurate measures of ecosystem services. However, the choice of input data is critical and there is a need for further validation in other parts of the worl

The SPTPoL extended cluster survey

We describe the observations and resultant galaxy cluster catalog from the 2770 deg2 SPTpol Extended Cluster Survey (SPT-ECS). Clusters are identified via the Sunyaev-Zel'dovich (SZ) effect and confirmed with a combination of archival and targeted follow-up data, making particular use of data from the Dark Energy Survey (DES). With incomplete follow-up we have confirmed as clusters 244 of 266 candidates at a detection significance ξ ≥ 5 and an additional 204 systems at 4 4 threshold, and 10% of their measured SZ flux. We associate SZ-selected clusters, from both SPT-ECS and the SPT-SZ survey, with clusters from the DES redMaPPer sample, and we find an offset distribution between the SZ center and central galaxy in general agreement with previous work, though with a larger fraction of clusters with significant offsets. Adopting a fixed Planck-like cosmology, we measure the optical richness-SZ mass (l - M) relation and find it to be 28% shallower than that from a weak-lensing analysis of the DES data-a difference significant at the 4σ level-with the relations intersecting at λ = 60. The SPT-ECS cluster sample will be particularly useful for studying the evolution of massive clusters and, in combination with DES lensing observations and the SPT-SZ cluster sample, will be an important component of future cosmological analyses

The status of the world's land and marine mammals: diversity, threat, and knowledge

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Detection of CMB-cluster lensing using polarization data from SPTpol

We report the first detection of gravitational lensing due to galaxy clusters using only the polarization of the cosmic microwave background (CMB). The lensing signal is obtained using a new estimator that extracts the lensing dipole signature from stacked images formed by rotating the cluster-centered Stokes Q U map cutouts along the direction of the locally measured background CMB polarization gradient. Using data from the SPTpol 500     deg 2 survey at the locations of roughly 18 000 clusters with richness λ ≥ 10 from the Dark Energy Survey (DES) Year-3 full galaxy cluster catalog, we detect lensing at 4.8 σ . The mean stacked mass of the selected sample is found to be ( 1.43 ± 0.40 ) × 10 14 M ⊙ which is in good agreement with optical weak lensing based estimates using DES data and CMB-lensing based estimates using SPTpol temperature data. This measurement is a key first step for cluster cosmology with future low-noise CMB surveys, like CMB-S4, for which CMB polarization will be the primary channel for cluster lensing measurements

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism