Developing a nationally appropriate mitigation measure from the greenhouse gas abatement potential from livestock production in the Brazilian Cerrado.

Brazil is one of the first major developing countries to commit to a national greenhouse gas (GHG) emissions target that requires a reduction of between 36.1% and 38.9% relative to baseline emissions by 2020. The country intends to submit to agricultural emissions reductions as part of this target with livestock production identified as offering significant abatement potentia

Identification of hypertensive patients with dominant affective temperaments might improve the psychopathological and cardiovascular risk stratification: a pilot, case-control study.

BACKGROUND: Although mood disorders and cardiovascular diseases have widely studied psychosomatic connections, data concerning the influence of the psychopathologically important affective temperaments in hypertension are scarce. To define a possibly higher cardiovascular risk subpopulation we investigated in well-treated hypertensive patients with dominant affective temperaments (DOM) and in well-treated hypertensive patients without dominant temperaments the level of depression and anxiety, arterial stiffness and serum Brain-derived Neurotrophic Factor (seBDNF). METHODS: 175 hypertensive patients, free of the history of psychiatric diseases, completed the TEMPS-A, Beck Depression Inventory and Hamilton Anxiety Scale questionnaires in two primary care practices. Of those 175 patients, 24 DOM patients and 24 hypertensive controls (matched in age, sex and the presence of diabetes) were selected for measurements of arterial stiffness and seBDNF level. RESULTS: Beck and Hamilton scores in DOM patients were higher compared with controls. Pulse wave velocity and augmentation index did not differ between the groups while in the DOM patients decreased brachial systolic and diastolic and central diastolic blood pressures were found compared with controls. SeBDNF was lower in the DOM group than in the controls (22.4 +/- 7.2 vs. 27.3 +/- 7.8 ng/mL, p < 0.05). CONCLUSIONS: Although similar arterial stiffness parameters were found in DOM patients, their increased depression and anxiety scores, the decreased brachial and central diastolic blood pressures as well as the decreased seBDNF might refer to their higher vulnerability regarding the development not only of major mood disorders, but also of cardiovascular complications. These data suggest that the evaluation of affective temperaments should get more attention both with regard to psychopathology and cardiovascular health management

Fitness Consequences of Advanced Ancestral Age over Three Generations in Humans

A rapid rise in age at parenthood in contemporary societies has increased interest in reports of higher prevalence of de novo mutations and health problems in individuals with older fathers, but the fitness consequences of such age effects over several generations remain untested. Here, we use extensive pedigree data on seven pre-industrial Finnish populations to show how the ages of ancestors for up to three generations are associated with fitness traits. Individuals whose fathers, grandfathers and great-grandfathers fathered their lineage on average under age 30 were ~13% more likely to survive to adulthood than those whose ancestors fathered their lineage at over 40 years. In addition, females had a lower probability of marriage if their male ancestors were older. These findings are consistent with an increase of the number of accumulated de novo mutations with male age, suggesting that deleterious mutations acquired from recent ancestors may be a substantial burden to fitness in humans. However, possible non-mutational explanations for the observed associations are also discussed

Grand challenges in sustainable intensification and ecosystem services

Arguably the greatest grand challenge for humankind is to keep the biosphere within its safe and just operating space, providing sufficient resources to meet people’s needs without exceeding the Earth’s capacity to supply them (Raworth, 2012). “Safe” is defined in terms of keeping planetary environmental processes, through mechanisms such as climate regulation and improved nutrient cycles, within limits over the long term (Rockstrom et al., 2009). “Just” is increasingly being interpreted in terms of meeting the UN Sustainable Development Goals, with targets addressing various forms of equity as well as biophysical needs (Griggs et al., 2013). Keeping the biosphere within the operating space requires that we produce the food we need, along with the ecosystem and socioeconomic goods and services we require (Garnett et al., 2013). By definition, achieving this challenge also means achieving the sustainable intensification (SI) of agriculture, whereby more food is produced from the same area of land (or water), with reduced or reversed negative environmental impacts accompanied by a range of positive societal and environmental co-benefits. SI is variously considered as a goal (Royal Society, 2009), a process (Firbank et al., 2013), a trade-off between economic production activity and ecological performance (Gadanakis et al., 2015), or a suite of interventions (Godfray and Garnett, 2014)

The potential for an agroecological approach in Scotland: policy brief

Agroecology is receiving increasing attention for its potential to reconcile environmental, sustainability and food production goals, through restoring the health of agricultural ecosystems and increasing the resilience of farms to future challenges. This study examined five different agroecological approaches that are currently practiced in Scotland to determine their potential to support the delivery of policy targets relating to climate change, biodiversity, and food production

A nitrogen budget for Scotland

UKCEH report to SEPA. The aim of this study was to quantify key nitrogen flows for Scotland, bringing together the most recent available data for soils, water, air and human consumption/production (with an emphasis on agriculture, nutrition and waste). Losses of N to water (132 kt N yr-1), air (80 kt N yr-1) and terrestrial systems (90 kt N through atmospheric deposition) estimated here are substantial, and these are mainly due to agricultural activities and, to a smaller extent, waste recycling/processing. Improved nutrient use efficiency is critical for delivering both environmental and economic benefits. However, further work is required to complete currently unquantified and uncertain flows and provide more detail on key activities, to enable the development of policy options, in conjunction with SEPA’s Sector Plans

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

Background The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. Findings High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. Conclusions This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture

Report on developing bottom-up Marginal Abatement Cost Curves (MACCS) for representative farm types.

bitstream/item/177181/1/D11.2-Report-on-developing-bottom-up-MACCs-for-representative-farm-types-0263D69D-63D3-4EA3-A333-EDA004AFDFCB1.pd

The quail genome:insights into social behaviour, seasonal biology and infectious disease response

Background: The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Results: We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. Conclusions: We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species

Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human

Background: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences. Results: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences. Conclusions: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics