Multi-experiment assessment of soil nitrous oxide emissions in sugarcane

Soil nitrous oxide (N 2O) fluxes comprise a significant part of the greenhouse gas emissions of agricultural products but are spatially and tempo-rally variable, due to complex interactions between climate, soil and management variables. This study aimed to identify the main factors that affect N2Oemissions under sugarcane, using a multi-site data-base from field experiments. Greenhouse gas fluxes, soil, climate, and management data were obtained from 13 field trials spanning the 2011–2017 period. We conducted exploratory, descriptive and inferential data analyses in experiments with varying fertiliser and stillage (vinasse) type and rate, and crop residue rates. The most relevant period of high N2O fluxes was the first 46 days after fertiliser application. The results indicate a strong positive correlation of cumulative N2O with nitrogen (N) fertiliser rate, soil fungi community (18S rRNA gene), soil ammonium(NH 4+ ) and nitrate (NO3−); and a moderate negative correlation with amoA genes of ammonia-oxidising archaea (AOA) and soil organic matter content. The regression analysis revealed that easily routinely measured climate and management-related variables explained over 50% of the variation in cumulativeN2O emissions, and that additional soil chemical and physical parameters improved the regression fit within R2 = 0.65. Cross-wavelet analysis indicated significant correlations of N2O fluxes with rainfall and air temperature up to 64 days, associated with temporal lags of 2 to 4 days in some experiments, and presenting a good environmental control over fluxes in general. The nitrogen fertiliser mean emission factors ranged from 0.03 to 1.17% of N applied, with urea and ammonium nitrate plus vinasse producing high emissions, while ammonium sulphate, ammonium nitrate without vinasse, calcium nitrate, and mitigation alternatives (nitrification inhibitors and timing of vinasse application) producing low N2O-EFs. Measurements from multiple sites spanning several crop-ping seasons were useful for exploring the influence of environmental and management-related variables on soil N 2O emissions in sugarcane production, providing support for global warming mitigation strategies, nitrogen management policies, and increased agricultural input efficiency

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Sexual reproduction allows transposable elements (TEs) to proliferate, leading to rapid divergence between populations and species. A significant outcome of divergence in the TE landscape is evident in hybrid dysgenic syndromes, a strong form of genomic incompatibility that can arise when (TE) family abundance differs between two parents. When TEs inherited from the father are absent in the mother's genome, TEs can become activated in the progeny, causing germline damage and sterility. Studies in Drosophila indicate that dysgenesis can occur when TEs inherited paternally are not matched with a pool of corresponding TE silencing PIWI-interacting RNAs (piRNAs) provisioned by the female germline. Using the D. virilis syndrome of hybrid dysgenesis as a model, we characterize the effects that divergence in TE profile between parents has on offspring. Overall, we show that divergence in the TE landscape is associated with persisting differences in germline TE expression when comparing genetically identical females of reciprocal crosses and these differences are transmitted to the next generation. Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic piRNA profile of the parents that arise though polymorphic TE insertions. Overall, these results support a model in which early germline events in dysgenesis establish a chronic, stable state of both TE and gene expression in the germline that is maintained through adulthood and transmitted to the next generation. This work demonstrates that divergence in the TE profile is associated with diverse piRNA-mediated transgenerational effects on gene expression within populations

A restatement of the natural science evidence base concerning grassland management, grazing livestock and soil carbon storage

Approximately a third of all annual greenhouse gas emissions globally are directly or indirectly associated with the food system, and over a half of these are linked to livestock production. In temperate oceanic regions, such as the UK, most meat and dairy is produced in extensive systems based on pasture. There is much interest in the extent to which such grassland may be able to sequester and store more carbon to partially or completely mitigate other greenhouse gas emissions in the system. However, answering this question is difficult due to context-specificity and a complex and sometimes inconsistent evidence base. This paper describes a project that set out to summarize the natural science evidence base relevant to grassland management, grazing livestock and soil carbon storage potential in as policy-neutral terms as possible. It is based on expert appraisal of a systematically assembled evidence base, followed by a wide stakeholders engagement. A series of evidence statements (in the appendix of this paper) are listed and categorized according to the nature of the underlying information, and an annotated bibliography is provided in the electronic supplementary material

Spatial and cell type transcriptional landscape of human cerebellar development

The human neonatal cerebellum is one-fourth of its adult size yet contains the blueprint required to integrate environmental cues with developing motor, cognitive and emotional skills into adulthood. Although mature cerebellar neuroanatomy is well studied, understanding of its developmental origins is limited. In this study, we systematically mapped the molecular, cellular and spatial composition of human fetal cerebellum by combining laser capture microscopy and SPLiT-seq single-nucleus transcriptomics. We profiled functionally distinct regions and gene expression dynamics within cell types and across development. The resulting cell atlas demonstrates that the molecular organization of the cerebellar anlage recapitulates cytoarchitecturally distinct regions and developmentally transient cell types that are distinct from the mouse cerebellum. By mapping genes dominant for pediatric and adult neurological disorders onto our dataset, we identify relevant cell types underlying disease mechanisms. These data provide a resource for probing the cellular basis of human cerebellar development and disease

Apolipoprotein E is a pancreatic extracellular factor that maintains mature β-cell gene expression.

The in vivo microenvironment of tissues provides myriad unique signals to cells. Thus, following isolation, many cell types change in culture, often preserving some but not all of their in vivo characteristics in culture. At least some of the in vivo microenvironment may be mimicked by providing specific cues to cultured cells. Here, we show that after isolation and during maintenance in culture, adherent rat islets reduce expression of key β-cell transcription factors necessary for β-cell function and that soluble pancreatic decellularized matrix (DCM) can enhance β-cell gene expression. Following chromatographic fractionation of pancreatic DCM, we performed proteomics to identify soluble factors that can maintain β-cell stability and function. We identified Apolipoprotein E (ApoE) as an extracellular protein that significantly increased the expression of key β-cell genes. The ApoE effect on beta cells was mediated at least in part through the JAK/STAT signaling pathway. Together, these results reveal a role for ApoE as an extracellular factor that can maintain the mature β-cell gene expression profile

What do changing weather and climate shocks and stresses mean for the UK food system?

In light of the publication of Henry Dimbleby’s National Food Strategy (www.nationalfoodstrategy. org/) and the COP26 climate meeting in Glasgow, it is timely to consider the impacts of weather and climate extremes on the UK food system. Climate change-driven changes in extreme weather events are one of the highest-risk future shocks to the UK food system [1], underlining the importance of preparedness across the food chain [2]. Here, we identify major knowledge gaps in the primary impacts of extreme weather and climate change across the UK’s food system, its functioning and their interactions to provide information to support adaptation and resilience planning. Research tends to focus on individual food system activities rather than taking a systematic approach [3, 4]. How- ever, strong evidence exists about the impacts of long- term climate trends and extremes [5] on primary food production [6]. The major knowledge gaps therefore concern post-primary production dimensions [4], notably food system activities between the ‘farm-gate’ and consumption—which are the core focus of this paper (supplementary material S1 available online at stacks.iop.org/ERL/17/051001/mmedia). These constitute major economic and social dimensions but are often the ‘missing middle’ in food system discus- sions. We use the UK food system as an illustrative case study, and consider both global and domestic risks and implications. We present methods, tools and frameworks for systemic analysis of climate impacts on food systems, consider the funding landscape, and highlight priorities for future research

Sink or source—The potential of coffee agroforestry systems to sequester atmospheric CO2 into soil organic carbon

Current carbon accounting methodologies often assume interactions between above-ground and below-ground carbon, without considering effects of land management. We used data from two long-term coffee agroforestry experiments in Costa Rica and Nicaragua to assess the effect on total soil organic carbon (SOC) stocks of (i) organic versus conventional management, (ii) higher versus moderate agronomic inputs, (iii) tree shade types. During the first nine years of coffee establishment total 0–40 cm depth SOC stocks decreased by 12.4% in Costa Rica and 0.13% in Nicaragua. Change in SOC differed consistently amongst soil layers: at 0–10 cm SOC stocks increased by 2.14 and 1.26 Mg C ha−1 in Costa Rica and Nicaragua respectively; however much greater reduction occurred at 20–40 cm (9.65 and 2.85 Mg C ha−1 respectively). Organic management caused a greater increase in 0–10 cm SOC but did not influence its reduction at depth. Effects of shade type were smaller, though heavily pruned legume shade trees produced a greater increase in 0–10 cm SOC than unpruned timber trees. No significant differences in SOC stocks were found between shaded and unshaded systems at any depth and SOC was poorly correlated with above-ground biomass stocks highlighting poor validity of “expansion factors” currently used to estimate SOC. SOC stock changes were significantly negatively correlated with initial SOC stock per plot, providing evidence that during establishment of these woody-plant-dominated agricultural systems SOC stocks tend to converge towards a new equilibrium as a function of the change in the quantity and distribution of organic inputs. Therefore it cannot be assumed that tree-based agricultural systems necessarily lead to increases in soil C stocks. While high inputs of organic fertiliser/tree pruning mulch increased surface-layer SOC stocks, this did not affect stocks in deeper soil, where decreases generally exceeded any gains in surface soil. Therefore site- and system-specific sampling is essential to draw meaningful conclusions for climate change mitigation strategies

HPV types and cofactors causing cervical cancer in Peru

We conducted a hospital-based case-control study in Peru of 198 women with histologically confirmed cervical cancer (173 squamous cell carcinomas and 25 cases of adenocarcinoma/adenosquamous carcinoma) and 196 control women. Information on risk factors was obtained by personal interview. Using PCR-based assays on exfoliated cervical cells and biopsy specimens, HPV DNA was detected in 95.3% of women with squamous cell carcinoma and in 92.0% of women with adenocarcinoma/adenosquamous carcinoma compared with 17.7% in control women. The age-adjusted odds ratio was 116.0 (95% Cl = 48.6–276.0) for squamous cell carcinoma and 51.4 (95% Cl = 11.4–232.0) for adenocarcinoma/adenosquamous carcinoma. The commonest types in women with cervical cancer were HPV 16, 18, 31, 52 and 35. The association with the various HPV types was equally strong for the two most common types (HPV 16 and 18) as for the other less common types. In addition to HPV, long-term use of oral contraceptives and smoking were associated with an increased risk. HPV is the main cause of both squamous cell carcinoma and adenocarcinoma in Peruvian women. © 2001 Cancer Research Campaignhttp://www.bjcancer.co