Farmers in low-elevation coastal zones in South Asia face numerous food security and environmental sustainability challenges. This study evaluated the effects of nitrogen (N) rate and source on the agronomic, economic, and environmental performance of transplanted and rainfed 'aman' (monsoon-season) rice in Bangladesh's non-saline coastal areas. Fifty-one farmers participated in trials distributed across two landscape positions described as 'highlands' (on which field water inundation depth typically remains <30 cm) and 'medium-highlands' (inundation depths 30-90 cm) planted singly with varieties appropriate to each position (BRRI dhan 39 for highlands and the traditional variety Bhushiara for medium-highlands). Researcher designed but farmer-managed dispersed plots were located across three district sub-units (Barisal Sadar, Hizla, Mehendigonj) and compared N source (broadcast prilled urea or deep-placed urea super granules (USG)) at four N rates. Rice grown on medium-highlands did not respond to increasing N rates beyond 28 kg N ha^-1, indicating that little fertilization is required to maintain yields and profitability while limiting environmental externalities. In highland locations, clear trade-offs between agronomic and environmental goals were observed. To increase yields and profits for BRRI dhan 39, 50 or 75 kg N ha^-1 was often needed, although these rates were associated with declining energy and increasing greenhouse gas (GHG) efficiencies. Compared to prilled urea, USG had no impact on yield, economic, energy and GHG efficiencies in medium-highland locations. USG conversely led to 4.2-5.8% yield improvements at higher N rates on highlands, while also increasing energy efficiency. Given the observed yield, agronomic and economic benefit of USG, our preliminary results that farmers can consider use of USG at 50 kg N ha^-1 to produce yields equivalent to 75 kg N ha^-1 of prilled urea in highland landscapes, while also reducing environmental externalities. These results suggest that when assessing sustainable intensification (SI) strategies for rice in South Asia's coastal zones, N requirements should be evaluated within specific production contexts (e.g. cultivar type within landscape position) to identify options for increasing yields without negatively influencing environmental and economic indicators. Similar studies in other parts of coastal South Asia could help policy-makers prioritize investments in agriculture with the aim of improving rice productivity while also considering income generation and environmental outcomes.

Diversification of smallholder rice-based cropping systems has the potential to increase cropping system intensity and boost food security. However, impacts on resource use efficiencies (e.g., nutrients, energy, and labor) remain poorly understood, highlighting the need to quantify synergies and trade-offs among different sustainability indicators under on-farm conditions. In southern coastal Bangladesh, aman season rice is characterized by low inputs and low productivity. We evaluated the farm-level impacts of cropping system intensification (adding irrigated boro season rice) and diversification (adding chili, groundnut, mungbean, or lathyrus) on seven performance indicators (rice equivalent yield, energy efficiency, partial nitrogen productivity, partial potassium productivity, partial greenhouse gas footprint, benefit-cost ratio, and hired labor energy productivity) based on a comprehensive survey of 501 households. Indicators were combined into a multi-criteria performance index, and their scope for improvement was calculated by comparing an individual farmer's performance to top-performing farmers (highest 20%). Results indicate that the baseline system (single-crop aman season rice) was the least productive, while double cropped systems increased rice equivalent yield 72-217%. Despite gains in productivity, higher cropping intensity reduced resource use efficiencies due to higher inputs of fertilizer and energy, which also increased production costs, particularly for boro season rice. However, trade-offs were smaller for diversified systems including legumes, largely owing to lower N fertilizer inputs. Aman season rice had the highest multi-criteria performance index, followed by systems with mungbean and lathyrus, indicating the latter are promising options to boost food production and profitability without compromising sustainability. Large gaps between individual and top-performing farmers existed for each indicator, suggesting significant scope for improvement. By targeting indicators contributing most to the multi-criteria performance index (partial nitrogen productivity, energy efficiency, hired labor energy productivity), results suggest further sustainability gains can be achieved through future field research studies focused on optimizing management within diversified systems.

Supplementary information

The online version contains supplementary material available at 10.1007/s13593-022-00795-3.

Large changes have taken place in smallholder farming systems in South Asia's coastal areas in recent decades, particularly related to cropping intensity, input availability, climate risks, and off-farm activities. However, few studies have investigated the extent to which these changes have impacted farm-level crop productivity, which is a key driver of food security and poverty in rainfed, low-input, rice-based systems. The objective of this study was to conduct an integrated assessment of variables related to socioeconomic status, farm characteristics, and crop management practices to understand the major factors influencing crop productivity and identify promising leverage points for sustainable development in coastal Bangladesh. Using a panel survey dataset of 32 variables from 502 farm households located within polder (coastal embankment) and outside polder systems during 2005-2015, we employed statistical factor analysis to characterize five independent latent factors named here as Farming Challenges, Economic Status, Crop Management Practices, Asset Endowment, and Farm Characteristics. The factor Farming Challenges explained the most variation among households (31%), with decreases observed over time, specifically households located outside polders. Individual variables contributing to this factor included perceived cyclone severity, household distance to main roads and input-output markets, cropping intensity, and access to extension services. The most important factors for increasing crop productivity on a household and per unit area basis were Asset Endowment and Crop Management Practices, respectively. The former highlights the need for increasing gross cropped area, which can be achieved through greater cropping intensity, while the latter was associated with increased fertilizer, labor, and pesticide input use. Despite the importance of these factors, household poverty trajectory maps showed that changes in off-farm income had played the strongest role in improving livelihoods in this coastal area. This study can help inform development efforts and policies for boosting farm-level crop productivity, specifically through agricultural intensification (higher cropping intensity combined with appropriate and efficient use of inputs) and expanding opportunities for off-farm income as key pathways to bring smallholder households out of poverty.

Objective

This study utilized Next Generation Sequencing (NGS) to identify differentially expressed transcripts in orbital adipose tissue from patients with active Thyroid Eye Disease (TED) versus healthy controls.

Method

This prospective, case-control study enrolled three patients with severe, active thyroid eye disease undergoing orbital decompression, and three healthy controls undergoing routine eyelid surgery with removal of orbital fat. RNA Sequencing (RNA-Seq) was performed on freshly obtained orbital adipose tissue from study patients to analyze the transcriptome. Bioinformatics analysis was performed to determine pathways and processes enriched for the differential expression profile. Quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) was performed to validate the differential expression of selected genes identified by RNA-Seq.

Results

RNA-Seq identified 328 differentially expressed genes associated with active thyroid eye disease, many of which were responsible for mediating inflammation, cytokine signaling, adipogenesis, IGF-1 signaling, and glycosaminoglycan binding. The IL-5 and chemokine signaling pathways were highly enriched, and very-low-density-lipoprotein receptor activity and statin medications were implicated as having a potential role in TED.

Conclusion

This study is the first to use RNA-Seq technology to elucidate differential gene expression associated with active, severe TED. This study suggests a transcriptional basis for the role of statins in modulating differentially expressed genes that mediate the pathogenesis of thyroid eye disease. Furthermore, the identification of genes with altered levels of expression in active, severe TED may inform the molecular pathways central to this clinical phenotype and guide the development of novel therapeutic agents.

Late-onset retinal degeneration (L-ORD) is an autosomal dominant macular degeneration characterized by the formation of sub-retinal pigment epithelium (RPE) deposits and neuroretinal atrophy. L-ORD results from mutations in the C1q-tumor necrosis factor-5 protein (CTRP5), encoded by the CTRP5/C1QTNF5 gene. To understand the mechanism underlying L-ORD pathology, we used a human cDNA library yeast two-hybrid screen to identify interacting partners of CTRP5. Additionally, we analyzed the Bruch's membrane/choroid (BM-Ch) from wild-type (Wt), heterozygous S163R Ctrp5 mutation knock-in (Ctrp5^S163R/wt ), and homozygous knock-in (Ctrp5^S163R/S163R ) mice using mass spectrometry. Both approaches showed an association between CTRP5 and HTRA1 via its C-terminal PDZ-binding motif, stimulation of the HTRA1 protease activity by CTRP5, and CTRP5 serving as an HTRA1 substrate. The S163R-CTRP5 protein also binds to HTRA1 but is resistant to HTRA1-mediated cleavage. Immunohistochemistry and proteomic analysis showed significant accumulation of CTRP5 and HTRA1 in BM-Ch of Ctrp5^S163R/S163R and Ctrp5^S163R/wt mice compared with Wt. Additional extracellular matrix (ECM) components that are HTRA1 substrates also accumulated in these mice. These results implicate HTRA1 and its interaction with CTRP5 in L-ORD pathology.

Late-onset retinal degeneration (L-ORD) is an autosomal dominant macular degeneration characterized by the formation of sub-retinal pigment epithelium (RPE) deposits and neuroretinal atrophy. L-ORD results from mutations in the C1q-tumor necrosis factor-5 protein (CTRP5), encoded by the CTRP5/C1QTNF5 gene. To understand the mechanism underlying L-ORD pathology, we used a human cDNA library yeast two-hybrid screen to identify interacting partners of CTRP5. Additionally, we analyzed the Bruch's membrane/choroid (BM-Ch) from wild-type (Wt), heterozygous S163R Ctrp5 mutation knock-in (Ctrp5^S163R/wt ), and homozygous knock-in (Ctrp5^S163R/S163R ) mice using mass spectrometry. Both approaches showed an association between CTRP5 and HTRA1 via its C-terminal PDZ-binding motif, stimulation of the HTRA1 protease activity by CTRP5, and CTRP5 serving as an HTRA1 substrate. The S163R-CTRP5 protein also binds to HTRA1 but is resistant to HTRA1-mediated cleavage. Immunohistochemistry and proteomic analysis showed significant accumulation of CTRP5 and HTRA1 in BM-Ch of Ctrp5^S163R/S163R and Ctrp5^S163R/wt mice compared with Wt. Additional extracellular matrix (ECM) components that are HTRA1 substrates also accumulated in these mice. These results implicate HTRA1 and its interaction with CTRP5 in L-ORD pathology.

In the most productive area of the Indo-Gangetic Plains in Northwest India where high yields of rice and wheat are commonplace, a medium-term cropping system trial was conducted in Haryana State. The goal of the study was to identify integrated management options for further improving productivity and profitability while rationalizing resource use and reducing environmental externalities (i.e., "sustainable intensification", SI) by drawing on the principles of diversification, precision management, and conservation agriculture. Four scenarios were evaluated: Scenario 1 - "business-as-usual" [conventional puddled transplanted rice (PTR) followed by (fb) conventional-till wheat]; Scenario 2 - reduced tillage with opportunistic diversification and precision resource management [PTR fb zero-till (ZT) wheat fb ZT mungbean]; Scenario 3 - ZT for all crops with opportunistic diversification and precision resource management [ZT direct-seeded rice (ZT-DSR) fb ZT wheat fb ZT mungbean]; and Scenario 4 - ZT for all crops with strategic diversification and precision resource management [ZT maize fb ZT wheat fb ZT mungbean]. Results of this five-year study strongly suggest that, compared with business-as-usual practices, SI strategies that incorporate multi-objective yield, economic, and environmental criteria can be more productive when used in these production environments. For Scenarios 2, 3, and 4, system-level increases in productivity (10-17%) and profitability (24-50%) were observed while using less irrigation water (15-71% reduction) and energy (17-47% reduction), leading to 15-30% lower global warming potential (GWP), with the ranges reflecting the implications of specific innovations. Scenario 3, where early wheat sowing was combined with ZT along with no puddling during the rice phase, resulted in a 13% gain in wheat yield compared with Scenario 2. A similar gain in wheat yield was observed in Scenario 4 vis-à-vis Scenario 2. Compared to Scenario 1, wheat yields in Scenarios 3 and 4 were 15-17% higher, whereas, in Scenario 2, yield was either similar in normal years or higher in warmer years. During the rainy (kharif) season, ZT-DSR provided yields similar to or higher than those of PTR in the first three years and lower (11-30%) in Years 4 and 5, a result that provides a note of caution for interpreting technology performance through short-term trials or simply averaging results over several years. The resource use and economic and environmental advantages of DSR were more stable through time, including reductions in irrigation water (22-40%), production cost (11-17%), energy inputs (13-34%), and total GWP (14-32%). The integration of "best practices" in PTR in Scenario 2 resulted in reductions of 24% in irrigation water and 21% in GWP, with a positive impact on yield (0.9 t/ha) and profitability compared to conventional PTR, demonstrating the power of simple management changes to generate improved SI outcomes. When ZT maize was used as a diversification option instead of rice in Scenario 4, reductions in resource use jumped to 82-89% for irrigation water and 49-66% for energy inputs, with 13-40% lower GWP, similar or higher rice equivalent yield, and higher profitability (27-73%) in comparison to the rice-based scenarios. Despite these advantages, maize value chains are not robust in this part of India and public procurement is absent. Results do demonstrate that transformative opportunities exist to break the cycle of stagnating yields and inefficient resource use in the most productive cereal-based cropping systems of South Asia. However, these SI entry points need to be placed in the context of the major drivers of change in the region, including market conditions, risks, and declining labor availability, and matching with the needs and interests of different types of farmers.

South Asian countries will have to double their food production by 2050 while using resources more efficiently and minimizing environmental problems. Transformative management approaches and technology solutions will be required in the major grain-producing areas that provide the basis for future food and nutrition security. This study was conducted in four locations representing major food production systems of densely populated regions of South Asia. Novel production-scale research platforms were established to assess and optimize three futuristic cropping systems and management scenarios (S2, S3, S4) in comparison with current management (S1). With best agronomic management practices (BMPs), including conservation agriculture (CA) and cropping system diversification, the productivity of rice- and wheat-based cropping systems of South Asia increased substantially, whereas the global warming potential intensity (GWPi) decreased. Positive economic returns and less use of water, labor, nitrogen, and fossil fuel energy per unit food produced were achieved. In comparison with S1, S4, in which BMPs, CA and crop diversification were implemented in the most integrated manner, achieved 54% higher grain energy yield with a 104% increase in economic returns, 35% lower total water input, and a 43% lower GWPi. Conservation agriculture practices were most suitable for intensifying as well as diversifying wheat-rice rotations, but less so for rice-rice systems. This finding also highlights the need for characterizing areas suitable for CA and subsequent technology targeting. A comprehensive baseline dataset generated in this study will allow the prediction of extending benefits to a larger scale.