The mitochondrial calcium uniporter transports Ca 2+ via a ligand-relay mechanism.

The mitochondrial calcium uniporter (mtCU) is a multicomponent Ca 2+ -specific channel that imparts mitochondria with the capacity to sense the cytosolic calcium signals. The metazoan mtCU comprises the pore-forming subunit MCU and the essential regulator EMRE, arranged in a tetrameric channel complex, and the Ca 2+ sensing peripheral proteins MICU1-3. The mechanism of mitochondrial Ca 2+ uptake by mtCU and its regulation is poorly understood. Our analysis of MCU structure and sequence conservation, combined with molecular dynamics simulations, mutagenesis, and functional studies, led us to conclude that the Ca 2+ conductance of MCU is driven by a ligand-relay mechanism, which depends on stochastic structural fluctuations in the conserved DxxE sequence. In the tetrameric structure of MCU, the four glutamate side chains of DxxE (the E-ring) chelate Ca 2+ directly in a high-affinity complex (site 1), which blocks the channel. The four glutamates can also switch to a hydrogen bond-mediated interaction with an incoming hydrated Ca 2+ transiently sequestered within the D-ring of DxxE (site 2), thus releasing the Ca 2+ bound at site 1. This process depends critically on the structural flexibility of DxxE imparted by the adjacent invariant Pro residue. Our results suggest that the activity of the uniporter can be regulated through the modulation of local structural dynamics. A preliminary account of this work was presented at the 67 th Annual Meeting of the Biophysical Society in San Diego, CA, February 18-22, 2023.

Discovery and molecular basis of subtype-selective cyclophilin inhibitors.

Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC50) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.

Demand for Crop Insurance in Developing Countries: New Evidence from India.

Determining farmers' real demand for crop insurance is difficult, especially in developing countries, where there is a lack of formal financial sector integration and a high reliance on informal risk mitigation options. We provide some new estimates of farmers' willingness-to-pay for insurance in the context of a large-scale subsidised programme in India. We conducted a discrete choice experiment with agricultural households across four states in India, enabling us to estimate preferences for specific insurance policy attributes such as coverage period, method of loss assessment, timing of indemnity payments and the cost of insurance. Our results suggest that farmers do value crop insurance under certain conditions and some are willing to pay a premium for such coverage in excess of the subsidised rates they are currently required to pay under this programme. In particular, farmers value the assurances that they will receive timely payouts when they incur losses, and may not have a strong preference for the method with which losses are assessed. On the other hand, farmers are quite sensitive to coverage periods. Our baseline assessment shows that when optimised to farmer requirements, there can be a sizeable demand for crop insurance by developing country farmers.

MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations.

The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine.

Drought-tolerant rice, weather index insurance, and comprehensive risk management for smallholders: evidence from a multi-year field experiment in India.

In rainfed production systems throughout India, agricultural activities are dependent upon the summer monsoon, and any aberration in monsoon rainfall patterns can have severe consequences for rice production. There is considerable policy interest in designing programs to lower small-scale farmers' exposure to these types of risk given the regularity with which adverse monsoon events occur. This paper introduces a field experiment conducted with two risk management options in the state of Odisha: a drought-tolerant rice cultivar; and a weather index insurance product designed to complement the performance of the cultivar. Uptake rates for the cultivar itself and for the joint product are compared across two years alongside an analysis of factors that predict uptake. Results indicate high levels of demand for both the products, albeit with a significant degree of price sensitivity. But this sensitivity is agnostic to the nature of price reductions, suggesting that public investments that lower the costs of risk management may be sufficient to encourage broad uptake, without necessarily relying upon distortionary subsidies as is so often done. Sustained demand between years one and two is primarily explained where individuals were indemnified in year one and had a large number of peers also purchasing the product.

Do farmers value rice varieties tolerant to droughts and floods? Evidence from a discrete choice experiment in Odisha, India.

Abiotic stresses such as droughts and floods significantly constrain rice production in India. New stress tolerant technologies have the potential to reduce yield variability and help insulate farmers from the risks posed by these hazards. Using discrete choice experiments conducted in rural Odisha, we estimate farmers' valuation for drought-tolerant (DT) and submergence-tolerant (SubT) traits embodied in rice cultivars. Our results demonstrate that farmers in both drought-prone as well as submergence prone regions value reduction in yield variability offered by new, stress-tolerant cultivars, and would generally be willing to pay a significant premium for these traits. While virtually all farmers perceive the threat of drought and are willing to pay for protection against drought risk, only farmers in flood-prone areas would be willing to pay for rice that can withstand being submerged for prolonged periods, suggesting the potential for market segmentation along geographical or ecological lines.

Social dynamics of short term variability in key measures of household and community wellbeing in Bangladesh.

High-frequency social data collection may facilitate improved recall, more inclusive reporting, and improved capture of intra-period variability. Although there are examples of small studies collecting particular variables at high frequency in the social science literature, to date there have been no significant efforts to collect a wide range of variables with high frequency. We have implemented the first such effort with a smartphone-based data collection approach, systematically varying the frequency of survey task and recall period, allowing the analysis of the relative merit of high-frequency data collection for different key variables in household surveys. This study of 480 farmers from northwestern Bangladesh over approximately one year of continuous data on key measures of household and community wellbeing could be particularly useful for the design and evaluation of development interventions and policies. While the data discussed here provide a snapshot of what is possible, we also highlight their strength for providing opportunities for interdisciplinary research in the household agricultural production, practices, seasonal hunger, etc., in a low-income agrarian society.

Corrigendum to 'Can differences in individual learning explain patterns of technology adoption? Evidence on heterogeneous learning patterns and hybrid rice adoption in Bihar, India' [World Dev. 115 (2018) 178-189].

[This corrects the article DOI: 10.1016/j.worlddev.2018.11.014.].

Ex ante and ex post effects of hybrid index insurance in Bangladesh.

This study assesses both the demand for and effectiveness of an index insurance product designed to help smallholder farmers in Bangladesh manage crop production risk during the monsoon season. Villages were randomized into either an insurance treatment or a comparison group, and discounts and rebates were randomly allocated across treatment villages to encourage insurance take-up and to allow for the estimation of the price-elasticity of insurance demand. Among those offered insurance, we find demand to be fairly price elastic, with discounts significantly more successful in stimulating demand than rebates. Purchasing insurance yields both ex ante risk management effects as well as ex post income effects on agricultural production practices. The risk management effects lead to an expansion of cultivated area with concomitant increases in agricultural input expenditures during the monsoon season. The income effects lead to more intensive rice production during the subsequent dry season, with more intensive use of both irrigation and fertilizers, resulting in higher yields and higher total rice production.

Can differences in individual learning explain patterns of technology adoption? Evidence on heterogeneous learning patterns and hybrid rice adoption in Bihar, India.

Much empirical research that has shown that an individual's decision to adopt a new technology is the result of learning - both in personal experimentation as well as observing the experimentation of others. Yet even casual observation would suggest significant heterogeneity learning processes, manifesting itself in widely varying patterns of adoption over space and time. In this paper we explore this heterogeneity in the context of early adoption of hybrid rice in rural India. Using specially-designed experiments conducted as part of a primary survey in the field, we are able to identify which of four broad learning heuristics most accurately reflects individuals' information processing strategies. Linking these learning heuristics with observed use of rice hybrids, we demonstrate that pure Bayesian learning is well suited for the tinkering and marginal adjustments that would be required to learn about a technology like hybrid rice, but is also more cognitively taxing, requiring a longer memory and more complex updating processes. Consequently, only about 25 percent of the farmers in our sample can be characterized as pure Bayesian learners. Present-biased learning and relying on first impressions will likely hinder adoption of a technology like hybrid rice, even after controlling for access to credit and a rudimentary proxy for intelligence.

Evaluating producer preferences and information processing strategies for drought risk management tools in Bangladesh.

We use stated preference data to study farmers' preferences for two alternative strategies to manage drought risks in Bangladesh. A choice experiment on drought tolerant rice varieties and weather index insurance was administered to 2306 farmers. Two overarching preference classes or meso-groups were identified using an equality constrained latent class model, each containing various patterns of attribute non-attendance. Our analysis finds that farmers rely on information processing strategies to simplify risk management tool decisions to mitigate drought risk. Differences in the use of farm inputs, and access to savings mechanisms, both formal and informal, are shown to affect decision making.

Lack of evidence for substrate channeling or flux between wildtype and mutant isocitrate dehydrogenase to produce the oncometabolite 2-hydroxyglutarate.

Monoallelic point mutations in the gene encoding the cytosolic, NADP+-dependent enzyme isocitrate dehydrogenase 1 (IDH1) cause increased production of the oncometabolite 2-hydroxyglutarate (2-HG) in multiple cancers. Most IDH1 mutant tumors retain one wildtype (WT) IDH1 allele. Several studies have proposed that retention of this WT allele is protumorigenic by facilitating substrate channeling through a WT-mutant IDH1 heterodimer, with the WT subunit generating a local supply of α-ketoglutarate and NADPH that is then consumed by the mutant subunit to produce 2-HG. Here, we confirmed that coexpression of WT and mutant IDH1 subunits leads to formation of WT-mutant hetero-oligomers and increases 2-HG production. An analysis of a recently reported crystal structure of the WT-R132H IDH1 heterodimer and of in vitro kinetic parameters for 2-HG production, however, indicated that substrate channeling between the subunits is biophysically implausible. We also found that putative carbon-substrate flux between WT and mutant IDH1 subunits is inconsistent with the results of isotope tracing experiments in cancer cells harboring an endogenous monoallelic IDH1 mutation. Finally, using a mathematical model of WT-mutant IDH1 heterodimers, we estimated that the NADPH:NADP+ ratio is higher in the cytosol than in the mitochondria, suggesting that NADPH is unlikely to be limiting for 2-HG production in the cytosol. These findings argue against supply of either substrate being limiting for 2-HG production by a cytosolic IDH1 mutant and suggest that the retention of a WT allele in IDH1 mutant tumors is not due to a requirement for carbon or cofactor flux between WT and mutant IDH1.

Smart subsidies for catchment conservation in Malawi.

Conservation agriculture (CA) is a management paradigm in which soil is covered outside of cropping seasons, minimally disturbed, and recharged with nitrogen-fixing legumes. Finding effective ways to encourage CA is a centuries-old problem playing out acutely today in Sub-Saharan Africa. To better understand this issue, we have collected data on rural livelihoods and CA adoption during a two-year intervention in southern Malawi. The intervention evaluated rates of CA adoption under two different structures of payment and three levels of monitoring. The dataset includes a baseline and endline survey covering 1,900 households, along with surveys conducted with participants opting into the intervention. Baseline and endline questions included modules on farm-level inputs and production at the plot-crop level; plot characteristics; household composition and assets; savings, loans, and other sources of income; neighborhood characteristics; and perceptions regarding CA. Registration questionnaires in the intervention included detailed assessments of recent production in plots being registered to the intervention, and basic information for all other plots; and basic information on household structure and assets.

New modalities for managing drought risk in rainfed agriculture: Evidence from a discrete choice experiment in Odisha, India.

Droughts have historically had large impacts on agricultural production in rainfed agricultural systems. Scientists and policymakers have proposed various strategies for managing risks, with limited success. In this study we consider two such strategies, specifically drought tolerant rice and weather index insurance. While neither drought tolerant cultivars nor weather index insurance products are perfect solutions for adequately managing drought risk in and of themselves, there is scope to exploit the benefits of each and bundle them into a complementary risk management product, specifically through proper index calibration and an optimized insurance design. In this study, we explore preferences for such a complementary risk management product using discrete choice experiments in Odisha, India. We are able to estimate the added value that farmers perceive in the bundled product above and beyond the value associated with each of the independent products. We also show that valuations are very sensitive to the basis risk implied by the insurance product, with farmers less enthusiastic about risk management products that leave significant risks uninsured.

Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia.

Genomic studies in acute myeloid leukemias (AML) have identified mutations that drive altered DNA methylation, including TET2 and IDH2 Here, we show that models of AML resulting from TET2 or IDH2 mutations combined with FLT3ITD mutations are sensitive to 5-azacytidine or to the IDH2 inhibitor AG-221, respectively. 5-azacytidine and AG-221 treatment induced an attenuation of aberrant DNA methylation and transcriptional output and resulted in a reduction in leukemic blasts consistent with antileukemic activity. These therapeutic benefits were associated with restoration of leukemic cell differentiation, and the normalization of hematopoiesis was derived from mutant cells. By contrast, combining AG-221 or 5-azacytidine with FLT3 inhibition resulted in a reduction in mutant allele burden, progressive recovery of normal hematopoiesis from non-mutant stem-progenitor cells, and reversal of dysregulated DNA methylation and transcriptional output. Together, our studies suggest combined targeting of signaling and epigenetic pathways can increase therapeutic response in AML.Significance: AMLs with mutations in TET2 or IDH2 are sensitive to epigenetic therapy through inhibition of DNA methyltransferase activity by 5-azacytidine or inhibition of mutant IDH2 through AG-221. These inhibitors induce a differentiation response and can be used to inform mechanism-based combination therapy. Cancer Discov; 7(5); 494-505. ©2017 AACR.See related commentary by Thomas and Majeti, p. 459See related article by Yen et al., p. 478This article is highlighted in the In This Issue feature, p. 443.

Disaster risk, social vulnerability, and economic development.

This paper examines the extent to which economic development decreases a country's risk of experiencing climate-related disasters as well as the societal impacts of those events. The paper proceeds from the underlying assumption that disasters are not inherently natural, but arise from the intersection of naturally-occurring hazards within fragile environments. It uses data from the International Disaster Database (EM-DAT), representing country-year-level observations over the period 1980-2007. The study finds that low-income countries are significantly more at risk of climate-related disasters, even after controlling for exposure to climate hazards and other factors that may confound disaster reporting. Following the occurrence of a disaster, higher income generally diminishes a country's social vulnerability to such happenings, resulting in lower levels of mortality and morbidity. This implies that continued economic development may be a powerful tool for lessening social vulnerability to climate change.

Real-Time Social Data Collection in Rural Bangladesh via a 'Microtasks for Micropayments' Platform on Android Smartphones.

The advent of cheap smartphones in rural areas across the globe presents an opportunity to change the mode with which researchers engage hard-to-reach populations. In particular, smartphones allow researchers to connect with respondents more frequently than standard household surveys, opening a new window into important short-term variability in key measures of household and community wellbeing. In this paper, we present early results from a pilot study in rural Bangladesh using a 'microtasks for micropayments' model to collect a range of community and household living standards data using Android smartphones. We find that more frequent task repetition with shorter recall periods leads to more inclusive reporting, improved capture of intra-seasonal variability, and earlier signals of events such as illness. Payments in the form of mobile talk time and data provide a positive development externality in the form of expanded access to mobile internet and social networks. Taken to scale, programs such as this have potential to transform data collection in rural areas, providing near-real-time windows into the development of markets, the spread of illnesses, or the diffusion of ideas and innovations.

Transient poverty, poverty dynamics, and vulnerability to poverty: An empirical analysis using a balanced panel from rural China.

China's economic reforms starting in the late 1970s have resulted in rapid economic growth, with annual growth in gross domestic product averaging greater than 10 percent per year for more than thirty years. Accompanying this rapid growth in national accounts have been rapid and widespread reductions in poverty. With these reductions in poverty, however, there has often been observed an increase in income inequality, both between as well as within rural and urban sectors. This rising income gap challenges the notion that economic reforms in China have been as successful as the poverty statistics would suggest. In this paper, we suggest that an alternative view would be to consider the effects of these reforms on changing the chronic nature of poverty and reducing household vulnerability to poverty. Using a balanced panel from rural China from 1991 through 2006, we find that most poverty among our sample has shifted from being chronic in nature to being transient, with households either shifting into a state of being non-poor moving in and out of poverty. Among our sample, vulnerability to poverty has been declining over time, but the declines are not uniform over time or space. We decompose household vulnerability status into two proximate causes: low expected income and high income variability, finding vulnerability increasingly due to income variability. Additionally, we demonstrate that vulnerable households have very different characteristics than non-vulnerable households.

DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia.

Somatic mutations in IDH1/IDH2 and TET2 result in impaired TET2-mediated conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The observation that WT1 inactivating mutations anticorrelate with TET2/IDH1/IDH2 mutations in acute myeloid leukemia (AML) led us to hypothesize that WT1 mutations may impact TET2 function. WT1 mutant AML patients have reduced 5hmC levels similar to TET2/IDH1/IDH2 mutant AML. These mutations are characterized by convergent, site-specific alterations in DNA hydroxymethylation, which drive differential gene expression more than alterations in DNA promoter methylation. WT1 overexpression increases global levels of 5hmC, and WT1 silencing reduced 5hmC levels. WT1 physically interacts with TET2 and TET3, and WT1 loss of function results in a similar hematopoietic differentiation phenotype as observed with TET2 deficiency. These data provide a role for WT1 in regulating DNA hydroxymethylation and suggest that TET2 IDH1/IDH2 and WT1 mutations define an AML subtype defined by dysregulated DNA hydroxymethylation.

Reimagining cost recovery in Pakistan's irrigation system through willingness-to-pay estimates for irrigation water from a discrete choice experiment.

It is widely argued that farmers are unwilling to pay adequate fees for surface water irrigation to recover the costs associated with maintenance and improvement of delivery systems. In this paper, we use a discrete choice experiment to study farmer preferences for irrigation characteristics along two branch canals in Punjab Province in eastern Pakistan. We find that farmers are generally willing to pay well in excess of current surface water irrigation costs for increased surface water reliability and that the amount that farmers are willing to pay is an increasing function of their existing surface water supply as well as location along the main canal branch. This explicit translation of implicit willingness-to-pay (WTP) for water (via expenditure on groundwater pumping) to WTP for reliable surface water demonstrates the potential for greatly enhanced cost recovery in the Indus Basin Irrigation System via appropriate setting of water user fees, driven by the higher WTP of those currently receiving reliable supplies.