George Daley and John Rinn and colleagues identify large intergenic non-coding RNAs that are upregulated during reprogramming of induced pluripotent stem cells, and they show a functional role for large intergenic non-coding RNA-RoR in induced pluripotent stem cell derivation. The conversion of lineage-committed cells to induced pluripotent stem cells (iPSCs) by reprogramming is accompanied by a global remodeling of the epigenome1,2,3,4,5, resulting in altered patterns of gene expression2,6,7,8,9. Here we characterize the transcriptional reorganization of large intergenic non-coding RNAs (lincRNAs)10,11 that occurs upon derivation of human iPSCs and identify numerous lincRNAs whose expression is linked to pluripotency. Among these, we defined ten lincRNAs whose expression was elevated in iPSCs compared with embryonic stem cells, suggesting that their activation may promote the emergence of iPSCs. Supporting this, our results indicate that these lincRNAs are direct targets of key pluripotency transcription factors. Using loss-of-function and gain-of-function approaches, we found that one such lincRNA (lincRNA-RoR) modulates reprogramming, thus providing a first demonstration for critical functions of lincRNAs in the derivation of pluripotent stem cells.

Transgenic zebrafish carrying the human oncogene BRAF(V600E), the most common mutation in melanoma patients, provide a convenient model for melanoma. Two papers from Leonard Zon and colleagues demonstrate the potential of this system in the study of cancer genetics and in drug development. Ceol et al. screen for genes that cooperate with mutated BRAF, and identify SETDB1 as capable of accelerating melanoma formation in fish. The gene is found in a region that is frequently amplified in human melanomas, and its gene product, SETDB1, is a histone methylating enzyme that is often overexpressed in those melanomas. This work establishes SETDB1 as an important oncogene. White et al. find expression of a gene signature in melanoma-susceptible zebrafish embryos that is indicative of disrupted differentiation of neural crest progenitors. A chemical screen identifies leflunomide, an immunomodulatory drug used to treat rheumatoid arthritis, as an inhibitor of neural crest stem cells. Leflunomide has antimelanoma activity in human melanoma xenografts and might prove useful as an anticancer drug, particularly in combination with BRAF inhibitors. In a zebrafish model of melanoma driven by activated BRAF, this study finds expression of a gene signature indicative of disrupted terminal differentiation of neural crest progenitors. A chemical screen led to the identification of leflunomide as an inhibitor of neural crest stem cells. Leflunomide inhibits dihydroorotate dehydrogenase and thereby transcriptional elongation, including genes involved in neural crest development and melanoma growth. Leflunomide has anti-melanoma activity in the zebrafish model and human melanoma xenografts, and might prove useful as an anticancer drug. Melanoma is a tumour of transformed melanocytes, which are originally derived from the embryonic neural crest. It is unknown to what extent the programs that regulate neural crest development interact with mutations in the BRAF oncogene, which is the most commonly mutated gene in human melanoma1. We have used zebrafish embryos to identify the initiating transcriptional events that occur on activation of human BRAF(V600E) (which encodes an amino acid substitution mutant of BRAF) in the neural crest lineage. Zebrafish embryos that are transgenic for mitfa:BRAF(V600E) and lack p53 (also known as tp53) have a gene signature that is enriched for markers of multipotent neural crest cells, and neural crest progenitors from these embryos fail to terminally differentiate. To determine whether these early transcriptional events are important for melanoma pathogenesis, we performed a chemical genetic screen to identify small-molecule suppressors of the neural crest lineage, which were then tested for their effects on melanoma. One class of compound, inhibitors of dihydroorotate dehydrogenase (DHODH), for example leflunomide, led to an almost complete abrogation of neural crest development in zebrafish and to a reduction in the self-renewal of mammalian neural crest stem cells. Leflunomide exerts these effects by inhibiting the transcriptional elongation of genes that are required for neural crest development and melanoma growth. When used alone or in combination with a specific inhibitor of the BRAF(V600E) oncogene, DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies. Taken together, these studies highlight developmental pathways in neural crest cells that have a direct bearing on melanoma formation.

Meeting the ever-increasing global food, feed, and fiber demands while conserving the quantity and quality of limited agricultural water resources and maintaining the sustainability of irrigated agriculture requires optimizing irrigation management using advanced technologies such as soil moisture sensors. In this study, the performance of five different soil moisture sensors was evaluated for their accuracy in two irrigated cropping systems, one each in central and southwest Oklahoma, with variable levels of soil salinity and clay content. With factory calibrations, three of the sensors had sufficient accuracies at the site with lower levels of salinity and clay, while none of them performed satisfactorily at the site with higher levels of salinity and clay. The study also investigated the performance of different approaches (laboratory, sensor-based, and the Rosetta model) to determine soil moisture thresholds required for irrigation scheduling, i.e., field capacity (FC) and wilting point (WP). The estimated FC and WP by the Rosetta model were closest to the laboratory-measured data using undisturbed soil cores, regardless of the type and number of input parameters used in the Rosetta model. The sensor-based method of ranking the readings resulted in overestimation of FC and WP. Finally, soil moisture depletion, a critical parameter in effective irrigation scheduling, was calculated by combining sensor readings and FC estimates. Ranking-based FC resulted in overestimation of soil moisture depletion, even for accurate sensors at the site with lower levels of salinity and clay.

Groundwater depletion is a serious issue in the southern and central parts of the High Plains Aquifer (HPA), USA. A considerable imbalance exists between the recharge process and groundwater extractions in these areas, which threatens the long-term sustainability of the aquifer. Irrigated agriculture has a major share in the economy, and it requires high pumping rates in regions vulnerable to large groundwater level declines. A literature review has been conducted to understand the state of affairs of irrigated agriculture in the HPA, along with the dynamics of groundwater decline and recharge using statistical and remote-sensing based datasets. Also, three irrigation management and technology-based approaches have been discussed from the perspective of sustainability. The southern and central parts of the HPA consist mostly of non-renewable groundwater formations, and the natural water storage is prone to exhaustion. Moreover, the aforementioned regions have comparatively higher crop water requirement due to the climate, and irrigating crops in these regions puts stringent pressure on the aquifer. The upper threshold of irrigation application efficiency (IAE) is high in the HPA, and could reach up to 95%; however, considerable room for improvement in irrigation water management exists. In general, the practices of irrigation scheduling used in the HPA are conventional and a small proportion of growers use modern methods to decide about irrigation timing. Among numerous ways to promote sustainable groundwater use in the HPA, deficit irrigation, use of soil moisture sensors, and subsurface drip irrigation can be considered as potential ways to attain higher lifespans in susceptible parts of the aquifer.

Mitochondrial iron is essential for the biosynthesis of heme and iron-sulfur ([Fe-S]) clusters in mammalian cells. In developing erythrocytes, iron is imported into the mitochondria by MFRN1 (mitoferrin-1, SLC25A37). Although loss of MFRN1 in zebrafish and mice leads to profound anemia, mutant animals showed no overt signs of porphyria, suggesting that mitochondrial iron deficiency does not result in an accumulation of protoporphyrins. Here, we developed a gene trap model to provide in vitro and in vivo evidence that iron regulatory protein-1 (IRP1) inhibits protoporphyrin accumulation. Mfrn1^+/gt;Irp1^−/− erythroid cells exhibit a significant increase in protoporphyrin levels. IRP1 attenuates protoporphyrin biosynthesis by binding to the 5′-iron response element (IRE) of alas2 mRNA, inhibiting its translation. Ectopic expression of alas2 harboring a mutant IRE, preventing IRP1 binding, in Mfrn1^gt/gt cells mimics Irp1 deficiency. Together, our data support a model whereby impaired mitochondrial [Fe-S] cluster biogenesis in Mfrn1^gt/gt cells results in elevated IRP1 RNA-binding that attenuates ALAS2 mRNA translation and protoporphyrin accumulation.