Nitrification, a key process in the global nitrogen cycle that generates nitrate through microbial activity, may enhance losses of fertilizer nitrogen by leaching and denitrification. Certain plants can suppress soil-nitrification by releasing inhibitors from roots, a phenomenon termed biological nitrification inhibition (BNI). Here, we report the discovery of an effective nitrification inhibitor in the root-exudates of the tropical forage grass Brachiaria humidicola (Rendle) Schweick. Named ''brachialactone,'' this inhibitor is a recently discovered cyclic diterpene with a unique 5-8-5-membered ring system and a ␥-lactone ring. It contributed 60 -90% of the inhibitory activity released from the roots of this tropical grass. Unlike nitrapyrin (a synthetic nitrification inhibitor), which affects only the ammonia monooxygenase (AMO) pathway, brachialactone appears to block both AMO and hydroxylamine oxidoreductase enzymatic pathways in Nitrosomonas. global warming ͉ nitrogen pollution ͉ nitrous oxide emissions ͉ root exudation ͉ climate change M ost modern agricultural systems are based on large inputs of inorganic nitrogen (N), with ammonium (NH 4 ϩ ) being the primary N source (1, 2). Also, current crop management practices result in the development of highly nitrifying soil environments (3, 4). Nitrification results in the transformation of the relatively immobile NH 4 ϩ to highly mobile nitrate (NO 3 Ϫ ), making inorganic N susceptible to losses through leaching of NO 3 Ϫ and/or gaseous N emissions, potentially initiating a cascade of environmental and health problems (1, 2, 5, 6). Nitrous oxide (N 2 O) is one of the three major biogenic greenhouse gases contributing to global warming, produced primarily from denitrification processes in agricultural systems (5, 7). Also, assimilation of NO 3 Ϫ by plants can result in further N 2 O emissions directly from plant canopies (8). The low agronomic N-use efficiency (NUE) found in many agricultural systems is largely the result of N losses associated with nitrification (i.e., N losses from NO 3 Ϫ leaching and denitrification) (9-11). Most plants have the ability to assimilate both NH 4 ϩ and NO 3 Ϫ (12); therefore, nitrification does not need to be a dominant process in the N cycle for efficient N use.Nitrification is low in some forest and grassland soils (13-17). Since the early 1960s, some tropical grasses have been suspected of having the capacity to inhibit nitrification (18-21). However, this concept remained controversial due to the lack of direct evidence showing such inhibitory effects or the identification of specific inhibitors (22).We adopted a very sensitive bioassay using a recombinant luminescent Nitrosomonas europaea to detect biological nitrification inhibition (BNI) in plant-soil systems with the inhibitory activity of roots expressed in allylthiourea units (ATU) (23). Using this methodology, we were able to show that certain plants release nitrification inhibitors from their roots (23-26). Such BNI capacity appears to be relatively widespread among...

Tumor protein p53 (TP53) is the most frequently mutated gene in cancer 1,2. In patients with myelodysplastic syndromes (MDS), TP53 mutations are associated with high-risk disease 3,4 , rapid transformation to acute myeloid leukemia (AML) 5 , resistance to conventional therapies 6-8 and dismal outcomes 9. Consistent with the tumor-suppressive role of TP53, patients harbor both mono-and biallelic mutations 10. However, the biological and clinical implications of TP53 allelic state have not been fully investigated in MDS or any other cancer type. We analyzed 3,324 patients with MDS for TP53 mutations and allelic imbalances and delineated two subsets of patients with distinct phenotypes and outcomes. One-third of TP53-mutated patients had monoallelic mutations whereas two-thirds had multiple hits (multi-hit) consistent with biallelic targeting. Established associations with complex karyotype, few co-occurring mutations, high-risk presentation and poor outcomes were specific to multi-hit patients only. TP53 multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System (IPSS-R) 11. Surprisingly, monoallelic patients did not differ from TP53 wild-type patients in outcomes and response to therapy. This study shows that consideration of TP53 allelic state is critical for diagnostic and prognostic precision in MDS as well as in future correlative studies of treatment response. In collaboration with the International Working Group for Prognosis in MDS (Supplementary Table 1), we assembled a cohort of 3,324 peridiagnostic and treatment-naive patients with MDS or closely related myeloid neoplasms (Extended Data Fig. 1 and Supplementary Fig. 1). Genetic profiling included conventional G-banding analyses (CBA) and tumor-only, capture-based, next-generation sequencing (NGS) of a panel of genes recurrently mutated in MDS, as well as genome-wide copy number probes. Allele-specific copy number profiles were generated from NGS data using the CNACS algorithm 7 (see Methods and Code availability). An additional 1,120 samples derived from the Japanese MDS consortium (Extended Data Fig. 2) were used as a validation cohort. To study the effect of TP53 allelic state on genome stability, clinical presentation, outcome and response to therapy, we performed a detailed characterization of alterations at the TP53 locus. First, we assessed genome-wide allelic imbalances in the cohort of 3,324 patients, to include arm-level or focal (~3 Mb) ploidy alterations and regions of copy-neutral loss of heterozygosity (cnLOH) (Extended Data Fig. 3, Supplementary Figs. 2-4 and Methods).

Nitrification, a microbial process, is a key component and integral part of the nitrogen (N) cycle. Soil N is in a constant state of flux, moving and changing chemical forms. During nitrification, a relatively immobile N-form (NH + 4) is converted into highly mobile nitrate-N (NO − 3). The nitrate formed is susceptible to losses via leaching and conversion to gaseous forms via denitrification. Often less than 30% of the applied N fertilizer is recovered in intensive agricultural systems, largely due to losses associated with and following nitrification. Nitrogen-use efficiency (NUE) is defined as the biomass produced per unit of assimilated N and is a conservative function in most biological systems. A better alternative is to define NUE as the dry matter produced per unit N applied and strive for improvements in agronomic yields through N recovery. Suppressing nitrification along with its associated N losses is potentially a key part in any strategy to improve N recovery and agronomic NUE. In many mature N-limited ecosystems, nitrification is reduced to a relatively minor flux. In such systems there is a high degree of internal N cycling with minimal loss of N. In contrast, in most highproduction agricultural systems nitrification is a major process in N cycling with the resulting N losses and inefficiencies. This review presents the current state of knowledge on nitrification and associated N losses, and discusses strategies for controlling nitrification in agricultural systems. Limitations of the currently available nitrification inhibitors are highlighted. The concept of biological nitrification inhibition (BNI) is proposed for controlling nitrification in agricultural systems utilizing traits found in natural ecosystems. It is emphasized that suppression of nitrification in agricultural systems is a critical step required for improving agronomic NUE and maintaining environmental quality.

A bioluminescence assay using recombinant Nitrosomonas europaea was adopted to detect and quantify natural nitrification inhibitors in plant-soil systems. The recombinant strain of N. europaea produces a distinct two-peak luminescence due to the expression of luxAB genes, introduced from Vibrio harveyi, during nitrification. The bioluminescence produced in this assay is highly correlated with NO 2 -production (r 2 = 0.94). Using the assay, we were able to detect significant amounts of a nitrification inhibitor produced by the roots of Brachiaria humidicola (Rendle) Schweick. We propose that the inhibitory activity produced/released from plants be termed 'biological nitrification inhibition' (BNI) to distinguish it from industrially produced inhibitors. The amount of BNI activity produced by roots was expressed in units defined in terms of the action of a standard inhibitor allylthiourea (AT). The inhibitory effect from 0.22 lM AT in an assay containing 18.9 mM of NH 4 + is defined as one AT unit of activity. A substantial amount of BNI activity was released from the roots of B. humidicola (15-25 AT unit g -1 root dry wt day -1 ). The BNI activity released was a function of the growth stage and N content of the plant. Shoot N levels were positively correlated with the release of BNI activity from roots (r 2 = 0.76). The inhibitor/s released from B. humidicola roots suppressed soil nitrification. Additions of 20 units of BNI per gram of soil completely inhibited NO 3 -formation in a 55-day study and remained functionally stable in the soil for 50 days. Both the ammonia monooxygenase and the hydroxylaminooxidoreductase enzymatic pathways in Nitrosomonas were effectively blocked by the BNI activity released from B. humidicola roots. The proposed bioluminescence assay can be used to characterize and determine the BNI activity of plant roots, thus it could become a powerful tool in genetically exploiting the BNI trait in crops and pastures.

Regulating nitrification could be a key strategy in improving nitrogen (N) recovery and agronomic N-use efficiency in situations where the loss of N following nitrification is significant. A highly sensitive bioassay using recombinant luminescent Nitrosomonas europaea, has been developed that can detect and quantify the amount of nitrification inhibitors produced by plants (hereafter referred to as BNI activity). A number of species including tropical and temperate pastures, cereals and legumes were tested for BNI in their root exudate. There was a wide range in BNI capacity among the 18 species tested; specific BNI (AT units activity g -1 root dry wt) ranged from 0 (i.e. no detectable activity) to 18.3 AT units. Among the tested cereal and legume crops, sorghum [Sorghum bicolor (L.)], pearl millet [Pennisetum glaucum (L.) R. Br.], and groundnut [Arachis hypogaea (L.)] showed detectable BNI in root exudate. Among pasture grasses, Brachiaria humidicola (Rendle) Schweick, B. decumbens Stapf showed the highest BNI capacity. Several high-and low-BNI genotypes were identified within the B. humidicola species. Soil collected from field plots of 10 year-old high-BNI genotypes of B. humidicola, showed a near total suppression (>90%) of nitrification; most of the soil inorganic N remained in the NH 4 + form after 30 days of incubation. In contrast, soils collected from low-BNI genotypes did not show any inhibitory effect; most of the soil inorganic N was converted to NO 3 -after 30 days of incubation. In both the high-and low-BNI genotypes, BNI was detected in root exudate only when plants were grown with NH 4 + , but not when grown with NO 3 -as the sole source of N. BNI compounds when added to the soil inhibited nitrification and the relationship was linear (r 2 = 0.92 ** ; n = 12). The BNI from high-and low-BNI types when added to N. europaea in pure culture, blocked both the ammonia monooxygenase (AMO) and the hydroxylamine oxidoreductase (HAO) pathways. Our results indicated that BNI capacity varies widely among and within species; and that some degree of BNI capacity is likely a widespread phenomenon in tropical pasture grasses. We suggest that the BNI capacity could either be managed and/or introduced into pastures/crops with an expression of this phenomenon, via genetic improvement approaches that combine high productivity along with some capacity to regulate soil nitrification process.

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SummaryFresh leukemic cells from patients with adult T cell leukemia (ATL) and some ATL-derived T cell hnes show adhesion to human umbilical vein endothelial cells (HUVECs) mainly through E-selectin, but a proportion of this binding remains unaffected by the addition of combinations of antibodies against known adhesion molecules. By immunizing mice with one of such cell hnes, we estabhshed monoclonal antibodies (mAbs), termed 131 and 315, that recognize a single cell surface antigen (Ag) and inhibit the remaining pathway of the adhesion. These mAbs did not react with normal resting peripheral blood mononuclear cells (PBMC) or most of the cell lines tested except for two other human T cell leukemia virus type I (HTLV-I)-infected T cell hnes. After stimulation with phytohemagglutinin (PHA), PBMC expressed Ag 131/315 transiently, indicating that these mAbs define a T cell activation Ag. Western blotting and immunoprecipitation revealed that Ag 131/315 has an apparent molecular mass of 50 kD. Expression cloning was done by transient expression in COS-7 cells and immunological selection to isolate a cDNA clone encoding Ag 131/315. Sequence analysis of the cDNA indicated that it is identical to human OX40, a member of the tumor necrosis factor/nerve growth factor receptor family. We then found that gp34, the hgand of OX40, was expressed on HUVECs and other types of vascular endothehal cells. Furthermore, it was shown that the adhesion ofCD4 + cells ofPHA-stimulated PBMC to unstimulated HUVECs was considerably inhibited by either 131 or 315. Finally, OX40 transfectants of Kit 225, a human interleukin 2-dependent T cell line, were bound specifically to gp34 transfectants of MMCE, a mouse epithelial cell hne, and this binding was blocked by either 315 or 5A8, an anti-gp34 mAb. These results indicate that the OX40/gp34 system directly mediates adhesion of activated T cells or OX40+-transformed T cells to vascular endothehal cells.

Peripheral T-cell lymphoma, not otherwise specified (PTCL, NOS) is a diagnosis of exclusion, being the most common entity in mature T-cell neoplasms, and its molecular pathogenesis remains significantly understudied. Here, combining whole-exome and targeted-capture sequencing, gene-expression profiling, and immunohistochemical analysis of tumor samples from 133 cases, we have delineated the entire landscape of somatic alterations, and discovered frequently affected driver pathways in PTCL, NOS, with and without a T-follicular helper (TFH) cell phenotype. In addition to previously reported mutational targets, we identified a number of novel recurrently altered genes, such as KMT2C, SETD1B, YTHDF2, and PDCD1. We integrated these genetic drivers using hierarchical clustering and identified a previously undescribed molecular subtype characterized by TP53 and/or CDKN2A mutations and deletions in non-TFH PTCL, NOS. This subtype exhibited different prognosis and unique genetic features associated with extensive chromosomal instability, which preferentially affected molecules involved in immune escape and transcriptional regulation, such as HLA-A/B and IKZF2. Taken together, our findings provide novel insights into the molecular pathogenesis of PTCL, NOS by highlighting their genetic heterogeneity. These results should help to devise a novel molecular classification of PTCLs and to exploit a new therapeutic strategy for this group of aggressive malignancies.