TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death.

2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known about the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have the NADase function necessary but insufficient to activate plant immune responses. Here, we show that plant TIR proteins, besides being NADases, act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data show that a TIR domain adopts distinct oligomers with mutually exclusive NADase and synthetase activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana (Nb), supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7, displays 2',3'-cAMP/cGMP but not 3',5'-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in Nb. Our study identifies a family of 2',3'-cAMP/cGMP synthetases and establishes a critical role for them in plant immune responses.

The impact of impervious surface, vegetation, and soil areas on land surface temperatures in a semi-arid region using Landsat satellite images enriched with Ndaisi method data.

Impervious surfaces are a significant issue of both urbanization and environmental assessment. However, it is a problem to classify impervious surface (IS) and soil areas as separate classes in land cover classification. The objectives of this study are to obtain impervious surface, vegetation, and soil areas clearly of an urban complex with a semi-arid climate and to better determine the relationships of IS, vegetation, and soil areas with land surface temperatures (LSTs). For this purpose, IS, vegetation, and soil areas in a semi-arid city of Turkey-Kayseri city were identified by using Normalized Difference Anthropogenic Impervious Surface Index (NDAISI) data and support vector machine (SVM) method together in the classification of different areas. Landsat 5, 7, and 8 satellite images of 1987, 2000, and 2013 were used, respectively, in this study. Afterward, the effects of these areas on LSTs were analyzed. Regression analysis was used to determine the relationships between land cover areas and surface temperatures. To better demonstrate these relationships, besides common pixel-based and classical regional-based approaches, a new density-based regional analysis approach was proposed. This study is an innovative one in terms of detecting IS and indicating relationships between land cover areas and surface temperatures in semi-arid regions. Another innovation of the study is related to the results produced. The results showed that decreasing LST values were observed with increasing IS and vegetation cover values and increasing LST values were observed with increasing soil areas. The present findings may provide significant contributions to the literature and will facilitate the development of urban planning strategies in semi-arid regions.

Investigation of iron ore potential in north-central Nigeria, using high-resolution aeromagnetic dataset and remote sensing approach.

The instability of fuel prices in the international market has adversely affected the economy of Nigeria, which is a developing country that solely relies on crude oil. This has led the country to consider diversifying its economy into mineral resources. The consideration of iron ore as an important mineral for global infrastructure, steel production, and wealth creation has prompted this study to consider its potential within north-central Nigeria. Additionally, no geophysical reports considering the regional distribution of iron ore potential in both the Basement Complex and the sedimentary basins within north-central Nigeria have been previously carried out. This study employs an analytical hierarchy process (AHP) and weighted overlay to integrate the analyses of the high-resolution aeromagnetic data set (HRAMD) and Landsat 8 OLI/TIRS to assess the iron ore potential of the different geological terrain in north-central Nigeria. The ferrous mineral band ratio technique was adopted in processing the Landsat data, and several signal enhancement techniques were performed on the HRAMD, including the first vertical derivative (1VD), analytical signal, center for exploration targeting (CET) grid analysis, Euler deconvolution, and radially averaged power spectrum (RAPS). The shallowest magnetic sources and the high amplitude zones were delineated, and the dominant structural trend of the area was revealed to be WNW-ESE and NE-SW, and both orientations appeared to be favorable for mineralization. The apparent depth estimates of shallow and deep-seated magnetic structures obtained from Euler deconvolution ranged from 127.65 to 3540.64 m, whereas RAPS delineated a range of 285-3710 m. The analytical signal (AS) categorized the magnetism of the area into low, intermediate, and high magnetic zones. The higher magnetic zones were considered to be favorable for mineralization. The ferrous mineral ratio map reveals areas of higher reflectance, which depict zones of iron ore potential. The iron ore potential map was validated using known iron ore mines and deposits, which showed a perfect correlation, and new sites of probable iron ore mineralization within north-central Nigeria were revealed. This article will serve as a guide for stakeholders in the exploration of iron ore deposits.

Geospatial approaches of TGSI and morphometric analysis in the Mahi River basin using Landsat 8 OLI/TIRS and SRTM-DEM.

The research objective is to assess the Mahi River basin, morphometric parameters, and structurally controlled morphological terrains about the topsoil grain size index (TGSI), based on satellite data including Landsat 8 OLI/TIRS and SRTM-DEM data, using ArcGIS processing software. According to morphometric analysis, the Mahi River basin has an area of 28,844.2 km2 and is a drainage basin of the 8th order. In the sub-basin (SB8), bifurcation ratio reveals structural and geomorphological disorder, and high sinuosity causes significant meandering. These positive dependency factors, such as drainage density (Dd) and stream frequency (Sf), are increasing in SB7, SB8, SB12, and SB13, which results in high permeability, strong runoff, a flat topography, and a gentle slope. TGSI has been performed to analyze the geomorphological features of the structurally controlled Mahi River. The Landsat 8 OLI/TIRS has been utilized for the TGSI analysis, and SRTM-DEM has been utilized for the extraction of structurally controlled lineaments of the river basin. The resultant structurally controlled terrains have been cross-verified based on the DN reflectance of TGSI and the lineament type in the river basin for the morphometry. The results of the TGSI reveal that the minimum and maximum values are -0.1324 and 0.4207; the dominant type of terrain is pediment pediplain complex (PPC), having the TGSI range 0.1322 to 0.4207 with the fracture-type structural dominance with an area of 56.7% of the total area. The results reveal that the structural linear features in the Mahi catchment consist of structural deformed bodies such as faults, fractures, and ridge plains. Thus, it can be observed from the findings that remote sensing data (SRTM-DEM) combined with GIS methodology prove to be an effective tool in morphometric analysis and TGSI data could be utilized in the future for basin management and other hydrological studies.

A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease.

BACKGROUND: DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms. RESULTS: Here we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea, Bryozoa, Chordata, and Echinodermata), and are especially rich in bivalves. Unlike other Kolobok families, KolobokP adopts a composite-like architecture: an internal region (INT) flanked by two long terminal direct repeats (LTDRs), which exhibit their own short terminal inverted repeats ranging up to 18 bps. The excision of LTDRs was strongly suggested. The LTDR lengths seem to be constrained to be either around 450-bp or around 660-bp. The internal region encodes a DDD/E transposase and a small His-Me finger nuclease, which likely originated from the homing endonuclease encoded by a group I intron from a eukaryotic species. The architecture of KolobokP resembles composite DNA transposons, usually observed in bacterial genomes, and long terminal repeat (LTR) retrotransposons. In addition to this monomeric LTDR-INT-LTDR structure, plenty of solo LTDRs and multimers represented as (LTDR-INT)n-LTDR are also observed. Our structural and phylogenetic analysis supported the birth of KolobokP in the late stage of the Kolobok evolution. We propose KolobokP families propagate themselves in two ways: the canonical transposition catalyzed by their transposase and the sequence-specific cleavage by their endonuclease followed by the multimerization through the unequal crossover. CONCLUSIONS: The presence of homing endonuclease and long terminal direct repeats of KolobokP families suggest their unique dual replication mechanisms: transposition and induced unequal crossover.

Demystifying uncertainty in PM10 susceptibility mapping using variable drop-off in extreme-gradient boosting (XGB) and random forest (RF) algorithms.

This study investigates uncertainty in machine learning that can occur when there is significant variance in the prediction importance level of the independent variables, especially when the ROC fails to reflect the unbalanced effect of prediction variables. A variable drop-off loop function, based on the concept of early termination for reduction of model capacity, regularization, and generalization control, was tested. A susceptibility index for airborne particulate matter of less than 10 µm diameter (PM10) was modeled using monthly maximum values and spectral bands and indices from Landsat 8 imagery, and Open Street Maps were used to prepare a range of independent variables. Probability and classification index maps were prepared using extreme-gradient boosting (XGBOOST) and random forest (RF) algorithms. These were assessed against utility criteria such as a confusion matrix of overall accuracy, quantity of variables, processing delay, degree of overfitting, importance distribution, and area under the receiver operating characteristic curve (ROC).

New insights into helitron transposable elements in the mesopolyploid species Brassica rapa.

Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs.