Decision Tree Classifiers for Star/Galaxy Separation

We study the star/galaxy classification efficiency of 13 different decision tree algorithms applied to photometric objects in the Sloan Digital Sky Survey Data Release Seven (SDSS DR7). Each algorithm is defined by a set of parameters which, when varied, produce different final classification trees. We extensively explore the parameter space of each algorithm, using the set of $884,126$ SDSS objects with spectroscopic data as the training set. The efficiency of star-galaxy separation is measured using the completeness function. We find that the Functional Tree algorithm (FT) yields the best results as measured by the mean completeness in two magnitude intervals: $14\le r\le21$ ($85.2$) and $r\ge19$ ($82.1$). We compare the performance of the tree generated with the optimal FT configuration to the classifications provided by the SDSS parametric classifier, 2DPHOT and Ball et al. (2006). We find that our FT classifier is comparable or better in completeness over the full magnitude range $15\le r\le21$, with much lower contamination than all but the Ball et al. classifier. At the faintest magnitudes ($r>19$), our classifier is the only one able to maintain high completeness ($>$80%) while still achieving low contamination ($\sim2.5$). Finally, we apply our FT classifier to separate stars from galaxies in the full set of $69,545,326$ SDSS photometric objects in the magnitude range $14\le r\le21$.Comment: Submitted to A

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded similar to 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of similar to 81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs

Ecoenzymatic stoichiometry reveals widespread soil phosphorus limitation to microbial metabolism across Chinese forests

8 páginas.- 4 figuras.- 57 referencias.- Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s43247-022-00523-5Forest soils contain a large amount of organic carbon and contribute to terrestrial carbon sequestration. However, we still have a poor understanding of what nutrients limit soil microbial metabolism that drives soil carbon release across the range of boreal to tropical forests. Here we used ecoenzymatic stoichiometry methods to investigate the patterns of microbial nutrient limitations within soil profiles (organic, eluvial and parent material horizons) across 181 forest sites throughout China. Results show that, in 80% of these forests, soil microbes were limited by phosphorus availability. Microbial phosphorus limitation increased with soil depth and from boreal to tropical forests as ecosystems become wetter, warmer, more productive, and is affected by anthropogenic nitrogen deposition. We also observed an unexpected shift in the latitudinal pattern of microbial phosphorus limitation with the lowest phosphorus limitation in the warm temperate zone (41-42 degrees N). Our study highlights the importance of soil phosphorus limitation to restoring forests and predicting their carbon sinks. Phosphorus limitation of soil microbial communities in forests is widespread, increases with soil depth, and is enhanced under wetter and warmer climates and elevated anthropogenic nitrogen deposition, according to ecoenzymatic stoichiometric analyses across 181 forests in China.This study was financially supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB40000000), Funds for International Cooperation and Exchange of National Natural Science Foundation of China (32061123007), National Natural Science Foundation of China (41977031), Program of State Key Laboratory of Loess and Quaternary Geology CAS (SKLLQGZR1803). Contributions from Dr. Chen are funded by H2020 Marie Skłodowska-Curie Actions (No. 839806). M.D.-B. acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by CIN/AEI/10.13039/501100011033. M.D.-B. is also supported by a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático “01–Refuerzo de la investigación, el desarrollo tecnológico y la innovación”) associated with the research project P20_00879 (ANDABIOMA).Peer reviewe

Whole Genome PCR Scanning Reveals the Syntenic Genome Structure of Toxigenic Vibrio cholerae Strains in the O1/O139 Population

Vibrio cholerae is commonly found in estuarine water systems. Toxigenic O1 and O139 V. cholerae strains have caused cholera epidemics and pandemics, whereas the nontoxigenic strains within these serogroups only occasionally lead to disease. To understand the differences in the genome and clonality between the toxigenic and nontoxigenic strains of V. cholerae serogroups O1 and O139, we employed a whole genome PCR scanning (WGPScanning) method, an rrn operon-mediated fragment rearrangement analysis and comparative genomic hybridization (CGH) to analyze the genome structure of different strains. WGPScanning in conjunction with CGH revealed that the genomic contents of the toxigenic strains were conservative, except for a few indels located mainly in mobile elements. Minor nucleotide variation in orthologous genes appeared to be the major difference between the toxigenic strains. rrn operon-mediated rearrangements were infrequent in El Tor toxigenic strains tested using I-CeuI digested pulsed-field gel electrophoresis (PFGE) analysis and PCR analysis based on flanking sequence of rrn operons. Using these methods, we found that the genomic structures of toxigenic El Tor and O139 strains were syntenic. The nontoxigenic strains exhibited more extensive sequence variations, but toxin coregulated pilus positive (TCP+) strains had a similar structure. TCP+ nontoxigenic strains could be subdivided into multiple lineages according to the TCP type, suggesting the existence of complex intermediates in the evolution of toxigenic strains. The data indicate that toxigenic O1 El Tor and O139 strains were derived from a single lineage of intermediates from complex clones in the environment. The nontoxigenic strains with non-El Tor type TCP may yet evolve into new epidemic clones after attaining toxigenic attributes

Genome Expression Profile Analysis of the Immature Maize Embryo during Dedifferentiation

Maize is one of the most important cereal crops worldwide and one of the primary targets of genetic manipulation, which provides an excellent way to promote its production. However, the obvious difference of the dedifferentiation frequency of immature maize embryo among various genotypes indicates that its genetic transformation is dependence on genotype and immature embryo-derived undifferentiated cells. To identify important genes and metabolic pathways involved in forming of embryo-derived embryonic calli, in this study, DGE (differential gene expression) analysis was performed on stages I, II, and III of maize inbred line 18-599R and corresponding control during the process of immature embryo dedifferentiation. A total of ∼21 million cDNA tags were sequenced, and 4,849,453, 5,076,030, 4,931,339, and 5,130,573 clean tags were obtained in the libraries of the samples and the control, respectively. In comparison with the control, 251, 324 and 313 differentially expressed genes (DEGs) were identified in the three stages with more than five folds, respectively. Interestingly, it is revealed that all the DEGs are related to metabolism, cellular process, and signaling and information storage and processing functions. Particularly, the genes involved in amino acid and carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis and signal transduction mechanism have been significantly changed during the dedifferentiation. To our best knowledge, this study is the first genome-wide effort to investigate the transcriptional changes in dedifferentiation immature maize embryos and the identified DEGs can serve as a basis for further functional characterization

Cloning and characterization of miRNAs from maize seedling roots under low phosphorus stress

MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. In this study, a small RNA library was constructed to identify conserved miRNAs as well as novel miRNAs in maize seedling roots under low level phosphorus stress. Twelve miRNAs were identified by high throughput sequencing of the library and subsequent analysis, two belong to conserved miRNA families (miRNA399b and miRNA156), and the remaining ten are novel and one of latter is conserved in gramineous species. Based on sequence homology, we predicted 125 potential target genes of these miRNAs and then expression patterns of 7 miRNAs were validated by semi-RT-PCR analysis. MiRNA399b, Zma-miR3, and their target genes (Zmpt1 and Zmpt2) were analyzed by real-time PCR. It is shown that both miRNA399b and Zma-miR3 are induced by low phosphorus stress and regulated by their target genes (Zmpt1 and Zmpt2). Moreover, Zma-miR3, regulated by two maize inorganic phosphate transporters as a newly identified miRNAs, would likely be directly involved in phosphate homeostasis, so was miRNA399b in Arabidopsis and rice. These results indicate that both conserved and maize-specific miRNAs play important roles in stress responses and other physiological processes correlated with phosphate starvation, regulated by their target genes. Identification of these differentially expressed miRNAs will facilitate us to uncover the molecular mechanisms underlying the progression of maize seedling roots development under low level phosphorus stress

Investigation of Residents’ Health Literacy Status and Its Risk Factors in Jiangsu Province of China

Health literacy has become an important public health concern. Multistage cluster random sampling was used to select 12 450 individuals. Using the 2009 Chinese Health Literacy questionnaire, participants were divided into groups with poor or not poor health literacy status. The knowledge rates for 6 areas of health literacy were determined with the following results: science concept of health (60.0%), literacy for preventing acute infectious disease (66.8%), literacy for preventing noncommunicable chronic disease (51.9%), safety and first aid (66.8%), obtaining and making use of basic medical care (55.3%), and comprehensive health literacy (52.5%). Multiple logistic regression showed that living in a rural area, fewer individuals in a household, younger age, low education, agricultural or rural migrant occupation workers, and low family income were associated with a poor health literacy status. Our results support the use of health education and promotion interventions to improve health literacy in this high-risk population in China