To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).

Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up-and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development. maize transcriptomes | coexpressed genes | cis binding site M aize (Zea mays) is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, the regulatory network that controls maize leaf development is still not well understood. In fact, the number of known maize transcription factor (TF)-binding sites (TFBSs) is far smaller than that for Arabidopsis thaliana (1-3).To understand better the regulation of maize leaf development, several recent studies used next-generation sequencing (NGS) technologies to survey transcriptomic differences among maize leaf cell types and developmental stages. The first large-scale study was by Li et al. (7) investigated the transcriptomes of Kranz (i.e., the foliar leaf blade) and non-Kranz (the husk leaf sheath) maize leaves to identify cohorts of genes associated with procambium initiation and vascular patterning. Recently, Wang et al. (8) conducted comparative transcriptomic and metabolomic analyses of developing leaves in maize and rice and identified putative structural and regulatory components important for C4 and C3 photosynthesis. These studies provided insights into the regulatory mechanisms underlying the development of Kranz leaf anatomy in maize.In the present study, we obtained nine transcriptomes of the second leaf from 84-192 h post imbibition at 12-h (6:00 AM and 6:00 PM) or 24-h (6:00 PM only) intervals. Together with the 13 SignificanceMaize is a major crop and a model plant for studying C4 leaf development. However, its regulatory network of leaf ...

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Heavy metal contamination in lake sediments is a serious problem, particularly in developing countries such as China. To evaluate heavy metal pollution and risk of contamination in lake sediments on a national scale in China, we collated available data in the literature of the last 10 years on lake sediments polluted with heavy metals from 24 provinces in China. Based on these data, we used sediment quality guidelines, geoaccumulation index, and potential ecological risk index to assess potential ecological risk levels. The results showed that approximately 20.6% of the lakes studied exceeded grade II level in Chinese soil quality standards for As, 31.3% for Cd, 4.6% for Cu, 20.8% for Ni, 2.8% for Zn, and 11.1% for Hg, respectively. Besides, the mean concentrations for As in 10.3% of lakes, Hg in 11.9% of lakes, and Ni in 31.3% of lakes surpassed the probable effect level. The potential ecological risk for toxic metals decreased in the order of Cd > Hg > As > Cu > Pb > Ni > Cr > Zn, and there were 21.8% of the lakes studied in the state of moderate risk, 10.9% in high risk, and 12.7% in very high risk. It can be concluded that Chinese lake sediments are polluted by heavy metals to varying degrees. In order to provide key management targets for relevant administrative agencies, based on the results of the pollution and ecological risk assessments, Cd, Hg, As, Cu, and Ni were selected as the priority control heavy metals, and the eastern coastal provinces and Hunan province were selected as the priority control provinces. This article, therefore, provides a comprehensive assessment of heavy metal pollution in lake sediments in China, while providing a reference for the development of lake sediment quality standards.