Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future

A Fine-Grained Hardware Security Approach for Runtime Code Integrity in Embedded Systems

Embedded systems are subjected to various adversaries including software attacks, physical attacks, and side channel attacks. Most of these malicious attacks can lead to the invalid execution of programs, and launch of destructive actions or reveal critical information. However, most previous security mechanisms suffer from coarse checking granularity and unacceptable performance overhead, due to strict restriction on system resources. This paper presents a fine-grained hardware-based security approach to ensure runtime code integrity in the embedded systems by offline profiling of the program features and runtime integrity check. We design a hardware implemented instruction stream integrity checker (ISIC) to perform runtime checking of pre-extracted features. Any invalid execution of the program will trigger the corresponding exception signal. We implement the ISIC with OR1200 processor on XC5VLX50T field-programmable gate array (FPGA). The experimental results show that the proposed approach can detect all the attacks destructing integrity of the instruction stream, and the performance overhead induced by the security mechanism is less than 3.45% according to the selected benchmarks

Embedded System Confidentiality Protection by Cryptographic Engine Implemented with Composite Field Arithmetic

Embedded systems are subjecting to various kinds of security threats. Some malicious attacks exploit valid code gadgets to launch destructive actions or to reveal critical details. Some previous memory encryption strategies aiming at this issue suffer from unacceptable performance overhead and resource consumption. This paper proposes a hardware based confidentiality protection method to secure the code and data stored and transferred in embedded systems. This method takes advantage of the I/D-cache structure to reduce the frequency of the cryptographic encryption and decryption processing. We implement the AES engine with composite field arithmetic to reduce the cost of hardware implementation. The proposed architecture is implemented on EP2C70 FPGA chip with OpenRisc 1200 based SoC. The experiment results show that the AES engine is required to work only in the case of I/D-cache miss and the hardware implementation overhead can save 53.24% and 13.39% for the AES engine and SoC respectively

Embedded System Confidentiality Protection by Cryptographic Engine Implemented with Composite Field Arithmetic

Embedded systems are subjecting to various kinds of security threats. Some malicious attacks exploit valid code gadgets to launch destructive actions or to reveal critical details. Some previous memory encryption strategies aiming at this issue suffer from unacceptable performance overhead and resource consumption. This paper proposes a hardware based confidentiality protection method to secure the code and data stored and transferred in embedded systems. This method takes advantage of the I/D-cache structure to reduce the frequency of the cryptographic encryption and decryption processing. We implement the AES engine with composite field arithmetic to reduce the cost of hardware implementation. The proposed architecture is implemented on EP2C70 FPGA chip with OpenRisc 1200 based SoC. The experiment results show that the AES engine is required to work only in the case of I/D-cache miss and the hardware implementation overhead can save 53.24% and 13.39% for the AES engine and SoC respectively

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure