Modification of the fatty acid composition in Arabidopsis and maize seeds using a stearoyl-acyl carrier protein desaturase-1 (ZmSAD1) gene

Composition of fatty acids in the transgenic ZmSAD1 Arabidopsis mature seeds (DOCX 17 kb

Modeling for Predicting the Time to Detection of Staphylococcal Enterotoxin A in Cooked Chicken Product

Staphylococcal enterotoxins (SEs) produced by Staphylococcus aureus (S. aureus) are the cause of Saphylococcal food poisoning (SFP) outbreaks. Thus, estimation of the time to detection (TTD) of SEs, that is, the time required to reach the SEs detection limit, is essential for food preservation and quantitative risk assessment. This study was conducted to explore an appropriate method to predict the TTD of SEs in cooked chicken product under variable environmental conditions. An S. aureus strain that produces staphylococcal enterotoxin A (SEA) was inoculated into cooked chicken meat. Initial inoculating concentrations (approximately 102, 103, 104 CFU/g) of S. aureus and incubation temperatures (15 ± 1, 22 ± 1, 29 ± 1, and 36 ± 1°C) were chosen as environmental variables. The counting of S. aureus colonies and the detection of SEA were performed every 3 or 6 h during the incubation. The TTD of SEA was considered a response of S. aureus to environmental variables. Linear polynomial regression was used to model the effects of environmental variables on the TTD of SEA. Result showed that the correlation coefficient (R2) of the regressed equation is higher than 0.98, which means the obtained equation was reliable. Moreover, the minimum concentration of S. aureus for producing a detectable amount of SEA under various environmental conditions was approximately 6.32 log CFU/g, which was considered the threshold for S. aureus to produce SEA. Hence, the TTD of SEA could be obtained by calculating the time required to reach the threshold by using an established S. aureus growth predictive model. Both established methods were validated through internal and external validation. The results of graphical comparison, RMSE, SEP, Af, and Bf showed that the accuracy of both methods were acceptable, and linear polynomial regression method showed more accurately

Genome‐Wide Association Study for Nine Plant Architecture Traits in Sorghum

Sorghum [ (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass-related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes. A total of 101 single-nucleotide polymorphism (SNP) representative regions were associated with at least one of the nine traits, and two of the significant markers correspond to GA candidate genes, () and (), affecting plant height and seed number, respectively. The resolution of a previously reported quantitative trait loci (QTL) for leaf angle on chromosome 7 was increased to a 1.67 Mb region containing seven candidate genes with good prospects for further investigation. This study provides new knowledge of the association of GA genes with plant architecture traits and the genomic regions controlling variation in leaf angle, stem circumference, internode number, tiller number, seed number, panicle exsertion, and panicle length. The GA gene affecting seed number variation () and the genomic region on chromosome 7 associated with variation in leaf angle are also important outcomes of this study and represent the foundation of future validation studies needed to apply this knowledge in breeding programs

Deep Learning in Indoor Human Activity Recognition with Millimeter Wave Radar

Human activity recognition (HAR) is an active field of study concerned with automatically identifying human activities by analyzing and classifying the data captured from sensors. HAR has received great attention due to its wide application in healthcare and eldercare. Deep learning models such as multilayer perceptron (MLP), convolutional neural network (CNN), and recurrent neural network (RNN) have been widely applied to HAR. Recently, Transformer emerges as a new type of deep learning neural network, which has been a breakthrough in natural language processing tasks, and is showing great promise in the field of computer vision. In our research, we experimented with three Transformer models and three non-transformer models using a public indoor millimeter wave radar dataset called MMActivity. The highest prediction accuracy of 96.10% was achieved by a Transformer model integrating CNN with the Transformer encoder, which is comparable to the prediction accuracy of 95.90% achieved by the non-transformer model BiLSTM. When applying to the dataset collected by our own millimeter wave radar, our Transformer model integrated with CNN also showed a high prediction accuracy of 93.6%

Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions

Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, especially when coupled with excessive light, and that greatly affect the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for seven photosynthetic gas exchange and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28 °C/24 °C), cold (15 °C/15 °C), and recovery (28 °C/24 °C). Cold stress significantly reduced the rate of photosynthetic CO2 uptake of sorghum plants, and a total of 143 unique genomic regions were discovered associated with at least one trait in a particular treatment or with derived variables. Ten regions on chromosomes 3, 4, 6, 7, and 8 that harbor multiple significant markers in linkage disequilibrium (LD) were consistently identified in gas exchange and chlorophyll fluorescence traits. Several candidate genes within those intervals have predicted functions related to carotenoids, phytohormones, thioredoxin, components of PSI, and antioxidants. These regions represent the most promising results for future validation and with potential application for the improvement of crop productivity under cold stress.This article is published as Ortiz, Diego, Jieyun Hu, and Maria G. Salas Fernandez. "Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions." Journal of experimental botany 68, no. 16 (2017): 4545-4557. doi: 10.1093/jxb/erx276. Posted with permission.</p

Simultaneous Removal of Nitrate and Phosphate in a Pyrrhotite and Sulfur-Circulating Packed Bed Reactor

A pyrrhotite and sulfur-circulating packed bed reactor (PS-CPBR) was constructed to study the removal process and mechanism of NO3−-N and PO43−-P with different electron donors. The results showed that the NO3−-N and PO43−-P removal performance of mixed electron donors (pyrrhotite and sulfur) was superior to the single electron donor (pyrrhotite). The optimum conditions of NO3−-N and PO43−-P removal in the PS-CPBR were a hydraulic retention time (HRT) of 12 h and a C/N of 0, and the average removal efficiency was 100% and 86.39%. The sulfur in mixed electron donors was able to promote the dissolution of pyrrhotite and the formation of polysulfide to increase the effectiveness of electron donors, promoting the removal of NO3−-N, while the PO43−-P was removed in the form of FePO4 precipitation. Microbial and functional gene analyses demonstrated that different electron donors were able to influence the abundance of microbial communities and denitrification functional genes. Meanwhile, mixed electron donors were able to increase the protein content of biofilms and reduce the resistance of electron transfer between microorganisms and electrons

Genome-Wide Association Study for Nine Plant Architecture Traits in Sorghum

Sorghum [Sorghum bicolor (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass-related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes. A total of 101 single-nucleotide polymorphism (SNP) representative regions were associated with at least one of the nine traits, and two of the significant markers correspond to GA candidate genes, GA2ox5 (Sb09 g028360) and KS3 (Sb06 g028210), affecting plant height and seed number, respectively. The resolution of a previously reported quantitative trait loci (QTL) for leaf angle on chromosome 7 was increased to a 1.67 Mb region containing seven candidate genes with good prospects for further investigation. This study provides new knowledge of the association of GA genes with plant architecture traits and the genomic regions controlling variation in leaf angle, stem circumference, internode number, tiller number, seed number, panicle exsertion, and panicle length. The GA gene affecting seed number variation (KS3, Sb06 g028210) and the genomic region on chromosome 7 associated with variation in leaf angle are also important outcomes of this study and represent the foundation of future validation studies needed to apply this knowledge in breeding programs.This article is published as Zhao, Jing, Maria B. Mantilla Perez, Jieyun Hu, and Maria G. Salas Fernandez. "Genome-wide association study for nine plant architecture traits in sorghum." The plant genome 9, no. 2 (2016). doi: 10.3835/plantgenome2015.06.0044. Posted with permission.</p

Additional file 1: Figure S1. of Modification of the fatty acid composition in Arabidopsis and maize seeds using a stearoyl-acyl carrier protein desaturase-1 (ZmSAD1) gene

Schematic diagrams of the different ZmSAD1 constructs. (a, d) ZmSAD1 constructs; (b) anti-ZmSAD1; and (c, e) ZmSAD1 RNAi (not to scale). a, b, and c were in the pBI121 vector and used for Arabidopsis transformation. d and e were in the pCAMBIA3301 vector and used for maize transformation. (f) Part of the ZmSAD1 cDNA sequence used for RNAi. (g) Sequence used as a loop in the RNAi construct. LB and RB, T-DNA left and right borders, respectively; Pnos, nopaline synthase gene promoter; Tnos, nopaline synthase gene terminator; NPTII, neomycin phosphotransferase II; FAE1, promoter of fatty acid elongation 1 condensing enzyme; SAD1, stearoyl-acyl carrier protein desaturase1; bar, phosphinothricin acetyltransferase; T35s, CaMV 35S terminator; and P35s: CaMV35S promoter. The full-length cDNA of ZmSAD1 was used in the ZmSAD1 and anti-ZmSAD1 constructs. (DOCX 964 kb