Genetics Etiologies Associated with Fetal Growth Restriction

Abstract. Fetal growth restriction (FGR) is associated with multiple adverse perinatal outcomes, such as increased risk of intrauterine death, neonatal morbidity and mortality, and long-term adverse outcomes. Genetic etiological factors are critical in fetuses with intrauterine growth restriction, including chromosomal abnormalities, copy number variants, single gene disorders, uniparental disomy, epigenetic changes, and confined placental mosaicism. This paper aims to provide an overview of genetic defects related to FGR and to highlight the importance of prenatal genetic counseling and testing for precise diagnosis and management of FGR

Deep Neural Network-Based Generation of Planar CH Distribution through Flame Chemiluminescence in Premixed Turbulent Flame

Flame front structure is one of the most fundamental characteristics and, hence, vital for understanding combustion processes. Measuring flame front structure in turbulent flames usually needs laser-based diagnostic techniques, mostly planar laser-induced fluorescence (PLIF). The equipment of PLIF, burdened with lasers, is often too sophisticated to be configured in harsh environments. Here, to shed the burden, we propose a deep neural network-based method to generate the structures of flame fronts using line-of-sight CH* chemiluminescence that can be obtained without the use of lasers. A conditional generative adversarial network (C-GAN) was trained by simultaneously recording CH-PLIF and chemiluminescence images of turbulent premixed methane/air flames. Two distinct generators of the C-GAN, namely Resnet and U-net, were evaluated. The former net performs better in this study in terms of both generating snap-shot images and statistics over multiple images. For chemiluminescence imaging, the selection of the camera's gate width produces a trade-off between the signal-to-noise (SNR) ratio and the temporal resolution. The trained C-GAN model can generate CH-PLIF images from the chemiluminescence images with an accuracy of over 91% at a Reynolds number of 5000, and the flame surface density at a higher Reynolds number of 10,000 can also be effectively estimated by the model. This new method has the potential to achieve the flame characteristics without the use of laser and significantly simplify the diagnosing system, also with the potential for high-speed flame diagnostics

Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain.

Rice foot rot caused by Dickeya zeae is an important bacterial disease of rice worldwide. In this study, we identified a new strain EC2 from rice in Guangdong province, China. This strain differed from the previously identified strain from rice in its biochemical characteristics, pathogenicity, and genomic constituents. To explore genomic discrepancies between EC2 and previously identified strains from rice, a complete genome sequence of EC2 was obtained and used for comparative genomic analyses. The complete genome sequence of EC2 is 4,575,125 bp in length. EC2 was phylogenetically closest to previously identified Dickeya strains from rice, but not within their subgroup. In terms of secretion systems, genomic comparisons revealed that EC2 harbored only type I (T1SS), typeⅡ (T2SS), and type VI (T6SS) secretion systems. The flagella cluster of this strain possessed specific genomic characteristics like other D. zeae strains from Guangdong and from rice; within this locus, the genetic diversity among strains from rice was much lower than that of within strains from non-rice hosts. Unlike other strains from rice, EC2 lost the zeamine cluster, but retained the clustered regularly interspaced short palindromic repeats-1 (CRISPR-1) array. Compared to the other D. zeae strains containing both exopolysaccharide (EPS) and capsular polysaccharide (CPS) clusters, EC2 harbored only the CPS cluster, while the other strains from rice carried only the EPS cluster. Furthermore, we found strain MS1 from banana, carrying both EPS and CPS clusters, produced significantly more EPS than the strains from rice, and exhibited different biofilm-associated phenotypes. Comparative genomics analyses suggest EC2 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings emphasize the emergence of a new type of D. zeae strain causing rice foot rot, an essential step in the early prevention of this rice bacterial disease

Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai

Abstract Background Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only the orchid-associated strains have been shown to cause soft rot symptoms. Methods We constructed the complete PA1 genome sequence and used comparative genomics to explore the differences in genomic features between D. fangzhongdai and other Dickeya species. Results PA1 has a 4,979,223-bp circular genome with 4269 predicted protein-coding genes. D. fangzhongdai was phylogenetically similar to Dickeya solani and Dickeya dadantii. The type I to type VI secretion systems (T1SS–T6SS), except for the stt-type T2SS, were identified in D. fangzhongdai. The three phylogenetically similar species varied significantly in terms of their T5SSs and T6SSs, as did the different D. fangzhongdai strains. Genomic island (GI) prediction and synteny analysis (compared to D. fangzhongdai strains) of PA1 also indicated the presence of T5SSs and T6SSs in strain-specific regions. Two typical CRISPR arrays were identified in D. fangzhongdai and in most other Dickeya species, except for D. solani. CRISPR-1 was present in all of these Dickeya species, while the presence of CRISPR-2 varied due to species differentiation. A large polyketide/nonribosomal peptide (PK/NRP) cluster, similar to the zeamine biosynthetic gene cluster in Dickeya zeae rice strains, was discovered in D. fangzhongdai and D. solani. The D. fangzhongdai and D. solani strains might recently have acquired this gene cluster by horizontal gene transfer (HGT). Conclusions Orchid-associated strains are the typical members of D. fangzhongdai. Genomic analysis of PA1 suggested that this strain presents the genomic characteristics of this novel species. Considering the absence of the stt-type T2SS, the presence of CRISPR loci and the zeamine biosynthetic gene cluster, D. fangzhongdai is likely a transitional form between D. dadantii and D. solani. This is supported by the later acquisition of the zeamine cluster and the loss of CRISPR arrays by D. solani. Comparisons of phylogenetic positions and virulence determinants could be helpful for the effective quarantine and control of this emerging species

CONSTANS-Like 9 (OsCOL9) Interacts with Receptor for Activated C-Kinase 1(OsRACK1) to Regulate Blast Resistance through Salicylic Acid and Ethylene Signaling Pathways

<div><p>In a previous transcriptome analysis of early response genes in rice during <i>Magnaporthe oryzae</i> infection, we identified a CONSTANS-like (<i>COL</i>) gene <i>OsCOL9</i>. In the present study, we investigated the functional roles of <i>OsCOL9</i> in blast resistance. <i>OsCOL9</i> belonged to group II of the COL protein family, and it contained a BB-box and a C-terminal CCT (CONSTANS, COL and TOC1) domain. <i>OsCOL9</i> was found in the nucleus of rice cells, and it exerted transcriptional activation activities through its middle region (MR). <i>Magnaporthe oryzae</i> infection induced <i>OsCOL9</i> expression, and transgenic <i>OsCOL9</i> knock-out rice plants showed increased pathogen susceptibility. <i>OsCOL9</i> was a critical regulator of pathogen-related genes, especially <i>PR1b</i>, which were also activated by exogenous salicylic acid (SA) and 1-aminocyclopropane-1-carboxylicacid (ACC), the precursor of ethylene (ET). Further analysis indicated that <i>OsCOL9</i> over-expression increased the expressions of phytohormone biosynthetic genes, <i>NPR1</i>, <i>WRKY45</i>, <i>OsACO1</i> and <i>OsACS1</i>, which were related to SA and ET biosynthesis. Interestingly, we found that OsCOL9 physically interacted with the scaffold protein OsRACK1 through its CCT domain, and the <i>OsRACK1</i> expression was induced in response to exogenous SA and ACC as well as <i>M</i>. <i>oryzae</i> infection. Taken together, these results indicated that the COL protein OsCOL9 interacted with OsRACK1, and it enhanced the rice blast resistance through SA and ET signaling pathways.</p></div