Particle-Associated Polycyclic Aromatic Hydrocarbons (PAHs) in the Atmosphere of Hefei, China: Levels, Characterizations and Health Risks

Airborne PM2.5 and PM10 samples were collected in summertime (August 2015) and wintertime (December 2015-January 2016) in an industrial complex area in Hefei, China. The average concentrations of PM2.5 and PM10 (90.5 and 114.5 mu g/m(3), respectively) were higher than the regulated levels of China National Ambient Air Quality Standard (grade I) and the WHO Ambient (outdoor) Air Quality and Health Guideline Value. Seasonal variations in PM2.5/PM10 indicated that the secondary sources of particulate matters, formed by gas-to-particle conversion, were enhanced in summer due to longer time of solar radiation and higher temperature. The total concentrations of PM2.5- and PM10-associated PAHs were 5.89 and 17.70 ng/m(3) in summer as well as 63.41 and 78.26 ng/m(3) in winter, respectively. Both PM2.5- and PM10-associated PAHs were dominated by 4- to 6-ring PAHs, suggesting that the fossil fuel combustion and vehicle emissions were the primary sources of PAHs in atmospheric particulate matters in Hefei. The total concentration of PAHs had a slightly higher correlation coefficient with PM2.5 (R = 0.499, P < 0.05) than PM10 (R = 0.431, P > 0.05), indicating the higher association tendency of PAHs with PM2.5. The coefficient of divergence analysis showed that the compositions of PAH were quite different between summer and winter. Total BaP equivalent concentration (BaP-TEQ) for particulate-bound PAHs in winter (58.87 ng/m(3)) was higher than that in summer (5.53 ng/m(3)). In addition, particulate-bound PAHs in winter had an inhalation cancer risk (ICR) value of 2.8 x 10(-3), which was higher than the safe range (10(-4)-10(-6))

Junior Recital

List of performers and performances

Novel bi-allelic variants of CHMP1A contribute to pontocerebellar hypoplasia type 8: additional clinical and genetic evidence

Pontocerebellar hypoplasia type 8(PCH8) is a rare neurodegenerative disorder, reportedly caused by pathogenic variants of the CHMP1A in autosomal recessive inheritance, and CHMP1A variants have also been implicated in other diseases, and yet none of the prenatal fetal features were reported in PCH8. In this study, we investigated the phenotype and genotype in a human subject with global developmental delay, including clinical data from the prenatal stage through early childhood. Prenatally, the mother had polyhydramnios, and the bilateral ventricles of the fetus were slightly widened. Postnatally, the infant was observed to have severely delayed psychomotor development and was incapable of visual tracking before 2 years old and could not fix on small objects. The young child had hypotonia, increased knee tendon reflex, as well as skeletal malformations, and dental crowding; she also had severe and recurrent pulmonary infections. Magnetic resonance imaging of the brain revealed a severe reduction of the cerebellum (vermis and hemispheres) and a thin corpus callosum. Through whole exome sequencing and whole genomics sequencing, we identified two novel compound heterozygous variations in CHMP1A [c.53 T > C(p.Leu18Pro)(NM_002768.5) and exon 1 deletion region (NC_000016.10:g.89656392_89674382del)]. cDNA analysis showed that the exon1 deletion region led to the impaired expression, and functional verification with zebrafish embryos using base edition indicated variant c.53 T > C (p.Leu18Pro), causing dysplasia of the cerebellum and pons. These results provide further evidence that CHMP1A variants in a recessive inheritance pattern contribute to the clinical characteristics of PCH8 and further expand our knowledge of the phenotype and genotype spectrum of PCH8

Identification of Heat-Tolerant Genes in Non-Reference Sequences in Rice by Integrating Pan-Genome, Transcriptomics, and QTLs.

The availability of large-scale genomic data resources makes it very convenient to mine and analyze genes that are related to important agricultural traits in rice. Pan-genomes have been constructed to provide insight into the genome diversity and functionality of different plants, which can be used in genome-assisted crop improvement. Thus, a pan-genome comprising all genetic elements is crucial for comprehensive variation study among the heat-resistant and -susceptible rice varieties. In this study, a rice pan-genome was firstly constructed by using 45 heat-tolerant and 15 heat-sensitive rice varieties. A total of 38,998 pan-genome genes were identified, including 37,859 genes in the reference and 1141 in the non-reference contigs. Genomic variation analysis demonstrated that a total of 76,435 SNPs were detected and identified as the heat-tolerance-related SNPs, which were specifically present in the highly heat-resistant rice cultivars and located in the genic regions or within 2 kbp upstream and downstream of the genes. Meanwhile, 3214 upregulated and 2212 downregulated genes with heat stress tolerance-related SNPs were detected in one or multiple RNA-seq datasets of rice under heat stress, among which 24 were located in the non-reference contigs of the rice pan-genome. We then mapped the DEGs with heat stress tolerance-related SNPs to the heat stress-resistant QTL regions. A total of 1677 DEGs, including 990 upregulated and 687 downregulated genes, were mapped to the 46 heat stress-resistant QTL regions, in which 2 upregulated genes with heat stress tolerance-related SNPs were identified in the non-reference sequences. This pan-genome resource is an important step towards the effective and efficient genetic improvement of heat stress resistance in rice to help meet the rapidly growing needs for improved rice productivity under different environmental stresses. These findings provide further insight into the functional validation of a number of non-reference genes and, especially, the two genes identified in the heat stress-resistant QTLs in rice

Molecular cloning and expression analysis of a zebrafish novel zinc finger protein gene rnf141

ZNF230 is a novel zinc finger gene cloned by our laboratory. In order to understand the potential functions of this gene in vertebrate development, we cloned the zebrafish orthologue of human ZNF230, named rnf141. The cDNA fragment of rnf141 was obtained by rapid amplification of cDNA ends (RACE). The open reading frame (ORF) encodes a polypeptide of 222 amino acids which shares 75.65% identity with the human ZNF230. RT-PCR analysis in zebrafish embryo and adult tissues revealed that rnf141 transcripts are maternally derived and that rnf141 mRNA has a broad distribution. Zygotic rnf141 message is strongly localized in the central nervous system, as shown by whole-mount in situ hybridization. Knockdown and over expression of rnf141 can induce abnormal phenotypes, including abnormal development of brain, as well as yolk sac and axis extendsion. Marker gene analysis showed that rnf141 may play a role in normal dorsoventral patterning of zebrafish embryos, suggesting that rnf141 may have a broad function during early development of vertebrates

Rice Stress-Resistant SNP Database.

BACKGROUND:Rice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Thus, it is of great importance to perform in-depth explorations on the genes that are closely associated with the stress-resistant traits in rice. The existing rice SNP databases have made considerable contributions to rice genomic variation information but none of them have a particular focus on integrating stress-resistant variation and related phenotype data into one web resource. RESULTS:Rice Stress-Resistant SNP database (http://bioinformatics.fafu.edu.cn/RSRS) mainly focuses on SNPs specific to biotic and abiotic stress-resistant ability in rice, and presents them in a unified web resource platform. The Rice Stress-Resistant SNP (RSRS) database contains over 9.5 million stress-resistant SNPs and 797 stress-resistant candidate genes in rice, which were detected from more than 400 stress-resistant rice varieties. We incorporated the SNPs function, genome annotation and phenotype information into this database. Besides, the database has a user-friendly web interface for users to query, browse and visualize a specific SNP efficiently. RSRS database allows users to query the SNP information and their relevant annotations for individual variety or more varieties. The search results can be visualized graphically in a genome browser or displayed in formatted tables. Users can also align SNPs between two or more rice accessions. CONCLUSION:RSRS database shows great utility for scientists to further characterize the function of variants related to environmental stress-resistant ability in rice

Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during <i>In Vitro</i> Plantlet Growth and Flowering in <i>Amaranthus tricolor</i> L.

<div><p><i>Amaranthus tricolor</i> L. is a C₄ plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, <i>Am. tricolor</i> readily bolts and blooms, degrading leaf quality. A preliminary <i>in vitro</i> flowering study demonstrated that the flowering control pathway in <i>Am. tricolor</i> may differ from that of <i>Arabidopsis</i>. Nevertheless, no transcriptome analysis of the flowering process in <i>Amaranthus</i> has been conducted. To study <i>Am. tricolor</i> floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from <i>Am. tricolor</i> at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to <i>in vitro</i> flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for <i>in vitro</i> flowering in <i>Am. tricolor</i>. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from <i>Am. tricolor</i> at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in <i>Am. tricolor</i> growth and development, but the results were somewhat similar to <i>Arabidopsis</i>. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate <i>in vitro</i> plantlet growth and flowering in <i>Am. tricolor</i>, the process appears to be highly complex in this species.</p></div

Elemental Composition, Morphology and Sources of Fine Particulates (PM2.5) in Hefei City, China

Elemental composition and morphology were studied for atmospheric fine particles (PM2.5) collected from a fast developing city, Hefei, with an aim of tracing the potential emission sources. The sampling was conducted every month at two urban sites between June 2014 and December 2015. We used X-ray fluorescence (XRF) to determine the elemental composition, and scanning electronic microscopy (SEM) and transmission electron microscope (TEM) to characterize the particles in morphology. Our results showed that PM2.5 contained large fractions of particles likely derived from fuel burning, construction and automobile emissions and was highly enriched in sulfur. Aggregations of particles suggested a strong secondary reaction under high SO2 levels. Some discrepancies in elemental composition at the two sampling sites were observed, which were attributed to the difference in traffic density and construction fugitive dust emissions. A negative correlation existed between the polluted elements in PM2.5 and the ambient temperature and a positive correlation existed with the pressure, likely caused by a reduction in the height of the terrestrial boundary layer and reaction rates of pollutants