Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings.

Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salt-tolerant phenotypes was observed in this population. Genome-wide association studies (GWAS) revealed 57 loci significantly associated with salt tolerance. Forty-nine candidate genes were detected from these loci. About 10% of these genes were co-localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling, stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt-tolerance-associated-gene 4 (SAG4, GRMZM2G077295) and SAG6 (GRMZM2G106056), which encode a protein transport protein and the double-strand break repair protein MRE11, respectively, had positive roles in plant salt tolerance, and their salt-tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt-tolerance in maize.

PCSK9 induces endothelial cell autophagy by regulating the PI3K/ATK pathway in atherosclerotic coronary heart disease.

OBJECTIVE: Atherosclerosis is a chronic inflammatory disease of the arteries, and its pathogenesis is related to endothelial dysfunction. It has been found that the protein convertase subtilin/kexin9 type (PCSK9) plays an important role in AS, but its specific mechanism is still unclear. METHODS: In this study, we first cultured human umbilical vein endothelial cells (HUVECs) with 50 or 100µg/ml oxidized low-density lipoprotein (ox-LDL) for 24 hours to establish a coronary atherosclerosis cell model. RESULTS: The results showed that ox-LDL induced HUVEC injury and autophagy and upregulated PCSK9 protein expression in HUVECs in a concentration-dependent manner. Silencing PCSK9 expression with siRNA inhibited ox-LDL-induced HUVEC endothelial dysfunction, inhibited the release of inflammatory factors, promoted HUVEC proliferation and inhibited apoptosis. In addition, ox-LDL increased the expression of LC3B-I and LC3B-II and decreased the expression of p62. However, these processes are reversed by sh-PCSK9. In addition, sh-PCSK9 can inhibit PI3K, AKT and mTOR phosphorylation and promote autophagy. CONCLUSION: Taken together, our research shows that silencing PCSK9 inhibits the PI3K/ATK/mTOR pathway to activate ox-LDL-induced autophagy in vascular endothelial cells, alleviating endothelial cell injury and inflammation.

Isolation and characterization of 13 new polymorphic microsatellite markers in the Phaseolus vulgaris L. (Common Bean) genome.

In this study, 13 polymorphic microsatellite markers were isolated from the Phaseolus vulgaris L. (common bean) by using the Fast Isolation by AFLP of Sequence COntaining Repeats (FIASCO) protocol. These markers revealed two to seven alleles, with an average of 3.64 alleles per locus. The polymorphic information content (PIC) values ranged from 0.055 to 0.721 over 13 loci, with a mean value of 0.492, and 7 loci having PIC greater than 0.5. The expected heterozygosity (H(E)) and observed heterozygosity (H(O)) levels ranged from 0.057 to 0.814 and from 0.026 to 0.531, respectively. Cross-species amplification of the 13 prime pairs was performed in its related specie of Vigna unguiculata L. Seven out of all these markers showed cross-species transferability. These markers will be useful for future genetic diversity and population genetics studies for this agricultural specie and its related species.

piRNA-guided intron removal from pre-mRNAs regulates density-dependent reproductive strategy.

Animal density-dependent experiences have profound effects on reproductive strategies with marked fecundity differences. Migratory locust adopts distinct population density-dependent reproductive strategies to cope with their respective life cycles, but the mechanisms remain poorly understood. Here, we report that Piwi-interacting RNAs (piRNAs) in the locust germline play key roles in this process. We find that the locust Piwi protein Liwi1 and piRNAs are highly expressed in early developing egg chambers in solitarious locusts, which have higher fecundity than gregarious locusts. Approximately 40% of solitarious locust-associated piRNAs map to protein-coding genes. We find that Liwi1/piRNAs facilitate pre-mRNA splicing of oocyte development-related genes, such as oo18 RNA-binding protein (Orb), in the germline by recruiting the splicing factor U2AF35 to piRNA-targeted introns, thereby increasing fecundity. Such piRNA-guided pre-mRNA splicing is also functional in Drosophila and mouse germ cells. We uncover a piRNA-guided splicing mechanism for processing reproduction-related mRNAs and determining animal reproductive strategies.

Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp.chinensis).

Long non-coding RNAs (lncRNAs) mediate important epigenetic regulation in various biological processes related to the stress response in plants. However, the systematic analysis of the lncRNAs expressed in Brassica rapa under heat stress has been elusive. In this study, we performed a genome-wide analysis of the lncRNA expression profiles in non-heading Chinese cabbage leaves using strand-specific RNA-sequencing. A total of 4594 putative lncRNAs were identified with a comprehensive landscape of dynamic lncRNA expression networks under heat stress. Co-expression networks of the interactions among the differentially expressed lncRNAs, mRNAs and microRNAs revealed that several phytohormones were associated with heat tolerance, including salicylic acid (SA) and brassinosteroid (BR) pathways. Of particular importance is the discovery of 25 lncRNAs that were highly co-expressed with 10 heat responsive genes. Thirty-nine lncRNAs were predicted as endogenous target mimics (eTMs) for 35 miRNAs, and five of them were validated to be involved in the heat tolerance of Chinese cabbage. Heat responsive lncRNA (TCONS_00048391) is an eTM for bra-miR164a, that could be a sponge for miRNA binding and may be a competing endogenous RNA (ceRNA) for the target gene NAC1 (Bra030820), affecting the expression of bra-miR164a in Chinese cabbage. Thus, these findings provide new insights into the functions of lncRNAs in heat tolerance and highlight a set of candidate lncRNAs for further studies in non-heading Chinese cabbage.

The Maize ABA Receptors ZmPYL8, 9, and 12 Facilitate Plant Drought Resistance.

Drought is one of the major abiotic stresses affecting world agriculture. Breeding drought-resistant crops is one of the most important challenges for plant biologists. PYR1/PYL/RCARs, which encode the abscisic acid (ABA) receptors, play pivotal roles in ABA signaling, but how these genes function in crop drought response remains largely unknown. Here we identified 13 PYL family members in maize (ZmPYL1-13). Changes in expression of these genes under different stresses indicated that ZmPYLs played important roles in responding to multiple abiotic stresses. Transgenic analyses of ZmPYL genes in Arabidopsis showed that overexpression of ZmPYL3, ZmPYL9, ZmPYL10, and ZmPYL13 significantly enhanced the sensitivity of transgenic plants to ABA. Additionally, transgenic lines overexpressing ZmPYL8, ZmPYL9, and ZmPYL12 were more resistant to drought. Accumulation of proline and enhanced expression of drought-related marker genes in transgenic lines further confirmed the positive roles of ZmPYL genes in plant drought resistance. Association analyses with a panel of 368 maize inbred lines identified natural variants in ZmPYL8 and ZmPYL12 that were significantly associated with maize drought resistance. Our results deepen the knowledge of the function of maize PYL genes in responses to abiotic stresses, and the natural variants identified in ZmPYL genes may serve as potential molecular markers for breeding drought-resistant maize cultivars.

Geo-spatial hotspots of hemorrhagic fever with renal syndrome and genetic characterization of Seoul variants in Beijing, China.

BACKGROUND: Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in mainland China, and has extended from rural areas to cities recently. Beijing metropolis is a novel affected region, where the HFRS incidence seems to be diverse from place to place. METHODOLOGY/PRINCIPAL FINDINGS: The spatial scan analysis based on geographical information system (GIS) identified three geo-spatial "hotspots" of HFRS in Beijing when the passive surveillance data from 2004 to 2006 were used. The Relative Risk (RR) of the three "hotspots" was 5.45, 3.57 and 3.30, respectively. The Phylogenetic analysis based on entire coding region sequence of S segment and partial L segment sequence of Seoul virus (SEOV) revealed that the SEOV strains circulating in Beijing could be classified into at least three lineages regardless of their host origins. Two potential recombination events that happened in lineage #1 were detected and supported by comparative phylogenetic analysis. The SEOV strains in different lineages and strains with distinct special amino acid substitutions for N protein were partially associated with different spatial clustered areas of HFRS. CONCLUSION/SIGNIFICANCE: Hotspots of HFRS were found in Beijing, a novel endemic region, where intervention should be enhanced. Our data suggested that the genetic variation and recombination of SEOV strains was related to the high risk areas of HFRS, which merited further investigation.

"Lock and key control" of photochromic reactivity by controlling the oxidation/reduction state.

A photochemical active triangle terarylene was synthesized and the photochromic behavior was investigated. Its photochromic reactivity can be strongly suppressed by selected oxidization of the sulfur atoms in the molecules. Reactivated photochromic reactivity was obtained by deoxidization of the S, S-dioxide moieties. The suppressed photoactivity of the oxidation state was attributed to the stronger intramolecular hydrogen bonding interactions.

[Study on the association between hantavirus infection and Rattus norvegicus].

OBJECTIVE: To further understand the association of hantavirus (HV) harbored and transmitted in wild brown rats. METHODS: Rattus norvegicus (n = 570) were trapped in 10 sites in Beijing. RT-PCR was used to test rodent lung samples for hantavirus infection. Unconditional multivariate logistic regression analysis was performed, with PCR positive as the dependent variable and the characteristics of Rattus norvegicus population as independent variables. RESULTS: The overall HV prevalence in Rattus norvegicus was 9.1% (52/570). Significant association between HV infection in Rattus norvegicus and some biological characteristics of host population was observed. Adult Rattus norvegicus had a higher HV prevalence than juveniles. Males in the reproduction periods and rats with wounds were more likely to be infected with HV than others. CONCLUSION: It was further confirmed that there existed parallel transmission of HV in Rattus norvegicus hosts. Aggression might be the primary mode of HV transmission among male Rattus norvegicus.

[Spatial analysis on the distribution of hemorrhagic fever with renal syndrome by geographic information system in Haidian district, Beijing].

OBJECTIVE: To analyze the spatial distribution of hemorrhagic fever with renal syndrome (HFRS) in Haidian district, Beijing and to explore the geographical characteristics of HFRS in highly endemic areas. METHODS: Administration boundary layer was established under the background of 1:100,000 map in the ArcInfo 8.1 software. The HFRS cases from 1997 to 2002 were positioned on the map. Highly endemic areas were identified by spatial cluster analysis using SaTScan 3.0 software. Distribution of HFRS cases was shown in different colors and contours by spatial analysis of geographic information system (GIS). RESULTS: Spatial Cluster Analysis of confirmed cases of HFRS identified in 1997 - 2002 in Haidian district showed that HFRS patients were not randomly distributed. The highly endemic areas were founded in Sujiatuo township, Yongfeng township, Shangzhuang township, Wenquan town and Bei'anhe township (relative risk = 4.43, P = 0.001). A thematic map of HFRS in haidian district was set up. CONCLUSION: HFRS infections were not randomly distributed, since the distribution was related to geographic-environmental factors.

[Epidemiological characteristics of 403 patients with severe acute respiratory syndrome in Haidian district, Beijing].

OBJECTIVE: To analyze epidemiological features of severe acute respiratory syndrome (SARS) in Haidian district, Beijing. METHODS: Each SARS case was interviewed by trained investigator using standardized questionnaire followed a descriptive analysis. RESULTS: Four hundred and three SARS cases were identified and 27 of them died from March 18 and May 31, 2003. The incidence rate of SARS was 18.0/100,000 with case fatality rate as 6.7% in Haidian district, Beijing. Seventy-four percent of patients were adults with higher risk in age group of 20 - 29 year. SARS patients were scattered around in 32 out of 33 streets and villages in this district. The disease appeared to be sporadic but the case of outbreaks in family or university only seen in three streets. The course of SARS epidemic in this district could be divided into three phases: initial-which last for days, peak-21 days and then rapid decline-for 26 days. Number of patients having had a history of close contact to other SARS were gradually decreasing along with the process of the epidemics (trend chi(2) = 8.800, P = 0.003). Seventy-two point seven percent of the SARS cases had been exposed to the injection in the hospital settings. When the epidemics came to a rapid decline, 85.7% of the patients diagnosed during that period could be traced down to have had the history of contacting SARS cases within their own families. The distribution of occupation was also showed significantly different in the three respective stages (chi(2) = 36.41, P < 0.01). Among the patients who could not be identified as having confirmed contact history, 26.6% having had outward activities and 47.6% of them visited hospitals, especially during the peak stage. CONCLUSION: The intensity of SARS epidemic among the residents of Haidian district was recognized as similar to the other parts of Beijing. Nosocomial infection in hospital settings was most important cause responsible for the transmission of SARS in this district.

[Study on the molecular epidemiology of hantaviruse carried by hosts in northern suburb of Beijing].

OBJECTIVE: To investigate hantanvirus infection of captured rodents in Haidian district and Changping district of Beijing and to type hantavirus using molecular technique. METHODS: The captured mice were classified and the density of distribution was calculated. Reverse transcription-polymerase chain reaction (RT-PCR) technique was used to amplify the partial M fragnments of hantaviruse. Several representative positive samples were sequenced and analysed by ClustalX (5.0) and DNAClub software. RESULTS: A total of 414 animals were captured, among which Battus norvegicus was the dominant group. In Haidian district, the median infection rates with hantavirus were 13.14% in Battus norvegicus and 0 in Mus musculus Linnaeus. In Changping district, the average infection rates were 17.46% in Battus norvegicus and 3.57% in Mus musculus Linnaeus. Nucleotide sequences analysis showed that the virus detected all belonged to SEO-type. They clustered with Z37 virus and could be branched into 2 different subclades. CONCLUSION: The major hosts of hantavirus in Haidian and Changping district were Battus norvegicus and the epidemic strains in the two districts of Beijing were genotyped as SEO-type. Nucleotide sequence and deduced amino acid sequence from different rodents were highly homologous, while nucleotide mutation had also been observed. Further studies are required to explore the possible virus sequence mutation.