Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2

BACKGROUND: TaGW2-6A, cloned in earlier research, strongly influences wheat grain width and TKW. Here, we mainly analyzed haplotypes of TaGW2-6B and their effects on TKW and interaction with haplotypes at TaGW2-6A. RESULTS: About 2.9 kb of the promoter sequences of TaGW2-6B and TaGW2-6D were cloned in 34 bread wheat cultivars. Eleven SNPs were detected in the promoter region of TaGW2-6B, forming 4 haplotypes, but no divergence was detected in the TaGW2-6D promoter or coding region. Three molecular markers including CAPS, dCAPS and ACAS, were developed to distinguish the TaGW2-6B haplotypes. Haplotype association analysis indicated that TaGW2-6B has a stronger influence than TaGW2-6A on TKW, and Hap-6B-1 was a favored haplotype increasing grain width and weight that had undergone strong positive selection in global wheat breeding. However, clear geographic distribution differences for TaGW2-6A haplotypes were found; Hap-6A-A was favored in Chinese, Australian and Russian cultivars, whereas Hap-6A-G was preferred in European, American and CIMMYT cultivars. This difference might be caused by a flowering and maturity time difference between the two haplotypes. Hap-6A-A is the earlier type. Haplotype interaction analysis between TaGW2-6A and TaGW2-6B showed additive effects between the favored haplotypes. Hap-6A-A/Hap-6B-1 was the best combination to increase TKW. Relative expression analysis of the three TaGW2 homoeologous genes in 22 cultivars revealed that TaGW2-6A underwent the highest expression. TaGW2-6D was the least expressed during grain development and TaGW2-6B was intermediate. Diversity of the three genes was negatively correlated with their effect on TKW. CONCLUSIONS: Genetic effects, expression patterns and historic changes of haplotypes at three homoeologous genes of TaGW2 influencing yield were dissected in wheat cultivars. Strong and constant selection to favored haplotypes has been found in global wheat breeding during the past century. This research also provides a valuable case for understanding interaction of genes that control complex traits in polyploid species

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as <it>Arabidopsis </it>and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants.</p> <p>Results</p> <p>In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (<it>Citrus trifoliata</it>) which is an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from <it>C. trifoliata </it>flower and fruit tissues. Based on sequence similarity and hairpin structure prediction, we found that 156,639 reads representing 63 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates whose precursors were all potentially generated from citrus ESTs. In addition, five miRNA* sequences were also sequenced. These sequences had not been earlier described in other plant species and accumulation of the 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes including one encoding IRX12 copper ion binding/oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in <it>C. trifoliata</it>.</p> <p>Conclusion</p> <p>Deep sequencing of short RNAs from <it>C. trifoliata </it>flowers and fruits identified 10 new potential miRNAs and 42 highly conserved miRNA families, indicating that specific miRNAs exist in <it>C. trifoliata</it>. These results show that regulatory miRNAs exist in agronomically important trifoliate orange and may play an important role in citrus growth, development, and response to disease.</p

Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

Invasive Pulmonary Aspergillosis, which is caused by the filamentous fungus Aspergillus fumigatus, is a life-threatening infection for immunosuppressed patients. Chromatin structure regulation is important for genome stability maintenance and has the potential to drive genome rearrangements and affect virulence and pathogenesis of pathogens. Here, we performed the first A. fumigatus global chromatin profiling of two histone modifications, H3K4me3 and H3K9me3, focusing on the two most investigated A. fumigatus clinical isolates, Af293 and CEA17. In eukaryotes, H3K4me3 is associated with active transcription, while H3K9me3 often marks silent genes, DNA repeats, and transposons. We found that H3K4me3 deposition is similar between the two isolates, while H3K9me3 is more variable and does not always represent transcriptional silencing. Our work uncovered striking differences in the number, locations, and expression of transposable elements between Af293 and CEA17, and the differences are correlated with H3K9me3 modifications and higher genomic variations among strains of Af293 background. Moreover, we further showed that the Af293 strains from different laboratories actually differ in their genome contents and found a frequently lost region in chromosome VIII. For one such Af293 variant, we identified the chromosomal changes and demonstrated their impacts on its secondary metabolites production, growth and virulence. Overall, our findings not only emphasize the influence of genome heterogeneity on A. fumigatus fitness, but also caution about unnoticed chromosomal variations among common laboratory strains.The Science and Technology Development Fund, Macao S.A.R (FDCT) (project reference number: 0106/2020/A and 0033/2021/A1) to KHW, Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 2016/07870-9 to GHG and 2018/14821-0 to ACC and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (301058/2019-9 and 404735/2018-5) to GHG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer Reviewed"Article signat per 15 autors/es: Ana Cristina Colabardini , Fang Wang, Zhengqiang Miao, Lakhansing Pardeshi, Clara Valero,Patrícia Alves de Castro,Daniel Yuri Akiyama,Kaeling Tan,Luisa Czamanski Nora,Rafael Silva-Rocha, Marina Marcet-Houben,Toni Gabaldón,Taicia Fill,Koon Ho Wong ,Gustavo H. Goldman"Postprint (published version

A jacalin-related lectin-like gene in wheat is a component of the plant defence system

Jacalin-related lectins (JRLs) are a subgroup of proteins with one or more jacalin-like lectin domains. Although JRLs are often associated with biotic or abiotic stimuli, their biological functions in plants, as well as their relationships to plant disease resistance, are poorly understood. A mannose-specific JRL (mJRL)-like gene (TaJRLL1) that is mainly expressed in stem and spike and encodes a protein with two jacalin-like lectin domains was identified in wheat. Pathogen infection and phytohormone treatments induced its expression; while application of the salicylic acid (SA) biosynthesis inhibitor paclobutrazol and the jasmonic acid (JA) biosynthesis inhibitor diethyldithiocarbamic acid, respectively, substantially inhibited its expression. Attenuating TaJRLL1 through virus-induced gene silencing increased susceptibility to the facultative fungal pathogen Fusarium graminearum and the biotrophic fungal pathogen Blumeria graminis. Arabidopsis thaliana transformed with TaJRLL1 displayed increased resistance to F. graminearum and Botrytis cinerea. JA and SA levels in transgenic Arabidopsis increased significantly. A loss or increase of disease resistance due to an alteration in TaJRLL1 function was correlated with attenuation or enhancement of the SA- and JA-dependent defence signalling pathways. These results suggest that TaJRLL1 could be a component of the SA- and JA-dependent defence signalling pathways

Air Quality over China

The strong economic growth in China in recent decades, together with meteorological factors, has resulted in serious air pollution problems, in particular over large industrialized areas with high population density. To reduce the concentrations of pollutants, air pollution control policies have been successfully implemented, resulting in the gradual decrease of air pollution in China during the last decade, as evidenced from both satellite and ground-based measurements. The aims of the Dragon 4 project “Air quality over China” were the determination of trends in the concentrations of aerosols and trace gases, quantification of emissions using a top-down approach and gain a better understanding of the sources, transport and underlying processes contributing to air pollution. This was achieved through (a) satellite observations of trace gases and aerosols to study the temporal and spatial variability of air pollutants; (b) derivation of trace gas emissions from satellite observations to study sources of air pollution and improve air quality modeling; and (c) study effects of haze on air quality. In these studies, the satellite observations are complemented with ground-based observations and modeling

Prenatal diagnosis of micrognathia: a systematic review

PurposeThis systematic review aimed to analyze the characteristics of different diagnostic techniques for micrognathia, summarize the consistent diagnostic criteria of each technique, and provide a simple and convenient prenatal diagnosis strategy for micrognathia.MethodsIn accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, the search was undertaken in three international databases (PubMed, Scopus, and Web of Science). The three reviewers assessed all papers and extracted the following variables: author's name and year of publication, country, study design, number of participants, gestational age, equipment for prenatal examination, biometric parameters related to micrognathia, main results.ResultsA total of 25 articles included in the analysis. Nineteen articles described cross-sectional studies (76 percent), 4 (16 percent) were case-control studies, and 2 (8 percent) were cohort studies. Fifteen studies (60 percent) had a prospective design, 9 (36 percent) had a retrospective design, and one (4 percent) had both prospective and retrospective design. Thirty-two percent of the studies (n = 8) were performed in USA, and the remaining studies were performed in China (n = 4), Israel (n = 3), Netherlands (n = 3), UK (n = 1), France (n = 1), Italy (n = 1), Belgium(n = 1), Germany (n = 1), Spain (n = 1), and Austria (n = 1). The prenatal diagnosis of micrognathia can be performed as early as possible in the first trimester, while the second and third trimester of pregnancy were the main prenatal diagnosis period. The articles that were included in the qualitative synthesis describe 30 biometric parameters related to the mandible.ConclusionOf the 30 biometric parameters related to the mandible, 15 can obtain the simple and convenient diagnostic criteria or warning value for micrognathia. Based on these diagnostic criteria or warning value, clinicians can quickly make a preliminary judgment on facial deformities, to carry out cytologic examination to further clarify the diagnosis of micrognathia

Inhibition of Topoisomerase IIA (Top2α) Induces Telomeric DNA Damage and T Cell Dysfunction During Chronic Viral Infection

T cells play a critical role in controlling viral infection; however, the mechanisms regulating their responses remain incompletely understood. Here, we investigated the role of topoisomerase IIA (Top2α, an enzyme that is essential in resolving entangled DNA strands during replication) in telomeric DNA damage and T cell dysfunction during viral infection. We demonstrated that T cells derived from patients with chronic viral (HBV, HCV, and HIV) infection had lower Top2α protein levels and enzymatic activity, along with an accumulation of the Top2α cleavage complex (Top2cc) in genomic DNA. In addition, T cells from virally infected subjects with lower Top2α levels were vulnerable to Top2α inhibitor-induced cell apoptosis, indicating an important role for Top2α in preventing DNA topological disruption and cell death. Using Top2α inhibitor (ICRF193 or Etoposide)-treated primary T cells as a model, we demonstrated that disrupting the DNA topology promoted DNA damage and T cell apoptosis via Top2cc accumulation that is associated with protein-DNA breaks (PDB) at genomic DNA. Disruption of the DNA topology was likely due to diminished expression of tyrosyl-DNA phosphodiesterase 2 (TDP2), which was inhibited in T cells in vitro by Top2α inhibitor and in vivo by chronic viral infection. These results suggest that immune-evasive viruses (HBV, HCV, and HIV) can disrupt T cell DNA topology as a mechanism of dysregulating host immunity and establishing chronic infection. Thus, restoring the DNA topologic machinery may serve as a novel strategy to protect T cells from unwanted DNA damage and to maintain immune competence

MiR-RACE, a New Efficient Approach to Determine the Precise Sequences of Computationally Identified Trifoliate Orange (Poncirus trifoliata) MicroRNAs

BACKGROUND: Among the hundreds of genes encoding miRNAs in plants reported, much more were predicted by numerous computational methods. However, unlike protein-coding genes defined by start and stop codons, the ends of miRNA molecules do not have characteristics that can be used to define the mature miRNAs exactly, which made computational miRNA prediction methods often cannot predict the accurate location of the mature miRNA in a precursor with nucleotide-level precision. To our knowledge, there haven't been reports about comprehensive strategies determining the precise sequences, especially two termini, of these miRNAs. METHODS: In this study, we report an efficient method to determine the precise sequences of computationally predicted microRNAs (miRNAs) that combines miRNA-enriched library preparation, two specific 5' and 3' miRNA RACE (miR-RACE) PCR reactions, and sequence-directed cloning, in which the most challenging step is the two specific gene specific primers designed for the two RACE reactions. miRNA-mediated mRNA cleavage by RLM-5' RACE and sequencing were carried out to validate the miRNAs detected. Real-time PCR was used to analyze the expression of each miRNA. RESULTS: The efficiency of this newly developed method was validated using nine trifoliate orange (Poncirus trifoliata) miRNAs predicted computationally. The miRNAs computationally identified were validated by miR-RACE and sequencing. Quantitative analysis showed that they have variable expression. Eight target genes have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in Poncirus trifoliate. CONCLUSION: The efficient and powerful approach developed herein can be successfully used to validate the sequences of miRNAs, especially the termini, which depict the complete miRNA sequence in the computationally predicted precursor