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AIMS: Soybean is an important food crop as well as a promising energy source. Because soybean is self-sufficient in nitrogen, phosphorus, in the orthophosphate form (Pi), becomes the most limiting macronutrient affecting the growth and productivity of soybean, especially in acidic and alkaline soils. It has been documented that plants have developed a series of physiological and biochemical strategies to adapt to Pi deficiency, but the mechanistic details of soybean response to Pi deficiency, especially those at the molecular level, are largely unknown. In this study, we aim to understand how soybean plants respond to Pi deficiency in soils by identifying and analysing Pi-responsive genes in the roots of soybean at the whole-genome scale. METHODS: The transcriptome in soybean roots under Pi-deficiency was analyzed using the Illumina’s digital gene expression (DGE) high-throughput sequencing platforms, and the expression profiles of arbitrarily selected Pi-responsive genes identified in the current research were validated by quantitative RT-PCR. RESULTS: A total of 1612 genes were found to be differentially expressed in soybean roots after Pi deficiency for seven days; 727 genes were up-regulated, and 885 genes were down-regulated. Gene ontology (GO) enrichment analysis showed that 17 GO terms of biological processes were significantly enriched including photosynthesis, iron ion transport, dUTP metabolism, cell wall organization, fatty acid metabolism and stress responses. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, homeostasis control of reactive oxygen species, calcium signaling, hormonal signaling and gene transcription were included in the differentially expressed genes. Quantitative RT-PCR was used to analyze the expression of 30 arbitrarily selected genes and 29 of them were confirmed to exhibit similar differential expression patterns under Pi deficiency as revealed by the high throughput DGE sequencing. CONCLUSIONS: These results provide useful information for identifying and characterizing important components in the Pi signaling network in soybean and enhance understanding of the molecular mechanisms by which plants adapt to low Pi stress.

Routine surveillance in live poultry markets in the northern regions of Vietnam from 2016 to 2017 resulted in the isolation of 27 highly pathogenic avian H5N1 and H5N6 viruses of 3 different clades (2.3.2.1c, 2.3.4.4f, and 2.3.4.4g). Sequence and phylogenetic analysis of these viruses revealed reassortment with various subtypes of low pathogenic avian influenza viruses. Deep-sequencing identified minor viral subpopulations encoding variants that may affect pathogenicity and sensitivity to antiviral drugs. Interestingly, mice infected with two different clade 2.3.2.1c viruses lost body weight rapidly and succumbed to virus infection, whereas mice infected with clade 2.3.4.4f or 2.3.4.4g viruses experienced non-lethal infections.

Background Colorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non‐targeted deep‐sequencing strategies enable nowadays full microbiome characterization up to species level. Aim We aimed to analyze both bacterial and viral communities in CRC using these strategies. Materials & Methods We analyzed bacterial and viral communities using both DNA and RNA deep‐sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples. Results No viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002). Discussion Sequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC. Conclusion Joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.

Pancreatic cancer is lethal due to lack of perceptible symptoms and effective treatment methods. Immunotherapy may provide promising therapeutic choices for malignant tumors like pancreatic cancer. Tumor‐infiltrating lymphocytes (TIL) in tumor mesenchyme could recognize peptide antigens presented on the surface of tumor cells. The present study aimed to test the relationship between the T cell receptor (TCR) β repertoire of the tumor and peripheral blood, and also to investigate the intra‐tumor spatial heterogeneity of the TCR β repertoire in pancreatic cancer. To the best of our knowledge, this is the first study to evaluate the clonal composition of TCR β repertoire in TIL across the spatial extent of pancreatic cancer. In this study, we studied 5 patients who were diagnosed with primary pancreatic cancer. Ultra‐deep sequencing was used to assess the rearrangement of the TCR β‐chain (TCR β) gene. HE staining and immunohistochemistry of CD3, CD4, CD8 and HLA class I were used to show histopathology and immune conditions macroscopically. TIL repertoire showed that different regions of the same tumor showed a greater number of repertoire overlaps between each other than between peripheral blood, which suggested that T cell clones in pancreatic cancer might be quite different from those in peripheral blood. In contrast, intra‐tumoral TCR β repertoires were spatially homogeneous between different regions of a single tumor tissue. Based on these results, we speculated that the cellular adaptive immune response in pancreatic cancer was spatially homogeneous; this may pave the way for immunotherapy for the treatment of pancreatic cancer patients. In this study, rearrangement genes in the TCR β‐chain (TCR β) of 5 pancreatic cancer patients were assessed by ultra‐deep sequencing. HE staining and immunohistochemistry of CD3, CD4, CD8 and HLA class I were used to show histopathology and immune conditions macroscopically. TIL repertoire showed that T cell clones within pancreatic cancer were quite different from those in peripheral blood, while intratumoral TCR β repertoires were spatially homogeneous in different regions of 1 tumor tissue.

Background Emery–Dreifuss muscular dystrophy (EDMD2) is a rare form of muscular dystrophy that is inherited as an autosomal dominant trait. In some patients, it is inherited from parental mosaicism, and this increases the recurrence risk significantly. The presence of mosaicism is underestimated due to the limitations of genetic testing and the difficulty in obtaining samples. Methods A peripheral blood sample from a 9‐year‐old girl with EDMD2 was analyzed by enhanced whole exome sequencing (WES). Sanger sequencing in her unaffected parents and younger sister was performed for validation. In the mother, ultra‐deep sequencing and droplet digital PCR (ddPCR) in multiple samples (blood, urine, saliva, oral epithelium, and nail clippings) were performed in order to identify the suspected mosaicism of the variant. Results WES revealed a heterozygous mutation (LMNA, c.1622G>A) in the proband. Sanger sequencing of the mother suggested the presence of mosaicism. The ratio of mosaic mutation was confirmed in different samples by ultra‐deep sequencing and ddPCR (19.98%–28.61% and 17.94%–28.33%, respectively). This inferred that the mosaic mutation may have occurred early during embryonic development and that the mother had gonosomal mosaicism. Conclusion We described a case of EDMD2 caused by maternal gonosomal mosaicism which was confirmed by using ultra‐deep sequencing and ddPCR. This study illustrates the importance of a systematic and comprehensive screening of parental mosaicism with more sensitive approaches and the use of multiple tissue samples. We confirmed the maternal gonosomal mosaicism by ultra‐deep sequencing and ddPCR in multiple samples from three layers. This study illustrated the importance of a systematic and comprehensive screening of parental mosaicism with more sensitive approaches and the use of multiple tissue samples.

1. There are a number of theories and processes relating to invasive alien species (IAS) and their interactions with natural enemies (predators, parasites and pathogens), including the enemy release hypothesis, spillover and spillback. 2. Most empirical studies focus on pairwise interactions and are limited to the population-level avoiding the complexities of a community approach. Oversimplified studies could result in misleading conclusions because of the importance of positive and negative feedback mechanisms, mediated by parasites, throughout communities and beyond. 3. Recent advances in ecological networks analysis (ENA) provide a powerful framework to investigate the complexity of interactions within ecological communities and response to disturbance, such as the arrival of an IAS. Molecular data, from either standard PCR or nextgeneration approaches, can be incorporated into ecological networks to enable the number and strength of interactions to be quantified; however, this has rarely been performed so far. 4. In this paper, we explore the contribution of parasite interactions, in the context of community ecology, to the success of invasive alien predatory insects with specific reference to the harlequin ladybird, Harmonia axyridis. We begin by defining the main theories and processes relating to parasite—host interactions in the context of invasion biology, before exploring the advantages of a community ecology approach, and particularly ENA, for revealing dominant mechanisms in determining the success of invasion.

Selenium (Se), an essential element, plays important roles in human health as well as environmental sustainability. Se hyperaccumulating plants are thought as an alternative selenium resource, recently. Astragalus species are known as hyperaccumulator of Se by converting it to nonaminoacid compounds. However, Se‐metabolism‐related hyperaccumulation is not elucidated in plants yet. MicroRNAs (miRNAs) are key molecules in many biological and metabolic processes via targeting mRNAs, which may also play an important role in Se accumulation in plants. In this study, we identified 418 known miRNAs, belonging to 380 families, and 151 novel miRNAs induced by Se exposure in Astragalus chyrsochlorus callus. Among known miRNAs, the expression of 287 families was common in both libraries, besides 71 families were expressed only in Se‐treated sample, whereas 60 conserved families were expressed in control tissue. miR1507a, miR1869 and miR2867‐3p were mostly up‐regulated, whereas miR1507‐5p and miR8781b were significantly down‐regulated by Se exposure. Computational analysis shows that the targets of miRNAs are involved in different types of biological mechanisms including 47 types of cellular component, 103 types of molecular function and 144 types of biological process. Degradome analysis shows that 1256 mRNAs were targeted by 499 miRNAs. We conclude that some known and novel miRNAs such as miR167a, miR319, miR1507a, miR4346, miR7767‐3p, miR7800, miR9748 and miR‐n93 target transcription factors, disease resistance proteins and some specific genes like cysteine synthase and might be related to plant hormone signal transduction, plant–pathogen interaction and sulphur metabolism pathways.

Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord. Finding key mRNAs is important for improving repair after nerve injury. This study aimed to investigate changes in mRNAs in the spinal cord following sciatic nerve injury by transcriptomic analysis. The left sciatic nerve denervation model was established in C57BL/6 mice. The left L4-6 spinal cord segment was obtained at 0, 1, 2, 4 and 8 weeks after severing the sciatic nerve. mRNA expression profiles were generated by RNA sequencing. The sequencing results of spinal cord mRNA at 1, 2, 4, and 8 weeks after severing the sciatic nerve were compared with those at 0 weeks by bioinformatic analysis. We identified 1915 differentially expressed mRNAs in the spinal cord, of which 4, 1909, and 2 were differentially expressed at 1, 4, and 8 weeks after sciatic nerve injury, respectively. Sequencing results indicated that the number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury. These mRNAs were associated with the cellular response to lipid, ATP metabolism, energy coupled proton transmembrane transport, nuclear transcription factor complex, vacuolar proton-transporting V-type ATPase complex, inner mitochondrial membrane protein complex, tau protein binding, NADH dehydrogenase activity and hydrogen ion transmembrane transporter activity. Of these mRNAs, Sgk1, Neurturin and Gpnmb took part in cell growth and development. Pathway analysis showed that these mRNAs were mainly involved in aldosterone-regulated sodium reabsorption, oxidative phosphorylation and collecting duct acid secretion. Functional assessment indicated that these mRNAs were associated with inflammation and cell morphology development. Our findings show that the number and type of spinal cord mRNAs involved in changes at different time points after peripheral nerve injury were different. The number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury. These results provide reference data for finding new targets for the treatment of peripheral nerve injury, and for further gene therapy studies of peripheral nerve injury and repair. The study procedures were approved by the Ethics Committee of the Peking University People's Hospital (approval No. 2017PHC004) on March 5, 2017.