Bisphenol A Exposure Disrupts Enamel Formation via EZH2-Mediated H3K27me3

Enamel formation is a serial and complex biological process, during which related genes are expressed progressively in a spatiotemporal manner. This process is vulnerable to environmental cues, resulting in developmental defects of enamel (DDE). However, how environmental factors are biologically integrated during enamel formation is still poorly understood. Here, we investigated the mechanism of DDE elicited by a model endocrine-disrupting chemical, bisphenol A (BPA), in mouse incisors. We show that BPA exposure leads to DDE in mouse incisors, as well as excessive proliferation in dental epithelial stem/progenitor cells. Western blotting, chromatin immunoprecipitation sequencing, and immunofluorescence staining revealed that this effect was accompanied by upregulation of a repressive mark, H3K27me3, in the labial cervical loop of mouse incisors. Perturbation of H3K27me3 methyltransferase EZH2 repressed the level of H3K27me3 and partially attenuated the excessive proliferation in dental epithelial stem/progenitor cells and DDE induced by BPA exposure. Overall, our results demonstrate the essential role of repressive histone modification H3K27me3 in DDE elicited by exposure to an endocrine-disrupting chemical.

Single-cell RNA expression profiling of SARS-CoV-2-related ACE2 and TMPRSS2 in human trophectoderm and placenta

OBJECTIVES

To examine the characteristics and distribution of possible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target cells in the human trophectoderm (TE) and placenta.

METHODS

Bioinformatics analysis was performed based on published single-cell transcriptomic datasets of early TE and first- and second-trimester human placentae. We conducted the transcriptomic analysis of 4198 early TE cells, 1260 first-trimester placental cells and 189 extravillous trophoblast cells (EVTs) from 24-week placentae (EVT_24W) using the SMART-Seq2 method. In addition, to confirm the bioinformatic results, we performed immunohistochemical staining of three first-trimester, three second-trimester and three third-trimester placentae from nine women recruited prospectively to this study. We evaluated the expression of the SARS-CoV-2-related molecules angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2).

RESULTS

Via bioinformatic analysis, we identified the existence of ACE2 and TMPRSS2 expression in human TE as well as in first- and second-trimester placentae. In the human TE, 54.4% of TE1 cells, 9.0% of cytotrophoblasts (CTBs), 3.2% of EVTs and 29.5% of syncytiotrophoblasts (STBs) were ACE2-positive. In addition, 90.7% of TE1 cells, 31.5% of CTBs, 22.1% of EVTs and 70.8% of STBs were TMPRSS2-positive. In placental cells, 20.4% of CTBs, 44.1% of STBs, 3.4% of EVTs from 8-week placentae (EVT_8W) and 63% of EVT_24W were ACE2-positive, while 1.6% of CTBs, 26.5% of STBs, 1.9% of EVT_8W and 20.1% of EVT_24W were TMPRSS2-positive. Pathway analysis revealed that EVT_24W cells that were positive for both ACE2 and TMPRSS2 (ACE2 + TMPRSS2-positive) were associated with morphogenesis of branching structure, extracellular matrix interaction, oxygen binding and antioxidant activity. The ACE2 + TMPRSS2-positive TE1 cells were correlated with an increased capacity for viral invasion, epithelial-cell proliferation and cell adhesion. Expression of ACE2 and TMPRSS2 was observed on immunohistochemical staining in first-, second- and third-trimester placentae.

CONCLUSIONS

ACE2- and TMPRSS2-positive cells are present in the human TE and placenta in all three trimesters of pregnancy, which indicates the possibility that SARS-CoV-2 could spread via the placenta and cause intrauterine fetal infection. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.

Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression

BACKGROUND

Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown.

RESULTS

We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity.

CONCLUSIONS

The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.

TubZIP28, a novel bZIP family transcription factor from Triticum urartu, and TabZIP28, its homologue from Triticum aestivum, enhance starch synthesis in wheat

Starch in wheat grain provides humans with carbohydrates and influences the quality of wheaten food. However, no transcriptional regulator of starch synthesis has been identified first in common wheat (Triticum aestivum) due to the complex genome. Here, a novel basic leucine zipper (bZIP) family transcription factor TubZIP28 was found to be preferentially expressed in the endosperm throughout grain-filling stages in Triticum urartu, the A genome donor of common wheat. When TubZIP28 was overexpressed in common wheat, the total starch content increased by c. 4%, which contributed to c. 5% increase in the thousand kernel weight. The grain weight per plant of overexpression wheat was also elevated by c. 9%. Both in vitro and in vivo assays showed that TubZIP28 bound to the promoter of cytosolic AGPase and enhanced both the transcription and activity of the latter. Knockout of the homologue TabZIP28 in common wheat resulted in declines of both the transcription and activity of cytosolic AGPase in developing endosperms and c. 4% reduction of the total starch in mature grains. To the best of our knowledge, TubZIP28 and TabZIP28 are transcriptional activators of starch synthesis first identified in wheat, and they could be superior targets to improve the starch content and yield potential of wheat.

Direct medical burden of antimicrobial-resistant healthcare-associated infections: empirical evidence from China

BACKGROUND

Antimicrobial resistance (AMR) and healthcare-associated infections (HAIs) are among the biggest global public health challenges, and overlap widely. These infections cause significant morbidity and mortality, put pressure on health systems, and incur rising direct and indirect costs.

AIM

This study analysed the direct medical burden attributable to AMR-HAIs in Chinese public tertiary hospitals, and aimed to inform both the medical regulators and hospital managers for better control of HAIs and containment of AMR.

METHODS

The propensity score matching method (γ= 0.25σ, nearest neighbor 1:1 matching) was applied to conduct a retrospective cohort study in five public tertiary hospitals in the Hubei province of China during 2013-2015. Descriptive analysis, Pearson's chi-squared test, Mann-Whitney U-test, Wilcoxon signed-rank test and paired/independent Z/T test were conducted. The statistically significant level was set at P<0.05.

FINDINGS

From 2013 to 2015 overall, the additional total medical expenditure per HAI-AMR inpatient was US$15,557.25 compared with that of the non-HAIs, and the additional length of per hospital stay of the HAI-AMR inpatient was 41 days compared with that of the non-HAIs (P<0.001).

CONCLUSIONS

In combination with AMR, HAIs caused significant additional medical expenses and affected the turnover rate of hospital beds. Most of the increased medical costs fell to patients and their families. These findings call for more effective control of HAIs and containment of AMR. A national study is needed to estimate the medical, social and economic burden of HAIs in combination with AMR.

Clinical outcomes of ultrasound-guided radiofrequency ablation for the treatment of primary papillary thyroid microcarcinoma

AIM

To evaluate the safety, efficacy, and long-term outcomes of ultrasound-guided radiofrequency ablation (RFA) for the treatment of primary papillary thyroid microcarcinoma (PTMC).

MATERIALS AND METHODS

A total of 37 patients with 38 PTMC nodules underwent RFA at a power of 20 W between September 2014 and December 2017. The clinical data of these patients were reviewed retrospectively and analysed. Imaging studies of the nodules were conducted, and the patients' thyroid function was assessed before RFA; 1, 3, 6, and 12 months after RFA; and every 6 months thereafter. The volumes and volume reduction rate (VRR) of the nodules were also calculated.

RESULTS

RFA with a low power of 20 W was used in the treatment of 37 patients with 38 PTMC nodules. All nodules achieved complete ablation, no complications occurred, and thyroid function was not affected. During follow-up, the volume of the nodules gradually decreased. Twelve months after ablation, the mean volumes of the nodules significantly decreased to 0.01±0.03 ml with a VRR of 99.34±3.49%. At a median follow-up of 6 (range: 1-18) months, 37 of the 38 nodules were completely absorbed, and no recurrence was observed in all 37 patients.

CONCLUSIONS

Low-power RFA showed good safety and promising efficacy outcomes for the treatment of PTMC. In addition to surgery and active surveillance, RFA may be an alternative treatment option for patients with PTMC.

[β-catenin nuclear translocation represses thyroid cancer stem cells differentiating into cells with sodium-iodine symporter functional expression]

Objective: To confirm whether β-catenin nuclear translocation in thyroid cancer stem cells can differentiate into thyroid cancer cells without functional membrane expression of sodium-iodine transporter (NIS) and be resistant to iodide 131 treatment. Methods: Thyroid cancer stem cells were firstly isolated as a side population (SP) from human thyroid cancer cell line FTC133. The SP cells from FTC133 were transfected with β-catenin, and then differentiated. The cells were further collected for Western blot, Transwell and MTT assay to investigate the epithelial-mesenchymal transition (EMT) characteristics, tumor growth, invasion, and iodine uptake potency in vitro. Functional NIS expression and iodide uptake in differentiated cells were detected with immunofluorescent staining and iodide uptake assay, respectively. Subcutaneous severe combined immunodeficient (SCID) mice tumor model was induced with differentiated cancer cells to explore the in vivo effect of radioiodine treatment. Further immunohistochemical staining was performed to reveal the changes of functional proteins involved in tumor radioiodine treatment. Results: Side population was isolated from FTC133 accounting for about 0.03%, with high expression of stem cell markers and decreased expression of differentiated cell markers. Western blot showed prominent EMT phenotype in the differentiated cells from β-catenin transfected stem cell model, with absence of epithelial expression of E-cadherin and cytokeratin 18, as well as abnormal expression of vimentin,fibronectin and urokinase-type plasminogen activator. Moreover,compared with cells differentiated from untransfected or empty plasmid transfected stem cells, in vitro proliferation markedly increased 85.4% and 81.0%, respectively (both P<0.01); while in vitro invasion augmented 78.8% and 84.4%, respectively (both P<0.01). Immunofluorescent staining identified that, after transfected with β-catenin, differentiated cells underwent β-catenin nuclear translocation and NIS localization transferred from membrane to plasma, compared with cells from untransfected or empty plasmid transfected stem cells. Cell iodide uptake in vitro decreased about 52.8% and 45.2%, respectively (both P<0.01). Furthermore, in vivo experiment further demonstrated that, cells differentiated from β-catenin transfected stem cells were found with much higher tumor proliferation,tumor growth rate and larger tumor mass after radioiodine 131 treatment (both P<0.05). Conclusion: Induction of β-catenin nuclear translocation in stem cells may generate differentiated thyroid cancer cells that are not sensitive to radioiodine treatment.

[The co-relation of BRAF V600E mutation and factors affecting occurrence and prognosis of papillary thyroid carcinoma]

Objective: To investigate the prevalence of BRAF V600E mutation in thyroid nodules and to analyze the relationship between BRAF V600E mutation and various clinicopathological features. Methods: BRAF V600E mutant gene test was done in 463 cases of thyroid nodules collected from April 2015 to July 2018 in Beijing Hospital. Pathologic sections of 444 cases of papillary thyroid carcinoma were reviewed and clinical information was collected.Statistical analysis of the relationship between BRAF V600E gene mutation and various clinicopathological features was performed with SPSS 21.0 statistical software. Results: There were 109 males and 354 females in the cohort, with a male to female ratio of 1.0∶3.2. The patient ranged in age from 16 to 82 years, with an average age of 46.1 years. The BRAF V600E mutation rates in papillary thyroid carcinoma, benign thyroid nodules and other thyroid carcinoma were 86.5%(384/444),0/15 and 1/4,respectively.There was significant correlation between BRAF V600E mutation and histological diagnosis of papillary thyroid carcinoma (P<0.05). There was no correlation with age, gender, multifocality, bilaterality, coexisting lymphocytic thyroiditis, nodular goiter, maximum diameter, capsule invasion, extrathyroidal extension and clinical stage (P>0.05). Conclusions: BRAF V600E gene mutation is closely related to the occurrence of papillary thyroid carcinoma. BRAF V600E has significant value in the diagnosis of papillary thyroid carcinoma. While BRAF V600E mutation is related to the histological diagnosis, it shows no correlation with other clinicopathologic features. BRAF V600E mutation is not an independent prognostic factor in papillary thyroid carcinoma patients.

Identification and characterization of CircRNAs involved in the regulation of wheat root length

BACKGROUND

Recent studies indicate that circular RNAs (circRNAs) may play important roles in the regulation of plant growth and development. Plant roots are the main organs of nutrient and water uptake. However, whether circRNAs involved in the regulation of plant root growth remains to be elucidated.

METHODS

LH9, XN979 and YN29 are three Chinese wheat varieties with contrasting root lengths. Here, the root circRNA expression profiles of LH9, XN979 and YN29 were examined by using high-throughput sequencing technology.

RESULTS

Thirty-three and twenty-two differentially expressed circRNAs (DECs) were identified in the YN29-LH9 comparison and YN29-XN979 comparison, respectively. Among them, ten DECs coexisted in both comparisons. As the roots of both LH9 and XN979 were significantly larger and deeper than YN29, the ten DECs coexisting in the two comparisons were highly likely to be involved in the regulation of wheat root length. Moreover, three of the ten DECs have potential miRNA binding sites. Real-time PCR analysis showed that the expression levels of the potential binding miRNAs exhibited significant differences between the long root plants and the short root plants.

CONCLUSIONS

The expression levels of some circRNAs exhibited significant differences in wheat varieties with contrasting root phenotypes. Ten DECs involved in the regulation of wheat root length were successfully identified in which three of them have potential miRNAs binding sites. The expression levels of putative circRNA-binding miRNAs were correlated with their corresponding circRNAs. Our results provide new clues for studying the potential roles of circRNAs in the regulation of wheat root length.

Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat

Using Wheat 90 K SNP assay, kernel-related traits of Chinese bread wheat were used to perform association mapping in 14 environments by GWAS. Results indicated that 996 and 953 of 4417 and 3172 significant SNPs for kernel length and thousand-kernel weight were located on the chromosome 7B. Haplotype analysis of these SNPs on 7B generated the block containing the predicted TaGW8-B1 gene. TaGW8-B1 gene was further cloned by sequencing in bread wheat and a 276-bp InDel was found in the first intron. TaGW8-B1 without and with the 276-bp InDel were designated as TaGW8-B1a and TaGW8-B1b, respectively. Analysis of agronomic traits indicated that cultivars with TaGW8-B1a possessed significantly wider kernel width, significantly more kernel number per spike, longer kernel length, higher thousand-kernel weight and more spikelet number per spike than cultivars with TaGW8-B1b. Furthermore, cultivars with TaGW8-B1a possessed significantly higher yield than cultivars with TaGW8-B1b. Therefore, TaGW8-B1a was considered as a potentially superior allele. Meanwhile, TaGW8-B1a possessed a significantly higher expression level than TaGW8-B1b in mature seeds by qRT-PCR. It possibly suggested that the high expression of TaGW8-B1 was positively associated with kernel size in bread wheat. Distribution of TaGW8-B1 allele indicated that TaGW8-B1a has been positively selected in Chinese wheat.

[Role of ash2 (absent, small, or homeotic)-like and Jumonji domain-containing protein 3 on histone methylation of interferon-gamma gene and their associations with vascular damage of Kawasaki disease]

Objective: To investigate the impacts of ash2 (absent, small, or homeotic)-like (Ash2L) and Jumonji domain-containing protein 3 (Jmjd3) on histone methylation of interferon-gamma(IFN-γ) gene and association with vascular damage of Kawasaki disease (KD) in acute phase. Methods: This study was performed among 36 children with KD in acute phase (KD group) and 28 age-matched health children (control group), who were treated or underwent physical examination in our hospital between February 2015 and June 2016. Patients were further divided into KD groups with or without coronary artery lesions (KD-CAL(+) , 16 cases; KD-CAL(-), 20 cases). All KD patients were treated with intravenous immunoglobulin. The proportion of type 1 helper T(Th1) cells and protein levels of IFN-γ, T-box expressed in T cells(T-bet), phosphorylated signal transducer and activator of transcription 1(pSTAT1) and phosphorylated signal transducer and activator of transcription 4(pSTAT4) were analyzed by flow cytometry.Chromatin immunoprecipitation was performed to determine histone methylation (histone H3 tri-methyl K4(H3K4me3), histone H3 tri-methyl K27(H3K27me3)) and binding levels of Ash2L, Jmjd3 and Ezh2 associated with IFN-γ in CD4(+) T cells. Quantitative real-time PCR was used to determine mRNA levels of IFN-γ, interferon γ receptor 1(IFN-γR1), interferon γ receptor 2(IFN-γR2), interleukin 12 receptor subunit beta 1(IL-12Rβ1), interleukin 12 receptor subunit beta 2(IL-12Rβ2), interleukin 18 receptor subunit beta α(IL-18Rα), interleukin 18 receptor subunit beta β(IL-18Rβ), tumor necrosis factor receptor 1(TNFR1), toll-like receptor 4(TLR4), receptor interacting serine/threonine kinase 1(RIP-1) and myeloid differentiation primary response gene 88(MyD88) in CD4(+) T cells. Plasma concentrations of IFN-γ, interleukin 12(IL-12), interleukin 18(IL-18) and tumor necrosis factor α(TNF-α) were measured by enzyme-linked Immunosorbent assay. Results: (1)The proportion of Th1 and its protein level of IFN-γ were significantly higher in KD group than those in control group and higher in KD-CAL(+) group than in KD-CAL(-) group (all P<0.05), and lower after treatment than before treatment (all P<0.05). (2)Compared with control group, mRNA level of IFN-γ and IFN-γ-associating H3K4me3 was increased, while level of IFN-γ associating H3K27me3 in CD4(+) T cells was reduced in KD group (all P<0.05), which resulted in a higher rate of H3K4me3/H3K27me3 (P<0.05) in KD group, which was positively correlated with IFN-γ mRNA in KD group(r=0.55, P<0.05). Similar results were found between KD-CAL(+) group and KD-CAL(-) group (all P<0.05). Level of IFN-γ associating H3K27me3 was increased, and mRNA level of IFN-γ and IFN-γ associating H3K4me3 was decreased after treatment than before treatment (all P<0.05). (3)Expression of T-bet protein and binding levels of Ash2L and Jmjd3 with IFN-γ gene were significantly higher in KD group than those in control group(all P<0.05), higher in KD-CAL(+) group than those in KD-CAL(-) group (all P<0.05). These parameters were significantly lower after treatment than before treatment (all P<0.05). Binding level of Ezh2 with IFN-γ gene was similar among various groups (all P>0.05). (4)In comparison with control or after treatment, surface receptors(IFN-γR1/2, IL-12Rβ1/2, IL-18Rα/β, TNFR1 and TLR4) and its downstream molecules(pSTAT1, pSTAT4, RIP(1) and MyD88) in CD4(+) T cells, and plasma concentrations of inflammatory cytokines(IFN-γ, IL-12, IL-18 and TNF-α) were found to be higher in KD group(all P<0.05). These parameters were also higher in KD-CAL(+) group than in KD-CAL(-) group (all P<0.05). Conclusion: Aberrant histone methylation of IFN-γ associating H3K4me3 and H3K27me3 caused by over-binding of Ash2L and Jmjd3 might be involved in immune dysfunction and vascular damage in KD in the acute phase.

Comparative Proteomic Analysis Provides New Insights Into Low Nitrogen-Promoted Primary Root Growth in Hexaploid Wheat

Nitrogen deficient environments can promote wheat primary root growth (PRG) that allows for nitrogen uptake in deep soil. However, the mechanisms of low nitrogen-promoted root growth remain largely unknown. Here, an integrated comparative proteome study using iTRAQ analysis on the roots of two wheat varieties and their descendants with contrasting response to low nitrogen (LN) stress was performed under control (CK) and LN conditions. In total, 84 differentially abundant proteins (DAPs) specifically involved in the process of LN-promoted PRG were identified and 11 pathways were significantly enriched. The Glutathione metabolism, endocytosis, lipid metabolism, and phenylpropanoid biosynthesis pathways may play crucial roles in the regulation of LN-promoted PRG. We also identified 59 DAPs involved in the common response to LN stress in different genetic backgrounds. The common responsive DAPs to LN stress were mainly involved in nitrogen uptake, transportation and remobilization, and LN stress tolerance. Taken together, our results provide new insights into the metabolic and molecular changes taking place in contrasting varieties under LN conditions, which provide useful information for the genetic improvement of root traits and nitrogen use efficiency in wheat.

High-throughput sequencing revealed that microRNAs were involved in the development of superior and inferior grains in bread wheat

High-throughput sequencing was employed to investigate the expression of miRNAs and their target genes in superior and inferior seeds of Aikang 58. Small RNA sequencing revealed 620 conserved and 64 novel miRNAs in superior grains, and 623 conserved and 66 novel miRNAs in inferior grains. Among these, 97 known miRNAs, and eight novel miRNAs showed differential expression between the superior and inferior seeds. Degradome sequencing revealed at least 140 candidate target genes associated with 35 miRNA families during the development of superior and inferior seeds. GO and KEGG pathway analysis showed that the differentially expressed miRNAs, both conserved and novel, were likely involved in hormone production, carbohydrate metabolic pathways, and cell division. We validated eight known and four novel grain development-related miRNAs and their target genes by quantitative real-time polymerase chain reaction to ensure the reliability of small RNA and degradome-seq results. Of these, miR160 and miR165/166 were knocked down in Arabidopsis using short-tandem target mimic (STTM160 and STTM165/166) technology, which confirmed their roles in seed development. Specifically, STTM160 showed significantly smaller grain size, lower grain weight, shorter siliques length, shorter plant height, and more serrated leaves, whereas STTM165/166 showed decreased seed number, disabled siliques, and curled upward leaves.

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BACKGROUND

Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.

RESULTS

Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.

CONCLUSIONS

Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

BACKGROUND

During asexual reproduction the embryogenic callus can differentiate into a new plantlet, offering great potential for fostering in vitro culture efficiency in plants. The immature embryos (IMEs) of wheat (Triticum aestivum L.) are more easily able to generate embryogenic callus than mature embryos (MEs). To understand the molecular process of embryogenic callus formation in wheat, de novo transcriptome sequencing was used to generate transcriptome sequences from calli derived from IMEs and MEs after 3d, 6d, or 15d of culture (DC).

RESULTS

In total, 155 million high quality paired-end reads were obtained from the 6 cDNA libraries. Our de novo assembly generated 142,221 unigenes, of which 59,976 (42.17%) were annotated with a significant Blastx against nr, Pfam, Swissprot, KOG, KEGG, GO and COG/KOG databases. Comparative transcriptome analysis indicated that a total of 5194 differentially expressed genes (DEGs) were identified in the comparisons of IME vs. ME at the three stages, including 3181, 2085 and 1468 DEGs at 3, 6 and 15 DC, respectively. Of them, 283 overlapped in all the three comparisons. Furthermore, 4731 DEGs were identified in the comparisons between stages in IMEs and MEs. Functional analysis revealed that 271transcription factor (TF) genes (10 overlapped in all 3 comparisons of IME vs. ME) and 346 somatic embryogenesis related genes (SSEGs; 35 overlapped in all 3 comparisons of IME vs. ME) were differentially expressed in at least one comparison of IME vs. ME. In addition, of the 283 overlapped DEGs in the 3 comparisons of IME vs. ME, excluding the SSEGs and TFs, 39 possessed a higher rate of involvement in biological processes relating to response to stimuli, in multi-organism processes, reproductive processes and reproduction. Furthermore, 7 were simultaneously differentially expressed in the 2 comparisons between the stages in IMEs, but not MEs, suggesting that they may be related to embryogenic callus formation. The expression levels of genes, which were validated by qRT-PCR, showed a high correlation with the RNA-seq value.

CONCLUSIONS

This study provides new insights into the role of the transcriptome in embryogenic callus formation in wheat, and will serve as a valuable resource for further studies addressing embryogenic callus formation in plants.

Comprehensive profiling of lysine ubiquitome reveals diverse functions of lysine ubiquitination in common wheat

Protein ubiquitination, which is a major post-translational modifications that occurs in eukaryotic cells, is involved in diverse biological processes. To date, large-scale profiling of the ubiquitome in common wheat has not been reported, despite its status as the major cereal crop in the world. Here, we performed the first ubiquitome analysis of the common wheat (Triticum aestivum L.) variety, Aikang 58. Overall, 433 lysine modification sites were identified in 285 proteins in wheat seedlings, and four putative ubiquitination motifs were revealed. In particular, 83 of the 285 ubiquitinated proteins had ubiquitination orthologs in Oryza sativa L., and Arabidopsis thaliana. Ubiquitylated lysines were found to have a significantly different preference for secondary structures when compared with the all lysines. In accordance with previous studies, proteins related to binding and catalytic activity were predicted to be the preferential targets of lysine ubiquitination. Besides, protein interaction network analysis reveals that diverse interactions are modulated by protein ubiquitination. Bioinformatics analysis revealed that the ubiquitinated proteins were involved in diverse biological processes. Our data provides a global view of the ubiquitome in common wheat for the first time and lays a foundation for exploring the physiological role of lysine ubiquitination in wheat and other plants.

An integrative model of prostate cancer interaction with the bone microenvironment

Despite advanced efforts in early diagnosis, aggressive surgical treatment, and use of targeted chemotherapies, the prognosis for many cancers is still dismal. This emphasizes the necessity to develop new strategies for understanding tumor growth and metastasis. Here we use a systems approach that combines mathematical modeling and numerical simulation to develop a predictive computational model for prostate cancer and its subversion of the bone microenvironment. This model simulates metastatic prostate cancer evolution, progressing from normal bone and hormone levels to quantifiable diseased states. The simulations clearly demonstrate phenomena similar to those found clinically in prostate cancer patients. In addition, the major prediction of this model is the existence of low and high osteogenic states that are markedly different from one another. The existence and potential realization of these steady states appear to be mediated by the Wnt signaling pathway and by the effects of PSA on TGF-β, which encourages the bone microenvironment to evolve. The model is used to explore several potential therapeutic strategies, with some potential drug targets showing more promise than others: in particular, completely blocking Wnt and greatly increasing DKK-1 had significant positive effects, while blocking RANKL did not improve the outcome.