Common Site Planning Initiatives for Abbey Gardens and Peterborough GreenUP: Includes Final Report

Finding Common Ground for Facilitating Collaborative Partnerships stemmed from a desire among several employees of Peterborough GreenUP and Abbey Gardens to explore the potential for collaboration between both organizations. In the winter of 2014, planning began for a meeting between members of GreenUP and Abbey Gardens facilitated by Trent graduate students in the Sustainability Studies program through the Community First: Impacts of Community Engagement (CFICE) project and Trent Centre for Community Based Education (TCCBE). What this meeting would look like and what would be discussed evolved over the next few weeks and culminated in a daylong workshop in Bobcaygeon on April 1st, 2014. This report summarizes the main ideas that came up in several activities and presentations. It contains resources on the background of the project, next steps, and the contact information of participants from both organizations. Appendices include the presentation slides from the respective organizations presentations, staff lists and contact information for each organization, and detailed activity notes from the workshop

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Background: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. Results: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). Conclusions: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level

Full-length single-cell RNA-seq applied to a viral human cancer:applications to HPV expression and splicing analysis in HeLa S3 cells

Background: Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied HeLa is a well characterized HPV+ cervical cancer cell line Result: We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins Conclusion: Our results reveal the heterogeneity of a virus-infected cell line It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers

Frequent alterations in cytoskeleton remodelling genes in primary and metastatic lung adenocarcinomas

The landscape of genetic alterations in lung adenocarcinoma derived from Asian patients is largely uncharacterized. Here we present an integrated genomic and transcriptomic analysis of 335 primary lung adenocarcinomas and 35 corresponding lymph node metastases from Chinese patients. Altogether 13 significantly mutated genes are identified, including the most commonly mutated gene TP53 and novel mutation targets such as RHPN2, GLI3 and MRC2. TP53 mutations are furthermore significantly enriched in tumours from patients harbouring metastases. Genes regulating cytoskeleton remodelling processes are also frequently altered, especially in metastatic samples, of which the high expression level of IQGAP3 is identified as a marker for poor prognosis. Our study represents the first large-scale sequencing effort on lung adenocarcinoma in Asian patients and provides a comprehensive mutational landscape for both primary and metastatic tumours. This may thus form a basis for personalized medical care and shed light on the molecular pathogenesis of metastatic lung adenocarcinoma

How Non-Uniform Stiffness Affects the Propulsion Performance of a Biomimetic Robotic Fish

Live fish in nature exhibit various stiffness characteristics. The anguilliform swimmer, like eels, has a relatively flexible body, while the thunniform swimmer, like the swordfishes, has a much stiffer body. Correspondingly, in the design of biomimetic robotic fish, how to balance the non-uniform stiffness to achieve better propulsion performance is an essential question needed to be answered. In this paper, we conduct an experimental study on this question. First, a customized experimental platform is built, which eases the adjustment of the non-uniform stiffness ratio, the stiffness of the flexible part, the flapping frequency, and the flapping amplitude. Second, extensive experiments are carried out, finding that to maximize the propulsion performance of the biomimetic robotic fish, the non-uniform stiffness ratio is required to adapt to different locomotor parameters. Specifically, the non-uniform stiffness ratio needs to be reduced when the robotic fish works at low frequency, and it needs to be increased when the robotic fish works at high frequency. Finally, detailed discussions are given to further analyze the experimental results. Overall, this study can shed light on the design of a non-uniform biomimetic robotic fish, which helps to increase its propulsion performance

Embolization of uterine arteriovenous malformation

Background: Uterine arteriovenous malformation is a rare but potential life-threatening source of bleeding. A high index of suspicion and accurate diagnosis of the condition in a timely manor are essential because instrumentation that is often used for other sources of uterine bleeding can be lead to massive hemorrhage. Case: We describe here a case of uterine arteriovenous malformation. A 32-year-old woman presented abnormal vaginal bleeding following the induced abortion. A diagnosis of uterine arteriovenous malformation made on the basis of Doppler ultrasonraphy was confirmed through pelvic angiography. The embolization of bilateral uterine arteries was performed successfully. Conclusion: Uterine arteriovenous malformation should be suspected in patient with abnormal vaginal bleeding, especially who had the past medical history incluing cesarean section, induced abortion, or Dillation and Curethage and so on. Although angiography remains the gold standard, Doppler ultrasonography is also a good noninvasive technique. The transcatheter uterine artery embolization offers a safe and effective treatment

Molecular Subtyping and Prognostic Assessment Based on Tumor Mutation Burden in Patients with Lung Adenocarcinomas

The distinct molecular subtypes of lung cancer are defined by monogenic biomarkers, such as EGFR, KRAS, and ALK rearrangement. Tumor mutation burden (TMB) is a potential biomarker for response to immunotherapy, which is one of the measures for genomic instability. The molecular subtyping based on TMB has not been well characterized in lung adenocarcinomas in the Chinese population. Here we performed molecular subtyping based on TMB with the published whole exome sequencing data of 101 lung adenocarcinomas and compared the different features of the classified subtypes, including clinical features, somatic driver genes, and mutational signatures. We found that patients with lower TMB have a longer disease-free survival, and higher TMB is associated with smoking and aging. Analysis of somatic driver genes and mutational signatures demonstrates a significant association between somatic RYR2 mutations and the subtype with higher TMB. Molecular subtyping based on TMB is a potential prognostic marker for lung adenocarcinoma. Signature 4 and the mutation of RYR2 are highlighted in the TMB-High group. The mutation of RYR2 is a significant biomarker associated with high TMB in lung adenocarcinoma

CAR modulates plasma membrane nano-organization and immune signaling downstream of RALF1-FERONIA signaling pathway

International audienceIn Arabidopsis, the receptor-like kinase (RLK) FERONIA (FER) senses peptide ligands in the plasma membrane (PM), modulates plant growth and development, and integrates biotic and abiotic stress signaling for downstream adaptive responses. However, the molecular interplay of these diverse processes is largely unknown.Here, we show that FER, the receptor of Rapid Alkalinization Factor 1 (RALF1), physically interacts with C2 domain ABA-related (CAR) proteins to control the nano-organization of the PM. During this process, the RALF1-FER pathway upregulates CAR protein translation, and then more CAR proteins are recruited to the PM. This acts as a rapid feedforward loop that stabilizes the PM liquid-ordered phase. FER interacts with and phosphorylates CARs, thereby reducing their lipid-binding ability and breaking the feedback regulation at later time points.The formation of the flg22-induced FLS2-BAK1 immune complex, which depends on the integrity of FER-containing nanodomains, is impaired in fer and pentuple car14569 mutant.Together, we propose that the FER-CAR module controls the formation of PM nano-organization during RALF signaling through a self-contained amplifying loop including both positive and negative feedback