The \u3cem\u3elet-7\u3c/em\u3e MicroRNA Family Members \u3cem\u3emir\u3c/em\u3e-48, \u3cem\u3emir\u3c/em\u3e-84, and mir-241 Function Together to Regulate Developmental Timing in \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e

The microRNA let-7 is a critical regulator of developmental timing events at the larval-to-adult transition in C. elegans. Recently, microRNAs with sequence similarity to let-7 have been identified. We find that doubly mutant animals lacking the let-7 family microRNA genes mir-48 and mir-84 exhibit retarded molting behavior and retarded adult gene expression in the hypodermis. Triply mutant animals lacking mir-48, mir-84, and mir-241 exhibit repetition of L2-stage events in addition to retarded adult-stage events. mir-48, mir-84, and mir-241 function together to control the L2-to-L3 transition, likely by base pairing to complementary sites in the hbl-1 3′ UTR and downregulating hbl-1 activity. Genetic analysis indicates that mir-48, mir-84, and mir-241 specify the timing of the L2-to-L3 transition in parallel to the heterochronic genes lin-28 and lin-46. These results indicate that let-7 family microRNAs function in combination to affect both early and late developmental timing decisions

Most \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e MicroRNAs are Individually Not Essential for Development or Viability

MicroRNAs (miRNAs), a large class of short noncoding RNAs found in many plants and animals, often act to post-transcriptionally inhibit gene expression. We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans, expanding the number of mutated miRNA genes to 95, or 83% of known C. elegans miRNAs. We find that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. These observations are consistent with the hypothesis that there is significant functional redundancy among miRNAs or among gene pathways regulated by miRNAs. This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs

Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA [version 1; peer review: 1 approved, 2 approved with reservations]

Background: Methylation of carbon-5 of cytosines (m5C) is a conserved post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. It can be further modified to yield 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C), 2´-O-methyl-5-hydroxymethylcytidine (hm5Cm) and 2´-O-methyl-5-formylcytidine (f5Cm). How m5C, and specially its derivates, contribute to biology mechanistically is poorly understood. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. Hence, identifying readers for RNA modifications can enhance our understanding in the biological roles of these modifications. Methods: To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Potential readers were identified using mass spectrometry. The interaction of two of the putative readers with m5C was validated using immunoblotting. Results: Our mass spectrometry analyses revealed unique binding proteins for each of the modifications. In silico analysis for phenotype enrichments suggested that hm5Cm unique readers are enriched in proteins involved in RNA processing, while readers for m5C, hm5C and f5C are involved in germline processes. We validated our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. Finally, sequence alignment analysis showed that several of the putative m5C readers contain the conserved RNA recognition motif (RRM), including ALY-1 and ALY-2. Conclusions: The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives. Furthermore, we demonstrate that ALY-1 and ALY-2 bind to m5C in C. elegans

Evaluation of the clinical effectiveness of bioactive glass (S53P4) in the treatment of non-unions of the tibia and femur: study protocol of a randomized controlled non-inferiority trial

Background: Treatment of non-union remains challenging and often necessitates augmentation of the resulting defect with an autologous bone graft (ABG). ABG is limited in quantity and its harvesting incurs an additional surgical intervention leaving the risk for associated complications and morbidities. Therefore, artificial bone graft substitutes that might replace autologous bone are needed. S53P4-type bioactive glass (BaG) is a promising material which might be used as bone graft substitute due to its osteostimulative, conductive and antimicrobial properties. In this study, we plan to examine the clinical effectiveness of BaG as a bone graft substitute in Masquelet therapy in comparison with present standard Masquelet therapy using an ABG with tricalciumphosphate to fill the bone defect. Methods/design: This randomized controlled, clinical non-inferiority trial will be carried out at the Department of Orthopedics and Traumatology at Heidelberg University. Patients who suffer from tibial or femoral non-unions with a segmental bone defect of 2–5 cm and who are receiving Masquelet treatment will be included in the study. The resulting bone defect will either be filled with autologous bone and tricalciumphosphate (control group, N = 25) or BaG (S53P4) (study group, N = 25). Subsequent to operative therapy, all patients will receive the same standardized follow-up procedures. The primary endpoint of the study is union achieved 1year after surgery. Discussion: The results from the current study will help evaluate the clinical effectiveness of this promising biomaterial in non-union therapy. In addition, this randomized trial will help to identify potential benefits and limitations regarding the use of BaG in Masquelet therapy. Data from the study will increase the knowledge about BaG as a bone graft substitute as well as identify patients possibly benefiting from Masquelet therapy using BaG and those who are more likely to fail, thereby improving the quality of non-union treatment. Trial registration: German Clinical Trials Register (DRKS), ID: DRKS00013882 . Registered on 22 January 2018

Plasticity in pentacene thin films

We have investigated the structure, defects and plasticity of thermally evaporated thin films of the organic molecular semiconductor pentacene using X-ray Diffraction (XRD), Optical microscopy (OM), Transmission Electron Microscopy (TEM), Electron Diffraction (ED), and High Resolution Electron Microscopy (HREM). Using XRD the degree of (001) texturing present in the as-grown films was characterized. The nature of pentacene plasticity and deformation-induced molecular alignment was investigated using rubbing and scratching techniques, as well as nanoindentation. Rubbing of the bulk powder produced thin oriented films, and a deformation length scale dependence was seen. Under stress pentacene crystals initially fail by cracking, until they reach a critical size of about one micron, when they tend to plastically deform into thin sheets. Alignment of thermally evaporated films was achieved under a controlled load scratch, and the degree of molecular orientation inside the scratched region was directly imaged using HREM. Finally, using nanoindentation we measured pentacene's plastic hardness to be 0.25 GPa at a loading rate 0.05 mN/s. A loading rate dependence of the hardness and stiffness was measured, with thin films behaving harder and stiffer at faster indentation rates.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44778/1/10853_2004_Article_5277106.pd

Geomorphological processes shape plant community traits in the Arctic

Aim Geomorphological processes profoundly affect plant establishment and distributions, but their influence on functional traits is insufficiently understood. Here, we unveil trait-geomorphology relationships in Arctic plant communities. Location High-Arctic Svalbard, low-Arctic Greenland and sub-Arctic Fennoscandia. Time period 2011-2018. Major taxa studied Vascular plants. Methods We collected field-quantified data on vegetation, geomorphological processes, microclimate and soil properties from 5,280 plots and 200 species across the three Arctic regions. We combined these data with database trait records to relate local plant community trait composition to dominant geomorphological processes of the Arctic, namely cryoturbation, deflation, fluvial processes and solifluction. We investigated the relationship between plant functional traits and geomorphological processes using hierarchical generalized additive modelling. Results Our results demonstrate that community-level traits are related to geomorphological processes, with cryoturbation most strongly influencing both structural and leaf economic traits. These results were consistent across regions, suggesting a coherent biome-level trait response to geomorphological processes. Main conclusions The results indicate that geomorphological processes shape plant community traits in the Arctic. We provide empirical evidence for the existence of generalizable relationships between plant functional traits and geomorphological processes. The results indicate that the relationships are consistent across these three distinct tundra regions and that geomorphological processes should be considered in future investigations of functional traits.Peer reviewe

Geomorphological processes shape plant community traits in the Arctic

Aim Geomorphological processes profoundly affect plant establishment and distributions, but their influence on functional traits is insufficiently understood. Here, we unveil trait-geomorphology relationships in Arctic plant communities. Location High-Arctic Svalbard, low-Arctic Greenland and sub-Arctic Fennoscandia. Time period 2011-2018. Major taxa studied Vascular plants. Methods We collected field-quantified data on vegetation, geomorphological processes, microclimate and soil properties from 5,280 plots and 200 species across the three Arctic regions. We combined these data with database trait records to relate local plant community trait composition to dominant geomorphological processes of the Arctic, namely cryoturbation, deflation, fluvial processes and solifluction. We investigated the relationship between plant functional traits and geomorphological processes using hierarchical generalized additive modelling. Results Our results demonstrate that community-level traits are related to geomorphological processes, with cryoturbation most strongly influencing both structural and leaf economic traits. These results were consistent across regions, suggesting a coherent biome-level trait response to geomorphological processes. Main conclusions The results indicate that geomorphological processes shape plant community traits in the Arctic. We provide empirical evidence for the existence of generalizable relationships between plant functional traits and geomorphological processes. The results indicate that the relationships are consistent across these three distinct tundra regions and that geomorphological processes should be considered in future investigations of functional traits.Peer reviewe

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were likely present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and mRNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders, scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.We thank A. McGregor, D. Leite, M. Akam, R. Jenner, R. Kilner, A. Duarte, C. Jiggins, R. Wallbank, A. Bourke, T. Dalmay, N. Moran, K. Warchol, R. Callahan, G. Farley and T. Livdahl for providing the arthropods. H. Robertson provided the D. virgifera genome sequence. This research was supported by a Leverhulme Research Project Grant (RPG-2016-210 to F.M.J., E.A.M. and P.S.), a European Research Council grant (281668 DrosophilaInfection to F.M.J.), a Medical Research Council grant (MRC MC-A652-5PZ80 to P.S.), an Imperial College Research Fellowship (to P.S.), Cancer Research UK (C13474/A18583 and C6946/A14492 to E.A.M.), the Wellcome Trust (104640/Z/14/Z and 092096/Z/10/Z to E.A.M.) and a National Institutes of Health R37 grant (GM62862 to P.D.Z.)

Time-resolved single-cell RNA-seq using metabolic RNA labelling

Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-seq), a method for massively parallel analysis of newly transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking newly transcribed mRNAs with T-to-C substitutions. Using scNT-seq, we jointly profiled new and old transcriptomes in ~55,000 single cells. These data revealed time-resolved transcription factor activities and cell-state trajectories at the single-cell level in response to neuronal activation. We further determined rates of RNA biogenesis and decay to uncover RNA regulatory strategies during stepwise conversion between pluripotent and rare totipotent two-cell embryo (2C)-like stem cell states. Finally, integrating scNT-seq with genetic perturbation identifies DNA methylcytosine dioxygenase as an epigenetic barrier into the 2C-like cell state. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms

The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription.

PIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate germ cell development and maintain germline integrity in many animals. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. piRNA biogenesis mechanisms are diverse and remain poorly understood. Here, we identify the RNA polymerase II (RNA Pol II) core subunit RPB-9 as required for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We show that rpb-9 initiates heritable piRNA-mediated gene silencing at two DNA transposon families and at a subset of somatic genes in the germline. We provide genetic and biochemical evidence that RPB-9 is required for piRNA biogenesis by recruiting the Integrator complex at piRNA genes, hence promoting transcriptional termination. We conclude that, as a part of its rapid evolution, the piRNA pathway has co-opted an ancient machinery for high-fidelity transcription