Critical Role of FLRT1 Phosphorylation in the Interdependent Regulation of FLRT1 Function and FGF Receptor Signalling

Background Fibronectin leucine rich transmembrane (FLRT) proteins have dual properties as regulators of cell adhesion and potentiators of fibroblast growth factor (FGF) mediated signalling. The mechanism by which the latter is achieved is still unknown and is the subject of this investigation. Principal Findings Here we show that FLRT1 is a target for tyrosine phosphorylation mediated by FGFR1 and implicate a non-receptor Src family kinase (SFK). We identify the target tyrosine residues in the cytoplasmic domain of FLRT1 and show that these are not direct substrates for Src kinase suggesting that the SFK may exert effects via potentiation of FGFR1 kinase activity. We show that whilst FLRT1 expression results in a ligand-dependent elevation of MAP kinase activity, a mutant version of FLRT1, defective as an FGFR1 kinase substrate (Y3F-FLRT1), has the property of eliciting ligand-independent chronic activation of the MAP kinase pathway which is suppressed by pharmacological inhibition of either FGFR1 or Src kinase. Functional investigation of FGFR1 and FLRT1 signalling in SH-SY5Y neuroblastoma cells reveals that FLRT1 alone acts to induce a multi-polar phenotype whereas the combination of FLRT1 and FGFR activation, or expression of Y3F-FLRT1, acts to induce neurite outgrowth via MAPK activation. Similar results were obtained in a dendrite outgrowth assay in primary hippocampal neurons. We also show that FGFR1, FLRT1 and activated Src are co-localized and this complex is trafficked toward the soma of the cell. The presence of Y3F-FLRT1 rather than FLRT1 resulted in prolonged localization of this complex within the neuritic arbour. Conclusions This study shows that the phosphorylation state of FLRT1, which is itself FGFR1 dependent, may play a critical role in the potentiation of FGFR1 signalling and may also depend on a SFK-dependent phosphorylation mechanism acting via the FGFR. This is consistent with an ‘in vivo’ role for FLRT1 regulation of FGF signalling via SFKs. Furthermore, the phosphorylation-dependent futile cycle mechanism controlling FGFR1 signalling is concurrently crucial for regulation of FLRT1-mediated neurite outgrowth

Cloudy, increasingly FAIR; Revisiting the FAIR Data guiding principles for the European Open Science Cloud

The FAIR Data Principles propose that all scholarly output should be Findable, Accessible, Interoperable, and Reusable. As a set of guiding principles, expressing only the kinds of behaviours that researchers should expect from contemporary data resources, how the FAIR principles should manifest in reality was largely open to interpretation. As support for the Principles has spread, so has the breadth of these interpretations. In observing this creeping spread of interpretation, several of the original authors felt it was now appropriate to revisit the Principles, to clarify both what FAIRness is, and is not

A scoping review of nurse-led randomised controlled trials

Background: Nurses comprise the largest portion of the healthcare workforce worldwide. However, nurse representation in the leadership of clinical research and research funding is largely unknown. The Australasian Nursing and Midwifery Clinical Trials Network was established to provide a coordinated network, focussed on building research capacity in nursing and midwifery. To support this work, this scoping review of nurse-led randomised controlled trials was conducted to summarise research activity, as well as highlight future research directions, gaps and resources. Midwife-led trials will be reported elsewhere. Aim: To quantify number, type and quality of nurse-led randomised controlled trials registered between 2000–2021. Design: A scoping review of RCTs. Data Sources: Medline, Emcare and Scopus were searched from 2000 to August 2021. ANZCTR, NHMRC, MRFF and HRC (NZ) registries were searched from inception to July 2021. Review Methods: This review was informed by the JBI scoping review framework using the PRISMA-ScR. Results: Our search yielded 186 nurse-led publications and 279 registered randomised controlled trials. Multiple trials had the same nurse leaders. There were more registrations than publications. Publications were predominantly of high methodological quality; however, there was a reliance on active controls and blinding low. Trial registrations indicate that universities and hospital/healthcare organisations were the major sources of funding, while publications indicate that Governments and the National Health and Medical Research Council were the main funding bodies. Conclusion: A small number of high-quality, large-scale, nationally funded randomised controlled trials were identified, with a larger number of locally funded small trials. There was a disparity between the number of registered trials and those published. Additional infrastructure, funding and career frameworks are needed to enable nurses to design, conduct and publish clinical trials that inform the health system and improve health outcomes. Relevance to Clinical Practice: Research initiated and led by nurses has the potential to improve the health and well-being of individuals and communities, and current nurse-led research is of high methodological quality; however, there were very few nurse-led RCTs, conducted by a small pool of nurse researchers. This gap highlights the need for support in the design, conduct and publishing of nurse-led RCTs. Patient or Public Contribution: This is a scoping review; therefore, patient or public contribution is not applicable

GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries generated by a number of these protocols. Our programmes suggested some empirical guidelines for library design; however, no information was provided regarding library diversity at the protein (rather than DNA) level. We have now updated our web server, enabling analysis of translated libraries constructed by site-saturation mutagenesis and error-prone PCR (epPCR). We introduce GLUE-Including Translation (GLUE-IT), which finds the expected amino acid completeness of libraries in which up to six codons have been independently varied (according to any user-specified randomization scheme). We provide two tools for assisting with experimental design: CodonCalculator, for assessing amino acids corresponding to given randomized codons; and AA-Calculator, for finding degenerate codons that encode user-specified sets of amino acids. We also present PEDEL-AA, which calculates amino acid statistics for libraries generated by epPCR. Input includes the parent sequence, overall mutation rate, library size, indel rates and a nucleotide mutation matrix. Output includes amino acid completeness and diversity statistics, and the number and length distribution of sequences truncated by premature termination codons. The web interfaces are available at http://guinevere.otago.ac.nz/stats.html

High resolution dynamical mapping of social interactions with active RFID

In this paper we present an experimental framework to gather data on face-to-face social interactions between individuals, with a high spatial and temporal resolution. We use active Radio Frequency Identification (RFID) devices that assess contacts with one another by exchanging low-power radio packets. When individuals wear the beacons as a badge, a persistent radio contact between the RFID devices can be used as a proxy for a social interaction between individuals. We present the results of a pilot study recently performed during a conference, and a subsequent preliminary data analysis, that provides an assessment of our method and highlights its versatility and applicability in many areas concerned with human dynamics

Rootlets, a malting by-product with great potential

Barley rootlets are the most abundant by-product from the malting industry. Due to the inherent association of the malting industry with brewing and distilling industries, it is also considered a by-product of these industries. Barley rootlets are produced during the germination step of malting. These rootlets are a valuable source of nutrition, with protein and fibre holding a large proportion of their composition. Barley rootlets are generally pelletised and used as animal fodder; however, their usage may not be limited to this. Efforts have been made to utilise barley rootlets as food ingredients, sources of enzymes, antioxidants, raw materials in fermentations, and in biochar production. Conversion of this by-product into other/new applications would reduce waste production from their industry origin and reduce some of the impending environmental concerns associated with by-product production. The current review focuses on providing information on the formation, production, and processing of barley rootlets, while also highlighting the composition, quality, and potential applications of barley rootlets

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)

Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were subsequently replaced with a randomized trinucleotide sequence donated by the DNA cassette termed SubSeqNNN. The bla gene encoding TEM-1 β-lactamase was used as a model to demonstrate the effectiveness of TriNEx. Sequence analysis revealed that the mutations were distributed throughout bla, with variants containing single, double and triple nucleotide changes. Many of the resulting amino acid substitutions had significant effects on the in vivo activity of TEM-1, including up to a 64-fold increased activity toward ceftazidime and up to an 8-fold increased resistance to the inhibitor clavulanate. Many of the observed amino acid substitutions were only accessible by exchanging at least two nucleotides per codon, including charge-switch (R164D) and aromatic substitution (W165Y) mutations. TriNEx can therefore generate a diverse range of protein variants with altered properties by combining the power of site-directed saturation mutagenesis with the capacity of whole-gene mutagenesis to randomly introduce mutations throughout a gene

An analysis of the feasibility of short read sequencing

Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that re-sequencing and de novo sequencing of the majority of a bacterial genome is possible with read lengths of 20-30 nt, and that reads of 50 nt can provide reconstructed contigs (a contiguous fragment of sequence data) of 1000 nt and greater that cover 80% of human chromosome 1

The State of Altmetrics: A Tenth Anniversary Celebration

Altmetric’s mission is to help others understand the influence of research online.We collate what people are saying about published research in sources such as the mainstream media, policy documents, social networks, blogs, and other scholarly and non-scholarly forums to provide a more robust picture of the influence and reach of scholarly work. Altmetric works with some of the biggest publishers, funders, businesses and institutions around the world to deliver this data in an accessible and reliable format. Contents Altmetrics, Ten Years Later, Euan Adie (Altmetric (founder) & Overton) Reflections on Altmetrics, Gemma Derrick (University of Lancaster), Fereshteh Didegah (Karolinska Institutet & Simon Fraser University), Paul Groth (University of Amsterdam), Cameron Neylon (Curtin University), Jason Priem (Our Research), Shenmeng Xu (University of North Carolina at Chapel Hill), Zohreh Zahedi (Leiden University) Worldwide Awareness and Use of Altmetrics, Yin-Leng Theng (Nanyang Technological University) Leveraging Machine Learning on Altmetrics Big Data, Saeed-Ul Hassan (Information Technology University), Naif R. Aljohani (King Abdulaziz University), Timothy D. Bowman (Wayne State University) Altmetrics as Social-Spatial Sensors, Vanash M. Patel (West Hertfordshire Hospitals NHS Trust), Robin Haunschild (Max Planck Institute for Solid State Research), Lutz Bornmann (Administrative Headquarters of the Max Planck Society) Altmetric’s Fable of the Hare and the Tortoise, Mike Taylor (Digital Science) The Future of Altmetrics: A Community Vision, Liesa Ross (Altmetric), Stacy Konkiel (Altmetric