A simple method for spray-on gene editing in planta, bioRxiv, 2019-10-26
Potential innovation in Plant research using gene-edited and genetically modified plants is currently being hindered by inefficient and costly plant transformation. We show that carbon dots formed from natural materials (quasi-spherical, <10nm nanoparticles) can act as a fast vehicle for carrying plasmids into mature plant cells, resulting in transient plant transformation in a number of important crop species with no negative impacts on photosynthesis or growth. We further show that GFP, Cas9, and gRNA introduced into wheat via foliar application (spraying on) of plasmid coated carbon dots are expressed and, in the case of Cas9, make genome edits in SPO11 genes. Therefore, we present a protocol for spray-on gene editing that is simple, inexpensive, fast, transforms in planta, and is applicable to multiple crop species. We believe this technique creates many opportunities for the future of plant transformation in research and shows great promise for plant protein production systems.
biorxiv plant-biology 200-500-users 2019Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis, bioRxiv, 2019-10-26
AbstractHere we use deep transfer learning to quantify histopathological patterns across 17,396 H&E stained histopathology image slides from 28 cancer types and correlate these with underlying genomic and transcriptomic data. Pan-cancer computational histopathology (PC-CHiP) classifies the tissue origin across organ sites and provides highly accurate, spatially resolved tumor and normal distinction within a given slide. The learned computational histopathological features correlate with a large range of recurrent genetic aberrations, including whole genome duplications (WGDs), arm-level copy number gains and losses, focal amplifications and deletions as well as driver gene mutations within a range of cancer types. WGDs can be predicted in 2527 cancer types (mean AUC=0.79) including those that were not part of model training. Similarly, we observe associations with 25% of mRNA transcript levels, which enables to learn and localise histopathological patterns of molecularly defined cell types on each slide. Lastly, we find that computational histopathology provides prognostic information augmenting histopathological subtyping and grading in the majority of cancers assessed, which pinpoints prognostically relevant areas such as necrosis or infiltrating lymphocytes on each tumour section. Taken together, these findings highlight the large potential of PC-CHiP to discover new molecular and prognostic associations, which can augment diagnostic workflows and lay out a rationale for integrating molecular and histopathological data.Key points<jatslist list-type=bullet><jatslist-item>Pan-cancer computational histopathology analysis with deep learning extracts histopathological patterns and accurately discriminates 28 cancer and 14 normal tissue types<jatslist-item><jatslist-item>Computational histopathology predicts whole genome duplications, focal amplifications and deletions, as well as driver gene mutations<jatslist-item><jatslist-item>Wide-spread correlations with gene expression indicative of immune infiltration and proliferation<jatslist-item><jatslist-item>Prognostic information augments conventional grading and histopathology subtyping in the majority of cancers<jatslist-item>
biorxiv bioinformatics 500+-users 2019Plants with self-sustained luminescence, bioRxiv, 2019-10-18
AbstractIn contrast to fluorescent proteins, light emission from luciferase reporters requires exogenous addition of a luciferin substrate. Bacterial bioluminescence has been the single exception, where an operon of five genes is sufficient to produce light autonomously. Although commonly used in prokaryotic hosts, toxicity of the aldehyde substrate has limited its use in eukaryotes1. Here we demonstrate autonomous luminescence in a multicellular eukaryotic organism by incorporating a recently discovered fungal bioluminescent system2 into tobacco plants. We monitored these light-emitting plants from germination to flowering, observing temporal and spatial patterns of luminescence across time scales from seconds to months. The dynamic patterns of luminescence reflected progression through developmental stages, circadian oscillations, transport, and response to injuries. As with other fluorescent and luminescent reporters, we anticipate that this system will be further engineered for varied purposes, especially where exogenous addition of substrate is undesirable.
biorxiv plant-biology 500+-users 2019Insights from a survey-based analysis of the academic job market, bioRxiv, 2019-10-09
AbstractApplying for a faculty position is a critical phase of many postdoctoral careers, but most postdoctoral researchers in STEM fields enter the academic job market with little knowledge of the process and expectations. A lack of data has made it difficult for applicants to assess their qualifications relative to the general applicant pool and for institutions to develop effective hiring policies. We analyzed responses to a survey of faculty job applicants between May 2018 and May 2019. We establish various background scholarly metrics for a typical faculty applicant and present an analysis of the interplay between those metrics and hiring outcomes. Traditional benchmarks of a positive research track record above a certain threshold of qualifications were unable to completely differentiate applicants with and without offers. Our findings suggest that there is no single clear path to a faculty job offer and that metrics such as career transition awards and publications in high impact factor journals were neither necessary nor sufficient for landing a faculty position. The applicants perceived the process as unnecessarily stressful, time-consuming, and largely lacking in feedback, irrespective of a successful outcome. Our findings emphasize the need to improve the transparency of the faculty job application process. In addition, we hope these and future data will help empower trainees to enter the academic job market with clearer expectations and improved confidence.
biorxiv scientific-communication-and-education 500+-users 2019The Future of OA A large-scale analysis projecting Open Access publication and readership, bioRxiv, 2019-10-09
Understanding the growth of open access (OA) is important for deciding funder policy, subscription allocation, and infrastructure planning. This study analyses the number of papers available as OA over time. The models includes both OA embargo data and the relative growth rates of different OA types over time, based on the OA status of 70 million journal articles published between 1950 and 2019. The study also looks at article usage data, analyzing the proportion of views to OA articles vs views to articles which are closed access. Signal processing techniques are used to model how these viewership patterns change over time. Viewership data is based on 2.8 million uses of the Unpaywall browser extension in July 2019. We found that Green, Gold, and Hybrid papers receive more views than their Closed or Bronze counterparts, particularly Green papers made available within a year of publication. We also found that the proportion of Green, Gold, and Hybrid articles is growing most quickly. In 2019- 31% of all journal articles are available as OA. - 52% of article views are to OA articles. Given existing trends, we estimate that by 2025 - 44% of all journal articles will be available as OA. - 70% of article views will be to OA articles. The declining relevance of closed access articles is likely to change the landscape of scholarly communication in the years to come.
biorxiv scientific-communication-and-education 200-500-users 2019A proximity biotinylation map of a human cell, bioRxiv, 2019-10-08
Compartmentalization is an essential characteristic of eukaryotic cells, ensuring that cellular processes are partitioned to defined subcellular locations. High throughput microscopy1 and biochemical fractionation coupled with mass spectrometry2-6 have helped to define the proteomes of multiple organelles and macromolecular structures. However, many compartments have remained refractory to such methods, partly due to lysis and purification artefacts and poor subcompartment resolution. Recently developed proximity-dependent biotinylation approaches such as BioID and APEX provide an alternative avenue for defining the composition of cellular compartments in living cells (e.g. 7-10). Here we report an extensive BioID-based proximity map of a human cell, comprising 192 markers from 32 different compartments that identifies 35,902 unique high confidence proximity interactions and localizes 4,145 proteins expressed in HEK293 cells. The recall of our localization predictions is on par with or better than previous large-scale mass spectrometry and microscopy approaches, but with higher localization specificity. In addition to assigning compartment and subcompartment localization for many previously unlocalized proteins, our data contain fine-grained localization information that, for example, allowed us to identify proteins with novel roles in mitochondrial dynamics. As a community resource, we have created humancellmap.org, a website that allows exploration of our data in detail, and aids with the analysis of BioID experiments.
biorxiv molecular-biology 200-500-users 2019