A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress

AbstractThe invariant lineage of Caenorhabditis elegans has powerful potential for quantifying developmental variability in normal and stressed embryos. Previous studies of division timing by automated lineage tracing suggested that variability in cell cycle timing is low in younger embryos, but manual lineage tracing of specific lineages suggested that variability may increase for later divisions. We developed improved automated lineage tracing methods that allowroutine lineage tracing through the last round of embryonic cell divisions and we applied these methods to trace the lineage of 18 wild-type embryos. Cell cycle lengths, division axes and cell positions are remarkably consistent among these embryos at all stages, with only slight increase in variability later in development. The resulting quantitative 4-dimensional model of embryogenesis provides a powerful reference dataset to identify defects in mutants or in embryos that have experienced environmental perturbations. We also traced the lineages of embryos imaged at higher temperatures to quantify the decay in developmental robustness under temperature stress. Developmental variability increases modestly at 25°C compared with 22°C and dramatically at 26°C, and we identify homeotic transformations in a subset of embryos grown at 26°C. The deep lineage tracing methods provide a powerful tool for analysis of normal development, gene expression and mutants and we provide a graphical user interface to allow other researchers to explore the average behavior of arbitrary cells in a reference embryo

Phone to Photoshop: Mobile workarounds in young people’s visual self-presentation strategies

Relatively few young South Africans are equipped to enter the creative industries, since access to these occupations requires a combination of economic, social and cultural capital. The South African schooling system does little to assist students to overcome the income and class barriers to these industries. Increasing use of online portfolios for professional self-presentation in creative fields constitutes another key hurdle to tertiary studies at elite institutions and also to freelance employment, given the local context of unequal access to digital technologies. While mobile phones are the most accessible form of digital media in the South African context, their use in portfolio creation necessitates extensive resourcefulness for mobile-centric students. This paper explores how mobile technologies are implicated in digital self-presentation and in the creation of e-portfolios, which involve both specific forms of cultural capital and specialised infrastructure. Similarly digital portfolio creation requires infrastructure which exceeds the capacities of most South African schools. We document the barriers and opportunities presented by digital networking for two young South African Visual Arts students. These two students attended very different secondary schools but both learned to showcase their work in digital portfolios and develop professional self-presentation strategies. We describe the visual strategies they adopted as they negotiated an unequal education system in two different parts of Cape Town. Their experiences suggest that educators should be open to accommodating the mobile practices and genres that young people already use as they help them assume and challenge ‘disciplined’ identities in the visual arts

Crystallographic observation of nonenzymatic RNA primer extension

The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5′-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process

Axonemal structures reveal mechanoregulatory and disease mechanisms

Motile cilia and flagella beat rhythmically on the surface of cells to power the flow of fluid and to enable spermatozoa and unicellular eukaryotes to swim. In humans, defective ciliary motility can lead to male infertility and a congenital disorder called primary ciliary dyskinesia (PCD), in which impaired clearance of mucus by the cilia causes chronic respiratory infections1. Ciliary movement is generated by the axoneme, a molecular machine consisting of microtubules, ATP-powered dynein motors and regulatory complexes2. The size and complexity of the axoneme has so far prevented the development of an atomic model, hindering efforts to understand how it functions. Here we capitalize on recent developments in artificial intelligence-enabled structure prediction and cryo-electron microscopy (cryo-EM) to determine the structure of the 96-nm modular repeats of axonemes from the flagella of the alga Chlamydomonas reinhardtii and human respiratory cilia. Our atomic models provide insights into the conservation and specialization of axonemes, the interconnectivity between dyneins and their regulators, and the mechanisms that maintain axonemal periodicity. Correlated conformational changes in mechanoregulatory complexes with their associated axonemal dynein motors provide a mechanism for the long-hypothesized mechanotransduction pathway to regulate ciliary motility. Structures of respiratory-cilia doublet microtubules from four individuals with PCD reveal how the loss of individual docking factors can selectively eradicate periodically repeating structures

Beside the Seaside. The archaeology of the twentieth-century English seaside holiday experience: a phenomenological context.

A recent survey commissioned by English Heritage highlights the rich cultural history of the traditional English seaside resort (Brodie and Winter 2007). Emerging in the eighteenth century, these towns grew in significance before the advent of cheaper continental holidays in the 1960s signalled their demise. Nevertheless they retain an affectionate place within English social memory, and are in their own right distinctive maritime communities. Using an archaeological case study and a broadly phenomenological approach this contribution analyses the experience of the resort holiday through reference to place, space and materiality. Further, it seeks to situate the English seaside resort, as a functionally distinctive post-medieval urban and maritime phenomenon, within a global context of the archaeology of tourism

Characterization of Granulations of Calcium and Apatite in Serum as Pleomorphic Mineralo-Protein Complexes and as Precursors of Putative Nanobacteria

Calcium and apatite granulations are demonstrated here to form in both human and fetal bovine serum in response to the simple addition of either calcium or phosphate, or a combination of both. These granulations are shown to represent precipitating complexes of protein and hydroxyapatite (HAP) that display marked pleomorphism, appearing as round, laminated particles, spindles, and films. These same complexes can be found in normal untreated serum, albeit at much lower amounts, and appear to result from the progressive binding of serum proteins with apatite until reaching saturation, upon which the mineralo-protein complexes precipitate. Chemically and morphologically, these complexes are virtually identical to the so-called nanobacteria (NB) implicated in numerous diseases and considered unusual for their small size, pleomorphism, and the presence of HAP. Like NB, serum granulations can seed particles upon transfer to serum-free medium, and their main protein constituents include albumin, complement components 3 and 4A, fetuin-A, and apolipoproteins A1 and B100, as well as other calcium and apatite binding proteins found in the serum. However, these serum mineralo-protein complexes are formed from the direct chemical binding of inorganic and organic phases, bypassing the need for any biological processes, including the long cultivation in cell culture conditions deemed necessary for the demonstration of NB. Thus, these serum granulations may result from physiologically inherent processes that become amplified with calcium phosphate loading or when subjected to culturing in medium. They may be viewed as simple mineralo-protein complexes formed from the deployment of calcification-inhibitory pathways used by the body to cope with excess calcium phosphate so as to prevent unwarranted calcification. Rather than representing novel pathophysiological mechanisms or exotic lifeforms, these results indicate that the entities described earlier as NB most likely originate from calcium and apatite binding factors in the serum, presumably calcification inhibitors, that upon saturation, form seeds for HAP deposition and growth. These calcium granulations are similar to those found in organisms throughout nature and may represent the products of more general calcium regulation pathways involved in the control of calcium storage, retrieval, tissue deposition, and disposal

Comprehensive molecular characterization of gastric adenocarcinoma

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies

The Atmospheric River Tracking Method Intercomparison Project (ARTMIP): Quantifying Uncertainties in Atmospheric River Climatology

Atmospheric rivers (ARs) are now widely known for their association with high‐impact weather events and long‐term water supply in many regions. Researchers within the scientific community have developed numerous methods to identify and track of ARs—a necessary step for analyses on gridded data sets, and objective attribution of impacts to ARs. These different methods have been developed to answer specific research questions and hence use different criteria (e.g., geometry, threshold values of key variables, and time dependence). Furthermore, these methods are often employed using different reanalysis data sets, time periods, and regions of interest. The goal of the Atmospheric River Tracking Method Intercomparison Project (ARTMIP) is to understand and quantify uncertainties in AR science that arise due to differences in these methods. This paper presents results for key AR‐related metrics based on 20+ different AR identification and tracking methods applied to Modern‐Era Retrospective Analysis for Research and Applications Version 2 reanalysis data from January 1980 through June 2017. We show that AR frequency, duration, and seasonality exhibit a wide range of results, while the meridional distribution of these metrics along selected coastal (but not interior) transects are quite similar across methods. Furthermore, methods are grouped into criteria‐based clusters, within which the range of results is reduced. AR case studies and an evaluation of individual method deviation from an all‐method mean highlight advantages/disadvantages of certain approaches. For example, methods with less (more) restrictive criteria identify more (less) ARs and AR‐related impacts. Finally, this paper concludes with a discussion and recommendations for those conducting AR‐related research to consider.Fil: Rutz, Jonathan J.. National Ocean And Atmospheric Administration; Estados UnidosFil: Shields, Christine A.. National Center for Atmospheric Research; Estados UnidosFil: Lora, Juan M.. University of Yale; Estados UnidosFil: Payne, Ashley E.. University of Michigan; Estados UnidosFil: Guan, Bin. California Institute of Technology; Estados UnidosFil: Ullrich, Paul. University of California at Davis; Estados UnidosFil: O'Brien, Travis. Lawrence Berkeley National Laboratory; Estados UnidosFil: Leung, Ruby. Pacific Northwest National Laboratory; Estados UnidosFil: Ralph, F. Martin. Center For Western Weather And Water Extremes; Estados UnidosFil: Wehner, Michael. Lawrence Berkeley National Laboratory; Estados UnidosFil: Brands, Swen. Meteogalicia; EspañaFil: Collow, Allison. Universities Space Research Association; Estados UnidosFil: Goldenson, Naomi. University of California at Los Angeles; Estados UnidosFil: Gorodetskaya, Irina. Universidade de Aveiro; PortugalFil: Griffith, Helen. University of Reading; Reino UnidoFil: Kashinath, Karthik. Lawrence Bekeley National Laboratory; Estados UnidosFil: Kawzenuk, Brian. Center For Western Weather And Water Extremes; Reino UnidoFil: Krishnan, Harinarayan. Lawrence Berkeley National Laboratory; Estados UnidosFil: Kurlin, Vitaliy. University of Liverpool; Reino UnidoFil: Lavers, David. European Centre For Medium-range Weather Forecasts; Estados UnidosFil: Magnusdottir, Gudrun. University of California at Irvine; Estados UnidosFil: Mahoney, Kelly. Universidad de Lisboa; PortugalFil: Mc Clenny, Elizabeth. University of California at Davis; Estados UnidosFil: Muszynski, Grzegorz. University of Liverpool; Reino Unido. Lawrence Bekeley National Laboratory; Estados UnidosFil: Nguyen, Phu Dinh. University of California at Irvine; Estados UnidosFil: Prabhat, Mr.. Lawrence Bekeley National Laboratory; Estados UnidosFil: Qian, Yun. Pacific Northwest National Laboratory; Estados UnidosFil: Ramos, Alexandre M.. Universidade Nova de Lisboa; PortugalFil: Sarangi, Chandan. Pacific Northwest National Laboratory; Estados UnidosFil: Viale, Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentin