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Results 1 through 20 out of 2465

in category cell biology

 

1: Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms

Tsung-Li Liu, Srigokul Upadhyayula et al.

12,675 downloads (posted 08 Jan 2018)

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution without inducing undue stress on either. We combined lattice light sheet microscopy with two-channel adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages, and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.

https://rxivist.org/papers/22539
https://doi.org/10.1101/243352

2: The Human Cell Atlas

Aviv Regev, Sarah Teichmann et al.

11,515 downloads (posted 08 May 2017)

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body, by undertaking a Human Cell Atlas Project as an international collaborative effort. The aim would be to define all human cell types in terms of distinctive molecular profiles (e.g., gene expression) and connect this information with classical cellular descriptions (e.g., location a...

https://rxivist.org/papers/22935
https://doi.org/10.1101/121202

3: Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris

The Tabula Muris Consortium, Stephen R. Quake et al.

11,164 downloads (posted 20 Dec 2017)

We have created a compendium of single cell transcriptome data from the model organism Mus musculus comprising more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, revealing gene expression in poorly characterized cell populations and allowing for direct and controlled comparison of gene expression in cell types shared between tissues, such as T-lymphocytes and endothelial cells from distinct anatomical locations. Two distinct technical approaches were used for most t...

https://rxivist.org/papers/22348
https://doi.org/10.1101/237446

4: Inter-homologue repair in fertilized human eggs?

Dieter Egli, Michael V. Zuccaro et al.

9,798 downloads (posted 28 Aug 2017)

Many human diseases have an underlying genetic component. The development and application of methods to prevent the inheritance of damaging mutations through the human germline could have significant health benefits, and currently include preimplantation genetic diagnosis and carrier screening. Ma et al. take this a step further by attempting to remove a disease mutation from the human germline through gene editing (1). They assert the following advances: (i) the correction of a pathogenic gene mutation responsible for ...

https://rxivist.org/papers/22772
https://doi.org/10.1101/181255

5: Investigation of the cellular reprogramming phenomenon referred to as stimulus-triggered acquisition of pluripotency (STAP)

Hitoshi Niwa

9,611 downloads (posted 28 Sep 2015)

In January 2014, it was reported that strong external stimuli, such as a transient low-pH stressor, was capable of inducing the reprogramming of mammalian somatic cells, resulting in the generation of pluripotent cells (Obokata et al. 2014a, b). This cellular reprograming event was designated 'stimulus-triggered acquisition of pluripotency' (STAP) by the authors of these reports. However, after multiple instances of scientific misconduct in the handling and presentation of the data were brought to light, both reports we...

https://rxivist.org/papers/23208
https://doi.org/10.1101/027730

6: Mitochondria Are Physiologically Maintained At Close To 50 °C

Dominique Chrétien, Paule Bénit et al.

7,254 downloads (posted 02 May 2017)

In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, while a noticeable proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under dif...

https://rxivist.org/papers/22785
https://doi.org/10.1101/133223

7: Atlas of Subcellular RNA Localization Revealed by APEX-seq

Furqan M Fazal, Shuo Han et al.

6,758 downloads (posted 26 Oct 2018)

We introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two disti...

https://rxivist.org/papers/35295
https://doi.org/10.1101/454470

8: CRISPR-Cas9 Genome Editing In Human Cells Works Via The Fanconi Anemia Pathway

Chris D. Richardson, Katelynn R. Kazane et al.

4,777 downloads (posted 09 May 2017)

CRISPR-Cas9 genome editing creates targeted double strand breaks (DSBs) in eukaryotic cells that are processed by cellular DNA repair pathways. Co-administration of single stranded oligonucleotide donor DNA (ssODN) during editing can result in high-efficiency (>20%) incorporation of ssODN sequences into the break site. This process is commonly referred to as homology directed repair (HDR) and here referred to as single stranded template repair (SSTR) to distinguish it from repair using a double stranded DNA donor (dsDon...

https://rxivist.org/papers/22934
https://doi.org/10.1101/136028

9: Zika Virus in the Human Placenta and Developing Brain: Cell Tropism and Drug Inhibition

Hanna Retallack, Elizabeth Di Lullo et al.

4,567 downloads (posted 15 Jun 2016)

The rapid spread of Zika virus (ZIKV) and its association with abnormal brain development constitute a global health emergency. Congenital ZIKV infection produces a range of mild to severe pathologies, including placental damage and microcephaly. However, the placenta's role in viral transmission and the mechanisms of microcephaly have not been addressed in primary human tissues. Moreover, there is an urgent need for drugs that can prevent developmental defects following infection. Here, we identify the placental and br...

https://rxivist.org/papers/23149
https://doi.org/10.1101/058883

10: Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system

Jennifer K Heppert, Daniel J Dickinson et al.

4,290 downloads (posted 19 Feb 2016)

Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamics in vivo. Recent advances in genome editing have enabled precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential of in vivo imaging experiments, and they facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been made in vit...

https://rxivist.org/papers/23188
https://doi.org/10.1101/040279

11: Automating multimodal microscopy with NanoJ-Fluidics

Pedro Almada, Pedro M. Pereira et al.

4,265 downloads (posted 14 May 2018)

Fluorescence microscopy can reveal all aspects of cellular mechanisms, from molecular details to dynamics, thanks to approaches such as super-resolution and live-cell imaging. Each of its modalities requires specific sample preparation and imaging conditions to obtain high-quality, artefact-free images, ultimately providing complementary information. Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows involving multiple sample preparation steps. We ...

https://rxivist.org/papers/22224
https://doi.org/10.1101/320416

12: Bright photoactivatable fluorophores for single-molecule imaging

Jonathan B. Grimm, Brian P English et al.

4,219 downloads (posted 29 Jul 2016)

Small molecule fluorophores are important tools for advanced imaging experiments. The development of self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in live-cell microscopy. We recently described a general method for improving the brightness and photostability of small, cell-permeable fluorophores, resulting in the azetidine-containing 'Janelia Fluor' (JF) dyes. Here, we refine and extend the utility of the JF dyes by synthesizing photoactivatable derivatives that ar...

https://rxivist.org/papers/23134
https://doi.org/10.1101/066779

13: Building a 3D Integrated Cell

Gregory R. Johnson, Rory M. Donovan-Maiye et al.

4,185 downloads (posted 21 Dec 2017)

We present a conditional generative model for learning variation in cell and nuclear morphology and predicting the location of subcellular structures from 3D microscopy images. The model generalizes well to a wide array of structures and allows for a probabilistic interpretation of cell and nuclear morphology and structure localization from fluorescence images. We demonstrate the effectiveness of the approach by producing and evaluating photo-realistic 3D cell images using the generative model, and show that the conditi...

https://rxivist.org/papers/22570
https://doi.org/10.1101/238378

14: Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy

Chawin Ounkomol, Sharmishtaa Seshamani et al.

4,170 downloads (posted 27 Mar 2018)

Understanding cells as integrated systems is a challenge central to modern biology. While different microscopy approaches may be used to probe diverse aspects of biological organization, each method presents limitations which ultimately restrict a view into unified cellular organization. For example, while fluorescence microscopy can resolve subcellular structure in living cells, it is expensive, slow, and can damage cells. Here, we present a label-free method for predicting 3D fluorescence directly from transmitted lig...

https://rxivist.org/papers/22191
https://doi.org/10.1101/289504

15: Spatial Organization of Rho GTPase signaling by RhoGEF/RhoGAP proteins

Paul Markus Mueller, Juliane Rademacher et al.

4,015 downloads (posted 24 Jun 2018)

Rho GTPases control cell shape formation and thus fundamental physiological processes in all eukaryotes. Their functions are regulated by 145 RhoGEF and RhoGAP multi-domain proteins in humans. To provide the framework for a systems-level understanding of how these regulators orchestrate cellular morphogenesis, we comprehensively characterized their substrate specificities, localization and interactome. The resulting resource places the RhoGEFs/RhoGAPs in functional context, serving as a foundation for targeted and integ...

https://rxivist.org/papers/22089
https://doi.org/10.1101/354316

16: Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER

Sinem K. Saka, Yu Wang et al.

3,964 downloads (posted 28 Dec 2018)

Probing the molecular organization of tissues requires in situ analysis by microscopy. However current limitations in multiplexing, sensitivity, and throughput collectively constitute a major barrier for comprehensive single-cell profiling of proteins. Here, we report Immunostaining with Signal Amplification By Exchange Reaction (Immuno-SABER), a rapid, highly multiplexed signal amplification method that simultaneously tackles these key challenges. Immuno-SABER utilizes DNA-barcoded antibodies and provides a method for ...

https://rxivist.org/papers/40648
https://doi.org/10.1101/507566

17: Long-term expanding human airway organoids for disease modelling.

Norman Sachs, Domenique D. Zomer-van Ommen et al.

3,930 downloads (posted 09 May 2018)

Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar biopsies or lavage material. The pseudostratified airway organoid epithelium consists of basal cells, functional multi-ciliated cells, mucus-producing goblet cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR funct...

https://rxivist.org/papers/22234
https://doi.org/10.1101/318444

18: Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

Brock Roberts, Amanda Haupt et al.

3,837 downloads (posted 31 Mar 2017)

We present a CRISPR/Cas9 genome editing strategy to systematically tag endogenous proteins with fluorescent tags in human inducible pluripotent stem cells. To date we have generated multiple human iPSC lines with GFP tags for 10 proteins representing key cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, lamin B1, non-muscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome editing methodology using Cas9 ribonuclear protein ...

https://rxivist.org/papers/22976
https://doi.org/10.1101/123042

19: A general method to fine-tune fluorophores for live-cell and in vivo imaging

Jonathan B. Grimm, Anand K Muthusamy et al.

3,482 downloads (posted 14 Apr 2017)

Pushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the 'Janelia Fluor' (JF) series of dyes. Here, we refine and extend this strategy, showing that incorporation of 3-substituted azetidine groups allows rational tuning of the spectral and chemical properties with un...

https://rxivist.org/papers/22958
https://doi.org/10.1101/127613

20: Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses

Eswar Prasad Ramachandran Iyer, Sukanya Punthambaker et al.

3,446 downloads (posted 13 Mar 2018)

We present Barcoded Oligonucleotides Ligated On RNA Amplified for Multiplexed and parallel In-Situ analysis (BOLORAMIS), a reverse-transcription (RT)-free method for spatially-resolved, targeted, in-situ RNA identification of single or multiple targets. For this proof of concept, we have profiled 154 distinct coding and small non-coding transcripts ranging in sizes 18 nucleotide (nt) in length and upwards, from over 200,000 individual human induced pluripotent stem cells (iPSC) and demonstrated compatibility with multip...

https://rxivist.org/papers/22378
https://doi.org/10.1101/281121