scholarly journals Microhomology-based CRISPR tagging tools for protein tracking, purification, and depletion

2019 ◽  
Vol 294 (28) ◽  
pp. 10877-10885 ◽  
Author(s):  
Da-Wei Lin ◽  
Benjamin P. Chung ◽  
Jia-Wei Huang ◽  
Xiaorong Wang ◽  
Lan Huang ◽  
...  
Keyword(s):  
Protein Function ◽  
Mammalian Cells ◽  
Gene Locus ◽  
End Joining ◽  
High Quality ◽  
Physiological Conditions ◽  
Protein Tracking ◽  
Endogenous Proteins ◽  
And Behavior ◽  
Fluorescence Tags

Work in yeast models has benefitted tremendously from the insertion of epitope or fluorescence tags at the native gene locus to study protein function and behavior under physiological conditions. In contrast, work in mammalian cells largely relies on overexpression of tagged proteins because high-quality antibodies are only available for a fraction of the mammalian proteome. CRISPR/Cas9-mediated genome editing has recently emerged as a powerful genome-modifying tool that can also be exploited to insert various tags and fluorophores at gene loci to study the physiological behavior of proteins in most organisms, including mammals. Here we describe a versatile toolset for rapid tagging of endogenous proteins. The strategy utilizes CRISPR/Cas9 and microhomology-mediated end joining repair for efficient tagging. We provide tools to insert 3×HA, His6FLAG, His6-Biotin-TEV-RGSHis6, mCherry, GFP, and the auxin-inducible degron tag for compound-induced protein depletion. This approach and the developed tools should greatly facilitate functional analysis of proteins in their native environment.

scholarly journals Comparative assessment of fluorescent transgene methods for quantitative imaging in human cells

2014 ◽  
Vol 25 (22) ◽  
pp. 3610-3618 ◽  
Author(s):  
Robert Mahen ◽  
Birgit Koch ◽  
Malte Wachsmuth ◽  
Antonio Z. Politi ◽  
Alexis Perez-Gonzalez ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Function ◽  
Mammalian Cells ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Quantitative Imaging ◽  
Live Cells ◽  
Single Molecule Spectroscopy ◽  
Mitotic Kinase ◽  
Endogenous Proteins

Fluorescence tagging of proteins is a widely used tool to study protein function and dynamics in live cells. However, the extent to which different mammalian transgene methods faithfully report on the properties of endogenous proteins has not been studied comparatively. Here we use quantitative live-cell imaging and single-molecule spectroscopy to analyze how different transgene systems affect imaging of the functional properties of the mitotic kinase Aurora B. We show that the transgene method fundamentally influences level and variability of expression and can severely compromise the ability to report on endogenous binding and localization parameters, providing a guide for quantitative imaging studies in mammalian cells.

scholarly journals Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons

2022 ◽  
Author(s):  
Lewis A Macdonald ◽  
Gillian C A Taylor ◽  
Jennifer M Brisbane ◽  
Ersi Christodoulou ◽  
Lucy Scott ◽  
...  
Keyword(s):  
Mouse Models ◽  
Protein Function ◽  
Mammalian Cells ◽  
Degradation Kinetics ◽  
Cell Types ◽  
Mouse Genetics ◽  
Chemical Genetic ◽  
Endogenous Proteins ◽  
Specific Degradation

Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. Using mouse genetics, we show that degradation kinetics depend upon the dose of the tagged protein, ligand, and the E3 ligase subunit Tir1. Rapid degradation of condensin I and condensin II, two essential regulators of mitotic chromosome structure, revealed that both complexes are individually required for cell division in precursor lymphocytes, but not in their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modelling drug activity in mammalian tissues.

scholarly journals Homogenous overexpression of the extracellular matrix protein Netrin-1 in a hollow fiber bioreactor

2021 ◽  
Author(s):  
Aniel Moya-Torres ◽  
Monika Gupta ◽  
Fabian Heide ◽  
Natalie Krahn ◽  
Scott Legare ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Hollow Fiber ◽  
Mammalian Cells ◽  
Matrix Protein ◽  
Continuous Production ◽  
Extracellular Matrix Protein ◽  
Close Monitoring ◽  
High Quality ◽  
Biolayer Interferometry ◽  
Hollow Fiber Bioreactor

Abstract The production of recombinant proteins for functional and biophysical studies, especially in the field of structural determination, still represents a challenge as high quality and quantities are needed to adequately perform experiments. This is in part solved by optimizing protein constructs and expression conditions to maximize the yields in regular flask expression systems. Still, work flow and effort can be substantial with no guarantee to obtain improvements. This study presents a combination of workflows that can be used to dramatically increase protein production and improve processing results, specifically for the extracellular matrix protein Netrin-1. This proteoglycan is an axon guidance cue which interacts with various receptors to initiate downstream signaling cascades affecting cell differentiation, proliferation, metabolism, and survival. We were able to produce large glycoprotein quantities in mammalian cells, which were engineered for protein overexpression and secretion into the media using the controlled environment provided by a hollow fiber bioreactor. Close monitoring of the internal bioreactor conditions allowed for stable production over an extended period of time. In addition to this, Netrin-1 concentrations were monitored in expression media through biolayer interferometry which allowed us to increase Netrin-1 media concentrations tenfold over our current flask systems while preserving excellent protein quality and in solution behavior. Our particular combination of genetic engineering, cell culture system, protein purification, and biophysical characterization permitted us to establish an efficient and continuous production of high-quality protein suitable for structural biology studies that can be translated to various biological systems. Key points • Hollow fiber bioreactor produces substantial yields of homogenous Netrin-1 • Biolayer interferometry allows target protein quantitation in expression media • High production yields in the bioreactor do not impair Netrin-1 proteoglycan quality Graphical abstract

scholarly journals Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joonas A. Jamsen ◽  
Akira Sassa ◽  
Lalith Perera ◽  
David D. Shock ◽  
William A. Beard ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Time Lapse ◽  
Strand Break ◽  
Structural Basis ◽  
End Joining ◽  
Strand Breaks ◽  
Nucleotide Pools ◽  
Nucleotide Insertion ◽  
Non Homologous End Joining

AbstractReactive oxygen species (ROS) oxidize cellular nucleotide pools and cause double strand breaks (DSBs). Non-homologous end-joining (NHEJ) attaches broken chromosomal ends together in mammalian cells. Ribonucleotide insertion by DNA polymerase (pol) μ prepares breaks for end-joining and this is required for successful NHEJ in vivo. We previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP), that can lead to mutagenesis, cancer, aging and human disease. Here we reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during DSB repair by pol μ. Time-lapse crystallography snapshots of structural intermediates during nucleotide insertion along with computational simulations reveal substrate, metal and side chain dynamics, that allow oxidized ribonucleotides to escape polymerase discrimination checkpoints. Abundant nucleotide pools, combined with inefficient sanitization and repair, implicate pol μ mediated oxidized ribonucleotide insertion as an emerging source of widespread persistent mutagenesis and genomic instability.

scholarly journals Positive Emotions Boost Enthusiastic Responsiveness to Capitalization Attempts. Dissecting Self-Report, Physiology, and Behavior

2021 ◽  
Author(s):  
Lukasz D. Kaczmarek ◽  
Todd B. Kashdan ◽  
Maciej Behnke ◽  
Martyna Dziekan ◽  
Ewelina Matuła ◽  
...  
Keyword(s):  
Positive Emotions ◽  
Negative Emotions ◽  
Emotional Valence ◽  
Self Report ◽  
Physiological Reactivity ◽  
Direct Effects ◽  
High Quality ◽  
Video Clips ◽  
And Behavior ◽  
Positive And Negative Emotions

AbstractWhen individuals communicate enthusiasm for good events in their partners' lives, they contribute to a high-quality relationship; a phenomenon termed interpersonal capitalization. However, little is known when individuals are more ready to react enthusiastically to the partner's success. To address this gap, we examined whether positive and negative emotions boost or inhibit enthusiastic responses to partner's capitalization attempts (RCA). Participants (N = 224 individuals) responded to their partner's success. Before each capitalization attempt (operationalized as responses following the news that their partner won money in a game), we used video clips to elicit positive (primarily amusement) or negative (primarily anger) or neutral emotions in the responder. We recorded emotional valence, smiling intensity, verbal RCA, and physiological reactivity. We found indirect (but not direct) effects such that eliciting positive emotions boosted and negative emotions inhibited enthusiastic RCA (smiling intensity and enthusiastic verbal RCA). These effects were relatively small and mediated by emotional valence and smiling intensity but not physiological reactivity. The results offer novel evidence that positive emotions fuel the capitalization process.

scholarly journals Phosphorylation: The Molecular Switch of Double-Strand Break Repair

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
K. C. Summers ◽  
F. Shen ◽  
E. A. Sierra Potchanant ◽  
E. A. Phipps ◽  
R. J. Hickey ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Genomic Stability ◽  
Molecular Switches ◽  
Strand Break ◽  
Nonhomologous End Joining ◽  
End Joining ◽  
Brca1 And Brca2 ◽  
Damage Response ◽  
Repair Mechanisms ◽  
Repair Pathways

Repair of double-stranded breaks (DSBs) is vital to maintaining genomic stability. In mammalian cells, DSBs are resolved in one of the following complex repair pathways: nonhomologous end-joining (NHEJ), homologous recombination (HR), or the inclusive DNA damage response (DDR). These repair pathways rely on factors that utilize reversible phosphorylation of proteins as molecular switches to regulate DNA repair. Many of these molecular switches overlap and play key roles in multiple pathways. For example, the NHEJ pathway and the DDR both utilize DNA-PK phosphorylation, whereas the HR pathway mediates repair with phosphorylation of RPA2, BRCA1, and BRCA2. Also, the DDR pathway utilizes the kinases ATM and ATR, as well as the phosphorylation of H2AX and MDC1. Together, these molecular switches regulate repair of DSBs by aiding in DSB recognition, pathway initiation, recruitment of repair factors, and the maintenance of repair mechanisms.

scholarly journals Secreted CXCL12 (SDF-1) forms dimers under physiological conditions

2012 ◽  
Vol 442 (2) ◽  
pp. 433-442 ◽  
Author(s):  
Paramita Ray ◽  
Sarah A. Lewin ◽  
Laura Anne Mihalko ◽  
Sasha-Cai Lesher-Perez ◽  
Shuichi Takayama ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Extracellular Space ◽  
Mammalian Cells ◽  
Cell Signalling ◽  
Xenograft Model ◽  
Physiological Conditions ◽  
Cxc Chemokine ◽  
Chemokine Ligand ◽  
Chemokine Cxcl12 ◽  
And Function

Chemokine CXCL12 (CXC chemokine ligand 12) signalling through CXCR (CXC chemokine receptor) 4 and CXCR7 has essential functions in development and underlies diseases including cancer, atherosclerosis and autoimmunity. Chemokines may form homodimers that regulate receptor binding and signalling, but previous studies with synthetic CXCL12 have produced conflicting evidence for homodimerization. We used bioluminescence imaging with GL (Gaussia luciferase) fusions to investigate dimerization of CXCL12 secreted from mammalian cells. Using column chromatography and GL complementation, we established that CXCL12 was secreted from mammalian cells as both monomers and dimers. Secreted CXCL12 also formed homodimers in the extracellular space. Monomeric CXCL12 preferentially activated CXCR4 signalling through Gαi and Akt, whereas dimeric CXCL12 more effectively promoted recruitment of β-arrestin 2 to CXCR4 and chemotaxis of CXCR4-expressing breast cancer cells. We also showed that CXCR7 preferentially sequestered monomeric CXCL12 from the extracellular space and had minimal effects on dimeric CXCL12 in cell-based assays and an orthotopic tumour xenograft model of human breast cancer. These studies establish that CXCL12 secreted from mammalian cells forms homodimers under physiological conditions. Since monomeric and dimeric CXCL12 have distinct effects on cell signalling and function, our results have important implications for ongoing efforts to target CXCL12 pathways for therapy.

Supporting Young Children’s Development of Executive Function Through Early Mathematics

2021 ◽  
Vol 8 (2) ◽  
pp. 192-199
Author(s):  
Christina Mulcahy ◽  
Crystal A. Day Hess ◽  
Douglas H. Clements ◽  
Jasmine R. Ernst ◽  
Sarah E. Pan ◽  
...  
Keyword(s):  
Executive Function ◽  
Mathematics Achievement ◽  
Mathematics Teaching ◽  
Early Childhood Teachers ◽  
Academic Skills ◽  
High Quality ◽  
Alternative Strategies ◽  
Early Mathematics ◽  
General Skills ◽  
And Behavior

Early childhood teachers face competing instructional priorities to support specific academic skills and general skills that underlie learning, such as executive function (EF) skills that allow children to control their own thinking and behavior. As the evidence shows, EF skills predict later mathematics achievement, and early mathematics predicts later EF. These relations between mathematics and EF suggest high-quality mathematics teaching has a dual benefit: Teachers can promote children’s math and EF competencies by embedding support for EF in high-quality mathematics activities. Children benefit when guided to reflect on solutions and alternative strategies, and teachers benefit from guidance on how to support both math and EF. Finally, research on teachers developing both domains can inform educational policy.

Optimizing Protocols for High-Quality RNA Extraction from Blood and Liver Tissues of the Broad-Snouted Caiman

2021 ◽  
Vol 28 (4) ◽  
pp. 197-204
Author(s):  
Evelyn Cecilia López González ◽  
Lucía Magdalena Odetti ◽  
Gisela Laura Poletta ◽  
Nancy Denslow ◽  
Kevin J. Kroll ◽  
...  
Keyword(s):  
Rna Extraction ◽  
Biological Processes ◽  
High Quality ◽  
Efficient Procedure ◽  
Physiological Conditions ◽  
Environmental Perturbation ◽  
Preservation Methods ◽  
Cell Tissue ◽  
And Storage ◽  
Liver Tissues

Transcriptomic information provides fundamental insights into biological processes and can be used to determine gene expression in cell, tissue, or organism under specific physiological conditions, or in response to any environmental perturbation. Extraction of high quality RNA is a challenging step mainly in non-traditional organisms, and protocols for preservation and isolation need to be adjusted in many cases. In the present work, we aimed to develop a protocol for preservation and isolation of high-quality and quantity of RNA from blood and liver tissues of Caiman latirostris. Three preservation methods were tested: 1) flash freezing (LN2) and storage at –80°C; 2) RNAlater® conservation with progressive cooling up to –80°C); 3) preservation in TRIzol® reagent, flash freezing in LN2 and storage at –80°C. Methods 1 and 2 were tested for liver, while 2 and 3 for blood. Our results showed that both preservation methods resulted in excellent outcomes for liver samples. For blood samples however, TRIzol® preservation was an efficient procedure for adequate RNA quality, quantity, and integrity, while conservation in RNAlater® solution was inadequate in both quality and quantity for an optimal RNA extraction. Appropriate protocols were established for each tissue and are being used now for transcriptomic studies in this sentinel organism.

Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction

1986 ◽  
Vol 6 (12) ◽  
pp. 4295-4304
Author(s):  
D B Roth ◽  
J H Wilson
Keyword(s):  
Mammalian Cells ◽  
Simian Virus 40 ◽  
Restriction Enzymes ◽  
Simian Virus ◽  
T Antigen ◽  
Short Sequence ◽  
End Joining ◽  
Nonhomologous Recombination ◽  
Sequence Homologies ◽  
Linear Molecules

Although DNA breakage and reunion in nonhomologous recombination are poorly understood, previous work suggests that short sequence homologies may play a role in the end-joining step in mammalian cells. To study the mechanism of end joining in more detail, we inserted a polylinker into the simian virus 40 T-antigen intron, cleaved the polylinker with different pairs of restriction enzymes, and transfected the resulting linear molecules into monkey cells. Analysis of 199 independent junctional sequences from seven constructs with different mismatched ends indicates that single-stranded extensions are relatively stable in monkey cells and that the terminal few nucleotides are critical for cell-mediated end joining. Furthermore, these studies define three mechanisms for end joining: single-strand, template-directed, and postrepair ligations. The latter two mechanisms depend on homologous pairing of one to six complementary bases to position the junction. All three mechanisms operate with similar overall efficiencies. The relevance of this work to targeted integration in mammalian cells is discussed.

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