scholarly journals Real Time de novo Deposition of Centromeric Histone-associated Proteins Using the Auxin Inducible Degradation system

2018 ◽  
Author(s):  
Sebastian Hoffmann ◽  
Daniele Fachinetti
Keyword(s):  
Real Time ◽  
Protein Dynamics ◽  
Protein Function ◽  
Genome Engineering ◽  
De Novo ◽  
Protein Complexes ◽  
Versatile Tool ◽  
Associated Proteins ◽  
Endogenous Proteins ◽  
Set Up

i.Summary/AbstractMeasuring protein dynamics is essential to uncover protein function and to understand the formation of large protein complexes such as centromeres. Recently, genome engineering in human cells has improved our ability to study the function of endogenous proteins. By combining genome editing techniques with the Auxin Inducible Degradation (AID) system, we created a versatile tool to study protein dynamics. This system allows us to analyze both protein function and dynamics by enabling rapid protein depletion and re-expression in the same experimental set-up. Here, we focus on the dynamics of the centromeric histone-associated protein CENP-C, responsible for the formation of the kinetochore complex. Following rapid removal and re-activation of a fluorescent version of CENP-C by auxin treatment and removal, we could follow CENP-C de novo deposition at centromeric regions during different stages of the cell cycle. In conclusion, the auxin degradation system is a powerful tool to assess and quantify protein dynamics in real time.

scholarly journals AI-based Spectroscopic Monitoring of Real-time Interactions between SARS-CoV-2 and Human ACE2

2020 ◽  
Author(s):  
Sheng Ye ◽  
Guozhen Zhang ◽  
Jun Jiang
Keyword(s):  
Machine Learning ◽  
Real Time ◽  
Protein Dynamics ◽  
Structural Information ◽  
Protein Complexes ◽  
Spike Protein ◽  
Proof Of Concept ◽  
Spectroscopy Study ◽  
Time Resolved ◽  
Spectroscopic Monitoring

<div> <p>Here we demonstrate by a proof-of-concept simulation of IR spectra of complex of spike protein of SARS-CoV-2 and human ACE2, that a time-resolved spectroscopy may monitor the real-time structural information of the protein-protein complexes of interest, with the help of a machine learning protocol. The significant speedup of our approach relative to conventional quantum chemistry approach suggests a promising way of accelerating the development of real-time spectroscopy study of protein dynamics.</p> </div>

scholarly journals The evaluation of RNA-Seq de novo assembly by PacBio long read sequencing

2019 ◽  
Author(s):  
Yifan Yang ◽  
Michael Gribskov
Keyword(s):  
Real Time ◽  
De Novo ◽  
Critical Issue ◽  
Evaluation Methods ◽  
Model Organisms ◽  
Rna Seq ◽  
Long Reads ◽  
Long Read ◽  
Set Up ◽  
Downstream Analysis

AbstractRNA-Seq de novo assembly is an important method to generate transcriptomes for non-model organisms before any downstream analysis. Given many great de novo assembly methods developed by now, one critical issue is that there is no consensus on the evaluation of de novo assembly methods yet. Therefore, to set up a benchmark for evaluating the quality of de novo assemblies is very critical. Addressing this challenge will help us deepen the insights on the properties of different de novo assemblers and their evaluation methods, and provide hints on choosing the best assembly sets as transcriptomes of non-model organisms for the further functional analysis. In this article, we generate a “real time” transcriptome using PacBio long reads as a benchmark for evaluating five de novo assemblers and two model-based de novo assembly evaluation methods. By comparing the de novo assmblies generated by RNA-Seq short reads with the “real time” transcriptome from the same biological sample, we find that Trinity is best at the completeness by generating more assemblies than the alternative assemblers, but less continuous and having more misassemblies; Oases is best at the continuity and specificity, but less complete; The performance of SOAPdenovo-Trans, Trans-AByss and IDBA-Tran are in between of five assemblers. For evaluation methods, DETONATE leverages multiple aspects of the assembly set and ranks the assembly set with an average performance as the best, meanwhile the contig score can serve as a good metric to select assemblies with high completeness, specificity, continuity but not sensitive to misassemblies; TransRate contig score is useful for removing misassemblies, yet often the assemblies in the optimal set is too few to be used as a transcriptome.

scholarly journals AI-based Spectroscopic Monitoring of Real-time Interactions between SARS-CoV-2 and Human ACE2

2020 ◽  
Author(s):  
Sheng Ye ◽  
Guozhen Zhang ◽  
Jun Jiang
Keyword(s):  
Machine Learning ◽  
Real Time ◽  
Protein Dynamics ◽  
Structural Information ◽  
Protein Complexes ◽  
Spike Protein ◽  
Proof Of Concept ◽  
Spectroscopy Study ◽  
Time Resolved ◽  
Spectroscopic Monitoring

<div> <p>Here we demonstrate by a proof-of-concept simulation of IR spectra of complex of spike protein of SARS-CoV-2 and human ACE2, that a time-resolved spectroscopy may monitor the real-time structural information of the protein-protein complexes of interest, with the help of a machine learning protocol. The significant speedup of our approach relative to conventional quantum chemistry approach suggests a promising way of accelerating the development of real-time spectroscopy study of protein dynamics.</p> </div>

scholarly journals Nanopores: a versatile tool to study protein dynamics

2020 ◽  
Author(s):  
Sonja Schmid ◽  
Cees Dekker
Keyword(s):  
Protein Dynamics ◽  
Single Molecule ◽  
Conformational Changes ◽  
Protein Function ◽  
Label Free ◽  
Cellular Functions ◽  
Ensemble Averaging ◽  
Time Resolved ◽  
Wide Range ◽  
Versatile Tool

Abstract Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins – involving conformational changes and interactions – remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics – one molecule at a time.

scholarly journals Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system

2019 ◽  
Author(s):  
Tyler S. Halpin-Healy ◽  
Sanne E. Klompe ◽  
Samuel H. Sternberg ◽  
Israel S. Fernández
Keyword(s):  
Genome Engineering ◽  
De Novo ◽  
Structural Basis ◽  
Functional Coupling ◽  
Type I ◽  
Loop Formation ◽  
Dna Targeting ◽  
Associated Proteins ◽  
Mechanistic Basis ◽  
Cascade Complex

AbstractBacteria have evolved adaptive immune systems encoded by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and the CRISPR-associated (Cas) genes to maintain genomic integrity in the face of relentless assault from pathogens and mobile genetic elements [1–3]. Type I CRISPR-Cas systems canonically target foreign DNA for degradation via the joint action of the ribonucleoprotein complex Cascade and the helicase-nuclease Cas3 [4,5] but nuclease-deficient Type I systems lacking Cas3 have been repurposed for RNA-guided transposition by bacterial Tn7-like transposons [6,7]. How CRISPR- and transposon-associated machineries collaborate during DNA targeting and insertion has remained elusive. Here we determined structures of a novel TniQ-Cascade complex encoded by the Vibrio cholerae Tn6677 transposon using single particle electron cryo-microscopy (cryo-EM), revealing the mechanistic basis of this functional coupling. The quality of the cryo-EM maps allowed for de novo modeling and refinement of the transposition protein TniQ, which binds to the Cascade complex as a dimer in a head-to-tail configuration, at the interface formed by Cas6 and Cas7 near the 3’ end of the crRNA. The natural Cas8-Cas5 fusion protein binds the 5’ crRNA handle and contacts the TniQ dimer via a flexible insertion domain. A target DNA-bound structure reveals critical interactions necessary for protospacer adjacent motif (PAM) recognition and R-loop formation. The present work lays the foundation for a structural understanding of how DNA targeting by TniQ-Cascade leads to downstream recruitment of additional transposon-associated proteins, and will guide protein engineering efforts to leverage this system for programmable DNA insertions in genome engineering applications.

DEVELOPMENT OF MULTIPLEX REAL-TIME PCR ASSAY FOR SIX PATHOGENS: RAPID TOOL FOR DIAGNOSIS OF BACTERIAL MENINGITIS

2019 ◽  
pp. 60-66
Author(s):  
Viet Quynh Tram Ngo ◽  
Thi Ti Na Nguyen ◽  
Hoang Bach Nguyen ◽  
Thi Tuyet Ngoc Tran ◽  
Thi Nam Lien Nguyen ◽  
...  
Keyword(s):  
Bacterial Meningitis ◽  
Real Time ◽  
Real Time Pcr ◽  
Diagnostic Methods ◽  
Type B ◽  
E Coli ◽  
Pcr Assays ◽  
Set Up ◽  
Etiological Agents ◽  
Suis Serotype

Introduction: Bacterial meningitis is an acute central nervous infection with high mortality or permanent neurological sequelae if remained undiagnosed. However, traditional diagnostic methods for bacterial meningitis pose challenge in prompt and precise identification of causative agents. Aims: The present study will therefore aim to set up in-house PCR assays for diagnosis of six pathogens causing the disease including H. influenzae type b, S. pneumoniae, N. meningitidis, S. suis serotype 2, E. coli and S. aureus. Methods: inhouse PCR assays for detecting six above-mentioned bacteria were optimized after specific pairs of primers and probes collected from the reliable literature resources and then were performed for cerebrospinal fluid (CSF) samples from patients with suspected meningitis in Hue Hospitals. Results: The set of four PCR assays was developed including a multiplex real-time PCR for S. suis serotype 2, H. influenzae type b and N. meningitides; three monoplex real-time PCRs for E. coli, S. aureus and S. pneumoniae. Application of the in-house PCRs for 116 CSF samples, the results indicated that 48 (39.7%) cases were positive with S. suis serotype 2; one case was positive with H. influenzae type b; 4 cases were positive with E. coli; pneumococcal meningitis were 19 (16.4%) cases, meningitis with S. aureus and N. meningitidis were not observed in any CSF samples in this study. Conclusion: our in-house real-time PCR assays are rapid, sensitive and specific tools for routine diagnosis to detect six mentioned above meningitis etiological agents. Key words: Bacterial meningitis, etiological agents, multiplex real-time PCR

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