scholarly journals Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

2020 ◽  
Vol 8 (5) ◽  
pp. 720 ◽  
Author(s):  
Meichen Pan ◽  
Matthew A. Nethery ◽  
Claudio Hidalgo-Cantabrana ◽  
Rodolphe Barrangou
Keyword(s):  
Genome Engineering ◽  
Rare Variants ◽  
Adaptive Immune System ◽  
Effector Proteins ◽  
Type I ◽  
Human Gut ◽  
Adaptive Immune ◽  
Naturally Occurring ◽  
History Of

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.

scholarly journals Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Open Biology ◽  
2016 ◽  
Vol 6 (4) ◽  
pp. 160009 ◽  
Author(s):  
Kerstin Howe ◽  
Philipp H. Schiffer ◽  
Julia Zielinski ◽  
Thomas Wiehe ◽  
Gavin K. Laird ◽  
...  
Keyword(s):  
Adaptive Immune System ◽  
Large Family ◽  
Immune Recognition ◽  
Adaptive Immune ◽  
New Family ◽  
The Family ◽  
History Of ◽  
Leucine Rich Repeats ◽  
Adaptive Immune Systems ◽  
B30.2 Domain

Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.

scholarly journals Repetitive DNA reeling by the Cascade-Cas3 complex in nucleotide unwinding steps

2017 ◽  
Author(s):  
Luuk Loeff ◽  
Stan J.J. Brouns ◽  
Chirlmin Joo
Keyword(s):  
Single Molecule ◽  
Adaptive Immune System ◽  
Dna Unwinding ◽  
Type I ◽  
Base Pairs ◽  
Spatiotemporal Resolution ◽  
Adaptive Immune ◽  
Single Molecule Fret ◽  
Target Dna ◽  
Loaded Mechanism

CRISPR-Cas loci provide an RNA-guided adaptive immune system against invading genetic elements. Interference in type I systems relies on the RNA-guided surveillance complex Cascade for target DNA recognition and the trans-acting Cas3 helicase/nuclease protein for target degradation. Even though the biochemistry of CRISPR interference has been largely covered, the biophysics of DNA unwinding and coupling of the helicase and nuclease domains of Cas3 remains elusive. Here we employed single-molecule FRET to probe the helicase activity with a high spatiotemporal resolution. We show that Cas3 remains tightly associated with the target-bound Cascade complex while reeling in the target DNA using a spring-loaded mechanism. This spring-loaded reeling occurs in distinct bursts of three base pairs, that each underlie three successive 1-nt unwinding events. Reeling is highly repetitive, compensating for inefficient nicking activity of the nuclease domain. Our study reveals that the discontinuous helicase properties of Cas3 and its tight interaction with Cascade ensure well controlled degradation of target DNA only.

scholarly journals Rare variants in Toll-like receptor 7 results in functional impairment and downregulation of cytokine-mediated signaling in COVID-19 patients

2021 ◽  
Author(s):  
Stefania Mantovani ◽  
Sergio Daga ◽  
Chiara Fallerini ◽  
Margherita Baldassarri ◽  
Elisa Benetti ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Rare Variants ◽  
Functional Characterization ◽  
Prior History ◽  
Type I ◽  
Mrna Levels ◽  
Loss Of Function ◽  
Peripheral Blood Mononuclear ◽  
Antiviral Responses ◽  
History Of

AbstractToll-like receptors (TLR) are crucial components in the initiation of innate immune responses to a variety of pathogens, triggering the production of pro-inflammatory cytokines and type I and II interferons, which are responsible for innate antiviral responses. Among the different TLRs, TLR7 recognizes several single-stranded RNA viruses including SARS-CoV-2. We and others identified rare loss-of-function variants in X-chromosomal TLR7 in young men with severe COVID-19 and with no prior history of major chronic diseases, that were associated with impaired TLR7 signaling as well as type I and II IFN responses. Here, we performed RNA sequencing to investigate transcriptome variations following imiquimod stimulation of peripheral blood mononuclear cells isolated from patients carrying previously identified hypomorphic, hypofunctional, and loss-of-function TLR7 variants. Our investigation revealed a profound impairment of the TLR7 pathway in patients carrying loss-of-function variants. Of note, a failure in IFNγ upregulation following stimulation was also observed in cells harboring the hypofunctional and hypomorphic variants. We also identified new TLR7 variants in severely affected male patients for which a functional characterization of the TLR7 pathway was performed demonstrating a decrease in mRNA levels in the IFNα, IFNγ, RSAD2, ACOD1, IFIT2, and CXCL10 genes.

scholarly journals CRISPR/Cas9 and cancer

2021 ◽  
Vol 53 (2) ◽  
Author(s):  
Nora Mimoune ◽  
Mohamed Wail Bahouh ◽  
Said Boukhechem ◽  
Djamel Khelef ◽  
Rachid Kaidi
Keyword(s):  
Cancer Research ◽  
Clinical Trials ◽  
Immune System ◽  
Genome Engineering ◽  
Adaptive Immune System ◽  
Powerful Method ◽  
Efficient Technology ◽  
Adaptive Immune ◽  
Mouse Models Of Cancer ◽  
The Impact

CRISPR/Cas9 has become a powerful method for making changes to the genome of many organisms. First discovered in bacteria as part of an adaptive immune system, CRISPR/Cas9 and modified versions have found widespread use in genome engineering and in the activation or repression of gen expression. As such, CRISPR/Cas9 promises to accelerate cancer research by providing an efficient technology to dissect mechanisms of tumorigenesis, identify targets for drug development, and possibly arm cells for cell-based therapies. Here, we review the current applications of the CRISPR/Cas9 technology for cancer research and therapy. We highlight the impact of CRISPR/Cas9 in generating organoid and mouse models of cancer. Finally, we provide an overview of the first clinical trials applying CRISPR/Cas9 as a therapeutic approach against cancer.

CRISPR/Cas-Systems: characteristics and possibilities of use for editing bacterial genomes

Bacteriology ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 38-48
Author(s):  
I.A. Blatov ◽  
◽  
A.S. Shchurova ◽  
D.Yu. Guschin ◽  
S.D. Zvereva ◽  
...  
Keyword(s):  
Immune System ◽  
Genome Editing ◽  
Bacterial Species ◽  
Adaptive Immune System ◽  
Bacterial Genomes ◽  
Modern Biology ◽  
Adaptive Immune ◽  
History Of ◽  
Genomic Editing ◽  
Classification Structure

CRISPR-Cas is the adaptive immune system of bacteria and archaea. Since 2012, when the first opportunity to use the CRISPR/Cas system for genome editing was realized, the number of studies in this area has been growing rapidly. Today, genomic editing to modify specific regions of the genomes of various organisms is considered one of the key methodologies of modern biology. This review is devoted to the history of discovery, classification, structure, operational mechanisms of CRISPRCas systems and strategies for editing the genomes of various bacterial species using this technology. Key words: genome editing, genome, CRISPR-Cas system, bacteria

Maladaptation to mental stress mitigated by the adaptive immune system via depletion of naturally occurring regulatory CD4+CD25+ cells

2006 ◽  
Vol 66 (6) ◽  
pp. 552-563 ◽  
Author(s):  
Hagit Cohen ◽  
Yaniv Ziv ◽  
Michal Cardon ◽  
Zeev Kaplan ◽  
Michael A. Matar ◽  
...  
Keyword(s):  
Immune System ◽  
Mental Stress ◽  
Adaptive Immune System ◽  
Adaptive Immune ◽  
Naturally Occurring

scholarly journals Defective innate immunity predisposes murine neonates to poor sepsis outcome but is reversed by TLR agonists

Blood ◽  
2008 ◽  
Vol 112 (5) ◽  
pp. 1750-1758 ◽  
Author(s):  
James L. Wynn ◽  
Philip O. Scumpia ◽  
Robert D. Winfield ◽  
Matthew J. Delano ◽  
Kindra Kelly-Scumpia ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Immune System ◽  
Adaptive Immune System ◽  
Neutrophil Recruitment ◽  
Polymicrobial Sepsis ◽  
Type I ◽  
Sepsis Mortality ◽  
Tlr Agonists ◽  
Adaptive Immune ◽  
Increased Risk

Abstract Neonates exhibit an increased risk of sepsis mortality compared with adults. We show that in contrast to adults, survival from polymicrobial sepsis in murine neonates does not depend on an intact adaptive immune system and is not improved by T cell–directed adaptive immunotherapy. Furthermore, neonates manifest an attenuated inflammatory and innate response to sepsis, and have functional defects in their peritoneal CD11b+ cells. Activation of innate immunity with either a Toll-like receptor 4 (TLR4) or TLR7/8 agonist, but not a TLR3 agonist, increased the magnitude, but abbreviated the early systemic inflammatory response, reduced bacteremia, and improved survival to polymicrobial sepsis. TLR4 agonist pretreatment enhanced peritoneal neutrophil recruitment with increased oxidative burst production, whereas the TLR7/8 agonist also enhanced peritoneal neutrophil recruitment with increased phagocytic ability. These benefits were independent of the adaptive immune system and type I interferon signaling. Improving innate immune function with select TLR agonists may be a useful strategy to prevent neonatal sepsis mortality.

scholarly journals Four-dimensional impedance manometry derived from esophageal high-resolution impedance-manometry studies: a novel analysis paradigm

2020 ◽  
Vol 13 ◽  
pp. 175628482096905
Author(s):  
Wenjun Kou ◽  
Dustin A. Carlson ◽  
Neelesh A. Patankar ◽  
Peter J. Kahrilas ◽  
John E. Pandolfino
Keyword(s):  
High Resolution ◽  
Flow Rate ◽  
Time History ◽  
Type I ◽  
Bolus Transit ◽  
Time Flow ◽  
Biophysical Analysis ◽  
History Of ◽  
Emptying Time

Background: This study aimed to introduce a novel analysis paradigm, referred to as 4-dimensional (4D) manometry based on biophysical analysis; 4D manometry enables the visualization of luminal geometry of the esophagus and esophagogastric junction (EGJ) using high-resolution-impedance-manometry (HRIM) data. Methods: HRIM studies from two asymptomatic controls and one type-I achalasia patient were analyzed. Concomitant fluoroscopy images from one control subject were used to validate the calculated temporal-spatial luminal radius and time-history of intraluminal bolus volume and movement. EGJ analysis computed diameter threshold for emptying, emptying time, flow rate, and distensibility index (DI), which were compared with bolus flow time (BFT) analysis. Results: For normal control, calculated volumes for 5 ml swallows were 4.1 ml–6.7 ml; for 30 ml swallows 21.3 ml–21.8 ml. With type-I achalasia, >4 ml of intraesophageal bolus residual was present both pre- and post-swallow. The four phases of bolus transit were clearly illustrated on the time-history of bolus movement, correlating well with the fluoroscopic images. In the control subjects, the EGJ diameter threshold for emptying was 8 mm for 5 ml swallows and 10 mm for 30 ml swallows; emptying time was 1.2–2.2 s for 5 ml swallows (BFT was 0.3–3 s) and 3.25–3.75 s for 30 ml swallows; DI was 2.4–3.4 mm2/mmHg for 5 ml swallows and 4.2–4.6 mm2/mmHg for 30 ml swallows. Conclusions: The 4D manometry system facilitates a comprehensive characterization of dynamic esophageal bolus transit with concurrent luminal morphology and pressure from conventional HRIM measurements. Calculations of flow rate and wall distensibility provide novel measures of EGJ functionality.

SLPI and elafin: one glove, many fingers

2005 ◽  
Vol 110 (1) ◽  
pp. 21-35 ◽  
Author(s):  
Steven E. Williams ◽  
Thomas I. Brown ◽  
Ali Roghanian ◽  
Jean-Michel Sallenave
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Immune Responses ◽  
Adaptive Immune Response ◽  
Adaptive Immune System ◽  
Innate Immune ◽  
Type I ◽  
Adaptive Immune ◽  
Pathological Conditions ◽  
Related Proteins

Elafin and SLPI (secretory leucocyte protease inhibitor) have multiple important roles both in normal homoeostasis and at sites of inflammation. These include antiprotease and antimicrobial activity as well as modulation of the response to LPS (lipopolysaccharide) stimulation. Elafin and SLPI are members of larger families of proteins secreted predominantly at mucosal sites, and have been shown to be modulated in multiple pathological conditions. We believe that elafin and SLPI are important molecules in the controlled functioning of the innate immune system, and may have further importance in the integration of this system with the adaptive immune response. Recent interest has focused on the influence of inflamed tissues on the recruitment and phenotypic modulation of cells of the adaptive immune system and, indeed, the local production of elafin and SLPI indicate that they are ideally placed in this regard. Functionally related proteins, such as the defensins and cathelicidins, have been shown to have direct effects upon dendritic cells with potential alteration of their phenotype towards type I or II immune responses. This review addresses the multiple functions of elafin and SLPI in the inflammatory response and discusses further their roles in the development of the adaptive immune response.

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