The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

Bacterial and archaeal CRISPR-Cas systems offer adaptive immune protection against foreign mobile genetic elements (MGEs). This function is regulated by sequence specific binding of CRISPR RNA (crRNA) to target DNA/RNA, with an additional requirement of a flanking DNA motif called the protospacer adjacent motif (PAM) in certain CRISPR systems. In this review, we discuss how the same fundamental mechanism of RNA-DNA and/or RNA-RNA complementarity is utilized by bacteria to regulate two distinct functions: to ward off intruding genetic materials and to modulate diverse physiological functions. The best documented examples of alternate functions are bacterial virulence, biofilm formation, adherence, programmed cell death, and quorum sensing. While extensive complementarity between the crRNA and the targeted DNA and/or RNA seems to constitute an efficient phage protection system, partial complementarity seems to be the key for several of the characterized alternate functions. Cas proteins are also involved in sequence-specific and non-specific RNA cleavage and control of transcriptional regulator expression, the mechanisms of which are still elusive. Over the past decade, the mechanisms of RNA-guided targeting and auxiliary functions of several Cas proteins have been transformed into powerful gene editing and biotechnological tools. We provide a synopsis of CRISPR technologies in this review. Even with the abundant mechanistic insights and biotechnology tools that are currently available, the discovery of new and diverse CRISPR types holds promise for future technological innovations, which will pave the way for precision genome medicine.

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CRISPR-Cas: biology, mechanisms and relevance

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0496 ◽

2016 ◽

Vol 371 (1707) ◽

pp. 20150496 ◽

Cited By ~ 100

Author(s):

Frank Hille ◽

Emmanuelle Charpentier

Keyword(s):

Dna Sequences ◽

Adaptive Immune System ◽

Crispr Locus ◽

Biochemical Processes ◽

Adaptive Immune ◽

Physiological Properties ◽

Target Dna ◽

Associated Proteins ◽

Cas Proteins

Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’.

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On-Surface Radical Oligomerisation: A New Approach to STM Tip-Induced Reactions

10.26434/chemrxiv.6860105 ◽

2018 ◽

Author(s):

Gaolei Zhan ◽

Younes Makoudi ◽

Judicael Jeannoutot ◽

Simon Lamare ◽

Michel Féron ◽

...

Keyword(s):

Sample Surface ◽

Scanning Tunnelling Microscope ◽

Transfer Event ◽

New Approach ◽

The Past ◽

Organic Nanostructures ◽

Scanning Tunnelling ◽

New Strategy ◽

Surface Fabrication ◽

And Control

Over the past decade, on-surface fabrication of organic nanostructures has been widely investigated for the development of molecular electronic devices, nanomachines, and new materials. Here, we introduce a new strategy to obtain alkyl oligomers in a controlled manner using on-surface radical oligomerisations that are triggered by the electrons/holes between the sample surface and the tip of a scanning tunnelling microscope. The resulting radical-mediated mechanism is substantiated by a detailed theoretical study. This electron transfer event only occurs when Vs < -3 V or Vs > + 3 V and allows access to reactive radical species under exceptionally mild conditions. This transfer can effectively ‘switch on’ a sequence leading to formation of oligomers of defined size distribution due to the on-surface confinement of reactive species. Our approach enables new ways to initiate and control radical oligomerisations with tunnelling electrons, leading to molecularly precise nanofabrication.

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Ten-year trends of hypertension treatment and control rate in Korea

Scientific Reports ◽

10.1038/s41598-021-86199-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kwang-il Kim ◽

Eunjeong Ji ◽

Jung-yeon Choi ◽

Sun-wook Kim ◽

Soyeon Ahn ◽

...

Keyword(s):

Age Groups ◽

Favorable Effect ◽

Age Group ◽

Hypertension Treatment ◽

Treatment Rate ◽

Cross Sectional ◽

The Past ◽

Nationally Representative ◽

Multistage Sampling ◽

And Control

AbstractWe analyzed the Korean National Health and Nutrition Examination Survey (KNHANES) database to determine the trends of hypertension treatment and control rate in Korea over the past 10 years. In addition, we tried to investigate the effect of chronic medical conditions on hypertension management. We investigated the hypertension prevalence, awareness, treatment, and control rate from 2008 to 2017. KNHANES, which uses a stratified multistage sampling design, is a cross-sectional, nationally representative survey conducted by the Korean government. A total of 59,282 adults (≥ 20 years) were included, which was representative of the total population of around 40 million Koreans per year. The mean age was 50.7 ± 16.4 years and 42.6% were male. The prevalence of hypertension, hypercholesterolemia, diabetes mellitus, and obesity significantly increased over the 10 years. During this period, the hypertension treatment and control rate significantly improved. Hypertension treatment rate was significantly lower in the younger age group compared to the older age group, but the control rate among the treated patients was not significantly different between age groups. The treatment and control rates of hypertension were higher in patients with multimorbidity, which implies that it has a favorable effect on the treatment and control of hypertension. Hypertension treatment and control rate have improved over the past 10 years. The higher treatment and control rate in patients with multimorbidity suggest that the more aggressive surveillance might be associated with the improvement of hypertension treatment and control rate in Korea.

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CRISPR as a Diagnostic Tool

Biomolecules ◽

10.3390/biom11081162 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1162

Author(s):

Seohyun Kim ◽

Sangmin Ji ◽

Hye Ran Koh

Keyword(s):

Diagnostic Tool ◽

Specific Binding ◽

Diagnostic Methods ◽

Specific Gene ◽

Guide Rna ◽

Engineering Technique ◽

Target Dna ◽

Target Binding ◽

Genetic Engineering Technique ◽

Disease Related Gene

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.

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An Introduction to Development of Centralized and Distributed Stochastic Approximation Algorithm with Expanding Truncations

Algorithms ◽

10.3390/a14060174 ◽

2021 ◽

Vol 14 (6) ◽

pp. 174

Author(s):

Wenxiao Zhao

Keyword(s):

Approximation Algorithm ◽

Stochastic Approximation ◽

Probabilistic Method ◽

Principal Component ◽

Stochastic Approximation Algorithm ◽

The Past ◽

Systems And Control ◽

Ode Method ◽

Centralized Algorithm ◽

And Control

The stochastic approximation algorithm (SAA), starting from the pioneer work by Robbins and Monro in 1950s, has been successfully applied in systems and control, statistics, machine learning, and so forth. In this paper, we will review the development of SAA in China, to be specific, the stochastic approximation algorithm with expanding truncations (SAAWET) developed by Han-Fu Chen and his colleagues during the past 35 years. We first review the historical development for the centralized algorithm including the probabilistic method (PM) and the ordinary differential equation (ODE) method for SAA and the trajectory-subsequence method for SAAWET. Then, we will give an application example of SAAWET to the recursive principal component analysis. We will also introduce the recent progress on SAAWET in a networked and distributed setting, named the distributed SAAWET (DSAAWET).

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The Origins of Domestic Sheep and Goats: a Reconsideration in the Light of the Fossil Evidence

Proceedings of the Prehistoric Society ◽

10.1017/s0079497x00013943 ◽

1969 ◽

Vol 34 ◽

pp. 368-384 ◽

Cited By ~ 8

Author(s):

Sebastian Payne

Keyword(s):

Direct Evidence ◽

Present Situation ◽

Wild Relatives ◽

The Other ◽

Domestic Sheep ◽

Sheep And Goats ◽

Animal Domestication ◽

The Past ◽

The One ◽

And Control

In recent discussions of the origins and process of animal domestication (Reed, 1961, Zeuner, 1963), both authors rely on two kinds of evidence: on the one hand, the present distributions and characteristics of the different breeds of whatever animal is being discussed, together with its feral and wild relatives, and, on the other hand, the past record, given by literary and pictorial sources and the bones from archaeological and geological sites. Increased recognition of the limitations of the past record, whether in the accuracy of the information it appears to give (as in the case of pictorial sources), or in the certainty of the deductions we are at present capable of drawing from it (this applies especially to the osteological record), has led these authors to argue mainly from the present situation, using the past record to confirm or amplify the existing picture.Arguing from the present, many hypotheses about the origins and process of domestication are available. The only test we have, when attempting to choose between these, lies in the direct evidence of the past record. The past record, it is freely admitted, is very fragmentary: the information provided by the present situation is more exact, ranges over a much wider field, and is more open to test and control. Nevertheless, the past record, however imperfect it is, is the only direct evidence we have about the process of domestication.

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Risk factors and biofilm formation analyses of hospital-acquired infection of Candida pelliculosa in a neonatal intensive care unit

BMC Infectious Diseases ◽

10.1186/s12879-021-06295-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhijie Zhang ◽

Yu Cao ◽

Yanjian Li ◽

Xufang Chen ◽

Chen Ding ◽

...

Keyword(s):

Risk Factors ◽

Intensive Care Unit ◽

Biofilm Formation ◽

Prevention And Control ◽

Neonatal Intensive Care ◽

Infection Prevention ◽

Infection Prevention And Control ◽

Anti Fungal ◽

Hospital Acquired ◽

And Control

Abstract Background Candida pelliculosa is an ecological fungal species that can cause infections in immunocompromised individuals. Numerous studies globally have shown that C. pelliculosa infects neonates. An outbreak recently occurred in our neonatal intensive care unit; therefore, we aimed to evaluate the risk factors in this hospital-acquired fungal infection. Methods We performed a case-control study, analysing the potential risk factors for neonatal infections of C. pelliculosa so that infection prevention and control could be implemented in our units. Isolated strains were tested for drug resistance and biofilm formation, important factors for fungal transmission that give rise to hospital-acquired infections. Results The use of three or more broad-spectrum antimicrobials or long hospital stays were associated with higher likelihoods of infection with C. pelliculosa. The fungus was not identified on the hands of healthcare workers or in the environment. All fungal isolates were susceptible to anti-fungal medications, and after anti-fungal treatment, all infected patients recovered. Strict infection prevention and control procedures efficiently suppressed infection transmission. Intact adhesin-encoding genes, shown by genome analysis, indicated possible routes for fungal transmission. Conclusions The use of three or more broad-spectrum antimicrobials or a lengthy hospital stay is theoretically associated with the risk of infection with C. pelliculosa. Strains that we isolated are susceptible to anti-fungal medications, and these were eliminated by treating all patients with an antifungal. Transmission is likely via adhesion to the cell surface and biofilm formation.

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The Problem of Energy

Theory Culture & Society ◽

10.1177/0263276414536747 ◽

2014 ◽

Vol 31 (5) ◽

pp. 3-20 ◽

Cited By ~ 53

Author(s):

John Urry

Keyword(s):

Social Theory ◽

21St Century ◽

Fossil Fuel ◽

Energy Systems ◽

Social Thought ◽

Human Intervention ◽

The West ◽

The Past ◽

And Control ◽

Global Growth

Energy forms and their extensive scale are remarkably significant for the ways that societies are organized. This article shows the importance of how societies are ‘energized’ and especially the global growth of ‘fossil fuel societies’. Much social thought remains oblivious to the energy revolution realized over the past two to three centuries which set the ‘West’ onto a distinct trajectory. Energy is troubling for social thought because different energy systems with their ‘lock-ins’ are not subject to simple human intervention and control. Analyses are provided here of different fossil fuel societies, of coal and oil, with the latter enabling the liquid, mobilized 20th century. Consideration is paid to the possibilities of reducing fossil fuel dependence but it is shown how unlikely such a ‘powering down’ will be. The author demonstrates how energy is a massive problem for social theory and for 21st-century societies. Developing post-carbon theory and especially practice is far away but is especially urgent.

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Plant MicroRNAs Responsive to Fungal Infection

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.941-944.1141 ◽

2014 ◽

Vol 941-944 ◽

pp. 1141-1145 ◽

Cited By ~ 1

Author(s):

Hui Li Zhang ◽

Lin Chen ◽

Wen Na Li ◽

Li Li Wang ◽

Hong Yu Xie

Keyword(s):

Fungal Pathogens ◽

High Throughput Sequencing ◽

Adaptive Immune System ◽

Messenger Rnas ◽

Disease Mechanism ◽

Adaptive Immune ◽

Alternative Approach ◽

Crop Disease ◽

Transcriptional Gene Regulation ◽

And Control

MicroRNAs (miRNAs) are endogenous small RNAs transcribed from non-coding DNA, which have the capacity to base pair with the target mRNAs (messenger RNAs) to repress their translation or resulted in cleavage. We have paid much attention on the DNA and its coded proteins, the discovery of miRNAs as gene negatively regulators has led to a fundamental change in understanding of post-transcriptional gene regulation in plants. Fungal pathogens infection is the main cause of most economic crops diseases. Unlike humans, plants don’t evolved to have a adaptive immune system, they protect themselves with a mechanism consists of activation and response. Recently, high throughput sequencing validated that miRNA play a crucial role in plant-fungus interaction. A better understanding of miRNA-mediated disease mechanism in fungi should clarify the strategy of crop disease control. MiRNA-based manipulations as gene suppressors, such as artificial miRNAs, may emerge as a new alternative approach for the improvement of crops and control of crop disease.

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Transition and the Pitfalls of Nondemocratic Institutions: A review of Constitutionality in Ethiopia

Africa Journal of Comparative Constitutional Law ◽

10.47348/ajcl/2021/a4 ◽

2021 ◽

Vol 2021 (1) ◽

pp. 67-87

Author(s):

Tadesse Melaku

Keyword(s):

Case Analysis ◽

Democratic Governance ◽

Institutional Reforms ◽

Constitutional Review ◽

The Past ◽

Government Power ◽

Review Mechanism ◽

And Control ◽

Regional Elections ◽

Do So

Ethiopia has undertaken important political reforms after the fall of authoritarianism in 2018. This article examines the performance of Ethiopia’s constitutional review mechanism amid the ongoing political and institutional reforms in the country. The study focuses on the process and merit of the constitutional ruling to delay the 2020 national and regional elections because of the coronavirus pandemic, thereby extending the government’s tenure. It further unravels the challenges posed by nondemocratic institutions of the past regime in navigating the transition. In doing so, this study draws on legal, documentary and case analysis, and a literature review. While the mandate extension comes as no surprise, the reasoning of the decision to do so was disappointing for many, dashing the hope and sense of a constitutional moment that accompanied the highly publicised constitutional hearing process in June 2020. The judgment reveals an endemic deficiency of the institutional system. Thus, it is imperative for Ethiopia to establish an independent constitutional umpire to check and control the exercise of government power and support the transition to multiparty democratic governance in the country.

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