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Molecular Therapy : the Journal of the... Sep 2020CRISPR-mediated DNA base editors, which include cytosine base editors (CBEs) and adenine base editors (ABEs), are promising tools that can induce point mutations at... (Review)
Review
CRISPR-mediated DNA base editors, which include cytosine base editors (CBEs) and adenine base editors (ABEs), are promising tools that can induce point mutations at desired sites in a targeted manner to correct or disrupt gene expression. Their high editing efficiency, coupled with their ability to generate a targeted mutation without generating a DNA double-strand break (DSB) or requiring a donor DNA template, suggests that DNA base editors will be useful for treating genetic diseases, among other applications. However, this hope has recently been challenged by the discovery of DNA base editor shortcomings, including off-target DNA editing, the generation of bystander mutations, and promiscuous deamination effects in both DNA and RNA, which arise from the main DNA base editor constituents, a Cas nuclease variant and a deaminase. In this review, we summarize information about the DNA base editors that have been developed to date, introduce their associated potential challenges, and describe current efforts to minimize or mitigate those issues of DNA base editors.
Topics: CRISPR-Associated Protein 9; CRISPR-Cas Systems; DNA; DNA Breaks, Double-Stranded; DNA Replication; Deamination; Gene Editing; Humans; Point Mutation; RNA, Guide, CRISPR-Cas Systems
PubMed: 32763143
DOI: 10.1016/j.ymthe.2020.07.021 -
Metallomics : Integrated Biometal... Apr 2021Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural... (Review)
Review
Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.
Topics: Base Pairing; Coordination Complexes; DNA-Directed DNA Polymerase; Metals; Nucleic Acids
PubMed: 33791776
DOI: 10.1093/mtomcs/mfab016 -
Synthetic and Systems Biotechnology Dec 2020CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA... (Review)
Review
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA guided Cas nucleases generate DNA double-strand break (DSB), triggering cellular repair systems mainly Non-homologous end-joining (NHEJ, imprecise repair) or Homology-directed repair (HDR, precise repair). However, DSB typically leads to unexpected DNA changes and lethality in some organisms. The establishment of bacteria and plants into major bio-production platforms require efficient and precise editing tools. Hence, in this review, we focus on the non-DSB and template-free genome editing, i.e., base editing (BE) and prime editing (PE) in bacteria and plants. We first highlight the development of base and prime editors and summarize their studies in bacteria and plants. We then discuss current and future applications of BE/PE in synthetic biology, crop improvement, evolutionary engineering, and metabolic engineering. Lastly, we critically consider the challenges and prospects of BE/PE in PAM specificity, editing efficiency, off-targeting, sequence specification, and editing window.
PubMed: 32954022
DOI: 10.1016/j.synbio.2020.08.003 -
Journal of Neurological Surgery. Part... Feb 2018Pediatric skull base and craniofacial reconstruction presents a unique challenge since the potential benefits of therapy must be balanced against the cumulative... (Review)
Review
Pediatric skull base and craniofacial reconstruction presents a unique challenge since the potential benefits of therapy must be balanced against the cumulative impact of multimodality treatment on craniofacial growth, donor-site morbidity, and the potential for serious psychosocial issues. To suggest an algorithm for skull base reconstruction in children and adolescents after tumor resection. Comprehensive literature review and summary of our experience. We advocate soft-tissue reconstruction as the primary technique, reserving bony flaps for definitive procedures in survivors who have reached skeletal maturity. Free soft-tissue transfer in microvascular technique is the mainstay for reconstruction of large, three-dimensional defects, involving more than one anatomic region of the skull base, as well as defects involving an irradiated field. However, to reduce total operative time, intraoperative blood loss, postoperative hospital stay, and donor-site morbidity, locoregional flaps are better be considered the flap of first choice for skull base reconstruction in children and adolescents, as long as the flap is large enough to cover the defect. Our "workhorse" for dural reconstruction is the double-layer fascia lata. Advances in endoscopic surgery, image guidance, alloplastic grafts, and biomaterials have increased the armamentarium for reconstruction of small and mid-sized defects. Skull base reconstruction using locoregional flaps or free flaps may be safely performed in pediatrics. Although the general principles of skull base reconstruction are applicable to nearly all patients, the unique demands of skull base surgery in pediatrics merit special attention. Multidisciplinary care in experienced centers is of utmost importance.
PubMed: 29404244
DOI: 10.1055/s-0037-1615806 -
AJNR. American Journal of Neuroradiology Mar 2021Skull base osteomyelitis is a relatively rare condition, generally occurring as a complication of advanced otologic or sinus infection in immunocompromised patients.... (Review)
Review
Skull base osteomyelitis is a relatively rare condition, generally occurring as a complication of advanced otologic or sinus infection in immunocompromised patients. Skull base osteomyelitis is generally divided into 2 broad categories: typical and atypical. Typical skull base osteomyelitis occurs secondary to uncontrolled infection of the temporal bone region, most often from necrotizing external otitis caused by in a patient with diabetes. Atypical skull base osteomyelitis occurs in the absence of obvious temporal bone infection or external auditory canal infection. It may be secondary to advanced sinusitis or deep face infection or might occur in the absence of a known local source of infection. Atypical skull base osteomyelitis preferentially affects the central skull base and can be caused by bacterial or fungal infections. Clinically, typical skull base osteomyelitis presents with signs and symptoms of otitis externa or other temporal bone infection. Both typical and atypical forms can produce nonspecific symptoms including headache and fever, and progress to cranial neuropathies and meningitis. Early diagnosis can be difficult both clinically and radiologically, and the diagnosis is often delayed. Radiologic evaluation plays a critical role in the diagnosis of skull base osteomyelitis, with CT and MR imaging serving complementary roles. CT best demonstrates cortical and trabecular destruction of bone. MR imaging is best for determining the overall extent of disease and best demonstrates involvement of marrow space and extraosseous soft tissue. Nuclear medicine studies can also be contributory to diagnosis and follow-up. The goal of this article was to review the basic pathophysiology, clinical findings, and key radiologic features of skull base osteomyelitis.
Topics: Diagnostic Imaging; Humans; Osteomyelitis; Skull Base
PubMed: 33478944
DOI: 10.3174/ajnr.A7015 -
Advances in Chronic Kidney Disease Sep 2017Acid-base disorders are in patients with chronic kidney disease, with chronic metabolic acidosis receiving the most attention clinically in terms of diagnosis and... (Review)
Review
Acid-base disorders are in patients with chronic kidney disease, with chronic metabolic acidosis receiving the most attention clinically in terms of diagnosis and treatment. A number of observational studies have reported on the prevalence of acid-base disorders in this patient population and their relationship with outcomes, mostly focusing on chronic metabolic acidosis. The majority have used serum bicarbonate alone to define acid-base status due to the lack of widely available data on other acid-base disorders. This review discusses the time course of acid-base alterations in CKD patients, their prevalence, and associations with CKD progression and mortality.
Topics: Acid-Base Equilibrium; Acid-Base Imbalance; Bicarbonates; Disease Progression; Humans; Prevalence; Renal Dialysis; Renal Insufficiency, Chronic; Risk Factors
PubMed: 29031354
DOI: 10.1053/j.ackd.2017.08.003 -
Journal of Chemical Theory and... Nov 2022Hoogsteen (HG) base pairs have a transient nature and can be structurally similar to Watson-Crick (WC) base pairs, making their occurrence and thermodynamic stability...
Hoogsteen (HG) base pairs have a transient nature and can be structurally similar to Watson-Crick (WC) base pairs, making their occurrence and thermodynamic stability difficult to determine experimentally. Herein, we employed the restrain-free-energy perturbation-release (R-FEP-R) method to calculate the relative free energy of the WC and HG base pairing modes in isolated and bound DNA systems and predict the glycosyl torsion conformational preference of purine bases. Notably, this method does not require prior knowledge of the transition pathway between the two end states. Remarkably, relatively fast convergence was reached, with results in excellent agreement with experimental data for all the examined DNA systems. The R-REP-R method successfully determined the stability of HG base pairing and more generally, the conformational preference of purine bases, in these systems. Therefore, this computational approach can help to understand the dynamic equilibrium between the WC and HG base pairing modes in DNA.
Topics: Base Pairing; DNA; Thermodynamics; Molecular Conformation; Purines; Nucleic Acid Conformation
PubMed: 36201305
DOI: 10.1021/acs.jctc.2c00848 -
Biochemistry Sep 2019Base editing is a genome editing strategy that induces specific single-nucleotide changes within genomic DNA. Two major DNA base editors, cytosine base editors and... (Review)
Review
Base editing is a genome editing strategy that induces specific single-nucleotide changes within genomic DNA. Two major DNA base editors, cytosine base editors and adenine base editors, that consist of a Cas9 protein linked to a deaminase enzyme that catalyzes targeted base conversion directed by a single-guide RNA have been developed. This strategy has been used widely for precise genome editing because, unlike CRISPR-Cas nuclease-based genome editing systems, this strategy does not create double-strand DNA breaks that often result in high levels of undesirable indels. However, recent papers have reported that DNA base editors can cause substantial off-target editing in both genomic DNA and RNA. The off-target editing described in these studies is primarily independent of guide RNA and arises from the promiscuous reactivity of the deaminase enzymes used in DNA base editors. In this Perspective, we discuss the development of DNA base editors, the guide RNA-independent off-target activity reported in recent studies, and strategies that improve the selectivity of DNA base editors.
Topics: Adenosine Deaminase; Animals; CRISPR-Associated Protein 9; CRISPR-Cas Systems; Cytidine Deaminase; DNA; Gene Editing; Humans; RNA Editing; RNA, Guide, CRISPR-Cas Systems
PubMed: 31433621
DOI: 10.1021/acs.biochem.9b00573 -
Frontiers in Immunology 2018In humans, acid-base balance is crucial to cell homeostasis. Acidosis is observed in numerous inflammatory processes, primarily acute conditions such as sepsis, trauma,... (Review)
Review
In humans, acid-base balance is crucial to cell homeostasis. Acidosis is observed in numerous inflammatory processes, primarily acute conditions such as sepsis, trauma, or acute respiratory distress where females tend to exhibit better prognosis compared with males. The mechanisms underlying these gender-dependent differences are multiple, probably involving hormonal and genetic factors, particularly the X chromosome. Although pH influences multiple immunological functions, gender differences in acid-base balance have been poorly investigated. In this review, we provide an update on gender differences in human susceptibility to inflammatory diseases. We additionally discuss the potential impact of acid-base balance on the gender bias of the inflammatory response in view of our recent observation that girls present higher neutrophilic inflammation and lower pH with a trend toward better prognosis in severe sepsis. We also highlight the potent role played by endothelial cells in gender differences of inflammation through activation of proton-sensing G protein-coupled receptors.
Topics: Acid-Base Equilibrium; Chromosomes, Human, X; Female; Humans; Hydrogen-Ion Concentration; Inflammation; Male; Sex Characteristics
PubMed: 29593728
DOI: 10.3389/fimmu.2018.00475 -
Journal of Cerebral Blood Flow and... Apr 2018Metabolic regulation of cerebrovascular tone directs blood flow to areas of increased neuronal activity and during disease states partially compensates for insufficient... (Review)
Review
Metabolic regulation of cerebrovascular tone directs blood flow to areas of increased neuronal activity and during disease states partially compensates for insufficient perfusion by enhancing blood flow in collateral blood vessels. Acid-base disturbances frequently occur as result of enhanced metabolism or insufficient blood supply, but despite definitive evidence that acid-base disturbances alter arterial tone, effects of individual acid-base equivalents and the underlying signaling mechanisms are still being debated. H is an important intra- and extracellular messenger that modifies cerebrovascular tone. In addition, low extracellular [HCO] promotes cerebrovascular contraction through an endothelium-dependent mechanism. CO alters arterial tone development via changes in intra- and extracellular pH but it is still controversial whether CO also has direct vasomotor effects. Vasocontractile responses to low extracellular [HCO] and acute CO-induced decreases in intracellular pH can counteract H-mediated vasorelaxation during metabolic and respiratory acidosis, respectively, and may thereby reduce the risk of capillary damage and cerebral edema that could be consequences of unopposed vasodilation. In this review, the signaling mechanisms for acid-base equivalents in cerebral arteries and the mechanisms of intracellular pH control in the arterial wall are discussed in the context of metabolic regulation of cerebrovascular tone and local perfusion.
Topics: Acid-Base Equilibrium; Acid-Base Imbalance; Animals; Cerebral Arteries; Cerebrovascular Circulation; Humans; Signal Transduction; Vasodilation
PubMed: 28984162
DOI: 10.1177/0271678X17733868