Article
Biochemistry & Molecular Biology
Marios Mejdani, April Pawluk, Karen L. Maxwell, Alan R. Davidson
Summary: Anti-CRISPRs are a diverse class of protein inhibitors produced by phages and mobile genetic elements to evade destruction by the CRISPR-Cas system. A study focused on AcrIE2, an anti-CRISPR inhibiting the Pseudomonas aeruginosa type I-E CRISPR-Cas system, revealed its unique ability to bind to the CRISPR-Cas complex without preventing DNA-binding, operating through a distinct mechanism compared to other type I anti-CRISPRs. AcrIE2 likely blocks DNA cleavage by inhibiting the recruitment of the Cas3 nuclease to the Cascade complex.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Medicine, General & Internal
Ivan Ivanov, Dimitri Livshits, Brenda Sokup, Angela Frisby, Nirav Patel
Summary: Describes the case of a young adult female who presented to the emergency department with headache and vomiting. After treatment, a noncontrast head CT scan was done and showed subarachnoid hemorrhage with edema and mass effect. The patient required blood pressure control with a nicardipine drip and recovered well.
CUREUS JOURNAL OF MEDICAL SCIENCE
(2023)
Article
Economics
B. Stitzel, C. L. Rogers
Summary: This study found that the adjustment of the water rate structure by the municipality resulted in different behavioral responses from different consumption groups, with ultra-low users increasing water consumption and high-volume users reducing consumption. The behavioral responses were greater in the longer run compared to the short term.
WATER RESOURCES AND ECONOMICS
(2021)
Article
Computer Science, Artificial Intelligence
Iacopo Ghinassi, Lin Wang, Chris Newell, Matthew Purver
Summary: This article systematically compares the performance of neural sentence encoders (NSE) in topic segmentation and finds that NSEs generally provide improvements, except in specific domains like news shows. The study also shows that although Transformers-based encoders improve over previous approaches, fine-tuning does not always lead to better performance. The proposed metric, ARP, can quantify the lexical cohesion of multi-topic documents, and it is found that traditional sentence encoders fail to create topically cohesive clusters of segments in conversational data.
PEERJ COMPUTER SCIENCE
(2023)
Editorial Material
Medicine, General & Internal
Wendy Stead
Summary: In this essay, the infectious diseases physician emphasizes the importance of forgiveness towards those possibly involved in COVID-19 transmission, drawing on the healing power of family absolution she witnessed as a child.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2021)
Article
Microbiology
Bowen Yang, Jinfang Zheng, Yanbin Yin
Summary: This paper introduces AcaFinder, the first tool for Aca genome mining. AcaFinder can predict Acas and their associated acr-aca operons, identify homologs of known Acas, and analyze potential prophages, CRISPR-Cas systems, and self-targeting spacers (STSs) in input genomes. The tool was applied to mining prokaryotic and gut phage genomes, resulting in the identification of 36 high-confident new Aca families. The study also reveals a complex association network between Acrs and Acas.
Article
Biochemistry & Molecular Biology
Sungwon Hwang, Chuxi Pan, Bianca Garcia, Alan R. Davidson, Trevor F. Moraes, Karen L. Maxwell
Summary: In this study, the activity of an anti-CRISPR protein isolated from a Haemophilus parainfluenzae prophage was investigated, revealing its ability to block CRISPR-Cas9 DNA cleavage activity. The researchers determined the three-dimensional crystal structure of this protein and found that it binds to the Cas9 Recognition Domain. Although the binding does not disrupt the interaction between the Cas9-anti-CRISPR complex and target DNA, it inhibits DNA cleavage by blocking the conformational changes required for the HNH and RuvC endonuclease domains to contact the DNA sites to be nicked.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sungwon Hwang, Megha Shah, Bianca Garcia, Noor Hashem, Alan R. Davidson, Trevor F. Moraes, Karen L. Maxwell
Summary: In this study, it was found that the AcrIIC5Nch protein can inhibit the CRISPR-Cas immune system by preventing Cas9 from binding to target DNA. AcrIIC5Nch targets the PAM-interacting domain (PID) of Nme1Cas9 for inhibition and requires guide RNA to be pre-loaded on Cas9. The crystal structure of AcrIIC5Nch was determined and critical amino acid residues for its function were identified. Protein docking analysis suggests that AcrIIC5Nch likely occupies the Cas9 DNA binding pocket, inhibiting target DNA binding through a mechanism similar to AcrIIA2 and AcrIIA4.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Medicine, General & Internal
Wendi Bao, Kendall L. Buchanan, Loretta S. Davis
Summary: AITL is a rare and aggressive lymphoma that often presents with skin involvement resembling viral or drug-induced rashes. Morbilliform rashes with systemic symptoms of unclear etiology should undergo thorough evaluation, and empiric corticosteroid therapy should be avoided to prevent delayed diagnosis of underlying malignancy like AITL.
CLINICAL CASE REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Benoit J. Pons, Stineke van Houte, Edze R. Westra, Anne Chevallereau
Summary: CRISPR-Cas is a defense system in prokaryotes that protects against invasion by mobile genetic elements, such as bacteriophages. Bacteriophages can overcome CRISPR-Cas defenses by encoding anti-CRISPR proteins, which inhibit the CRISPR-Cas machinery and promote phage replication. This review summarizes the current understanding of the distribution of anti-CRISPR genes in mobile genetic elements, the ecology of phages encoding anti-CRISPR proteins, and their coevolution with bacterial defense mechanisms. The need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in mobile genetic element-host interactions is highlighted.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Computer Science, Theory & Methods
Theodoros Apostolopoulos, Vasilios Katos, Kim-Kwang Raymond Choo, Constantinos Patsakis
Summary: Dynamic malware analysis involves debugging binary files and monitoring changes in sandboxed environments. It allows investigators to manipulate code execution paths to understand malware behavior, but malware may incorporate defenses against virtual environments and debugging. Software vendors may also use similar methods to protect their intellectual property.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Helen B. Belato, George P. Lisi
Summary: The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs), has revolutionized the field of CRISPR-Cas technology. These inhibitors have diverse structures and functions, and can act as orthosteric or allosteric inhibitors, as well as modify CRISPR-Cas components. Understanding the mechanisms of Acrs is crucial for the development of more precise and controllable CRISPR-Cas tools.
Article
Biotechnology & Applied Microbiology
Camilo Calvache, Marta Vazquez-Vilar, Sara Selma, Mireia Uranga, Asun Fernandez-del-Carmen, Jose-Antonio Daros, Diego Orzaez
Summary: This study demonstrates that anti-CRISPR proteins AcrIIA4 and AcrVA1 can prevent CRISPR/Cas-mediated gene editing in plants, opening up new possibilities for customized control of gene editing and gene expression.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Gi Eob Kim, So Yeon Lee, Hyun Ho Park
Summary: The study revealed the crystal structure of AcrIIC4, showing it adopts a helical bundle fold comprising four helixes, can form a monomer in solution, and directly interacts with Cas9 and Cas9/sgRNA complex. This discovery of AcrIIC4's structure and interaction mode with Cas9 will help understand the diversity in the inhibitory mechanisms of the Acr protein family.
Article
Biochemical Research Methods
Richard G. Lahr, Pragya Sharma, Anthony Maus, Loralie J. Langman, Paul J. Jannetto
Summary: This study describes an assay for quantitation of two common ethanol metabolites, PEth 16:0/18:1 and PEth 16:0/18:2, from human whole blood. The developed method utilizes supported liquid extraction and liquid chromatography-tandem mass spectrometry, enabling automated sample preparation and accurate analysis, while overcoming challenges in the sample preparation process.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
