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Article ; Online: Death after High-Dose rAAV9 Gene Therapy in a Patient with Duchenne's Muscular Dystrophy.

Palaz, Fahreddin

2023 Volume 389, Issue 23, Page(s) 2210–2211

MeSH term(s)	Humans ; Muscular Dystrophy, Duchenne/genetics ; Muscular Dystrophy, Duchenne/therapy ; Patients
Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2312288
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Article ; Online: Applications of CRISPR Epigenome Editors in Tumor Immunology and Autoimmunity.

Yahsi, Berkay / Palaz, Fahreddin / Dincer, Pervin

ACS synthetic biology

2024 Volume 13, Issue 2, Page(s) 413–427

Abstract: Over the past decade, CRISPR-Cas systems have become indispensable tools for genetic engineering and have been used in clinical trials for various diseases. Beyond genome editing, CRISPR-Cas systems can also be used for performing programmable epigenetic ...

Abstract	Over the past decade, CRISPR-Cas systems have become indispensable tools for genetic engineering and have been used in clinical trials for various diseases. Beyond genome editing, CRISPR-Cas systems can also be used for performing programmable epigenetic modifications. Recent efforts in enhancing CRISPR-based epigenome modifiers have yielded potent tools enabling targeted DNA methylation/demethylation capable of sustaining epigenetic memory through numerous cell divisions. Moreover, it has been understood that during chronic inflammatory states, including cancer, T cells encounter a state called T cell exhaustion that involves elevated inhibitory receptors (e.g., LAG-3, TIM3, PD-1, CD39) and reduced effector T cell-related protein levels (IFN-γ, granzyme B, and perforin). Importantly, epigenetic dysregulation has been identified as one of the key drivers of T cell exhaustion, and it remains one of the biggest obstacles in the field of immunotherapy and decreases the efficiency of chimeric antigen receptor T (CAR-T) cell therapy. Similarly, autoimmune diseases exhibit epigenetically dysfunctional regulatory T (Treg) cells. For instance,
MeSH term(s)	Humans ; Epigenome ; Autoimmunity ; CRISPR-Cas Systems/genetics ; Gene Editing ; Autoimmune Diseases/genetics ; Autoimmune Diseases/therapy ; Neoplasms/genetics ; Neoplasms/therapy
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.3c00524
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Article ; Online: Improving recombinant protein production in CHO cells using the CRISPR-Cas system.

Kalkan, Ali Kerem / Palaz, Fahreddin / Sofija, Semeniuk / Elmousa, Nada / Ledezma, Yuri / Cachat, Elise / Rios-Solis, Leonardo

Biotechnology advances

2023 Volume 64, Page(s) 108115

Abstract: Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering ...

Abstract	Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
MeSH term(s)	Cricetinae ; Animals ; CRISPR-Cas Systems/genetics ; Cricetulus ; CHO Cells ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Genetic Engineering
Chemical Substances	Recombinant Proteins
Language	English
Publishing date	2023-02-07
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	47165-3
ISSN	1873-1899 ; 0734-9750
ISSN (online)	1873-1899
ISSN	0734-9750
DOI	10.1016/j.biotechadv.2023.108115
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Article ; Online: Clinical Validation and Evaluation of a Colorimetric SARS-CoV-2 RT-LAMP Assay Against RT-PCR.

Erdem, Murat / Andaç-Özketen, Ayşe / Özketen, Ahmet Çağlar / Karahan, Gizem / Tozluyurt, Abdullah / Palaz, Fahreddin / Alp, Alpaslan / Ünal, Serhat

Infectious diseases & clinical microbiology

2023 Volume 5, Issue 2, Page(s) 136–143

Abstract: Objective: Reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) is one of the time-saving, accurate, and cost-effective alternative methods to real-time polymerase chain reaction (RT-PCR). This study aimed to identify the robustness of ...

Abstract	Objective: Reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) is one of the time-saving, accurate, and cost-effective alternative methods to real-time polymerase chain reaction (RT-PCR). This study aimed to identify the robustness of a colorimetric RT-LAMP assay kit that we developed, detecting SARS-COV-2 viral RNA within 30 minutes using a primer set special to the N gene against RT-PCR, the gold standard. Materials and methods: Both symptomatic and asymptomatic subjects were included from a single university hospital and the status of both RT-PCR and RT-LAMP assay results were compared, and the consistency of these two assays was analyzed. Results: We showed that the RT-LAMP and RT-PCR assay results confirmed 90% consistency. When we consider the epidemiologic, clinical, and radiologic evaluation, the consistency reached 97%. Conclusion: The results revealed that the colorimetric RT-LAMP assay was efficient, robust, and rapid to be used as in vitro diagnostic tool to display competitiveness compared with RT-PCR.
Language	English
Publishing date	2023-06-23
Publishing country	Turkey
Document type	Journal Article
ISSN	2667-646X
ISSN (online)	2667-646X
DOI	10.36519/idcm.2023.210
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Article ; Online: CRISPR-based tools: Alternative methods for the diagnosis of COVID-19.

Palaz, Fahreddin / Kalkan, Ali Kerem / Tozluyurt, Abdullah / Ozsoz, Mehmet

Clinical biochemistry

2021 Volume 89, Page(s) 1–13

Abstract: The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spread all over the world rapidly and caused a global pandemic. To prevent the virus from spreading to more individuals, it is of great importance to identify and isolate ... ...

Abstract	The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spread all over the world rapidly and caused a global pandemic. To prevent the virus from spreading to more individuals, it is of great importance to identify and isolate infected individuals through testing. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the gold standard method for the diagnosis of coronavirus disease (COVID-19) worldwide. However, performing RT-qPCR is limited to centralized laboratories because of the need for sophisticated laboratory equipment and skilled personnel. Further, it can sometimes give false negative or uncertain results. Recently, new methods have been developed for nucleic acid detection and pathogen diagnosis using CRISPR-Cas systems. These methods present rapid and cost-effective diagnostic platforms that provide high sensitivity and specificity without the need for complex instrumentation. Using the CRISPR-based SARS-CoV-2 detection methods, it is possible to increase the number of daily tests in existing laboratories, reduce false negative or uncertain result rates obtained with RT-qPCR, and perform testing in resource-limited settings or at points of need where performing RT-qPCR is not feasible. Here, we briefly describe the RT-qPCR method, and discuss its limitations in meeting the current diagnostic needs. We explain how the unique properties of various CRISPR-associated enzymes are utilized for nucleic acid detection and pathogen diagnosis. Then, we highlight the important features of CRISPR-based diagnostic methods developed for SARS-CoV-2 detection. Finally, we examine the advantages and limitations of these methods, and discuss how they can contribute to improving the efficiency of the current testing systems for combating SARS-CoV-2.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/virology ; COVID-19 Testing/methods ; CRISPR-Cas Systems ; Humans ; Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
Language	English
Publishing date	2021-01-09
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	390372-2
ISSN	1873-2933 ; 0009-9120
ISSN (online)	1873-2933
ISSN	0009-9120
DOI	10.1016/j.clinbiochem.2020.12.011
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Article ; Online: Improving recombinant protein production in CHO cells using the CRISPR-Cas system

Kalkan, Ali Kerem / Palaz, Fahreddin / Sofija, Semeniuk / Elmousa, Nada / Ledezma, Yuri / Cachat, Elise / Rios-Solis, Leonardo

Biotechnology Advances. 2023 Feb. 07, p.108115-

2023 , Page(s) 108115–

Abstract	Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
Keywords	CRISPR-Cas systems ; Cricetulus griseus ; biopharmaceutical industry ; biopharmaceuticals ; biotechnology ; cost effectiveness ; genetic engineering ; mammals ; protein synthesis ; recombinant proteins ; synthetic biology ; CRISPR system ; CHO cells ; Recombinant protein ; Bioprocessing ; Glycan composition ; Mammalian cells
Language	English
Dates of publication	2023-0207
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	47165-3
ISSN	0734-9750
ISSN	0734-9750
DOI	10.1016/j.biotechadv.2023.108115
Database	NAL-Catalogue (AGRICOLA)

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Article: RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods.

Selvam, Kasturi / Najib, Mohamad Ahmad / Khalid, Muhammad Fazli / Mohamad, Suharni / Palaz, Fahreddin / Ozsoz, Mehmet / Aziah, Ismail

Diagnostics (Basel, Switzerland)

2021 Volume 11, Issue 9

Abstract: Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription-quantitative polymerase chain ... ...

Abstract	Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription-quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2.
Language	English
Publishing date	2021-09-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics11091646
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Article ; Online: A Highly Potent SARS-CoV-2 Blocking Lectin Protein.

Ahan, Recep E / Hanifehnezhad, Alireza / Kehribar, Ebru Ş / Oguzoglu, Tuba C / Földes, Katalin / Özçelik, Cemile E / Filazi, Nazlican / Öztop, Sıdıka / Palaz, Fahreddin / Önder, Sevgen / Bozkurt, Eray U / Ergünay, Koray / Özkul, Aykut / Şeker, Urartu Özgür Şafak

ACS infectious diseases

2022 Volume 8, Issue 7, Page(s) 1253–1264

Abstract: The COVID-19 (coronavirus disease-19) pandemic affected more than 180 million people around the globe, causing more than five million deaths as of January 2022. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the new coronavirus, has been ... ...

Abstract	The COVID-19 (coronavirus disease-19) pandemic affected more than 180 million people around the globe, causing more than five million deaths as of January 2022. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the new coronavirus, has been identified as the primary cause of the infection. The number of vaccinated people is increasing; however, prophylactic drugs are highly demanded to ensure secure social contact. A number of drug molecules have been repurposed to fight against SARS-CoV-2, and some of them have been proven to be effective in preventing hospitalization or ICU admissions. Here, we demonstrated griffithsin (GRFT), a lectin protein, to block the entry of SARS-CoV-2 and its variants, Delta and Omicron, into the Vero E6 cell lines and IFNAR
MeSH term(s)	Animals ; COVID-19/drug therapy ; COVID-19/prevention & control ; Humans ; Lectins ; Mice ; Pandemics ; SARS-CoV-2
Chemical Substances	Lectins
Language	English
Publishing date	2022-04-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2373-8227
ISSN (online)	2373-8227
DOI	10.1021/acsinfecdis.2c00006
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Article ; Online: CRISPR-Cas13 System as a Promising and Versatile Tool for Cancer Diagnosis, Therapy, and Research.

Palaz, Fahreddin / Kalkan, Ali Kerem / Can, Özgür / Demir, Ayça Nur / Tozluyurt, Abdullah / Özcan, Ahsen / Ozsoz, Mehmet

ACS synthetic biology

2021 Volume 10, Issue 6, Page(s) 1245–1267

Abstract: Over the past decades, significant progress has been made in targeted cancer therapy. In precision oncology, molecular profiling of cancer patients enables the use of targeted cancer therapeutics. However, current diagnostic methods for molecular ... ...

Abstract	Over the past decades, significant progress has been made in targeted cancer therapy. In precision oncology, molecular profiling of cancer patients enables the use of targeted cancer therapeutics. However, current diagnostic methods for molecular analysis of cancer are costly and require sophisticated equipment. Moreover, targeted cancer therapeutics such as monoclonal antibodies and small-molecule drugs may cause off-target effects and they are available for only a minority of cancer driver proteins. Therefore, there is still a need for versatile, efficient, and precise tools for cancer diagnostics and targeted cancer treatment. In recent years, the CRISPR-based genome and transcriptome engineering toolbox has expanded rapidly. Particularly, the RNA-targeting CRISPR-Cas13 system has unique biochemical properties, making Cas13 a promising tool for cancer diagnosis, therapy, and research. Cas13-based diagnostic methods allow early detection and monitoring of cancer markers from liquid biopsy samples without the need for complex instrumentation. In addition, Cas13 can be used for targeted cancer therapy through degrading and manipulating cancer-associated transcripts with high efficiency and specificity. Moreover, Cas13-mediated programmable RNA manipulation tools offer invaluable opportunities for cancer research, identification of drug-resistance mechanisms, and discovery of novel therapeutic targets. Here, we review and discuss the current use and potential applications of the CRISPR-Cas13 system in cancer diagnosis, therapy, and research. Thus, researchers will gain a deep understanding of CRISPR-Cas13 technologies, which have the potential to be used as next-generation cancer diagnostics and therapeutics.
MeSH term(s)	CRISPR-Cas Systems ; Early Detection of Cancer/methods ; Gene Editing/methods ; Genome, Human ; Humans ; Liquid Biopsy ; Molecular Targeted Therapy/methods ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/pathology ; Neoplasms/therapy ; Precision Medicine/methods ; RNA/genetics ; Transcriptome
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2021-05-26
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.1c00107
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Article ; Online: RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods

Kasturi Selvam / Mohamad Ahmad Najib / Muhammad Fazli Khalid / Suharni Mohamad / Fahreddin Palaz / Mehmet Ozsoz / Ismail Aziah

Diagnostics, Vol 11, Iss 1646, p

2021 Volume 1646

Abstract	Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2.
Keywords	COVID-19 ; SARS-CoV-2 ; RT-LAMP ; CRISPR ; Cas12 ; Cas13 ; Medicine (General) ; R5-920
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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