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Book: Synthetic DNA

Hughes, Randall A.

methods and protocols

(Methods in molecular biology ; 1472 ; Springer protocols)

2017

Author's details	edited by Randall A. Hughes
Series title	Methods in molecular biology ; 1472 Springer protocols
Collection
Keywords	BASIC ; COOL program ; DNA sequences ; chemically synthesized DNA ; oligonucleotide synthesis ; synthetic oligonucleotide sequences
Language	English
Size	xiii, 248 Seiten, Illustrationen, Diagramme, 25.4 cm x 17.8 cm, 0 g
Publisher	Humana Press
Publishing place	New York
Publishing country	United States
Document type	Book
HBZ-ID	HT019126285
ISBN	978-1-4939-6341-6 ; 1-4939-6341-4 ; 9781493963430 ; 1493963430
Database	Catalogue ZB MED Medicine, Health

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Zs A 7042 -1472-	verfügbar in Königswinter	Königswinter

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Book: Synthetic DNA

Hughes, Randall A

methods and protocols

(Methods in molecular biology, ; 1472 ; Springer protocols)

2017

Author's details	edited by Randall A. Hughes
Series title	Methods in molecular biology, ; 1472 Springer protocols
MeSH term(s)	Genes, Synthetic/genetics ; DNA/biosynthesis ; Computational Biology/methods
Language	English
Size	xiii, 248 pages :, illustrations (some color) ;, 26 cm.
Document type	Book
Note	"Published In: United States, 28 October 2016 " --Distributor's website.
ISBN	9781493963416 ; 1493963414 ; 9781493963430 ; 1493963430
Database	Catalogue of the US National Library of Medicine (NLM)

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Article ; Online: Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology.

Hughes, Randall A / Ellington, Andrew D

Cold Spring Harbor perspectives in biology

2017 Volume 9, Issue 1

Abstract: The chemical synthesis of DNA oligonucleotides and their assembly into synthons, genes, circuits, and even entire genomes by gene synthesis methods has become an enabling technology for modern molecular biology and enables the design, build, test, learn, ...

Abstract	The chemical synthesis of DNA oligonucleotides and their assembly into synthons, genes, circuits, and even entire genomes by gene synthesis methods has become an enabling technology for modern molecular biology and enables the design, build, test, learn, and repeat cycle underpinning innovations in synthetic biology. In this perspective, we briefly review the techniques and technologies that enable the synthesis of DNA oligonucleotides and their assembly into larger DNA constructs with a focus on recent advancements that have sought to reduce synthesis cost and increase sequence fidelity. The development of lower-cost methods to produce high-quality synthetic DNA will allow for the exploration of larger biological hypotheses by lowering the cost of use and help to close the DNA read-write cost gap.
MeSH term(s)	DNA/chemistry ; DNA Replication ; Oligonucleotide Array Sequence Analysis ; Synthetic Biology
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2017-01-03
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1943-0264
ISSN (online)	1943-0264
DOI	10.1101/cshperspect.a023812
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Recovery of Information Stored in Modified DNA with an Evolved Polymerase.

Shroff, Raghav / Ellefson, Jared W / Wang, Siyuan S / Boulgakov, Alexander A / Hughes, Randall A / Ellington, Andrew D

ACS synthetic biology

2022 Volume 11, Issue 2, Page(s) 554–561

Abstract: DNA is increasingly being explored as an alternative medium for digital information storage, but the potential information loss from degradation and associated issues with error during reading challenge its wide-scale implementation. To address this, we ... ...

Abstract	DNA is increasingly being explored as an alternative medium for digital information storage, but the potential information loss from degradation and associated issues with error during reading challenge its wide-scale implementation. To address this, we propose an atomic-scale encoding standard for DNA, where information is encoded in degradation-resistant analogues of natural nucleic acids (xNAs). To better enable this approach, we used directed evolution to create a polymerase capable of transforming 2'-
MeSH term(s)	DNA/genetics ; Nucleic Acids/genetics ; RNA/genetics ; RNA-Directed DNA Polymerase/metabolism
Chemical Substances	Nucleic Acids ; RNA (63231-63-0) ; DNA (9007-49-2) ; RNA-Directed DNA Polymerase (EC 2.7.7.49)
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.1c00575
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Survival and disease progression following solitary locoregional recurrence after head and neck radiotherapy.

Zhao, Lucian / Day, Andrew T / Moon, Dominic / Avkshtol, Vladimir / Sumer, Baran D / Hughes, Randall / Sher, David J

Head & neck

2022 Volume 44, Issue 5, Page(s) 1153–1163

Abstract: Purpose: The management of solitary locoregional recurrence (sLRR) of head and neck squamous cell carcinoma (HNSCC) previously treated with radiotherapy (RT) is challenging. We aimed to identify characteristics associated with improved outcome.: ... ...

Abstract	Purpose: The management of solitary locoregional recurrence (sLRR) of head and neck squamous cell carcinoma (HNSCC) previously treated with radiotherapy (RT) is challenging. We aimed to identify characteristics associated with improved outcome. Methods: We identified patients treated with non-sinus, mucosal HNSCC who initially received IMRT. We characterized overall survival (OS) and locoregional control (LRC). Multivariable analysis (MVA) on survival and patterns-of-failure were performed using Cox and Fine-Gray competing risks analysis. Results: We identified 90 patients with available follow-up. In total, 67 (74%) patients received curative-intent salvage, while 23 (26%) received palliative care. On MVA, significantly improved OS and LRC were associated with lower initial N-classification and use of salvage total laryngectomy (TL) or neck dissection (ND). Conclusion: A nontrivial number of patients with sLRR cannot undergo salvage. Among patients treated with curative intent, TL or ND were clearly associated with improved OS and LRC.
MeSH term(s)	Carcinoma, Squamous Cell/radiotherapy ; Carcinoma, Squamous Cell/surgery ; Disease Progression ; Head and Neck Neoplasms/radiotherapy ; Head and Neck Neoplasms/surgery ; Humans ; Neoplasm Recurrence, Local/pathology ; Retrospective Studies ; Squamous Cell Carcinoma of Head and Neck/radiotherapy
Language	English
Publishing date	2022-02-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	645165-2
ISSN	1097-0347 ; 0148-6403 ; 1043-3074
ISSN (online)	1097-0347
ISSN	0148-6403 ; 1043-3074
DOI	10.1002/hed.27012
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Highly variable timing renders immunotherapy efficacy and toxicity impractical biomarkers of one another in clinical practice.

von Itzstein, Mitchell S / Yang, Yuqiu / Wang, Yiqing / Hsiehchen, David / Sheffield, Thomas Y / Fattah, Farjana / Popat, Vinita / Ahmed, Murtaza / Homsi, Jade / Dowell, Jonathan E / Rashdan, Sawsan / Lohrey, Jay / Hammers, Hans J / Hughes, Randall S / Wang, Tao / Xie, Yang / Gerber, David E

Frontiers in immunology

2024 Volume 15, Page(s) 1351739

Abstract: Background: A useful clinical biomarker requires not only association but also a consistent temporal relationship. For instance, chemotherapy-induced neutropenia and epidermal growth-factor inhibitor-related acneiform rash both occur within weeks of ... ...

Abstract	Background: A useful clinical biomarker requires not only association but also a consistent temporal relationship. For instance, chemotherapy-induced neutropenia and epidermal growth-factor inhibitor-related acneiform rash both occur within weeks of treatment initiation, thereby providing information prior to efficacy assessment. Although immune checkpoint inhibitor (ICI)-associated immune-related adverse events (irAE) have been associated with therapeutic benefit, irAE may have delayed and highly variable onset. To determine whether ICI efficacy and irAE could serve as clinically useful biomarkers for predicting each other, we determined the temporal relationship between initial efficacy assessment and irAE onset in a diverse population treated with ICI. Methods: Using two-sided Fisher exact and Cochran-Armitage tests, we determined the relative timing of initial efficacy assessment and irAE occurrence in a cohort of 155 ICI-treated patients (median age 68 years, 40% women). Results: Initial efficacy assessment was performed a median of 50 days [interquartile range (IQR) 39-59 days] after ICI initiation; median time to any irAE was 77 days (IQR 28-145 days) after ICI initiation. Median time to first irAE was 42 days (IQR 20-88 days). Overall, 58% of any irAE and 47% of first irAE occurred after initial efficacy assessment. For clinically significant (grade ≥2) irAE, 60% of any and 53% of first occurred after initial efficacy assessment. The likelihood of any future irAE did not differ according to response (45% for complete or partial response vs. 47% for other cases; Conclusions: In contrast to that seen with chemotherapy and molecularly targeted therapies, the temporal relationship between ICI efficacy and toxicity is complex and bidirectional. In practice, neither parameter can be routinely relied on as a clinical biomarker to predict the other.
MeSH term(s)	Humans ; Female ; Male ; Aged ; Immune Checkpoint Inhibitors/adverse effects ; Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Neoplasms/drug therapy ; Neoplasms/immunology ; Neoplasms/therapy ; Biomarkers ; Immunotherapy/adverse effects ; Immunotherapy/methods ; Treatment Outcome ; Time Factors
Chemical Substances	Immune Checkpoint Inhibitors ; Biomarkers
Language	English
Publishing date	2024-04-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1351739
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: EBNA1 Inhibitors Block Proliferation of Spontaneous Lymphoblastoid Cell Lines From Patients With Multiple Sclerosis and Healthy Controls.

Monaco, Maria Chiara G / Soldan, Samantha S / Su, Chenhe / Clauze, Annaliese / Cooper, John F / Patel, Rishi J / Lu, Fang / Hughes, Randall J / Messick, Troy E / Andrada, Frances C / Ohayon, Joan / Lieberman, Paul M / Jacobson, Steven

Neurology(R) neuroimmunology & neuroinflammation

2023 Volume 10, Issue 5

Abstract: Background and objectives: Epstein-Barr virus (EBV) is a ubiquitous herpesvirus that establishes lifelong latency in memory B cells and has been identified as a major risk factor of multiple sclerosis (MS). B cell depletion therapies have disease- ... ...

Abstract	Background and objectives: Epstein-Barr virus (EBV) is a ubiquitous herpesvirus that establishes lifelong latency in memory B cells and has been identified as a major risk factor of multiple sclerosis (MS). B cell depletion therapies have disease-modifying benefit in MS. However, it is unclear whether this benefit is partly attributable to the elimination of EBV Methods: In this study, we describe the establishment of spontaneous lymphoblastoid cell lines (SLCLs) generated ex vivo with the endogenous EBV of patients with MS and controls and treated with either an Epstein-Barr virus nuclear antigen 1 (EBNA1) inhibitor (VK-1727) or cladribine, a nucleoside analog that eliminates B cells. Results: We showed that a small molecule inhibitor of EBNA1, a critical regulator of the EBV life cycle, blocks the proliferation and metabolic activity of these SLCLs. In contrast to cladribine, a highly cytotoxic B cell depleting therapy currently used in MS, the EBNA1 inhibitor VK-1727 was cytostatic rather than cytotoxic and selective for EBV Discussion: This study shows that patient-derived SLCLs provide a useful tool for interrogating the role of EBV
MeSH term(s)	Humans ; Cell Line ; Cell Proliferation ; Cladribine/pharmacology ; Epstein-Barr Virus Infections/complications ; Epstein-Barr Virus Infections/drug therapy ; Epstein-Barr Virus Infections/genetics ; Epstein-Barr Virus Nuclear Antigens ; Herpesvirus 4, Human ; Multiple Sclerosis ; Case-Control Studies
Chemical Substances	Cladribine (47M74X9YT5) ; Epstein-Barr Virus Nuclear Antigens
Language	English
Publishing date	2023-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2767740-0
ISSN	2332-7812 ; 2332-7812
ISSN (online)	2332-7812
ISSN	2332-7812
DOI	10.1212/NXI.0000000000200149
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Efficacy and Quality-of-Life Following Involved Nodal Radiotherapy for Head and Neck Squamous Cell Carcinoma: The INRT-AIR Phase II Clinical Trial.

Sher, David J / Moon, Dominic H / Vo, Dat / Wang, Jing / Chen, Liyuan / Dohopolski, Michael / Hughes, Randall / Sumer, Baran D / Ahn, Chul / Avkshtol, Vladimir

Clinical cancer research : an official journal of the American Association for Cancer Research

2023 Volume 29, Issue 17, Page(s) 3284–3291

Abstract: Purpose: Elective neck irradiation (ENI) has long been considered mandatory when treating head and neck squamous cell carcinoma (HNSCC) with definitive radiotherapy, but it is associated with significant dose to normal organs-at-risk (OAR). In this ... ...

Abstract	Purpose: Elective neck irradiation (ENI) has long been considered mandatory when treating head and neck squamous cell carcinoma (HNSCC) with definitive radiotherapy, but it is associated with significant dose to normal organs-at-risk (OAR). In this prospective phase II study, we investigated the efficacy and tolerability of eliminating ENI and strictly treating involved and suspicious lymph nodes (LN) with intensity-modulated radiotherapy. Patients and methods: Patients with newly diagnosed HNSCC of the oropharynx, larynx, and hypopharynx were eligible for enrollment. Each LN was characterized as involved or suspicious based on radiologic criteria and an in-house artificial intelligence (AI)-based classification model. Gross disease received 70 Gray (Gy) in 35 fractions and suspicious LNs were treated with 66.5 Gy, without ENI. The primary endpoint was solitary elective volume recurrence, with secondary endpoints including patterns-of-failure and patient-reported outcomes. Results: Sixty-seven patients were enrolled, with 18 larynx/hypopharynx and 49 oropharynx cancer. With a median follow-up of 33.4 months, the 2-year risk of solitary elective nodal recurrence was 0%. Gastrostomy tubes were placed in 14 (21%), with median removal after 2.9 months for disease-free patients; no disease-free patient is chronically dependent. Grade I/II dermatitis was seen in 90%/10%. There was no significant decline in composite MD Anderson Dysphagia Index scores after treatment, with means of 89.1 and 92.6 at 12 and 24 months, respectively. Conclusions: These results suggest that eliminating ENI is oncologically sound for HNSCC, with highly favorable quality-of-life outcomes. Additional prospective studies are needed to support this promising paradigm before implementation in any nontrial setting.
MeSH term(s)	Humans ; Artificial Intelligence ; Head and Neck Neoplasms/radiotherapy ; Prospective Studies ; Quality of Life ; Radiotherapy, Intensity-Modulated/adverse effects ; Squamous Cell Carcinoma of Head and Neck/radiotherapy
Language	English
Publishing date	2023-09-06
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-23-0334
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Viral Immune signatures from cerebrospinal fluid extracellular vesicles and particles in HAM and other chronic neurological diseases.

Pleet, Michelle L / Welsh, Joshua A / Stack, Emily H / Cook, Sean / Johnson, Dove-Anna / Killingsworth, Bryce / Traynor, Tim / Clauze, Annaliese / Hughes, Randall / Monaco, Maria Chiara / Ngouth, Nyater / Ohayon, Joan / Enose-Akahata, Yoshimi / Nath, Avindra / Cortese, Irene / Reich, Daniel S / Jones, Jennifer C / Jacobson, Steven

Frontiers in immunology

2023 Volume 14, Page(s) 1235791

Abstract: Background and objectives: Extracellular vesicles and particles (EVPs) are released from virtually all cell types, and may package many inflammatory factors and, in the case of infection, viral components. As such, EVPs can play not only a direct role ... ...

Abstract	Background and objectives: Extracellular vesicles and particles (EVPs) are released from virtually all cell types, and may package many inflammatory factors and, in the case of infection, viral components. As such, EVPs can play not only a direct role in the development and progression of disease but can also be used as biomarkers. Here, we characterized immune signatures of EVPs from the cerebrospinal fluid (CSF) of individuals with HTLV-1-associated myelopathy (HAM), other chronic neurologic diseases, and healthy volunteers (HVs) to determine potential indicators of viral involvement and mechanisms of disease. Methods: We analyzed the EVPs from the CSF of HVs, individuals with HAM, HTLV-1-infected asymptomatic carriers (ACs), and from patients with a variety of chronic neurologic diseases of both known viral and non-viral etiologies to investigate the surface repertoires of CSF EVPs during disease. Results: Significant increases in CD8+ and CD2+ EVPs were found in HAM patient CSF samples compared to other clinical groups ( Discussion: These data suggest that CD8+ and CD2+ CSF EVPs may be important as: 1) potential biomarkers and indicators of disease pathways for viral-mediated neurological diseases, particularly HAM, and 2) as possible meditators of the disease process in infected individuals.
MeSH term(s)	Humans ; Paraparesis, Tropical Spastic ; Central Nervous System ; Extracellular Vesicles ; Nervous System Diseases ; CD40 Antigens ; Chronic Disease
Chemical Substances	CD40 Antigens
Language	English
Publishing date	2023-08-09
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1235791
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Limited effects of source population identity and number on seagrass transplant performance.

Novak, Alyssa B / Plaisted, Holly K / Hays, Cynthia G / Hughes, Randall A

PeerJ

2017 Volume 5, Page(s) e2972

Abstract: Global declines in coastal foundation species highlight the importance of effective restoration. In this study, we examined the effects of source population identity and diversity (one vs. three sources per plot) on seagrass ( ...

Abstract	Global declines in coastal foundation species highlight the importance of effective restoration. In this study, we examined the effects of source population identity and diversity (one vs. three sources per plot) on seagrass (
Language	English
Publishing date	2017-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.2972
Database	MEDical Literature Analysis and Retrieval System OnLINE

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