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  1. Article ; Online: Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

    Judith Hyle / Mohamed Nadhir Djekidel / Justin Williams / Shaela Wright / Ying Shao / Beisi Xu / Chunliang Li

    Genome Biology, Vol 24, Iss 1, Pp 1-

    2023  Volume 30

    Abstract: Abstract Background CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription ... ...

    Abstract Abstract Background CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations in investigating the function of CTCF. Results We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcript changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF. Conclusions By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID-tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.
    Keywords CTCF ; Transcription ; Auxin-inducible degron ; CRISPR ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 570
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: microbiomeDASim

    Justin Williams / Hector Corrada Bravo / Jennifer Tom / Joseph Nathaniel Paulson

    F1000Research, Vol

    Simulating longitudinal differential abundance for microbiome data [version 2; peer review: 2 approved]

    2020  Volume 8

    Abstract: An increasing emphasis on understanding the dynamics of microbial communities in various settings has led to the proliferation of longitudinal metagenomic sampling studies. Data from whole metagenomic shotgun sequencing and marker-gene survey studies ... ...

    Abstract An increasing emphasis on understanding the dynamics of microbial communities in various settings has led to the proliferation of longitudinal metagenomic sampling studies. Data from whole metagenomic shotgun sequencing and marker-gene survey studies have characteristics that drive novel statistical methodological development for estimating time intervals of differential abundance. In designing a study and the frequency of collection prior to a study, one may wish to model the ability to detect an effect, e.g., there may be issues with respect to cost, ease of access, etc. Additionally, while every study is unique, it is possible that in certain scenarios one statistical framework may be more appropriate than another. Here, we present a simulation paradigm implemented in the R Bioconductor software package microbiomeDASim available at http://bioconductor.org/packages/microbiomeDASim microbiomeDASim. microbiomeDASim allows investigators to simulate longitudinal differential abundant microbiome features with a variety of known functional forms with flexible parameters to control desired signal-to-noise ratio. We present metrics of success results on one particular method called metaSplines.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Re-purposed drive-through vaccination set-up for Mpox, New York Metropolitan Area

    Marina Keller / Vishnu Chaturvedi / Rebecca Glassman / Donald S. Chen / Marc El-Khoury / Mary Dundas / Nicholas Feola / Varghese Thankachen / Marie Yezzo / Keri Tone / Justin Williams / Renee Garrick

    Infection Prevention in Practice, Vol 5, Iss 4, Pp 100316- (2023)

    2023  

    Abstract: Summary: Background: This report details how one large medical center in the Metropolitan New York area re-purposed a drive-through COVID-19 vaccination structure to handle a surge in Mpox cases in July 2022.Methods/Results: Simultaneous to on-going ... ...

    Abstract Summary: Background: This report details how one large medical center in the Metropolitan New York area re-purposed a drive-through COVID-19 vaccination structure to handle a surge in Mpox cases in July 2022.Methods/Results: Simultaneous to on-going COVID -19 vaccination and testing, Mpox vaccination was rolled out in the same drive through structure. More than 1,820 Jynneos (Smallpox and Monkeypox Vaccine, Live, Non-replicating) vaccine dosages were delivered subcutaneously and then intradermally to 1,123 individuals through the open window of their vehicles, averaging 8–10 patients an hour. Five vaccine recipients suffered Mpox rash; there was no exposure among healthcare providers. Conclusion: Drive-through vaccination is an efficient model to be redeployed for future unexpected vaccine initiatives.
    Keywords Monkeypox ; Mpox ; Vaccine drive-through ; Epidemic surge ; Jynneos ; Intradermal ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Teaching Incision and Drainage of Abscess

    Megan Freeman / Patricia Wathen / Justin Williams / Maggie Zhang

    MedEdPORTAL, Vol

    2014  Volume 10

    Abstract: Abstract Introduction This module provides instruction on how to teach the incision and drainage of the cutaneous abscess. It is best intended for application in small groups and can be applied in interdisciplinary team-based learner settings. Methods ... ...

    Abstract Abstract Introduction This module provides instruction on how to teach the incision and drainage of the cutaneous abscess. It is best intended for application in small groups and can be applied in interdisciplinary team-based learner settings. Methods This teaching module utilizes simulation techniques to improve learner competence. It is designed to allow the instructor to create a simulation-based curriculum for learners at any level of training for teaching incision and drainage of the cutaneous abscess. It provides instruction on making low-cost simulated models as well as tools and tips for implementation of the course. Additionally, this module provides the instructor with pre- and posttesting tools, a procedure checklist, and tools for teaching informed consent. The module takes about 90 minutes to complete. Results The pre- and posttests for this module were given to third-year medical students, who demonstrated a significant improvement in their ability to list the equipment needed and the essential steps of the procedure. Most learners also felt that it was a valuable learning experience that should be provided to all third-year medical students. Discussion Benefits of this model of teaching incision and drainage of abscesses include little expense of materials (approximately $1.00 per abscess) and minimal odor due to the use of toothpaste as “pus.”
    Keywords Patient Simulation ; Abscess ; Drainage ; Medicine (General) ; R5-920 ; Education ; L
    Subject code 370
    Language English
    Publishing date 2014-03-01T00:00:00Z
    Publisher Association of American Medical Colleges
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Graded recruitment of pupil-linked neuromodulation by parametric stimulation of the vagus nerve

    Zakir Mridha / Jan Willem de Gee / Yanchen Shi / Rayan Alkashgari / Justin Williams / Aaron Suminski / Matthew P. Ward / Wenhao Zhang / Matthew James McGinley

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: Despite its wide and growing use, the mechanisms by which in vivo vagus nerve stimulation (VNS) exerts its therapeutic benefits are still largely unknown. Here, the authors show in mice that pupil dilation is a reliable and noninvasive biosensor for ... ...

    Abstract Despite its wide and growing use, the mechanisms by which in vivo vagus nerve stimulation (VNS) exerts its therapeutic benefits are still largely unknown. Here, the authors show in mice that pupil dilation is a reliable and noninvasive biosensor for titratable VNS-evoked cortical neuromodulation by acetylcholine.
    Keywords Science ; Q
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Carbon in Mature Native Forests in Australia

    Fabiano A. Ximenes / Amrit Kathuria / Michael McLean / Rebecca Coburn / David Sargeant / Michael Ryan / Justin Williams / Ken Boer / Matthew Mo

    Forests, Vol 9, Iss 2, p

    The Role of Direct Weighing in the Derivation of Allometric Equations

    2018  Volume 60

    Abstract: Accurate estimates of forest biomass are essential to understand the contribution of forests to climate change mitigation efforts. In this manuscript, we report on biomass determinations for 586 directly weighed trees located in three important native ... ...

    Abstract Accurate estimates of forest biomass are essential to understand the contribution of forests to climate change mitigation efforts. In this manuscript, we report on biomass determinations for 586 directly weighed trees located in three important native forest areas in Australia. The sites were paired according to management strategy; i.e., managed for periodic cycles of harvest or conservation only. The key aim of the work was to test whether non-site specific available biomass relationships are reliable, especially in the estimation of the biomass of trees with a large diameter at breast height (DBH). The above-ground carbon (AGC) estimates for largely undisturbed forests ranged from approximately 200–400 t C ha−1. Existing allometric equations were generally poor at estimating biomass for mature trees, especially those of large DBH. Direct weighing of biomass ensured a degree of certainty in the results that cannot be associated with previous studies that relied on sub-sampling, or with studies that relied on existing allometric equations. Thus, caution should be exercised when interpreting the results of previous studies that did not rely on direct weighing of the biomass in the context of decisions around optimum forest management regimens, and the contribution of mature forest stands to the global carbon balance.
    Keywords native ; forests ; biomass ; weighing ; production ; conservation ; allometric ; Plant ecology ; QK900-989
    Subject code 333
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Analysis of the modern distribution of South African Gerbilliscus (Rodentia

    Timothy Campbell / Patrick Lewis / Justin Williams

    South African Journal of Science, Vol 107, Iss 1/

    Gerbillinae) with implications for Plio-Pleistocene palaeoenvironmental reconstruction

    2011  Volume 2

    Abstract: There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the ... ...

    Abstract There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the palaeontological and archaeological sites in the region. We used a geographic information systems analysis to examine the distribution of modern Gerbilliscus by georeferencing museum specimens. The distribution of Gerbilliscus was then compared to the latest treatment of the vegetation of South Africa, Lesotho and Swaziland in order to quantify the genus's environmental tolerances and propose a new niche model for this taxon. Palaeoenvironmental reconstructions are made possible by defining the tolerance limits of modern taxa that have persisted relatively unchanged throughout the Plio-Pleistocene. Tolerance limits can then be applied to fossil-bearing localities where these taxa are known to have occurred in the past. Results from our analysis indicated that Gerbilliscus exhibits a wide range of environmental tolerances that must be considered when reconstructing palaeoenvironments.
    Keywords Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Academy of Science of South Africa
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Analysis of the modern distribution of South African Gerbilliscus (Rodentia

    Timothy Campbell / Patrick Lewis / Justin Williams

    South African Journal of Science, Vol 107, Iss 1/

    Gerbillinae) with implications for Plio-Pleistocene palaeoenvironmental reconstruction

    2011  Volume 2

    Abstract: There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the ... ...

    Abstract There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the palaeontological and archaeological sites in the region. We used a geographic information systems analysis to examine the distribution of modern Gerbilliscus by georeferencing museum specimens. The distribution of Gerbilliscus was then compared to the latest treatment of the vegetation of South Africa, Lesotho and Swaziland in order to quantify the genus's environmental tolerances and propose a new niche model for this taxon. Palaeoenvironmental reconstructions are made possible by defining the tolerance limits of modern taxa that have persisted relatively unchanged throughout the Plio-Pleistocene. Tolerance limits can then be applied to fossil-bearing localities where these taxa are known to have occurred in the past. Results from our analysis indicated that Gerbilliscus exhibits a wide range of environmental tolerances that must be considered when reconstructing palaeoenvironments.
    Keywords Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Academy of Science of South Africa
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  9. Article ; Online: Analysis of the modern distribution of South African Gerbilliscus (Rodentia

    Timothy Campbell / Patrick Lewis / Justin Williams

    South African Journal of Science, Vol 107, Iss 1/

    Gerbillinae) with implications for Plio-Pleistocene palaeoenvironmental reconstruction

    2011  Volume 2

    Abstract: There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the ... ...

    Abstract There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the palaeontological and archaeological sites in the region. We used a geographic information systems analysis to examine the distribution of modern Gerbilliscus by georeferencing museum specimens. The distribution of Gerbilliscus was then compared to the latest treatment of the vegetation of South Africa, Lesotho and Swaziland in order to quantify the genus's environmental tolerances and propose a new niche model for this taxon. Palaeoenvironmental reconstructions are made possible by defining the tolerance limits of modern taxa that have persisted relatively unchanged throughout the Plio-Pleistocene. Tolerance limits can then be applied to fossil-bearing localities where these taxa are known to have occurred in the past. Results from our analysis indicated that Gerbilliscus exhibits a wide range of environmental tolerances that must be considered when reconstructing palaeoenvironments.
    Keywords Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Academy of Science of South Africa
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  10. Article ; Online: Analysis of the modern distribution of South African Gerbilliscus (Rodentia

    Timothy Campbell / Patrick Lewis / Justin Williams

    South African Journal of Science, Vol 107, Iss 1/

    Gerbillinae) with implications for Plio-Pleistocene palaeoenvironmental reconstruction

    2011  Volume 2

    Abstract: There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the ... ...

    Abstract There are four extant species of Gerbilliscus, formally classified as Tatera, native to the southern African subregion, each exhibiting varying degrees of environmental tolerance. These species are also routinely reported from many of the palaeontological and archaeological sites in the region. We used a geographic information systems analysis to examine the distribution of modern Gerbilliscus by georeferencing museum specimens. The distribution of Gerbilliscus was then compared to the latest treatment of the vegetation of South Africa, Lesotho and Swaziland in order to quantify the genus's environmental tolerances and propose a new niche model for this taxon. Palaeoenvironmental reconstructions are made possible by defining the tolerance limits of modern taxa that have persisted relatively unchanged throughout the Plio-Pleistocene. Tolerance limits can then be applied to fossil-bearing localities where these taxa are known to have occurred in the past. Results from our analysis indicated that Gerbilliscus exhibits a wide range of environmental tolerances that must be considered when reconstructing palaeoenvironments.
    Keywords Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Academy of Science of South Africa
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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