Biological Sciences

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    Protocols in Current Issue
    HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes in vivo

    Chromatin immunoprecipitation (ChIP) maps, on a genome-wide scale, transcription factor binding sites, and the distribution of other chromatin-associated proteins and their modifications. As such, it provides valuable insights into mechanisms of

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    HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes in vivo
    [Abstract]

    Chromatin immunoprecipitation (ChIP) maps, on a genome-wide scale, transcription factor binding sites, and the distribution of other chromatin-associated proteins and their modifications. As such, it provides valuable insights into mechanisms of gene regulation. However, successful ChIP experiments are dependent on the availability of a

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    Protocol to Study Spatial Subgoal Learning Using Escape Behavior in Mice
    Authors:  Philip Shamash and Tiago Branco, date: 06/20/2022, view: 775, Q&A: 0
    [Abstract]

    Rodent spatial navigation is a key model system for studying mammalian cognition and its neural mechanisms. Of particular interest is how animals memorize the structure of their environments and compute multi-step routes to a goal. Previous work on multi-step spatial reasoning has generally involved placing rodents at the start of a maze until

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    Time-off-pick Assay to Measure Caenorhabditis elegans Motility
    Authors:  Alyssa C. Walker, Rohan Bhargava, Amanda S. Brust, Ali A. Owji and Daniel M. Czyż, date: 06/20/2022, view: 921, Q&A: 0
    [Abstract]

    Caenorhabditis elegans is a simple metazoan that is often used as a model organism to study various human ailments with impaired motility phenotypes, including protein conformational diseases. Numerous motility assays that measure neuro-muscular function have been employed using C. elegans. Here, we describe “time-off-pick" (TOP), a novel

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    Protocol for High Throughput Screening of Antibody Phage Libraries
    [Abstract]

    Phage display is a proven and widely used technology for selecting specific antibodies against desired targets. However, an immense amount of effort is required to identify and screen the desired positive clones from large and diverse combinatorial libraries. On the other hand, the selection of positive binding clones

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    Electroporation of Small Interfering RNAs into Tibialis Anterior Muscles of Mice
    Authors:  Anna Stephan, Flavia A. Graca, Liam C. Hunt and Fabio Demontis, date: 06/05/2022, view: 788, Q&A: 0
    [Abstract]

    Aging and wasting of skeletal muscle reduce organismal fitness. Regrettably, only limited interventions are currently available to address this unmet medical need. Many methods have been developed to study this condition, including the intramuscular electroporation of DNA plasmids. However, this technique requires surgery and high electrical

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    A Modified Fluctuation Assay with a CAN1 Reporter in Yeast
    Authors:  Pengyao Jiang, Anja R. Ollodart and Maitreya J. Dunham, date: 06/05/2022, view: 524, Q&A: 0
    [Abstract]

    Understanding the generation of mutations is fundamental to understanding evolution and genetic disease; however, the rarity of such events makes experimentally identifying them difficult. Mutation accumulation (MA) methods have been widely used. MA lines require serial bottlenecks to fix de novo mutations, followed by whole-genome sequencing.

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    Protocol to Isolate Germinal Centers by Laser Microdissection
    Authors:  Farbod Bahreini, Markus Niebuhr, Julia Belde, Jürgen Westermann and Kathrin Kalies, date: 06/05/2022, view: 512, Q&A: 0
    [Abstract]

    During adaptive immune responses, germinal centers (GC) appear as transient microstructures, in which antigen-specific B and T cells interact with each other. Because only the antigen-activated B and T cells, such as Plasmablasts or follicular T helper (Tfh) cells, are present in GC, the in depth-analysis of GC is of great interest. To identify

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    Efficient Superovulation and Egg Collection from Mice
    Authors:  Miyuki Shindo, Kenji Miyado, Woojin Kang, Maki Fukami and Mami Miyado, date: 06/05/2022, view: 555, Q&A: 0
    [Abstract]

    Superovulation is a method used to reduce the number of mice used per experiment by increasing the egg number. Conventionally, superovulation for obtaining mouse eggs involves the use of equine chorionic gonadotropin (eCG) for stimulation and human CG for induction. Female mice of the C57BL/6 inbred strain spontaneously ovulate approximately 10

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    Quantification of Soil-surface Roots in Seedlings and Mature Rice Plants
    Authors:  Eiko Hanzawa, Yuka Kitomi, Yusaku Uga and Tadashi Sato, date: 05/05/2022, view: 1079, Q&A: 0
    [Abstract]

    Soil-surface roots (SORs) in rice are primary roots that elongate over or near the soil surface. SORs help avoid excessive reduction of stress that occurs in paddy, such as in saline conditions. SORs may also be beneficial for rice growth in phosphorus-deficient paddy fields. Thus, SOR is a useful trait for crop adaptation to certain environmental

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    Bacterial Growth Curve Measurements with a Multimode Microplate Reader
    Authors:  Ariel T. Rogers, Kaitlin R. Bullard, Akash C. Dod and Yong Wang, date: 05/05/2022, view: 1006, Q&A: 0
    [Abstract]

    Bacterial studies based on growth curves are common in microbiology and related fields. Compared to the standard photometer and cuvette based protocols, bacterial growth curve measurements with microplate readers provide better temporal resolution, higher efficiency, and are less laborious, while analysis and interpretation of the microplate-based

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