• Volume 11, 2021
  • Volume 10, 2020
  • Volume 9, 2019
  • Volume 8, 2018
  • Volume 7, 2017
  • Volume 6, 2016
  • Volume 5, 2015
  • Volume 4, 2014
  • Volume 3, 2013
  • Volume 2, 2012
  • Volume 1, 2011
Image Credit: BioProtoc.4013

Current Issue in 2021

Volume: 11, Issue: 9

Biochemistry

Proteomics Profiling of S-sulfurated Proteins in Acinetobacter baumannii Authors:  Brenna J. C. Walsh and David P. Giedroc, date: 05/05/2021, view: 243, Q&A: 0

Hydrogen sulfide (H2S) is emerging as an important modulator in bacterial cytoprotection against the host immune response in infected animals, which may well be attributed to downstream highly oxidized sulfur species, termed reactive sulfur species (RSS), derived from H2S. One mechanism by which H2S/RSS may signal in the cell is through proteome

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Click Chemistry for Imaging in-situ Protein Palmitoylation during the Asexual Stages of Plasmodium falciparum Author:  Mansoor A. Siddiqui, date: 05/05/2021, view: 385, Q&A: 0

Palmitoylation refers to the modification of the cysteine thiols in proteins by fatty acids, most commonly palmitic acid, through ‘thioester bond’ formation. In vivo, palmitoylation of proteins is catalyzed by palmitoyl acyltransferases (PATs or DHHC-PATs). Palmitoylation has recently emerged as a crucial post-translational

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Chromatographic Assays for the Enzymatic Degradation of Chitin Authors:  Sophanit Mekasha, Tina R. Tuveng, Gustav Vaaje-Kolstad and Vincent G. H. Eijsink, date: 05/05/2021, view: 307, Q&A: 0

Chitin is an insoluble linear polymer of β(1→4)-linked N-acetylglucosamine. Enzymatic cleavage of chitin chains can be achieved using hydrolytic enzymes, called chitinases, and/or oxidative enzymes, called lytic polysaccharide monooxygenases (LPMOs). These two groups of enzymes have different modes of action and yield different product

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Characterising Plant Deubiquitinases with in vitro Activity-based Labelling and Ubiquitin Chain Disassembly Assays Authors:  Michael J. Skelly and Steven H. Spoel, date: 05/05/2021, view: 242, Q&A: 0

Post-translational modification of proteins by ubiquitin is an essential cellular signaling mechanism in all eukaryotes. Ubiquitin is removed from target proteins by a wide range of deubiquitinase (DUB) enzymes with different activities and substrate specificities. Understanding how DUBs function in vitro is a vital first step to uncovering their

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Biological Engineering

Inkjet 3D Printing of Polymers Resistant to Fungal Attachment Authors:  Yinfeng He, Cindy Vallieres, Morgan R. Alexander, Ricky D. Wildman and Simon V. Avery, date: 05/05/2021, view: 310, Q&A: 0

Inkjet 3D printing is an additive manufacturing method that allows the user to produce a small batch of customized devices for comparative study versus commercial products. Here, we describe the use of a commercial 2D ink development system (Dimatix material printing) to manufacture small batches of 3D medical or other devices using a recently

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Biophysics

Spin Labeling of RNA Using “Click” Chemistry for Coarse-grained Structure Determination via Pulsed Electron-electron Double Resonance Spectroscopy Authors:  Maria F. Vicino, Tobias Hett and Olav Schiemann, date: 05/05/2021, view: 222, Q&A: 0

Understanding the function of oligonucleotides on a molecular level requires methods for studying their structure, conformational changes, and internal dynamics. Various biophysical methods exist to achieve this, including the whole toolbox of Electron Paramagnetic Resonance (EPR or ESR) spectroscopy. An EPR method widely used in this regard is

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Cancer Biology

ATAC-Seq-based Identification of Extrachromosomal Circular DNA in Mammalian Cells and Its Validation Using Inverse PCR and FISH Authors:  Zhangli Su, Shekhar Saha, Teressa Paulsen, Pankaj Kumar and Anindya Dutta, date: 05/05/2021, view: 336, Q&A: 0

Recent studies from multiple labs including ours have demonstrated the importance of extrachromosomal circular DNA (eccDNA) from yeast to humans (Shibata et al., 2012; Dillon et al., 2015; Møller et al., 2016; Kumar et al., 2017; Turner et al., 2017; Kim et al., 2020). More recently, it has been found that cancer cells obtain a selective

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Immunology

Analysis of Monocyte Cell Fate by Adoptive Transfer in a Murine Model of TLR7-induced Systemic Inflammation Authors:  Jaba Gamrekelashvili, Hermann Haller and Florian P. Limbourg, date: 05/05/2021, view: 281, Q&A: 0

Myeloid plasticity is a hallmark of the innate immune response to Toll-like receptor (TLR) activation. Here, we provide a protocol for monocyte cell fate tracking by adoptive transfer in the context of systemic inflammation induced by TLR7 activation, the principal innate immune receptor sensing viral RNA in mice. Defined monocyte subsets are

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Microbiology

High-throughput Method for Detecting Siderophore Production by Rhizosphere Bacteria Authors:  ShaoHua Gu, Wen Wan, ZhengYing Shao and Wei Zhong, date: 05/05/2021, view: 220, Q&A: 0

Siderophores, a key substance that microorganisms produce to obtain iron under iron-limited conditions, play an important role in regulating interactions between beneficial bacteria and pathogenic bacteria. A large number of bacteria were isolated from the rhizosphere, and we used the method presented here to assay the siderophore production by

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COVID-19 Sample Pooling: From RNA Extraction to Quantitative Real-time RT-PCR Authors:  Kenny Voon, Nur Alia Johari, Khai Lone Lim, Siew Tung Wong, Loke Tim Khaw, Shew Fung Wong, Elaine W. L. Chan, Kok Keong Chan, Boon Keat Tan, Nurul Hanis Ramzi, Patricia K. C. Lim and Lokman H. Sulaiman, date: 05/05/2021, view: 320, Q&A: 0

The COVID-19 pandemic requires mass screening to identify those infected for isolation and quarantine. Individually screening large populations for the novel pathogen, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is costly and requires a lot of resources. Sample pooling methods improve the efficiency of mass screening and consume

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Isolation of GFP-expressing Malarial Hypnozoites by Flow Cytometry Cell Sorting Authors:  Annemarie Voorberg-van der Wel, Sam O. Hoffman and Clemens H. M. Kocken, date: 05/05/2021, view: 192, Q&A: 0

Hypnozoites are dormant liver-stage parasites unique to relapsing malarial species, including the important human pathogen Plasmodium vivax, and pose a barrier to the elimination of malaria. Little is known regarding the biology of these stages, largely due to their inaccessible location. Hypnozoites can be cultured in vitro but these cultures

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Assessing Swarming of Aerobic Bacteria from Human Fecal Matter Authors:  Arjun S. Byju, Deeti Patel, Weijie Chen and Sridhar Mani, date: 05/05/2021, view: 200, Q&A: 0

Swarming – swift movement across a surface via flagella propulsion – is a unique property of many bacteria. The role of swarming, particularly among bacterial populations of the human gut microbiome, is not yet fully understood; although, it is becoming an area of increased scientific and clinical inquiry. To further characterize

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Molecular Biology

Identification of R-loop-forming Sequences in Drosophila melanogaster Embryos and Tissue Culture Cells Using DRIP-seq Authors:  Célia Alecki and Nicole J. Francis, date: 05/05/2021, view: 273, Q&A: 0

R-loops are non-canonical nucleic structures composed of an RNA–DNA hybrid and a displaced ssDNA. Originally identified as a source of genomic instability, R-loops have been shown over the last decade to be involved in the targeting of proteins and to be associated with different histone modifications, suggesting a regulatory function. In

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Neuroscience

Activity-based Anorexia for Modeling Vulnerability and Resilience in Mice Authors:  Jeff A. Beeler and Nesha S. Burghardt, date: 05/05/2021, view: 206, Q&A: 0

Activity-based anorexia (ABA) is a widely used rodent model of anorexia nervosa. It involves combining limited access to food with unlimited access to a running wheel, leading to a paradoxical decrease in food intake, hyperactivity, and life-threatening weight loss. Although initially characterized in rats, ABA has been tested in mice with results

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Plant Science

Age, Wound Size and Position of Injury – Dependent Vascular Regeneration Assay in Growing Leaves Authors:  Dhanya Radhakrishnan, Anju Pallipurath Shanmukhan, Abdul Kareem, Mabel Maria Mathew, Vijina Varaparambathu, Mohammed Aiyaz, Raji Krishna Radha, Krishnaprashanth Ramesh Mekala, Anil Shaji and Kalika Prasad, date: 05/05/2021, view: 286, Q&A: 0

Recurring damage to the aerial organs of plants necessitates their prompt repair, particularly their vasculature. While vascular regeneration assays for aerial plant parts such as the stem and inflorescence stalk are well established, those for leaf vasculature remain unexplored. Recently, we established a new vascular regeneration assay in

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Histological Methods to Detect Early-stage Plant Defense Responses during Artificial Inoculation of Lolium perenne with Epichloë festucae Authors:  Mostafa Rahnama, Damien J. Fleetwood and Richard D. Johnson, date: 05/05/2021, view: 180, Q&A: 0

Epichloë species form agriculturally important symbioses with many cool season grasses. To study these symbioses, such as the interaction of Epichloë festucae with perennial ryegrass (Lolium perenne), host plants can be infected by artificial inoculation of etiolated seedlings. This inoculation is performed by placing mycelium into an

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