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1. Exploring FlyBase Data Using QuickSearch

   https://doi.org/10.1002/cpz1.731  

   Marygold, Steven J. ; the FlyBase Consortium ( April 2023 , Current Protocols)

   FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information aboutDrosophila melanogaster. The long and rich history ofDrosophilaresearch, combined with recent surges in genomic‐scale and high‐throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

   Basic Protocol 1: Using the “Search FlyBase” tab of QuickSearch

   Basic Protocol 2: Using the “Data Class” tab of QuickSearch

   Basic Protocol 3: Using the “References” tab of QuickSearch

   Basic Protocol 4: Using the “Gene Groups” tab of QuickSearch

   Basic Protocol 5: Using the “Pathways” tab of QuickSearch

   Basic Protocol 6: Using the “GO” tab of QuickSearch

   Basic Protocol 7: Using the “Protein Domains” tab of QuickSearch

   Basic Protocol 8: Using the “Expression” tab of QuickSearch

   Basic Protocol 9: Using the “GAL4 etc” tab of QuickSearch

   Basic Protocol 10: Using the “Phenotype” tab of QuickSearch

   Basic Protocol 11: Using the “Human Disease” tab of QuickSearch

   Basic Protocol 12: Using the “Homologs” tab of QuickSearch

   Support Protocol 1: Managing FlyBase hit lists

    

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2. The eigensplitting of the fiber of the cyclotomic trace for the sphere spectrum

   https://doi.org/10.1090/tran/8822  

   Blumberg, Andrew ; Mandell, Michael ( January 2022 , Transactions of the American Mathematical Society)

   Let p ∈ Z p\in {\mathbb {Z}} be an odd prime. We show that the fiber sequence for the cyclotomic trace of the sphere spectrum S {\mathbb {S}} admits an “eigensplitting” that generalizes known splittings on K K -theory and T C TC . We identify the summands in the fiber as the covers of Z p {\mathbb {Z}}_{p} -Anderson duals of summands in the K ( 1 ) K(1) -localized algebraic K K -theory of Z {\mathbb {Z}} . Analogous results hold for the ring Z {\mathbb {Z}} where we prove that the K ( 1 ) K(1) -localized fiber sequence is self-dual for Z p {\mathbb {Z}}_{p} -Anderson duality, with the duality permuting the summands by i ↦ p − i i\mapsto p-i (indexed mod p − 1 p-1 ). We explain an intrinsic characterization of the summand we call Z Z in the splitting T C ( Z ) p ∧ ≃ j ∨ Σ j ′ ∨ Z TC({\mathbb {Z}})^{\wedge }_{p}\simeq j \vee \Sigma j’\vee Z in terms of units in the p p -cyclotomic tower of Q p {\mathbb {Q}}_{p} . 

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3. Bounds for exit times of Brownian motion and the first Dirichlet eigenvalue for the Laplacian

   https://doi.org/10.1090/tran/8903  

   Bañuelos, Rodrigo ; Mariano, Phanuel ; Wang, Jing ( August 2023 , Transactions of the American Mathematical Society)

   For domains in R d \mathbb {R}^d , d ≥ 2 d\geq 2 , we prove universal upper and lower bounds on the product of the bottom of the spectrum for the Laplacian to the power p > 0 p>0 and the supremum over all starting points of the p p -moments of the exit time of Brownian motion. It is shown that the lower bound is sharp for integer values of p p and that for p ≥ 1 p \geq 1 , the upper bound is asymptotically sharp as d → ∞ d\to \infty . For all p > 0 p>0 , we prove the existence of an extremal domain among the class of domains that are convex and symmetric with respect to all coordinate axes. For this class of domains we conjecture that the cube is extremal. 

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4. Towards a nomenclatural clarification of the Peltigera ponojensis/monticola clade including metagenomic sequencing of type material and the introduction of P. globulata Miadl. & Magain sp. nov.

   https://doi.org/10.1017/S0024282923000373  

   Miadlikowska, Jolanta ; Magain, Nicolas ; Medeiros, Ian D. ; Pardo-De la Hoz, Carlos J. ; Carbone, Ignazio ; LaGreca, Scott ; Barlow, Thomas ; Myllys, Leena ; Schmull, Michaela ; Lutzoni, François ( September 2023 , The Lichenologist)

   Abstract Peltigera globulata Miadl. & Magain, a new species in the P. ponojensis/monticola species complex of section Peltigera , is formally described. This clade was previously given the interim designation Peltigera sp. 17. It is found in sun-exposed and xeric habitats at high altitudes in Peru and Ecuador. Peltigera globulata can be easily recognized by its irregularly globulated margins covered mostly by thick, white pruina, somewhat resembling the sorediate thallus margins of P. soredians , another South American species from section Peltigera . The hypervariable region of ITS1 (ITS1-HR), which is in general highly variable among species of section Peltigera , does not have diagnostic value for species identification within the P. ponojensis/monticola complex. Nevertheless, no significant level of gene flow was detected among eight lineages representing a clade of putative species (including P. globulata ) within this complex. ITS sequences from the holotype specimens of P. monticola Vitik. (collected in 1979) and P. soredians Vitik. (collected in 1981) and lectotype specimens of P. antarctica C. W. Dodge (collected in 1941) and P. aubertii C. W. Dodge (collected in 1952) were successfully obtained through Sanger and Illumina metagenomic sequencing. BLAST results of these sequences revealed that the type specimen of P. monticola falls within the P. monticola/ponojensis 7 clade, which represents P. monticola s. str., and confirmed that the type specimen of P. aubertii falls within a clade identified previously as P. aubertii based on morphology. The ITS sequence from the type specimen of P. soredians , which superficially resembles P. globulata , confirms its placement in the P. rufescens clade. Finally, we discovered that the name P. antarctica was erroneously applied to a lineage in the P. ponojensis/monticola clade. The ITS sequence from the type specimen of P. antarctica represents a lineage within the P. rufescens clade, which is sister to the P. ponojensis/monticola clade. 

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5. A Rapid and Facile Purification Method for Glycan‐Binding Proteins and Glycoproteins

   https://doi.org/10.1002/cpps.113  

   Welch, Christina J. ; Kadav, Priyanka D. ; Edwards, Jared L. ; Krycia, Jessica ; Talaga, Melanie L. ; Bandyopadhyay, Purnima ; Dam, Tarun K. ( September 2020 , Current Protocols in Protein Science)

   Glycosylated proteins, namely glycoproteins and proteoglycans (collectively called glycoconjugates), are indispensable in a variety of biological processes. The functions of many glycoconjugates are regulated by their interactions with another group of proteins known as lectins. In order to understand the biological functions of lectins and their glycosylated binding partners, one must obtain these proteins in pure form. The conventional protein purification methods often require long times, elaborate infrastructure, costly reagents, and large sample volumes. To minimize some of these problems, we recently developed and validated a new method termed capture and release (CaRe). This method is time‐saving, precise, inexpensive, and it needs a relatively small sample volume. In this approach, targets (lectins and glycoproteins) are captured in solution by multivalent ligands called target capturing agents (TCAs). The captured targets are then released and separated from their TCAs to obtain purified targets. Application of the CaRe method could play an important role in discovering new lectins and glycoconjugates. © 2020 Wiley Periodicals LLC.

   Basic Protocol 1: Preparation of crude extracts containing the target proteins from soybean flour

   Alternate Protocol 1: Preparation of crude extracts from Jack bean meal

   Alternate Protocol 2: Preparation of crude extracts from the corms ofColocasia esculenta,Xanthosoma sagittifolium, and from the bulbs ofAllium sativum

   Alternate Protocol 3: Preparation ofEscherichia colicell lysates containing human galectin‐3

   Alternate Protocol 4: Preparation of crude extracts from chicken egg whites (source of ovalbumin)

   Basic Protocol 2: Preparation of 2% (v/v) red blood cell suspension

   Basic Protocol 3: Detection of lectin activity of the crude extracts

   Basic Protocol 4: Identification of multivalent inhibitors as target capturing agents by hemagglutination inhibition assays

   Basic Protocol 5: Testing the capturing abilities of target capturing agents by precipitation/turbidity assays

   Basic Protocol 6: Capturing of targets (lectins and glycoproteins) in the crude extracts by target capturing agents and separation of the target‐TCA complex from other components of the crude extracts

   Basic Protocol 7: Releasing the captured targets (lectins and glycoproteins) by dissolving the complex

   Basic Protocol 8: Separation of the targets (lectins and glycoproteins) from their respective target capturing agents

   Basic Protocol 9: Verification of the purity of the isolated targets (lectins or glycoproteins)

    

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