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1. CRISPR‐Cas9 Genome Editing in the Moss Physcomitrium (Formerly Physcomitrella ) patens

   https://doi.org/10.1002/cpz1.725  

   Wu, Shu‐Zon ; Ryken, Samantha E. ; Bezanilla, Magdalena ( April 2023 , Current Protocols)

   Until recently, precise genome editing has been limited to a few organisms. The ability of Cas9 to generate double stranded DNA breaks at specific genomic sites has greatly expanded molecular toolkits in many organisms and cell types. Before CRISPR‐Cas9 mediated genome editing,P. patenswas unique among plants in its ability to integrate DNA via homologous recombination. However, selection for homologous recombination events was required to obtain edited plants, limiting the types of editing that were possible. Now with CRISPR‐Cas9, molecular manipulations inP. patenshave greatly expanded. This protocol describes a method to generate a variety of different genome edits. The protocol describes a streamlined method to generate the Cas9/sgRNA expression constructs, design homology templates, transform, and quickly genotype plants. © 2023 Wiley Periodicals LLC.

   Basic Protocol 1: Constructing the Cas9/sgRNA transient expression vector

   Alternate Protocol 1: Shortcut to generating single and pooled Cas9/sgRNA expression vectors

   Basic Protocol 2: Designing the oligonucleotide‐based homology‐directed repair (HDR) template

   Alternate Protocol 2: Designing the plasmid‐based HDR template

   Basic Protocol 3: Inducing genome editing by transforming CRISPR vector intoP. patensprotoplasts

   Basic Protocol 4: Identifying edited plants.

    

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2. JEDI: J oint E stimation D iffusion I maging of macroscopic and microscopic tissue properties

   https://doi.org/10.1002/mrm.28141  

   Frank, Lawrence_R ; Zahneisen, Benjamin ; Galinsky, Vitaly_L ( January 2020 , Magnetic Resonance in Medicine)

   A new method for enhancing the sensitivity of diffusion MRI (dMRI) by combining the data from single (sPFG) and double (dPFG) pulsed field gradient experiments is presented.

   This method uses our JESTER framework to combine microscopic anisotropy information from dFPG experiments using a new method called diffusion tensor subspace imaging (DiTSI) to augment the macroscopic anisotropy information from sPFG data analyzed using our guided by entropy spectrum pathways method. This new method, called joint estimation diffusion imaging (JEDI), combines the sensitivity to macroscopic diffusion anisotropy of sPFG with the sensitivity to microscopic diffusion anisotropy of dPFG methods.

   Its ability to produce significantly more detailed anisotropy maps and more complete fiber tracts than existing methods within both brain white matter (WM) and gray matter (GM) is demonstrated on normal human subjects on data collected using a novel fast, robust, and clinically feasible sPFG/dPFG acquisition.

   The potential utility of this method is suggested by an initial demonstration of its ability to mitigate the problem of gyral bias. The capability of more completely characterizing the tissue structure and connectivity throughout the entire brain has broad implications for the utility and scope of dMRI in a wide range of research and clinical applications.

    

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3. The L p chord Minkowski problem

   https://doi.org/10.1515/ans-2022-0041  

   Xi, Dongmeng ; Yang, Deane ; Zhang, Gaoyong ; Zhao, Yiming ( January 2023 , Advanced Nonlinear Studies)

   Abstract Chord measures are newly discovered translation-invariant geometric measures of convex bodies in R n {{\mathbb{R}}}^{n} , in addition to Aleksandrov-Fenchel-Jessen’s area measures. They are constructed from chord integrals of convex bodies and random lines. Prescribing the L p {L}_{p} chord measures is called the L p {L}_{p} chord Minkowski problem in the L p {L}_{p} Brunn-Minkowski theory, which includes the L p {L}_{p} Minkowski problem as a special case. This article solves the L p {L}_{p} chord Minkowski problem when p > 1 p\gt 1 and the symmetric case of 0 < p < 1 0\lt p\lt 1 . 

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4. Upper Crustal Structure and Magmatism in Southwest Washington: V p , V s , and V p / V s Results From the iMUSH Active‐Source Seismic Experiment

   https://doi.org/10.1029/2018JB016203  

   Kiser, E. ; Levander, A. ; Zelt, C. ; Schmandt, B. ; Hansen, S. ( July 2019 , Journal of Geophysical Research: Solid Earth)

   Structural details of the crust play an important role in controlling the distribution of volcanic activity in arc systems. In southwest Washington, several different regional structures associated with accretion and magmatism have been invoked to explain the broad distribution of Cascade volcanism in this region. In order to image these regional structures in the upper crust, Pg and Sg travel times from the imaging Magma Under St. Helens (iMUSH) active‐source seismic experiment are inverted forV_p,V_s, andV_p/V_smodels in the region surrounding Mount St. Helens. Several features of these models provide new insights into the regional structure of the upper crust. A large section of the Southern Washington Cascades Conductor is imaged as a lowV_p/V_sanomaly that is inferred to represent a broad sedimentary/metasedimentary sequence that composes the upper crust in this region. The accreted terrane Siletzia is imaged west of Mount St. Helens as north/south trending highV_pandV_p/V_sbodies. TheV_p/V_smodel shows relatively highV_p/V_sregions near Mount St. Helens and the Indian Heaven Volcanic Field, which could be related to the presence of magmatic fluids. Separating these two volcanic regions below 6‐km depth is a northeast trending series of highV_pandV_sbodies. These bodies have the same orientation as several volcanic/magmatic features at the surface, including Mount St. Helens and Mount Rainier, and it is argued that these high‐velocity features are a regional‐scale group of intrusive bodies associated with a crustal weak zone that focuses magma ascent.

    

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5. Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

   https://doi.org/10.1111/nph.15687  

   Morin, Emmanuelle ; Miyauchi, Shingo ; San Clemente, Hélène ; Chen, Eric C. H. ; Pelin, Adrian ; de la Providencia, Ivan ; Ndikumana, Steve ; Beaudet, Denis ; Hainaut, Mathieu ; Drula, Elodie ; et al ( February 2019 , New Phytologist)

   Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology.

   We compared the genomes of Glomerales (Rhizophagus irregularis,Rhizophagus diaphanus,Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota,to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle.

   Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein‐coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis‐related genes inR. irregularisandG. roseaare specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation.

   The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis‐related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology ofAMfungi.

    

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