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1. Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

   https://doi.org/10.1029/2024GB008174  

   Wang, Yuhan; Bing, Haijian; Moorhead, Daryl L; Hou, Enqing; Wu, Yanhong; Wang, Jipeng; Duan, Chengjiao; Cui, Qingliang; Zhang, Zhiqin; Zhu, He; et al (October 2024, Global Biogeochemical Cycles)

   Abstract Microbes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession. 

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2. Reconstruction of the Crossing Type of a Point Set from the Compatible Exchange Graph of Noncrossing Spanning Trees

   https://doi.org/10.1007/978-3-030-14085-4_19  

   Marcos Oropeza, Csaba D. (February 2019, International Conference on Discrete Geometry for Computer Imagery)

   Let P be a set of n points in the plane in general position. The order type of P specifies, for every ordered triple, a positive or negative orientation; and the x-type (a.k.a. crossing type) of P specifies, for every unordered 4-tuple, whether they are in convex position. Geometric algorithms on P typically rely on primitives involving the order type or x-type (i.e., triples or 4-tuples). In this paper, we show that the x-type of P can be reconstructed from the compatible exchange graph G1(P) of noncrossing spanning trees on P. This extends a recent result by Keller and Perles (2016), who proved that the x-type of P can be reconstructed from the exchange graph G0(P) of noncrossing spanning trees, where G1(P) is a subgraph of G0(P) . A crucial ingredient of our proof is a structure theorem on the maximal sets of pairwise noncrossing edges (msnes) between two components of a planar straight-line graph on the point set P. 

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3. Fluorescence Intensity Fluctuation Analysis of Protein Oligomerization in Cell Membranes

   https://doi.org/10.1002/cpz1.384  

   Killeen, Tom D.; Rahman, Sadia; Badu, Dammar N.; Biener, Gabriel; Stoneman, Michael R.; Raicu, Valerică (March 2022, Current Protocols)

   Abstract Fluorescence fluctuation spectroscopy (FFS) encompasses a bevy of techniques that involve analyzing fluorescence intensity fluctuations occurring due to fluorescently labeled molecules diffusing in and out of a microscope's focal region. Statistical analysis of these fluctuations may reveal the oligomerization (i.e., association) state of said molecules. We have recently developed a new FFS‐based method, termed Two‐Dimensional Fluorescence Intensity Fluctuation (2D FIF) spectrometry, which provides quantitative information on the size and stability of protein oligomers as a function of receptor concentration. This article describes protocols for employing FIF spectrometry to quantify the oligomerization of a membrane protein of interest, with specific instructions regarding cell preparation, image acquisition, and analysis of images given in detail. Application of the FIF Spectrometry Suite, a software package designed for applying FIF analysis on fluorescence images, is emphasized in the protocol. Also discussed in detail is the identification, removal, and/or analysis of inhomogeneous regions of the membrane that appear as bright spots. The 2D FIF approach is particularly suited to assess the effects of agonists and antagonists on the oligomeric size of membrane receptors of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of live cells expressing protein constructs Basic Protocol 2: Image acquisition and noise correction Basic Protocol 3: Drawing and segmenting regions of interest Basic Protocol 4: Calculating the molecular brightness and concentration of individual image segments Basic Protocol 5: Combining data subsets using a manual procedure (Optional) Alternate Protocol 1: Combining data subsets using the advanced FIF spectrometry suite (Optional; alternative to Basic Protocol 5) Basic Protocol 6: Performing meta‐analysis of brightness spectrograms Alternate Protocol 2: Performing meta‐analysis of brightness spectrograms (alternative to Basic Protocol 6) Basic Protocol 7: Spot extraction and analysis using a manual procedure or by writing a program (Optional) Alternate Protocol 3: Automated spot extraction and analysis (Optional; alternative to Protocol 7) Support Protocol: Monomeric brightness determination 

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4. Computing the Caratheodory Number of a Point

   Bereg, Sergey; Haghpanah, Mohammadreza (August 2020, Canadian Conference on Computational Geometry)

   Caratheodory’s theorem says that any point in the convex hull of a set $$P$$ in $R^d$ is in the convex hull of a subset $P'$ of $$P$$ such that $$|P'| \le d + 1$$. For some sets P, the upper bound d + 1 can be improved. The best upper bound for P is known as the Caratheodory number [2, 15, 17]. In this paper, we study a computational problem of finding the smallest set $P'$ for a given set $$P$$ and a point $$p$$. We call the size of this set $P'$, the Caratheodory number of a point p or CNP. We show that the problem of deciding the Caratheodory number of a point is NP-hard. Furthermore, we show that the problem is k-LDT-hard. We present two algorithms for computing a smallest set $P'$, if CNP= 2,3. Bárány [1] generalized Caratheodory’s theorem by using d+1 sets (colored sets) such that their convex hulls intersect. We introduce a Colorful Caratheodory number of a point or CCNP which can be smaller than d+1. Then we extend our results for CNP to CCNP. 

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5. 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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