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1. Role of Phosphorus Type and Biodegradable Polymer on Phosphorus Fate and Efficacy in a Plant–Soil System

   https://doi.org/10.1021/acs.jafc.3c04735  

   Sigmon, Leslie R.; Vaidya, Shital R.; Thrasher, Corey; Mahad, Sumaya; Dimkpa, Christian O.; Elmer, Wade; White, Jason C.; Fairbrother, D. Howard (November 2023, Journal of Agricultural and Food Chemistry)

   Phosphorus (P) is critical for crop production but has a high nutrient use inefficiency. Tomato was grown in soil amended with five P-sources, used as-is, or embedded within a biodegradable polymer, polyhydroxyalkanoate (PHA). Correlation analysis identified treatments that maintain plant growth, improve bioavailable soil P, and reduce P loss. Three performance classes were identified: (i) micro- and nanohydroxyapatite, which did not increase bioavailable P, plant P-uptake, or change P in runoff/leaching compared to controls; (ii) monocalcium phosphate (MCP), dicalcium phosphate (DCP), calcium pyrophosphate nanoparticles (CAP), and PHA-MCP that increased P-uptake and/or bioavailable P but also increased P loss in runoff/leaching; and (iii) PHA-DCP and PHA-CAP, where increased bioavailable P and plant P-uptake were achieved with minimal P loss in runoff/leaching. In addition to identifying treatments that maintain plant growth, increase bioavailable P, and minimize nutrient loss, correlation plots also revealed that (i) bioavailable P was a good indicator of plant P-uptake; (ii) leached P could be predicted from water solubility; and (iii) P loss through runoff versus leaching showed similar trends. This study highlights that biopolymers can promote plant P-uptake and improve bioavailable soil P, with implications for mitigating the negative environmental impacts of P loss from agricultural systems. 

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2. Underestimated Neotropical diversity: Integrative taxonomy reveals two unrelated look-alike species in a suboscine bird ( Pachyramphus albogriseus )

   https://doi.org/10.1093/ornithology/ukac047  

   Musher, Lukas J.; Krabbe, Niels K.; Areta, Juan I. (August 2022, Ornithology)

   Abstract We applied an integrative taxonomic framework to evaluate the systematics of the Neotropical Black-and-white Becard (Pachyramphus albogriseusSclater 1857). Combining phylogenomic (ultraconserved elements), morphological, and vocalization data, we confirmed that this species is polyphyletic; some individuals form a clade sister to P. polychopterus and should be afforded species rank as P. salviniRichmond 1899 (Slender-billed Becard), whereas the remaining subspecies of P. albogriseus (Broad-banded Becard) are sister to P. major. We found that P. salvini differs from P. albogriseus in song, color of the lores, wing-bar width, body size, and bill width. Whereas P. albogriseus occurs in montane forest in Costa Rica and Panama (ssp. ornatus) and along the eastern slope of the Andes from northern Venezuela to southern Peru (ssp. albogriseus), P. salvini is found in the lowlands from Pacific Colombia south to northwest Peru and in the Río Marañón drainage. The latter also occurs, possibly only seasonally, along the eastern slope of the Andes, where the two species’ ranges approach closely. We treat P. a. guayaquilensisZimmer 1936 as a junior synonym of P. salviniRichmond 1899, and P. a. coronatusPhelps and Phelps 1953 as a junior synonym of P. a. albogriseusSclater 1857. This study provides a striking example of a major problem for comparative biology: underestimated and mischaracterized diversity. We argue that there are likely many more cases like this awaiting discovery. 

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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. 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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5. Dependent type systems as macros

   https://doi.org/10.1145/3371071  

   Chang, Stephen; Ballantyne, Michael; Turner, Milo; Bowman, William_J (December 2019, Proceedings of the ACM on Programming Languages)

   We present Turnstile+, a high-level, macros-based metaDSL for building dependently typed languages. With it, programmers may rapidly prototype and iterate on the design of new dependently typed features and extensions. Or they may create entirely new DSLs whose dependent type ``power'' is tailored to a specific domain. Our framework's support of language-oriented programming also makes it suitable for experimenting with systems of interacting components, e.g., a proof assistant and its companion DSLs. This paper explains the implementation details of Turnstile+, as well as how it may be used to create a wide-variety of dependently typed languages, from a lightweight one with indexed types, to a full spectrum proof assistant, complete with a tactic system and extensions for features like sized types and SMT interaction. 

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