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1. 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)

   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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2. Neurological Assessment Using a Physical-Virtual Patient (PVP)

   https://doi.org/10.1177/1046878120947462  

   Gonzalez, Laura ; Daher, Salam ; Welch, Greg ( August 2020 , Simulation & Gaming)

   Background. Simulation has revolutionized teaching and learning. However, traditional manikins are limited in their ability to exhibit emotions, movements, and interactive eye gaze. As a result, students struggle with immersion and may be unable to authentically relate to the patient.

   Intervention. We developed a new type of patient simulator called the Physical-Virtual Patients (PVP) which combines the physicality of manikins with the richness of dynamic visuals. The PVP uses spatial Augmented Reality to rear project dynamic imagery (e.g., facial expressions, ptosis, pupil reactions) on a semi-transparent physical shell. The shell occupies space and matches the dimensions of a human head.

   Methods. We compared two groups of third semester nursing students (N=59) from a baccalaureate program using a between-participant design, one group interacting with a traditional high-fidelity manikin versus a more realistic PVP head. The learners had to perform a neurological assessment. We measured authenticity, urgency, and learning.

   Results. Learners had a more realistic encounter with the PVP patient (p=0.046), they were more engaged with the PVP condition compared to the manikin in terms of authenticity of encounter and cognitive strategies. The PVP provoked a higher sense of urgency (p=0.002). There was increased learning for the PVP group compared to the manikin group on the pre and post-simulation scores (p=0.027).

   Conclusion. The realism of the visuals in the PVP increases authenticity and engagement which results in a greater sense of urgency and overall learning.

    

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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)

   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. 1D 1 H NMR as a Tool for Fecal Metabolomics

   https://doi.org/10.1002/cpch.83  

   Ganobis, Caroline M. ; Al‐Abdul‐Wahid, M. Sameer ; Renwick, Simone ; Yen, Sandi ; Carriero, Charley ; Aucoin, Marc G. ; Allen‐Vercoe, Emma ( August 2020 , Current Protocols in Chemical Biology)

   Metabolomic studies allow a deeper understanding of the processes of a given ecological community than nucleic acid–based surveys alone. In the case of the gut microbiota, a metabolic profile of, for example, a fecal sample provides details about the function and interactions within the distal region of the gastrointestinal tract, and such a profile can be generated in a number of different ways. This unit elaborates on the use of 1D¹H NMR spectroscopy as a commonly used method to characterize small‐molecule metabolites of the fecal metabonome (meta‐metabolome). We describe a set of protocols for the preparation of fecal water extraction, storage, scanning, measurement of pH, and spectral processing and analysis. We also compare the effects of various sample storage conditions for processed and unprocessed samples to provide a framework for comprehensive analysis of small molecules from stool‐derived samples. © 2020 Wiley Periodicals LLC

   Basic Protocol 1: Extracting fecal water from crude fecal samples

   Alternate Protocol 1: Extracting fecal water from small crude fecal samples

   Basic Protocol 2: Acquiring NMR spectra of metabolite samples

   Alternate Protocol 2: Acquiring NMR spectra of metabolite samples using Bruker spectrometer running TopSpin 3.x

   Alternate Protocol 3: Acquiring NMR spectra of metabolite samples by semiautomated process

   Basic Protocol 3: Measuring sample pH

   Support Protocol 1: Cleaning NMR tubes

   Basic Protocol 4: Processing raw spectra data

   Basic Protocol 5: Profiling spectra

   Support Protocol 2: Spectral profiling of sugars and other complex metabolites

    

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5. Updating SWAT+ to Clarify Understanding of In‐Stream Phosphorus Retention and Remobilization: SWAT+P.R&R

   https://doi.org/10.1029/2022WR033283  

   Wallington, Kevin ; Cai, Ximing ( March 2023 , Water Resources Research)

   Efforts to reduce riverine phosphorus (P) loads have not been as fruitful as expected or hoped. One reason for the failure of these efforts appears to be that models used for watershed P management have understated and misrepresented the role of in‐stream processes in shaping watershed P export. Here, we update the latest release of the Soil and Water Assessment Tool (SWAT+), a widely used watershed management model, to better represent in‐stream P retention and remobilization (SWAT+P.R&R). We add new streambed pools where P is stored and tracked, and we incorporate three new processes driving in‐stream P dynamics: (a) deposition and resuspension of sediment‐associated P, (b) diffusion of dissolved P between the water column and streambed, and (c) adsorption and desorption of mineral P. The objective of this modeling work is to provide a diagnostic tool that enables researchers to challenge existing assumptions regarding how watersheds store, transform, and transport P. Here, in a first diagnostic analysis, SWAT+P.R&R helps reconcile in‐stream P retention theory (that P is retained at low flows and remobilized at high flows) and a discordant data set in our validation watershed. SWAT+P.R&R results (a) clarify that the theorized relationship between P retention and flow is only valid (for this point‐source affected testbed, at least) at the temporal scale of a single rising‐or‐falling hydrograph limb and (b) illustrate that hysteresis obscures the relationship at longer temporal scales. Future work using SWAT+P.R&R could further challenge assumptions regarding timescales of in‐stream P legacies and sources of P load variability.

    

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