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1. Guiding Protein Conformation Sampling with Conformation Space Maps

   https://doi.org/10.29007/gfdc  

   Zaman, Ahmed Bin ; De Jong, Kenneth ; Shehu, Amarda ( March 2022 , EPiC Series in Computing)

   Deep learning research, from ResNet to AlphaFold2, convincingly shows that deep learning can predict the native conformation of a given protein sequence with high accu- racy. Accounting for the plasticity of protein molecules remains challenging, and powerful algorithms are needed to sample the conformation space of a given amino-acid sequence. In the complex and high-dimensional energy surface that accompanies this space, it is critical to explore a broad range of areas. In this paper, we present a novel evolutionary algorithm that guides its optimization process with a memory of the explored conformation space, so that it can avoid searching already explored regions and search in the unexplored regions. The algorithm periodically consults an evolving map that stores already sampled non- redundant conformations to enhance exploration during selection. Evaluation on diverse datasets shows superior performance of the algorithm over the state-of-the-art algorithms.

    

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2. Indian Ocean Dipole leads to Atlantic Niño

   https://doi.org/10.1038/s41467-021-26223-w  

   Zhang, Lei ; Han, Weiqing ( October 2021 , Nature Communications)

   Atlantic Niño is the Atlantic equivalent of El Niño-Southern Oscillation (ENSO), and it has prominent impacts on regional and global climate. Existing studies suggest that the Atlantic Niño may arise from local atmosphere-ocean interaction and is sometimes triggered by the Atlantic Meridional Mode (AMM), with overall weak ENSO contribution. By analyzing observational datasets and performing numerical model experiments, here we show that the Atlantic Niño can be induced by the Indian Ocean Dipole (IOD). We find that the enhanced rainfall in the western tropical Indian Ocean during positive IOD weakens the easterly trade winds over the tropical Atlantic, causing warm anomalies in the central and eastern equatorial Atlantic basin and therefore triggering the Atlantic Niño. Our finding suggests that the cross-basin impact from the tropical Indian Ocean plays a more important role in affecting interannual climate variability than previously thought.

    

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3. Biochemical Analysis Leads to Improved Orthogonal Bioluminescent Tools

   https://doi.org/10.1002/cbic.202200726  

   Williams, Sierra J. ; Gewing‐Mullins, Jordan A. ; Lieberman, Whitney K. ; Kolbaba‐Kartchner, Bethany ; Iqbal, Reema ; Burgess, Hana M. ; Colee, Clair M. ; Ornelas, Marya Y. ; Reid‐McLaughlin, Edison S. ; Mills, Jeremy H. ; et al ( February 2023 , ChemBioChem)

   Engineered luciferase‐luciferin pairs have expanded the number of cellular targets that can be visualized in tandem. While light production relies on selective processing of synthetic luciferins by mutant luciferases, little is known about the origin of selectivity. The development of new and improved pairs requires a better understanding of the structure−function relationship of bioluminescent probes. In this work, we report a biochemical approach to assessing and optimizing two popular bioluminescent pairs: Cashew/d‐luc and Pecan/4′‐BrLuc. Single mutants derived from Cashew and Pecan revealed key residues for selectivity and thermal stability. Stability was further improved through a rational addition of beneficial residues. In addition to providing increased stability, the known stabilizing mutations surprisingly also improved selectivity. The resultant improved pair of luciferases are >100‐fold selective for their respective substrates and highly thermally stable. Collectively, this work highlights the importance of mechanistic insight for improving bioluminescent pairs and provides significantly improved Cashew and Pecan enzymes which should be immediately suitable for multicomponent imaging applications.

    

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4. Overexpression of NDR1 leads to pathogen resistance at elevated temperatures

   https://doi.org/10.1111/nph.18190  

   Samaradivakara, Saroopa P. ; Chen, Huan ; Lu, Yi‐Ju ; Li, Pai ; Kim, Yongsig ; Tsuda, Kenichi ; Mine, Akira ; Day, Brad ( May 2022 , New Phytologist)

   Abiotic and biotic environments influence a myriad of plant‐related processes, including growth, development, and the establishment and maintenance of interaction(s) with microbes. In the case of the latter, elevated temperature has been shown to be a key factor that underpins host resistance and pathogen virulence.

   In this study, we elucidate a role forArabidopsisNON‐RACE‐SPECIFIC DISEASE RESISTANCE1 (NDR1) by exploiting effector‐triggered immunity to define the regulation of plant host immunity in response to both pathogen infection and elevated temperature.

   We generated time‐series RNA sequencing data of WT Col‐0, anNDR1overexpression line, andndr1andics1‐2mutant plants under elevated temperature. Not surprisingly, theNDR1‐overexpression line showed genotype‐specific gene expression changes related to defense response and immune system function.

   The results described herein support a role for NDR1 in maintaining cell signaling during simultaneous exposure to elevated temperature and avirulent pathogen stressors.

    

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5. Adult sex change leads to extensive forebrain reorganization in clownfish

   https://doi.org/10.1186/s13293-024-00632-0  

   Parker, Coltan_G ; Gruenhagen, George_W ; Hegarty, Brianna_E ; Histed, Abigail_R ; Streelman, Jeffrey_T ; Rhodes, Justin_S ; Johnson, Zachary_V ( July 2024 , Biology of Sex Differences)

   Sexual differentiation of the brain occurs in all major vertebrate lineages but is not well understood at a molecular and cellular level. Unlike most vertebrates, sex-changing fishes have the remarkable ability to change reproductive sex during adulthood in response to social stimuli, offering a unique opportunity to understand mechanisms by which the nervous system can initiate and coordinate sexual differentiation.

   This study explores sexual differentiation of the forebrain using single nucleus RNA-sequencing in the anemonefishAmphiprion ocellaris, producing the first cellular atlas of a sex-changing brain.

   We uncover extensive sex differences in cell type-specific gene expression, relative proportions of cells, baseline neuronal excitation, and predicted inter-neuronal communication. Additionally, we identify the cholecystokinin, galanin, and estrogen systems as central molecular axes of sexual differentiation. Supported by these findings, we propose a model of sexual differentiation in the conserved vertebrate social decision-making network spanning multiple subtypes of neurons and glia, including neuronal subpopulations within the preoptic area that are positioned to regulate gonadal differentiation.

   This work deepens our understanding of sexual differentiation in the vertebrate brain and defines a rich suite of molecular and cellular pathways that differentiate during adult sex change in anemonefish.

    

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