New articles from eLife – July 15, 2024

[Prash]

 

July 15, 2024 New articles from eLife Our Special Issue highlights advances in understanding regulation of kinase activity in physiological and pathophysiological processes MAGAZINE Biochemistry and Chemical Biology, Structural Biology and Molecular Biophysics Allosteric regulation of kinase activity Amy H Andreotti, Volker Dötsch The articles in this special issue highlight how modern cellular, biochemical, biophysical and computational techniques are allowing deeper and more detailed studies of allosteric kinase regulation. Neuroscience Unraveling the enigmatic role of the subthalamic nucleus Qianli Yang Subpopulations of neurons in the subthalamic nucleus have distinct activity patterns that relate to the three hypotheses of the Drift Diffusion Model. REVIEWED PREPRINTS Evolutionary Biology The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles in Arabidopsis halleri and A. lyrata Audrey Le Veve, Mathieu Genete ... Vincent Castric Cell Biology, Medicine Adventitial fibroblasts direct smooth muscle cell-state transition in pulmonary vascular disease Slaven Crnkovic, Helene Thekkekara Puthenparampil ... Grazyna Kwapiszewska Structural Biology and Molecular Biophysics RNA tertiary structure and conformational dynamics revealed by BASH MaP Maxim Oleynikov, Samie R Jaffrey Cell Biology, Evolutionary Biology Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25 P Richard J Yulo, Nicolas Desprat ... Heather L Hendrickson Neuroscience Microstructural asymmetries of the planum temporale predict functional lateralization of auditory-language processing Peipei Qin, Qiuhui Bi ... Gaolang Gong Structural Biology and Molecular Biophysics Elucidating ATP’s Role as Solubilizer of Biomolecular Aggregate Susmita Sarkar, Saurabh Gupta ... Jagannath Mondal Ecology Developmental stage determines the realized energy landscape for a flight specialist Elham Nourani, Louise Faure ... Kamran Safi Biochemistry and Chemical Biology, Cell Biology Two-way Dispatched function in Sonic hedgehog shedding and transfer to high-density lipoproteins Kristina Ehring, Sophia F Ehlers ... Kay Grobe Genetics and Genomics PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking Thomas E Forman, Marcin P Sajek ... Katherine A Fantauzzo Immunology and Inflammation, Cancer Biology Androgen deprivation triggers a cytokine signaling switch to induce immune suppression and prostate cancer recurrence Kai Sha, Renyuan Zhang ... John J Krolewski Structural Biology and Molecular Biophysics Conservation of the cooling agent binding pocket within the TRPM subfamily Kate Huffer, Elisabeth V Oskoui, Kenton J Swartz Chromosomes and Gene Expression CyAbrB2 is a nucleoid-associated protein in Synechocystis controlling hydrogenase expression during fermentation Ryo Kariyazono, Takashi Osanai Biochemistry and Chemical Biology A synthetic method to assay polycystin channel biophysics Megan Larmore, Orhi Esarte Palomero ... Paul G DeCaen Medicine, Immunology and Inflammation NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis Yong Jin, Jiayu Xing ... Qingsheng Yu Biochemistry and Chemical Biology Intracellular Expression of a Fluorogenic DNA Aptamer Using Retron Eco2 Mahesh A Vibhute, Corbin Machatzke ... Hannes Mutschler Biochemistry and Chemical Biology, Structural Biology and Molecular Biophysics Deciphering the actin structure-dependent preferential cooperative binding of cofilin Kien Xuan Ngo, Huong T Vu ... Taro QP Uyeda Genetics and Genomics, Epidemiology and Global Health Ethnic and region-specific genetic risk variants of stroke and its comorbid conditions can define the variations in the burden of stroke and its phenotypic traits Rashmi Sukumaran, Achuthsankar S. Nair, Moinak Banerjee Structural Biology and Molecular Biophysics, Neuroscience A Kv2 inhibitor combination reveals native neuronal conductances consistent with Kv2/KvS heteromers Robert G Stewart, Matthew James Marquis ... Jon T Sack Neuroscience Cell-type-specific origins of locomotor rhythmicity at different speeds in larval zebrafish Moneeza A Agha, Sandeep Kishore, David L McLean Neuroscience, Computational and Systems Biology Human EEG and artificial neural networks reveal disentangled representations of object real-world size in natural images Zitong Lu, Julie D Golomb Neuroscience Sequential replacement of PSD95 subunits in postsynaptic supercomplexes is slowest in the cortex Katie Morris, Edita Bulovaite ... Mathew H Horrocks Neuroscience Ih Block Reveals Separation of Timescales in Pyloric Rhythm Response to Temperature Changes in Cancer borealis Kyra A Schapiro, JD Rittenberg ... Eve Marder Microbiology and Infectious Disease, Computational and Systems Biology Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction Saugat Poudel, Jason Hyun ... Bernhard O Palsson Neuroscience Sex Differences in Discrimination Behavior and Orbitofrontal Engagement During Context-Gated Reward Prediction Sophie Peterson, Amanda Maheras ... Ronald Keiflin Neuroscience behaviorMate: An Intranet of Things Approach for Adaptable Control of Behavioral and Navigation-Based Experiments John C Bowler, George Zakka ... Attila Losonczy Neuroscience Synaptic interactions between stellate cells and parvalbumin interneurons in layer 2 of the medial entorhinal cortex are organized at the scale of grid cell clusters Li-Wen Huang, Derek LF Garden ... Matthew Nolan Genetics and Genomics, Cancer Biology Patient-derived xenografts and single-cell sequencing identifies three subtypes of tumor-reactive lymphocytes in uveal melanoma metastases Joakim Karlsson, Vasu R Sah ... Jonas A Nilsson Neuroscience Dynamic control of sequential retrieval speed in networks with heterogeneous learning rules Maxwell Gillett, Nicolas Brunel Neuroscience Cholinergic input to mouse visual cortex signals a movement state and acutely enhances layer 5 responsiveness Baba Yogesh, Georg B Keller Neuroscience Infralimbic parvalbumin neural activity facilitates cued threat avoidance Yi-Yun Ho, Qiuwei Yang ... Melissa R Warden Neuroscience Drosophila HCN mediates gustatory homeostasis by preserving sensillar transepithelial potential in sweet environments MinHyuk Lee, Se Hoon Park ... KyeongJin Kang Neuroscience A dynamic generative model can extract interpretable oscillatory components from multichannel neurophysiological recordings Proloy Das, Mingjian He, Patrick L Purdon Biochemistry and Chemical Biology The TTLL10 polyglycylase is stimulated by tubulin glutamylation and inhibited by polyglycylation Steven W Cummings, Yan Li ... Antonina Roll-Mecak Structural Biology and Molecular Biophysics Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K Lirong Zheng, Bingxin Zhou ... Liang Hong Ecology Habitat fragmentation mediates the mechanisms underlying long-term climate-driven thermophilization in birds Juan Liu, Morgan W Tingley ... Xingfeng Si Neuroscience, Computational and Systems Biology Reconstructing Voice Identity from Noninvasive Auditory Cortex Recordings Charly Lamothe, Etienne Thoret ... Pascal Belin Neuroscience, Stem Cells and Regenerative Medicine Circulating Platelets Modulate Oligodendrocyte Progenitor Cell Differentiation During Remyelination Amber R Philp, Carolina R Reyes ... Francisco J Rivera Neuroscience Human iPSC-derived Microglial Cells Integrated into Mouse Retina and Recapitulated Features of Endogenous Microglia Wenxin Ma, Lian Zhao ... Wei Li Immunology and Inflammation, Microbiology and Infectious Disease Released Bacterial ATP Shapes Local and Systemic Inflammation during Abdominal Sepsis Daniel Spari, Annina Schmid ... Guido Beldi Microbiology and Infectious Disease, Evolutionary Biology The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference Mahboobeh Behruznia, Maximillian Marin ... Conor J Meehan VERSIONS OF RECORD Developmental Biology Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis Siyuan Cheng, Ivan Fan Xia ... Stefania Nicoli Flow hemodynamic activation of endothelial klf2a is a mechanism regulating initial vascular smooth muscle cell differentiation on circle of Willis arteries. Neuroscience Multi-day neuron tracking in high-density electrophysiology recordings using earth mover’s distance Augustine Xiaoran Yuan, Jennifer Colonell ... Timothy D Harris Neurons can be tracked in mice implanted with Neuropixels 2.0 probes for up to 8 weeks using visual receptive fields to score tracking in the absence of reference data. Neuroscience Statistical learning shapes pain perception and prediction independently of external cues Jakub Onysk, Nicholas Gregory ... Flavia Mancini Statistical learning shapes pain perception by allowing the brain to predict and modulate pain intensity based on temporal patterns, providing insights into pain regulation and their relevance to chronic pain. Ecology Adipokinetic hormone signaling mediates the enhanced fecundity of Diaphorina citri infected by ‘Candidatus Liberibacter asiaticus’ Jiayun Li, Paul Holford ... Xiaoge Nian Molecular mechanism that Candidatus Liberibacter asiaticus improves the lipid metabolism and fecundity of Diaphorina citri through adipokinetic hormone and its receptor. Biochemistry and Chemical Biology, Chromosomes and Gene Expression Human DDX6 regulates translation and decay of inefficiently translated mRNAs Ramona Weber, Chung-Te Chang DDX6 triggers inefficiently translated mRNA decay by interacting with the ribosome through its FDF motif via the 5'-3' mRNA decay pathway. Neuroscience Chronic activation of a negative engram induces behavioral and cellular abnormalities Alexandra L Jellinger, Rebecca L Suthard ... Steve Ramirez Repeatedly activating negative memory-bearing cells produces cellular and behavioral abnormalities. Microbiology and Infectious Disease The target of rapamycin signaling pathway regulates vegetative development, aflatoxin biosynthesis, and pathogenicity in Aspergillus flavus Guoqi Li, Xiaohong Cao ... Shihua Wang Exploration of the target of rapamycin pathway in Aspergillus flavus reveals critical regulatory elements influencing aflatoxin synthesis and stress tolerance, offering potential targets for antifungal strategies. Microbiology and Infectious Disease Bacteria are a major determinant of Orsay virus transmission and infection in Caenorhabditis elegans Brian G Vassallo, Noemie Scheidel ... Dennis H Kim Distinct members of the Caenorhabditis elegans microbiota can have widely divergent effects on Orsay virus transmission, such that associated bacteria can effectively determine host susceptibility versus resistance to viral infection. Neuroscience Clustered synapses develop in distinct dendritic domains in visual cortex before eye opening Alexandra H Leighton, Juliette E Cheyne, Christian Lohmann In vivo calcium imaging in visual cortex neurons before eye opening shows that clustered synaptic inputs develop in dendritic domains, which may be precursors of computational subunits after eye opening. Medicine Human HPSE2 gene transfer ameliorates bladder pathophysiology in a mutant mouse model of urofacial syndrome Filipa M Lopes, Celine Grenier ... Neil A Roberts Proof of concept that viral vector-mediated gene transfer improves bladder function in a preclinical model of an inherited early-onset lower urinary tract disease. Physics of Living Systems Gendered hiring and attrition on the path to parity for academic faculty Nicholas LaBerge, Kenneth Hunter Wapman ... Daniel B Larremore Achieving gender parity among U.S. tenured and tenure-track faculty will require changes to hiring, which has substantially greater impacts on faculty gender representation than gendered differences in attrition rates. Cell Biology Vacuolar H+-ATPase determines daughter cell fates through asymmetric segregation of the nucleosome remodeling and deacetylase complex Zhongyun Xie, Yongping Chai ... Wei Li Asymmetric segregation of V-ATPase may cause distinct acidification levels in the two daughter cells, enabling asymmetric epigenetic inheritance that specifies their respective life-versus-death fates. Chromosomes and Gene Expression, Genetics and Genomics Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals Lisa Baumgartner, Jonathan J Ipsaro ... Julius Brennecke Genetic and biochemical characterization reveals how a single amino acid change in the chromodomain of the HP1 protein Rhino enables its specific interaction with the guidance factor Kipferl. Cancer Biology RBM7 deficiency promotes breast cancer metastasis by coordinating MFGE8 splicing switch and NF-kB pathway Fang Huang, Zhenwei Dai ... Yang Wang RBM7 functions as a novel regulator of MFGE8 alternative splicing and p65 phosphorylation to counteract the metastatic potential of breast cancer, offering novel mechanistic insights into how abnormal splicing contributes to tumor aggressiveness. Biochemistry and Chemical Biology Uncovering the BIN1-SH3 interactome underpinning centronuclear myopathy Boglarka Zambo, Evelina Edelweiss ... Gergo Gogl The SH3 domain of BIN1 mediates an unexpectedly large array of interactions, which is perturbed by missense variants. Medicine An atlas of brain-bone sympathetic neural circuits in mice Vitaly Ryu, Anisa Azatovna Gumerova ... Mone Zaidi Central SNS outflow sites originating from 87 brain nuclei and sub-nuclei in six brain divisions innervate bone. ACCEPTED MANUSCRIPTS Structural Biology and Molecular Biophysics Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation Hitendra Negi, Aravind Ravichandran ... Ranabir Das Neuroscience The components of an electrical synapse as revealed by expansion microscopy of a single synaptic contact Sandra P Cárdenas-García, Sundas Ijaz, Alberto E Pereda DIGESTS Neuroscience A picture is worth more than one word The brain’s visual areas independently process rich levels of information from a scene to help identify objects while retaining other details. Cell Biology Breaking a sweat A heat-sensitive ion channel known as TRPV4 helps regulate sweating in mice, a finding that offers insights into human sweat disorders. Neuroscience Running scared Pavlovian fear conditioning triggers active fear responses as well as freezing.

                                                           

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Prashanth N Suravajhala, Ph.D.
Principal Scientist, Systems Genomics
Room # 301, Amrita School of Biotechnology

Amrita University, Amritapuri, Kerala 690525, India. 

Group page: http://www.bioinformatics.org/wiki/Prash 

E mail:  prashATamDOTamritaDOTedu 

Twitter: @prashbio

"One rule is important in science- only courageous people win "   ~ Max Planck