Alonosphere – January 2023

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iScience

Rules for body fat interventions based on an operating point mechanism.

2023-01-25

PubMed:36818281; DOI:10.1016/j.isci.2023.106047

Alon Bar1, Omer Karin1, Avi Mayo1, Danny Ben-Zvi2, Uri Alon1

AI-generated cartoon-styled profile picture of Uri Alon

Affiliations
  1. Department Molecular Cell Biology, Weizmann Institute, Rehovot, Israel
  2. Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
Interventions to reduce fat are key,
Effects can be complex, you’ll agree.
Exercise may burn fat,
But more food might be had,
Leptin resistance adds to the spree.

Some interventions lead to an overshoot,
From diets, rebound cravings take root.
The “”operating point model”” shines,
Leptin controls as the plot aligns.

Steady-state fat and food intersect,
Determining outcomes we inspect.
Opposing or coherent, it’s clear,
Effects may differ, far or near.

In rodents, the model’s agreed,
Quadratic relation, humans indeed.
Understanding fat regulation’s art,
Guidance for disorders, we impart.

meteng-synbio

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Frontiers in bioengineering and biotechnology

Optimizing E. coli as a formatotrophic platform for bioproduction via the reductive glycine pathway.

2023-01-16

PubMed:36726742; DOI:10.3389/fbioe.2023.1091899

Seohyoung Kim1, Néstor Giraldo1, Vittorio Rainaldi1, Fabian Machens1, Florent Collas2, Armin Kubis2, Frank Kensy2, Arren Bar-Even1, Steffen N Lindner1

Affiliations
  1. Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
  2. b.fab GmbH, Köln, Germany
Metabolic engineering

Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol.

2023-01-31

PubMed:36731627; DOI:10.1016/j.ymben.2023.01.011

Lennart Schada von Borzyskowski1, Helena Schulz-Mirbach2, Mauricio Troncoso Castellanos3, Francesca Severi3, Paul A Gómez-Coronado2, Nicole Paczia4, Timo Glatter5, Arren Bar-Even6, Steffen N Lindner7, Tobias J Erb8

Affiliations
  1. Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
  2. Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
  3. Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
  4. Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
  5. Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
  6. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
  7. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany.
  8. Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany.

human-physiology

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Cell systems

Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition.

2023-01-19

PubMed:36657390; DOI:10.1016/j.cels.2022.12.003

Omer Karin1, Eric A Miska2, Benjamin D Simons3

Affiliations
  1. Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Mathematics, Imperial College London, London, SW7 2AZ, UK.
  2. Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
  3. Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
In biological systems, memories reside,
Brain and immune, where they hide.
Long-term memory’s persistence unknown,
Epigenetic inheritance, a pathway shown.

Caenorhabditis elegans takes the lead,
Transgenerational, memories proceed.
Silencing target genes for generations,
Resisting dilution, with lasting foundations.

Bistability’s dance, finely tuned,
Rates of biochemicals festooned.
Self-organization around a critical state,
Silencing timescales, memories innate.

Predictions emerge, insights come alive,
Design principles, long-term memory’s drive.
In the depths of memory’s grand theme,
Nature’s secrets, a fascinating dream.

Developmental psychology

Mind-bending geometry: Children’s and adults’ intuitions about linearity on spheres.

2023-01-05

PubMed:36603121; DOI:10.1037/dev0001509

Holly Huey1, Matthew Jordan2, Yuval Hart3, Moira R Dillon4

Affiliations
  1. Department of Psychology, University of California, San Diego
  2. Arts and Science Program, McMaster University
  3. Department of Psychology, Hebrew University of Jerusalem
  4. Department of Psychology, New York University
bioRxiv

Learning accelerates the evolution of slow aging but obstructs negligible senescence

2023-01-24

DOI:10.1101/2023.01.24.525295

P. Lenart, S. Psalmon, B. D. Towbin

Affiliations
  1. University of Bern
bioRxiv

Circuit to target approach defines an autocrine myofibroblast loop that drives cardiac fibrosis

2023-01-03

DOI:10.1101/2023.01.01.522422

S. Miyara, M. Adler, E. Bassat, Y. Divinsky, K. B. Umansky, J. Elkahal, A. Genzelinakh, D. Kain, D. Lendengolts, T. Shalit, M. Gershovits, A. Shakked, L. Zhang, J. Wang, D. M. Kimchi, A. Baehr, R. Sarig, C. Kupatt, E. M. Tanaka, R. Medzhitov, A. Mayo, U. Alon, E. Tzahor

AI-generated cartoon-styled profile picture of Uri Alon

Affiliations
  1. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
Wiley interdisciplinary reviews. RNA

Functional and regulatory impact of chimeric RNAs in human normal and cancer cells.

2023-01-12

PubMed:36633099; DOI:10.1002/wrna.1777

Sumit Mukherjee1, Sunanda Biswas Mukherjee1, Milana Frenkel-Morgenstern1

Affiliations
  1. Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
The FEBS journal

The landscape of differential splicing and transcript alternations in severe COVID-19 infection.

2023-01-11

PubMed:36628954; DOI:10.1111/febs.16723

Sunanda Biswas Mukherjee1, Sumit Mukherjee1, Rajesh Detroja1, Milana Frenkel-Morgenstern1

Affiliations
  1. Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
Science translational medicine

An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis.

2023-01-04

PubMed:36599008; DOI:10.1126/scitranslmed.add3949

Shuang Wang1, Kenneth Li1, Eliana Pickholz1, Ross Dobie2, Kylie P Matchett2, Neil C Henderson2, Chris Carrico3, Ian Driver3, Martin Borch Jensen3, Li Chen4, Mathieu Petitjean4, Dipankar Bhattacharya1, Maria I Fiel5, Xiao Liu6, Tatiana Kisseleva6, Uri Alon7, Miri Adler8, Ruslan Medzhitov9, Scott L Friedman1

AI-generated cartoon-styled profile picture of Uri Alon

Affiliations
  1. Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
  2. Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
  3. Gordian Biotechnology, San Francisco, CA 94107, USA
  4. PharmaNest Inc., Princeton, NJ 08540, USA
  5. Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
  6. Department of Surgery, University of California, San Diego, La Jolla, CA 92093, USA
  7. Department Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
  8. Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT 06510, USA
  9. Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
Advanced hepatic fibrosis, HSC’s role profound,
In NASH, a predictor, mortality abound,
Antifibrotic therapies yet to be,
Targets to find, a quest to decree,
Transcriptomic and morphological, insights unbound.

Single-nucleus RNA sequencing, data they store,
Tissue clearing, murine NASH, we explore,
Autocrine HSC signaling, it emerged,
68 receptor-ligand interactions converged,
Stellate cell-cell contacts, their secrets we adore.

Proof of principle, inhibition takes flight,
Neurotrophic receptor tyrosine kinase 3-neurotrophin 3’s might,
In culture, human HSC activation recedes,
Murine NASH fibrosis, the outcome exceeds,
A therapeutic paradigm, antifibrotic insight.

Repertoire of drug targets, a treasure map,
Underlying advanced fibrosis’s mishap,
Stage-specific therapies, the plan to enact,
Enhanced efficacy, a promising fact,
For advanced hepatic fibrosis, a therapeutic mishap.

animal physiology

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Proceedings of the National Academy of Sciences of the United States of America

The synaptic organization in the Caenorhabditis elegans neural network suggests significant local compartmentalized computations.

2023-01-11

PubMed:36630454; DOI:10.1073/pnas.2201699120

Rotem Ruach1, Nir Ratner1, Scott W Emmons2, Alon Zaslaver1

AI-generated cartoon-styled profile picture of Alon Zaslaver

Affiliations
  1. Department of Genetics, Silberman Institute of Life Science, The Hebrew University, Jerusalem 9190401, Israel
  2. Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York 10461, NY
Neurons, dendritic structures so grand,
Integrate inputs, computations they command,
Can simple neurons with few threads entwine,
Perform local computations, a question to define,
Caenorhabditis elegans, the network we understand.

Synaptic positions, not by randomness planned,
Clusters form, organization so grand,
Compartmentalized computations, they enthrall,
Positive and negative feedback, they install,
Triple-neuron circuits, where roles expand.

Facilitating signal integration, they stand,
Coordinated activation, a function so grand,
Synaptic topology guides the way,
Parallel functions, computational array,
Neural capacity, across a single strand.

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