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

Affiliations

Department Molecular Cell Biology, Weizmann Institute, Rehovot, Israel
Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel

1/14 We consume about a million calories every year, yet our weight stays nearly constant. What circuit can do that? What determines our weight? A new graphical model sheds light on fat mass regulation.
@iScience_CP @AlonBar10
#obesity #systemsphysiology
https://sciencedirect.com/science/article/pii/S2589004223001244?via%3Dihub…

2023-02-28

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

Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
b.fab GmbH, Köln, Germany

How far can you push formate assimilation via the reductive glycine pathway in E. coli? Find out in Kim’s and his kimdom’s recent paper of @WeTheBarEvenLab published in @FrontBioeng. Work done at @MPIMP_Potsdam together with http://bfab.bio.

2023-01-16

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

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.
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
Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
Facility for Mass Spectrometry and Proteomics, 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
Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany.
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.

I am very happy to see this one out (https://sciencedirect.com/science/article/pii/S1096717623000198…) at metabolic engineering. Bridging @mirbachh work of @WeTheBarEvenLab, @erblabs and @LennartSchada. Great collaboration on establishing the β-hydroxyaspartate pathway to optimize growth on PET-derived ethylene glycol.

2023-02-03

Our study on implementation of the β-hydroxyaspartate shunt in E. coli and P. putida to increase biomass yields for growth on ethylene glycol is out now in #Metabolic #Engineering @ElsevierConnect ! Congrats @LennartSchada .

2023-02-02

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

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.
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
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

Department of Psychology, University of California, San Diego
Arts and Science Program, McMaster University
Department of Psychology, Hebrew University of Jerusalem
Department of Psychology, New York University

Paper published “Mind-Bending Geometry: Children’s and adults’ intuitions about linearity on spheres” in DevPsych @APA_Journals with @hollyahuey @mattyj612 @uvhart! https://psycnet.apa.org/record/2023-35044-001… 1/8

2023-01-09

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

University of Bern

“…the ability to learn initially accelerated the evolution of slower aging but constrained the slowest possible rate of aging that can evolve”

2023-01-25

Check out the first theory preprint from the lab on the relation of learning and aging by the remarkable @PeterLenartj

2023-01-25

I am excited to share our preprint on #aging #learning #growth and #evolution https://biorxiv.org/content/10.1101/2023.01.24.525295v1… with @betowbin and Sacha Psalmon at @IZB_unibern @unibe funded by @SNF_ch. We show that *Learning accelerates the evolution of slow aging but obstructs negligible senescence*

2023-01-25

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

Affiliations

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel

Preprint and song: Minimal mathematical model cuts through the complexity of fibrosis to reveal a therapeutic target that reduces scarring in mice after heart attack. @Tzahore @MiyaraShoval @MiriAdler @RMedzhitov
https://biorxiv.org/content/10.1101/2023.01.01.522422v1…

2023-01-08

I’m so excited this episode of @MotionPod is finally out!! I had a blast chatting and diving deep into hot and cold #fibrosis in light of our recent @biorxivpreprint with @JACoates. Thanks for having me!
https://biorxiv.org/content/10.1101/2023.01.01.522422v1…

2023-04-13

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

Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel

We have published a comprehensive and most updated review paper on chimeric RNAs in WIREs RNA…
@Milana_FM
#ChimericRNA #Fusiongene #Cancers #Precisionmedicine

2023-01-12

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

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

Affiliations

Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
Gordian Biotechnology, San Francisco, CA 94107, USA
PharmaNest Inc., Princeton, NJ 08540, USA
Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Department of Surgery, University of California, San Diego, La Jolla, CA 92093, USA
Department Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT 06510, USA
Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA

A study of #NonAlcoholicSteatohepatitis in mice reveals a circuit of 60+ receptor-ligand interactions that drive liver #fibrosis, offering a compendium of potential therapeutic targets.

Learn more in @ScienceTM https://scim.ag/1b9

2023-01-16

In advanced fibrosis, Dr. Scott Friedman at @IcahnMountSinai and colleagues found that an autocrine hepatic stellate cell signaling circuit emerged that was composed of 68 receptor-ligand interactions conserved between murine and human NASH.

https://bit.ly/3IuFkNq

2023-01-09

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

Affiliations

Department of Genetics, Silberman Institute of Life Science, The Hebrew University, Jerusalem 9190401, Israel
Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York 10461, NY

Our recent in @PNASNews. https://pnas.org/doi/full/10.1073/pnas.2201699120…
The C. elegans neural network shows a clustered synaptic organization that may support local compartmentalized computations. Led by @RotemRuach with help of @NirRatner and a wonderful collaboration with Scott Emmons.
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2023-01-24

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.

Alonosphere – January 2023

kedalionlabs.com

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