Alonosphere February 2023

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

The global biomass of wild mammals.

2023-02-27

PubMed:36848563; DOI:10.1073/pnas.2204892120

Lior Greenspoon¹, Eyal Krieger¹, Ron Sender¹, Yuval Rosenberg¹, Yinon M Bar-On¹, Uri Moran¹, Tomer Antman¹, Shai Meiri², Uri Roll³, Elad Noor¹, Ron Milo¹

Affiliations

Department of Plant and Environmental Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
School of Zoology, Tel-Aviv University, Tel-Aviv, 6997801, Israel
Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel

Wild animals make up just 6% of mammals (biomass)

The rest is us & farmed animals

Through extreme land use & culling predators, animal ag has also created an unbalanced pop. of what’s left of wild animals

40% of them are concentrated in only 10 species:
https://pnas.org/doi/epdf/10.1073/pnas.2204892120…

2023-06-13

Wild mammals, they roam and they graze,
Icons of nature’s wondrous displays,
Their biomass unknown,
In data it’s shown,
A global estimate, through scientific ways.

Biomass unites creatures of size and of might,
Comparing their presence, a scientific light,
From tiny to grand,
Across every land,
A tale of wild mammals, in nature’s flight.

White-tailed deer, boar, and elephant grand,
Large herbivores shaping the land,
In millions of tonnes,
A weight that dawns,
Nature’s orchestra, a symphony so grand.

Baleen whales in oceans, majestic and free,
Wild marine mammals, a sight to see,
Their biomass immense,
A watery expanse,
In the world’s embrace, they dance with glee.

Yet livestock and humans, a staggering load,
Dominating the scale, a truth to be told,
Wild mammals we count,
In nature’s account,
A benchmark of balance, a story to be bold.

bioRxiv

A comprehensive rRNA variation atlas in health and disease

2023-02-02

DOI:10.1101/2023.01.30.526360

D. Rothschild, T. T. Susanto, J. P. Spence, N. R. Genuth, N. Sinnott-Armstrong, J. K. Pritchard, M. Barna

Affiliations

Stanford University

I love rRNA!

2023-02-03

Ribosome subtypes in human.

2023-02-03

Super important and incredible interesting work! Congrats to the whole team!

2023-02-03

A much needed comprehensive resource documenting the full diversity of human rRNA sequences, paving the path to so much more. Congrats @D_Rothschild_ and @mbarnalab

2023-02-03

This is a milestone in mapping tissue-specific rRNA variants in ribosomes using long-read sequencing from the amazing @D_Rothschild_ and Theo in the @mbarnalab and @jkpritch labs! Implications for healthy and cancer ribosomes!

2023-02-03

Such an important contribution to the field – revealing the unknown variations of rRNA within ribosomes leading to cell-type-specific ribosomes!

2023-02-03

eLife

Dynamics of co-substrate pools can constrain and regulate metabolic fluxes.

2023-02-17

PubMed:36799616; DOI:10.7554/eLife.84379

Robert West¹, Hadrien Delattre¹, Elad Noor², Elisenda Feliu³, Orkun S Soyer¹

Affiliations

School of Life Sciences, University of Warwick, Warwick, United Kingdom
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
Department of Mathematics, University of Copenhagen, Copenhagen, Denmark

What controls metabolic fluxes? Our latest work highlights the relevance of co-substrate cycles as a distinct alternative to enzyme levels:

2023-04-03

Dynamics of co-substrate pools can constrain and regulate metabolic fluxes

2023-02-19

In metabolism’s dance, a tale we unfold,
Co-substrates cycle, their stories untold,
Energy carriers, well-known in their role,
ATP, NAD(P)H, a part of the whole.

Yet others, too, in the intricate scheme,
Metabolic flux, like a flowing stream,
A mathematical framework, we create,
To analyze cycling’s intricate fate.

A limit imposed, an additional bound,
By co-substrate dynamics, we’re bound,
Turnover rate and total pool size,
Factors that shape metabolic skies.

Branched pathways, coupled and fine,
Co-substrate cycling, their design,
Regulation’s key, in our control,
Unlocking the secrets, a metabolic goal.

Through analytical gaze and simulations too,
We explore the flux, in its debut,
In central carbon’s intricate sphere,
Limitations emerge, becoming clear.

Experimental hints, hypotheses born,
Co-substrate dynamics, a light newly sworn,
Understanding flux, a metabolic quest,
Co-substrate dynamics, our insights best.

In cells’ hidden chambers, where secrets entwine,
Measuring and controlling, a path we define,
Co-substrate’s embrace, a crucial key,
To unlock the secrets of metabolic glee.

quant-bio-classic

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Science advances

The global biomass and number of terrestrial arthropods.

2023-02-03

PubMed:36735788; DOI:10.1126/sciadv.abq4049

Yuval Rosenberg¹, Yinon M Bar-On¹, Amir Fromm¹, Meital Ostikar¹, Aviv Shoshany¹, Omer Giz¹, Ron Milo¹

Affiliations

Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

Do arthropods outweigh humanity? Our new paper, “The global biomass and number of terrestrial arthropods,” is out now @ScienceAdvances. https://science.org/doi/10.1126/sciadv.abq4049….
https://wis-wander.weizmann.ac.il/environment/answering-question-has-bugged-ecologists-decades….
#arthropods #insects #ecology #biomass #anthropocene

2023-02-03

human-physiology

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bioRxiv

p16-dependent upregulation of PD-L1 impairs immunosurveillance of senescent cells

2023-02-01

DOI:10.1101/2023.01.30.524522

J. Majewska, A. Agrawal, A. Mayo, L. Roitman, R. Chatterjee, J. Kralova, T. Landsberger, Y. Katzenelenbogen, T. M. Salame, E. Hagai, N. Stanojevic, I. Amit, U. Alon, V. Krizhanovsky

Affiliations

Weizmann Institute of Science

New preprint from our lab: Senescent cells upregulate PD-L1 in p16 dependent manner! Activating anti-PDL1 antibody eliminates p16+ cells from inflamed lungs! Congratulations @JuliaMMagdalena and @amitmechaging! Thanks @UriAlonWeizmann
@IdoAmitLab
https://biorxiv.org/cgi/content/short/2023.01.30.524522v1…

2023-02-02

Viruses

The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients.

2023-02-04

PubMed:36851647; DOI:10.3390/v15020433

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

Affiliations

Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel

Knowledge leads to breakthroughs vs disease – fellow Dr. Sumit Mukherjee in @theNCI @NCIResearchCtr CDSL https://bit.ly/2VP5jr4 contributed to a paper about the landscape of expressed chimeric transcripts in severe COVID-19 patients published in Viruses https://bit.ly/3ZHVVD7

2023-03-15

Stem cell reports

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.

2023-02-23

PubMed:36827975; DOI:10.1016/j.stemcr.2023.01.011

Lisiena Hysenaj¹, Samantha Little¹, Kayla Kulhanek¹, Melia Magnen², Kriti Bahl¹, Oghenekevwe M Gbenedio¹, Morgan Prinz¹, Lauren Rodriguez³, Christopher Andersen⁴, Arjun Arkal Rao⁵, Alan Shen⁶, Jean-Christophe Lone⁷, Leonard C Lupin-Jimenez⁴, Luke R Bonser⁸, Nina K Serwas⁹, Eran Mick¹⁰, Mir M Khalid¹¹, Taha Y Taha¹¹, Renuka Kumar¹¹, Jack Z Li¹², Vivianne W Ding¹², Shotaro Matsumoto¹³, Mazharul Maishan¹³, Bharath Sreekumar¹¹, Camille Simoneau¹¹, Irina Nazarenko¹⁴, Michael G Tomlinson¹⁵, Khajida Khan¹⁶, Anne von Gottberg¹⁷, Alex Sigal¹⁸, Mark R Looney¹⁹, Gabriela K Fragiadakis²⁰, David M Jablons²¹, Charles R Langelier²², Michael Matthay²³, Matthew Krummel²⁴, David J Erle²⁵, Alexis J Combes⁵, Anita Sil²⁶, Melanie Ott²⁷, Johannes R Kratz²⁸, Jeroen P Roose²⁹

Affiliations

Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
School of Life Science, University of Essex, C04 3SQ Colchester, UK
Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center, Heidelberg, Germany
School of Biosciences, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Centre for the AIDS Program of Research, Durban, South Africa
ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA
Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.

March 14 @stemcellreports. Learned a lot, analyzing human airway #organoids & #COVID. https://cell.com/stem-cell-reports/fulltext/S2213-6711(23)00014-0…. THX @TheOttLab @alexis_combes @GabiFragiadakis @lisiena_lissi @sigallab @NIAID @TheMarkFdn. Now back to tumor organoids & immune cells. Postdoc positions.

2023-03-14

Do not hesitate to join @roose_jeroen if you are looking for a post doc position.
The projects in the lab are extremely diverse and interesting. Jeroen is extremely collaborative, cool but also extremely hard working…
#postdocposition #CaliforniaAdventure

2023-03-14

Drs. @lisiena_lissi, @roose_jeroen, and colleagues biobanked airway #organoids by preserving stem cell function, and then used them to study epithelial responses #SARSCoV2 infection. @UCSFAnatomy
@stemcellreports | https://bit.ly/3m2MoYw

2023-02-24

THX! Note that this paper has extensive characterization of (passages) of organoids. Something that (we think) should become standard in organoid research, specially when this technology will start to impact the clinic. See recent piece on @HansClevers https://nature.com/articles/d41573-023-00030-y…

2023-02-25

Thank you @organoidscience for advertiaong our work!

@immunox @UCSF_Postdocs

2023-02-24

Viruses

Dynamics of SARS-CoV-2 VOC Neutralization and Novel mAb Reveal Protection against Omicron.

2023-02-14

PubMed:36851745; DOI:10.3390/v15020530

Linhui Hao¹, Tien-Ying Hsiang¹, Ronit R Dalmat², Renee Ireton¹, Jennifer F Morton², Caleb Stokes¹, Jason Netland¹, Malika Hale¹, Chris Thouvenel¹, Anna Wald³, Nicholas M Franko⁴, Kristen Huden⁴, Helen Y Chu⁴, Alex Sigal⁵, Alex L Greninger⁶, Sasha Tilles⁷, Lynn K Barrett⁷, Wesley C Van Voorhis⁷, Jennifer Munt⁸, Trevor Scobey⁸, Ralph S Baric⁸, David J Rawlings¹, Marion Pepper¹, Paul K Drain², Michael Gale¹

Affiliations

Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109, USA
International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA 98104, USA
Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA
Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA 98195, USA
Africa Health Research Institute, Durban 4001, South Africa
Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
Center for Emerging & Re-Emerging Infectious Diseases, University of Washington, Seattle, WA 98109, USA
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27695, USA

Nature medicine

High- or low-dose preoperative ipilimumab plus nivolumab in stage III urothelial cancer: the phase 1B NABUCCO trial.

2023-02-02

PubMed:36732628; DOI:10.1038/s41591-022-02199-y

Jeroen van Dorp¹, Christodoulos Pipinikas², Britt B M Suelmann³, Niven Mehra³, Nick van Dijk³, Giovanni Marsico², Maurits L van Montfoort³, Sophie Hackinger², Linde M Braaf⁴, Tauanne Amarante², Charlaine van Steenis⁵, Kirsten McLay², Antonios Daletzakis⁶, Daan van den Broek⁷, Maaike W van de Kamp³, Kees Hendricksen³, Jeantine M de Feijter³, Thierry N Boellaard³, Richard P Meijer³, Toine G van der Heijden³, Nitzan Rosenfeld², Bas W G van Rhijn³, Greg Jones⁸, Michiel S van der Heijden⁹

Affiliations

Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
Inivata Ltd., Babraham Research Park, Cambridge, UK
Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
Inivata Ltd., Babraham Research Park, Cambridge, UK.
Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands.

High dose ipilimumab plus nivolumab in locoregionally advanced urothelial cancer led to a higher pathological complete response rate than low dose ipilimumab in cohort 2 of the NABUCCO trial.
#UrothelialCancer #NMEDClinical @NKI_nl

2023-02-03

International journal of molecular sciences

Characterization of Continuous Transcriptional Heterogeneity in High-Risk Blastemal-Type Wilms’ Tumors Using Unsupervised Machine Learning.

2023-02-09

PubMed:36834944; DOI:10.3390/ijms24043532

Yaron Trink¹, Achia Urbach², Benjamin Dekel³, Peter Hohenstein⁴, Jacob Goldberger¹, Tomer Kalisky¹

Affiliations

Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
Pediatric Stem Cell Research Institute and Division of Pediatric Nephrology, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer 5262000, Israel
Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands

Cellular and molecular gastroenterology and hepatology

Distal Fecal Wash Host Transcriptomics Identifies Inflammation Throughout the Colon and Terminal Ileum.

2023-02-14

PubMed:36791991; DOI:10.1016/j.jcmgh.2023.02.002

Stav Dan¹, Bella Ungar², Shani Ben-Moshe¹, Keren Bahar Halpern¹, Miri Yavzori², Ella Fudim², Orit Picard², Chaya Mushka Abitbol², Sivan Harnik², Iris Barshack³, Uri Kopylov², Shomron Ben-Horin², Shalev Itzkovitz⁴

Affiliations

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
Department of Pathology, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.

In our paper published today in @AGA_CMGH we show that transcriptome of shed cells in feces exposes active inflammation, its severity and segmental location in #IBD: https://cmghjournal.org/article/S2352-345X(23)00021-8/fulltext…. Great work by Stav Dan and Bella Ungar.

2023-02-14

Noninvasive methods, the aim,
To assess inflammation’s flame,
Fecal wash shed-cell transcriptomics doth show,
Endoscopic and histologic clues in a row,
Proximal segments, their role to acclaim.

Prospective study, patients enrolled,
Inflammatory bowel disease, the story unfold,
Biopsy specimens and fecal washes we sought,
Distal colon, proximal, terminal ileum, we fought,
Concurrent parameters, the results they beheld.

Distal fecal washes, a classifier strong,
In Crohn’s disease, histologic assessment prolong,
Even without distal colonic display,
Robust classification, inflammation’s array,
Capturing gene expression, responses to belong.

algo

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Journal of chemical information and modeling

Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves.

2023-02-20

PubMed:36802628; DOI:10.1021/acs.jcim.3c00005

Dmitrij Rappoport¹, Adrian Jinich²

Affiliations

Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, California 92697, United States
Weill Cornell Medicine, 1300 York Avenue, Box 65, New York, New York 10065, United States

“Enzyme Substrate Prediction from 3D Feature Representations Using Space-Filling Curves”

With my friend Dmitrij Rappoport, we explore space-filling curves (SFCs) as feature representations of protein structures for enzyme substrate prediction.

https://tinyurl.com/23xm87yb

2023-02-21

In the realm of proteins, a quest takes flight,
To predict properties, with accuracy so bright,
Structural features compact, interpretable lore,
Aiding predictions, what lies in store.

Space-filling curves, mapping a graceful ballet,
From three dimensions, to one they convey,
Hilbert andMorton curves, weaving patterns anew,
Molecular structures, in a simplified view.

Enzyme substrates, challenges embrace,
SDRs and SAM-MTases, their roles we trace,
SFC’s magic, encoding secrets within,
Predictions emerge, as science begins.

kedalionlabs.com

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