The paper identifies a novel dynamic site of Plk1 recruitment to the inner centromere during mitosis, regulated by Cdk1 and counteracted by Bub1/PP2A.

bioRxiv · Jul 3, 2024 · PreprintCell Biology

The Mammalian KU70 C-terminus SAP Domain Is Required to Repair Exogenous DNA Damage

Y. Wang, M. Czap, H. Kim, H. Lu, J. Liu, Y. Chang, P. Romanienko, C. Montagna, Z. Shen

This study shows that the KU70 SAP domain is essential for repairing exogenous DNA damage but not for V(D)J recombination or development.

bioRxiv · Jun 30, 2024 · PreprintCancer Biology

Urine Proteomics in Methamphetamine Addicted Patients

Z. Shen, J. Liang, S. Tang, X. Pan, Y. Bao, Y. Deng, Y. Gao

This study compares urine proteomes of methamphetamine users, withdrawers, and healthy individuals, identifying differentially expressed proteins linked to addiction and neurotoxicity.

bioRxiv · Jun 18, 2024 · PreprintBiochemistry

Changes in urinary proteome in healthy individuals taking multi-vitamin/mineral supplements

Z. Shen, H. Wang, M. Yang, Y. Gao

This study shows that taking multi-vitamin/mineral supplements for 2 or 4 weeks changes the urinary proteome, with erythropoietin receptor levels increasing significantly in some individuals.

bioRxiv · Jun 18, 2024 · PreprintBiochemistry

Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine

A. Yisimayi, W. Song, J. Wang, F. Jian, Y. Yu, X. Chen, Y. Xu, R. An, Y. Wang, J. Wang, H. Sun, P. Wang, L. Yu, F. Shao, R. Jin, , Y. Cao

The paper investigates how Omicron-specific naive B cell maturation after breakthrough infection alleviates immune imprinting from inactivated SARS-CoV-2 vaccines.

bioRxiv · May 13, 2024 · PreprintImmunology

Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1

F. Jian, J. Wang, A. Yisimayi, W. Song, Y. Xu, X. Chen, X. Niu, S. Yang, Y. Yu, P. Wang, H. Sun, L. Yu, J. Wang, Y. Wang, R. An, , Y. Cao

This study analyzes the humoral immune response to SARS-CoV-2 XBB and JN.1 lineages, showing JN.1 elicits superior neutralization and highlights the need for JN.1-based vaccine boosters.

bioRxiv · Apr 19, 2024Immunology

Effects of arbuscular mycorrhizal fungi on nitrogen uptake in cotton (Gossypium hirsutum L.) under low-nitrogen conditions

H. Wang, y. wang, X. cheng, Y. He, z. shen, W. zhang, x. pu

This study examines how arbuscular mycorrhizal fungi affect nitrogen uptake in cotton under low-nitrogen conditions, finding increased root biomass and soil enzyme activity with AMF symbiosis.

bioRxiv · Mar 17, 2024 · PreprintPlant Biology

Changes of urine proteome after intragastric administration of polysaccharide iron complex in rats

Z. Shen, M. Yang, H. Wang, Y. Gao

This study compares urine proteomes of rats before and after polysaccharide-iron complex administration, identifying iron-related proteins and pathways.

bioRxiv · Mar 5, 2024 · PreprintBiochemistry

Changes of urinary proteome in rats after intragastric administration of zinc gluconate

Z. Shen, M. Yang, H. Wang, Y. Gao

This study compares the urinary proteome of rats before and after zinc gluconate administration, identifying zinc-related differential proteins and their biological functions.

bioRxiv · Mar 4, 2024 · PreprintBiochemistry

Changes of urinary proteome in rats after intragastric administration of calcium gluconate

Z. Shen, M. Yang, H. Wang, Y. Gao

The paper examines changes in the urinary proteome of rats after calcium gluconate administration, identifying calcium-related proteins and their pathway associations.

bioRxiv · Mar 4, 2024 · PreprintBiochemistry

GTPase-activating protein ARAP1 regulates circular dorsal ruffles as a nutrient uptake mechanism in the Hep3B hepatocellular carcinoma cell line

X. Sun, Y. Li, Y. He, L. Cheng, J. Wei, L. Du, Z. Shen, S. Yoshida

This study shows that ARAP1 regulates circular dorsal ruffles in Hep3B cells, and its deletion reduces malignant potential, suggesting CDRs contribute to cancer development through nutrient uptake.

bioRxiv · Dec 31, 2023 · PreprintCell Biology

Nuclear Pyruvate Dehydrogenase Complex Regulates Histone Acetylation and Transcriptional Regulation in the Ethylene Response

Z. Shao, L. Bian, S. K. Ahmadi, T. J. Daniel, M. A. Belmonte, J. G. Burns, P. Kotla, Y. Bi, Z. Shen, S.-L. Xu, Z.-Y. Wang, S. P. Briggs, H. Qiao

This study identifies the nuclear pyruvate dehydrogenase complex (PDC) as a key regulator of histone acetylation and transcription during ethylene response in plants.

bioRxiv · Oct 25, 2023Plant Biology

Platelet proteo-transcriptomic profiling validates mediators of thrombosis and proteostasis in patients with myeloproliferative neoplasms

S. Kelliher, S. Gamba, L. Weiss, Z. Shen, M. Marchetti, F. Schieppati, C. Scaife, S. Madden, K. Bennett, A. Fortune, S. Maung, M. Fay, F. Ni Ainle, P. Maguire, A. Falanga, , A. Krishnan

The paper profiles the platelet proteome in MPN patients to identify mediators of thrombosis and proteostasis, validating key transcriptome findings.

bioRxiv · Oct 23, 2023 · PreprintPathology

Changes in the urinary proteome of rats after short-term intake of magnesium threonate

Z. Shen, M. Yang, Y. Liu, H. Wang, Y. Gao

This study examines changes in the urinary proteome of rats after short-term magnesium threonate intake, identifying differential proteins linked to magnesium's biological functions.

bioRxiv · Sep 29, 2023 · PreprintBiochemistry

Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86

S. Yang, Y. Yu, F. Jian, W. Song, A. Yisimayi, X. Chen, Y. Xu, P. Wang, L. Yu, J. Wang, X. Niu, J. Wang, T. Xiao, R. An, Y. Wang, , Y. R. Cao

This study characterizes the antigenic properties and infectivity of the SARS-CoV-2 BA.2.86 variant, finding it evades immune responses but has reduced infectivity compared to previous variants.

bioRxiv · Sep 1, 2023 · PreprintImmunology

Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding

F. Jian, L. Feng, S. Yang, Y. Yu, L. Wang, W. Song, A. Yisimayi, X. Chen, Y. Xu, P. Wang, L. Yu, J. Wang, L. Liu, X. Niu, J. Wang, , Y. R. Cao

This study shows that convergent evolution of SARS-CoV-2 XBB lineages at RBD positions 455-456 synergistically enhances antibody evasion and ACE2 binding through epistatic interactions.

bioRxiv · Aug 30, 2023Immunology

Molecular basis of Gabija anti-phage supramolecular assemblies

X. Yang, Z. Shen, Q. Lin, T. Fu

This study reveals the structure and function of the Gabija anti-phage system, showing GajA forms tetramers and GajAB forms octamers, with GajB enhancing DNA cleavage activity.

bioRxiv · Aug 7, 2023Immunology

Vacuolar H+-ATPase Determines Daughter Cell Fates through Asymmetric Segregation of the Nucleosome Remodeling and Deacetylase Complex

Z. Xie, Y. Chai, Z. Zhu, Z. Shen, Z. Guo, Z. Zhao, L. Xiao, Z. Du, G. Ou, W. Li

The paper shows that V-ATPase asymmetrically segregates the NuRD complex during cell division, influencing daughter cell survival or apoptosis through pH differences.

bioRxiv · Jun 25, 2023Cell Biology

Biological condensates form percolated networks with molecular motion properties distinctly different from dilute solutions

Z. Shen, B. Jia, Y. Xu, J. Wessen, T. Pal, H. S. Chan, S. Du, M. Zhang

This study develops a single molecule imaging method to analyze molecular motion in biological condensates, revealing distinct motion behaviors compared to dilute solutions.

eLife · Jun 1, 2023Peer-reviewedCell Biology

IL-10 inhibits STAT1-dependent macrophage accumulation during microbiota-induced colitis

I. Patik, N. S. Redhu, A. Eran, B. Bao, A. Nandy, Y. Tang, S. El Sayed, Z. Shen, J. Glickman, J. G. Fox, S. Snapper, B. H. Horwitz

The paper shows IL-10R inhibits STAT1-dependent macrophage accumulation in colitis by preventing a cell-extrinsic signal, not directly affecting STAT1 function.

Mucosal Immunology · Jun 1, 2023Peer-reviewedImmunology

Lipid Bilayer Strengthens the Cooperative Network of Membrane Proteins

S. Muhammednazaar, J. Yao, M. R. Nicelis, Y. C. Park, Z. Shen, M. D. Bridges, R. Guo, N. Swope, M. S. Rhee, M. Kim, K. H. Kim, W. L. Hubbell, K. G. Fleming, L. Columbus, S.-g. Kang, H. Hong

This study shows that lipid bilayers enhance membrane protein stability and their response to external stimuli by influencing hydrophobic thickness and amphiphile packing.

bioRxiv · May 30, 2023Biophysics

Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting

A. Yisimayi, W. Song, J. Wang, F. Jian, Y. Yu, X. Chen, Y. Xu, S. Yang, X. Niu, T. Xiao, J. Wang, L. Zhao, H. Sun, R. An, N. Zhang, , Y. Cao

This study shows repeated Omicron exposures reduce immune imprinting from wildtype vaccines, leading to higher neutralizing antibodies against XBB variants.

bioRxiv · May 1, 2023Immunology

CD45 limits Natural Killer cell development from common lymphoid progenitors

L. G. Meza Guzman, C. D. Hyland, G. M. Bidgood, E. Leong, Z. Shen, W. Goh, T. Kratina, J. Rautela, J. Vince, S. Nicholson, N. Huntington

This study shows that CD45 deficiency in common lymphoid progenitors causes NK cell developmental defects, not enhanced persistence, suggesting CD45 inhibition could improve in vitro NK cell generation for therapy.

bioRxiv · Apr 17, 2023 · PreprintCell Biology

High-level production of nervonic acid in the oleaginous yeast Yarrowia lipolytica by systematic metabolic engineering

H. Su, P. Shi, Z. Shen, H. Meng, Z. Meng, X. Han, Y. chen, W. Fan, Y. Fa, C. Yang, F. Li, S. Wang

This study engineered Yarrowia lipolytica to overproduce nervonic acid through metabolic pathway modifications, achieving high titers and purity.

bioRxiv · Mar 28, 2023 · PreprintBioengineering

Protective effect of plasma neutralization from prior SARS-CoV-2 Omicron infection against BA.5 subvariant symptomatic reinfection

X. Chen, Y. Xu, Y. Xie, W. Song, Y. Hu, A. Yisimayi, F. Shao, L. Geng, Y. Wang, H. Gao, Y. Shi, S. Zhang, R. Jin, Z. Shen, Y. R. Cao

The paper assesses the protective effect of neutralizing antibodies from prior Omicron BA.5 infection against symptomatic reinfection with BA.5, BF.7, CH.1.1, and XBB.1.5 subvariants, finding a strong correlation between antibody titers and reduced reinfection risk.

bioRxiv · Feb 14, 2023Immunology

Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion

C. Yue, W. Song, L. Wang, F. Jian, X. Chen, F. Gao, Z. Shen, Y. Wang, X. Wang, Y. R. Cao

This study shows XBB.1.5 has higher ACE2 binding and moderate antibody evasion, contributing to its increased transmissibility compared to other variants.

bioRxiv · Jan 3, 2023Immunology

Urine proteomic analysis of the rat e-cigarette model

Y. Liu, Z. Shen, C. Zhao, Y. Gao

This study uses urine proteomics to analyze the effects of e-cigarettes on rats, identifying differential proteins and pathways linked to immune, cardiovascular, and respiratory systems.

bioRxiv · Nov 19, 2022 · PreprintBiochemistry

The mechanism of nicotinamide phosphoribosyltransferase whereby positive allosteric modulation elevates cellular NAD+

K. M. Ratia, Z. Shen, J. Gordon-Blake, H. Lee, M. S. Laham, I. S. Krider, N. Christie, M. S. Ackerman-Berrier, C. Penton, N. G. Knowles, S. R. Musku, J. Fu, G. R. Musku, R. Xiong, G. R. J. Thatcher

This study identifies the mechanism by which NAMPT is activated by positive allosteric modulators, revealing how this enhances NAD+ biosynthesis and regulates NAM binding.

bioRxiv · Oct 21, 2022 · PreprintBiochemistry

Molecular Mechanisms of Holliday Junction Branch Migration Catalyzed by an Asymmetric RuvB Hexamer

A. D. Rish, Z. Shen, Z. Chen, T.-M. Fu

This study reports cryo-EM structures of RuvB in complex with DNA and nucleotides, revealing the mechanism of Holliday junction branch migration and the ATP hydrolysis cycle in RuvB.

bioRxiv · Sep 22, 2022Biochemistry