Biology subjects

Wu, C.

Publications and source records attributed to Wu, C..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

PRR adjuvants restrain high stability peptides presentation on APCs

Adjuvants can affect APCs function and boost adaptive immune responses post-vaccination. However, whether they modulate the specificity of immune responses, particularly immunodominant epitope responses, and the mechanisms of regulating antigen processing and presentation remain poorly defined. Here, using overlapping synthetic peptides, we screened the dominant epitopes of Th1 responses in mice post-vaccination with different adjuvants and found that the adjuvants altered the antigen-specific CD4+ T-cell immunodominant epitope hierarchy. MHC-II immunopeptidomes demonstrated that the peptide repertoires presented by APCs were significantly altered by the adjuvants. Unexpectedly, no novel peptide presentation was detected after adjuvant treatment, whereas peptides with high binding stability for MHC-II presented in the control group were missing after adjuvant stimulation, particularly in the MPLA- and CpG-stimulated groups. The low-stability peptide present in the adjuvant groups effectively elicited robust T-cell responses and formed immune memory. Collectively, our results suggest that adjuvants (MPLA and CpG) inhibit high-stability peptide presentation instead of revealing cryptic epitopes, which may alter the specificity of CD4+ T-cell-dominant epitope responses. The capacity of adjuvants to modify peptide-MHC (pMHC) stability and antigen-specific T-cell immunodominant epitope responses has fundamental implications for the selection of suitable adjuvants in the vaccine design process and epitope vaccine development.

immunology↗

bioRxiv2024

Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics

The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the transcriptional trajectories toward cardiomyocyte in early mouse embryo, and characterize the epigenetic landscapes underlying the early mesodermal lineage specification by single-cell multi-omics analyses. The analyses also reveal distinct core regulatory networks (CRN) in controlling specification of mesodermal lineages. We further demonstrate the essential role HAND1 and FOXF1 in driving the earliest cardiac progenitors specification. These key transcription factors occupy at distinct enhancers, but function synergistically and hierarchically to regulate the expression of cardiac-specific genes. In addition, HAND1 is required for exiting from the nascent mesoderm program, while FOXF1 is essential for driving cardiac differentiation during juxta-cardiac field (JCF) specification. Our findings establish transcriptional and epigenetic determinants specifying the early cardiac lineage, providing insights for the investigation of congenital heart defects.

molecular biology↗

bioRxiv2024

Channel width modulates the permeability of DNA origami based nuclear pore mimics

Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importin-{beta}1 substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.

biophysics↗

bioRxiv2024

Virtual Growing Child (VGC): A general normative comparative system via quantitative dynamic MRI for quantifying pediatric regional respiratory anomalies with application in thoracic insufficiency syndrome (TIS)

BackgroundA normative database of regional respiratory structure and function in healthy children does not exist. MethodsVGC provides a database with four categories of regional respiratory measurement parameters including morphological, architectural, dynamic, and developmental. The database has 3,820 3D segmentations (around 100,000 2D slices with segmentations). Age and gender group analysis and comparisons for healthy children were performed using those parameters via two-sided t-testing to compare mean measurements, for left and right sides at end-inspiration (EI) and end-expiration (EE), for different age and gender specific groups. We also apply VGC measurements for comparison with TIS patients via an extrapolation approach to estimate the association between measurement and age via a linear model and to predict measurements for TIS patients. Furthermore, we check the Mahalanobis distance between TIS patients and healthy children of corresponding age. FindingsThe difference between male and female groups (10-12 years) behave differently from that in other age groups which is consistent with physiology/natural growth behavior related to adolescence with higher right lung and right diaphragm tidal volumes for females(p<0.05). The comparison of TIS patients before and after surgery show that the right and left components are not symmetrical, and the left side diaphragm height and tidal volume has been significantly improved after surgery (p <0.05). The left lung volume at EE, and left diaphragm height at EI of TIS patients after surgery are closer to the normal children with a significant smaller Mahalanobis distance (MD) after surgery (p<0.05). InterpretationThe VGC system can serve as a reference standard to quantify regional respiratory abnormalities on dMRI in young patients with various respiratory conditions and facilitate treatment planning and response assessment. FundingThe grant R01HL150147 from the National Institutes of Health (PI Udupa).

bioengineering↗

bioRxiv2024

L-Shaped Distributions of the Relative Substitution Rates (c/micro) in SARS-COV-2 with or without Molecular Clocks, Challenging Mainstream Evolutionary Theories

A definitive test to quantify fitness changes of mutations is required to end a continuing 50-year "neutralist-selectionist" debate in evolutionary biology. Our previous work introduced a substitution-mutation rate ratio c/{micro} test (c: substitution rate in Translated Region/TR or UnTranslated Region/UTR; {micro}: mutation rate) to quantify the selection pressure and thus the proportions of strictly neutral, nearly neutral, beneficial, and deleterious mutations in a genome. Intriguingly, both a L-shaped probability distribution of c/{micro} and molecular clock were observed for SARS-COV-2s genome. We found that the proportion of the different mutation types from the distribution is not consistent with the hypotheses of the three existing evolution theories (Kimuras Neutral Theory/KNT, Ohtas Nearly Neutral Theory/ONNT and the Selectionist Theory/ST), and a balance condition explains the molecular clock, thus we proposed a new theory named as Near-Neutral Balanced Selectionist Theory (NNBST). In this study, the c/{micro} analysis was extended beyond the genome to 26 TRs, 12 UTRs, and 10 TRSs (Transcriptional Regulatory Sequences) of SARS-COV-2. While L-shaped probability distributions of c/{micro} were observed for all of 49 segments, molecular clocks were observed for only 24 segments, supporting NNBST and Near-Neutral Unbalanced Selectionist Theory (NNUST) to explain the molecular evolution of 24/25 segments with/without molecular clocks. Thus, the Near-Neutral Selectionist Theory (NNST) integrates traditional neutral and selectionist theories to deepen our understanding of how mutation, selection, and genetic drift influence genomic evolution. Author SummaryThe "neutralist-selectionist" debate in molecular evolution has been unresolved for 50 years due to the three main theories of molecular evolution (Kimuras Neutral Theory/KNT, Ohtas Nearly-Neutral Theory/ONNT, Selectionist Theory/ST) disagreeing on the proportion of neutral mutations (KNT), nearly-neutral deleterious mutations (ONNT) and adaptive mutations (ST) within species. We recently developed a robust method, the c/{micro} relative substitution rate test, to quantify the proportion of each mutation type within >11K genomic sequences of SARS-COV-2 RNA virus. Our previous analysis revealed an L-shaped c/{micro} probability distribution and a constant substitution rate (e.g., molecular clock) for the SARS-COV-2 genome over 19 months, and the proportions of mutation types were inconsistent with those predicted by the three theories. We thus proposed the Near-Neutral Balanced Selectionist Theory (NNBST) to explain the molecular clock-feature and L-shaped probability distribution for SARS-COV-2. In this study, we extended this analysis to the 25 protein-coding gene segments and 24 non-protein-coding segments of SARS-COV-2. We observed that all 49 segments exhibited an L-shaped probability distribution and 24 out of the 49 segments exhibited a molecular clock, however the remaining 25 segments did not exhibit a molecular clock. We thus propose the Near-Neutral Unbalanced Selectionist Theory (NNUST) and NNBST to explain the segments without/with molecular clock features, respectively. We also coin the Near-Neutral Selectionist Theory (NNST) to combine traditional KNT, ONNT and ST to deepen our understanding of how mutation, selection, and genetic drift influence genomic evolution.

evolutionary biology↗

bioRxiv2024

Targeting oncogenic K-Ras mutants with a small-molecule degrader through Nedd4-1

K-Ras mutations represent a most prevalent oncogenic alteration in human cancers. Despite of tremendous efforts, it remains a big challenge to develop inhibitors that can target the oncogenic K-Ras mutants, especially mutants without specific active or charged side chains such as K-RasG12V. Here, taking advantage of our previous finding that Nedd4-1 is a bona fide E3 ubiquitin ligase for wild-type Ras proteins, we developed a compound XMU-MP-9 that can promote ubiquitination and degradation of various K-Ras mutants including K-RasG12V, and significantly inhibit proliferation and tumor development of K-Ras mutant harboring cells. Mechanistically, XMU-MP-9 acts as a bifunctional compound to bind the C2 domain of Nedd4-1 and an allosteric site of K-Ras to enhance Nedd4-1 and K-Ras interaction, and to induce a conformational change of Nedd4-1/K-Ras complex to allow Nedd4-1 targeting K128 of K-Ras for ubiquitination. Hence, our study presents a robust strategy to develop small-molecule degrader of K-Ras mutants, and also sheds light on the development of small-molecule degraders for H-Ras and N-Ras mutants.

cancer biology↗

bioRxiv2024

Specific oncogene activation of the cell of origin in mucosal melanoma

Mucosal melanoma (MM) is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics, we developed a zebrafish model in which all melanocytes experienced CCND1 expression and loss of PTEN and TP53. Surprisingly, melanoma only developed from melanocytes lining internal organs, analogous to the location of patient MM. We found that zebrafish MMs had a unique chromatin landscape from cutaneous melanoma. Internal melanocytes could be labeled using a MM-specific transcriptional enhancer. Normal zebrafish internal melanocytes shared a gene expression signature with MMs. Patient and zebrafish MMs have increased migratory neural crest gene and decreased antigen presentation gene expression, consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors, allowing this model to be used for MM therapeutic discovery.

cancer biology↗

bioRxiv2024

Current forest carbon offset buffer pools do not adequately insure against disturbance-driven carbon losses

Nature-based climate solutions in Earths forests could strengthen the land carbon sink and contribute to climate mitigation, but must adequately account for climate risks to the durability of carbon storage. Forest carbon offset protocols use a buffer pool to insure against disturbance risks that may compromise durability. However, current buffer pool tools and allocations are not based on existing scientific data or models. Here, we use a tropical forest stand biomass model and an extensive set of long-term tropical forest plots to test whether current buffer pools are adequate to insure against observed disturbance regimes. We find that forest age and disturbance regime both influence necessary buffer pool sizes. In the vast majority of disturbance scenarios, current buffer pools are substantially smaller than required by carbon cycle science. Buffer pool estimates urgently need to be updated based on rigorous, open scientific datasets for nature-based climate solutions to succeed. Plain Language SummaryForests could contribute to climate mitigation through conservation and restoration activities. Carbon offsets are a widespread pathway to fund these nature-based climate solutions in forests, but must account for the risks to durability that forests face in a changing climate. Current carbon offset protocols have a buffer pool to insure against risk in different disturbance regimes, but the buffer pool contributions have not been tested with observed disturbance regimes and rigorous models. We tested these contributions using widespread tropical forest plot data and a carbon cycle model and find that the current buffer pool contributions are generally not adequate for most disturbance regimes. Our results highlight that better datasets, models, and tools are urgently needed in forest carbon offset protocols. Key pointsO_LINature-based climate solutions in forests face substantial and rising climate risks to durability C_LIO_LICarbon offsets use a buffer pool to insure against disturbance, which is not currently based on rigorous evidence C_LIO_LIOur results reveal current carbon offset protocols do not have an adequate buffer pool for most tropical forest disturbance regimes C_LI

ecology↗

bioRxiv2024

CADTAD: CAncer Driver Topologically Associated Domains identify oncogenic and tumor suppressive lncRNAs

Cancer long noncoding RNAs (lncRNAs) have been identified by experimental and in silico methods. However, current approaches for identifying cancer lncRNAs are not sufficient and effective. To uncover them, we focused on the core cancer driver lncRNAs, which directly interact with cancer driver protein-coding genes (PCGs). We investigated various aspects of cancer lncRNAs, including their expression patterns, genomic locations, and direct interactions with cancer driver PCGs, and developed a pipeline to unearth candidate cancer driver lncRNAs. Finally, we validated the reliability of potential cancer driver lncRNAs through functional analysis of bioinformatics data and CRISPR-Cas9 knockout experiments. We found that cancer lncRNAs were more concentrated in cancer driver topologically associated domains (CDTs), and CDT is an important feature in identifying cancer lncRNAs. Moreover, cancer lncRNAs showed a high tendency to co-express with and bind to cancer driver PCGs. Utilizing these distinctive characteristics, we developed a pipeline CADTAD to unearth candidate cancer driver lncRNAs in pan-cancer, including 256 oncogenic lncRNAs, 177 tumor suppressive lncRNAs, and 75 dual-function lncRNAs, as well as in three individual cancer types, and validated their cancer-related function. More importantly, the function of 10 putative cancer driver lncRNAs in prostate cancer was subsequently validated to influence cancer phenotype through cell studies. In light of these findings, our study offers a new perspective from the 3D genome to study the roles of lncRNAs in cancer. Furthermore, we provide a valuable set of potential lncRNAs that could deepen our understanding of the oncogenic mechanism of cancer driver lncRNAs.

genomics↗

bioRxiv2024

Mechanical confinement induces ferroptosis through mitochondrial dysfunction

Cells exist in highly crowded environments where they are exposed to fluctuating mechanical forces arising from surrounding cells and the extracellular matrix microenvironment. In these settings, external forces are transmitted to intracellular organelles including the nucleus. While cells can survive confinement, extended duration of confinement or confinement in settings where cells are unable to escape, can result in cell death. How cells sense and respond to prolonged confinement to trigger cell death remains unclear. Here, we demonstrate that nuclear deformation generated by axial confinement triggers the programmed cell death pathway - ferroptosis. We show that axial confinement results in Drp1-dependent mitochondrial fragmentation and cPLA2 translocation to mitochondria, where Drp1 undergoes acute phase separation. Ensuing mitochondrial ROS accumulation and arachidonic acid production concertedly leads to lipid peroxidation evoking ferroptosis. Finally, of clinical relevance, we find that in human osteoarthritis tissue cPLA2 exhibits mitochondrial localization and high ROS levels. Together, our findings unveil a pivotal role for Drp1 and cPLA2 in linking mechanical confinement with mitochondrial dysfunction resulting in ferroptosis, which sheds new light on a mechanical mechanism of pathophysiology in osteoarthritis.

cell biology↗

bioRxiv2024

Closed-loop electrical stimulation to prevent focal epilepsy progression and long-term memory impairment

Interictal epileptiform discharges (IEDs) are ubiquitously expressed in epileptic networks and disrupt cognitive functions. It is unclear whether addressing IED-induced dysfunction could improve epilepsy outcomes as most therapeutics target seizures. We show in a model of progressive hippocampal epilepsy that IEDs produce pathological oscillatory coupling which is associated with prolonged, hypersynchronous neural spiking in synaptically connected cortex and expands the brain territory capable of generating IEDs. A similar relationship between IED-mediated oscillatory coupling and temporal organization of IEDs across brain regions was identified in human subjects with refractory focal epilepsy. Spatiotemporally targeted closed-loop electrical stimulation triggered on hippocampal IED occurrence eliminated the abnormal cortical activity patterns, preventing spread of the epileptic network and ameliorating long-term spatial memory deficits in rodents. These findings suggest that stimulation-based network interventions that normalize interictal dynamics may be an effective treatment of epilepsy and its comorbidities, with a low barrier to clinical translation. One-Sentence SummaryTargeted closed-loop electrical stimulation prevents spread of the epileptic network and ameliorates long-term spatial memory deficits.

neuroscience↗

bioRxiv2024

IL-1beta-induced epithelial cell and fibroblast transdifferentiation fuels neutrophil recruitment in chronic rhinosinusitis with nasal polyps

Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases, including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated with an unfavorable prognosis. Here, using single-cell RNA sequencing (scRNA-seq) to profile human nasal mucosa obtained from the inferior turbinates, middle turbinates, and nasal polyps of CRSwNP patients, we identified two IL-1 signaling-induced cell subsets--LY6D+ club cells and IDO1+ fibroblasts--that promote neutrophil recruitment by respectively releasing S100A8/A9 and CXCL1/2/3/5/6/8 into inflammatory regions. IL-1{beta}, a pro-inflammatory cytokine involved in IL-1 signaling, induces the transdifferentiation of LY6D+ club cells and IDO1+ fibroblasts from primary epithelial cells and fibroblasts, respectively. In an LPS-induced neutrophilic CRSwNP mouse model, blocking IL-1{beta} activity with a receptor antagonist significantly reduced the numbers of LY6D+ club cells and IDO1+ fibroblasts and mitigated nasal inflammation. This study reveals the roles of two cell subsets in neutrophil recruitment and demonstrates an IL-1-based intervention for mitigating neutrophilic inflammation in CRSwNP.

immunology↗

bioRxiv2024

Prevotella are major contributors of sialidases in the human vaginal microbiome.

Elevated bacterial sialidase activity in the female genital tract is strongly associated with poor health outcomes including preterm birth and bacterial vaginosis. These negative effects may arise from sialidase-mediated degradation of the protective mucus layer in the cervicovaginal environment. Prior biochemical studies of vaginal bacterial sialidases have focused solely on the bacterial vaginosis-associated organism Gardnerella vaginalis. Despite their implications for sexual and reproductive health, sialidases from other vaginal bacteria have not been characterized. Here, we show that vaginal Prevotella species produce active sialidases that possess variable activity toward mucin. These sialidases are highly conserved across clades of Prevotella from different geographies, hinting at their importance globally. Finally, we find that Prevotella sialidases, including mucin-degrading enzymes from Prevotella timonensis, are highly prevalent and abundant in human vaginal metagenomes and metatranscriptomes, Together, our results identify Prevotella as a critical source of sialidases in the vaginal microbiome, improving our understanding of this detrimental bacterial activity. Significance StatementSialidase activity in the vaginal microbiome is increased in bacterial vaginosis and strongly associated with other adverse health outcomes. Sialidase enzymes release sialic acid from host-derived glycans in the vaginal environment, altering their structures and functions. However, biochemical studies of vaginal bacterial sialidases have been limited to one genus, Gardnerella. In this work, we identify and characterize multiple active sialidase enzymes in vaginal bacteria of the genus Prevotella. We find that Prevotella sialidases are more prevalent and abundant in vaginal microbial communities than Gardnerella sialidases. Our work highlights Prevotella bacteria as an underappreciated source of sialidase activity with important implications for both our understanding of vaginal health and therapeutic development.

microbiology↗

bioRxiv2023

Exposure and resistance to lantibiotics impact microbiota composition and function

The intestinal microbiota is composed of hundreds of distinct microbial species that interact with each other and their mammalian host. Antibiotic exposure dramatically impacts microbiota compositions and leads to acquisition of antibiotic-resistance genes. Lantibiotics are ribosomally synthesized and post-translationally modified peptides produced by some bacterial strains to inhibit the growth of competing bacteria. Nisin A is a lantibiotic produced by Lactococcus lactis that is commonly added to food products to reduce contamination with Gram-positive pathogens. Little is known, however, about lantibiotic-resistance of commensal bacteria inhabiting the human intestine. Herein, we demonstrate that Nisin A administration to mice alters fecal microbiome compositions and the concentration of taurine-conjugated primary bile acids. Lantibiotic Resistance System genes (LRS) are encoded by lantibiotic-producing bacterial strains but, we show, are also prevalent in microbiomes across human cohorts spanning vastly different lifestyles and 5 continents. Bacterial strains encoding LRS have enhanced in vivo fitness upon dietary exposure to Nisin A but reduced fitness in the absence of lantibiotic pressure. Differential binding of host derived, secreted IgA contributes to fitness discordance between bacterial strains encoding or lacking LRS. Although LRS are associated with mobile genetic elements, sequence comparisons of LRS encoded by distinct bacterial species suggest they have been long-term components of their respective genomes. Our study reveals the prevalence, abundance and physiologic significance of an underappreciated subset of antimicrobial resistance genes encoded by commensal bacterial species constituting the human gut microbiome, and provides insights that will guide development of microbiome augmenting strategies.

microbiology↗

bioRxiv2023

Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques

For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34+ cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34+ cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP+ cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.

cell biology↗

bioRxiv2023

Structure basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor

The neuropeptide 26RFa, a member of the RF-amide peptide family, activates the pyroglutamylated RF-amide peptide receptor (QRFPR), a class A GPCR. The 26RFa/QRFPR system plays critical roles in energy homeostasis, making QRFPR an attractive drug target for treating obesity, diabetes, and eating disorders. However, the lack of structural information has hindered our understanding of the peptide recognition and regulatory mechanism of QRFPR, impeding drug design efforts. In this study, we determined the cryo-EM structure of the Gq-coupled QRFPR bound to 26RFa. The structure reveals a unique assembly mode of the receptor extracellular regions and the peptide N-terminus and elucidates the recognition mechanism of the C-terminal heptapeptide of 26RFa within the transmembrane binding pocket of QRFPR. The study also clarifies the similarities and distinctions in the binding pattern of the RF-amide moiety in five RF-amide peptides and the RY-amide segment in neuropeptide Y. These findings deepen our understanding of the RF-amide peptides recognition, aiding in the rational design of drugs targeting QRFPR and other RF-amide receptors.

biophysics↗

bioRxiv2023

Effects of greening-induced warming and cooling on tree phenology in temperate and boreal forests

Tree phenology, periodic biological events in trees, is highly sensitive to climate change. It has been reported that forest greening can influence the local climate by altering the seasonal surface energy budget. However, tree phenological responses to forest greening remains poorly understood at large spatial scales. Combining remote-sensing derived phenological and leaf area indices since 2001, herein we show that forest greening led to earlier spring (-1.05 {+/-} 0.17 d) and autumn phenology (-1.95 {+/-} 0.14 d) in temperate and boreal forests. Our results show that forest greening in winter and spring decreased surface albedo and thus resulted in biophysical warming that caused earlier spring leaf phenology. In contrast, forest greening in summer and autumn triggered biophysical cooling by enhancing evapotranspiration, which led to earlier autumn leaf phenology. These findings suggest that forest greening could significantly alter tree phenology through seasonal biophysical impacts. Therefore, it is essential to incorporate these complicated biophysical impacts of greening into tree phenology models to accurately predict future shifts in tree phenology under future climate change.

ecology↗

bioRxiv2023

Filter-aided expansion proteomics

Integration of hydrogel-based tissue expansion and mass spectrometry-based proteomics enables high spatial resolution analysis of global protein expression in tissues. Here, we introduce a filter-aided tissue expansion proteomics (FAXP) method with optimized hydrogel preparation and treatment steps for spatial proteomics analysis of formalin-fixed paraffin-embedded (FFPE) specimens. Compared with our original ProteomEx method, FAXP, partially automated with robotics, exhibited 14.5-fold higher volumetric resolution, increased peptide yield leading to 250% more protein identifications, and 50% time consumption for sample preparation. We demonstrated its application in clinical colorectal tissue samples. We further integrated it with laser capture microdissection for proteomic analysis of subcellular organelles.

biochemistry↗