Biology subjects

Berry, S.

Publications and source records attributed to Berry, S..

18 recordsLinked to original sources

bioRxiv2026

Supramolecular Site-Specific Antibody Drug Conjugates Outperform Cysteine-Conjugated Analogs in Pancreatic Peritoneal Carcinomatosis

Antibody drug conjugates (ADCs) are a burgeoning class of targeted therapies. However, limitations in their synthesis and efficiency of payload delivery restrict their clinical utility. Here we report a supramolecular assembly (SMA) ADC conjugation method, which allows site-specific, uniform drug loading, resulting in an enhanced pharmacokinetic profile and in vivo efficacy. This peptide conjugation strategy relies on spontaneous heterotetrameric coiled-coil formation between a pair of peptides appended on the C-terminus and a drug-loaded complementary pair in aqueous solution. Pairing this SMA conjugation with an antibody that targets the dual-endothlin-1/VEGF signal peptide receptor (DEspR), a pancreatic ductal adenocarcinoma (PDAC) specific receptor, retains antibody binding and plasma stability. When the anti-DEspR monoclonal antibody is conjugated with monomethyl auristatin E (MMAE), the ensuing ADC internalizes following cell surface binding and induces selected cell death in multiple DEspR positive PDAC cell lines. In vivo, the ADC exhibits favorable pharmacokinetics, high tumor specificity, and improves overall survival in a rat orthotopic model of pancreatic peritoneal carcinomatosis, compared to conventional ADC conjugation. A heterotetrameric coiled-coil structure enables the efficient synthesis of a potent ADC, further documenting the versatility of supramolecular scaffolds as key orthogonal building block for site-specific conjugation in biopharmaceutical and biomaterial drug delivery systems. One Sentence SummaryCombining site-specific conjugation of monomethyl auristatin E, via the use of biologically inspired heterotetrameric coiled-coils, with a tumor-selective antibody targeting the dual-endothlin-1/VEGF signal peptide receptor affords a highly effective, ADC, which improves survival in a rat orthotopic model of pancreatic peritoneal carcinomatosis compared to standard cysteine-conjugated analogues with higher drug loading.

bioengineering↗

bioRxiv2026

Differences between protein fitness models can be used to design variants of altered specificity

The vastness of sequence space makes it challenging for directed evolution to efficiently traverse the fitness landscape. In recent years, unsupervised probabilistic models trained on natural sequences have shown promise for predicting the functional effects of mutations and designing new proteins, leading many to suggest that these models may be useful for guiding directed evolution campaigns toward functional regions of sequence space. However, many directed evolution campaigns are interested in evolving new substrate or ligand specificity, and the behavior of unsupervised sequence models on predicting and designing activity against altered substrates or ligands has not been tested. We have built a curated database of multiplexed functional assay results profiling substrate or ligand specificity and systematically how assessed various popular unsupervised protein fitness models score and design variants that alter selectivity in these datasets. We find that sequence models that learn from the surrounding sequence context, especially protein language models, systematically bias against variants that alter specificity. This bias leads them to design altered-specificity variants at similar or lower rates than random chance. However, we propose a simple strategy to exploit this bias by taking weighted differences of model scores to enrich libraries for altered-specificity variants. These findings and our database should help guide how biologists best use protein fitness models and provide a framework to help machine learning researchers develop a new generation of machine learning models that can better design novelty.

Systems Biology↗

bioRxiv2026

Unified sampling framework and experimental benchmarking of sequence- and structure-based protein models

Generative models are increasingly used for protein design, but the lack of standardized evaluation frameworks limits comparison across model classes and hinders translation to experimental success. Here, we introduce a unified sampling and benchmarking framework that enables controlled sequence generation across alignment, protein language, and structure-based models, and apply it to Tobacco etch virus (TEV) protease. Across hundreds of thousands of designed sequences, different models explore distinct regions of sequence space with no clear computational selection metrics to assess enzymatic function. Experimental evaluation reveals large differences in functional outcomes, ranging from non-functional variants to sequences with 9-fold higher activity than wildtype. Machine learning-designed libraries achieve a 39.32% hit rate (percentage of variants matching or exceeding wildtype activity) compared to 6.06% for an error-prone PCR baseline. Structure-based models perform best overall, with hit rates of 74.4% and 66.8% for ESM-IF1 and ProteinMPNN, respectively. Commonly used selection metrics do not strongly correlate with experimental activity, highlighting a gap between in silico evaluation and enzyme function. Together, these results establish a generalizable framework for benchmarking generative protein models and demonstrate the necessity of experimental validation for guiding model development and sequence prioritization.

bioinformatics↗

bioRxiv2025

Hierarchical buffering of cellular RNA polymerase II pools maintains transcriptional homeostasis

RNA polymerase II (Pol II) abundance and transcriptional output are coordinated across diverse conditions to maintain mRNA homeostasis. To determine whether Pol II acts as a limiting factor for transcription, we combined acute perturbations with quantitative single-cell imaging and genome-wide profiling. We find that transcription remains stable across 70-180% of normal Pol II levels in human cells. This robustness emerges from hierarchical buffering mechanisms operating on distinct timescales. Within tens of minutes after monoallelic depletion of Pol II subunit POLR2A, cells maintain steady transcriptional output by drawing polymerases from a nucleoplasmic reserve pool. However, over hours, cellular Pol II holoenzyme levels also recover, driven by constitutive excess POLR2A subunit production rather than feedback sensing. Finally, strong depletion over days activates additional compensatory mechanisms. Together, these results reveal how temporal separation of buffering mechanisms provides robustness to perturbations of essential machinery, illuminating how cells maintain homeostatic control of essential complexes.

cell biology↗

bioRxiv2025

In Situ Photoactivated Hydrogel Adhesive Dressings for Post Colon Polypectomies (PolypCures)

Colon polypectomy is a widely performed endoscopic procedure that reduces the incidence of colorectal cancer but leaves exposed colonic wounds susceptible to bleeding, perforation, and infection. The current standard of wound care, mechanical clips, is limited by technical complexity, high cost, and poor efficacy for large (> 2 cm in diameter) or difficult-to-access lesions. Here, we present PolypCure, an in situ photoactivated hydrogel adhesive dressing delivered via a single catheter, through either oozing or spraying methods, to achieve rapid, spatiotemporally controlled sealing and hemostasis (within 2 min) of colon lesions using the white light source integrated into standard endoscopic instruments. The hydrogel, composed of norbornene- and thiol-functionalized polyethylene glycol, carboxymethyl cellulose, and Eosin Y, exhibits mechanical properties comparable to colon tissue (G [~] 6 kPa), strong shear strength (> 15 kPa), low swelling (< 200%), and small pore size ([~] 20 {micro}m), ensuring long-term stability (up to 30 days) and protection against bacterial infiltration. The formulation also demonstrates biocompatibility and hemocompatibility. In an in vivo pig colon endoscopic mucosal resection (EMR) model, PolypCure fully adheres to large lesions for at least 3 days and promotes early-stage wound healing. Overall, PolypCure is a promising solution to wound management post-polypectomy.

bioengineering↗

bioRxiv2025

High-content imaging reveals the ability of microexons to shape protein localisation

Alternative splicing provides a pervasive means to expand proteome complexity, yet how it reorganises protein interactions and constrains where proteins act within cell remains unclear. By constructing an interface-resolved interaction network composed of 17,660 experimentally defined contact sites, we reveal that tissue-specific alternative splicing remodels protein connectivity by reshaping modular protein architecture. Longer exons reshape local interaction patterns whereas microexons fine-tune key interfaces linking distinct cellular processes. Integration of subcellular localisation data further indicates that such rewiring can redistribute proteins within cells. To test this, we developed a high-content imaging approach to systematically evaluate the influence of individual exons on protein localisation and screened a targeted library of protein isoforms differing in individual exons. 38% of the tested isoform pairs altered localisation, with microexons, although typically shorter than five amino acids, accounting for a substantial proportion of these effects. Bioinformatic and structural analyses identified that microexons can extend secondary structural regions and reposition charged residues, suggesting a potential to modulate local electrostatic environments. Consistent with this, biochemical analysis of a four-amino acid microexon in sorting nexin 2 - identified through our screen - confirmed that residue insertion, rather than side chain chemistry, was driving differences in protein localisation through repositioning of a flanking, charged residue. Together, these findings describe a principle by which alternative splicing fine-tunes interface architecture to coordinate protein assembly, localisation, and proteome organisation.

molecular biology↗

bioRxiv2025

Maize kernel composition and morphology influences pericarp retention during nixtamalization

Background and ObjectivesPericarp retention during nixtamalization directly influences masa quality, affecting texture, machinability, and nutritional content of staple foods such as tortillas and chips. Despite its industrial relevance, the underlying kernel traits that govern pericarp retention remain poorly characterized. This study aimed to assess an existing staining method to quantify pericarp retention based on visual evaluation, and identify the compositional and morphological characteristics of maize kernels that most strongly predict pericarp retention during nixtamalization. FindingsStain-based scoring of pericarp retention showed moderate correlation with directly measured pericarp mass, achieving a Pearsons correlation coefficient of 0.77 in the rapid cook test and 0.56 in the benchtop cook test. Pearson correlation coefficients of 18 compositional and morphological traits range from -0.294 to 0.538. Ground kernel ash content and initial pericarp quantity were the most correlated and predictive variables associated with pericarp retention. ConclusionsStain-based methods lack the resolution necessary for quantitative pericarp assessment. Initial pericarp quantity and ground kernel ash content are likely key determinants of nixtamalization pericarp retention. Significance and NoveltyThis study provides a first assessment on the impacts of morphological and compositional variation for pericarp retention, which can be built upon to develop improved varieties and cooking methods for product optimization.

plant biology↗

bioRxiv2023

Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker-trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

plant biology↗

bioRxiv2023

Disruption of Aldehyde Dehydrogenase 2 protects against 1 bacterial infection

The ALDH2*2 (rs671) variant present in >500 million individuals reduces ALDH2 function, impairing aldehyde detoxification. While aldehyde accumulation in these individuals is associated with numerous negative health consequences, a previous study showed a cohort of ALDH2*2 carriers are less likely to develop active pulmonary tuberculosis. Here, we present additional human data that support this finding and show ALDH2-deficiency in mice provides a fitness advantage during bacterial infections. We found aldehydes normally detoxified by ALDH2 killed the bacterial pathogens Mycobacterium tuberculosis and Francisella tularensis. Infected macrophages from Aldh2-/-mice had higher levels of formaldehyde and 4-hydroxynonenal, which enhanced their microbicidal capacity. Aldh2-/- mice were more resistant to infection with Mycobacterium tuberculosis and Francisella tularensis than parental mice and displayed elevated inflammatory cytokine and chemokine levels, accompanied by an increased accumulation of inflammatory monocytes and macrophages. These findings support a model in which host-derived aldehydes are robust innate immune effectors, limiting bacterial infection through both direct microbicidal activity and immune modulation. Collectively, this work may explain why the ALDH2*2 allele was selected for in humans.

microbiology↗

bioRxiv2022

Integrating analog and digital modes of gene expression at Arabidopsis FLC

Quantitative gene regulation at the cell population-level can be achieved by two fundamentally different modes of regulation at individual gene copies. A "digital" mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an "analog" mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), "digital" Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population-level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.

molecular biology↗

bioRxiv2022

Robust and Versatile Arrayed Libraries for Human Genome-Wide CRISPR Activation, Deletion and Silencing

Arrayed CRISPR libraries extend the scope of gene-perturbation screens but require large numbers of efficacious sgRNA-expressing vectors. Using a newly invented liquid-phase plasmid cloning methodology, we constructed genome-wide arrayed libraries for human gene ablation (19,936 plasmids), activation, and epigenetic silencing (22,442 plasmids). At least 76% of each plasmid preparation encoded an intact array of 4 non-overlapping sgRNAs designed to tolerate most human DNA polymorphisms. We achieved perturbation efficacies of 75-99%, 76-92% and up to 10,000x in deletion, silencing and activation experiments, respectively. Upon conversion into massively parallel lentiviral vectors, an arrayed activation screen of 1,634 human transcription factors yielded 11 novel regulators of the cellular prion protein PrPC. Furthermore, a screen using a pooled version of the ablation library identified 5 novel modifiers of autophagy that went undetected with either of two 1sgRNA libraries. The CRISPR libraries described here represent a powerful resource for the targeted perturbation of human protein-coding genes.

genomics↗

bioRxiv2022

Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps

Highly multiplexed quantitative subcellular imaging holds enormous promise for understanding how spatial context shapes the activity of our genome and its products at multiple scales. Yet unbiased analysis of subcellular organisation across experimental conditions remains challenging, because differences in molecular profiles between conditions confound differences in molecular profiles across space. Here, we introduce a deep-learning framework called CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis), which uses a variational autoencoder conditioned on cellular states and perturbations to learn consistent molecular signatures. Clustering the learned representations into subcellular landmarks allows quantitative comparisons of landmark sizes, shapes, molecular compositions and relative spatial organisation between conditions. By performing high-resolution multiplexed immunofluorescence on human cells, we use CAMPA to reveal how subnuclear organisation changes upon different perturbations of RNA production or processing, and how different membraneless organelles scale with cell size. Furthermore, by integrating information across the cellular and subcellular scales, we uncover new links between the molecular composition of membraneless organelles and bulk RNA synthesis rates of single cells. We anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organisation to identify the rules by which context shapes physiology and disease.

systems biology↗

bioRxiv2021

Nuclear RNA concentration coordinates RNA production with cell size in human cells

Unlike its DNA template, RNA abundance and synthesis rates increase with cell size, as part of a mechanism of cellular RNA concentration homeostasis. Here, we study this scaling phenomenon in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations remain highly constant. Systems-level analysis indicates that perturbations that would lead to increased nuclear mRNA abundance result in downregulation of mRNA synthesis. This is associated with reduced levels of several transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (Pol II) itself. Acute shut-down of nuclear RNA degradation, elevation of nuclear mRNA levels, and mathematical modelling indicate that mammalian cells achieve RNA concentration homeostasis by an mRNA-based negative feedback on transcriptional activity in the nucleus. Ultimately, this acts to robustly scale Pol II abundance with cell volume and coordinate mRNA synthesis and degradation.

molecular biology↗

bioRxiv2021

Genetic resistance to yellow rust infection of the wheat ear is controlled by genes controlling foliar resistance and flowering time

Yellow rust (YR), or stripe rust, is a fungal infection of wheat (Triticum aestivum L.) caused by the pathogen Puccinia striiformis Westend f. sp. tritici (Pst). While much research has focused on YR infection of wheat leaves, we are not aware of reports investigating the genetic control of YR resistance in other wheat structures, such as the ears. Here we use an eight-founder population to undertake genetic analysis of glume YR infection in wheat ears. Five quantitative trait loci (QTL) were identified, each explaining between ~3-7% of the phenotypic variation. Of these, three (QYrg.niab-2D.2, QYrg.niab-4D.1 and QYrg.niab-5A.1) co-located with QTL for leaf YR resistance previously identified in the same population, with evidence suggesting QYrg.niab-5A.1 may correspond to the adult plant resistance locus Yr34 which originates from T. monococcum ssp. monococcum and that resistance at QYrg.niab-2D.2 may be conferred by chromosomal introgression from a wheat relative. Additional leaf YR resistance QTL previously identified in the population were not detected as controlling glume resistance, with the remaining two glume YR QTL linked to genetic loci controlling flowering time. The first of these, QYrg.niab-2D.1, mapped to the major flowering time locus Photoperiod-D1 (Ppd-D1), with the early-flowering allele from the MAGIC founder Soissons conferring reduced glume YR resistance. The second, QYrg.niab-4A.1, was identified in one trial only, and was located close to a flowering time QTL. This indicates earlier flowering results in increased glume YR susceptibility, likely due to exposure of tissues during environmental conditions more favourable for Pst infection. Collectively, our results provide first insights into the genetic control of YR resistance in glumes, controlled by subsets of QTL for leaf YR resistance and flowering time. This work provides specific genetic targets for the control of YR resistance in both the leaves and the glumes, and may be especially relevant in Pst-prone agricultural environments where earlier flowering is favoured. Core ideasO_LIPuccinia striiformis Westend f. sp. tritici (Pst) causes yellow rust (YR) in wheat leaves and ears. C_LIO_LIWe present the first reports for the genetic control of YR on the wheat ear. C_LIO_LIEar YR infection is controlled by subsets of QTL controlling leaf resistance and flowering time. C_LIO_LIThe findings are relevant to wheat breeding for Pst-prone environments. C_LI

genetics↗

bioRxiv2020

Resolving a QTL complex for height, heading, and grain yield on chromosome 3A in bread wheat

Crop height (Ht), heading date (Hd), and grain yield (GY) are interrelated traits in wheat. Independent manipulation of each is important for adaptation and performance. Validated QTL for all three collocate on chromosome 3A in the Avalon x Cadenza population. We asked if these are linked or pleiotropic effects. The region was dissected using recombinants derived from Near Isogenic Lines. It was shown that Ht and Hd are controlled by independent genes. The newly defined Ht QTL interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is much larger and rearranged compared to the reference genome but FT2 is a candidate of particular interest. The Hd effect was shown to act independently of photoperiod and vernalization but did exhibit genotype x environment interaction suggesting a role in ambient temperature sensitivity. It was the Hd locus that was most associated with increased GY of Cadenza alleles, supporting physiological studies proposing that late alleles at this locus increase spike fertility and grain number. The work has uncoupled height from heading and yield and shown that one of very few validated GY QTL in wheat is probably mediated by phenological variation. HighlightThere only are three validated wheat yield QTL. Here, one of them was genetically dissected. This showed that the physiological basis of the yield effect is likely to be phenological.

genetics↗

bioRxiv2018

The effects of training population design on genomic prediction accuracy in wheat

Genomic selection offers several routes for increasing genetic gain or efficiency of plant breeding programs. In various species of livestock there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeders equation. Accurate predictions of genomic breeding value are central to this and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable accurate predictions.\n\nTo quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and triparental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25,000 segregating single nucleotide polymorphism markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Within cross genomic prediction accuracies of yield BLUEs were 0.125 - 0.127 using two different cross-validation approaches, and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasize the importance of the training set design in relation to the genetic material to which the resulting prediction model is to be applied.

genetics↗

bioRxiv2018

HOPS-dependent endosomal fusion required for efficient cytosolic delivery of therapeutic peptides and small proteins

Protein therapeutics represent a significant and growing component of the modern pharmacopeia, but their potential to treat human disease is limited because most proteins fail to traffic across biological membranes. Recently, we discovered that cell-permeant miniature proteins (CPMPs) containing a precisely defined, penta-arginine motif traffic readily to the cytosol and nucleus with efficiencies that rival those of hydrocarbon-stapled peptides active in animals and man. Like many cell-penetrating peptides (CPPs), CPMPs enter the endocytic pathway; the difference is that CPMPs are released efficiently from endosomes while other CPPs are not. Here, we seek to understand how CPMPs traffic from endosomes into the cytosol and what factors contribute to the efficiency of endosomal release. First, using two complementary cell-based assays, we exclude endosomal rupture as the primary means of endosomal escape. Next, using a broad spectrum of techniques, including an RNA interference (RNAi) screen, fluorescence correlation spectroscopy (FCS), and confocal imaging, we identify VPS39--a gene encoding a subunit of the homotypic fusion and protein sorting (HOPS) complex--as a critical determinant in the trafficking of CPMPs and hydrocarbon-stapled peptides to the cytosol. Although CPMPs neither inhibit nor activate HOPS function, HOPS activity is essential to efficiently deliver CPMPs to the cytosol. Subsequent multi-color confocal imaging studies identify CPMPs within the endosomal lumen, particularly within the intraluminal vesicles (ILVs) of Rab7+ and Lamp1+ endosomes that are the products of HOPS-mediated fusion. These results suggest that CPMPs require HOPS to reach ILVs--an environment that serves as a prerequisite for efficient endosomal escape.

biochemistry↗

bioRxiv2018

BED-domain containing immune receptors confer diverse resistance spectra to yellow rust

Introductory paragraph Introductory paragraph Main Methods Author contributions Data availability Competing interests References Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security1. Genetic resistance can reduce crop losses in the field and can be selected for through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst)2. This highlights the need to (i) identify genes that alone or in combination provide broad-spectrum resistance and (ii) increase our understanding of the underlying molecular mod ...

plant biology↗