Biology subjects

Morris, C.

Publications and source records attributed to Morris, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Caught a chill? The relationship between canker disease susceptibility and the vulnerability to freeze events in apricot trees.

Bacterial canker remains a major constraint affecting apricot production in South-East of France. It is primarily caused by Pseudomonas syringae, a Gram-negative bacterium, many strains of which exhibit ice nucleation activity. By promoting ice formation at relatively high subzero temperatures, ice nucleation-active bacteria may facilitate tissue disruption and pathogen entry. Concurrently, climate-driven shifts toward warmer winter-spring periods have advanced flowering phenology, increasing exposure to late frost events. Despite breeders having developed less susceptible varieties to bacterial canker and early flowering varieties, the link between these traits and frost sensitivity, an emerging risk in this location, remains unresolved. Here, we have evaluated the links between canker susceptibility and frost sensitivity using three cultivar pairs contrasting in disease response and flowering time. Ice nucleation temperature was measured in excised buds under controlled conditions throughout the frost-risk period, alongside field-based diameter variation monitoring over two years. Disease susceptibility (P < 0.001), phenology (P = 0.003), varieties (P < 0.001), locations (P < 0.001), and sampling date (P < 0.001) significantly affected nucleation temperature, whereas epiphytic bacterial abundance and xylem vessel diameter did not. Trees froze at higher temperatures in situ than in laboratory assays (1 to -2{degrees}C versus -3 to 4{degrees}C, respectively), indicating strong environmental modulation of freezing processes beyond Psy-like bacterial activity, which is reflected in contrasting disease susceptibilities (P < 0.001) and precocities (P < 0.001). These results shed light on the complexity of the freezing process in trees under natural conditions. We discuss the potential roles of microclimatic conditions and alternative ice nucleation sources beyond Psy-like bacteria in driving these physiological processes.

plant biology↗

bioRxiv2026

Engineering CAR T Cells for Hepatocellular Carcinoma Recurrence after Liver Transplantation

Background & AimsLiver transplantation improves outcomes in hepatocellular carcinoma (HCC), yet treatment options for patients with tumor recurrence remain limited to tyrosine kinase inhibitors. Glypican-3 (GPC3)-targeted CAR T cells offer a tumor-directed immune-based therapeutic strategy, but their efficacy may be limited by post-transplant immunosuppression. We developed a CAR T cell platform combining CRISPR/Cas9-mediated FKBP1A disruption to confer resistance to FKBP12-dependent immunosuppressive agents, including tacrolimus, everolimus, and sirolimus, with TRAC knockout to eliminate endogenous T cell receptor expression and reduce alloreactivity. MethodsHuman T cells were edited using Cas9 ribonucleoprotein complexes targeting FKBP1A and TRAC, expanded, and transduced with an anti-GPC3 CAR construct. Cytokine production and cytotoxicity were assessed in vitro. Antitumor activity under tacrolimus treatment was evaluated in a Hep G2 xenograft model, and xenoreactivity was assessed in a graft-versus-host disease model. FKBP1A/TRAC double-knockout T cells were enriched using mTOR inhibitor selection combined with CD3-based MACS depletion. PBMCs from liver transplant recipients were used to evaluate feasibility for clinical translation during the early post-transplant period. ResultsTacrolimus suppressed wild-type CAR T cell function but not FKBP1A/TRAC double-knockout CAR T cells, which retained cytokine production, cytotoxicity, and in vivo antitumor activity. Cyclosporine A remained suppressive, enabling its potential use as a pharmacologic control strategy. TRAC disruption reduced xenoreactivity. CD3-based MACS depletion and mTOR inhibition achieved functional double-knockout efficiencies greater than 98%, without compromising cell viability. Functional FKBP1A/TRAC knockout CAR T cells were generated from patient PBMC samples 30 days post-transplant. ConclusionsDual-edited GPC3 CAR T cells resist tacrolimus-based immunosuppression while limiting alloreactivity, supporting their use for recurrent HCC after liver transplantation. Sequential, high-viability selection in a modular cellular engineering framework enables adaptation to alternative tumor targets and next-generation CAR T cell designs. Impact and implicationsO_LIEngineering armored GPC3-targeting CAR T cells for hepatocellular carcinoma in the post-transplant setting C_LIO_LIDemonstrating safety and therapeutic efficacy in the presence of immunosuppressive drugs in preclinical models C_LIO_LILeveraging mTOR inhibitor resistance and CD3 destabilization enables high-efficiency, high-purity selection of genetically modified T cells C_LIO_LIA modular cellular engineering platform enables utilization for alternative tumor targets and next-generation CAR T cells C_LI

immunology↗

bioRxiv2026

Bulb bankruptcy: energy dynamics in Eucomis autumnalis, a South African mesic grassland geophyte

Intense grazing and trampling by livestock reduce forb populations in South African mesic grasslands by limiting photosynthesis, thereby depleting carbohydrate reserves in underground storage organs (USOs) required for persistence. The effects of simulated herbivory on above- and below-ground growth, bulb starch reserves, and water content in the bulbous geophyte, Eucomis autumnalis, were assessed over a 468-day pot experiment, with seasonal dynamics described using Generalised Additive Models. Four intense summer and autumn defoliations reduced seasonally integrated above-ground dry matter (-83.7%), bulb mass (-51.7%), starch concentration (-32.3%), total starch pool (-68.9%), and bulb water pool (-35.1%), while increasing bulb water content (+29.4%) relative to controls. Bulb growth and starch pools (bulb mass x starch concentration) were most strongly suppressed during late summer and autumn, when control plants increased bulb mass and replenished starch reserves. Repeated defoliation forced plants to divert assimilates to regrowth, disrupting seasonal source-sink dynamics and driving progressive depletion of reserves; bulbs were consequently pushed towards energetic bankruptcy, potentially unable to sustain future growth and persistence under chronic grazing. These findings highlight the need to avoid high stocking densities, protect plants from intense autumn grazing, and provide periodic full-year recovery rests to conserve geophytic forbs in mesic grasslands.

ecology↗

bioRxiv2026

Condensate-Like Organization in Respiratory Aerosols Modulates the Dynamics of an Airborne Virus

The molecular behavior of viruses within respiratory aerosols plays a critical role in airborne disease transmission yet remains largely inaccessible to experimental characterization. Here, we use a billion-atom all-atom molecular dynamics simulation of a virus-laden respiratory aerosol to uncover how respiratory proteins, lipids, ions, and water collectively assemble around SARS-CoV-2, giving rise to structured microenvironments that influence viral stability and spike dynamics. We find that respiratory components rapidly evolve into heterogeneous networks characterized by protein-rich aggregates, patchy lipid assemblies, and spatially structured ion and water dynamics. These features create distinct microenvironments that constrain molecular transport and stabilize regions surrounding the virion. Within this crowded aerosol context, we observe sustained and selective interactions between aerosol components and the viral spike protein, including preferential recruitment of surfactant lipids and persistent coordination by divalent cations. These interactions modulate spike conformational dynamics, enhancing domain breathing motions and flexibility at key hinge regions while preserving a stable membrane anchor. Together, these observations reveal a condensate-like physical regime in which multivalent aerosol components coalesce into a soft, heterogeneous matrix that selectively modulates viral protein dynamics under extreme crowding. By framing virus-laden respiratory aerosols within this physical context, this work establishes an in situ molecular framework for understanding how aerosols influence viral persistence and offers a platform for exploring mechanisms relevant to airborne disease transmission and mitigation strategies. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/721971v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@4d0f60org.highwire.dtl.DTLVardef@12c9d1forg.highwire.dtl.DTLVardef@1ff6c29org.highwire.dtl.DTLVardef@15feec_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisRespiratory aerosols exhibit condensate-like physical properties that govern the evolution of the particle and modulate the behavior of airborne SARS-CoV-2.

biophysics↗

bioRxiv2026

Poly(acrylamido) PEG-alternatives Enhance mRNA-LNP Efficacy in Immune Cells and Evade anti-PEG Antibodies During Repeated Dosing

Following the successes of the messenger RNA (mRNA) lipid nanoparticle (LNP) vaccines during the COVID-19 pandemic, mRNA-LNPs are being explored for many critical disease indications including infectious disease vaccination, cancer immunotherapies, and protein replacement therapies. LNPs require a polymer coating to provide stability in storage, and to minimise clearance from the body by reducing protein adsorption after injection. Poly(ethylene glycol)-lipids (PEG-lipids) have fulfilled this role to date, however increasing prevalence of antibodies against PEG in the general population jeopardises the efficacy of future PEGylated LNP doses and increases the likelihood of adverse pseudo-allergic responses. There is, therefore, an urgent unmet need to develop LNPs with new surfaces of PEG-alternative polymers which can evade anti-PEG antibodies, particularly where repeat dosing is required. Here, we present a family of polymer lipids, poly(acrylamido) (PAM) lipids, which effectively replace conventional PEG-lipids in mRNA-LNP formulations. We identify key design parameters to show that PAM-lipid monomer chemistry, molar mass and end-group all have critical effects on LNP size, polydispersity and in vitro transfection efficiencies, while having little impact on LNP morphology or internal structure. We determine that side-group (monomer) chemistry is a key mediator in alleviating anti-polymer antibody cross-reactivity. Compared to clinical benchmark PEGylated LNPs, several PAM-LNPs displayed improved transfection efficacy across multiple mRNA cargos in diverse cell types, organs, and routes of administration, both in vitro and in vivo. In particular, mRNA transfection improved in immune cells both in vitro (up-to 120-fold), and in vivo (up-to 5-fold), including superior mRNA expression in lymph nodes (2.5-fold). In part, this is likely because PAMs increase LNP uptake/association with primary immune cells (BMDCs), and increase biodistribution to the lymphoid tissues (LNs, spleen). Crucially, PAM-LNPs avoid circulating anti-PEG antibodies to recover lost mRNA efficacy after repeated dosing in vivo, 300% higher than PEG-LNPs. Overall, our findings establish the PAM-lipid family as a versatile platform of chemically varied PEG-alternatives, towards the next generation of therapeutic mRNA-LNP technologies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/708093v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@107de1aorg.highwire.dtl.DTLVardef@186b6eforg.highwire.dtl.DTLVardef@1542371org.highwire.dtl.DTLVardef@e2d47f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Loss of dispersal via ice nucleation activity constrains microbial evolution

The ability to disperse over long distances through the atmosphere is a common trait across the tree of life, facilitating resource access and increasing long-range gene flow. Loss of dispersal mechanisms, viz. flight, can occur in animals found on islands where documented phenotypic changes like loss of wingspan impedes longer distance travel to mate with the metapopulation. Bacteria also experience atmospheric flight and descend via bioprecipitation by catalyzing the freezing of cloud droplets with protein InaZ. InaZ triggers ice nucleation at temperatures near 0{circ}C(1). This ice nucleation activity (INA), a biophysical trait, enhances bacterial deposition through precipitation. The role of InaZ-mediated ice nucleation on bacterial dispersal is well documented, but the impact of loss of INA and thus reduction or loss of atmospheric dispersal on bacterial ecology and evolution has not been described. Here we show that the loss of the ancestral inaZ gene restricts bacterial dispersal and leads to significant genetic and ecological isolation across multiple genera. Through the analysis of available complete genomes, we demonstrate that lineages lacking functional inaZ experience major gene loss events, reduced recombination rates and a marked dependence on human-mediated or insect transmission. These INA-lacking bacteria exhibit an increased ecological signature of isolation that parallels the distribution of geographically isolated animals. Our results establish InaZ as a keystone biophysical trait that defines microbial dispersal strategies. We anticipate these findings will provide a framework for understanding how shifts in biophysical traits drive niche differentiation and changes in dispersal with downstream consequences for Earth system processes. Significance StatementSome microorganisms catalyze freezing of cloud droplets near 0{degrees}C via ice nucleation activity (INA) enhancing their deposition. We determined that loss of the gene encoding the INA protein in Gammaproteobacteria restricts bacterial dispersal. Bacteria that lost this ancestral trait compared to relatives with INA experienced distinct, major gene loss events, altered gene flow and marked dependence on transmission by plant tissues or insects and an increased ecological signature of isolation paralleling the geographically isolated plants and animals. We posit that gene loss for biophysical traits such as INA is a keystone example of the consequences of a biological trait defining microbial dispersal.

evolutionary biology↗

bioRxiv2026

Viral Infections Drive Functional Remodeling of Ribosome-Associated Proteins

Viruses hijack host ribosomes to synthesize their proteins and have evolved various strategies to manipulate translation, including the association of numerous non-ribosomal proteins, known as ribosome-associated proteins (RAPs), with the core ribosome. However, current methods of capturing RAPs that associate transiently and/or in small amounts with ribosomes are suboptimal. To address this issue, we developed an enhanced ribosome affinity purification (eRAP) method that enables the capture of over 500 previously unreported RAPs. Using eRAP, we investigated whether the composition of ribosomes changes during infection by two very different viruses: herpes simplex virus 1 (HSV-1) and Sindbis virus (SINV). Our results revealed that viral infection does not substantially alter the composition of core ribosomes but does drive extensive remodeling of RAPs in a virus-specific manner. Functional analyses with SINV showed that several of these RAPs are critical for viral propagation. Additionally, we discovered that the RAP ASCC3 plays a novel role in promoting the expression of secretory proteins, including viral glycoproteins. This occurs independently of ASCC3s canonical function of rescuing ribosome collisions. Together, our findings establish the ribosome as a dynamic regulatory hub that undergoes remodeling to achieve virus-specific translational output, highlighting the functional significance of ribosomal heterogeneity.

molecular biology↗

bioRxiv2025

Seventy-five years of insight: the impact of the Ukulinga very long-term grassland experiments

Two of the worlds oldest grassland experiments began in 1950-51 in Pietermaritzburg, South Africa. The Burning and Mowing Trial (BMT) tests how summer mowing and dormant-season burning or mowing regimes affect mesic grassland. The Veld Fertiliser Trial (VFT) examines how nitrogen, phosphorus fertilisers and lime influence grassland productivity, composition, and diversity. Seventy-five years later, their impact was assessed through research output and value for education and networking. All published papers and their citations were identified, with key themes, leading authors, and citation patterns of the top ten papers from each trial analysed. A total of 25 and 24 peer-reviewed papers, cited 1,652 times, have been published from the BMT and VFT, respectively, with publication rates rising since 2000. Studies addressed treatment effects on soil, plants, invertebrates, microbes, regional comparisons, and remote sensing. South Africans led authorship, with strong USA participation, and the top-10 papers reached a wide multinational audience. The Ukulinga LTEs demonstrated the vital role of regular burning or mowing, revealed how fertilisers can negatively impact grassland, and highlighted the importance of treatment interactions in shaping ecosystem dynamics. As key sites for research collaboration and education, they should be maintained long-term to advance understanding and address new questions.

ecology↗

bioRxiv2025

G-Quadruplexes Act as an On/Off Switch While i-Motifs Regulate Insulin Expression in Reporter Gene Assays

The insulin-linked polymorphic region (ILPR) is a variable number tandem repeat located in the promoter of the human insulin gene. This G-rich sequence can fold into four-stranded G-quadruplex DNA structures, while its complementary C-rich strand forms i-motifs. The ILPR varies in repeat number and sequence composition, but the relationship between sequence diversity, DNA structure, and insulin gene regulation remains poorly understood. Although both G-quadruplexes and i-motifs have been implicated in transcriptional control, their relative contributions, particularly when formed on complementary strands of the same locus, are unclear. Here, we characterised the structure and stability of nine ILPR-based sequences using biophysical techniques and luciferase reporter assays. We demonstrate that transcriptional activation in response to high glucose occurs only when both G-quadruplex and i-motif structures can form. Other combinations of structures do not induce transcription. Moreover, promoter activity correlated positively with i-motif stability, but not with G-quadruplex stability. These results suggest a model in which G-quadruplexes function as an on/off switch, while i-motifs act as modulators of gene expression. Our findings underscore the importance of treating G-quadruplexes and i-motifs as a dynamic, interdependent system in both the regulation of gene expression and also the potential of these structures as therapeutic targets. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/651924v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@16ae322org.highwire.dtl.DTLVardef@65e893org.highwire.dtl.DTLVardef@884ab3org.highwire.dtl.DTLVardef@1e0311e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Regulatory interactions between APOBEC3B N- and C-terminal domains

APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) active site is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared dynamics of the truncated (A3Bctd) to the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD-CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics of fl-A3B, which may offer new avenues for therapeutic intervention in cancer.

biophysics↗

bioRxiv2024

Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening

The APOBEC3 (A3) family of enzymes are zinc metalloenzymes that catalyze the conversion of 2'- deoxycytidine to 2'-deoxyuridine in single stranded DNA. APOBEC3B (A3B), a member of the A3 family, has emerged as a key driver of genomic instability in many cancer types by mutating host DNA to drive tumorigenesis and therapy resistance. Small molecule inhibitors of A3B would extend the durability of current therapies by limiting mutations that promote tumor escape and therapy resistance. Consequently, a computer aided drug discovery (CADD) campaign was employed to identify inhibitors of A3B. Through molecular dynamics (MD) simulations and computational solvent mapping analysis, we identified a novel putative allosteric pocket on the c-terminal domain of A3B and virtually screened the ChemBridge Diversity Set ([~]110,000 small molecules) against both the active and predicted allosteric sites. High scoring compounds were selected for in vitro testing and triage, resulting in 13 candidate inhibitors. Using cysteine reactive probes, one of the original hit compounds was mapped to the computationally identified allosteric pocket. However, after resynthesis of representative chemotypes and further investigation using in vitro assays, none of the chemotypes retained inhibitory activity. Further analysis revealed that most of the inhibition observed in the primary assay was due to metal contamination in the screening sample, which resulted in the removal of the catalytic zinc from the enzyme active site. Although validated A3B inhibitors were not discovered in this study, we report a ligandable allosteric site on A3B and several cautionary insights for researchers developing small molecule inhibitors of zinc metalloenzymes. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/591187v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@b7e577org.highwire.dtl.DTLVardef@13a1a43org.highwire.dtl.DTLVardef@192309eorg.highwire.dtl.DTLVardef@b60a31_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

CCQM-P199: Interlaboratory comparability study of HIV-1 RNA copy number quantification

Infection with human immunodeficiency virus (HIV)-1 leads to acquired immunodeficiency syndrome (AIDS) if left untreated. According to UN figures, approximately 39 million people globally were living with HIV in 2022, with 76% of those individuals accessing antiretroviral therapy. Measurement of plasma viral RNA load using calibrated nucleic acid amplification tests (like reverse transcription quantitative PCR, RT-qPCR) is routinely performed to monitor response to treatment and ultimately prevent viral transmission. RNA quantities measured by commercial tests can vary over many orders of magnitude, from trace single copy levels to, in cases, over 109 /mL of plasma, presenting an analytical challenge for calibrating across a broad measurement range. Interlaboratory study CCQM-P199 "HIV-1 RNA copy number quantification" (April to September 2019) was conducted under the auspices of the Consultative Committee for Amount of Substance (CCQM) Nucleic Acid analysis Working Group (NAWG), with the aims of supporting national metrology institutes (NMIs) and designated institutes (DIs) development of the capacity and evaluating candidate reference measurement procedures for applied viral nucleic acid measurements. Thirteen laboratories participated in CCQM-P199 and were requested to report the RNA copy number concentration, expressed in copies per microliter, of the HIV-1 group specific antigen (gag) gene of in vitro transcribed RNA molecules at low ({approx} 103 /L) and high concentration ({approx} 109 /L) (Study Materials 1 and 2, linked by gravimetric dilution) and purified genomic RNA from cultured virus (Study Material 3). Study Materials 1 and 3 were measured by participants using one-step reverse transcription digital PCR (RT-dPCR) (Bio-Rad reagents) and/or two-step RT-dPCR with alternative cDNA synthesis reagents. Study Material 2 was measured by both RT-dPCR (one-step) (n = 4) and orthogonal methods: single molecule flow cytometric counting (n = 2), high performance liquid chromatograph (HPLC) (n = 1) and isotype dilution-mass spectrometry (ID-MS) (n = 1). Interlaboratory reproducibilities (expressed as %CV) were 21.4 %, 15.3 % and 22.0 % for Study Materials 1, 2 and 3 respectively. Analysis of overdispersion showed that the interlaboratory variation for all three Study Materials was not accounted for in their reported uncertainties, indicating uncharacterized sources of variation remain. Although the mean values of RT-dPCR and orthogonal method results were not statistically significantly different (p = 0.46), the extrapolated mean Study Material 2 results were higher than mean Study Material 1 results (1196 vs. 808 /L; p < 0.05). Follow-up analysis of Study Material 2 purity by ultra-performance liquid chromatography (UPLC) indicated higher molecular weight (MW) impurities constituted 16.6 % of the molecules, which are hypothesised to be the cause of the HPLC and ID-MS results being higher than the majority of Study Material 1 and 2 results. This study demonstrates that reproducible measurement of RNA templates was achieved by metrology laboratories, illustrating the potential of RT-dPCR combined with complimentary orthogonal approaches to support traceability and precision of contemporary methods for RNA quantification. This study also highlighted that detailed characterization of RNA materials and sources of bias affecting measurements such as RT efficiency is needed to further establish RT-dPCR as a primary reference measurement procedure for RNA copy number quantification.

molecular biology↗

bioRxiv2024

CCQM-P199b: Interlaboratory comparability study of SARS-CoV-2 RNA copy number quantification

Nucleic acid amplification tests including reverse transcription quantitative PCR (RT-qPCR) are used to detect RNA from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Standardized measurements of RNA can facilitate comparable performance of laboratory tests in the absence of existing reference measurement systems early on in a pandemic. Interlaboratory study CCQM P199b "SARS-CoV-2 RNA copy number quantification" was designed to test the fitness-for-purpose of developed candidate reference measurement procedures (RMPs) for SARS-CoV-2 genomic targets in purified RNA materials, and was conducted under the auspices of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM) to evaluate the measurement comparability of national metrology institutes (NMIs) and designated institutes (DIs), thereby supporting international standardization. Twenty-one laboratories participated in CCQM P199b and were requested to report the RNA copy number concentration, expressed in number of copies per microliter, of the SARS-CoV-2 nucleocapsid (N) gene partial region (NC_045512.2: 28274-29239) and envelope (E) gene (NC_045512.2: 26245-26472) (optional measurements) in samples consisting of in vitro transcribed RNA or purified RNA from lentiviral constructs. Materials were provided in two categories: lower concentration ({approx} (101-104) /L in aqueous solution containing human RNA background) and high concentration ({approx} 109 /L in aqueous solution without any other RNA background). For the measurement of N gene concentration in the lower concentration study materials, the majority of laboratories (n = 17) used one-step reverse transcription-digital PCR (RT-dPCR), with three laboratories applying two-step RT-dPCR and one laboratory RT-qPCR. Sixteen laboratories submitted results for E gene concentration. Reproducibility (% CV or equivalent) for RT-dPCR ranged from 19 % to 31 %. Measurements of the high concentration study material by orthogonal methods (isotope dilution-mass spectrometry and single molecule flow cytometry) and a gravimetrically linked lower concentration material were in a good agreement, suggesting a lack of overall bias in RT-dPCR measurements. However methodological factors such as primer and probe (assay) sequences, RT-dPCR reagents and dPCR partition volume were found to be potential sources of interlaboratory variation which need to be controlled when applying this technique. This study demonstrates that the accuracy of RT-dPCR is fit-for-purpose as a RMP for viral RNA target quantification in purified RNA materials and highlights where metrological approaches such as the use of in vitro transcribed controls, orthogonal methods and measurement uncertainty evaluation can support standardization of molecular methods.

molecular biology↗

bioRxiv2023

A paper based microfluidic platform combining LAMP-CRISPR/Cas12a for fluorometric detection of nucleic acids

Nucleic acid isothermal amplification methods are advantageous for point-of-care (POC) diagnostics because of their precision, sensitivity, and low power requirements. Loop-mediated isothermal amplification (LAMP) is an established method, renowned for its nucleic acid amplification efficiency and robust amplification of semi purified target nucleic acids. However, LAMP may be prone to non-specific amplification causing false positives and therefore fails to replace PCR as the gold standard method in clinical testing. We show that LAMP combined with clustered regularly interspaced short palindromic repeats (CRISPR) technology is an effective alternative for overcoming the limitations of LAMP alone. Nucleic acids are first isothermally pre-amplified to enrich for targets, then specific amplification detection signals are generated by sequences of RNA guided recognition of amplicons. We are the first to demonstrate a paper based microfluidic system for detecting pathogen nucleic acids in samples by combining the power of LAMP and CRISPR technology. We show that although LAMP may produce non-specific amplification, the possibility of detecting a false positive can be eliminated by combining LAMP with CRISPR based detection. We demonstrate that a paper based microfluidic platform has the potential to compete with the conventional Nucleic acid testing (NAT) technologies not only in terms of robustness but also in terms of cost and complexity.

bioengineering↗

bioRxiv2022

Associative nitrogen fixation could be common in South African mesic grassland

Non-symbiotic nitrogen-fixing bacterial diazotrophs closely associated with the roots of grasses probably contribute most of the new nitrogen acquired to sustain productive natural grasslands, yet their ecology is poorly understood, especially in southern Africa. We looked for genetic evidence, using qPCR and gel electrophoresis, for the presence of the bacterial nifH gene associated with the roots of four grass species (20 plants each) in a mesic grassland in South Arica, which would indicate the potential for N fixation by diazotrophs. Grasses most tolerant of low N (Aristida junciformis) were predicted to harbour the most diazotrophs, especially compared to those most responsive to fertiliser N (Eragrostis curvula). However, the nifH gene was found in all 80 root samples and did not differ in copy number between species. Sequencing of a representative sample confirmed the identity of the nifH gene. The recently burned half of the grassland had 60% more nifH genes than the area burned 15 months previously, suggesting that grass growth stimulated by fire could recruit diazotrophs. Given their ubiquity and importance in the N economy of grasslands, research is required to characterise root-associated diazotroph communities, quantify their N fixation rates, and understand their environmental controls.

ecology↗

bioRxiv2022

Will The Grass Be Greener On The Other Side Of Climate Change?

Increasing atmospheric [CO2] is stimulating photosynthesis and plant production, increasing the demand for nitrogen relative to soil supply with declining global foliar nitrogen concentrations as a consequence. The effect of such oligotrophication on the forage quality of sweetveld, mixedveld, and sourveld grasslands in South Africa, which support livestock production and native ungulates, are unknown. Soil characteristics and the herbage quality of an abundant grass are described from baseline historical (mid 1980s) data collected across a sweet-mixed-sour grassland gradient in KwaZulu-Natal. Sourveld occurred on the most acidic, dystrophic soils and exhibited a pronounced decline in leaf N, digestibility, and other macronutrients during winter, in sharp contrast to sweetveld, on nutrient-rich soils, where forage quality varied little seasonally. In a carbon enriched, warmer, and most likely drier future climate, we predict that forage quality will be little altered in sweetveld where soil nutrients and temperature are not limiting but that sourveld could become sourer because soil nutrients will be inadequate to match higher plant production promoted by elevated [CO2] and warmer and longer growing seasons. Reassessing historical data and seasonal and spatial monitoring of forage quality will enable past and future impacts of climate change on grassland forage quality to be assessed. SignificanceO_LIGrassland forage quality will likely decline with elevated [CO2] and warming, particularly in sourveld. C_LIO_LIClimate change could deepen and widen the sourveld winter forage bottleneck, necessitating greater supplementary feeding of livestock. C_LI

ecology↗

bioRxiv2022

Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control

Waste from dairy production is one of the worlds largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs). However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with >99% reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for prevalence and control of AMR, and that measures to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.

microbiology↗

bioRxiv2021

Vascular proteome responses precede organ dysfunction in sepsis

Vascular dysfunction and organ failure are two distinct, albeit highly interconnected clinical outcomes linked to morbidity and mortality in human sepsis. The mechanisms driving vascular and parenchymal damage are dynamic and display significant molecular crosstalk between organs and tissues. Therefore, assessing their individual contribution to disease progression is technically challenging. Here, we hypothesize that dysregulated vascular responses predispose the organism to organ failure. To address this hypothesis, we have evaluated four major organs in a murine model of S. aureus sepsis by combining in vivo labeling of the endothelial proteome, data-independent acquisition (DIA) mass spectrometry, and an integrative computational pipeline. The data reveal, with unprecedented depth and throughput, that a septic insult evokes organ-specific proteome responses that are highly compartmentalized, synchronously coordinated, and significantly correlated with the progression of the disease. Vascular proteome changes were found to precede bacterial invasion and leukocyte infiltration into the organs, as well as to precede changes in various well-established cellular and biochemical correlates of systemic coagulopathy and tissue dysfunction. Importantly, our data suggests a potential role for the vascular proteome as a determinant of the susceptibility of the organs to undergo failure during sepsis.

immunology↗