Biology subjects

Collins, K.

Publications and source records attributed to Collins, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Senescent tenocytes drive an age-associated loss of cell-extracellular matrix homeostasis, which can be partially restored using dihydroresveratrol

Tendons are commonly injured, not only in athletes, but also during normal everyday activities, particularly in older age. Tendons are rich in extracellular matrix proteins, many of which are turned over extremely slowly during an individuals lifetime. As a result, tight regulation of the extracellular matrix is essential for tendons to remain resilient to the mechanical load placed on them. However, tendons are prone to age-associated functional decline, characterised by chronic inflammation, accumulation of damaged collagen, and matrix remodelling. These degenerative changes often precede injury, wherein additional inflammation and fibrotic tissue deposition make treatment difficult and reinjury highly likely. Understanding and preventing the causes of tendon functional decline is therefore vital to improving quality of life in the ageing population. Using an equine model, here we show that tendon fibroblasts, or tenocytes, isolated from aged tendons exhibit markers of senescence when cultured in vitro. Further, we describe how senescence in tenocytes drives inflammation, hypercontractility, and dysregulation of tendon matrix components. By replicatively senescing tenocytes isolated from young tendons, we observed that senescent tenocytes instigated proinflammatory signalling, had impaired capacity in wound healing assays, increased contractility, and secreted factors that induced senescence in healthy tenocytes. Further, tenocyte senescence dysregulated matrix turnover both at the gene and protein level. Finally, we demonstrate how senotherapeutic treatment of senescent tenocytes can reduce expression of senescence markers and restore proliferative capacity. Our results uncover systemic links between tendon ageing and cellular senescence, and identify mechanisms and therapeutic strategies for age-associated tendon degeneration.

cell biology↗

bioRxiv2026

OTTR-CLASH: improved biochemical and bioinformatic identification of Argonaute 2-mediated microRNA-target RNA interactions

Various methods have detected miRNA-target interactions via immunoprecipitation of UV-crosslinked Argonaute ribonucleoprotein complexes, followed by intermolecular ligation of bound miRNAs to target strands, forming chimeric RNAs. To date, these methods have relied on conventional viral reverse transcriptases (RTs) to generate cDNAs for sequencing. However, crosslinked RNAs often retain adducts after purification, which can make them poor templates for viral RTs. Here, we adapted OTTR (Ordered Two-Template Relay) techniques to generate cDNAs from Ago2-bound RNAs. OTTR makes use of a modified retroelement-encoded RT, which is strongly processive even on templates with modifications or adducts. We show that this "OTTR-CLASH" method increases the frequency of generating chimeric RNAs compared to previous methods. We also developed an improved bioinformatic pipeline for analysis of these data, and we use this to catalog miRNA-target interactions not previously described in the literature. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/738487v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@16d62f8org.highwire.dtl.DTLVardef@7c8da4org.highwire.dtl.DTLVardef@13727fborg.highwire.dtl.DTLVardef@21f443_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

A versatile method to pattern surfaces within microfluidic devices

Microfluidic devices with surface-bound biomolecular patterns enable localised detection arrays, enzymatic catalysis, and gene expression. Photolithography is a well-established method to pattern open surfaces with high spatial control. However, patterning enclosed microfluidic channels remains technically challenging. Such capability would enable in situ surface modification and precise pattern alignment to channel geometries. Here, we present a photolithographic method using commercially available reagents to pattern sealed microfluidic devices. We first coat surfaces with (3-Aminopropyl)triethoxysilane (APTES) to bond microfluidic chips and provide surface amine groups onto which photocleavable polyethylene glycol (PC PEG) compounds are bound. UV exposure using standard photolithography equipment selectively deprotects the amine groups, which can subsequently bind amine-reactive cargos. We demonstrate the versatility of this method by patterning both poly(dimethylsiloxane) (PDMS) and glass surfaces with diverse cargoes: DNA, proteins, and gold nanoparticles. We also compare covalent versus noncovalent DNA patterning. Covalently bound DNA patterns are denser and could be used for sequence-specific target DNA capture. However, noncovalently bound DNA yielded higher cell-free gene expression from surface-bound GFP templates.

systems biology↗

bioRxiv2026

Intricate asymbiotic hyphal interactions of Rhizophagus irregularis revealed with single-plane observations in a new microfluidic device

Arbuscular mycorrhizal fungi (AMF) are essential symbionts to most land plants. There is great interest in using AMF inoculation treatments to enhance restoration or agricultural efforts. However, little is known about AMF asymbiotic interactions that could shape soil ecosystems and inoculation outcomes. Studying these early traits is challenging given the obligate nature of AMF. Microfluidic devices enable high-resolution, single-plane, time-resolved observation of AMF hyphal traits in controlled, plant-less environments. The AMF-AnastomosisChip, introduced in this work, additionally separates spores and hyphae into lanes for detailed observations prior to entering a shared interaction zone. Using this device with Rhizophagus irregularis, we phenotyped key hyphal traits from germination to anastomosis. We compared the effect of a fatty acid (FA) treatment to other environmental factors in shaping AMF growth and fusion (anastomosis). Among our results, we confirm known effects of the FA treatment in increasing hyphal branching and longevity but interestingly show that multiple hyphae in a lane can negate FA effects. We also newly reveal that anastomosis occurs for 100% of interactions among hyphae from different lanes, but only for 50% of in-lane interactions, potentially linked to spore origin. Our findings validate the AMF-AnastomosisChip as a versatile platform for increasing discovery in trait-based microbial ecology, including for asymbiotic AMF interactions with environmental factors. This work sets the foundation for future studies with the AMF-AnastomosisChip on the effects of nutrient content, plant-derived molecules, or microbial community members on the AMF traits characterized in this study.

microbiology↗

bioRxiv2025

Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies

All eukaryotic cells secrete exosomes, a type of extracellular vesicles (EVs) derived from the endocytic compartments known as multivesicular bodies (MVBs), or late endosomes (LEs). Exosomes contain a diverse range of cargo such as nucleic acids, proteins, lipids and small molecules but whether these contents have a biological function remains an area of intense investigation. Over the last decade, numerous studies have described the transcriptome of exosomes but very little is known about the RNA content of the MVBs, the source compartment for exosome biogenesis. Here we determine the small-RNA transcriptome of highly purified MVBs and report that various classes of nuclear small regulatory RNAs such as small-Cajal body associated RNAs (scaRNAs), small-nucleolar RNAs (snoRNAs) and small-nuclear RNAs (snRNAs) traffic to MVBs. We show that this RNA-trafficking requires the function of ESCRT machinery but is independent of canonical LC3 lipidation mediated selective autophagy. Furthermore, blocking the activity of a PI3K Class 3 enzyme, VPS34, required for recruitment of the ESCRT machinery to the endosome, prevents the turnover of these nuclear RNAs in MVBs. Our results provide a mechanism for targeting nuclear ribonucleoprotein complexes (RNPs), such as Cajal bodies, for degradation and turnover by the cytoplasmic endo-lysosomal pathway. Significance StatementEndosomes are cytoplasmic, membrane-bound subcellular organelles that are sites for biogenesis of exosomes, a class of extracellular vesicles, thought to mediate intercellular communication via their packaged cargo such as RNA. Previous studies have focused on the transcriptome of exosomes however very little is known about the identity of RNAs and mechanisms by which they are sorted into endosomes. Here we report a comprehensive endosome transcriptome and provide evidence that several nuclear RNA-protein complexes (RNPs) sort into endosomes, a previously unappreciated phenomenon. We show that this process requires the activity of endosomal sorting complexes and phospholipids characteristic of cellular endocytic compartments. Our study provides a mechanism for recycling and disposal of unwanted nuclear RNPs by the cytoplasmic endolysosomal pathway.

biochemistry↗

bioRxiv2025

Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals

Retrotransposons play outsized roles in the evolution of gene regulation, genome function, and disease pathogenesis and more recently, have sparked interest as workhorses for new gene therapy approaches. R2 retrotransposons insert site-specifically to the multicopy genes encoding 28S ribosomal RNA at a target sequence conserved broadly across eukaryotic evolution. R2 retrotransposons have been detected in many animals, but previous surveys have been limited in scope and methodology. Here, we substantially expand the known distribution of R2 retrotransposons from previously unrepresented or underrepresented taxonomic groups ranging from ctenophores to amphibians and reptiles. We discover diverse R2 domain architectures and motifs and identify many new avian R2 candidates for genome engineering development. Overall, phylogenetic analyses reveal two highly successful R2 lineages. We observe properties of each lineage in several features of the domains that mediate DNA recognition and in co-evolving signatures within the reverse transcriptase domain. Within each of the two lineages, R2 protein sequences do not necessarily preserve the unifying configuration of N-terminal DNA-binding domains implied in the current clade classification scheme. We show that recombinant R2 proteins with distinctive domain architectures and distribution across major animal classes support target-primed reverse transcription with conserved site specificity. Our analysis of the surprisingly varied domain architectures that support target-site specificity informs new R2 classification criteria and provides a greatly expanded foundation for additional structure/function insights about DNA binding selectivity. This expanded perspective on R2 evolution informs approaches for engineering therapeutic gene insertion technologies and offers an opportunity to investigate the conservation and diversification of retrotransposons.

evolutionary biology↗

bioRxiv2025

Managing populations after a disease outbreak: exploration of epidemiological consequences of managed host reintroduction following disease-driven host decline

Disease outbreaks in wild populations around the globe can lead to widespread mortality within populations, where recovery of individuals can be rare. An example of this population is the sunflower sea star Pyc-nopodia helianthioides in the Northeastern Pacific coast. The populations of this species, as well as many other sea star populations, have experienced massive mortality events due to an unidentified disease called Sea Star Wasting Disease (SSWD). Pycnopodia play a key role in providing top-down control of kelp grazers in rocky reefs across the Northeastern Pacific coast. This, combined with the massive declines in kelp coverage observed during the 2015-2016 marine heat wave observed in the Northeastern Pacific, has sparked an interest in reintroducing Pycnopodia individuals in the coast to potentially assist in recovery of the populations. However, the epidemiological implications of reintroducing healthy sea stars into the wild populations is an under-explored question. This work explores this question using a dynamical population model of Pycnopodia. We use this model to estimate the impacts of reintroducing healthy individuals into a wild sea star population. This analysis will provide valuable information for managers interested in restoring Pycnopodia populations.

ecology↗

bioRxiv2025

Sequencing by Expansion (SBX) -- a novel, high-throughput single-molecule sequencing technology

Remarkable advances in high-throughput sequencing have enabled major biological discoveries and clinical applications, but achieving wider distribution and use depends critically on further improvements in scale and cost reduction. Nanopore sequencing has long held the promise for such progress, but has had limited market penetration. This is because efficient and accurate nanopore sequencing of nucleic acids has been challenged by fundamental signal-to-noise limitations resulting from the poor spatial resolution and molecular distinction of nucleobases. Here, we describe Sequencing by Expansion (SBX), a single-molecule sequencing technology that overcomes these limitations by using a biochemical conversion process to encode the sequence of a target nucleic acid molecule into an Xpandomer, a highly measurable surrogate polymer. Expanding over 50 times longer than the parent DNA templates, Xpandomers are engineered with high signal-to-noise reporter codes to enable facile, high-accuracy nanopore sequencing. We demonstrate the performance of SBX and present the specialized molecular structures, chemistries, enzymes and methods that enable it. The innovative molecular and systems engineering in SBX create a transformative technology to address the needs of existing and emerging sequencing applications.

genomics↗

bioRxiv2025

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree.

genomics↗

bioRxiv2024

Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second strand nicking

R2 retrotransposons are model site-specific eukaryotic non-LTR retrotransposons that copy-and-paste into gene loci encoding ribosomal RNAs. Recently we demonstrated that avian A-clade R2 proteins achieve efficient and precise insertion of transgenes into their native safe-harbor loci in human cells. The features of A-clade R2 proteins that support gene insertion are not characterized. Here, we report high resolution cryo-electron microscopy structures of two vertebrate A-clade R2 proteins, avian and testudine, at the initiation of target-primed reverse transcription and one structure after cDNA synthesis and second strand nicking. Using biochemical and cellular assays we discover the basis for high selectivity of template use and unique roles for each of the expanded A-clade zinc-finger domains in nucleic acid recognition. Reverse transcriptase active site architecture is reinforced by an unanticipated insertion motif in vertebrate A-clade R2 proteins. Our work brings first insights to A-clade R2 protein structure during gene insertion and enables further improvement and adaptation of R2-based systems for precise transgene insertion.

biochemistry↗

bioRxiv2024

Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing

Sequencing RNAs that are biologically processed or degraded to less than [~]100 nucleotides typically involves multi-step, low-yield protocols with bias and information loss inherent to ligation and/or polynucleotide tailing. We recently introduced Ordered Two-Template Relay (OTTR), a method that captures obligatorily end-to-end sequences of input molecules and, in the same reverse transcription step, also appends 5' and 3' sequencing adapters of choice. OTTR has been thoroughly benchmarked for optimal production of microRNA, tRNA and tRNA fragments, and ribosome-protected mRNA footprint libraries. Here we sought to characterize, quantify, and ameliorate any remaining bias or imprecision in the end-to-end capture of RNA sequences. We introduce new metrics for the evaluation of sequence capture and use them to optimize reaction buffers, reverse transcriptase sequence, adapter oligonucleotides, and overall workflow. Modifications of the reverse transcriptase and adapter oligonucleotides increased the 3' and 5' end-precision of sequence capture and minimized overall library bias. Improvements in recombinant expression and purification of the truncated Bombyx mori R2 reverse transcriptase used in OTTR reduced non-productive sequencing reads by minimizing bacterial nucleic acids that compete with low-input RNA molecules for cDNA synthesis, such that with miRNA input of 3 picograms (less than 1 fmol), fewer than 10% of sequencing reads are bacterial nucleic acid contaminants. We also introduce a rapid, automation-compatible OTTR protocol that enables gel-free, length-agnostic enrichment of cDNA duplexes from unwanted adapter-only side products. Overall, this work informs considerations for unbiased end-to-end capture and annotation of RNAs independent of their sequence, structure, or post-transcriptional modifications.

biochemistry↗

bioRxiv2024

Prebiotic Supplementation Modulates the Gut Microbiome for Improving Oral Antipsychotic Bioavailability

Atypical antipsychotics are crucial for the management of schizophrenia and bipolar disorder, yet they exhibit significant pharmacokinetic variability which leads to inconsistent therapeutic responses. This study investigates the hypothesis that gut microbiome composition critically influences the oral bioavailability of lurasidone, a poorly soluble weak base antipsychotic with pH-dependent solubility. To investigate this, male Sprague-Dawley rats underwent systematic gut microbiome manipulation through pretreatment with antibiotics or prebiotics (inulin) for 14 days prior to a single oral dose of lurasidone. Pharmacokinetic analysis of collected plasma samples revealed a significant 4.3-fold increase in lurasidone bioavailability following prebiotic pretreatment, compared to a control (no pretreatment) group. Conversely, lurasidone bioavailability was highly variable in rats with a depleted microbiome (i.e., antibiotic treatment group), with 80% of animals demonstrating lower bioavailability than the control group. Characterisation of gut microbiome composition and short-chain fatty acid (SCFA) concentrations demonstrated positive correlations between lurasidone bioavailability, microbial diversity, and SCFA levels, mediated by modulation of luminal pH. Elevated SCFA levels created a favourable environment for lurasidone solubilisation by lowering intestinal pH. These findings highlight the potential for optimising antipsychotic pharmacokinetics through personalised microbiome interventions. Furthermore, the correlation between SCFAs and lurasidone bioavailability suggests their potential as biomarkers for predicting inter-patient pharmacokinetic variability, particularly for poorly soluble weak bases. Thus, new avenues are opened for developing novel co-therapies and screening tools to enhance antipsychotic pharmacokinetic performance, potentially improving treatment outcomes for patients with schizophrenia and bipolar disorder. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/604016v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@7dac6borg.highwire.dtl.DTLVardef@c2cf1corg.highwire.dtl.DTLVardef@1ab5460org.highwire.dtl.DTLVardef@130ab14_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs

Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing. ImportanceDiverse conditions of infection and cellular stress incite the cleavage of transfer RNAs, leading to the formation of tRNA fragments which can directly regulate gene expression. In our study of gammaherpesviruses, such as the murine herpesvirus 68 and human oncogenic Kaposi Sarcoma associated Herpesvirus, we discovered that transfer RNA regulation and cleavage is a key component of gene reprogramming during infection. We present the first in-depth profile of tRNA fragment generation in response to DNA virus infection, using state-of-the-art sequencing techniques that overcome several challenges with tRNA sequencing. We present several lines of evidence that tRNA fragments are made from newly-transcribed premature tRNAs and propose that this may be a defining characteristic of tRNA cleavage in some contexts. Finally, we show that tRNA splicing machinery is involved with the formation of some MHV68-induced tRNA fragments, with a key regulator of splicing, CLP1, required for maximal viral titer. Together, we posit that tRNA processing may be integral to the elegant shift in gene expression that occurs during viral take-over of the host cell.

microbiology↗

bioRxiv2024

The atypical antipsychotic lurasidone positively modulates the gut microbiota in rats: A comparative study to olanzapine

Background and PurposeAntipsychotics like olanzapine are associated with significant metabolic dysfunction, attributable to gut microbiota dysbiosis. A recent notion that most psychotropics are detrimental to the gut microbiota has arisen from consistent findings of metabolic adverse effects. However, unlike olanzapine, the metabolic effects of lurasidone are conflicting, with most reports observing weight loss rather than gain. Thus, this study investigates the contrasting effects of olanzapine and lurasidone on the gut microbiota to explore the hypothesis of "gut neutrality" for lurasidone exposure. Experimental ApproachUsing a Sprague-Dawley rat model, the impact of olanzapine and lurasidone administration on the gut microbiota was explored. Faecal and blood samples were collected weekly over a 21-day period to analyse changes to the gut microbiota and related metabolic markers. Key ResultsLurasidone triggered no significant weight gain or metabolic alterations, instead positively modulating gut microbiota through increases in mean OTUs (+50 OTUs) and alpha diversity (+0.5 increase in Shannons index). This novel finding suggests an underlying mechanism for lurasidones metabolic inertia. In contrast, olanzapine triggered a statistically significant decrease in mean OTUs (-75 OTUs) and substantial compositional variation, suggesting a decrease in microbial richness. Microbiota alterations correlated with metabolic dysfunction, evidenced through a statistically significant 30% increase in weight gain, increase in pro-inflammatory cytokine expression, and increase in blood triglycerides and glycaemic levels. Conclusion and ImplicationsThe study challenges the notion that all antipsychotics disrupt the gut microbiota similarly and highlights the potential benefits of gut positive or neutral antipsychotics like lurasidone in managing metabolic side effects. Further research is warranted to validate these findings in humans to guide personalised pharmacological treatment regimens for schizophrenia. Bullet point summary- What is already known: O_LIOlanzapine induces weight gain by disrupting the gut microbiome. C_LIO_LIThe impact of lurasidone on the gut microbiome is unknown and weight gaining propensities unclear. C_LI - What this study adds: O_LILurasidone positively modulates gut microbiota through enhancement of microbial diversity and richness. C_LIO_LIPotential mechanisms underlying lurasidones weight and metabolic neutrality are elucidated. C_LI - Clinical significance: O_LIGut neutral antipsychotics like lurasidone could be favourable alternatives for patients unable to tolerate olanzapine. C_LIO_LIPersonalised treatment for schizophrenia considering individual sensitivities to metabolic effects is emphasised. C_LI

pharmacology and toxicology↗

bioRxiv2024

Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage

Withdrawal statementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2024/592122. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: https://doi.org/10.1101/2024.05.01.592122.

microbiology↗

bioRxiv2024

Human Soluble Prorenin Receptor Expressed in Adipose Tissue Improves Insulin Sensitivity and Endothelial Function in Obese Female Mice

Soluble prorenin receptor (sPRR) is a component of the renin-angiotensin system (RAS) identified as a plasma biomarker for human metabolic disease. However, what tissue source of sPRR is implicated in the modulation of metabolic function remains unclear. This study investigated the contribution of human sPRR (HsPRR) produced in the adipose tissue (Adi) on the metabolic and cardiovascular function of lean and obese male and female mice. Adi-HsPRR mice, generated by crossing human sPRR-Myc-tag and Adiponectin/Cre mice, were fed a low-fat or high-fat diet (10% and 60% kCal from fat, respectively) for 20 weeks. Obese Adi-HsPRR mice showed elevated sPRR levels in adipose tissue without affecting adipocyte size or fat depot weight. Despite plasma sPRR being similar between obese Adi-HsPRR and control female mice, a positive correlation between plasma sPRR and adiposity was present only in controls. Obese Adi-HsPRR male mice showed elevated plasma sPRR compared with controls, but no correlation with adiposity was found in either group. Nevertheless, Adi-HsPRR expression improved insulin sensitivity and endothelial function, reduced adipogenic genes mRNA abundance (PPARg, SEBP1C and CD36), and increased plasma Angiotensin 1-7 levels only in obese HsPPR female mice. Taken together, elevated HsPRR in adipose tissue improved metabolic and vascular function in obese female mice despite normal circulating levels of sPRR, whereas increased local and circulating levels of HsPRR did not influence metabolic and cardiovascular function in obese male mice. Our data suggest that increased plasma sPRR associated with metabolic disease could be produced by other tissues rather than adipocytes.

physiology↗

bioRxiv2023

A transmission bottleneck for malaria? Quantification of sporozoite expelling from laboratory and natural P. falciparum infections

It is currently unknown whether all Plasmodium falciparum infected mosquitoes are equally infectious. We assessed sporogonic development using cultured gametocytes in the Netherlands and naturally circulating strains in Burkina Faso. We quantified the number of sporozoites expelled into artificial skin in relation to intact oocysts, ruptured oocysts, and residual salivary gland sporozoites. Sporozoites were quantified by highly sensitive qPCR; intact and ruptured oocysts by fluorescence microscopy following antibody staining of circumsporozoite protein. In laboratory conditions, higher total sporozoite burden in mosquitoes was associated with a shorter duration of sporogony (p<0.001). Overall, 53% (116/216) of P. falciparum infected An. stephensi mosquitoes expelled sporozoites into artificial skin. The medians of expelled and residual salivary gland sporozoites were 136 (IQR: 34-501) and 23,947 (IQR: 9127-78,380), respectively. There was a strong positive correlation between ruptured oocyst number and salivary gland sporozoite load ({rho}=0.8; p<0.0001) and a weaker positive correlation between salivary gland sporozoite load and the number of sporozoites expelled ({rho}=0.35; p=0.0002). In Burkina Faso, An. coluzzii mosquitoes were infected by natural gametocyte carriers. Among mosquitoes that were salivary gland sporozoite positive, 89% (33/37) expelled sporozoites with a median of 1035 expelled sporozoites (IQR: 171-2969) and harbored a median of 45,100 residual salivary gland sporozoites (IQR: 20,310-164,900). Again, we observed a strong correlation between ruptured oocyst number and salivary gland sporozoite load ({rho}=0.9; p<0.0001) and a positive correlation between salivary gland sporozoite load and the number of sporozoites expelled ({rho}=0.7; p<0.0001). Mosquito salivary glands in Burkina Faso harbored 1-3 distinct parasite clones; several mosquitoes expelled multiple parasite clones during probing. Whilst sporozoite expelling was regularly observed from mosquitoes with low infection burdens, our findings indicate that mosquito infection burden is associated with the number of expelled sporozoites. Future work is required to determine the direct implications of these findings for transmission potential.

microbiology↗

bioRxiv2023

Secondary Structure Detection Through Direct Nanopore RNA Sequencing

Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT from Bombyx mori with single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were able to quantify the RTs dwell time at every single nucleotide step along its RNA template. By challenging the enzyme with various RNA structures, we found that during cDNA synthesis the RT can sense and actively destabilize RNA structures 11-12 nt downstream of its front boundary. The ability to sequence single molecules of RNA with nanopores paves the way to investigate the single-nucleotide activity of other processive RNA translocases.

biophysics↗