Biology subjects

Baker, R.

Publications and source records attributed to Baker, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Type 2B VWD substitutions trigger enhanced macrophage-mediated clearance that is attenuated by the BT200 aptamer

Type 2B von Willebrand disease (VWD) is characterized by missense variants in exon 28 of the von Willebrand factor (VWF) gene that encodes the VWF-A1 domain. These missense mutations result in single amino acid residue substitutions that cause activation of VWF-A1 and promote spontaneous interaction with platelet GPIba;. Importantly, enhanced VWF clearance has been shown to play a key pathogenic role in >90% patients with Type 2B VWD. Although this VWF clearance occurs via mechanisms that are independent of VWF-platelet complex formation, the biological mechanisms responsible for the increased clearance of type 2B VWD variants remain poorly understood. In this study, we investigated a series of different type 2B amino acid substitutions within the VWF-A1 domain (R1306W, R1308C, W1313C and R1379L). We demonstrate that these variants all exhibit significantly increased macrophage binding. In part, the enhanced macrophage interactions are mediated via increased binding of type 2B VWD variants to LRP1 extracellular cluster II and IV. Our findings further demonstrate that the K1405-K1408 lysine cluster in the VWF-A1 domain plays a key role in enabling enhanced LRP1 interactions for type 2B VWD variants. In addition, we show that type 2B VWF variants demonstrate significantly enhanced interaction with the macrophage MGL receptor. Finally, and importantly from a clinical perspective, we demonstrate that the increase in macrophage binding for type 2B variants is significantly attenuated in the presence of BT200. Collectively, our findings have direct translational relevance with respect to the clinical heterogeneity and treatment of type 2B VWD.

biochemistry↗

bioRxiv2026

QuadCleave: Enzymatic cleavage and analysis of DNA G-quadruplexes.

Prediction of G-quadruplexes (G4), noncanonical DNA secondary structures containing guanine tetrads, can have profound relevance across cancer, neurodegenerative and other genetic diseases, but require experimental validation by instrument intensive methods including CD spectroscopy, fluorescence, NMR, or crystallography. We report a novel, inexpensive, efficient and scalable 2-enzyme system for confirmation of G4 formation and copy number repeat count. First, QuadCleave, in which Mismatch Endonuclease I was used to repeatably, site-specifically and selectively cleave oligodeoxynucleotides containing exclusively G4-forming sequences. Second, HaeIII enzyme identified G4-forming sequences that can also generate GG/CC base pairs, and a sequences cleavage by both established it in C9ORF72, the most mutated gene in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These findings establish ubiquitously accessible experimental validation of G4 forming sequences and their copy number repeat assessment, with specificity to C9ORF72 oligodeoxynucleotides whose repeat expansion has critical clinical implications in a subpopulation of ALS and FTD patients.

molecular biology↗

bioRxiv2025

Thermally activated irreversible homogenization of G-quadruplexes in an ALS/FTD-associated nucleotide expansion

A significant proportion of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases exhibit a substantial copy number expansion of the hexanucleotide GGGGCC/GGCCCC sequence in the C9ORF72 gene. The GGGGCC sequence forms a non-canonical DNA structure called a G-quadruplex (G4) which has been associated with the disease states and with nucleic acid condensate formation. G4s can fold into various topologies, which can differentially impact fidelity of DNA synthesis. However, how G4 conformational heterogeneity and its regulation impact hexanucleotide repeat expansion is unclear, and important clues may lie in the thermodynamic properties of different G4 topologies. Here, we use temperature-swept CD spectroscopy to observe configurational homogenization of an initially heterogeneous population of G4s over a small range of temperatures, demonstrating thermally activated behavior. We further show that this reaction is irreversible, since subsequent temperature sweeps do not show CD shifts from non-parallel to parallel G4 topologies. Finally, we provide an analytical theory based on a two-state thermodynamic model which is compatible with experimental evidence, and we discuss alternate mechanisms for the homogenization transition. These findings suggest that kinetic regulation of non-canonical DNA structures may play a role in cellular homeostasis or disease pathogenesis. SIGNIFICANCEThe GGGGCC repeats in the C9ORF72 gene expand in copy number in certain neurodegenerative diseases, forming non-canonical DNA structures called G-quadruplexes (G4) which are associated with the pathological state. However, why the repeat expansion occurs is not known, and a key may lie in the thermodynamic stability of certain G4 conformations. Here, we use CD spectroscopy to experimentally report thermally activated heat-induced G4 conformation homogenization, from a heterogeneous population to the parallel configuration. We derive an analytical biophysical theory which is compatible with this experimental observation, which is shown to be irreversible. Our in vitro tuning of the free energy landscape that modulates G4 conformational fidelity motivates a search for possible in vivo enzymatic regulators.

biophysics↗

bioRxiv2024

A new mechanochemical vertex model with Ca2+ signalling, for apical constriction in neural tube closure

Apical constriction during neural tube closure is driven by cell contractions which are preceded by asynchronous and cell-autonomous Ca2+ flashes, as demonstrated in recent experiments. Disruption of these Ca2+ signals and contractions leads to neural tube defects, such as anencephaly and spina bifida. A good understanding of the two-way mechanochemical coupling of Ca2+ signalling and mechanics remains elusive, while live-cell imaging is difficult. Thus, mathematical modelling is essential but existing models do not exhibit good agreement with experiments. We present two new mechanochemical vertex models of apical constriction during neural tube closure and simulate them using CelluLink, a new user-friendly open-source Python package for vertex modelling. The first, one-way mechanochemical model only studies the effect of Ca2+ signalling on cell mechanics. It improves previous models, reproducing some key experimental observations, such as the reduction of the neural plate size to 2%-8% of its initial area. Other novel features of the one-way model is the incorporation of the surface ectoderm and of the experimental amplitude and frequency profiles of the Ca2+ flashes. Furthermore, guided by experiments, the damping coefficient of the vertices and cell-cell adhesion are modelled as functions of the actomyosin concentration and cell size. Furthermore, we develop a two-way model which improves the one-way model by capturing the two-way coupling between Ca2+ signalling and cell mechanics, through the incorporation of stretch-sensitive Ca2+ channels. These channels enable cells to sense mechanical stimuli and encode them into Ca2+ signals. In the two-way model, the Ca2+ flash frequency and amplitude profiles are model outputs and are not inputs as in the one-way model. Finally, we use both models to propose a series of hypotheses for future experiments. Author summaryAs a baby is growing in the womb, its neural tube closes to form the brain and the spinal cord. During neural tube closure, cells are contracting in a ratchet-like way while experiencing a choreography of Ca2+ flashes. If the Ca2+ flashes or the contractions go wrong, serious birth defects like spina bifida and anencephaly may arise. Understanding how Ca2+ flashes and contractions work together is complex, especially since studying living cells is challenging. To address this challenge, we developed two new mathematical models. The first model captures how Ca2+ flashes affect contractions, improving previous models and accurately capturing some experimental results. For example, it incorporates recent experimental measurements of the amplitude of Ca2+ flashes (brightness) and their frequency (how frequently the flashes appear). The second model builds on the first model by additionally capturing the effect contractions have on the Ca2+ flashes. We capture this two-way coupling by enabling cells to sense mechanical stimuli through stretch-sensitive Ca2+ channels. In this case, the amplitude and frequency of the Ca2+ flashes arise as outputs. Both models inform future experiments that will further elucidate embryo malformations.

systems biology↗

bioRxiv2024

Cellular cruise control: energy expenditure as a regulator of collective migration in epithelia

Epithelial migration is implicit in processes ranging from gastrula development to the healing of skin, and involves the coordinated motion, force production, and resulting energy expenditure of thousands of constitutive cells. However, the spatiotemporal patterning and regulation of energy expenditure during epithelial migration remains poorly understood. Here, we propose a continuum mechan-ics framework and use it to explore how energy expenditure regulates epithelial migration. We use canonical mechanical metrics such as force, work and power to define what it means for a tissue to migrate efficiently and show that freely expanding epithelia actively regulate themselves to operate within a maximally efficient regime. We then leverage electrotaxis (directed motion in response to an externally applied electric field) as a tool to study non-homeostatic migra-tion using this new framework. We show that regulation of migration is robust to external cues and acts to to attenuate a tissues response to stimuli.

biophysics↗

bioRxiv2024

The global fish and invertebrate abundance value of mangroves

Mangroves are a critical coastal habitat that provides a suite of ecosystem services and supports livelihoods. We undertake the first global analysis to estimate density and abundance of 37 commercially important fish and invertebrates that are known to extensively use mangroves. Geomorphic mangrove type, sea surface salinity and temperature, and length of mangrove forest edge were important in predicting the density of commercial fish and invertebrates, with deltaic systems supporting the highest densities. The model predicted high densities throughout parts of southeast Asia, the northern coast of South America, the Red Sea, and the Caribbean and Central America. Application of our model onto the global mangrove extent, estimates that mangroves support the annual abundance of nearly 800 billion young-of-year fish and invertebrates contained in our model. Our results confirm the critical role of mangroves globally in supporting fish and fisheries, and further builds the case for their conservation and restoration.

ecology↗

bioRxiv2023

Stable isotopes disentangle niche partitioning and species co-occurrence in a multi-level marine mutualism

Ecologists have long sought general explanations for the co-occurrence of ecologically similar taxa. Niche theory explains co-occurrence via functional differences among taxa that reduce competition and promote resource partitioning. Alternatively, the unified neutral theory of biodiversity and biogeography suggests that co-occurrence can be attributed to stochastic processes, and thus, presupposes that ecologically similar species that occur in sympatry are functionally analogous. We test these alternative hypotheses in multiple dimensions using the most diverse crustacean-sea anemone symbiosis from coral reefs in the Tropical Western Atlantic. {delta}13C and {delta}15N stable isotope analyses of six crustacean symbionts that co-occur around the host anemone Bartholomea annulata exhibit highly differentiated isotopic niche space spanning three trophic levels. As multiple crustacean species within the symbiosis have been documented as cleaners that remove parasites from reef fishes, we extended our investigation into the broader cleaner community. Our stable isotope analyses of cleaners shows that only Pedersons cleaner shrimp Ancylomenes pedersoni exhibits {delta}15N isotopic signatures that are consistent with a dedicated cleaning lifestyle. Co-occurring species that have been previously described to clean reef fishes such as Periclimenes yucatanicus, Stenopus hispidus, and Stenorhynchus seticornis all occupy trophic levels well below An. pedersoni. Taken together, our data are consistent with the expectations of niche theory: co-occurring symbiotic crustaceans have highly partitioned niche space with low levels of functional redundancy. Finally, our findings reinforce and extend the ecological importance of An. pedersoni as likely the only dedicated cleaner shrimp on coral reefs in the Tropical Western Atlantic.

ecology↗

bioRxiv2022

Voluntary and forced exposure to ethanol vapor produces similar escalation of alcohol drinking but differential recruitment of brain regions related to stress, habit, and reward in male rats.

A major limitation of the most widely used current animal models of alcohol dependence is that they use forced exposure to ethanol including ethanol-containing liquid diet and chronic intermittent ethanol (CIE) vapor to produce clinically relevant blood alcohol levels (BAL) and addiction-like behaviors. We recently developed a novel animal model of voluntary induction of alcohol dependence using ethanol vapor self-administration (EVSA). In this model, naive outbred rats given intermittent access to alcohol vapor self-administration exhibit BAL in the 150-300 mg% range and develop somatic signs of withdrawal during acute abstinence. However, it is unknown whether EVSA leads to an escalation of alcohol drinking per se, and whether such escalation is associated with neuroadaptations in brain regions related to stress, reward, and habit. To address these issues, we compared the levels of alcohol drinking during withdrawal between rats passively exposed to alcohol (CIE) or voluntarily exposed to EVSA and measured the number of Fos+ neurons during acute withdrawal (16 h) in the central nucleus of the amygdala (CeA), dorsomedial striatum (DMS), dorsolateral striatum (DLS), nucleus accumbens core (Nacc), periaqueducal grey area (PAG), lateral Habenula (HbL), and the paraventricular nucleus of the thalamus (PVT). The rats were first trained to orally self-administer alcohol in standard operant chambers and then divided in 4 groups (CIE, CI-Air, EVSA and Air-SA) and exposed to intermittent ethanol vapor (passive or active) or intermittent air (passive or active) for 8 h/day, 3 days a week. CIE and EVSA rats exhibited similar BAL (150-300 mg% range) and similar escalation of alcohol drinking during withdrawal, while no changes in terms of drinking were observed in the air exposed rats. CIE and EVSA also increased the motivation for alcohol compared to their respective air control groups under a progressive ratio schedule of reinforcement. Acute withdrawal from EVSA and CIE recruited a similar number of Fos+ neurons in the CeA, however, acute withdrawal from EVSA recruited a higher number of Fos+ neurons in every other brain region analyzed compared to acute withdrawal from CIE. Moreover, acute withdrawal from EVSA specifically recruited the DMS and PVT, a pattern not observed in CIE rats. In summary, these results demonstrate that EVSA produces similar escalation of alcohol drinking, motivation to drink, and blood-alcohol levels than the CIE model, while letting animals voluntary initiate alcohol exposure and maintain alcohol dependence. Moreover, while the behavioral measures of alcohol dependence between the voluntary (EVSA) and passive (CIE) model was similar, the recruitment of neuronal ensembles during acute withdrawal was very different with a higher recruitment of Fos+ neurons in key brain regions important for stress, reward and habit-related processes. The EVSA model may be particularly useful to unveil the neuronal networks and pharmacology responsible for the voluntary induction and maintenance of alcohol dependence and may improve translational studies by providing preclinical researchers with an animal model with better face validity for alcohol use disorder.

neuroscience↗

bioRxiv2022

Human and murine Cryptococcus neoformans infection selects for common genomic changes in an environmental isolate.

A pet cockatoo was the suspected source of Cryptococcus neoformans recovered from the cerebral spinal fluid (CSF) of an immunocompromised patient with cryptococcosis based on the molecular analyses available in 2000. Here we report whole genome sequence analysis of the clinical and cockatoo strains. Both are closely related MAT strains belonging to the VNII lineage, confirming that the human infection likely originated from pet bird exposure. The two strains differ by 61 single nucleotide polymorphisms, including 8 nonsynonymous changes involving 7 genes. To ascertain whether changes in these genes are selected during mammalian infection, we passaged the cockatoo strain in mice. Remarkably, isolates obtained from mouse tissue possess a frame-shift mutation in one of the seven genes altered in the human sample, a gene predicted to encode a SWI-SNF chromatin-remodeling complex protein. Both cockatoo and patient strains as well as mouse passaged isolates obtained from brain tissue had a premature stop codon in a homolog of ZFC3, a predicted single-zinc finger containing protein, which is associated with larger capsules when deleted and appears to have reverted to a full-length protein in the mouse passaged isolates obtained from lung tissue. The patient strain and mouse passaged isolates show variability in the expression of virulence factors, with differences in capsule size, melanization, and rates on non-lytic expulsion from macrophages observed. Our results establish that environmental strains undergo genomic and phenotypic changes during mammalian passage, suggesting that animal virulence can be a mechanism for genetic change and that the genomes of clinical isolates may provide a readout of mutations acquired during infection.

genomics↗

bioRxiv2021

GLS1 is a Protective Factor Rather than a Molecular Target in ARID1A-Mutated Ovarian Clear Cell Carcinoma

Targeting glutamine metabolism has emerged as a novel therapeutic strategy for several human cancers, including ovarian cancer. The primary target of this approach is the kidney isoform of glutaminase, glutaminase 1 (GLS1), a key enzyme in glutamine metabolism that is overexpressed in several human cancers. A first-in-class inhibitor of GLS1, called CB839 (Telaglenastat), has been investigated in several clinical trials, with promising results. The first clinical trial of CB839 in platinum-resistant ovarian cancer patients is forthcoming. ARID1A-mutated ovarian clear cell carcinoma (OCCC) is a relatively indolent and chemoresistant ovarian cancer histotype. In OCCC-derived cells in vitro and mouse models, loss of ARID1A leads to upregulation of GLS1. Thus, targeting of GLS1 with CB839 has been suggested as a targeted approach for OCCC patients with tumors harboring ARID1A-mutations. Here, we investigated whether GLS1 is differentially expressed between OCCC patients whose tumors are ARID1A positive and patients whose tumors are ARID1A negative. In clinical specimens of OCCC, we found that GLS1 overexpression was not correlated with ARID1A loss. In addition, GLS1 overexpression was associated with better clinical outcomes. Our findings suggest that GLS1 expression in OCCC may be a protective factor and that caution should be taken when considering the use of CB839 to treat OCCC patients.

cancer biology↗

bioRxiv2021

Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition

Gut microbiome succession impacts infant development. However, it remains unclear what factors promote persistence of initial bacterial colonists in the developing gut. Here, we performed strain-resolved metagenomic analyses to compare gut colonization of preterm and full-term infants throughout the first year of life and evaluated links between strain persistence and strain origin as well as genetic potential. Analysis of 206 fecal metagenomes collected from full-term and preterm infants and their mothers revealed that infants initially distinct microbial communities converged by age one. Approximately 11% of early colonists, primarily Bacteroides and Bifidobacterium, persisted during the first year of life, and these were more prevalent in full-term compared to preterm infants. Gut-associated strains from mothers were significantly more likely to persist in the infant gut than other strains. Enrichment in genes for surface adhesion, iron acquisition and carbohydrate degradation may explain persistence of some strains through the first year of life.

microbiology↗

bioRxiv2020

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae

Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region, readthrough allows translation into the mRNA 3-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5 of the stop codon, six nucleotides 3 of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 and mRNA secondary structure in the 3-UTR had milder effects. Additionally, we found low readthrough genes to have shorter 3-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features affecting the efficiency of translation termination and readthrough. AUTHOR SUMMARYOf the 64 codons that exist for translation of the genetic code into a polypeptide chain, only UAA, UAG, and UGA signify termination of continued protein synthesis. However, the efficiency of termination is not the same for different mRNAs and is likely influenced by mRNA sequences proximal to these "stop" codons. Here, we sought to expand current understanding of termination efficiency to a genome-wide scale. Our analysis identifies novel mRNA features that may regulate the efficiency of translation termination, including the identities of the stop codon, the penultimate codon, the proximal nucleotides, and the length of mRNA 3-untranslated region. As [~]11% of human diseases are caused by mutations that introduce premature stop codons, resulting in both accelerated mRNA decay and truncated protein product, our findings are valuable for understanding and developing therapeutics targeting the termination step of mRNA translation.

genetics↗

bioRxiv2020

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species viability from total RNA sequencing.

microbiology↗

bioRxiv2020

A computer vision approach for studying fossorial and cryptic crabs

Despite the increasing need to catalogue and describe biodiversity and the ecosystem processes it underpins, these tasks remain inherently challenging. This is particularly true for species that are difficult to observe in their natural environment, such as fossorial and cryptic crabs that inhabit intertidal sediments. Traditional sampling techniques for intertidal crabs are often invasive, labour intensive and/or inconsistent. These factors can limit the amount and type of data that can be collected which in turn hinders our ability to obtain reliable ecological estimates and compare findings between studies. Computer vision and machine learning algorithms present an opportunity to innovate and improve sampling approaches. Moreover, cheaper and tougher recording devices and the diversity of open source software further boost the possibilities of achieving rigorous image-based sampling, which can broaden the range of questions that can be addressed from the data collected. Despite its significant potential, the software and algorithms associated with image-based sampling may be daunting to researchers without expertise in computer vision. Therefore, there is a need to develop protocols and data processing workflows to showcase the value of embracing new technologies. This paper presents a non-invasive computer vision and learning protocol for sampling fossorial and cryptic crabs in their natural environment. The image-based protocol is underpinned by fit-for-purpose and off-the-shelf software. We demonstrate this approach using fiddler crab and sediment recordings to study and quantify crab abundance, motion patterns, behaviour, intraspecific interactions, and estimate bioturbation rates. We discuss current limitations in this protocol and identify opportunities for improvement and additional data stream options that can be obtained from this approach. We conclude that this protocol can overcome some of the limitations associated with traditional techniques for sampling intertidal crabs, and could be applied to other taxa or ecosystems that present similar challenges. We believe this sampling and analytical framework represents an important step forward in understanding the ecology of species and their functional role within ecosystems.

ecology↗

bioRxiv2020

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics

Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in microbiome context. Here, we reconstructed five unique C. parapsilosis genomes from premature infant fecal samples and analyzed their genome structure, population diversity and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have four to sixteen copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis coexisted with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

microbiology↗

bioRxiv2019

Continuum descriptions of spatial spreading for heterogeneous cell populations: theory and experiment

Variability in cell populations is frequently observed in both in vitro and in vivo settings. Intrinsic differences within populations of cells, such as differences in cell sizes or differences in rates of cell motility, can be present even within a population of cells from the same cell line. We refer to this variability as cell heterogeneity. Mathematical models of cell migration, for example, in the context of tumour growth and metastatic invasion, often account for both undirected (random) migration and directed migration that is mediated by cell-to-cell contacts and cell-to-cell adhesion. A key feature of standard models is that they often assume that the population is composed of identical cells with constant properties. This leads to relatively simple single-species homogeneous models that neglect the role of heterogeneity. In this work, we use a continuum modelling approach to explore the role of heterogeneity in spatial spreading of cell populations. We employ a three-species heterogeneous model of cell motility that explicitly incorporates different types of experimentally-motivated heterogeneity in cell sizes: (i) monotonically decreasing; (ii) uniform; (iii) non-monotonic; and (iv) monotonically increasing distributions of cell size. Comparing the density profiles generated by the three-species heterogeneous model with density profiles predicted by a more standard single-species homogeneous model reveals that when we are dealing with monotonically decreasing and uniform distributions a simple and computationally efficient single-species homogeneous model can be remarkably accurate in describing the evolution of a heterogeneous cell population. In contrast, we find that the simpler single-species homogeneous model performs relatively poorly when applied to non-monotonic and monotonically in-creasing distributions of cell sizes. Additional results for heterogeneity in parameters describing both undirected and directed cell migration are also considered, and we find that similar results apply.

biophysics↗

bioRxiv2019

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors

Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1,163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids and growth rates. A machine learning classifier found that samples collected prior to NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher two days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.

microbiology↗

bioRxiv2019

Dynamic architecture of the Escherichia coli structural maintenance of chromosomes (SMC) complex, MukBEF

Structural Maintenance of Chromosomes (SMC) complexes use a proteinaceous ring-shaped architecture to organise chromosomes, thereby facilitating chromosome segregation. They utilise cycles of ATP binding and hydrolysis to transport themselves rapidly with respect to DNA, a process requiring protein conformational changes and multiple DNA contacts. We have analysed changes in the architecture of the Escherichia coli SMC complex, MukBEF, as a function of nucleotide binding to MukB and subsequent ATP hydrolysis. This builds upon previous work showing that MukF kleisin directs formation of a MukBEF tripartite ring as a consequence of functional interactions between the C- and N-terminal domains of MukF with the MukB head and neck, respectively (Zawadzka et al., 2018). Using both model truncated substrates and complexes containing full length MukB, we now demonstrate formation of MukBEF dimers of dimers, dependent on MukF dimerization, MukB head-engagement and MukE, which plays an essential role in organizing MukBEF complexes.

biochemistry↗