Biology subjects

Sim, A.

Publications and source records attributed to Sim, A..

5 recordsLinked to original sources

bioRxiv2026

Light-harvesting strategies and competition drive niche partitioning among Ostreobium lineages in the spectral architecture of the coral reef

Ostreobium, a siphonous green alga capable of living inside of calcium carbonate substrates, including the skeletons of reef-building corals. This study investigates spectral niche preferences and physiological strategies of Ostreobium using community-wide experiments. We exposed natural Ostreobium communities from Porites lutea collected across shallow, mid, and deeper-water sites to three light conditions: far-red, blue, and white light, simulating healthy shallow-water corals, deeper water conditions, and bleached coral skeletons respectively. Using 16S rRNA metabarcoding and chlorophyll analysis, we assessed community changes and physiological responses over 16 weeks. We show significant variation in spectral preferences among Ostreobium OTUs, with clear evidence for both generalist and specialist strategies. Chlorophyll analysis showed photoacclimation responses through changes in pigment compositions. Our work shows that the spectral architecture of the reef plays a role in structuring Ostreobium communities, but the many mismatches between spectral preferences of OTUs and their observed presence in nature, suggests that inter-species competition is likely to be an even stronger contributor to community structure across the reefs microhabitats. We show that physiological heterogeneity within Ostreobium is strongly phylogenetically structured, and our results clearly highlight the importance of considering OTU-level differences when predicting community responses to environmental disturbances such as coral bleaching. While generalist OTUs dominate natural communities, these do poorly in incubations, and we hypothesise that white light specialists may become key players during coral bleaching events. Our work is a substantial advance in our understanding of Ostreobium ecology and provides a framework for interpreting future environmental sequencing data, offering insights into the functional roles of the different OTUs.

ecology↗

bioRxiv2021

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.

genomics↗

bioRxiv2019

BceAB-type antibiotic resistance transporters appear to act by target protection of cell wall synthesis

Resistance against cell wall-active antimicrobial peptides in bacteria is often mediated by transporters. In low GC-content Gram-positive bacteria, a wide-spread type of such transporters are the BceAB-like systems, which frequently provide a high level of resistance against peptide antibiotics that target intermediates of the lipid II cycle of cell wall synthesis. How a transporter can offer protection from drugs that are active on the cell surface, however, has presented researchers with a conundrum. Multiple theories have been discussed, ranging from removal of the peptides from the membrane, internalisation of the drug for degradation, to removal of the cellular target rather than the drug itself. To resolve this much-debated question, we here investigated the mode of action of the transporter BceAB of Bacillus subtilis. We show that it does not inactivate or import its substrate antibiotic bacitracin. Moreover, we present evidence that the critical factor driving transport activity is not the drug itself, but instead the concentration of drug-target complexes in the cell. Our results, together with previously reported findings, lead us to propose that BceAB-type transporters act by transiently freeing lipid II cycle intermediates from the inhibitory grip of antimicrobial peptides, and thus provide resistance through target protection of cell wall synthesis. Target protection has so far only been reported for resistance against antibiotics with intracellular targets, such as the ribosome. However, this mechanism offers a plausible explanation for the use of transporters as resistance determinants against cell wall-active antibiotics in Gram-positive bacteria where cell wall synthesis lacks the additional protection of an outer membrane.

microbiology↗

bioRxiv2019

From modules to networks: A systems-level analysis of the bacitracin stress response in Bacillus subtilis

Bacterial resistance against antibiotics often involves multiple mechanisms that are interconnected to ensure robust protection. So far, the knowledge about underlying regulatory features of those resistance networks is sparse, since they can hardly be determined by experimentation alone. Here, we present the first computational approach to elucidate the interplay between multiple resistance modules against a single antibiotic, and how regulatory network structure allows the cell to respond to and compensate for perturbations of resistance. Based on the response of B. subtilis towards the cell wall synthesis-inhibiting antibiotic bacitracin, we developed a mathematical model that comprehensively describes the protective effect of two well-studied resistance modules (BceAB and BcrC) on the progression of the lipid II cycle. By integrating experimental measurements of expression levels, the model accurately predicts the efficacy of bacitracin against the B. subtilis wild-type as well as mutant strains lacking one or both of the resistance modules. Our study reveals that bacitracin-induced changes in the properties of the lipid II cycle itself control the interplay between the two resistance modules. In particular, variations in the concentrations of UPP, the lipid II cycle intermediate that is targeted by bacitracin, connect the effect of the BceAB transporter and the homeostatic response via BcrC to an overall resistance response. We propose that monitoring changes in pathway properties caused by a stressor allows the cell to fine-tune deployment of multiple resistance systems and may serve as a cost-beneficial strategy to control the overall response towards this stressor.\n\nImportanceAntibiotic resistance poses a major threat to global health and systematic studies to understand the underlying resistance mechanisms are urgently needed. Although significant progress has been made in deciphering the mechanistic basis of individual resistance determinants, many bacterial species rely on the induction of a whole battery of resistance modules, and the complex regulatory networks controlling these modules in response to antibiotic stress are often poorly understood. In this work we combine experiments and theoretical modelling to decipher the resistance network of Bacillus subtilis against bacitracin, which inhibits cell wall biosynthesis in Gram-positive bacteria. In response to bacitracin stress we find a high level of cross-regulation between the two major resistance modules and quantify their effects on bacterial resistance. To rationalize our experimental data, we expand a previously established computational model for the lipid II cycle through incorporating the quantitative action of the resistance modules. This leads us to a systems-level description of the bacitracin stress response network that captures the complex interplay between resistance modules and the essential lipid II cycle of cell wall biosynthesis and accurately predicts the minimal inhibitory bacitracin concentration in all the studied mutants. With this, our study highlights how bacterial resistance emerges from an interlaced network of redundant homeostasis and stress response modules.

systems biology↗

bioRxiv2018

Structure mapping of dengue and Zika viruses reveals new functional long-range interactions

Dengue and Zika are clinically important members of the Flaviviridae family that utilizes an 11kb positive strand RNA for genome regulation. While structures have been mapped primarily in the UTRs, much remains to be learnt about how the rest of the genome folds to enable function. Here, we performed secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains in their native virus particles and infected cells. Comparative analysis of SHAPE reactivities across serotypes nominated potentially functional regions that are highly structured, show structure conservation, and low synonymous mutation rates, including a structure associated with ribosome pausing. Pair-wise interaction mapping by SPLASH further reveals new pair-wise interactions, in addition to the known circularization sequence. 40% of pair-wise interactions form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared pair-wise interactions between serotypes revealed macro-organization whereby interactions are preserved at their physical locations, beyond their sequence identities. In addition, structure mapping of virus genomes released in solution-as well as inside host cells-showed that other helicases, in addition to the ribosome, play a role in unwinding viral structures inside cells. Mutational experiments that disrupt in cell and in virion pair-wise interactions result in virus attenuation, demonstrating their importance during the virus life-cycle.

genomics↗