BMAC Weekly — 2026-W41
8 papers selected for 2026-W41.
2026-09-29–2026-10-05 · 8 papers
Large-deviations theory for growing chemical reaction networks
P Gagrani, I Madrid, TJ Kobayashi
2026-09-25 · arXiv preprint arXiv:2609.30970
TL;DR. The authors develop a large-deviation theory for exponentially growing stochastic chemical reaction networks by decomposing abundance into volume and composition, showing composition fluctuations obey a large-deviation principle with speed equal to system volume.
Key signal. Composition fluctuations satisfy a large-deviation principle whose quasipotential solves a contact Hamilton-Jacobi equation, and covariances of accumulated observables decay with accumulated volume rather than physical time.
Why it matters here. It directly addresses stochasticity in growing biochemical reaction networks, connecting to Fangzhou's interests in microbial growth laws, cell-size homeostasis, and biomolecular reaction networks as a null model for single-cell heterogeneity.
Spatiotemporal dynamics and stability of multi-kingdom microbial communities in hospital sinks acting as persistent pathogen reservoirs
Iván Linares‐Ambohades, Natalia Guerra-Pinto, Sandra Mingo-Ramirez, Silvia Serrano-Calleja, Francisco Amaro, Ana Alastruey‐Izquierdo, Cruz Soriano, Raul de Pablo Sánchez, Val F. Lanza, Rafael Cantón, Fernando Baquero, Teresa M. Coque, Ana Elena Pérez‐Cobas
2026-09-26 · bioRxiv
TL;DR. A 17-month multi-kingdom study of 14 hospital sink drains combined 16S/ITS/18S profiling, culturomics, and resistance testing to track community assembly and stability through renovation and clinical use.
Key signal. Former-ICU drains harbor a highly conserved multi-kingdom core that remains resilient to structural changes and inactivity, with multidrug-resistant pathogens deeply embedded in integrated ecological networks.
Why it matters here. It ties to Fangzhou's microbial population dynamics and community ecology interests by showing how environmental structure and anthropogenic shifts shape persistent, sink-specific multi-kingdom communities.
Microbial Communities in Composting Processes:Succession, Functional Ecology, and Biotechnological Applications
Wijdan Hameed Abd Al-Razzaq Al-Kubaisy
2026-10-01 · Al-Turath Journal for Biology
TL;DR. A review of composting microbiology spanning 2021-2026 uses genome-resolved metagenomics, metatranscriptomics, and ecological network analysis to examine microbial succession, functional ecology, and biotechnological applications.
Key signal. Taxonomic biodiversity plays only a minor role in maintaining stability during composting, thermophilic fungi cannot be replaced by bacteria, and keystone taxa and interaction networks not detected by abundance-based profiling promote process efficiency.
Why it matters here. It connects to Fangzhou's microbial community ecology and population dynamics interests, particularly the roles of keystone taxa, functional redundancy, and antibiotic resistance gene dynamics in managed microbial systems.
Synthetic genetic circuits that count developmental cues in plant roots
Soyeon Choi, Jennifer A. N. Brophy
2026-09-29 · bioRxiv (Cold Spring Harbor Laboratory)
TL;DR. The authors built synthetic genetic circuits in Arabidopsis thaliana that use root primordium-specific promoters to express large serine recombinases, irreversibly inverting DNA segments each time a new lateral root initiates to count developmental cues.
Key signal. Circuit architectures were developed that produce distinct fluorescence outputs in primary, secondary, and tertiary roots by counting long-duration input pulses over the roughly two-day root branch specification period.
Why it matters here. It directly addresses Fangzhou's synthetic biology circuits interest by demonstrating how repeated developmental signals can be converted into heritable DNA states for branch-resolution engineering.
A Modified Rao-Blackwellised Particle Filter Based on Updated Process Noise Covariance for Chemical Reaction Networks
Suryasnata Dash, Abhishek Dey
2026-09-25 · arXiv (Cornell University)
TL;DR. The authors apply a modified Rao-Blackwellised particle filter with recursively updated process noise covariance, based on the chemical Langevin equation, to jointly estimate parameters and states in a reduced-order gene expression system.
Key signal. The RBPF with updated noise covariance balances parameter estimation accuracy, state estimation error, and innovation whiteness compared with fixed noise covariance choices.
Why it matters here. It connects to Fangzhou's biomolecular control and reaction network interests by providing an estimation framework for stochastic chemical reaction networks relevant to synthetic and natural biological systems.
N-acyl-homoserine lactonase–nanosilver composite modulates the bacterial community of an in vitro enriched biofilm model of early childhood caries
Chuang Nie, Ran Xia, Liqiong Ma, Song Li, Jing Zhang
2026-10-02 · Frontiers in Oral Health
TL;DR. An N-acyl-homoserine lactonase-nanosilver composite was tested on in vitro enriched biofilms from children with early childhood caries, with effects assessed by 16S rRNA sequencing, SEM, and biomass assays.
Key signal. The composite reduced microbial alpha diversity and total biomass, disrupted biofilm architecture, decreased Actinomyces and Lactobacillus, and enriched Haemophilus and Granulicatella, with predicted functional changes in carbohydrate and nucleotide metabolism.
Why it matters here. It relates to Fangzhou's microbial community ecology and quorum-sensing interests by showing how a quorum-quenching enzyme combined with nanosilver alters community composition and metabolic function in a biofilm model.
Pathogen detection and microbial community characterization in clinically symptomatic pigs from commercial farms
Se Hui Park, Doo Sung Cheon, Tae Jin Cho, Sun Ae Kim
2026-10-01 · Frontiers in Veterinary Science
TL;DR. The study combined molecular pathogen diagnostics with 16S rRNA sequencing of lung, oral fluid, and fecal samples from clinically symptomatic pigs on South Korean commercial farms.
Key signal. Most respiratory pathogens were detected more often in oral fluid than lung, while lung microbiota showed lowest diversity and dominance by Escherichia-Shigella and Actinobacillus, and Clostridium perfringens presence was associated with distinct gut community composition and predicted functions.
Why it matters here. It connects to Fangzhou's microbial population and community ecology interests by characterizing how pathogen presence associates with site-specific microbiota structure and predicted functional profiles in a production animal system.
Effects of Inoculum Source and Incubation Temperature on Bacterial Community Structure and Predicted Functional Potential Associated with Polylactic Acid (PLA) Degradation
Subin Hwang, Soo Yeon Lee, Kyung-Suk Cho
2026-09-21 · Microbiology and Biotechnology Letters
TL;DR. Two compost inocula were enriched with polylactic acid under mesophilic and thermophilic conditions for 100 days to assess bacterial community structure and predicted functional potential.
Key signal. Community structure was primarily shaped by inoculum source followed by incubation temperature, with distinct genus-KO associations such as Pseudoxanthomonas with K12686 and K10804 in one inoculum.
Why it matters here. It relates to Fangzhou's community ecology and dynamic metabolism interests by demonstrating how inoculum and temperature select taxa and predicted functions linked to ester-bond hydrolysis and lactic acid metabolism.