Biology subjects

Thutupalli, S.

Publications and source records attributed to Thutupalli, S..

10 recordsLinked to original sources

bioRxiv2026

Interplay of mechanics, growth and viral infection dynamics in a spatially expanding bacterial colony

We investigate the dynamics of the spread of the infection due to a phage- during the range expansion of an E coli colony. We find a rich panoply of spatio-temporal dynamics at large colony-level length scales, arising due to the interplay of mechanical forces, growth and viral infection dynamics at smaller cellular length scales. Strikingly, the phages "surf" the front of the growing bacterial colony by hitchhiking on E coli that are advected due to the growth of bacteria in the colony, resulting in an anisotropic spread of the phages. We identify microscopic processes - of the phage release during lysis (occurring on short millisecond timescales at length scales close to that of a single bacterium) and local nematic alignment of the rod-like E coli bacteria (occurring on timescales comparable to the bacterial growth rate and the length scales of a few bacterial cells) - that enhance the advective effects driving the hitchhiking behavior. Combining our experiments with a mathematical model, we explain the multiple spatio-temporal dynamical regimes - from the coexistence of uninfected bacteria, resistant (lysogenic) cells and phages, to fixed points where the entire population turns resistant or remains uninfected. Our work broaches a new frontier in the investigation of eco-evolutionary processes arising from the mechanical and ecological forces due to the interactions between viruses and their hosts.

biophysics↗

bioRxiv2025

Physical confinement regulates transition in nematode motility

How do worms navigate their complex natural surroundings? Undulatory microswimmers such as nematodes typically inhabit environments such as soil, vegetable matter, and host tissues. While the natural habitats of nematodes are often three-dimensional granular niches with spatiotemporally varying visco-elasto-plastic material properties that impose physical constraints on their motion, current knowledge about nematode motility patterns broadly comes from investigating model organisms such as Caenorhabditis elegans either inside liquid cultures or the surface of soft agar pads. How nematodes move through 3D granular niches across different degrees of physical confinement remains poorly understood due to a lack of optically transparent 3D granular matrices. We bridge this gap by engineering an optically transparent granular matrix to directly visualise and quantitatively analyse nematode motion. Importantly, nematodes can freely move through this matrix by generating a minimal yield stress; once the nematode moves away, the matrix self-heals to ensure the material properties remain invariant. Using these platforms, we observe that the propulsive speed of nematodes shows a non-monotonic relation with the yield stress of their microenvironment. This non-monotonicity emerges as nematodes optimize for efficient navigation at higher yield stress, wherein, their forward propulsive speed matches the wave speed along their body. This regulation of locomotory behaviour is purely dictated by the physical interaction of the nematode with its environment without involving soft-touch sensory neurons. Remarkably, predictions from a slender body theory of undulatory motion exactly capture the scaling behaviour for both efficiency and mode of motion as obtained from the experimental data. Finally, in a phase space described by non-dimensional propulsive efficiency and a non-dimensional time scale of motility, we capture a gait transition from poorly efficient thrashing under low confinement to more efficient crawling under high confinement. Thus, our work establishes a new regulatory paradigm describing how distinct modes of undulatory motion emerge under different degrees of physical confinement.

biophysics↗

bioRxiv2024

Convergent cellular adaptation to a quiescence-like state in response to freeze-thaw stress

Extreme stress, such as freeze-thaw, poses a severe challenge to many organisms, but the mechanisms underlying their adaptation to survive such stress remain elusive. Here, we show that Saccharomyces cerevisiae can rapidly evolve freeze-thaw tolerance through a physiological state transition, with survival increasing nearly two orders of magnitude from {approx}2% to {approx}70% in about 25 cycles of stress exposure. Evolved yeast cells exhibit a quiescence-like state, characterized by altered cellular physiology: increased intracellular trehalose accumulation, reduced membrane damage, cytoplasmic stiffening and an exit from a proliferative cycle. This mechano-chemically reinforced survival strategy emerges across independent evolutionary lines despite distinct genetic backgrounds, suggesting a convergent mechanism of adaptation. By integrating experimental evolution, biophysical measurements, genomic analysis, and a quantitative model that captures the adaptation dynamics, we reveal that stress tolerance can arise via a potentially generalizable, physiologically mediated adaptation strategy. These findings provide new insights into microbial survival under extreme conditions and suggest broader implications for cellular stress responses beyond yeast.

evolutionary biology↗

bioRxiv2024

Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast

The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism -- spontaneous fluid flows arising from metabolically-generated density gradients -- can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a biophysical scaffold to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how cooption of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.

evolutionary biology↗

bioRxiv2023

Constrained dynamics of oligonucleotides in the phase-separated droplets

Phase-separated droplets are excellent means of compartmentalizing functional molecules and have been shown as excellent models for protocells. Although complex functions based on oligonucleotides have been studied, we still lack an understanding of how the oligonucleotide dynamics are affected by the condensed internal environment of these droplets. Particularly, we lack high-resolution experimental measurements of the dynamical parameters that control oligonucleotide diffusion inside the phase-separated droplets. In addition, there is no clarity on how these dynamical parameters differ in the charged (coacervates) vs non-charged (aqueous two-phase system, ATPS) environment of these droplets. In this study, using fluorescence correlation spectroscopy (FCS), we demonstrate the constrained dynamics of oligonucleotides inside membraneless phase-separated droplets at an unprecedented resolution. We further compare transport properties at different lengths of oligonucleotides as well as salt concentrations. We observe that among all the parameters the oligonucleotides caging (spatial restriction in the movement) inside the matrix has a considerable impact on the diffusive dynamics. Our study provides a way of unravelling, quantifying and understanding physical parameters governing the polymer transport dynamics inside the phase-separated droplets.

biophysics↗

bioRxiv2022

Multispecies autocatalytic RNA reaction networks in coacervates

Robust and dynamic localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of an RNA system within charge-rich coacervates where catalytic RNAs are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates -- both in micron sized droplets as well as a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, these collectively autocatalytic reaction networks endow unique compositional identities to the coacervates which in turn transiently protect the identity against external perturbations, due to differential molecular transport and reaction rates. Our results establish a compartmentalised chemical system possessing a compositional identity possessing a balance between robustness and variability required for chemical evolution.

evolutionary biology↗

bioRxiv2022

Rethinking Population Bottlenecks: Intrinsic Fluctuations, Mutation and Dynamical Demographic Phases

By abruptly changing the size and composition of a population, bottlenecks can dramatically alter evolutionary trajectories. In the traditional picture, the faster a population recovers from a bottleneck, the more rapidly finite-size intrinsic fluctuations are suppressed and therefore the greater the likelihood of fixation to the attractor within whose basin the bottleneck constrained the population, initially. We now argue that this intuition is misleading; demonstrating that precisely the opposite behaviour is also possible. Depending critically on the rate of mutation, increased population growth can drive fixation to attractors that are different to that from whose basin it started. These findings are explained in terms of statistically distinct regimes of demographic behaviour, drawing parallels with the notion of non-equilibrium phase transitions. Such dynamical demographic phases are delimited by sharp transitions in time, as a population grows, and ultimately result from a time-dependent antagonism between mutation and the stochastically-induced effects of frequency-dependent birth.

evolutionary biology↗

bioRxiv2022

GTPase-dependent cyclic flexibility transitions drive the two-component EEA1-Rab5 molecular motor

The recognition of vesicles by their correct target compartment depends on the pairing of small GTPases with effector proteins (1-3). Whereas ATPases can cyclically convert the free energy of ATP hydrolysis into mechanical work, the function of small GTPases is predominantly associated with signal transduction processes, and their role in mechano-transduction is less established (4-6). However, binding of the GTPase Rab5 to the long coiled-coil tethering protein EEA1 on an early endosome induces a rigidity transition resulting in a large conformational change in EEA1 from a rigid and extended to a flexible and collapsed state. This entropic collapse of EEA1 gives rise to an effective force that can pull tethered membranes closer (7). It currently remains unclear if EEA1 can return from the collapsed to the extended conformation without the aid of chaperones. Here, we use fluorescence correlation spectroscopy to reveal that EEA1 in bulk solution can undergo multiple flexibility transition cycles that are associated with the binding and release of Rab5(GTP) and Rab5(GDP). Using semi-flexible polymer theory we provide evidence that the cyclic transitioning of Rab5-EEA1 between extended and collapsed conformations is driven by the energetics of Rab5 binding/unbinding and GTP hydrolysis. Cyclic flexibility transitions represent a complete mechanical work cycle that is able to perform up to 20 kBT of mechanical work per cycle, against an opposing force. Hence, Rab5 and EEA1 constitute a two-component molecular motor driven by the chemical energy derived from GTP hydrolysis by Rab5. We conclude that coiled-coil tethering proteins and their small GTPase partners can have active mechanical roles in membrane trafficking.

biophysics↗

bioRxiv2020

THE IMPACT OF MISTRANSLATION ON PHENOTYPIC VARIABILITY AND FITNESS

Phenotypic variation is widespread in natural populations, and can significantly alter their ecology and evolution. Phenotypic variation often reflects underlying genetic variation, but also manifests via non-heritable mechanisms. For instance, translation errors result in about 10% of cellular proteins carrying altered sequences. Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations. However, this link remains unverified. We manipulated mistranslation levels in Escherichia coli, and measured phenotypic variability between single cells (individual level variation), as well as replicate populations (population level variation). Monitoring growth and survival, we find that mistranslation indeed increases variation across E. coli cells, but does not consistently increase variability in growth parameters across replicate populations. Interestingly, although any deviation from the wild type (WT) level of mistranslation reduces fitness in an optimal environment, the increased variation is associated with a survival benefit under stress. Hence, we suggest that mistranslation-induced phenotypic variation can impact growth and survival and has the potential to alter evolutionary trajectories.

evolutionary biology↗

bioRxiv2020

In vivo multi-dimensional information-keeping in Halobacterium salinarum

Shortage of raw materials needed to manufacture components for silicon-based digital memory storage has led to a search for alternatives, including systems for storing texts, images, movies and other forms of information in DNA. Use of DNA as a medium for storage of 3-D information has also been investigated. However, two problems have yet to be addressed: first, storage of 3-D information in DNA has used objects and coding schemes which require large volumes of data; second, the medium used for DNA information-keeping has been inconsistent with qualities needed for long-term data storage. Here, we address these problems. First, we created in vivo DNA-encoded digital archives holding precise specifications for 3- and 4-dimensional figures with unprecedented efficiency. Second, we have demonstrated more robust and longer-lasting information-carriers than earlier repositories for DNA-based data archives by inserting digital information into the halophile, Halobacterium salinarum, an extremophilic archaeon. We then embedded Information-keeping halophiles into crystalline mineral salts in which similar organisms have been shown to persist in stasis for hundreds of millions of years. We propose that digital information archives composed in 3 or more dimensions may be inserted into halophilic organisms and preserved intact for indefinite periods of time.

synthetic biology↗