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bioRxiv2023

Active Transport by Cytoplasmic Dynein Maintains the Localization of MAP-2 in Developing Neurons

MAP2 has been widely used as a marker of neuronal dendrites because of its extensive restriction in the somatodendritic region of neurons. Despite that, how the precise localization of such a soluble protein is established and maintained against thermal forces and diffusion has been elusive and long remained a mystery in neuroscience. In this study, we aimed to uncover the mechanism behind how MAP2 is retained in the somatodendritic region. Using GFP-tagged MAP2 expressed in cultured hippocampal neurons, we discovered a crucial protein region responsible for the localization of MAP2, the serine/proline-rich (S/P) region. Our pulse-chase live-cell imaging revealed the slow but steady migration of MAP2 toward distal dendrites, which was not observed in a MAP2 mutant lacking the S/P region, indicating that S/P-dependent transport is vital for the proper localization of MAP2. Furthermore, our experiments using an inhibitor of cytoplasmic Dynein, ciliobrevin D, as well as Dynein knockdown, showed that cytoplasmic Dynein is involved in the transport of MAP2 in dendrites. We also found that Dynein complex binds to MAP2 through the S/P region in heterologous cells. Using mathematical modeling based on experimental data, we confirmed that an intermittent active transport mechanism is essential. Thus, we propose that the cytoplasmic Dynein recruits and transports free MAP2 toward distal dendrites, thereby maintaining the precise dendritic localization of MAP2 in neurons. Our findings shed light on the previously unknown mechanism behind MAP2 localization and provide a new direction for soluble protein trafficking research in the field of cell biology of neurons.

neuroscience↗

bioRxiv2023

Small ADP-ribosylation factor-like GTPase TITAN5 (TTN5/ARL2) is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER1

Iron acquisition is crucial for plants. The abundance of IRON-REGULATED TRANSPORTER 1 (IRT1) at the plasma membrane is controlled through endomembrane trafficking. Vesicular trafficking requires small ARF-like GTPases, one of them is TITAN 5 (TTN5). Its physiological functions during the life cycle and cellular targets remain unknown. Little is known how the vesicular trafficking mechanism affects IRT1 localization. We show that TTN5 interacts with the large cytoplasmic variable region and protein-regulatory platform of IRT1. ttn5-1+/- plants have a reduced activity of root iron reductase, needed for iron uptake via IRT1. Fluorescent fusion proteins of TTN5 and IRT1 colocalize at the plasma membrane and in endosomes/multivesicular bodies, where IRT1 sorting and cycling between the plasma membrane and the vacuole are coordinated. Colocalization at the plasma membrane depends partly on the interaction ability of TTN5. TTN5 can also interact with peripheral membrane proteins that are components of the IRT1 regulation machinery, like the trafficking factor SNX1, the C2 domain protein EHB1 and the SEC14-GOLD protein PATL2. Hence, this work links iron acquisition and vesicular trafficking involving a small GTPase of the ARF family. This opens up the possibility to study the involvement of TTN5 in nutritional cell biology in the endomembrane system. HighlightsO_LITTN5 interacts with the large intracellular loop and variable region of IRON-REGULATED TRANSPORTER 1 (IRT1) C_LIO_LITTN5 has a positive effect on root iron (Fe) reductase activity. C_LIO_LITTN5 and IRT1 colocalize at the plasma membrane and in the endomembrane system related to vesicle transport C_LIO_LITTN5 can interact with peripheral membrane proteins of the IRT1 interactome, EHB1, PATL2 and SNX1 suggesting a coordinating role in IRT1 regulation C_LI One-sentence summaryTTN5, a small ARF-like GTPase, is connected to the dynamic regulation of IRON-REGULATED TRANSPORTER 1 (IRT1) in the vesicular trafficking system through direct protein interaction and colocalization, linking with various peripheral membrane proteins of the IRT1 interactome and iron reductase activity.

plant biology↗

bioRxiv2023

Direct detection of deformation modes on varying length scales in active biopolymer networks

Correlated flows and forces that emerge from active matter orchestrate complex processes such as shape regulation and deformations in biological cells and tissues. The active materials central to cellular mechanics are cytoskeletal networks, where molecular motor activity drives deformations and remodeling. Here, we investigate deformation modes in contractile actin networks driven by the molecular motor myosin II through quantitative fluorescence microscopy. We examine the deformation anisotropy at different length scales in networks of sparsely cross-linked and bundled actin. In sparsely cross-linked networks, we find myosin-dependent biaxial buckling modes across length scales. Interestingly, both long and short-wavelength buckling may contribute to network contractility. In cross-linked bundled networks, uniaxial contraction predominates on long length scales, while the uniaxial or biaxial nature of the deformation depends on bundle microstructure at shorter length scales. The anisotropy of deformations may provide insight to the mechanical origins of contractility in actin networks and regulation of collective behavior in a variety of active materials.

biophysics↗

bioRxiv2023

The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation

Extra-chromosomal selfish DNA elements can evade the risk of being lost at every generation by behaving as chromosome appendages, thereby ensuring high fidelity segregation and stable persistence in host cell populations. The yeast 2-micron plasmid and episomes of the mammalian gammaherpes and papilloma viruses that tether to chromosomes and segregate by hitchhiking on them exemplify this strategy. We document for the first time the utilization of a SWI/SNF-type chromatin remodeling complex as a conduit for chromosome association by a selfish element. One principal mechanism for chromosome tethering by the 2-micron plasmid is the bridging interaction of the plasmid partitioning proteins (Rep1 and Rep2) with the yeast RSC2 complex and the plasmid partitioning locus STB. We substantiate this model by multiple lines of evidence derived from genomics, cell biology and interaction analyses. We describe a Rep-STB bypass system in which a plasmid engineered to non-covalently associate with the RSC complex mimics segregation by chromosome hitchhiking. Given the ubiquitous prevalence of SWI/SNF family chromatin remodeling complexes among eukaryotes, it is likely that the 2-micron plasmid paradigm or analogous ones will be encountered among other eukaryotic selfish elements.

molecular biology↗

bioRxiv2023

Unravelling a novel role for Cannabidivarin in the modulation of subventricular zone postnatal neurogenesis

Postnatal neurogenesis has been shown to rely on the endocannabinoid system. Here we aimed at unravelling the role of Cannabidivarin (CBDV), a non-psychoactive cannabinoid, with high affinity for the non-classical cannabinoid receptor TRPV1, on subventricular zone (SVZ) postnatal neurogenesis. Using the neurosphere assay, SVZ-derived neural stem/progenitor cells (NSPCs) were incubated with CBDV and/or 5-Iodoresinferotoxin (TRPV1 antagonist), and their role on cell viability, proliferation, and differentiation were dissected. CBDV was able to promote, through a TRPV1-dependent mechanism, cell survival, cell proliferation and neuronal differentiation. Furthermore, pulse-chase experiments revealed that CBDV-induced neuronal differentiation was a result of cell cycle exit of NSPCs. Regarding oligodendrocyte differentiation, CBDV inhibited oligodendrocyte differentiation and maturation. Since our data suggested that the CBDV-induced modulation of NSPCs acted via TRPV1, a sodium-calcium channel, and that intracellular calcium levels are known regulators of NSPCs fate and neuronal maturation, single cell calcium imaging was performed to evaluate the functional response of SVZ-derived cells. We observed that CBDV-responsive cells displayed a two-phase calcium influx profile, being the initial phase dependent on TRPV1 activation. Taken together, this work unveiled a novel and untapped neurogenic potential of CBDV via TRPV1 modulation. These findings pave the way to future neural stem cell biological studies and repair strategies by repurposing this non-psychoactive cannabinoid as a valuable therapeutic target.

neuroscience↗

bioRxiv2023

Novel TRPM7 inhibitors with potent anti-inflammatory effects in vivo

TRPM7, a TRP channel with ion conductance and kinase activities, has emerged as an attractive drug target for immunomodulation. Reverse genetics and cell biological studies have already established a key role for TRPM7 in the inflammatory activation of macrophages. Advancing TRPM7 as a viable molecular target for immunomodulation requires selective TRPM7 inhibitors with in vivo tolerability and efficacy. Such inhibitors have the potential to interdict inflammatory cascades mediated by systemic and tissue-specialized macrophages. FTY720, an FDA-approved drug for multiple sclerosis inhibits TRPM7. However, FTY720 is a prodrug and its metabolite, FTY720-phosphate, is a potent agonist of sphingosine 1-phosphate (S1P) receptors. In this study, we tested non-phosphorylatable FTY720 analogs, which are inert against S1PRs and well tolerated in vivo, for activity against TRPM7 and tissue bioavailability. Using patch clamp electrophysiology, we show that VPC01091.4 and AAL-149 block TRPM7 current at low micromolar concentrations. In culture, they act directly on macrophages to blunt LPS-induced inflammatory cytokine expression, an effect that is predominantly but not solely mediated by TRPM7. We found that VPC01091.4 has significant and rapid accumulation in the brain and lungs, along with direct anti-inflammatory action on alveolar macrophages and microglia. Finally, using a mouse model of endotoxemia, we show VPC01091.4 to be an efficacious anti-inflammatory agent that arrests systemic inflammation in vivo. Together, these findings identify novel small molecule inhibitors that allow TRPM7 channel inhibition independent of S1P receptor targeting. These inhibitors exhibit potent anti-inflammatory properties that are mediated by TRPM7 and likely other molecular targets that remain to be identified.

immunology↗

bioRxiv2023

Pain hypersensitivity is dependent on autophagy protein Beclin 1 in males but not females

Chronic pain is a pervasive health, social, and economic problem affecting 1 in 5 individuals around the world. Increasingly, it is understood that alterations in fundamental cell biological processes are critical for chronic pain. A prominent cellular process is autophagy but whether it plays a role in pain is unknown. To investigate whether autophagy is involved in pain processing and is targetable for pain relief, we focused on Beclin 1, a component of the class III phosphatidylinositol 3-kinase (PI3K) complex necessary for initiating autophagy. Here, we found that inflammatory pain hypersensitivity in male mice lacking one allele of Becn1 is significantly greater than that in wild type mice. By contrast, in female mice, loss of Becn1 did not affect inflammation-induced pain hypersensitivity. Further, intrathecal delivery of an activator of Beclin 1, tat-beclin 1, reversed mechanical hypersensitivity induced by peripheral inflammation or peripheral nerve injury in males. Tat-beclin 1 also prevented mechanical hypersensitivity induced by exogenous brain-derived neurotrophic factor (BDNF), a core mediator of inflammatory and neuropathic pain in the spinal dorsal horn in males. Pain signaling pathways converge on enhancement of N-methyl-D-aspartate receptors (NMDARs) in spinal dorsal horn neurons. We found that loss of Beclin 1 increases expression of the pain-critical NMDAR subunit, GluN2B, in the dorsal horn and upregulates synaptic NMDAR-mediated currents in dorsal horn neurons from males but not females. From our converging lines of evidence, we conclude that inhibition of Beclin 1 in the dorsal horn is critical in mediating inflammatory and neuropathic pain signaling pathways in males. Our findings provide the basis for sex-specific therapeutic approaches targeting pain with a new class of analgesics - activators of Beclin 1.

neuroscience↗

bioRxiv2023

The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling

Desmosomes mediate cell-cell adhesion and are prevalent in tissues under mechanical stress. However, their detailed structural characterization is not available. Here, we characterized the molecular architecture of the desmosomal outer dense plaque (ODP) using Bayesian integrative structural modeling via the Integrative Modeling Platform. Starting principally from the structural interpretation of an electron cryo-tomogram, we integrated information from X-ray crystallography, an immuno-electron microscopy study, biochemical assays, in-silico predictions of transmembrane and disordered regions, homology modeling, and stereochemistry information. The integrative structure was validated by information from imaging, tomography, and biochemical studies that were not used in modeling. The ODP resembles a densely packed cylinder with a PKP layer and a PG layer; the desmosomal cadherins and PKP span these two layers. Our integrative approach allowed us to localize disordered regions, such as N-PKP and PG-C. We refined previous protein-protein interactions between desmosomal proteins and provided possible structural hypotheses for defective cell-cell adhesion in several diseases by mapping disease-related mutations on the structure. Finally, we point to features of the structure that could confer resilience to mechanical stress. Our model provides a basis for generating experimentally verifiable hypotheses on the structure and function of desmosomal proteins in normal and disease states. Significance statementDesmosomes are cell-cell junctions that possess a hyper-adhesive property and are prevalent in tissues under mechanical stress. However, their detailed structural characterization has eluded experimental structural biologists so far. Here, we use an integrative approach that allows us to rigorously combine biochemical, biophysical, and cell biological data at multiple scales in order to determine the molecular architecture of the outer dense plaque region of desmosomes. We validate the structural model by several pieces of information not used to compute it. The model allows us to generate hypotheses on the desmosomal proteins in normal and disease states.

biophysics↗

bioRxiv2023

Maternal regulation of the vertebrate oocyte-to-egg transition

Maternally-loaded factors in the egg accumulate during oogenesis and are essential for the oocyte and egg to acquire developmental competence and ensure the production of viable embryos. The oocyte-to-egg transition consists of the regulation of multiple molecular processes both cytoplasmic and nuclear acting in the late oocyte during a process called oocyte maturation. However, the molecular nature and functional importance of factors acting at this stage remain poorly understood. Here, we present a collection of 5 recessive maternal-effect mutants identified in a zebrafish forward genetic screen that reveal unique molecular insights into the mechanisms controlling the vertebrate oviparous oocyte-to-egg transition. We identified critical cytoplasmic regulators of yolk globule formation and maturation that are essential for egg development and embryogenesis. Specifically, the maternal-effect genes, over easy, poached, p33bjta, and black caviar control yolk globule sizing and/or protein cleavage during oogenesis, likely through endolysosomal organization independent of nuclear oocyte maturation. Furthermore, we cloned one of the mutant genes, identifying a subunit of the Adaptor Protein complex 5, which regulates intracellular trafficking, and yolk vesicle formation. Together, these mutant genes represent novel genetic entry points to decipher the molecular mechanisms functioning in the oocyte-to-egg transition, fertility, and human disease. Additionally, our genetic screen provides valuable functional tools for exploring the evolutionary fates of maternal factors and their contribution to developmental strategies for reproductive success in metazoans. Author SummaryThe oocyte-to-egg transition consists of the coordinated regulation of multiple molecular processes acting in the late oocyte. This transcriptionally silent period requires the precisely timed function of maternally-supplied gene products during oogenesis. However, knowledge of their molecular nature and in vivo function remains incomplete. The mutants reported here provide access to maternal factors regulating the processes that prepare an oocyte for reproductive competence and embryogenesis. We have identified essential regulators of yolk granule formation and protein processing. Specifically, we found that the highly conserved maternal Ap5m1 protein regulates yolk granule maturation, which generate essential nutrients and immunity for growth and development in oviparous animals. The mutants presented here represent attractive genetic models to investigate the molecular and cell biological mechanisms that control the oocyte-to-egg transition, as well as reveal a collection of genetic factors indispensable for reproduction and survival. Importantly, knowledge of their genetic underpinnings and biological importance in reproduction will also pave the way to investigate the evolution of maternal genes during vertebrate development.

developmental biology↗

bioRxiv2023

Dynamics of giant vesicle assembly from thin lipid films

Giant unilamellar vesicles (GUVs) are micrometer-scale lipid assemblies that emulate key characteristics of biological cell membranes. GUVs can be obtained when solid-supported thin films of lipids are hydrated in aqueous solutions. However, a comprehensive understanding of their assembly dynamics has been lacking, impeding mechanistic insights. Here, we report the time dependence of the distribution of sizes and molar yield of GUVs obtained through a novel stopped-time technique. We compare three commonly used techniques, PAPYRUS (Paper-Abetted amPhiphile hYdRation in aqUeous Solutions) gentle hydration, and electroformation. We demonstrate that all three techniques show sigmoidal yield curves. Yields increase monotonically before reaching a plateau, with surprisingly high yields 60 seconds after hydration. Gentle hydration shows limited time evolution in contrast to PAPYRUS and electroformation. Exploration of bud dynamics on the surfaces uncovers bud emergence, diameter growth, and merging phenomena. To provide a comprehensive explanation of our observations, we employ the thermodynamic budding and merging model. This work expands our understanding of GUV assembly dynamics and offers fundamental insights into the underlying thermodynamic principles governing this process.

biophysics↗

bioRxiv2023

In vitro reconstitution of the M.tb proteasome core particle reveals conserved aspects of bacterial proteasome assembly

According to the WHO, one in three people in the world has a latent tuberculosis infection. Tuberculosis is caused by the bacterium Mycobacterium tuberculosis (M.tb). The development of multi-drug resistant (MDR) tuberculosis indicates a need for novel treatments. Hence, it is important to find a second line of treatment for patients infected with MDR tuberculosis. The proteasome is known to be necessary for survival under stress and pathogenicity in M.tb. However, our ability to use the proteasome as drug target has been limited by our abilities to screen for inhibitor compounds in vitro. The proteasome is a protease complex that degrades proteins and is crucial for the maintenance of protein homeostasis within cells. Like many protein complexes, the proteasome must assemble into a specific quaternary structure in order to be active. Specifically, the proteolytically-active proteasome Core Particle (CP) consists of 28 subunits (14 and 14 {beta}) that must assemble into a barrel-like structure in order to become catalytically active. Hence, understanding the assembly process in not only important from a basic cell biological perspective, but may also serve as the basis for the discovery of novel assembly inhibitors. In this study, we have established for the first time a protocol to express and purify the M.tb and {beta} subunits separately in vitro. The subunits are soluble monomers on purification and only assemble into active CPs upon reconstitution. Our assembly experiments revealed that M.tb CP assembly pathway is almost certainly identical to that seen in previous experiments on the CP from the bacterium Rhodococcus erythropolis (R.e), but assembly in M.tb is much slower. Interestingly, we found that subunits from M.tb and R.e spontaneously self-assembled into active hybrid proteasomes on reconstitution with each other, despite having only 65% sequence similarity. Our work thus strongly suggests that the CP assembly pathway is conserved across bacteria, and the ability to perform in vitro assembly experiments on the M.tb proteasome opens up the possibility of performing critical experiments, including screening for potential molecules that could inhibit assembly, directly in this clinically-relevant organism.

biochemistry↗

bioRxiv2023

Probing the in-situ volumes of Arabidopsis leaf plastids using 3D confocal and scanning electron microscopy

Leaf plastids harbor a plethora of biochemical reactions including photosynthesis, one of the most important metabolic pathways on earth. Scientists are eager to unveil the physiological processes within the organelle but also their interconnection with the rest of the plant cell. An increasingly important feature of this venture is to use experimental data in the design of metabolic models. A remaining obstacle has been the limited in situ volume information of plastids and other cell organelles. To fill this gap for chloroplasts, we established three microscopy protocols delivering in situ volumes based on: 1) chlorophyll fluorescence emerging from the thylakoid membrane, 2) a CFP marker embedded in the envelope, and 3) calculations from serial block-face scanning electron microscopy (SBFSEM). The obtained data were corroborated by comparing wild-type data with two mutant lines affected in the plastid division machinery known to produce small and large mesophyll chloroplasts, respectively. Furthermore, we also determined the volume of the much smaller guard cell plastids. Interestingly, their volume is not governed by the same components of the division machinery which defines mesophyll plastid size. Based on our three approaches the average volume of a mature Col-0 wild-type mesophyll chloroplasts is 93 {micro}m3. Wild-type guard cell plastids are approximately 18 {micro}m3. Lastly, our comparative analysis shows that the chlorophyll fluorescence analysis can accurately determine chloroplast volumes, providing an important tool to research groups without access to transgenic marker lines expressing genetically encoded fluorescence proteins or costly SBFSEM equipment. Significance statement -sentence summaryThis work describes and compares three different strategies to obtain accurate volumes of leaf plastids from Arabidopsis, the most widely used model plant. We hope our contribution will support quantitative metabolic flux modeling and spark other projects aimed at a more metric-driven plant cell biology.

plant biology↗

bioRxiv2023

Massively Concurrent Sub-Cellular Traction Force Videography enabled by Single-Pixel Optical Tracers (SPOTs)

We report a large field-of-view and high-speed videography platform for measuring the sub-cellular traction forces of more than 10,000 biological cells over 13mm2 at 83 frames per second. Our Single-Pixel Optical Tracers (SPOT) tool uses 2-dimensional diffraction gratings embedded into a soft substrate to convert cells mechanical traction stress into optical colors detectable by a video camera. The platform measures the sub-cellular traction forces of diverse cell types, including tightly connected tissue sheets and near isolated cells. We used this platform to explore the mechanical wave propagation in a tightly connected sheet of Neonatal Rat Ventricular Myocytes (NRVMs) and discovered that the activation time of some tissue regions are heterogeneous from the overall spiral wave behavior of the cardiac wave. One-Sentence SummaryAn optical platform for fast, concurrent measurements of cell mechanics at 83 frames per second, over a large area of 13mm2.

bioengineering↗

bioRxiv2023

Vascularized tumor on a microfluidic chip to study mechanisms promoting tumor neovascularization and vascular targeted therapies

The cascade of events leading to tumor formation includes induction of a tumor supporting neovasculature as a primary hallmark of cancer. Developing vasculature is difficult to evaluate in vivo but can be captured using microfluidic chip technology and patient derived cells. Herein, we established an on chip approach to investigate the mechanisms promoting tumor vascularization and vascular targeted therapies via co-culture of metastatic renal cell carcinoma spheroids and endothelial cells in a 3D environment. Our model permitted real-time, high-resolution observation and assessment of tumor-induced angiogenesis, where endothelial cells sprout towards the tumor and mimic a vascular network. Bevacizumab, an angiogenic inhibitor, disrupted interactions between vessels and tumors, destroying the vascular network. The on chip approach enabled assessment of endothelial cell biology, vessels functionality, drug delivery, and molecular expression of PSMA. Finally, observations in the vascularized tumor on chip permitted direct and conclusive quantification of this therapy in weeks as opposed to months in a comparable animal model. TeaserVascularized tumor on microfluidic chip provides opportunity to study targeted therapies and improves preclinical drug discovery.

cancer biology↗

bioRxiv2023

Machine learning of cellular metabolic rewiring

Metabolic rewiring allows cells to adapt their metabolism in response to evolving environmental conditions. Traditional metabolomics techniques, whether targeted or untargeted, often struggle to interpret these adaptive shifts. Here, we introduce MetaboLiteLearner, a machine learning framework that harnesses the detailed fragmentation patterns from electron ionization (EI) collected in scan mode during gas chromatography/mass spectrometry (GC/MS) to predict abundance changes in metabolically adapted cells. When tested on breast cancer cells with different preferences to metastasize to specific organs, MetaboLiteLearner predicted the impact of metabolic rewiring on metabolites withheld from the training dataset using only the EI spectra, without metabolite identification or pre-existing knowledge of metabolic networks. The model learned captures shared and unique metabolomic shifts between brain- and lung-homing metastatic lineages, suggesting potential organ-tailored cellular adaptations. Integrating machine learning and metabolomics paves the way for new insights into complex cellular adaptations. SignificanceMetabolic rewiring--the cellular adaptation to shifts in environment and nutrients--plays key roles in many contexts, including cancer metastasis. Traditional metabolomics often falls short of capturing the nuances of these metabolic shifts. This work introduces MetaboLiteLearner, a machine learning approach that harnesses the rich fragmentation patterns from electron ionization collected in scan mode during gas chromatography/mass spectrometry, paving the way for new insights into metabolic adaptations. Demonstrating its robustness on a breast cancer model, we highlight MetaboLiteLearners potential to reshape our understanding of metabolic rewiring, with implications in diagnostics, therapeutics, and basic cell biology.

bioinformatics↗

bioRxiv2023

Genome replication in asynchronously growing microbial populations

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and genome stability. Qualitatively, in a growing cell culture, one expects that genomic regions that are replicated early should be more abundant than regions that are replicated late. This abundance pattern can be experimentally measured using deep sequencing. However, a general quantitative theory to explain these data is still lacking. In this paper, we predict the abundance of DNA fragments in asynchronously growing cultures from any given stochastic model of the DNA replication program. As key examples, we present stochastic models of the DNA replication programs in Escherichia coli and in budding yeast. In both cases, our approach leads to analytical predictions that are in excellent agreement with experimental data and permit to infer key information about the replication program. In particular, our method is able to infer the locations of known replication origins in budding yeast with high accuracy. These examples demonstrate that our method can provide insight into a broad range of organisms, from bacteria to eukaryotes.

biophysics↗

bioRxiv2023

Onsager's variational principle in proliferating biological tissues, in presenceof activity and anisotropy

A hallmark of biological cells is their ability to proliferate and of tissues their ability to grow. This is common in morphogenesis and embryogenesis but also in pathological conditions such as tumour growth. To consider these tissues from a physical point of view, it is necessary to derive fundamental relationships, in particular for velocities and density components, taking into account growth terms, chemical factors and the symmetry of cells and tissues. The aim is then to develop a consistent coarse-grained approach to these complex systems, which exhibit proliferation, disorder, anisotropy and activity at small scales. To this end, Onsagers variational principle allows the systematic derivation of flux-force relations in systems out of equilibrium and the principle of the extremum of dissipation, first formulated by Rayleigh and revisited by Onsager, finally leads to a consistent formulation for a continuous approach in terms of a coupled set of partial differential equations. Considering the growth and death rates as fluxes, as well as the chemical reactions driving the cellular activities, we derive the momentum equations based on a leading order physical expansion. Furthermore, we illustrate the different interactions for systems with nematic or polar order at small scales, and numerically solve the resulting system of partial differential equations in relevant biophysical growth examples. To conclude, we show that Onsagers variational principle is useful for systematically exploring the different scenarios in proliferating systems, and how morphogenesis depends on these interactions.

biophysics↗

bioRxiv2023

Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as fission yeasts. As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available short-read genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNAs, transfer RNAs, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics. Take-awayO_LIA telomere-to-telomere genome assembly of the fission yeast S. japonicus C_LIO_LIChromosome 2 harbours a previously unknown second centromere-like region C_LIO_LIThe estimated genome size of S. japonicus may be up to 18.12 Mb C_LI

genomics↗