Biology subjects

Barak, Y.

Publications and source records attributed to Barak, Y..

9 recordsLinked to original sources

bioRxiv2026

Multi-scale histology reveals localized ageing signatures in normal human colon

Ageing is accompanied by heterogeneous changes in tissue structure, cellular composition, and microenvironments, yet how these changes are reflected in routine human histology remains poorly understood. Here, we introduce a histology-first, multi-scale digital pathology framework to study human colon ageing using hematoxylin and eosin (H&E) whole-slide images from clinically normal colon biopsies. The framework combines pathology foundation-model patch embeddings, attention-based multiple-instance learning, cell-level morphometric profiling, and prototype-based tissue compartmentalization. We show that chronological age can be predicted from normal colon tissue using mesoscopic representations derived from pathology foundation-model patch embeddings and attention-based multiple-instance learning. Incorporating cell-type-level morphometric features further improves prediction and refines the spatial allocation of model attention. By integrating attention maps with prototype-defined tissue compartments, we identify localized age-associated differences within stromal, epithelial, and lymphoid mucosal niches. Finally, we show that prediction discordant cases exhibit cellular profiles shifted toward the model-assigned age group, suggesting that some apparent model errors may reflect tissue-level age discordance beyond chronological age. Together, these findings show that routine H&E histology captures spatially localized signatures of normal human colon ageing and provides a scalable framework for linking tissue morphology with biological ageing state.

pathology↗

bioRxiv2025

Silk fibroin as a modulator of the amyloidogenic α-synuclein aggregation

AO_SCPLOWBSTRACTC_SCPLOWThe aggregation of fiber-forming proteins presents a duality of biological functions, where certain proteins, such as -synuclein, are implicated in neurodegenerative disorders like Parkinsons, while others, like silk fibroin, serve as essential building blocks for functional biomaterials. Despite ongoing investigations into the interplay between these contrasting protein groups, existing reports suggest that the presence of "functional" fibrillar proteins can accelerate amyloid growth via a crowding effect. In this study, we report a counterintuitive outcome, demonstrating that silk fibroin inhibits amyloidogenic aggregation of -synuclein protein. Our findings reveal that although the fibrillar aggregation of both proteins--individually and in mixtures--remains affected by environmental factors such as concentration and temperature, silk fibroin significantly alters the rheological behavior of the mixed solutions. Our structural and kinetic analyses reveal that silk modifies the structural transitions and self-assembly dynamics of -synuclein through macromolecular crowding and non-specific interactions that eventually suppressed the amyloidogenic aggregation of the -synuclein. Notably, when nanofibrillar amyloidogenic assemblies are forced to form in the presence of silk, they exhibit a markedly increased susceptibility to enzymatic degradation, a phenomenon not observed with pure -synuclein fibrillar constructs. These results prompt further investigation into the potential role of "functional" fiber-forming proteins in modulating protein aggregation processes and their implications for therapeutic strategies against neurodegenerative diseases.

biochemistry↗

bioRxiv2025

Refractive index as an indicator for dynamic protein condensation in cell nuclei

Protein condensation is the basis for formation of membrane-less organelles in the cell. Most famously, weak, polyvalent interactions, often including RNA, may lead to a liquid-liquid phase separation. This effect greatly enhances local concentrations and is thought to promote interactions that would remain rare in dilute solution. Synthetic systems provide a means to clarify the underlying biophysical mechanisms at play, both in vitro and in the cell via exogenous expression. In this regard, ferritin is a useful substrate, as its composition of 24 subunits with octahedral symmetry supports self-assembly by close packing in 3D. The conventional diagnostic tool for protein condensation is fluorescence imaging. In this work we explore the use of refractive index mapping to detect states of condensation and decondensation. Using two related ferritin-based self-assembly systems, we find that refractive index is a sensitive indicator for reversible condensation. Surprisingly, refractive index indicates a rapid decondensation even when molecular dispersal kinetics are slow according to fluorescence. Conversely, in a photo-activated condensation where long activation results in slow decondensation kinetics, the refractive index provides reliable evidence for the physical state independent of fluorescence. The observations suggest a distinction between condensation to a sparse biomolecular network, or to a material continuum that supports an optical polarizability distinct from that of the dilute phase in solution.

biophysics↗

bioRxiv2025

Millisecond bidirectional protein translocation by a HSP100 machine

How biological machines harness ATP to drive mechanical work remains a crucial question. Structural studies of protein-translocating AAA+ machines proposed a coupled and sequential translocation process, whereby ATP hydrolysis events lead to short threading steps. Yet, direct real-time observation of these events remains elusive. Here, we employ single-molecule FRET spectroscopy to track substrate translocation through ClpB, a quality control AAA+ machine. We isolate ClpB and its substrate within lipid vesicles and find that translocation events, while dependent on ATP, take milliseconds, much faster than ATP hydrolysis times. Surprisingly, the translocation rate depends weakly on temperature and ATP concentration. Using three-color FRET experiments, we find that translocation events can occur bidirectionally but are not always complete. Replacing ATP with the slowly hydrolysable analog ATP{gamma}S abolishes both rapid translocation and directionality. These results indicate a fast, stochastic Brownian-motor-like mechanism, redefining how ATP is coupled with mechanical action in AAA+ machines.

biophysics↗

bioRxiv2024

Autonomous biogenesis of the entire protein translation machinery excluding ribosomes

Recreating the conditions for autonomous biogenesis of the protein translation machinery is fundamental to our understanding of living systems and is essential for the assembly of minimal cell models. All components of the translation machinery, including the ribosomes, translation factors and aminoacyl tRNA synthetases, are made of proteins and are therefore involved in their own synthesis, posing a unique challenge for self-biogenesis. Here, we created physicochemical conditions for autonomous biogenesis of all the translation machinery, excluding the ribosome. We surface-immobilized synthetic genes coding for all thirty components as densely packed DNA brushes forming a reaction center that localizes, concentrates and catalyzes their simultaneous synthesis. To demonstrate their activity, we first determined empirically the minimal critical concentration of each translation protein required to initiate its own self-biogenesis in bulk solution. We then assembled a minimal gene expression reaction with all translation proteins at their critical concentrations. Under these dilute conditions, reporter proteins were not synthesized unless the DNA brushes encoded all the translation proteins, thereby demonstrating their co-synthesis, functionality and engagement in their own synthesis. This scenario of a complex biochemical process that amplifies itself can be generalized and extended to impact our understanding toward the design of autonomous self-replicating biological system.

synthetic biology↗

bioRxiv2023

A genetic circuit on a single DNA molecule as autonomous dissipative nanodevice

Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcriptiontranslation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we used a genetically encoded fluorescent reporter system with improved spatiotemporal resolution and observed the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally designed a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibited enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that coexpressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.

synthetic biology↗

bioRxiv2023

From Microstates to Macrostates in the Conformational Dynamics of GroEL: a Single-Molecule FRET Study

The chaperonin GroEL is a multi-subunit molecular machine that assists in protein folding in the E. coli cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. However, a measurement of subunit dynamics and their relation to the allosteric cycle of GroEL has been missing. Here, we report single-molecule FRET measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the co-chaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-liganded conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis, confirming the essential role of the observed dynamics in the function of GroEL. Significance StatementGroEL is a large protein-folding machine whose activity is accompanied by considerable conformational motions. Here, we use single-molecule FRET spectroscopy in combination with photon-by-photon statistical analysis to characterize the motions of a single GroEL subunit in real time and in the presence of ADP, ATP, and the co-chaperone GroES. Our results reveal transitions between four conformations on a timescale much faster than the functional cycle. We show that the motions of an individual subunit are directly coupled to the concerted allosteric mechanism of GroEL. This work, therefore, further demonstrates the impact of fast conformational dynamics on the biochemical function of molecular machines.

biophysics↗

bioRxiv2021

Water and Electrolyte Homeostasis in a Mouse Model with Reduced ENaC Gamma Subunit Expression

The epithelial Na+ channel (ENaC) promotes the absorption of Na+ in the aldosterone-sensitive distal nephron, colon, and respiratory epithelia. Deletion of genes encoding ENaCs subunits results in early post-natal mortality. We present initial characterization of a mouse with dramatically suppressed expression of the {gamma} subunit. We use this hypomorphic ({gamma}mt) allele to explore the importance of ENaCs {gamma} subunit in homeostasis of electrolytes and body fluid volume. At baseline, {gamma} subunit expression in {gamma}mt/mt mice is markedly suppressed in kidney and lung, while electrolytes resemble those of littermate controls. Challenge with a high K+ diet does not cause significant differences in blood K+, but provokes higher aldosterone in {gamma}mt/mt mice than controls. Quantitative magnetic resonance (QMR) measurement of body composition reveals similar baseline body water, lean tissue mass, and fat tissue mass in {gamma}mt/mt mice and controls. Surprisingly, euvolemia is sustained without significant changes in aldosterone or atrial natriuretic peptide. {gamma}mt/mt mice exhibit a more rapid decline in body water and lean tissue mass in response to a low Na+ diet than controls. Replacement of drinking water with 2% saline induces dramatic increases in body fat in both genotypes, and a selective transient increase in body water and lean tissue mass in {gamma}mt/mt mice. While ENaC in renal tubules and colon work to prevent extracellular fluid volume depletion, our observations suggest that ENaC in non-epithelial tissues may have a role in preventing extracellular fluid volume overload.

physiology↗

bioRxiv2018

Dynamic interactions of type I cohesin modules fine-tune the structure of the cellulosome of Clostridium thermocellum

Efficient degradation of plant cell walls by selected anaerobic bacteria is performed by large extracellular multienzyme complexes termed cellulosomes. The spatial arrangement within the cellulosome is organized by a protein called scaffoldin, which recruits the cellulolytic subunits through interactions between cohesin modules on the scaffoldin and dockerin modules on the enzymes. Although many structural studies of the individual components of cellulosomal scaffoldins have been performed, the role of interactions between individual cohesin modules and the flexible linker regions between them are still not entirely understood. Here, we report single-molecule measurements using Forster resonance energy transfer to study the conformational dynamics of a bimodular tandem cohesin segment of the scaffoldin protein CipA of Clostridium thermocellum. Our data reveal the existence of compacted structures in solution that persist on the timescale of milliseconds. The compacted conformation is found to be in dynamic equilibrium with an extended state that shows distance fluctuations on the microsecond timescale. Shortening of the inter-cohesin linker does not significantly alter the structural dynamics. Upon addition of dockerin-containing enzymes, an extension of the flexible state is observed but the cohesin-cohesin interactions persist. This suggests that the dockerin-binding interfaces are not involved in cohesin-cohesin interactions. The formation of cohesin-cohesin interactions is also observed in all-atom molecular dynamics simulations of the system. From the simulations, we identify possible inter-cohesin binding modes, none of which show obstruction of the cohesin-dockerin binding interfaces. Our results go beyond the view of scaffoldin as \"beads on a string\". We propose that both the flexibility and cohesin-cohesin interactions are important factors for the precise spatial arrangement of the enzymatic subunits in the cellulosome that leads to the high catalytic synergy in these assemblies. Hence, the flexibility of the linker region and cohesin-cohesin interactions should be considered when designing cellulosomes for industrial applications.

biophysics↗