Publications by authors named "Ariel Amir"

Take a drinking straw and bend it from its ends. After sufficient bending, the tube buckles forming a kink, where the curvature is localized in a very small area. This instability, known generally as the Brazier effect, is inherent to thin-walled cylindrical shells, which are particularly ubiquitous in living systems, such as rod-shaped bacteria.

View Article and Find Full Text PDF

The Luria-Delbrück model is a classic model of population dynamics with random mutations, that has been used historically to prove that random mutations drive evolution. In typical scenarios, the relevant mutation rate is exceedingly small, and mutants are counted only at the final time point. Here, inspired by recent experiments on DNA repair, we study a mathematical model that is formally equivalent to the Luria-Delbrück setup, with the repair rate p playing the role of mutation rate, albeit taking on large values, of order unity per cell division.

View Article and Find Full Text PDF

A critical cell cycle checkpoint for most bacteria is the onset of constriction when the septal peptidoglycan synthesis starts. According to the current understanding, the arrival of FtsN to midcell triggers this checkpoint in Escherichia coli. Recent structural and in vitro data suggests that recruitment of FtsN to the Z-ring leads to a conformational switch in actin-like FtsA, which links FtsZ protofilaments to the cell membrane and acts as a hub for the late divisome proteins.

View Article and Find Full Text PDF
Article Synopsis
  • The study investigates how Mycobacterium tuberculosis (Mtb) grows differently compared to other bacteria, particularly focusing on its cell growth patterns and behaviors at the single-cell level.
  • Using time-lapse imaging and mathematical modeling, it was found that Mtb has an asymmetric growth pattern and displays variability in cell size, growth speed, and division times.
  • Unlike typical bacteria that grow exponentially, Mtb grows in a linear fashion, indicating that its growth regulation mechanisms might differ significantly from those of other bacterial species.
View Article and Find Full Text PDF

Surging interest in individual differences has faced setbacks in light of recent replication crises in psychology, for example in brain-wide association studies exploring brain-behavior correlations. A crucial component of replicability for individual differences studies, which is often assumed but not directly tested, is the reliability of the measures we use. Here, we evaluate the reliability of different cognitive tasks on a dataset with over 250 participants, who each completed a multi-day task battery.

View Article and Find Full Text PDF

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited.

View Article and Find Full Text PDF

Neutrophils collectively migrate to sites of injury and infection. How these swarms are coordinated to ensure the proper level of recruitment is unknown. Using an ex vivo model of infection, we show that human neutrophil swarming is organized by multiple pulsatile chemoattractant waves.

View Article and Find Full Text PDF

Error correction is central to many biological systems and is critical for protein function and cell health. During mitosis, error correction is required for the faithful inheritance of genetic material. When functioning properly, the mitotic spindle segregates an equal number of chromosomes to daughter cells with high fidelity.

View Article and Find Full Text PDF

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population's mean fitness are poorly understood.

View Article and Find Full Text PDF

Cell growth and gene expression, two essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in experimental single-cell methods have invigorated theoretical studies into these processes. However, until recently, there was little dialog between the two areas of study.

View Article and Find Full Text PDF

Bacteria undergo cycles of growth and starvation to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. Although high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear.

View Article and Find Full Text PDF

In the past decade, great strides have been made to quantify the dynamics of single-cell growth and division in microbes. In order to make sense of the evolutionary history of these organisms, we must understand how features of single-cell growth and division influence evolutionary dynamics. This requires us to connect processes on the single-cell scale to population dynamics.

View Article and Find Full Text PDF

Unlabelled: Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited.

View Article and Find Full Text PDF

Neutrophils exhibit self-amplified swarming to sites of injury and infection. How swarming is controlled to ensure the proper level of neutrophil recruitment is unknown. Using an model of infection, we find that human neutrophils use active relay to generate multiple pulsatile waves of swarming signals.

View Article and Find Full Text PDF

The statistics of noise emitted by ultrathin crumpled sheets is measured while they exhibit logarithmic relaxations under load. We find that the logarithmic relaxation advanced via a series of discrete, audible, micromechanical events that are log-Poisson distributed (i.e.

View Article and Find Full Text PDF

The ability of bacterial pathogens to regulate growth is crucial to control homeostasis, virulence, and drug response. Yet, we do not understand the growth and cell cycle behaviors of (Mtb), a slow-growing pathogen, at the single-cell level. Here, we use time-lapse imaging and mathematical modeling to characterize these fundamental properties of Mtb.

View Article and Find Full Text PDF

How cells regulate their cell cycles is a central question for cell biology. Models of cell size homeostasis have been proposed for bacteria, archaea, yeast, plant, and mammalian cells. New experiments bring forth high volumes of data suitable for testing existing models of cell size regulation and proposing new mechanisms.

View Article and Find Full Text PDF

Many bacterial species are helical in shape, including the widespread pathogen . Motivated by recent experiments on showing that cell wall synthesis is not uniform [J. A.

View Article and Find Full Text PDF

Background: Double-strand break repair (DSBR) is a highly regulated process involving dozens of proteins acting in a defined order to repair a DNA lesion that is fatal for any living cell. Model organisms such as Saccharomyces cerevisiae have been used to study the mechanisms underlying DSBR, including factors influencing its efficiency such as the presence of distinct combinations of microsatellites and endonucleases, mainly by bulk analysis of millions of cells undergoing repair of a broken chromosome. Here, we use a microfluidic device to demonstrate in yeast that DSBR may be studied at a single-cell level in a time-resolved manner, on a large number of independent lineages undergoing repair.

View Article and Find Full Text PDF
Article Synopsis
  • Dynamic instability in biopolymers involves the phases of growth, catastrophe, and shrinkage in quasi-one-dimensional filaments.
  • Catastrophic events are primarily influenced by the balance of hydrolysis and polymerization at the polymer's tip, leading to predictable exponential catastrophe time distributions.
  • Depletion of monomers from a limited pool significantly alters the shape of this distribution, even if the overall polymerization rate remains relatively unchanged.
View Article and Find Full Text PDF

We study the dynamics of flow networks in porous media using two and three dimensional pore-network models. We consider a class of erosion dynamics for a single phase flow with no deposition, chemical reactions, or topology changes assuming a constitutive law depending on flow rate, local velocities, or shear stress at the walls. We show that depending on the erosion law, the flow may become uniform and homogenized or become unstable and develop channels.

View Article and Find Full Text PDF
Article Synopsis
  • The Escherichia coli cell cycle features two main checkpoints: the start of DNA replication and the start of cell constriction.
  • Using advanced fluorescence microscopy and microfluidic devices, researchers have studied how the timing of constriction relates to DNA replication at different growth rates.
  • Findings suggest that during slower growth, constriction initiation is influenced by the presence of the mid-cell chromosome, which impedes constriction independently of the usual control proteins, indicating a new mechanism of nucleoid-mediated regulation in E. coli.
View Article and Find Full Text PDF

A thin-walled tube, e.g., a drinking straw, manifests an instability when bent by localizing the curvature change in a small region.

View Article and Find Full Text PDF

Adaptation dynamics on fitness landscapes is often studied theoretically in the strong-selection, weak-mutation regime. However, in a large population, multiple beneficial mutants can emerge before any of them fixes in the population. Competition between mutants is known as clonal interference, and while it is known to slow down the rate of adaptation (when compared to the strong-selection, weak-mutation model with the same parameters), how it affects the shape of long-term fitness trajectories in the presence of epistasis is an open question.

View Article and Find Full Text PDF

Collection of high-throughput data has become prevalent in biology. Large datasets allow the use of statistical constructs such as binning and linear regression to quantify relationships between variables and hypothesize underlying biological mechanisms based on it. We discuss several such examples in relation to single-cell data and cellular growth.

View Article and Find Full Text PDF

A PHP Error was encountered

Severity: Warning

Message: fopen(/var/lib/php/sessions/ci_sessionbm6suhh21bcdgv7t64dsaaasvlcv026h): Failed to open stream: No space left on device

Filename: drivers/Session_files_driver.php

Line Number: 177

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: session_start(): Failed to read session data: user (path: /var/lib/php/sessions)

Filename: Session/Session.php

Line Number: 137

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once