SciTech Daily January 6, 2023 Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering the mechanical code which impacts the diverse deforming processes has been a challenge. Utilizing high-throughput measurements of DNA bendability an international team of researchers (UK, USA – Johns Hopkins University, Howard Hughes Medical Institute, Spain) quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. They used the measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. […]
Tag Archives: Biology
Physicists model cell migration to learn how cancer cells navigate tissue
Phys.org January 5, 2023 To learn more about how cancer cells size up surrounding tissue for stiffness and adapt their gecko-like movements in response a team of researchers at Virginia Polytechnic Institute developed a multiscale chemo mechanical whole-cell theory for mesenchymal migration. They developed a framework that coupled the subcellular focal adhesion dynamics at the cell-substrate interface with the cellular cytoskeletal mechanics and the chemical signaling pathways involving Rho GTPase proteins. In the presence of stiffness gradients and absence of chemical polarization, the cell moved toward an optimally stiff region from softer regions during durotaxis and from stiffer regions during […]
New study shows transmission of epigenetic memory across multiple generations
Phys.org September 26, 2022 Researchers at UC Santa Cruz have shown how a common type of epigenetic modification can be transmitted via sperm not only from parents to offspring, but to the next generation (“grand offspring”) as well. This “transgenerational epigenetic inheritance,” may explain how a person’s health and development could be influenced by the experiences of his or her parents and grandparents. They focused on epigenetic mark (called H3K27me3) in C. elegans. This mark is known to turn off or “repress” the affected genes. They selectively stripped the histone mark from the chromosomes of C. elegans sperm, which were […]
Physics meets biology: How bacteria synchronize to build complex structures
Phys.org August 29, 2022 Observable characteristics—phenotypes—at the cellular scale underpins homeostasis and the fitness of living systems. However, how they shape properties at the population level remains poorly understood. An international team of researchers (Luxembourg, the Netherlands) found that phenotypic noise self-regulates with growth and coordinates collective structural organization, the kinetics of topological defects and the emergence of active transport around confluent colonies. They cataloged key phenotypic traits in bacteria growing under diverse conditions. The results revealed a statistically precise critical time for the transition from a monolayer biofilm to a multilayer biofilm, despite the strong noise in the cell […]
How Pathogens Learn To Be Pathogens: Partnerships Between Microbes Lead to Human Disease
SciTech Daily February 21, 2022 Microbes compete for resources and must also hide from or fight predators. Using the fungus Rhizopus, which grows in the soil and on spoiled food, an international team of researchers (UK, USA – UCLA) showed how it fights back against this predator by partnering with a bacteria called Ralstonia in a two-way partnership. By living inside Rhizopus, Ralstonia hides from the predator. In return, Ralstonia makes a toxin that Rhizopus can use to neutralize the predator, preventing it from feeding on the pair. By learning to fight off predators in the soil, Rhizopus has also […]
A step toward “living biotherapeutics”
MIT News December 10, 2021 One of the obstacles to developing “living biotherapeutics” is that many of the species that could be beneficial are harmed by oxygen, making it difficult to manufacture, store, and deliver them. Researchers at MIT have shown that they can protect those bacteria with a coating that helps them to survive the manufacturing process. They developed a self-assembling cellular coating to improve the viability and stability of the next generation biotherapeutic Bacteroides thetaiotaomicron. They have demonstrated protection from both harsh processing conditions and oxygen exposure, even in the absence of canonical cryoprotectants. According to the researchers […]
New database of 660,000 assembled bacterial genomes sheds light on the evolution of bacteria
Phys.com November 10, 2021 Open sharing of genomic data consists of genomes assembled with different tools and levels of quality checking, and large volumes of completely unprocessed raw sequence data. Considerable computational effort is required before biological questions can be addressed. Researchers in the UK assembled and characterized 661,405 bacterial genomes retrieved from the European Nucleotide Archive (ENA) using a uniform standardized approach and produced a searchable COmpact Bit-sliced Signature (COBS) index, facilitating the easy interrogation of the entire dataset for a specific sequence. Additional MinHash and pp-sketch indices support genome-wide comparisons and estimations of genomic distance. 639,981 high-quality genomes […]
Fighting viruses with interchangeable defense genes
Science Daily October 21, 2021 Although it is generally accepted that phages drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. An international team of researchers (USA – MIT, Vienna, France) found that susceptibility to viral killing in marine Vibrio is mediated by large and highly diverse mobile genetic elements. These phage defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection is cumulative, and a single bacterial genome can harbor 6 to 12 defense elements, accounting for more than 90% of the […]
Study shows how some bacteria withstand antibiotic onslaught
Phys.org April 20, 2021 Bacteria that survive antibiotics, called persisters. Researchers at Princeton University explored how the number of DNA copies in a cell affects whether a cell persists despite exposure to DNA-damaging antibiotics called fluoroquinolones. The study confirmed the researchers’ expectation that bacteria with backup chromosomal copies of DNA proved to be persisters at a much greater rate than cells with just one copy. The experiments revealed a second and separate pathway to persistence in cells with a lone DNA copy. Unlike fully antibiotic resistant “superbugs,” persisters do not possess mutated genes; in fact, persisters are genetically identical to […]
Biological ‘rosetta stone’ brings scientists closer to deciphering how the body is built
Science News August 29, 2019 Every animal, from an ant to a human, contains in their genome pieces of DNA called Hox genes which dictate how embryos grow into adults, including where a developing animal puts its head, legs and other body parts. An international team of researchers (Spain, Columbia University) stumbled upon a small piece of regulatory DNA, called vvI1+2, that appeared to be regulated by all the fruit fly’s eight Hox genes. Their analyses provided a precise road map of Hox binding sites in vvI1+2, which could be applied to a living fruit fly. By employing a combination […]