We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

Increasing evidence indicates that metabolic disorders in offspring can result from the father's diet, but the mechanism remains unclear. In a paternal mouse model given a high-fat diet (HFD), we showed that a subset of sperm transfer RNA-derived small RNAs (tsRNAs), mainly from 5' transfer RNA halves and ranging in size from 30 to 34 nucleotides, exhibited changes in expression profiles and RNA modifications. Injection of sperm tsRNA fractions from HFD males into normal zygotes generated metabolic disorders in the F1 offspring and altered gene expression of metabolic pathways in early embryos and islets of F1 offspring, which was unrelated to DNA methylation at CpG-enriched regions. Hence, sperm tsRNAs represent a paternal epigenetic factor that may mediate intergenerational inheritance of diet-induced metabolic disorders.

/pdf/sperm-tsrnas-contribute-to-intergenerational-inheritance-of-3uj7sxfvu0.pdf

Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder

https://www.cell.com/cell/pdf/S0092-8674%2815%2900186-5.pdf

Promoting Health and Longevity through Diet: From Model Organisms to Humans

Diverse classes of RNA, ranging from small to long non-coding RNAs, have emerged as key regulators of gene expression, genome stability and defence against foreign genetic elements. Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds and then mediating the recruitment of histone and DNA methyltransferases. In addition, recent advances suggest that chromatin-associated long non-coding RNA scaffolds also recruit chromatin-modifying complexes independently of small RNAs. These co-transcriptional silencing mechanisms form powerful RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops.

RNA-mediated epigenetic regulation of gene expression

Many genes and molecules that drive tissue patterning during organogenesis and tissue regeneration have been discovered. Yet, we still lack a full understanding of how these chemical cues induce the formation of living tissues with their unique shapes and material properties. Here, we review work based on the convergence of physics, engineering and biology that suggests that mechanical forces generated by living cells are as crucial as genes and chemical signals for the control of embryological development, morphogenesis and tissue patterning.

/pdf/mechanical-control-of-tissue-and-organ-development-2seygtgtc3.pdf

Mechanical control of tissue and organ development

Starvation-induced transgenerational inheritance of small RNAs in C. elegans

Neuronal Small RNAs Control Behavior Transgenerationally.

https://www.cell.com/biophysj/pdf/S0006-3495(08)03228-1.pdf

The Regulative Role of Neurite Mechanical Tension in Network Development

The organization of neurons and glia cells on substrates composed of pristine carbon nanotube islands was investigated using high resolution scanning electron microscopy, immunostaining and confocal microscopy. Neurons were found bound and preferentially anchored to the rough surfaces; moreover, the morphology of the neuronal processes on the small, isolated islands of high density carbon nanotubes was found to be conspicuously curled and entangled. We further demonstrate that the roughness of the surface must match the diameter of the neuronal processes in order to allow them to bind. The results presented here suggest that entanglement, a mechanical effect, may constitute an additional mechanism by which neurons (and possibly other cell types) anchor themselves to rough surfaces. Understanding the nature of the interface between neurons and carbon nanotubes is essential to effectively harness carbon nanotube technology in neurological applications such as neuro-prosthetic and retinal electrodes.

https://iopscience.iop.org/article/10.1088/0957-4484/20/1/015101/pdf

Sarit Anava

Papers

Starvation-induced transgenerational inheritance of small RNAs in C. elegans

Neuronal Small RNAs Control Behavior Transgenerationally.

The Regulative Role of Neurite Mechanical Tension in Network Development

Process entanglement as a neuronal anchorage mechanism to rough surfaces.

MET-2-Dependent H3K9 Methylation Suppresses Transgenerational Small RNA Inheritance