Verma S et al. (2015) IUBMB Life "Understanding the complexities of Salmonella-host crosstalk as revealed by in vivo model organisms."

Srikanth CV, Verma S

[IUBMB Life, 2015]

Foodborne infections caused by non-typhoidal Salmonellae, such as Salmonella enterica serovar Typhimurium (ST), pose a major challenge in the developed and developing world. With constant rise of drug-resistant strains, understanding the epidemiology, microbiology, pathogenesis and host-pathogen interactions biology is a mandatory requirement to enable health systems to be ready to combat these illnesses. Patient data from hospitals, at least from some parts of the world, have aided in epidemiological understanding of ST-mediated disease. Most of the other aspects connected to Salmonella-host crosstalk have come from model systems that offer convenience, genetic tractability and low maintenance costs that make them extremely valuable tools. Complex model systems such as the bovine model have helped in understanding key virulence factors needed for infection. Simple systems such as fruit flies and Caenorhabditis elegans have aided in identification of novel virulence factors, host pathways and mechanistic details of interactions. Some of the path-breaking concepts of the field have come from mice model of ST colitis, which allows genetic manipulations as well as high degree of similarity to human counterpart. Together, they are invaluable for correlating in vitro findings of ST-induced disease progression in vivo. The current review is a compilation of various advances of ST-host interactions at cellular and molecular levels that has come from investigations involving model organisms.

Hoogstrate SW et al. (2014) Worm "Nematode endogenous small RNA pathways."

Snoek LB, Volkers RJ, Sterken MG, Hoogstrate SW, Kammenga JE

[Worm, 2014]

The discovery of small RNA silencing pathways has greatly extended our knowledge of gene regulation. Small RNAs have been presumed to play a role in every field of biology because they affect many biological processes via regulation of gene expression and chromatin remodeling. Most well-known examples of affected processes are development, fertility, and maintenance of genome stability. Here we review the role of the three main endogenous small RNA silencing pathways in Caenorhabditis elegans: microRNAs, endogenous small interfering RNAs, and PIWI-interacting RNAs. After providing an entry-level overview on how these pathways function, we discuss research on other nematode species providing insight into the evolution of these small RNA pathways. In understanding the differences between the endogenous small RNA pathways and their evolution, a more comprehensive picture is formed of the functions and effects of small RNAs.

Rechavi O et al. (2017) Curr Biol "Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans."

Lev I, Rechavi O

[Curr Biol, 2017]

Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations. We focus on the intricate interactions between heritable small RNAs and histone modifications, deposited on specific loci. A trace of heritable chromatin marks, in particular trimethylation of histone H3 lysine 9, is deposited on RNAi-targeted loci. However, how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.

Naqvi AR et al. (2009) Int J Biol Sci "The fascinating world of RNA interference."

Naqvi AR, Haq QM, Islam MN, Choudhury NR

[Int J Biol Sci, 2009]

Micro- and short-interfering RNAs represent small RNA family that are recognized as critical regulatory species across the eukaryotes. Recent high-throughput sequencing have revealed two more hidden players of the cellular small RNA pool. Reported in mammals and Caenorhabditis elegans respectively, these new small RNAs are named piwi-interacting RNAs (piRNAs) and 21U-RNAs. Moreover, small RNAs including miRNAs have been identified in unicellular alga Chlamydomonas reinhardtii, redefining the earlier concept of multi-cellularity restricted presence of these molecules. The discovery of these species of small RNAs has allowed us to understand better the usage of genome and the number of genes present but also have complicated the situation in terms of biochemical attributes and functional genesis of these molecules. Nonetheless, these new pools of knowledge have opened up avenues for unraveling the finer details of the small RNA mediated pathways.

Claycomb JM (2012) DNA Cell Biol "Caenorhabditis elegans small RNA pathways make their mark on chromatin."

Claycomb JM

[DNA Cell Biol, 2012]

Endogenous small-RNA-mediated gene silencing pathways are generally recognized for their functions in halting gene expression by the degradation of a transcript or by translational inhibition. However, another important mode of gene regulation by small RNAs is mediated at the level of chromatin modulation. Over the past decade a great deal of progress on understanding the molecular mechanisms by which small RNAs can influence chromatin has been made for fungi, ciliated protozoans, and plants, while less is known about the functions and consequences of such chromatin-directed small RNA pathways in animals. Several recent studies in the nematode Caenorhabditis elegans have provided mechanistic insights into small RNA pathways that impact chromatin throughout development. The "worm" has been instrumental in uncovering the mechanisms of RNA interference and remains a powerful system for dissecting the molecular means by which small RNA pathways impact chromatin in animals. This review summarizes our current knowledge of the various chromatin-directed small RNA pathways in C. elegans and provides insights for future study.

Houri-Zeevi L et al. (2016) Trends Genet "A Matter of Time: Small RNAs Regulate the Duration of Epigenetic Inheritance."

Houri-Zeevi L, Rechavi O

[Trends Genet, 2016]

Small RNAs are increasingly emerging as transgenerational carriers of epigenetic information in Caenorhabditis elegans and in other organisms. Recent studies have identified factors that are required for the inheritance of small RNAs and for heritable RNAi in worms, which typically persist for a finite number of generations. We examine here recent insights into the mechanisms that control the duration of transgenerational inheritance of small RNAs. We discuss current understanding of two types of regulatory mechanisms: those that prolong RNAi inheritance through amplification and maintenance of heritable small RNAs, and those that limit the persistence of ancestral RNAi by, for example, employing negative feedback loops to reset the transmission of epigenetic information. Collectively, these machineries result in the precise and intricate regulation of small RNA inheritance across generations.

Nelson P et al. (2003) Trends in Biochemical Sciences "The microRNA world: small is mighty."

Nelson P, Mourelatos Z, Kiriakidou M, Maniataki E, Sharma A

[Trends in Biochemical Sciences, 2003]

A new paradigm of RNA-directed gene expression regulation has emerged recently, profound in scope but arresting in the apparent simplicity of its core mechanism. Cells express numerous small ( approximately 22 nucleotide) RNAs that act as specificity determinants to direct destruction or translational repression of their mRNA targets. These small RNAs arise from processing of double-stranded RNA by the Dicer nuclease and incorporate with proteins that belong to the Argonaute family. Small RNAs might also target and silence homologous DNA sequences. The immense potential of small RNAs as controllers of gene networks is just beginning to unfold.

Van Wynsberghe PM et al. (2013) Adv Exp Med Biol "Epigenetic control of germline development."

Maine EM, Van Wynsberghe PM

[Adv Exp Med Biol, 2013]

Dynamic regulation of histone modifications and small noncoding RNAs is observed throughout the development of the C. elegans germ line. Histone modifications are differentially regulated in the mitotic vs meiotic germ line, on X chromosomes vs autosomes and on paired chromosomes vs unpaired chromosomes. Small RNAs function in transposon silencing and developmental gene regulation. Histone modifications and small RNAs produced in the germ line can be inherited and impact embryonic development. Disruption of histone-modifying enzymes or small RNA machinery in the germ line can result in sterility due to degeneration of the germ line and/or an inability to produce functional gametes.

Li R et al. (2021) Food Funct "Small berries as health-promoting ingredients: a review on anti-aging effects and mechanisms in Caenorhabditis elegans."

Pan S, Li R, Xu T, Tao M, Xu X, Wu T

[Food Funct, 2021]

Aging is an inevitable, irreversible, and complex process of damage accumulation and functional decline, increasing the risk of various chronic diseases. However, for now no drug can delay aging process nor cure aging-related diseases. Nutritional intervention is considered as a key and effective strategy to promote healthy aging and improve life quality. Small berries, as one of the most common and popular fruits, have been demonstrated to improve cognitive function and possess neuroprotective activities. However, the anti-aging effects of small berries have not been systematically elucidated yet. This review mainly focuses on small berries' anti-aging activity studies involving small berry types, active components, the utilized model organism <i>Caenorhabditis elegans</i> (<i>C. elegans</i>), related signaling pathways, and molecular mechanisms. The purpose of this review is to propose effective strategies to evaluate the anti-aging effects of small berries and provide guidance for the development of anti-aging supplements from small berries.

Hwang H et al. (2013) Biotechnol J "Microfluidic tools for developmental studies of small model organisms--nematodes, fruit flies, and zebrafish."

Lu H, Hwang H

[Biotechnol J, 2013]

Studying the genetics of development with small model organisms such as the zebrafish (Danio Rerio), the fruit fly (Drosophila melanogaster), and the soil-dwelling nematode (Caenorhabditis elegans), provide unique opportunities for understanding related processes and diseases in humans. These model organisms also have potential for use in drug discovery and toxicity-screening applications. There have been sweeping developments in microfabrication and microfluidic technologies for manipulating and imaging small objects, including small model organisms, which allow high-throughput quantitative biological studies. Here, we review recent progress in microfluidic tools able to manipulate small organisms and project future directions and applications of these techniques and technologies.