Statistical epistasis is a generic feature of gene regulatory networks

Functional dependencies between genes are a defining characteristic of gene networks underlying quantitative traits. However, recent studies show that the proportion of the genetic variation that can be attributed to statistical epistasis varies from almost zero to very high. It is thus of fundamental as well as instrumental importance to better understand whether different functional dependency patterns among polymorphic genes give rise to distinct statistical interaction patterns or not. Here we address this issue by combining a quantitative genetic model approach with genotype-phenotype models capable of translating allelic variation and regulatory principles into phenotypic variation at the level of gene expression. We show that gene regulatory networks with and without feedback motifs can exhibit a wide range of possible statistical genetic architectures with regard to both type of effect explaining phenotypic variance and number of apparent loci underlying the observed phenotypic effect. Although all motifs are capable of harboring significant interactions, positive feedback gives rise to higher amounts and more types of statistical epistasis. The results also suggest that the inclusion of statistical interaction terms in genetic models will increase the chance to detect additional QTL as well as functional dependencies between genetic loci over a broad range of regulatory regimes. This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation.     

Mutational spectrum of dihydropyrimidine dehydrogenase gene (DPYD) in the Tunisian population

Dihydropyrimidine dehydrogenase enzyme (DPD) deficiency is a pharmacogenetic syndrome leading to severe side-effects in patients receiving therapies containing the anticancer drug 5-fluorouracil (5-FU). The aim of this population study is to evaluate gene variations in the coding region of the dihydropyrimidine dehydrogenase gene (DPYD) in the Tunisian population. One hundred and six unrelated healthy Tunisian volunteers were genotyped by denaturing HPLC (DHPLC). Twelve variants in the coding region of the DPYD were detected. Allele frequencies of DPYD*5 (A1627G), DPYD*6 (G2194A), DPYD*9A (T85C), A496G, and G1218A were 12.7%, 7.1%, 13.7%, 5.7%, and 0.5%, respectively. The DPYD alleles DPYD*2A (IVS 14+1g>1), DPYD*3 (1897 del C) and DPYD*4 (G1601A) associated with DPD deficiency were absent from the examined subjects. We describe for the first time a new intronic polymorphism IVS 6-29 g>t, found in an allelic frequency of 4.7% in the Tunisian population. Comparing our data with that obtained in Caucasian, Egyptian, Japanese and African-American populations, we found that the Tunisian population resembles Egyptian and Caucasian populations with regard to their allelic frequencies of DPYD polymorphisms. This study describes for the first time the spectrum of DPYD sequence variations in the Tunisian population.     

Community response grids: using information technology to help communities respond to bioterror emergencies

Access to accurate and trusted information is vital in preparing for, responding to, and recovering from an emergency. To facilitate response in large-scale emergency situations, Community Response Grids (CRGs) integrate Internet and mobile technologies to enable residents to report information, professional emergency responders to disseminate instructions, and residents to assist one another. CRGs use technology to help residents and professional emergency responders to work together in community response to emergencies, including bioterrorism events. In a time of increased danger from bioterrorist threats, the application of advanced information and communication technologies to community response is vital in confronting such threats. This article describes CRGs, their underlying concepts, development efforts, their relevance to biosecurity and bioterrorism, and future research issues in the use of technology to facilitate community response.     

Leaf functional traits and monodominance in Southern Amazonia tropical forests

Tropical monodominant forests are rare communities with low tree species diversity. Species monodominance is not the product of a single mechanism, but the result of a set of not yet fully understood integrated ecological factors acting together. We compared populations of Brosimum rubescens in monodominant and mixed forests in Southern Amazonia to test whether leaf functional traits are ecological factors related to monodominance. Individuals of B. rubescens in the mixed forest invest in conservative strategies, while those in the monodominant forest invest in acquisitive strategies. Leaf functional traits, such as petiole length and adaxial cuticle thickness, could be associated with the monodominance of B. rubescens. Our study highlights for the first time the power of integrating leaf functional traits as a component of the set of ecological conditions to explain species monodominance. B. rubescens showed different functional strategies to establish and maintain its population in different forests, which makes it a strong competitor for resources, such as water and light, through variation in its leaf functional traits. We also suggest that such high plasticity can be an important condition for the persistence of the species over time.

     

Genistein protects intervertebral discs from degeneration via Nrf2-mediated antioxidant defense system: An in vitro and in vivo study

Oxidative stress has been reported to be closely associated with the development of intervertebral disc degeneration (IDD). IDD is one of the major causes of low back pain. Genistein (GES), one of the main isoflavones of soybean, has been shown to exert multiple biological functions on different diseases. Here, we tested the therapeutic potential of GES for IDD. In vitro experiments, we confirmed GES was nontoxic to rat nucleus pulposus cells (NPCs) within the concentration of 100 μM. Furthermore, GES was able to suppress apoptosis in tert-butyl hydroperoxide (TBHP)-treated NPCs. In the aspect of extracellular matrix (ECM), GES not only reduced metalloproteinase-13 (MMP-13) and a disintegrin-like and MMP thrombospondin type 1 motif 5 expression, but also increased aggrecan and type II collagen levels. Also, we found GES might rescue TBHP-induced NPCs degeneration by enhancing Nrf2-mediated antioxidant defense system. Silencing Nrf2 partly abolished the protective effects of GES on apoptosis and ECM disruption in TBHP-treated NPCs. Correspondingly, GES ameliorated IDD in a rat model by preserving morphology of degenerative intervertebral discs and promoting Nrf2 expression. To sum up, our study suggests that GES exerts protective effects in NPCs against degeneration and reveals the underlying mechanism of GES on Nrf2 activation in NPCs.     

Myosin light chain kinase: expression in neurons and upregulation during axon regeneration

Myosin light-chain kinase (MLCK) regulates actin-myosin II interactions in nonskeletal muscle cells, and the use of specific pharmacological inhibitors has implicated MLCK in retinal growth cone motility and neurite outgrowth. To further establish the existence and functions of MLCK in neurons, we isolated cDNAs encoding two forms of goldfish MLCK that were differentially expressed in the brain and gut and we sequenced the form most abundantly expressed in the brain (GFMLCK1). In situ hybridization with a cRNA probe specific to GFMLCK1 revealed widespread expression in CNS neurons, including tectal periventricular neurons and cerebellar and medullary neurons. After optic nerve crush, expression was markedly increased in the retinal ganglion cells. Expression peaked during the phase of axonal outgrowth, which, when taken together with our previous pharmacological studies, further supports a role for MLCK in growth cone motility. © 1996 John Wiley & Sons, Inc.     

Mechanotransduction by Membrane Proteins: Worms find PEZO-1’s function easy to swallow

JGP study finds that the C. elegans orthologue of the PIEZO family is a mechanosensitive ion channel that regulates pharyngeal pumping and food sensation.

The PIEZO family of mechanosensitive cation channels has been implicated in a wide variety of physiological processes in mammals and is also associated with human disease. Mammalian genomes encode two family members, known as Piezo1 and Piezo2, but invertebrates such as the nematode Caenorhabditis elegans only possess a single Piezo-related gene (1). The function of the C. elegans orthologue, known as pezo-1, has largely remained obscure, but, in this issue of JGP, Millet et al. reveal that it encodes a bona fide mechanosensitive ion channel that regulates pharyngeal activity (2).Jonathan Millet (left), Valeria Vásquez (center), and colleagues reveal that pezo-1, the sole PIEZO family member in C. elegans, is a mechanosensitive ion channel that regulates pharyngeal pumping and food sensation, particularly when worms are fed with large and stiff bacterial filaments that are difficult to swallow (graphic created with BioRender.com).In 2020, an elegant study demonstrated that pezo-1 controls C. elegans ovulation and fertilization (3). However, explains Valeria Vásquez from the University of Tennessee Health Science Center, whether pezo-1 encodes for a mechanosensitive ion channel was unknown. “PEZO-1 is expressed in many tissues, including the pharynx, which is the organ we decided to concentrate on in our study,” Vásquez says.Muscle cells in the C. elegans pharynx rhythmically contract and relax to pump food into the worm’s intestine. Vásquez and colleagues, including first author Jonathan Millet, found that PEZO-1 is expressed in several different pharyngeal cell types (2), including the gland cells whose secretions lubricate the pharynx, and the proprioceptive NSM neurons that are thought to sense the presence of food within the pharynx lumen and release serotonin to increase the rate of pharyngeal pumping.Millet et al. analyzed pharyngeal pumping in worms lacking pezo-1, as well as in animals expressing a pezo-1 point mutant that, in human Piezo1, increases channel function by slowing channel deactivation and inactivation. Loss or gain of pezo-1 function had surprisingly little effect on pharyngeal activity, causing only mild alterations in the duration and frequency of pumping induced by serotonin, and more obvious effects when challenged with high osmolarity solutions.Worms cultured in the laboratory are usually fed a diet of small, easily ingested Escherichia coli cells and, both loss and gain of pezo-1 function increased the pharynx’s response to this type of food. In their natural habitat, however, C. elegans encounter bacteria of various shapes and sizes, some of which might be harder to swallow. “It occurred to me that it might make a difference if we fed the worms with bacteria that were stiffer and longer,” Vásquez says.The researchers therefore provided their pezo-1 mutants with E. coli treated with cephalexin, an antibiotic that inhibits cell separation and causes the bacteria to form long, spaghetti-like filaments. Compared with wild-type worms fed with this diet, pharyngeal activity was markedly enhanced by the gain-of-function pezo-1 mutant, but substantially reduced in the absence of pezo-1, almost as if the worms were “choking” on the bacterial filaments.Crucially, by performing patch-clamp experiments on both cultured C. elegans cells and insect cells expressing recombinant pezo-1, Millet et al. confirmed that PEZO-1 is, indeed, a mechanosensitive ion channel. However, it remains to be seen exactly how PEZO-1 helps the pharynx sense the physical parameters of food and adjust its pumping activity accordingly. One possibility is that the channel acts within the proprioceptive neurons to regulate the release of serotonin.Intriguingly, the Drosophila PIEZO orthologue controls feeding behavior in flies (4). “However, it’s not known which mechanosensitive channels are important in the pharyngeal system of mammals,” Vásquez says. “Our studies in C. elegans could therefore open an opportunity to understand food sensation in humans.”