A TRAF3-NIK module differentially regulates DNA vs RNA pathways in innate immune signaling.

Detection of viral genomes by the innate immune system elicits an antiviral gene program mediated by type I interferons (IFNs). While viral RNA and DNA species induce IFN via separate pathways, the mechanisms by which these pathways are differentially modulated are unknown. Here we show that the positive regulator of IFN in the RNA pathway, TRAF3, has an inhibitory function in the DNA pathway. Loss of TRAF3 coincides with increased expression of the alternative NF-κB-inducing molecule, NIK, which interacts with the DNA pathway adaptor, STING, to enhance IFN induction. Cells lacking NIK display defective IFN activation in the DNA pathway due to impaired STING signaling, and NIK-deficient mice are more susceptible to DNA virus infection. Mechanistically, NIK operates independently from alternative NF-κB signaling components and instead requires autophosphorylation and oligomerization to activate STING. Thus a previously undescribed pathway for NIK exists in activating IFN in the DNA pathway

Pathway Tools version 23.0: Integrated Software for Pathway/Genome Informatics and Systems Biology

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings, and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. The software creates and manages a type of organism-specific database called a Pathway/Genome Database (PGDB), which the software enables database curators to interactively edit. It supports web publishing of PGDBs and provides a large number of query, visualization, and omics-data analysis tools. Scientists around the world have created more than 9,800 PGDBs by using Pathway Tools, many of which are curated databases for important model organisms. Those PGDBs can be exchanged using a peer-to-peer database-sharing system called the PGDB Registry.Comment: Reflects Pathway Tools version 23.0 in 2019; new information since the previous version is in blue text. 111 pages, 40 figure

Knockdown of piRNA pathway proteins results in enhanced Semliki forest virus production in mosquito cells

The exogenous siRNA pathway is important in restricting arbovirus infection in mosquitoes. Less is known about the role of the PIWI-interacting RNA pathway, or piRNA pathway, in antiviral responses. Viral piRNA-like molecules have recently been described following infection of mosquitoes and derived cell lines with several arboviruses. The piRNA pathway has thus been suggested to function as an additional small RNA-mediated antiviral response to the known infection-induced siRNA response. Here we show that piRNA-like molecules are produced following infection with the naturally mosquito-borne Semliki Forest virus in mosquito cell lines. We show that knockdown of piRNA pathway proteins enhances the replication of this arbovirus and defines the contribution of piRNA pathway effectors, thus characterizing the antiviral properties of the piRNA pathway. In conclusion, arbovirus infection can trigger the piRNA pathway in mosquito cells, and knockdown of piRNA proteins enhances virus production

Evaluating the role of the Hippo pathway in the onset and disease progression of the SOD1 mouse model of amyotrophic lateral sclerosis

The Hippo pathway is a cell signaling pathway involved in organ size regulation and tumorigenesis in mammals. This pathway regulates the activity of Yes-associated protein (YAP), a transcriptional coactivator which binds to the transcription factor TEAD to promote expression of genes controlling growth and proliferation of tissues, as well as inhibition of apoptosis. The Hippo pathway has recently been implicated as a pathogenic mechanism in neurodegenerative disorders. Specifically, mammalian sterile 20 (Ste20)-like kinase 1 (MST1), a protein kinase in the Hippo pathway, has been found to promote neuronal death under conditions of oxidative stress. Moreover, homozygous deletion of MST1 in a mouse model of Amyotrophic Lateral Sclerosis (ALS) significantly delayed onset of neurodegenerative symptoms. We examined the expression levels of key Hippo pathway components in cortex, lumbar spinal cord, and gastrocnemius muscle samples of male and female G39A SOD1 mice using western blots. Our results revealed a significant increase in phosphorylated MST1 (pMST1) in lumbar spinal cord of presymptomatic transgenic animals, and found this increase to be sex and gene copy number dependent. These results suggest that the Hippo pathway is dysregulated in the SOD1 mouse model and that MST1 may play a critical role in pathogenesis and disease progression in ALS

Generalized Measure of Entropy, Mathai's Distributional Pathway Model, and Tsallis Statistics

The pathway model of Mathai (2005) mainly deals with the rectangular matrix-variate case. In this paper the scalar version is shown to be associated with a large number of probability models used in physics. Different families of densities are listed here, which are all connected through the pathway parameter 'alpha', generating a distributional pathway. The idea is to switch from one functional form to another through this parameter and it is shown that basically one can proceed from the generalized type-1 beta family to generalized type-2 beta family to generalized gamma family when the real variable is positive and a wider set of families when the variable can take negative values also. For simplicity, only the real scalar case is discussed here but corresponding families are available when the variable is in the complex domain. A large number of densities used in physics are shown to be special cases of or associated with the pathway model. It is also shown that the pathway model is available by maximizing a generalized measure of entropy, leading to an entropic pathway. Particular cases of the pathway model are shown to cover Tsallis statistics (Tsallis, 1988) and the superstatistics introduced by Beck and Cohen (2003).Comment: LaTeX, 13 pages, title changed, introduction, conclusions, and references update

Mechanistic target of rapamycin (mTOR) activation during ruminant mammary development and function : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand

This thesis examines the abundance of total and activated mechanistic target of rapamycin (mTOR) pathway components in the developing and functional ruminant mammary gland. mTOR pathway activation is stimulated by a wide range of intra- and extracellular signals, such as amino acids (AA) and hormones, making the mTOR pathway a potential candidate for the development of intervention strategies designed to increase ruminant lactation potential. Tissues from two trials shown to improve lactation potential; dam-fetal nutrition and exogenous growth hormone (GH) administration during lactation, were used to measure changes in total and activated mTOR pathway protein abundance. Results show mammary glands of d 140 fetal lambs carried by maintenance fed dams and dairy cows administered exogenous GH, had increased abundance of total and activated mTOR and mitogen activated protein kinase (MAPK) pathway proteins. Increased abundance was associated with changes in biochemical indices. In the GH study MAPK pathway activation was stimulated by IGF-1 signaling whilst mTOR pathway activation was proposed to be mediated by AA signalling. Data from the GH study shows, L-arginine a known activator of the mTOR pathway, was the only AA reduced in both plasma and the lactating gland. Upstream factors were not identified for the phenotype observed in the dam-fetal nutrition study, but similar mechanisms were proposed. To elucidate the potential regulation of mTOR pathway activation by L-arginine and examine the effect on milk production, in vitro bovine cell culture models were evaluated. Results show that none of the models evaluated produced a lactating phenotype – a pre-requisite to accurately study the lactating gland in vitro. Finally, this thesis shows L-arginine administration from d 100 to d 140 of pregnancy, in twin bearing ewes had no effect on mTOR protein abundance or activation. However, administration from d 100 to parturition improved maternal gland health. In summary, this thesis associates improved lactation potential with increased total and activated mTOR pathway protein abundance, and the administration of L-arginine during late gestation with improved gland health. These findings provide fundamental knowledge that may lead to the development of novel technologies to increase ruminant gland performance and health

Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi.

The acetyl-CoA "Wood-Ljungdahl" pathway couples the folate-mediated one-carbon (C1) metabolism to either CO2 reduction or acetate oxidation via acetyl-CoA. This pathway is distributed in diverse anaerobes and is used for both energy conservation and assimilation of C1 compounds. Genome annotations for all sequenced strains of Dehalococcoides mccartyi, an important bacterium involved in the bioremediation of chlorinated solvents, reveal homologous genes encoding an incomplete Wood-Ljungdahl pathway. Because this pathway lacks key enzymes for both C1 metabolism and CO2 reduction, its cellular functions remain elusive. Here we used D. mccartyi strain 195 as a model organism to investigate the metabolic function of this pathway and its impacts on the growth of strain 195. Surprisingly, this pathway cleaves acetyl-CoA to donate a methyl group for production of methyl-tetrahydrofolate (CH3-THF) for methionine biosynthesis, representing an unconventional strategy for generating CH3-THF in organisms without methylene-tetrahydrofolate reductase. Carbon monoxide (CO) was found to accumulate as an obligate by-product from the acetyl-CoA cleavage because of the lack of a CO dehydrogenase in strain 195. CO accumulation inhibits the sustainable growth and dechlorination of strain 195 maintained in pure cultures, but can be prevented by CO-metabolizing anaerobes that coexist with D. mccartyi, resulting in an unusual syntrophic association. We also found that this pathway incorporates exogenous formate to support serine biosynthesis. This study of the incomplete Wood-Ljungdahl pathway in D. mccartyi indicates a unique bacterial C1 metabolism that is critical for D. mccartyi growth and interactions in dechlorinating communities and may play a role in other anaerobic communities

A C35 Carotenoid Biosynthetic Pathway

Upon coexpression with Erwinia geranylgeranyldiphosphate (GGDP) synthase in Escherichia coli, C30 carotenoid synthase CrtM from Staphylococcus aureus produces novel carotenoids with the asymmetrical C35 backbone. The products of condensation of farnesyldiphosphate and GDP, C35 structures comprise 40 to 60% of total carotenoid accumulated. Carotene desaturases and carotene cyclases from C40 or C30 pathways accepted and converted the C35 substrate, thus creating a C35 carotenoid biosynthetic pathway in E. coli. Directed evolution to modulate desaturase step number, together with combinatorial expression of the desaturase variants with lycopene cyclases, allowed us to produce at least 10 compounds not previously described. This result highlights the plastic and expansible nature of carotenoid pathways and illustrates how combinatorial biosynthesis coupled with directed evolution can rapidly access diverse chemical structures