Information Transmission in G Protein-Coupled Receptors.

G protein-coupled receptors (GPCRs) are the largest class of receptors in the human genome and constitute about 30% of all drug targets. In this article, intended for a non-mathematical audience, both experimental observations and new theoretical results are compared in the context of information transmission across the cell membrane. The amount of information actually currently used or projected to be used in clinical settings is a small fraction of the information transmission capacity of the GPCR. This indicates that the number of yet undiscovered drug targets within GPCRs is much larger than what is currently known. Theoretical studies with some experimental validation indicate that localized heat deposition and dissipation are key to the identification of sites and mechanisms for drug action.

Australian Cool-Season Pulse Seed-Borne Virus Research: 1. Alfalfa and Cucumber Mosaic Viruses and Less Important Viruses.

Here, we review the research undertaken since the 1950s in Australia's grain cropping regions on seed-borne virus diseases of cool-season pulses caused by alfalfa mosaic virus (AMV) and cucumber mosaic virus (CMV). We present brief background information about the continent's pulse industry, virus epidemiology, management principles and future threats to virus disease management. We then take a historical approach towards all past investigations with these two seed-borne pulse viruses in the principal cool-season pulse crops grown: chickpea, faba bean, field pea, lentil, narrow-leafed lupin and white lupin. With each pathosystem, the main focus is on its biology, epidemiology and management, placing particular emphasis on describing field and glasshouse experimentation that enabled the development of effective phytosanitary, cultural and host resistance control strategies. Past Australian cool-season pulse investigations with AMV and CMV in the less commonly grown species (vetches, narbon bean, fenugreek, yellow and pearl lupin, grass pea and other Lathyrus species) and those with the five less important seed-borne pulse viruses also present (broad bean stain virus, broad bean true mosaic virus, broad bean wilt virus, cowpea mild mottle virus and peanut mottle virus) are also summarized. The need for future research is emphasized, and recommendations are made regarding what is required.

Candidate composite biomarker to inform drug treatments for diabetic kidney disease.

Introduction: Current guidelines recommend renin angiotensin system inhibitors (RASi) as key components of treatment of diabetic kidney disease (DKD). Additional options include sodium-glucose cotransporter-2 inhibitors (SGLT2i), glucagon-like peptide 1 receptor agonists (GLP1a), and mineralocorticoid receptor antagonists (MCRa). The identification of the optimum drug combination for an individual is difficult because of the inter-, and longitudinal intra-individual heterogeneity of response to therapy. Results: Using data from a large observational study (PROVALID), we identified a set of parameters that can be combined into a meaningful composite biomarker that appears to be able to identify which of the various treatment options is clinically beneficial for an individual. It uses machine-earning techniques to estimate under what conditions a treatment of RASi plus an additional treatment is different from the treatment with RASi alone. The measure of difference is the annual percent change (ΔeGFR) in the estimated glomerular filtration rate (ΔeGFR). The 1eGFR is estimated for both the RASi-alone treatment and the add-on treatment. Discussion: Higher estimated increase of eGFR for add-on patients compared with RASi-alone patients indicates that prognosis may be improved with the add-on treatment. The personalized biomarker value thus identifies which patients may benefit from the additional treatment.

Arabinose- and xylose-modified analogs of 2',3'-cGAMP act as STING agonists.

Stimulator of interferon genes (STING) agonists are promising candidates for vaccine adjuvants and antitumor immune stimulants. The most potent natural agonist of STING, 2',3'-cyclic GMP-AMP (2',3'-cGAMP), is subject to nuclease-mediated inherent metabolic instability, thereby placing limits on its clinical efficacy. Here, we report on a new class of chemically synthesized sugar-modified analogs of 2',3'-cGAMP containing arabinose and xylose sugar derivatives that bind mouse and human STING alleles with high affinity. The co-crystal structures demonstrate that such analogs act as 2',3'-cGAMP mimetics that induce the "closed" conformation of human STING. These analogs show significant resistance to hydrolysis mediated by ENPP1 and increased stability in human serum, while retaining similar potency as 2',3'-cGAMP at inducing IFN-ß secretion from human THP1 cells. The arabinose- and xylose-modified 2',3'-cGAMP analogs open a new strategy for overcoming the inherent nuclease-mediated vulnerability of natural ribose cyclic nucleotides, with the additional benefit of high translational potential as cancer therapeutics and vaccine adjuvants.

Host Resistance to Virus Diseases Provides a Key Enabler towards Fast Tracking Gains in Grain Lupin Breeding.

Four lupin species, Lupinus angustifolius, L. albus, L. luteus, and L. mutabilis, are grown as cool-season grain legume crops. Fifteen viruses infect them. Two of these, bean yellow mosaic virus (BYMV) and cucumber mosaic virus (CMV), cause diseases that threaten grain lupin production. Phytosanitary and cultural control measures are mainly used to manage them. However, breeding virus-resistant lupin cultivars provides an additional management approach. The need to develop this approach stimulated a search for virus resistance sources amongst cultivated lupin species and their wild relatives. This review focuses on the progress made in optimizing virus resistance screening procedures, identifying host resistances to BYMV, CMV, and additional viral pathogen alfalfa mosaic virus (AMV), and the inclusion of BYMV and CMV resistance within lupin breeding programs. The resistance types found in different combinations of virus and grain lupin species include localized hypersensitivity, systemic hypersensitivity, extreme resistance, and partial resistance to aphid or seed transmission. These resistances provide a key enabler towards fast tracking gains in grain lupin breeding. Where studied, their inheritance depended upon single dominant genes or was polygenic. Although transgenic virus resistance was incorporated into L. angustifolius and L. luteus successfully, it proved unstable. Priorities for future research are discussed.

Model of ligand-triggered information transmission in G-protein coupled receptor complexes.

We present a model for the effects of ligands on information transmission in G-Protein Coupled Receptor (GPCR) complexes. The model is built ab initio entirely on principles of statistical mechanics and tenets of information transmission theory and was validated in part using agonist-induced effector activity and signaling bias for the angiotensin- and adrenergic-mediated signaling pathways, with in vitro observations of phosphorylation sites on the C tail of the GPCR complex, and single-cell information-transmission experiments. The model extends traditional kinetic models that form the basis for many existing models of GPCR signaling. It is based on maximizing the rates of entropy production and information transmission through the GPCR complex. The model predicts that (1) phosphatase-catalyzed reactions, as opposed to kinase-catalyzed reactions, on the C-tail and internal loops of the GPCR are responsible for controlling the signaling activity, (2) signaling favors the statistical balance of the number of switches in the ON state and the number in the OFF state, and (3) biased-signaling response depends discontinuously on ligand concentration.

Quantification of damage to plasmid DNA from 35 MeV electrons, 228 MeV protons and 300 kVp X-rays in varying hydroxyl radical scavenging environments.

The pBR322 plasmid DNA was irradiated with 35 MeV electrons, 228 MeV protons and 300 kVp X-rays to quantify DNA damage and make comparisons of DNA damage between radiation modalities. Plasmid was irradiated in a medium containing hydroxyl radical scavengers in varying concentrations. This altered the amount of indirect hydroxyl-mediated DNA damage, to create an environment that is more closely associated with a biological cell. We show that increasing hydroxyl scavenger concentration significantly reduced post-irradiation DNA damage to pBR322 plasmid DNA consistently and equally with three radiation modalities. At low scavenging capacities, irradiation with both 35 MeV electrons and 228 MeV protons resulted in increased DNA damage per dose compared with 300 kVp X-rays. We quantify both single-strand break (SSB) and double-strand break (DSB) induction between the modalities as a ratio of yields relative to X-rays, referred to as relative biological effectiveness (RBE). RBESSB values of 1.16 ± 0.15 and 1.18 ± 0.08 were calculated for protons and electrons, respectively, in a low hydroxyl scavenging environment containing 1 mM Tris-HCl for SSB induction. In higher hydroxyl scavenging capacity environments (above 1.1 × 106 s-1), no significant differences in DNA damage induction were found between radiation modalities when using SSB induction as a measure of RBE. Considering DSB induction, significant differences were only found between X-rays and 35 MeV electrons, with an RBEDSB of 1.72 ± 0.91 for 35 MeV electrons, indicating that electrons result in significantly more SSBs and DSBs per unit of dose than 300 kVp X-rays.

Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications.

In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Nigde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP's, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603-0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.

One-Flask Synthesis of Cyclic Diguanosine Monophosphate (c-di-GMP).

The bacterial signaling molecule cyclic diguanosine monophosphate (c-di-GMP) plays a key role in controlling biofilm formation and pathogenic virulence, among many other functions. It has widespread consequences for human health, and current research is actively exploring its molecular mechanisms. The convenient one-flask, gram-scale synthesis of c-di-GMP described here has facilitated these efforts and has been applied to a variety of analogs. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Preparation of DNA and RNA Fragments Containing Guanine N2 -Thioalkyl Tethers.

This article describes procedures for preparation of deoxyguanosine and guanosine derivatives in which the guanine N2 contains a thiopropyl tether, protected as a tert-butyl disulfide. After incorporation into a DNA or RNA fragment, this tether allows site-specific cross-linking to a thiol of a protein or another nucleic acid. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of diisopropyl-1-(tert-butylthio)-1,2-hydrazinedicarboxylate (4) Basic Protocol 2: Preparation of the 2'-deoxyguanosine N2 -propyl-tert-butyl disulfide phosphoramidite (12) Basic Protocol 3: Preparation of the guanosine N2 -propyl-tert-butyl disulfide phosphoramidite (20) Basic Protocol 4: Preparation of DNA fragments containing N2 -propyl-tert-butyl disulfide guanine Alternate Protocol: Preparation of RNA fragments containing N2 -propyl-tert-butyl disulfide guanine Basic Protocol 5: Conversion of N2 -propyl-tert-butyl disulfide to the free thiol, disulfide 5-thio-2-nitrobenzoic acid disulfide, or ethylamine disulfide.

Genomic High Plains Wheat Mosaic Virus Sequences from Australia: Their Phylogenetics and Evidence for Emaravirus Recombination and Reassortment.

High Plains wheat mosaic virus (HPWMoV) causes a serious disease in major wheat-growing regions worldwide. We report here the complete or partial genomic sequences of five HPWMoV isolates from Australian wheat samples. Phylogenetic analysis of the nucleotide sequences of the eight genomic segments of these five isolates together with others from Genbank found all eight genes formed two lineages, L1 and L2. L1 contained a single isolate from Colorado in the North American Great Plains Region (GPR), and L2 had two unresolved clusters, A and B, of isolates from Australia and the GPR. A quarter of the L2B isolate sequences of the nucleocapsid gene (RNA3) were recombinant, which is unexpected as little evidence of recombination exists in viruses with negative single-stranded RNA genomes. Phylogenies calculated from the amino acid sequences of HPWMoV's RNA-dependent RNA-polymerase (RNA1), glycoprotein (RNA2), and nucleocapsid protein (RNA3) showed they were closest to those of Palo Verde broom virus. However, its movement protein (RNA4) was closer to those of Ti ringspot-associated and common oak ringspot-associated viruses, indicating the RNA4 segments of their ancestors reassorted to produce the current emaraviruses. To avoid increased yield losses from co-infection, biosecurity measures are advised to avoid HPWMoV introduction to countries where wheat streak mosaic virus already occurs.

Regioselective 2'-Silylation of Purine Ribonucleosides for Phosphoramidite RNA Synthesis.

This article describes high-yield procedures for protection of purine ribonucleosides based on a reaction that allows highly regioselective 2'-silylation. Each protocol makes use of two transient protection steps. In the case of tritylation of the 5' hydroxyl, the 2',3'-diol is protected by reaction with N,N-dimethylformamide dimethylacetal (Zemlicka, 1963) to prevent the small, but potentially troublesome, tritylation of the 2'-hydroxyl that otherwise accompanies tritylation of the 5'-hydroxyl (Zhang et al., 1997). The phenoxyacetylation of the amino group is carried out after transient hydroxyl and guanine O6 protection with trimethylchlorosilane using the hydroxybenzotriazole active ester of phenoxyacetic acid. These protocols give overall yields that are three times the best yields available by conventional procedures for adenosine and guanosine, but offer no advantage for cytidine or uridine. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5'-O-(4,4'-dimethoxytrityl)-2'-O-tert-butyldimethylsilyl-6-N-acyladenosine Basic Protocol 2: Synthesis of 5'-O-(4,4'-dimethoxytrityl)-2'-O-tert-butyldimethysilyl-2-N-acylguanosine.

Syntheses of Specifically 15 N-Labeled Adenosine and Guanosine.

This article describes the specific incorporation of 15 N into the N7 and amino positions of adenosine (Basic Protocol 1), and conversion of the adenosine to guanosine labeled at the N1, N7, and amino positions (Basic Protocol 2). Two variations of the procedures are also presented that include either 12 C or 13 C at the C8 position of adenosine, and 13 C at either the C8 or C2 position of guanosine. These 13 C tags permit the incorporation of two 15 N-labeled nucleosides into an RNA strand while ensuring that their nuclear magnetic resonance (NMR) signals can be distinguished from each other by the presence or absence of C-N coupling. While the major application of these specifically 15 N-labeled nucleosides is NMR, the additional mass makes them useful in mass spectrometry (MS) as well. The procedures can also be adapted to synthesize the labeled deoxynucleosides. The Support Protocol describes the synthesis of 7-methylguanosine. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Syntheses of [7,NH2 -15 N2 ]- and [8-13 C-7,NH2 -15 N2 ]adenosine Support Protocol: Synthesis of 7-methylguanosine Basic Protocol 2: Synthesis of [2-13 C-1,7,NH2 -15 N3 ]- and [8-13 C-1,7,NH2 -15 N3 ]guanosine.

Enhanced Apiaceous Potyvirus Phylogeny, Novel Viruses, and New Country and Host Records from Sequencing Apiaceae Samples.

The family Apiaceae comprises approximately 3700 species of herbaceous plants, including important crops, aromatic herbs and field weeds. Here we report a study of 10 preserved historical or recent virus samples of apiaceous plants collected in the United Kingdom (UK) import interceptions from the Mediterranean region (Egypt, Israel and Cyprus) or during surveys of Australian apiaceous crops. Seven complete new genomic sequences and one partial sequence, of the apiaceous potyviruses apium virus Y (ApVY), carrot thin leaf virus (CaTLV), carrot virus Y (CarVY) and celery mosaic virus (CeMV) were obtained. When these 7 and 16 earlier complete non-recombinant apiaceous potyvirus sequences were subjected to phylogenetic analyses, they split into 2 separate lineages: 1 containing ApVY, CeMV, CarVY and panax virus Y and the other CaTLV, ashitabi mosaic virus and konjac virus Y. Preliminary dating analysis suggested the CarVY population first diverged from CeMV and ApVY in the 17th century and CeMV from ApVY in the 18th century. They also showed the "time to most recent common ancestor" of the sampled populations to be more recent: 1997 CE, 1983 CE and 1958 CE for CarVY, CeMV and ApVY, respectively. In addition, we found a new family record for beet western yellows virus in coriander from Cyprus; a new country record for carrot torradovirus-1 and a tentative novel member of genus Ophiovirus as a co-infection in a carrot sample from Australia; and a novel member of the genus Umbravirus recovered from a sample of herb parsley from Israel.

Allochthony, fatty acid and mercury trends in muscle of Eurasian perch (Perca fluviatilis) along boreal environmental gradients.

Environmental change, including joint effects of increasing dissolved organic carbon (DOC) and total phosphorus (TP) in boreal northern lakes may affect food web energy sources and the biochemical composition of organisms. These environmental stressors are enhanced by anthropogenic land-use and can decrease the quality of polyunsaturated fatty acids (PUFAs) in seston and zooplankton, and therefore, possibly cascading up to fish. In contrast, the content of mercury in fish increases with lake browning potentially amplified by intensive forestry practises. However, there is little evidence on how these environmental stressors simultaneously impact beneficial omega-3 fatty acid (n3-FA) and total mercury (THg) content of fish muscle for human consumption. A space-for-time substitution study was conducted to assess whether environmental stressors affect Eurasian perch (Perca fluviatilis) allochthony and muscle nutritional quality [PUFA, THg, and their derivative, the hazard quotient (HQ)]. Perch samples were collected from 31 Finnish lakes along pronounced lake size (0.03-107.5 km2), DOC (5.0-24.3 mg L-1), TP (5-118 µg L-1) and land-use gradients (forest: 50.7-96.4%, agriculture: 0-32.6%). These environmental gradients were combined using principal component analysis (PCA). Allochthony for individual perch was modelled using source and consumer δ2H values. Perch allochthony increased with decreasing lake pH and increasing forest coverage (PC1), but no correlation between lake DOC and perch allochthony was found. Perch muscle THg and omega-6 fatty acid (n6-FA) content increased with PC1 parallel with allochthony. Perch muscle DHA (22:6n3) content decreased, and ALA (18:3n3) increased towards shallower murkier lakes (PC2). Perch allochthony was positively correlated with muscle THg and n6-FA content, but did not correlate with n3-FA content. Hence, the quality of perch muscle for human consumption decreases (increase in HQ) with increasing forest coverage and decreasing pH, potentially mediated by increasing fish allochthony.

Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes.

Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato's Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 nonrecombinant open reading frame sequences showed that the PVV population had two major phylogroups, one of which formed three minor phylogroups (A1 to A3) of isolates, all of which are found only in the Andean region of South America (Peru and Colombia), and the other formed two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region, with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A1 and A3, there were two subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated nonrecombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so "subtree dating" was done via a single maximum likelihood phylogeny of PVV and PVY sequences, and PVY's well-supported 157 ce "time to most common recent ancestor" was extrapolated to date that of PVV as 29 bce. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose ≥2,000 years ago in the Andes and was taken to Europe during the Columbian Exchange, where it diversified around 1853 ce, soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realized and is of biosecurity relevance for world regions that have not yet recorded its presence.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges.

This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.