Adenovirus flow in host cell networks

Viruses are obligatory parasites that take advantage of intracellular niches to replicate. During infection, their genomes are carried in capsids across the membranes of host cells to sites of virion production by exploiting cellular behaviour and resources to guide and achieve all aspects of delivery and the downstream virus manufacturing process. Successful entry hinges on execution of a precisely tuned viral uncoating program where incoming capsids disassemble in consecutive steps to ensure that genomes are released at the right time, and in the right place for replication to occur. Each step of disassembly is cell-assisted, involving individual pathways that transmit signals to regulate discrete functions, but at the same time, these signalling pathways are organized into larger networks, which communicate back and forth in complex ways in response to the presence of virus. In this review, we consider the elegant strategy by which adenoviruses (AdVs) target and navigate cellular networks to initiate the production of progeny virions. There are many remarkable aspects about the AdV entry program; for example, the virus gains targeted control of a large well-defined local network neighbourhood by coupling several interacting processes (including endocytosis, autophagy and microtubule trafficking) around a collective reference state centred on the interactional topology and multifunctional nature of protein VI. Understanding the network targeting activity of protein VI, as well as other built-in mechanisms that allow AdV particles to be efficient at navigating the subsystems of the cell, can be used to improve viral vectors, but also has potential to be incorporated for use in entirely novel delivery systems.Peer reviewe

Conventional Breeding and Molecular Techniques to Improve Phytochemical Concentrations in Pepper (Capsicum spp.)

Five separate field experiments were conducted across different environmental locations in Texas for the purpose of quantifying concentrations of different phytochemical groups (ascorbic acid, capsaicinoids, and flavonoids) within various pepper species, as well as, to identify the most optimum environment to promote expression of the aforementioned phytochemical. Depending on the particular experiment, quantitative measurements were then used in more detail in one of three ways: for identification of the most superior individuals and optimum environmental locations to express elevated concentrations of a particular phytochemical (first three experiments), to calculate heritability and % heterosis estimates for various fruit characteristics and phytochemical levels (fourth experiment), or for use in a specific biotechnology technique to potentially identify a molecular marker linked to elevated levels of ascorbic acid (AA) and flavonoids (quercetin and luteolin) (fifth experiment). In the first experiment, significant differences in fruit weight, capsaicin, and dihydrocapsaicin (DHC) were revealed in fruit tissue of five Habanero (Capsicum chinense) hybrids in comparison to a popular, commercial check (Kukulkan F1) after being grown across three different environmental locations (College Station, Uvalde, and Weslaco). Fruit grown at the Weslaco location was found to be larger and contained more capsaicin and DHC than those produced in Uvalde or College Station. While flavonoid contents were variable and low in all genotypes and locations, a few hybrids showed some potential for use in future crossing schemes to compete against the commercial check. Our results further suggested that variation in phytochemicals in fruit tissue of Habanero genotypes can be exploited by selecting in an appropriate environment. In the second experiment, analysis of four jalapeño hybrids in comparison to three commercial checks (Dragon, Ixtapa, and J1845), as well as, two cayenne hybrids in comparison to one commercial check (Mesilla) were compared after growing in three different locations (Amarillo, College Station, and Uvalde). Results demonstrated that the College Station location contributed to production of fruit containing higher concentrations of both AA and flavonoids, while those grown in Amarillo produced fruit with higher capsaicinoids. As expected, cayenne samples contained more AA and flavonoids than jalapeño samples. In comparison to the commercial jalapeño checks, all jalapeño hybrids generally expressed less capsaicinoids. With respect to AA and flavonoid concentrations, a few jalapeño hybrids proved to have some potential to compete against their respective commercial cultivars. For the cayenne market, one genotype revealed its potential use in mild markets and for farmers interested in a new hybrid expressing both appreciable levels of phytochemicals, as well as, more visually aesthetic attributes. Statistical analyses from the third experiment found all the F-values for each characteristic to be significant except the Location x Genotype (L x G) component for fruit wall thickness. For this experiment, a total of 21 different C. annuum (jalapeño, Serrano, and cayenne) genotypes were evaluated after growing in two diverse environmental locations (Uvalde and Weslaco). In general, peppers grown in Weslaco produced fruit with higher concentrations of AA and capsaicinoids, with a few exceptions, while fruit grown at Uvalde generally was larger in size and contained higher concentrations of flavonoids. In comparison to their respective commercial checks (jalapeño – Dragon, Tormenta; Serrano – Halcon, Magnum45; cayenne – Mesilla), a few hybrids were arguably more desirable for their respective markets with respect to different fruit measurements, AA, capsaicinoid, and flavonoid concentrations. This evidence further suggested the potential benefit this material could have for growers interested in replacing current material in the industry and to more successfully provide consumers with a healthier ingredient to better sustain their lives. In the fourth experiment, results confirmed our hypotheses that paprika type material has higher AA and flavonoid concentrations than Serrano peppers, while the opposite is possible for capsaicinoid expression. For this experiment, our goal was to identify the relative ease of incorporating different traits of interest into an improved specimen evaluating a combination of 29 F1 paprika and Serrano pepper (C. annuum) hybrids along with 19 of their respective parents. We were also able to identify how productive certain crossing combinations were at expressing a significant amount of positive heterosis for different characteristics of interest. From our correlation analyses, we were able to identify that a significant association can exist between fruit weight and fruit diameter, as well as when other characteristics were evaluated. In all, our results were able to reveal how effective certain combinations of parent material are towards production of offspring with improved traits expressing appreciable fruit characteristics and elevated phytochemical concentrations. Finally, the quantitative measurements produced in our F2 molecular marker experiment found significant amounts of variation for both flavonoids (quercetin and luteolin) and AA expression. It was evident that incorporation of the necessary genes of interest present within fruit tissue across this F2 family for these different phytochemicals were passed from ‘Ca377’ (P1) to several of these offspring. Three candidate primers were eventually identified for their potential polymorphic expression. However, after statistically analyzing the results, only one primer was identified as expressing a significant association (although the value was still relatively low) of variability with respect to luteolin. We also identified a significant association between quercetin and luteolin, quercetin and total flavonoids (quercetin+luteolin), as well as, luteolin and total flavonoids (quercetin+luteolin) in fruit tissues of different pepper material. From our results, we were able to arguably conclude that an environmental component may serve a more essential role in activating the necessary physiological processes to produce specific secondary metabolites. Although our RAPD technique was fairly straightforward and useful, some may argue that a more reliable technique would have been better. Therefore, we postulate that success may be possible in the near future if a different molecular marker technique is used

An indole-containing dauer pheromone component with unusual dauer inhibitory activity at higher concentrations

In Caenorhabdltls elegans, the dauer pheromone, which consists of a number of derivatives of the 3,6-dideoxysugar ascarylose, is the primary cue for entry into the stress-resistant, nonaging dauer larval stage. Here, using activity-guided fractionation and NMR-based structure elucidation, a structurally novel, indole-3-carboxyl-modified ascaroside is identified that promotes dauer formation at low nanomolar concentrations but inhibits dauer formation at higher concentrations. © 2009 American Chemical Society

A 2.8-Angstrom-Resolution Cryo-Electron Microscopy Structure of Human Parechovirus 3 in Complex with Fab from a Neutralizing Antibody

Human parechovirus 3 (HPeV3) infection is associated with sepsis characterized by significant immune activation and subsequent tissue damage in neonates. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and the lack of a vaccine or specific antiviral therapy. Toward the latter, we present a 2.8-angstrom-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody, AT12-015, using cryo-electron microscopy (cryo-EM) and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally, at high resolution, it was possible to model a stretch of RNA inside the virion and, from this, identify the key features that drive and stabilize protein-RNA association during assembly. IMPORTANCE Human parechovirus 3 (HPeV3) is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, for which, despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Toward this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high resolution, it was possible to precisely define the epitope that, when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interactions and viral pathogenesis mechanisms and for finding potential cures for infection and disease.Peer reviewe

A Novel ascaroside controls the parasitic life cycle of the entomopathogenic nematode heterorhabditis bacteriophora

Entomopathogenic nematodes survive in the soil as stress-resistant infective juveniles that seek out and infect insect hosts. Upon sensing internal host cues, the infective juveniles regurgitate bacterial pathogens from their gut that ultimately kill the host. Inside the host, the nematode develops into a reproductive adult and multiplies until unknown cues trigger the accumulation of infective juveniles. Here, we show that the entomopathogenic nematode Heterorhabditis bacteriophora uses a small-molecule pheromone to control infective juvenile development. The pheromone is structurally related to the dauer pheromone ascarosides that the free-living nematode Caenorhabditis elegans uses to control its development. However, none of the C. elegans ascarosides are effective in H. bacteriophora, suggesting that there is a high degree of species specificity. Our report is the first to show that ascarosides are important regulators of development in a parasitic nematode species. An understanding of chemical signaling in parasitic nematodes may enable the development of chemical tools to control these species. © 2012 American Chemical Society

Queensland SharkSmart Drone Trial Final Report

Remotely Piloted Aircraft Systems, commonly called drones, provide a high-definition aerial view of a wide expanse of ocean, allowing the detection of potentially dangerous sharks in real-time, whilst having a negligible impact on the environment and non-target species. In addition, they are capable of spotting a range of marine hazards and can assist in beach rescue operations, thus providing numerous safety benefits for water users. The beaches of South-East Queensland (SEQ) have relatively good water clarity and a high level of visitation, making them an ideal location to test drones for detecting sharks and improving the safety of water users (Cardno, 2019). North Queensland beaches typically have lower water clarity, although it is important to test drones under these conditions to assess whether they can be effective at detecting sharks. The Queensland SharkSmart drone trial commenced on 19 September 2020, as a partnership between the Queensland Government Department of Agriculture and Fisheries (DAF) and Surf Life Saving Queensland (SLSQ). The trial was part of the Queensland Government’s commitment to research and trialling alternatives to traditional shark control measures. Drones were operated at two beaches on the Sunshine Coast (Alexandra Headland and Coolum North), two beaches on the Gold Coast (Southport Main Beach and Burleigh Beach) and one beach on North Stradbroke Island (NSI; Ocean beach) between 19 September 2020 and 4 October 2021. Additionally, to assess the effectiveness of drones at detecting sharks under the different environmental conditions found at North Queensland (NQ) beaches, drones were operated at Palm Cove, Cairns and Alma Bay, Magnetic Island, from 26 June 2021 to 31 October 2021. Drones were operated on weekends, public holidays and school holidays by SLSQ pilots, with two flights per hour from approximately 8am until midday. Flights lasted 15 - 20 minutes and followed a 400 m transect behind the surf break. All footage was collected in 4K and securely archived for later analysis with key operational and environmental data collected for every flight. When a shark was sighted, the drone pilot lowered the aircraft to determine the species and size while estimating distance of the animal from water users. Data analysis quantified the numbers of sharks sighted at each beach and the rate of sightings as a percentage across the whole trial from 19 September 2020 to 31 October 2021. Generalised Linear Mixed Models (GLMMs) were applied to quantify the influence of environmental and operational factors on the sightability (probability of a shark being sighted) of sharks. The movement tracks of sharks were mapped to analyse their behaviour and identify if there was clustering of movements in certain areas. Sighting rates from drones were also compared with shark catch in adjacent nets and drumlines deployed as part of the Queensland Shark Control Program (SCP)

A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses

Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are capsid binders that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhibitors and by means of cryo-electron microscopy (EM), followed by resistance selection and reverse genetics, we discovered a hitherto unknown druggable pocket that is formed by viral proteins VP1 and VP3 and that is conserved across entero-/rhinovirus species. We propose that these inhibitors stabilize a key region of the virion, thereby preventing the conformational expansion needed for viral RNA release. A medicinal chemistry effort resulted in the identification of analogues targeting this pocket with broad-spectrum activity against Coxsackieviruses B (CVBs) and compounds with activity against enteroviruses (EV) of groups C and D, and even rhinoviruses (RV). Our findings provide novel insights in the biology of the entry of entero-/rhinoviruses and open new avenues for the design of broad-spectrum antivirals against these pathogens.Peer reviewe

Shock compression experiments using the DiPOLE 100-X laser on the high energy density instrument at the European x-ray free electron laser: quantitative structural analysis of liquid Sn

X-ray free electron laser (XFEL) sources coupled to high-power laser systems offer an avenue to study the structural dynamics of materials at extreme pressures and temperatures. The recent commissioning of the DiPOLE 100-X laser on the high energy density (HED) instrument at the European XFEL represents the state-of-the-art in combining x-ray diffraction with laser compression, allowing for compressed materials to be probed in unprecedented detail. Here, we report quantitative structural measurements of molten Sn compressed to 85(5) GPa and ∼ 3500 K. The capabilities of the HED instrument enable liquid density measurements with an uncertainty of ∼ 1 % at conditions which are extremely challenging to reach via static compression methods. We discuss best practices for conducting liquid diffraction dynamic compression experiments and the necessary intensity corrections which allow for accurate quantitative analysis. We also provide a polyimide ablation pressure vs input laser energy for the DiPOLE 100-X drive laser which will serve future users of the HED instrument

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead