Toward Understanding Microbiome-Neuronal Signaling.

Host-associated microbiomes are emerging as important modifiers of brain activity and behavior. Metabolic, immune, and neuronal pathways are proposed to mediate communication across the so-called microbiota-gut-brain axis. However, strong mechanistic evidence, especially for direct signaling between microbes and sensory neurons, is lacking. Here, we discuss microbial regulation of short-chain fatty acids, neurotransmitters, as-yet-uncharacterized biochemicals, and derivatives of neuromodulatory drugs as important areas for assessing microbial interactions with the nervous system.

Learned linear models for detecting watercraft in a maritime environment.

This work provides a new, to the best of our knowledge, approach to constructing linear models for object detection in a scene. Specifically, we use representative training data in order to estimate the parameters describing a generalized wavelet model for the express purpose of detecting the presence of maritime targets in a scene. The parameter estimates are taken as those that maximize the probability of detecting the targets for a fixed probability of false alarm. The approach is then demonstrated on a database of short-wave infrared imagery containing various watercraft. Results are then compared to some of the more standard wavelet bases used in detection applications.

Correction: Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.

[This corrects the article DOI: 10.1371/journal.pgen.1005310.].

Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein.

Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to down-regulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.

Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available.

Nutritional depletion of total mixed rations by European starlings: Projected effects on dairy cow performance and potential intervention strategies to mitigate damage.

European starlings are an invasive bird species in North America that are known to cause damage to commercial dairies through the consumption of total mixed rations (TMR) destined for dairy cows. We hypothesized that large foraging flocks of starlings alter the physical composition of TMR, and that this change may be significant enough to affect milk production. To better determine if production losses could potentially occur in commercial dairies as a consequence of feed consumption by foraging flocks of starlings, we conducted controlled feeding experiments using a TMR sourced from a commercial dairy that is chronically plagued with seasonal starling damage. European starlings selected the high-energy fraction of the TMR and reduced starch and crude fat availability. Using the dairy National Research Council production model equations, the nutritional changes measured in the controlled feeding experiments could potentially reduce the productivity of dairies. Model output suggests that for Holsteins producing 32 kg of milk/d, total required net energy intake (NEI) was 31.5 Mcal/d. Within the reference TMR, NEI supplied was 29.3 Mcal/d, whereas within the starling-consumed TMR NEI supplied was 27.7 Mcal/d. Following our nutrition experiments, we assessed the efficacy of pelleted feed as a deterrent strategy for bird damage management in commercial dairies. Six different pelleted feed treatments of differing diameter were offered to starlings. All pellets of 0.95 cm diameter or larger inhibited starling consumption by ≥79%.

Monkey prefrontal neurons during Sternberg task performance: full contents of working memory or most recent item?

To explore the brain mechanisms underlying multi-item working memory, we monitored the activity of neurons in the dorsolateral prefrontal cortex while macaque monkeys performed spatial and chromatic versions of a Sternberg working-memory task. Each trial required holding three sequentially presented samples in working memory so as to identify a subsequent probe matching one of them. The monkeys were able to recall all three samples at levels well above chance, exhibiting modest load and recency effects. Prefrontal neurons signaled the identity of each sample during the delay period immediately following its presentation. However, as each new sample was presented, the representation of antecedent samples became weak and shifted to an anomalous code. A linear classifier operating on the basis of population activity during the final delay period was able to perform at approximately the level of the monkeys on trials requiring recall of the third sample but showed a falloff in performance on trials requiring recall of the first or second sample much steeper than observed in the monkeys. We conclude that delay-period activity in the prefrontal cortex robustly represented only the most recent item. The monkeys apparently based performance of this classic working-memory task on some storage mechanism in addition to the prefrontal delay-period firing rate. Possibilities include delay-period activity in areas outside the prefrontal cortex and changes within the prefrontal cortex not manifest at the level of the firing rate.NEW & NOTEWORTHY It has long been thought that items held in working memory are encoded by delay-period activity in the dorsolateral prefrontal cortex. Here we describe evidence contrary to that view. In monkeys performing a serial multi-item working memory task, dorsolateral prefrontal neurons encode almost exclusively the identity of the sample presented most recently. Information about earlier samples must be encoded outside the prefrontal cortex or represented within the prefrontal cortex in a cryptic code.

A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.

Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.

Range performance of the DARPA AWARE wide field-of-view visible imager.

In a prior paper, we described a new imaging architecture that addresses the need for wide field-of-view imaging combined with the resolution required to identify targets at long range. Over the last two years substantive improvements have been made to the system, both in terms of the size, weight, and power of the camera as well as to the optics and data management software. The result is an overall improvement in system performance, which we demonstrate via a maritime target identification experiment.

High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment.

UNLABELLED: Viral proteins often display several functions which require multiple assays to dissect their genetic basis. Here, we describe a systematic approach to screen for loss-of-function mutations that confer a fitness disadvantage under a specified growth condition. Our methodology was achieved by genetically monitoring a mutant library under two growth conditions, with and without interferon, by deep sequencing. We employed a molecular tagging technique to distinguish true mutations from sequencing error. This approach enabled us to identify mutations that were negatively selected against, in addition to those that were positively selected for. Using this technique, we identified loss-of-function mutations in the influenza A virus NS segment that were sensitive to type I interferon in a high-throughput fashion. Mechanistic characterization further showed that a single substitution, D92Y, resulted in the inability of NS to inhibit RIG-I ubiquitination. The approach described in this study can be applied under any specified condition for any virus that can be genetically manipulated. IMPORTANCE: Traditional genetics focuses on a single genotype-phenotype relationship, whereas high-throughput genetics permits phenotypic characterization of numerous mutants in parallel. High-throughput genetics often involves monitoring of a mutant library with deep sequencing. However, deep sequencing suffers from a high error rate (∼0.1 to 1%), which is usually higher than the occurrence frequency for individual point mutations within a mutant library. Therefore, only mutations that confer a fitness advantage can be identified with confidence due to an enrichment in the occurrence frequency. In contrast, it is impossible to identify deleterious mutations using most next-generation sequencing techniques. In this study, we have applied a molecular tagging technique to distinguish true mutations from sequencing errors. It enabled us to identify mutations that underwent negative selection, in addition to mutations that experienced positive selection. This study provides a proof of concept by screening for loss-of-function mutations on the influenza A virus NS segment that are involved in its anti-interferon activity.

Adherence to abiraterone among the first 86 recipients after release in Saskatchewan.

Metastatic castration-resistant prostate cancer is now commonly treated with abiraterone, an orally administered chronic medication. Although abiraterone has certain advantages over docetaxel-based therapy, patients are now responsible for ensuring optimal adherence to their medication. To our knowledge, adherence to abiraterone in a real-world setting has never been described. The objective of the present study was to measure adherence to abiraterone among the first patients to receive the drug in Saskatchewan. Electronic pharmacy claims were obtained from the Saskatchewan Cancer Agency after removal of patient names and identifiers. All patients with at least 1 dispensation for abiraterone between August 2011 and October 2013 were eligible. The primary endpoint was the percentage of patients achieving optimal adherence at 6 months, defined as a medication possession ratio (mpr) of 80% or better. During the study period, 141 patients received abiraterone, among whom 86 could be followed for at least 6 months. Optimal adherence was achieved in 82.6% of patients (71 of 86) at 6 months, with 79.1% achieving a mpr of at least 90%. Of patients with available follow-up to 1 year, 81.6% (31 of 38) maintained optimal adherence during the entire period.

High-throughput profiling of point mutations across the HIV-1 genome.

BACKGROUND: The HIV-1 pandemic is not the result of a static pathogen but a large genetically diverse and dynamic viral population. The virus is characterized by a highly mutable genome rendering efforts to design a universal vaccine a significant challenge and drives the emergence of drug resistant variants upon antiviral pressure. Gaining a comprehensive understanding of the mutational tolerance of each HIV-1 genomic position is therefore of critical importance. RESULTS: Here we combine high-density mutagenesis with the power of next-generation sequencing to gauge the replication capacity and therefore mutational tolerability of single point mutations across the entire HIV-1 genome. We were able to achieve the evaluation of point mutational effects on viral replicative capacity for 5,553 individual HIV-1 nucleotide positions - representing 57% of the viral genome. Replicative capacity was assessed at 3,943 nucleotide positions for a single alternate base change, 1,459 nucleotide positions for two alternate base changes, and 151 nucleotide positions for all three possible alternate base changes. This resulted in the study of how a total of 7,314 individual point mutations impact HIV-1 replication on a single experimental platform. We further utilize the dataset for a focused structural analysis on a capsid inhibitor binding pocket. CONCLUSION: The approach presented here can be applied to any pathogen that can be genetically manipulated in a laboratory setting. Furthermore, the methodology can be utilized under externally applied selection conditions, such as drug or immune pressure, to identify genetic elements that contribute to drug or host interactions, and therefore mutational routes of pathogen resistance and escape.

Modelling clinical data shows active tissue concentration of daclatasvir is 10-fold lower than its plasma concentration.

OBJECTIVES: Daclatasvir is a highly potent inhibitor of hepatitis C virus. We estimated the active tissue concentration of daclatasvir in vivo. METHODS: We developed a mathematical model incorporating pharmacokinetic/pharmacodynamic and viral dynamics. By fitting the model to clinical data reported previously, we estimated the ratio between plasma drug concentration and active tissue concentration in vivo. RESULTS: The modelling results show that the active tissue concentration of daclatasvir is ∼9% of the concentration measured in plasma (95% CI 1%-29%). CONCLUSIONS: Using plasma concentrations as surrogates for clinical recommendations may lead to substantial underestimation of the risk of resistance.

Characterization of the AWARE 10 two-gigapixel wide-field-of-view visible imager.

System requirements for many military electro-optic and IR camera systems reflect the need for both wide-field-of-view situational awareness as well as high-resolution imaging for target identification. In this work we present a new imaging system architecture designed to perform both functions simultaneously and the AWARE 10 camera as an example at visible wavelengths. We first describe the basic system architecture and user interface followed by a laboratory characterization of the system optical performance. We then describe a field experiment in which the camera was used to identify several maritime targets at varying range. The experimental results indicate that users of the system are able to correctly identify ~10 m targets at between 4 and 6 km with 70% accuracy.

Denoising infrared maritime imagery using tailored dictionaries via modified K-SVD algorithm.

Recent work has shown that tailored overcomplete dictionaries can provide a better image model than standard basis functions for a variety of image processing tasks. Here we propose a modified K-SVD dictionary learning algorithm designed to maintain the advantages of the original approach but with a focus on improved convergence. We then use the learned model to denoise infrared maritime imagery and compare the performance to the original K-SVD algorithm, several overcomplete "fixed" dictionaries, and a standard wavelet denoising algorithm. Results indicate the superiority of overcomplete representations and show that our tailored approach provides similar peak signal-to-noise ratios as the traditional K-SVD at roughly half the computational cost.

Orthodontic tooth movement causes decreased promoter expression of collagen type 1, bone sialoprotein and alpha-smooth muscle actin in the periodontal ligament.

OBJECTIVE: To evaluate the effects of orthodontic tooth movement on the promoter expression of collagen type 1 (3.6Col1), bone sialoprotein (BSP) and alpha-smooth muscle actin (αSMA) in the periodontal ligament (PDL) using transgenic mice containing transgenes of these promoters fused to green fluorescent proteins (GFP). MATERIALS AND METHODS: The maxillary first molars of 10-12 week-old transgenic mice were loaded with 10-12 g of force for 12, 48 h, or 7 days. Mice were transgenic for one of the following GFP-tagged bone markers of osteoblast lineage cells: 3.6-kb fragment of the rat collagen type 1 promoter (3.6Col1), BSP or α-smooth muscle actin (αSMA). Loaded molars under compression and tension were compared with contra-lateral unloaded controls. RESULTS: On the compression side of the PDL, orthodontic tooth movement caused a significant decrease in GFP expression of all the promoters at each time point. On the tension side, there was a significant increase in BSP-GFP expression, 12 h following loading compared to the contralateral unloaded controls. CONCLUSIONS: An in vivo tooth movement model using transgenic mice with promoter-GFP constructs provides an efficient and effective way of investigating the cellular events underlying orthodontic tooth movement. PDL cells may undergo decreased differentiation in response to the compressive force.

Single-round, multiplexed antibody mimetic design through mRNA display.

In a single round: By combining the high-efficiency enrichment through the continuous-flow magnetic separation (CFMS) technique with the analytical power of next-generation sequencing, the generation of antibody mimetics with a single round of mRNA display is made possible. This approach eliminates iterative selection cycles and provides a path to fully automated ligand generation (see picture).

Multi-objective utilization of wood waste recycled from construction and demolition (C&D): Products and characterization.

Producing energy and higher value bio-products from waste materials has been proposed as an economically viable opportunity in the renewable energy sector. However, several challenges associated with the integrated biomass conversion processes remain to be resolved. The present study introduces a multi-faceted plant production of thermal energy and biochar from construction and demolition (C&D) wood chips. The overarching objective of the study is to reduce waste materials while simultaneously producing a self-independent clean thermal energy resource along with value-added co-products such as biochar, biogases and/or activated carbon. The combined thermal energy and slow pyrolysis unit relies on 95% of its energy from waste wood chips to produce thermal energy and high value carbon products. The system not only supplies the energy required for the indirect pyrolysis unit but also provides a major portion of thermal energy demanded for the site. A multi-purpose objective of wood waste management, energy production from waste material, high-quality biochar from waste wood (over 80% carbon), and carbon offsets is demonstrated through the utilization of this plant by addressing some of the major previously problems and challenges faced. The information is useful for techno-economic and life cycle analysis in the next study.

Heterologous saRNA Prime, DNA Dual-Antigen Boost SARS-CoV-2 Vaccination Elicits Robust Cellular Immunogenicity and Cross-Variant Neutralizing Antibodies.

We assessed if immune responses are enhanced in CD-1 mice by heterologous vaccination with two different nucleic acid-based COVID-19 vaccines: a next-generation human adenovirus serotype 5 (hAd5)-vectored dual-antigen spike (S) and nucleocapsid (N) vaccine (AdS+N) and a self-amplifying and -adjuvanted S RNA vaccine (AAHI-SC2) delivered by a nanostructured lipid carrier. The AdS+N vaccine encodes S modified with a fusion motif to increase cell-surface expression and an N antigen modified with an Enhanced T-cell Stimulation Domain (N-ETSD) to direct N to the endosomal/lysosomal compartment and increase MHC class I and II stimulation potential. The S sequence in the AAHI-SC2 vaccine comprises the D614G mutation, two prolines to stabilize S in the prefusion conformation, and 3 glutamines in the furin cleavage region to confer protease resistance. CD-1 mice received vaccination by homologous and heterologous prime > boost combinations. Humoral responses to S were the highest with any regimen that included the AAHI-SC2 vaccine, and IgG bound to wild type and Delta (B.1.617.2) variant S1 at similar levels. An AAHI-SC2 prime followed by an AdS+N boost particularly enhanced CD4+ and CD8+ T-cell responses to both wild type and Delta S peptides relative to all other vaccine regimens. Sera from mice receiving AAHI-SC2 homologous or heterologous vaccination were found to be highly neutralizing for all pseudovirus strains tested: Wuhan, Beta, Delta, and Omicron strains. The findings here, taken in consideration with the availability of both vaccines in thermostable formulations, support the testing of heterologous vaccination by an AAHI-SC2 > AdS+N regimen in animal models of SARS-CoV-2 infection to assess its potential to provide increased protection against emerging SARS-CoV-2 variants particularly in regions of the world where the need for cold-chain storage has limited the distribution of other vaccines.