Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-ß Autocrine Stimulation.

Since the discovery of oncogenes, there has been tremendous interest to understand their mechanistic basis and to develop broadly actionable therapeutics. Some of the most frequently activated oncogenes driving diverse cancers are c-MYC, EGFR, HER2, AKT, KRAS, BRAF, and MEK. Using a reductionist approach, we explored how cellular proteomes are remodeled in isogenic cell lines engineered with or without these driver oncogenes. The most striking discovery for all oncogenic models was the systematic downregulation of scores of antiviral proteins regulated by type 1 interferon. These findings extended to cancer cell lines and patient-derived xenograft models of highly refractory pancreatic cancer and osteosarcoma driven by KRAS and MYC oncogenes. The oncogenes reduced basal expression of and autocrine stimulation by type 1 interferon causing remarkable convergence on common phenotypic and functional profiles. In particular, there was dramatically lower expression of dsRNA sensors including DDX58 (RIG-I) and OAS proteins, which resulted in attenuated functional responses when the oncogenic cells were treated with the dsRNA mimetic, polyI:C, and increased susceptibility to infection with an RNA virus shown using SARS-CoV-2. Our reductionist approach provides molecular and functional insights connected to immune evasion hallmarks in cancers and suggests therapeutic opportunities.

To Approve or not to Approve? A Comparative Analysis of State-Company-Indigenous Community Interactions in Mining in Canada and Sweden.

This Special Section explores the interplay between Indigenous peoples, industry, and the state in five proposed and active mining projects in Canada and Sweden. The overall aim is to identify factors shaping the quality of Indigenous community-industry-state interactions in mining and mine development. An ambition underlying the research is to develop knowledge to help manage mining related land-use conflicts in Sweden by drawing on Canadian comparisons and experience. This paper synthesizes the comparative research that has been conducted across jurisdictions in three Canadian provinces and Sweden. It focuses on the interplay between the properties of the governance system, the quality of interaction and governance outcomes. We combine institutional and interactive governance theory and use the concept of governability to assess how and why specific outcomes, such as mutually beneficial interaction, collaboration, or opposition, occurred. The analysis suggests there are measures that can be taken by the Swedish Government to improve the governability of mining related issues, by developing alternative, and more effective, avenues to recognize, and protect, Sámi rights and culture, to broaden the scope and increase the legitimacy and transparency of the EIAs, to raise the quality of interaction and consultation, and to develop tools to actively stimulate and support collaboration and partnerships on equal terms. Generally, we argue that Indigenous community responses to mining must be understood within a larger framework of Indigenous self-determination, in particular the communities' own assessments of their opportunities to achieve their long-term objectives using alternative governing modes and types of interactions.

Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics.

Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, e.g., HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges: finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra. Here, we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, e.g., at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, e.g., ± 0.01 Da. Also, new is glycan "wildcard" search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally, the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.

Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes.

The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here we apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK, and AKT. We find that each oncogene has somewhat different surfaceomes, but the functions of these proteins are harmonized by common biological themes including up-regulation of nutrient transporters, down-regulation of adhesion molecules and tumor suppressing phosphatases, and alteration in immune modulators. Addition of a potent MEK inhibitor that blocks MAPK signaling brings each oncogene-induced surfaceome back to a common state reflecting the strong dependence of the oncogene on the MAPK pathway to propagate signaling. Cell surface protein capture is mediated by covalent tagging of surface glycans, yet current methods do not afford sequencing of intact glycopeptides. Thus, we complement the surfaceome data with whole cell glycoproteomics enabled by a recently developed technique called activated ion electron transfer dissociation (AI-ETD). We found massive oncogene-induced changes to the glycoproteome and differential increases in complex hybrid glycans, especially for KRAS and HER2 oncogenes. Overall, these studies provide a broad systems-level view of how specific driver oncogenes remodel the surfaceome and the glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery.

Institutional Determinants of Mining Projects in Canada and Sweden: Insights from the Prosperity and Kallak Cases.

Mining has proven to be a controversial form of resource development throughout the circumpolar north. This article compares two mining projects-the proposed Prosperity gold and copper mine in central British Columbia, Canada and the proposed Kallak iron ore mine in Norrbotten County in northern Sweden-that have endured long and protracted approval processes that have caused tensions and disputes between mining companies, Indigenous peoples, communities and state actors. In an effort understand the particular development paths taken by these two mining projects, this article examines the institutional determinants that structure relationships between industry, Indigenous communities and the state in Canada and Sweden. Using an historical institutionalist theoretical approach, the article focuses on the manner in which the structural features of the political systems and the environmental assessment and permitting processes in both countries have shaped the mine approval process. It also identifies particular critical junctures-important events and decisions that influenced the trajectory of the approval processes in profound and consequential ways. The article finds that institutional determinants, both historical and contemporary, have played a critical role in determining outcomes in both cases. In particular, it demonstrates the ways in which the structures of the Canadian and Swedish political systems have historically excluded Indigenous peoples from the decision-making process for resource development projects such as mines. It also shows how broader institutional contexts, as well as specific events and decisions, have complicated and politicized the mine approval processes, a situation that has heightened tensions on all sides.

Phosphorylation controls RNA binding and transcription by the influenza virus polymerase.

The influenza virus polymerase transcribes and replicates the viral genome. The proper timing and balance of polymerase activity is important for successful replication. Genome replication is controlled in part by phosphorylation of NP that regulates assembly of the replication machinery. However, it remains unclear whether phosphorylation directly regulated polymerase activity. Here we identified polymerase phosphosites that control its function. Mutating phosphosites in the catalytic subunit PB1 altered polymerase activity and virus replication. Biochemical analyses revealed phosphorylation events that disrupted global polymerase function by blocking the NTP entry channel or preventing RNA binding. We also identified a regulatory site that split polymerase function by specifically suppressing transcription. These experiments show that host kinases phospho-regulate viral RNA synthesis directly by modulating polymerase activity and indirectly by controlling assembly of replication machinery. Further, they suggest polymerase phosphorylation may bias replication versus transcription at discrete times or locations during the infectious cycle.

A deep analysis of the proteomic and phosphoproteomic alterations that occur in skeletal muscle after the onset of immobilization.

KEY POINTS: A decrease in protein synthesis plays a major role in the loss of muscle mass that occurs in response to immobilization. In mice, immobilization leads to a rapid (within 6 h) and progressive decrease in the rate of protein synthesis and this effect is mediated by a decrease in translational efficiency. Deep proteomic and phosphoproteomic analyses of mouse skeletal muscles revealed that the rapid immobilization-induced decrease in protein synthesis cannot be explained by changes in the abundance or phosphorylation state of proteins that have been implicated in the regulation of translation. ABSTRACT: The disuse of skeletal muscle, such as that which occurs during immobilization, can lead to the rapid loss of muscle mass, and a decrease in the rate of protein synthesis plays a major role in this process. Indeed, current dogma contends that the decrease in protein synthesis is mediated by changes in the activity of protein kinases (e.g. mTOR); however, the validity of this model has not been established. Therefore, to address this, we first subjected mice to 6, 24 or 72 h of unilateral immobilization and then used the SUnSET technique to measure changes in the relative rate of protein synthesis. The result of our initial experiments revealed that immobilization leads to a rapid (within 6 h) and progressive decrease in the rate of protein synthesis and that this effect is mediated by a decrease in translational efficiency. We then performed a deep mass spectrometry-based analysis to determine whether this effect could be explained by changes in the expression and/or phosphorylation state of proteins that regulate translation. From this analysis, we were able to quantify 4320 proteins and 15,020 unique phosphorylation sites, and surprisingly, the outcomes revealed that the rapid immobilization-induced decrease in protein synthesis could not be explained by changes in either the abundance, or phosphorylation state, of proteins. The results of our work not only challenge the current dogma in the field, but also provide an expansive resource of information for future studies that are aimed at defining how disuse leads to loss of muscle mass.

Chemical Sensitivity Analysis and Uncertainty Analysis of Ozone Production in the Comprehensive Air Quality Model with Extensions Applied to Eastern Texas.

Chemical sensitivity analysis (CSA) is a new probing tool for sampling sensitivities to chemistry parameters during a three-dimensional (3-D) simulation. CSA was applied to rank all of the parameters in the Carbon Bond 6 revision 4 (CB6r4) mechanism and to create an ensemble of six chemical mechanisms representing higher and lower O3 formations than CB6r4. This ensemble of mechanisms was used to estimate the uncertainty from the chemistry in a 3-D simulation and combined with uncertainties from other model inputs obtained from calculations of their sensitivities. The overall uncertainty (1σ) in O3 predictions for eastern Texas was 10-11 ppb in the Gulf of Mexico near Galveston and 7-8 ppb in much of the rest of the domain on the higher O3 days of June 2012. As a percent of the O3 concentration, the uncertainty was more uniform over the domain, 11-14%. Chemistry and emissions make the largest contributions to the O3 uncertainty. Uncertainty in the dry deposition velocities is less important in urban areas and the Gulf, but it is similar in importance to the uncertainty in chemistry and emissions at most other locations. Uncertainty in O3 boundary concentrations is the least important.

Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts.

BACKGROUND: The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host by transitioning from the fast growing tachyzoite morphology to latent bradyzoite morphology. A hallmark of the bradyzoite is the development of neuronal cysts that are resilient against host immune response and current therapeutics. The bradyzoite parasites within the cyst have a carbohydrate and protein-rich wall and a slow-replication cycle, allowing them to remain hidden from the host. The intracellular, encysted lifestyle of T. gondii has made them recalcitrant to molecular analysis in vivo. RESULTS: Here, we detail the results from transcriptional and proteomic analyses of bradyzoite-enriched fractions isolated from mouse brains infected with T. gondii over a time course of 21 to 150 days. The enrichment procedure afforded consistent identification of over 2000 parasitic peptides from the mixed-organism sample, representing 366 T. gondii proteins at 28, 90, and 120 day timepoints. Deep sequencing of transcripts expressed during these three timepoints revealed that a subpopulation of genes that are transcriptionally expressed at a high level. Approximately one-third of these transcripts are more enriched during bradyzoite conditions compared to tachyzoites and approximately half are expressed at similar levels during each phase. The T. gondii transcript which increased the most over the course of chronic infection, sporoAMA1, shows stage specific isoform expression of the gene. CONCLUSIONS: We have expanded the transcriptional profile of in vivo bradyzoites to 120 days post-infection and provided the first in vivo proteomic profile of T. gondii bradyzoites. The RNA sequencing depth of in vivo bradyzoite T. gondii was over 250-fold greater than previous reports and allowed us to identify low level transcripts and a novel bradyzoite-specific isoform of sporoAMA1.

SURGICAL AND POSTOPERATIVE TREATMENT OF INTERVERTEBRAL DISC DISEASE IN A MOUNTAIN COATI (NASUELLA OLIVACEA) USING BEHAVIORAL MANAGEMENT AND PHYSICAL THERAPY.

A captive 8-yr-old female mountain coati, Nasuella olivacea, presented with intermittent paresis of the pelvic limbs. The coati was anesthetized for radiographs, which showed mineralized discs in the thoracolumbar region. After 3 mo of daily prednisone, its condition further declined. Magnetic resonance imaging confirmed extradural disc herniation, spinal cord compression, and requirement for a left-sided hemilaminectomy. Postoperatively, the coati received prednisolone, gabapentin, tramadol, and clavamox. An established history of positive reinforcement training allowed caretakers to implement physical therapy walks and novel exercises designed for its condition. The coati showed improvement with appropriate proprioceptive positioning and improved balance. Intervertebral disc disease is common in dogs and cats, and although physical therapy is routinely implemented in recovering neurologic patients of those species, it is relatively new in zoologic medicine. This report highlights the benefits of behavioral management in postoperative management of nondomestic species.

Identifying Novel Signaling Pathways: An Exercise Scientists Guide to Phosphoproteomics.

We propose that phosphoproteomic-based studies will radically advance our knowledge about exercise-regulated signaling events. However, these studies use cutting-edge technologies that can be difficult for nonspecialists to understand. Hence, this review is intended to help nonspecialists 1) understand the fundamental technologies behind phosphoproteomic analysis and 2) use various bioinformatic tools that can be used to interrogate phosphoproteomic datasets.

Nitric oxide targets oligodendrocytes and promotes their morphological differentiation.

In the central nervous system, nitric oxide (NO) transmits signals from one neurone to another, or from neurones to astrocytes or blood vessels, but the possibility of oligodendrocytes being physiological NO targets has been largely ignored. By exploiting immunocytochemistry for cGMP, the second messenger generated on activation of NO receptors, oligodendrocytes were found to respond to both exogenous and endogenous NO in cerebellar slices from rats aged 8 days to adulthood. Atrial natriuretic peptide, which acts on membrane-associated guanylyl cyclase-coupled receptors, also raised oligodendrocyte cGMP in cerebellar slices. The main endogenous source of NO accessing oligodendrocytes appeared to be the neuronal NO synthase isoform, which was active even under basal conditions and in a manner that was independent of glutamate receptors. Oligodendrocytes in brainstem slices were also shown to be potential NO targets. In contrast, in the optic nerve, oligodendrocyte cGMP was raised by natriuretic peptides but not NO. When cultures of cerebral cortex were continuously exposed to low NO concentrations (estimated as 40-90 pM), oligodendrocytes responded with a striking increase in arborization. This stimulation of oligodendrocyte growth could be replicated by low concentrations of 8-bromo-cGMP (maximum effect at 1 µM). It is concluded that oligodendrocytes are probably widespread targets for physiological NO (or natriuretic peptide) signals, with the resulting rise in cGMP serving to enhance their growth and maturation. NO might help coordinate the myelination of axons to the ongoing level of neuronal activity during development and could potentially contribute to adaptive changes in myelination in the adult.

Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice.

BACKGROUND: The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In this study, we build upon our HuGX ('high-throughput human genes on the X chromosome') strategy to expand our understanding of human gene regulation in vivo. RESULTS: In all, ten human genes known to express in therapeutically important brain regions were chosen for study. For eight of these genes, human bacterial artificial chromosome clones were identified, retrofitted with a reporter, knocked single-copy into the Hprt locus in mouse embryonic stem cells, and mouse strains derived. Five of these human genes expressed in mouse, and all expressed in the adult brain region for which they were chosen. This defined the boundaries of the genomic DNA sufficient for brain expression, and refined our knowledge regarding the complexity of gene regulation. We also characterized for the first time the expression of human MAOA and NR2F2, two genes for which the mouse homologs have been extensively studied in the central nervous system (CNS), and AMOTL1 and NOV, for which roles in CNS have been unclear. CONCLUSIONS: We have demonstrated the use of the HuGX strategy to functionally delineate non-coding-regulatory regions of therapeutically important human brain genes. Our results also show that a careful investigation, using publicly available resources and bioinformatics, can lead to accurate predictions of gene expression.

In vitro efficacy of cefovecin against anaerobic bacteria isolated from subgingival plaque of dogs and cats with periodontal disease.

Periodontal disease is a common disease of dogs and cats often requiring antimicrobial treatment as an adjunct to mechanical debridement. However, correct compliance with oral antimicrobial therapy in companion animals is often difficult. Cefovecin is a recently introduced veterinary cephalosporin that has demonstrated prolonged concentrations in extracellular fluid, allowing for dosing intervals of up to 14 days. Subgingival samples were collected from the oral cavity of 29 dogs and eight cats exhibiting grade 2 or grade 3 periodontal disease. Samples were cultivated on Wilkin Chalgrens agar and incubated in an anaerobic chamber for seven days. Selected anaerobic bacteria were isolated and identified to species level using 16S rRNA gene sequence analysis. Minimum inhibitory concentrations were determined for cefovecin and six additional antimicrobials using the agar dilution methodology recommended by the Clinical and Laboratory Standards Institute. The 65 clinical isolates were identified as Porphyromonas gulae (n = 45), Porphyromonas crevioricanis (n = 12), Porphyromonas macacae (n = 1), Porphyromonas cangingivalis (n = 1) Fusobacterium nucleatum (n = 2), Fusobacterium russii (n = 1) and Solobacterium moorei (n = 3). This is the first report of S. moorei being isolated from companion animals with periodontal disease. All isolates were highly susceptible to cefovecin, with a MIC90 of ≤0.125 µg/ml. Conversely, different resistance rates to ampicillin, amoxicillin and erythromycin between isolates were detected. Cefovecin is thus shown to be effective in vitro against anaerobic bacteria isolated from dogs and cats with periodontal disease.

Variability in oxidative stress biomarkers following a maximal exercise test.

The oxidative stress response to maximal exercise may provide useful clinical biomarkers for assessing redox homeostasis. The aim was to determine the between-individual variability in the exercise-induced change in oxidative stress measures and investigate predictors of these responses. Plasma F2-isoprostanes (Isop), protein carbonyls (PCs), glutathione peroxidase (GPX) activity and total antioxidant capacity (TAC) were measured before and after a maximal treadmill exercise test. Exercise produced significant increases in Isop (27.0%), PC (6.2%) and GPX (7.8%). There were large between-individual coefficients of variation: Isop (152%), PC, (240%), GPX (130%) and TAC (243%).

Modeling of secondary organic aerosols (SOA) based on two commonly used air quality models in China: Consistent S/IVOCs contribution but large differences in SOA aging.

Secondary organic aerosol (SOA) is an important component of atmospheric fine particulate matter (PM2.5), with contributions from anthropogenic and biogenic volatile organic compounds (AVOC and BVOC) and semi- (SVOC) and intermediate volatility organic compounds (IVOC). Policymakers need to know which SOA precursors are important but accurate simulation of SOA magnitude and contributions remain uncertain. Findings from existing SOA modeling studies have many inconsistencies due to differing emission inventory methodologies/assumptions, air quality model (AQM) algorithms, and other aspects of study methodologies. To address some of the inconsistencies, we investigated the role of different AQM SOA algorithms by applying two commonly used models, CAMx and CMAQ, with consistent emission inventories to simulate SOA concentrations and contributions for July and November 2018 in China. Both models have a volatility basis set (VBS) SOA algorithm but with different parameters and treatments of SOA photochemical aging. SOA generated from BVOC (i.e., BSOA) is found to be more important in southern China. In contrast, SOA generated from anthropogenic precursors is more prevalent in the North China Plain (NCP), Yangtze River Delta (YRD), Sichuan Basin and Central China. Both models indicate negligible SOA formation from SVOC emissions compared to other precursors. In July, when BVOC emissions are abundant, SOA is predominantly contributed by BSOA (except for NCP), followed by IVOC-SOA (i.e., SOA produced from IVOC) and ASOA (i.e., SOA produced from anthropogenic VOC). In contrast, in November, IVOC became the leading SOA contributor for all selected regions except PRD, illustrating the important contribution of IVOC emissions to SOA formation. While both models generally agree in terms of the spatial distributions and seasonal variations of different SOA components, CMAQ tends to predict higher BSOA, while CAMx generates higher ASOA concentrations. As a result, CMAQ results suggest that BSOA concentration is always higher than ASOA in November, while CAMx emphasizes the importance of ASOA. Utilizing a conceptual model, we found that different treatment of SOA aging between the two models is a major cause of differences in simulated ASOA concentrations. The step-wise SOA aging scheme implemented in the CAMx VBS (based on gas-phase reactions with OH radical and similar to other models) exhibits a strong enhancement effect on simulated ASOA concentrations, and this effect increases with the ambient organic aerosol (OA) concentrations. The CMAQ aerosol module implements a different SOA aging scheme that represents particle-phase oligomerization and has smaller impacts on total OA. Different structures and/or parameters of the SOA aging schemes are being used in current models, which could greatly affect model simulations of OA in ways that are difficult to anticipate. Our results indicate that future control policies should aim at reducing IVOC emissions as well as traditional VOC emissions. In addition, aging schemes are the major driver in CMAQ vs. CAMx treatments of ASOA and their resulting predicted mass. More sophisticated measurement data (e.g., with resolved OA components) and/or chamber experiments (e.g., investigating how aging influences SOA yields) are needed to better characterize SOA aging and constrain model parameterizations.

A continent-wide detailed geological map dataset of Antarctica.

A dataset to describe exposed bedrock and surficial geology of Antarctica has been constructed by the GeoMAP Action Group of the Scientific Committee on Antarctic Research (SCAR) and GNS Science. Our group captured existing geological map data into a geographic information system (GIS), refined its spatial reliability, harmonised classification, and improved representation of glacial sequences and geomorphology, thereby creating a comprehensive and coherent representation of Antarctic geology. A total of 99,080 polygons were unified for depicting geology at 1:250,000 scale, but locally there are some areas with higher spatial resolution. Geological unit definition is based on a mixed chronostratigraphic- and lithostratigraphic-based classification. Description of rock and moraine polygons employs the international Geoscience Markup Language (GeoSciML) data protocols to provide attribute-rich and queryable information, including bibliographic links to 589 source maps and scientific literature. GeoMAP is the first detailed geological map dataset covering all of Antarctica. It depicts 'known geology' of rock exposures rather than 'interpreted' sub-ice features and is suitable for continent-wide perspectives and cross-discipline interrogation.

The development of an oral health charting system for koalas (Phascolarctos cinereus).

The koala is one of Australia's most highly specialized folivores with a diet exclusively of eucalyptus leaves to provide all nutritive needs and therefore requires to be free of oral disease as they are dependent on good dentition for optimal health and quality of life. We developed an oral examination methodology based on protocols for companion animals and human dentistry to chart the oral health of koalas. Thirty free-ranging koalas from South-East Queensland, Australia were examined for general body and oral health. Inspection of the oral cavity was conducted for the presence or absence of the indicators oforal disease such as caries or periodontal disease. Univariate and multivariate analyses were performed on the examination data and a prototype oral health chart developed. The prototype was then trialled and the methodology validated by the Kappa statistic using ten additional koalas examined by four multidisciplinary personnel involved in koala care. Trauma associated fractures, tooth displacement, abnormal occlusion and tooth wear compacted vegetation, extrinsic stain deposits, periodontal bone loss, gingivitis, tooth mobility, and calculus were present in the oral cavities of the examined koalas. A system of scoring between 0 and 3 was constructed in accordance with current koala general health charting formats. Validation of the charting method using Kappa coefficients of agreement statistics indicated that there was a good agreement among observers on recorded results except for inflammation and calculus scoring. Modifications were made and visual aids and index scales produced to further assist observers. Oral health surveillance has been proven in other species to be significant in diagnosing physiological disturbances derived from environmental genetic, and developmental causes. Veterinarians, dental researchers, and koala husbandry personnel will benefit in using this charting method and reporting the oral health of koala populations in their future findings. This unique form of oral health monitoring would be adaptable to other mammals.

Mapping of the contraction-induced phosphoproteome identifies TRIM28 as a significant regulator of skeletal muscle size and function.

Mechanical signals, such as those evoked by maximal-intensity contractions (MICs), can induce an increase in muscle mass. Rapamycin-sensitive signaling events are widely implicated in the regulation of this process; however, recent studies indicate that rapamycin-insensitive signaling events are also involved. Thus, to identify these events, we generate a map of the MIC-regulated and rapamycin-sensitive phosphoproteome. In total, we quantify more than 10,000 unique phosphorylation sites and find that more than 2,000 of these sites are significantly affected by MICs, but remarkably, only 38 of the MIC-regulated events are mediated through a rapamycin-sensitive mechanism. Further interrogation of the rapamycin-insensitive phosphorylation events identifies the S473 residue on Tripartite Motif-Containing 28 (TRIM28) as one of the most robust MIC-regulated phosphorylation sites, and extensive follow-up studies suggest that TRIM28 significantly contributes to the homeostatic regulation of muscle size and function as well as the hypertrophy that occurs in response to increased mechanical loading.

Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin.

Using immunoprecipitation, mass spectrometry, and western blot analysis we investigated cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin in mammalian cells. We identified novel interactions with members of the exocyst, dynactin and chaperonin containing T-complex protein complexes, and we confirmed interactions reported previously with all members of the biogenesis of lysosome-related organelles complex-1 and the adaptor-related protein complex 3. We report interactions between dysbindin and the exocyst and dynactin complex that confirm a link between two important schizophrenia susceptibility genes: dysbindin and disrupted-in-schizophrenia-1. To expand upon this network of interacting proteins we also investigated protein interactions for members of the exocyst and dynactin complexes in mammalian cells. Our results are consistent with the notion that impairment of aspects of the synaptic vesicle life cycle may be a pathogenic mechanism in schizophrenia.