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1.
J Immunother Cancer ; 11(1)2023 01.
Article in English | MEDLINE | ID: mdl-36599469

ABSTRACT

BACKGROUND: Groundbreaking studies have linked the gut microbiome with immune homeostasis and antitumor immune responses. Mounting evidence has also demonstrated an intratumoral microbiome, including in soft tissue sarcomas (STS), although detailed characterization of the STS intratumoral microbiome is limited. We sought to characterize the intratumoral microbiome in patients with STS undergoing preoperative radiotherapy and surgery, hypothesizing the presence of a distinct intratumoral microbiome with potentially clinically significant microbial signatures. METHODS: We prospectively obtained tumor and stool samples from adult patients with non-metastatic STS using a strict sterile collection protocol to minimize contamination. Metagenomic classification was used to estimate abundance using genus and species taxonomic levels across all classified organisms, and data were analyzed with respect to clinicopathologic factors. RESULTS: Fifteen patients were enrolled. Most tumors were located at an extremity (67%) and were histologic grade 3 (87%). 40% were well-differentiated/dedifferentiated liposarcoma histology. With a median follow-up of 24 months, 4 (27%) patients developed metastases, and 3 (20%) died. Despite overwhelming human DNA (>99%) intratumorally, we detected a small but consistent proportion of bacterial DNA (0.02-0.03%) in all tumors, including Proteobacteria, Bacteroidetes, and Firmicutes, as well as viral species. In the tumor microenvironment, we observed a strong positive correlation between viral relative abundance and natural killer (NK) infiltration, and higher NK infiltration was associated with superior metastasis-free and overall survival by immunohistochemical, flow cytometry, and multiplex immunofluorescence analyses. CONCLUSIONS: We prospectively demonstrate the presence of a distinct and measurable intratumoral microbiome in patients with STS at multiple time points. Our data suggest that the STS tumor microbiome has prognostic significance with viral relative abundance associated with NK infiltration and oncologic outcome. Additional studies are warranted to further assess the clinical impact of these findings.


Subject(s)
Sarcoma , Soft Tissue Neoplasms , Adult , Humans , Virome , Sarcoma/genetics , Prognosis , Extremities/pathology , Killer Cells, Natural , Tumor Microenvironment
2.
Curr Treat Options Oncol ; 21(8): 68, 2020 07 04.
Article in English | MEDLINE | ID: mdl-32623530

ABSTRACT

OPINION STATEMENT: Denosumab is a RANK ligand inhibitor approved for the treatment of giant cell tumor of bone. While the role of denosumab in the setting of advanced and unresectable disease is well established, its role in surgically resectable disease is currently under discussion. Several prospective and retrospective series on neoadjuvant therapy in potentially resectable tumor with high morbidity surgery reported a relapse rate of 10-20% after resection and 30-40% after curettage. At the same time, less morbid surgery has obvious clinical advantages for the patient, and several studies have shown the efficacy of denosumab in downgrading of the surgical procedure. Currently, the role of neoadjuvant denosumab in operable GCTB is limited to selected cases in which a diffuse reactive bone formation and peripheral ossification can make an easier surgical procedure, for example, in tumors with a large soft tissue component. A planned resection may become less morbid when preoperative denosumab is administered. Whenever a segmental resection is thought to be indicated at diagnosis, denosumab may be considered in the neoadjuvant setting. A preoperative course of 6 months is considered safe and effective. Two case scenarios are presented and critically discussed. Because of the high recurrence rates after denosumab treatment followed by curettage, we discourage the use of denosumab when curettage is considered feasible. In this setting, a short course of preoperative denosumab (2-6 months) may be considered for highly selected cases, for example in pathological fractures. The role of adjuvant denosumab needs further investigation. Long-term disease control has been reported in case of non-surgical lesions, even after treatment interruption, but there is no consensus on ideal treatment duration and dosage for these scenarios. In all cases, multidisciplinary discussion with oncology, pathologist, radiologist, and surgeons is mandatory. Patient's comorbidities, dental conditions, and preferences, including family planning, should always be taken into account.


Subject(s)
Bone Density Conservation Agents/therapeutic use , Bone Neoplasms/complications , Denosumab/therapeutic use , Giant Cell Tumor of Bone/complications , Osteolysis/drug therapy , Osteolysis/etiology , Biopsy , Bone Density Conservation Agents/administration & dosage , Bone Neoplasms/diagnosis , Bone and Bones/diagnostic imaging , Bone and Bones/pathology , Denosumab/administration & dosage , Female , Giant Cell Tumor of Bone/diagnosis , Humans , Image-Guided Biopsy , Middle Aged , Neoadjuvant Therapy , Osteolysis/diagnosis , Radiography , Tomography, X-Ray Computed
3.
Nat Commun ; 10(1): 3907, 2019 08 29.
Article in English | MEDLINE | ID: mdl-31467278

ABSTRACT

Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose a framework for binary protein-protein interaction (PPI) mapping based on optimally combining assays and/or assay versions to maximize detection of true positive interactions, while avoiding detection of random protein pairs. We have engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions, differing by protein expression systems and tagging configurations. The resulting union of N2H versions recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our findings should be applicable to systematic mapping of other biological landscapes.


Subject(s)
Biological Assay/methods , Protein Interaction Mapping/methods , Proteome/analysis , Databases, Protein , HEK293 Cells , HeLa Cells , High-Throughput Screening Assays/methods , Humans , Protein Interaction Maps , Proteins/metabolism , Proteomics/methods , Two-Hybrid System Techniques
4.
Front Microbiol ; 9: 2596, 2018.
Article in English | MEDLINE | ID: mdl-30429836

ABSTRACT

After a pandemic wave in 2009 following their introduction in the human population, the H1N1pdm09 viruses replaced the previously circulating, pre-pandemic H1N1 virus and, along with H3N2 viruses, are now responsible for the seasonal influenza type A epidemics. So far, the evolutionary potential of influenza viruses has been mainly documented by consensus sequencing data. However, like other RNA viruses, influenza A viruses exist as a population of diverse, albeit related, viruses, or quasispecies. Interest in this quasispecies nature has increased with the development of next generation sequencing (NGS) technologies that allow a more in-depth study of the genetic variability. NGS deep sequencing methodologies were applied to determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide polymorphism profiles between seasons for a given subtype also revealed the constant genetic drift that human influenza A virus quasispecies undergo.

5.
Exp Clin Psychopharmacol ; 26(2): 125-131, 2018 04.
Article in English | MEDLINE | ID: mdl-29648860

ABSTRACT

Despite considerable health risks due to lower levels of estrogen production and the compounding antiestrogenic effects of nicotine, postmenopausal females continue to smoke. These females face significant barriers to cessation, including negative affect, weight concerns, and menopausal symptom severity. The current pilot study explored the effect of negative affect, weight concerns, and menopausal symptom severity on motivation and readiness to quit smoking. Eighteen postmenopausal smokers were randomized to receive brief motivational interviewing (B-MI; n = 8) or control treatment (i.e., a 1-hour video, n = 10). Participants completed measures of negative affect, weight concerns, and menopausal symptoms, as well as measures of motivation and readiness to quit. Motivation and readiness to quit were reassessed one week following treatment. At baseline, weight concerns, specifically surrounding smoking to prevent overeating, were identified as related to increased motivation to quit smoking. Menopausal symptom severity, specifically somatic symptoms, assessed at baseline, was associated with increased readiness for cessation. B-MI did not increase motivation or readiness to quit; however, results indicate that cigarettes per day decreased from baseline to follow-up by approximately 20-30%. These results provide valuable insight into enhancing engagement in a cessation treatment among this population. (PsycINFO Database Record


Subject(s)
Cigarette Smoking , Motivation , Motivational Interviewing/methods , Nicotine/pharmacology , Postmenopause , Smoking Cessation , Tobacco Use Disorder , Cigarette Smoking/adverse effects , Cigarette Smoking/physiopathology , Female , Humans , Middle Aged , Pilot Projects , Postmenopause/drug effects , Postmenopause/physiology , Postmenopause/psychology , Smokers/psychology , Smoking Cessation/methods , Smoking Cessation/psychology , Symptom Assessment/methods , Tobacco Use Disorder/physiopathology , Tobacco Use Disorder/psychology , Tobacco Use Disorder/therapy , Treatment Outcome
6.
J Orthop Trauma ; 32(4): e139-e144, 2018 04.
Article in English | MEDLINE | ID: mdl-29558376

ABSTRACT

The mission of any academic orthopaedic training program can be divided into 3 general areas of focus: clinical care, academic performance, and research. Clinical care is evaluated on clinical volume, patient outcomes, patient satisfaction, and becoming increasingly focused on data-driven quality metrics. Academic performance of a department can be used to motivate individual surgeons, but objective measures are used to define a residency program. Annual in-service examinations serve as a marker of resident knowledge base, and board pass rates are clearly scrutinized. Research productivity, however, has proven harder to objectively quantify. In an effort to improve transparency and better account for conflicts of interest, bias, and self-citation, multiple bibliometric measures have been developed. Rather than using individuals' research productivity as a surrogate for departmental research, we sought to establish an objective methodology to better assess a residency program's ability to conduct meaningful research. In this study, we describe a process to assess the number and quality of publications produced by an orthopaedic residency department. This would allow chairmen and program directors to benchmark their current production and make measurable goals for future research investment. The main goal of the benchmarking system is to create an "h-index" for residency programs. To do this, we needed to create a list of relevant articles in the orthopaedic literature. We used the Journal Citation Reports. This publication lists all orthopaedic journals that are given an impact factor rating every year. When we accessed the Journal Citation Reports database, there were 72 journals included in the orthopaedic literature section. To ensure only relevant, impactful journals were included, we selected journals with an impact factor greater than 0.95 and an Eigenfactor Score greater than 0.00095. After excluding journals not meeting these criteria, we were left with 45 journals. We performed a Scopus search over a 10-year period of these journals and created a database of articles and their affiliated institutions. We performed several iterations of this to maximize the capture of articles attributed to institutions with multiple names. Based off of this extensive database, we were able to analyze all allopathic US residency programs based on their quality research productivity. We believe this as a novel methodology to create a system by which residency program chairmen and directors can assess progress over time and accurate comparison with other programs.


Subject(s)
Biomedical Research/statistics & numerical data , Efficiency , Internship and Residency , Orthopedics/education , Bibliometrics , Humans , Orthopedics/statistics & numerical data
7.
Oncotarget ; 9(17): 13102-13115, 2018 Mar 02.
Article in English | MEDLINE | ID: mdl-29568343

ABSTRACT

The SRC Kinase Adaptor Phosphoprotein 2 (SKAP2) is a broadly expressed adaptor associated with the control of actin-polymerization, cell migration, and oncogenesis. After activation of different receptors at the cell surface, this dimeric protein serves as a platform for assembling other adaptors such as FYB and some SRC family kinase members, although these mechanisms are still poorly understood. The goal of this study is to map the SKAP2 interactome and characterize which domains or binding motifs are involved in these interactions. This is a prerequisite to finely analyze how these pathways are integrated in the cell machinery and to study their role in cancer and other human diseases when this network of interactions is perturbed. In this work, the domain and the binding motif of fourteen proteins interacting with SKAP2 were precisely defined and a new interactor, FAM102A was discovered. Herein, a fine-tuning between the binding of SRC kinases and their activation was identified. This last process, which depends on SKAP2 dimerization, indirectly affects the binding of FYB protein. Analysis of conformational changes associated with activation/inhibition of SRC family members, presently limited to their effect on kinase activity, is extended to their interactive network, which paves the way for therapeutic development.

8.
mSphere ; 2(6)2017.
Article in English | MEDLINE | ID: mdl-29202037

ABSTRACT

The optimized exploitation of cell resources is one cornerstone of a successful infection. Differential mapping of host-pathogen protein-protein interactions (PPIs) on the basis of comparative interactomics of multiple strains is an effective strategy to highlight correlations between host proteome hijacking and biological or pathogenic traits. Here, we developed an interactomic pipeline to deliver high-confidence comparative maps of PPIs between a given pathogen and the human ubiquitin proteasome system (UPS). This subarray of the human proteome represents a range of essential cellular functions and promiscuous targets for many viruses. The screening pipeline was applied to the influenza A virus (IAV) PB2 polymerase proteins of five strains representing different levels of virulence in humans. An extensive PB2-UPS interplay has been detected that recapitulates the evolution of IAVs in humans. Functional validation with several IAV strains, including the seasonal H1N1pdm09 and H3N2 viruses, confirmed the biological relevance of most identified UPS factors and revealed strain-independent and strain-specific effects of UPS factor invalidation on IAV infection. This strategy is applicable to proteins from any other virus or pathogen, providing a valuable resource with which to explore the UPS-pathogen interplay and its relationship with pathogenicity. IMPORTANCE Influenza A viruses (IAVs) are responsible for mild-to-severe seasonal respiratory illness of public health concern worldwide, and the risk of avian strain outbreaks in humans is a constant threat. Elucidating the requisites of IAV adaptation to humans is thus of prime importance. In this study, we explored how PB2 replication proteins of IAV strains with different levels of virulence in humans hijack a major protein modification pathway of the human host cell, the ubiquitin proteasome system (UPS). We found that the PB2 protein engages in an extended interplay with the UPS that evolved along with the virus's adaptation to humans. This suggests that UPS hijacking underlies the efficient infection of humans and can be used as an indicator for evaluation of the potential of avian IAVs to infect humans. Several UPS factors were found to be necessary for infection with circulating IAV strains, pointing to potential targets for therapeutic approaches.

9.
FEBS J ; 284(19): 3171-3201, 2017 10.
Article in English | MEDLINE | ID: mdl-28786561

ABSTRACT

Protein ubiquitination and its reverse reaction, deubiquitination, regulate protein stability, protein binding activity, and their subcellular localization. These reactions are catalyzed by the enzymes E1, E2, and E3 ubiquitin (Ub) ligases and deubiquitinases (DUBs). The Ub-proteasome system (UPS) is targeted by viruses for the sake of their replication and to escape host immune response. To identify novel partners of human papillomavirus 16 (HPV16) E6 and E7 proteins, we assembled and screened a library of 590 cDNAs related to the UPS by using the Gaussia princeps luciferase protein complementation assay. HPV16 E6 was found to bind to the homology to E6AP C terminus-type Ub ligase (E6AP), three really interesting new gene (RING)-type Ub ligases (MGRN1, LNX3, LNX4), and the DUB Ub-specific protease 15 (USP15). Except for E6AP, the binding of UPS factors did not require the LxxLL-binding pocket of HPV16 E6. LNX3 bound preferentially to all high-risk mucosal HPV E6 tested, whereas LNX4 bound specifically to HPV16 E6. HPV16 E7 was found to bind to several broad-complex tramtrack and bric-a-brac domain-containing proteins (such as TNFAIP1/KCTD13) that are potential substrate adaptors of Cullin 3-RING Ub ligases, to RING-type Ub ligases implicated in innate immunity (RNF135, TRIM32, TRAF2, TRAF5), to the substrate adaptor DCAF15 of Cullin 4-RING Ub ligase and to some DUBs (USP29, USP33). The binding to UPS factors did not require the LxCxE motif but rather the C-terminal region of HPV16 E7 protein. The identified UPS factors interacted with most of E7 proteins across different HPV types. This study establishes a strategy for the rapid identification of interactions between host or pathogen proteins and the human ubiquitination system.


Subject(s)
Host-Pathogen Interactions , Human papillomavirus 16/genetics , Oncogene Proteins, Viral/genetics , Papillomavirus E7 Proteins/genetics , Proteasome Endopeptidase Complex/metabolism , Repressor Proteins/genetics , Ubiquitin-Protein Ligase Complexes/genetics , Ubiquitin/genetics , Adaptor Proteins, Signal Transducing , Apoptosis , Carrier Proteins/genetics , Carrier Proteins/metabolism , Computational Biology , Gene Expression Regulation , Genes, Reporter , Human papillomavirus 16/metabolism , Humans , Luciferases/genetics , Luciferases/metabolism , Molecular Sequence Annotation , Oncogene Proteins, Viral/metabolism , Papillomavirus E7 Proteins/metabolism , Peptide Library , Protein Binding , Protein Interaction Mapping , Proteins/genetics , Proteins/metabolism , Repressor Proteins/metabolism , Ubiquitin/metabolism , Ubiquitin-Protein Ligase Complexes/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Specific Proteases/genetics , Ubiquitin-Specific Proteases/metabolism , Ubiquitination , Virus Replication
10.
Nat Microbiol ; 2: 16185, 2016 Oct 10.
Article in English | MEDLINE | ID: mdl-27723724

ABSTRACT

Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.


Subject(s)
Epidemiological Monitoring , Genome, Bacterial , Genotyping Techniques/methods , Listeria monocytogenes/classification , Listeria monocytogenes/genetics , Listeriosis/epidemiology , Listeriosis/microbiology , Genetic Variation , Global Health , Humans , Molecular Epidemiology/methods , Phylogeography
11.
Methods Mol Biol ; 1282: 213-29, 2015.
Article in English | MEDLINE | ID: mdl-25720483

ABSTRACT

Over the last 2 decades, yeast two-hybrid became an invaluable technique to decipher protein-protein interaction networks. In the field of virology, it has proven instrumental to identify virus-host interactions that are involved in viral embezzlement of cellular functions and inhibition of immune mechanisms. Here, we present a yeast two-hybrid protocol that has been used in our laboratory since 2006 to search for cellular partners of more than 300 viral proteins. Our aim was to develop a robust and straightforward pipeline, which minimizes false-positive interactions with a decent coverage of target cDNA libraries, and only requires a minimum of equipment. We also discuss reasons that motivated our technical choices and compromises that had to be made. This protocol has been used to screen most non-structural proteins of murine hepatitis virus (MHV), a member of betacoronavirus genus, against a mouse brain cDNA library. Typical results were obtained and are presented in this report.


Subject(s)
Murine hepatitis virus/physiology , Nerve Tissue Proteins/metabolism , Two-Hybrid System Techniques , Viral Proteins/metabolism , Animals , Host-Pathogen Interactions , Mice , Virus Attachment
12.
Emerg Infect Dis ; 20(11): 1812-20, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25341126

ABSTRACT

Multidrug-resistant and highly virulent Klebsiella pneumoniae isolates are emerging, but the clonal groups (CGs) corresponding to these high-risk strains have remained imprecisely defined. We aimed to identify K. pneumoniae CGs on the basis of genome-wide sequence variation and to provide a simple bioinformatics tool to extract virulence and resistance gene data from genomic data. We sequenced 48 K. pneumoniae isolates, mostly of serotypes K1 and K2, and compared the genomes with 119 publicly available genomes. A total of 694 highly conserved genes were included in a core-genome multilocus sequence typing scheme, and cluster analysis of the data enabled precise definition of globally distributed hypervirulent and multidrug-resistant CGs. In addition, we created a freely accessible database, BIGSdb-Kp, to enable rapid extraction of medically and epidemiologically relevant information from genomic sequences of K. pneumoniae. Although drug-resistant and virulent K. pneumoniae populations were largely nonoverlapping, isolates with combined virulence and resistance features were detected.


Subject(s)
Drug Resistance, Multiple, Bacterial/genetics , Genomics , Klebsiella Infections/microbiology , Klebsiella pneumoniae/genetics , Anti-Bacterial Agents/pharmacology , Cluster Analysis , Genome, Bacterial , Humans , Klebsiella Infections/epidemiology , Klebsiella pneumoniae/classification , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/pathogenicity , Multilocus Sequence Typing , Phylogeny , Serotyping , Virulence/genetics
13.
ACS Nano ; 7(11): 10094-104, 2013 Nov 26.
Article in English | MEDLINE | ID: mdl-24138532

ABSTRACT

We have synthesized model hydrophobic silicone thin films on gold surfaces by a two-step covalent grafting procedure. An amino-functionalized gold surface reacts with monoepoxy-terminated polydimethylsiloxane (PDMS) via a click reaction, resulting in a covalently attached nanoscale thin film of PDMS, and the click chemistry synthesis route provides great selectivity, reproducibility, and stability in the resulting model hydrophobic silicone thin films. The asymmetric interaction forces between the PDMS thin films and mica surfaces were measured with the surface forces apparatus in aqueous sodium chloride solutions. At an acidic pH of 3, attractive interactions are measured, resulting in instabilities during both approach (jump-in) and separation (jump-out from adhesive contact). Quantitative analysis of the results indicates that the Derjaguin-Landau-Verwey-Overbeek theory alone, i.e., the combination of electrostatic repulsion and van der Waals attraction, cannot fully describe the measured forces and that the additional measured adhesion is likely due to hydrophobic interactions. The surface interactions are highly pH-dependent, and a basic pH of 10 results in fully repulsive interactions at all distances, due to repulsive electrostatic and steric-hydration interactions, indicating that the PDMS is negatively charged at high pH. We describe an interaction potential with a parameter, known as the Hydra parameter, that can account for the extra attraction (low pH) due to hydrophobicity as well as the extra repulsion (high pH) due to hydrophilic (steric-hydration) interactions. The interaction potential is general and provides a quantitative measure of interfacial hydrophobicity/hydrophilicity for any set of interacting surfaces in aqueous solution.


Subject(s)
Silicones/chemistry , Adsorption , Aluminum Silicates/chemistry , Biocompatible Materials/chemistry , Dimethylpolysiloxanes/chemistry , Gold/chemistry , Hydrogen-Ion Concentration , Hydrophobic and Hydrophilic Interactions , Membrane Potentials , Nanotechnology , Polymers/chemistry , Solutions , Static Electricity , Surface Properties , Water/chemistry
14.
Tenn Med ; 106(3): 41-3, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23544291

ABSTRACT

OBJECTIVE: Describe the characteristics of the Tennessee (TN) Emergency Medicine (EM) workforce. METHODS: A cross-sectional mail survey of all non-government emergency departments (EDs) in TN was performed between January and April 2009. Data collected included: number and residency training of physicians, ED volume, employment and type of mid-level providers. Survey datawere compared to recent national EM workforce data. Subgroup analysis of rural EDs using Rural-Urban Commuting Area Code (RUCA) criteria was conducted. RESULTS: We received responses from 50 of the 100 emergency departments surveyed. Roughly half (53 percent) were rural, based on RUCA criteria. Mid-level providers worked with physicians in 31 departments, with physician assistants(PAs) being employed more commonly than nurse practitioners(NPs). Paramedics and emergency medical technicians (EMTs) were employed less frequently. Most EM residency trained physicians in Tennessee are working in EDs with approximately 39,000 annual visits per year or greater. Subspecialty physicians such as neurosurgeons, gastroenterologists and otorhinolaryngologists are generally not available to rural EDs, except by patient transfer, illustrating the marked differences in the work environments. CONCLUSION: While there is clearly a need for more emergency medicine residency training programs in Tennessee, the need to continue to provide advanced training for family medicine residency trained physicians is also clear. Family medicine doctors provide most of the rural emergency medicine in Tennessee.


Subject(s)
Emergency Medicine/education , Emergency Service, Hospital , Internship and Residency/statistics & numerical data , Cross-Sectional Studies , Emergency Service, Hospital/statistics & numerical data , Humans , Medically Underserved Area , Physician Assistants/supply & distribution , Rural Health Services , Tennessee , Utilization Review/statistics & numerical data , Workforce , Workload/statistics & numerical data
15.
Methods ; 58(4): 349-59, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22898364

ABSTRACT

Comparative interactomics is a strategy for inferring potential interactions among orthologous proteins or "interologs". Herein we focus, in contrast to standard homology-based inference, on the divergence of protein interaction profiles among closely related organisms, showing that the approach can correlate specific traits to phenotypic differences. As a model, this new comparative interactomic approach was applied at a large scale to human papillomaviruses (HPVs) proteins. The oncogenic potential of HPVs is mainly determined by the E6 and E7 early proteins. We have mapped and overlapped the virus-host protein interaction networks of E6 and E7 proteins from 11 distinct HPV genotypes, selected for their different tropisms and pathologies. We generated robust and comprehensive datasets by combining two orthogonal protein interaction assays: yeast two-hybrid (Y2H), and our recently described "high-throughput Gaussia princeps protein complementation assay" (HT-GPCA). HT-GPCA detects protein interaction by measuring the interaction-mediated reconstitution of activity of a split G. princeps luciferase. Hierarchical clustering of interaction profiles recapitulated HPV phylogeny and was used to correlate specific virus-host interaction profiles with pathological traits, reflecting the distinct carcinogenic potentials of different HPVs. This comparative interactomics constitutes a reliable and powerful strategy to decipher molecular relationships in virtually any combination of microorganism-host interactions.


Subject(s)
Alphapapillomavirus/physiology , Host-Pathogen Interactions , Luciferases/genetics , Plant Proteins/genetics , Two-Hybrid System Techniques , Alphapapillomavirus/genetics , Arecaceae/enzymology , Biomarkers/metabolism , Cluster Analysis , Genotype , HEK293 Cells , Humans , Luciferases/biosynthesis , Oncogene Proteins, Viral/genetics , Oncogene Proteins, Viral/metabolism , Papillomavirus E7 Proteins/genetics , Papillomavirus E7 Proteins/metabolism , Phylogeny , Plant Proteins/biosynthesis , Protein Binding , Protein Interaction Mapping , Protein Interaction Maps , Proteome/metabolism , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/genetics , Repressor Proteins/genetics , Repressor Proteins/metabolism , Viral Tropism
16.
PLoS Pathog ; 8(6): e1002761, 2012.
Article in English | MEDLINE | ID: mdl-22761572

ABSTRACT

Human Papillomaviruses (HPV) cause widespread infections in humans, resulting in latent infections or diseases ranging from benign hyperplasia to cancers. HPV-induced pathologies result from complex interplays between viral proteins and the host proteome. Given the major public health concern due to HPV-associated cancers, most studies have focused on the early proteins expressed by HPV genotypes with high oncogenic potential (designated high-risk HPV or HR-HPV). To advance the global understanding of HPV pathogenesis, we mapped the virus/host interaction networks of the E2 regulatory protein from 12 genotypes representative of the range of HPV pathogenicity. Large-scale identification of E2-interaction partners was performed by yeast two-hybrid screenings of a HaCaT cDNA library. Based on a high-confidence scoring scheme, a subset of these partners was then validated for pair-wise interaction in mammalian cells with the whole range of the 12 E2 proteins, allowing a comparative interaction analysis. Hierarchical clustering of E2-host interaction profiles mostly recapitulated HPV phylogeny and provides clues to the involvement of E2 in HPV infection. A set of cellular proteins could thus be identified discriminating, among the mucosal HPV, E2 proteins of HR-HPV 16 or 18 from the non-oncogenic genital HPV. The study of the interaction networks revealed a preferential hijacking of highly connected cellular proteins and the targeting of several functional families. These include transcription regulation, regulation of apoptosis, RNA processing, ubiquitination and intracellular trafficking. The present work provides an overview of E2 biological functions across multiple HPV genotypes.


Subject(s)
Host-Parasite Interactions/genetics , Oncogene Proteins, Viral/genetics , Papillomaviridae/genetics , Papillomavirus Infections/genetics , Cell Line , Genotype , Humans , Papillomaviridae/pathogenicity , Papillomavirus Infections/virology , Two-Hybrid System Techniques
17.
Small ; 8(3): 468-73, 2012 Feb 06.
Article in English | MEDLINE | ID: mdl-22213635

ABSTRACT

Polyvinylpyrollidone (PVP)-capped platinum nanoparticles (NPs) are found to change shape from spherical to flat when deposited on mesoporous silica substrates (SBA-15). Transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and extended X-ray absorption fine structure (EXAFS) analyses are used in these studies. The SAXS results indicate that, after deposition, the 2 nm NPs have an average gyration radius 22% larger than in solution, while the EXAFS measurements indicate a decrease in first neighbor co-ordination number from 9.3 to 7.4. The deformation of these small capped NPs is attributed to interactions with the surface of the SBA-15 support, as evidenced by X-ray absorption near-edge structure (XANES).

18.
J Virol ; 86(6): 3121-34, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22258240

ABSTRACT

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has been responsible for an epidemic outbreak of unprecedented magnitude in recent years. Since then, significant efforts have been made to better understand the biology of this virus, but we still have poor knowledge of CHIKV interactions with host cell components at the molecular level. Here we describe the extensive use of high-throughput yeast two-hybrid (HT-Y2H) assays to characterize interactions between CHIKV and human proteins. A total of 22 high-confidence interactions, which essentially involved the viral nonstructural protein nsP2, were identified and further validated in protein complementation assay (PCA). These results were integrated to a larger network obtained by extensive mining of the literature for reports on alphavirus-host interactions. To investigate the role of cellular proteins interacting with nsP2, gene silencing experiments were performed in cells infected by a recombinant CHIKV expressing Renilla luciferase as a reporter. Collected data showed that heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and ubiquilin 4 (UBQLN4) participate in CHIKV replication in vitro. In addition, we showed that CHIKV nsP2 induces a cellular shutoff, as previously reported for other Old World alphaviruses, and determined that among binding partners identified by yeast two-hybrid methods, the tetratricopeptide repeat protein 7B (TTC7B) plays a significant role in this activity. Altogether, this report provides the first interaction map between CHIKV and human proteins and describes new host cell proteins involved in the replication cycle of this virus.


Subject(s)
Alphavirus Infections/metabolism , Alphavirus Infections/virology , Chikungunya virus/metabolism , Host-Pathogen Interactions , Protein Interaction Maps , Viral Nonstructural Proteins/metabolism , Carrier Proteins/metabolism , Cell Line , Chikungunya Fever , Chikungunya virus/genetics , Heterogeneous-Nuclear Ribonucleoprotein K/metabolism , Humans , Nuclear Proteins/metabolism , Viral Nonstructural Proteins/genetics
19.
Am J Physiol Heart Circ Physiol ; 302(1): H340-8, 2012 Jan 01.
Article in English | MEDLINE | ID: mdl-22003055

ABSTRACT

We have shown that obese Zucker rats with orthopedic trauma (OZT) exhibit a loss of arteriolar tone in skeletal muscle. We hypothesize that the loss of arteriolar tone in OZT blunts vasoconstrictor responses to hemorrhage, resulting in an impaired blood pressure recovery. Orthopedic trauma was induced with soft tissue injury and local injection of bone components in both hindlimbs in lean (LZT) and OZT (11-13 wk). One day after the orthopedic trauma, blood pressure responses following hemorrhage were measured in conscious control lean, control obese, LZT, and OZT. In another set of experiments, the spinotrapezius muscle of control and trauma animals was prepared for microcirculatory observation. Arteriolar responses to phenylephrine (PE) or hemorrhage were determined. Hemorrhage resulted in similar blood pressure responses in control animals and LZT, but the blood pressure recovery following hemorrhage was blunted in the OZT. In the spinotrapezius, OZT exhibited decreased arteriolar tone and blunted vasoconstrictor responses to PE and hemorrhage. Treatment with glibenclamide improved the blood pressure recovery in the conscious OZT and improved the arteriolar tone, and PE induced vasoconstriction in the spinotrapezius of the OZT. Thus, ATP-dependent K(+) channel-mediated loss of arteriolar tone in OZT blunts the arteriolar constriction to hemorrhage, resulting in impaired blood pressure recovery.


Subject(s)
Blood Pressure , Femoral Fractures/complications , Hemorrhage/physiopathology , Muscle, Skeletal/blood supply , Obesity/complications , Soft Tissue Injuries/complications , Animals , Arterioles/physiopathology , Blood Pressure/drug effects , Disease Models, Animal , Dose-Response Relationship, Drug , Femoral Fractures/physiopathology , Glyburide/pharmacology , Heart Rate , Hemorrhage/complications , Hemorrhage/metabolism , KATP Channels/antagonists & inhibitors , KATP Channels/metabolism , Male , Microcirculation , Obesity/physiopathology , Phenylephrine/pharmacology , Potassium Channel Blockers/pharmacology , Rats , Rats, Zucker , Recovery of Function , Soft Tissue Injuries/physiopathology , Time Factors , Vasoconstriction , Vasoconstrictor Agents/pharmacology
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