Random access DNA memory using Boolean search in an archival file storage system.

DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 106 files, which thereby enables one in 106N selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets.

Using Evidence: A Nursing Assessment Protocol for Acute Geropsychiatric Patients.

INTRODUCTION: The Centers for Disease Control and Prevention estimates that approximately 20% of the United States population lives with at least one mental health issue. The most common mental illnesses affecting older Americans include anxiety, cognitive, and mood disorders. These patients may exhibit behaviors indicating agitation or anxiety during necessary hospital stays that warrant de-escalation techniques and appropriate medications to help manage emergent symptoms. AIMS: This quality improvement intervention was intended to demonstrate enhancement of the nursing assessment and reassessment of patients demonstrating symptoms of agitation and anxiety requiring intervention. METHODS: Assessment of the established nursing practice demonstrated compromised patient safety and led to planning and implementation of a new practice standard that incorporated an evidence-based tool. Nurses utilized a protocol that employed the Pittsburgh Agitation Scale to augment documentation of the nursing assessment for patients exhibiting symptoms of marked anxiety and agitation. RESULTS: Following a 3-month trial, chart audits were completed to assess results of the protocol's implementation. Significant improvement was noted in the nursing assessment process as evidenced in required documentation of nursing assessment and reassessment including use of the protocol. CONCLUSIONS: Implementing standards to guide nursing care can support both patient safety and professional practice.

Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction.

Molecular recognition is critical for the fidelity of signal transduction in biology. Conversely, the disruption of protein-protein interactions can lead to disease. Thus, comprehension of the molecular determinants of specificity is essential for understanding normal biological signaling processes and for the development of precise therapeutics. Although high-resolution structures have provided atomic details of molecular interactions, much less is known about the influence of cooperativity and conformational dynamics. Here, we used the Tiam2 PSD-95/Dlg/ZO-1 (PDZ) domain and a quadruple mutant (QM), engineered by swapping the identity of four residues important for specificity in the Tiam1 PDZ into the Tiam2 PDZ domain, as a model system to investigate the role of cooperativity and dynamics in PDZ ligand specificity. Surprisingly, equilibrium binding experiments found that the ligand specificity of the Tiam2 QM was switched to that of the Tiam1 PDZ. NMR-based studies indicated that Tiam2 QM PDZ, but not other mutants, had extensive microsecond to millisecond motions distributed throughout the entire domain suggesting structural cooperativity between the mutated residues. Thermodynamic analyses revealed energetic cooperativity between residues in distinct specificity subpockets that was dependent upon the identity of the ligand, indicating a context-dependent binding mechanism. Finally, isothermal titration calorimetry experiments showed distinct entropic signatures along the mutational trajectory from the Tiam2 wild-type to the QM PDZ domain. Collectively, our studies provide unique insights into how structure, conformational dynamics, and thermodynamics combine to modulate ligand-binding specificity and have implications for the evolution, regulation, and design of protein-ligand interactions.

De novo design and synthesis of a 30-cistron translation-factor module.

Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0.

Telehealth in Psychiatric Nursing Education: Lessons From the Field.

BACKGROUND: This article summarizes the experiences that a Midwest college of nursing had when telepsychiatry was introduced for psychiatric-mental health post-master's nurse practitioner students to use in a clinical internship. AIMS: Implications for nurse practitioner educators will be identified, and recommendations for future research will be explored. METHOD: Described are the following: (1) policies and procedures the institution considered, (2) challenges that were encountered by faculty and students, and (3) strategies and limitations of these strategies defining best practice, what didactic content should be taught, and how clinical placements needed to be structured. RESULTS: Implications for nurse practitioner educators, practice, and research are identified. CONCLUSIONS: It is clear that telepsychiatry has an important role in the clinical education of psychiatric-mental health nurse practitioners. It is working well as a clinical internship option. The college of nursing is continuing to examine and address issues and is looking forward to enhancing the telepsychiatry experiences for students in the future.

Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges.

PURPOSE: Chromosomal microarray analysis (CMA) is currently considered first-tier testing in pediatric care and prenatal diagnosis owing to its high diagnostic sensitivity for chromosomal imbalances. The aim of this study was to determine the efficacy and diagnostic power of CMA in both fresh and formalin-fixed paraffin-embedded (FFPE) samples of products of conception (POCs). METHODS: Over a 44-month period, 8,118 consecutive samples were received by our laboratory for CMA analysis. This included both fresh (76.4%) and FFPE samples (22.4%), most of which were ascertained for recurrent pregnancy loss and/or spontaneous abortion (83%). The majority of samples were evaluated by a whole-genome single-nucleotide polymorphism (SNP)-based array (81.6%); the remaining samples were evaluated by array-comparative genomic hybridization (CGH). RESULTS: A successful result was obtained in 7,396 of 8,118 (91.1%), with 92.4% of fresh tissue samples and 86.4% of FFPE samples successfully analyzed. Clinically significant abnormalities were identified in 53.7% of specimens (3,975 of 7,396), 94% of which were considered causative. CONCLUSION: Analysis of POC specimens by karyotyping fails in 20-40% of cases. SNP-based CMA is a robust platform, with successful results obtained in >90% of cases. SNP-based CMA can identify aneuploidy, polyploidy, whole-genome homozygosity, segmental genomic imbalances, and maternal cell contamination, thus maximizing sensitivity and decreasing false-negative results. Understanding the etiology of fetal loss enables clarification of recurrence risk and assists in determining appropriate management for future family planning.Genet Med 19 1, 83-89.

Comparison of Selected Nonlethal Samples from Adult Steelhead for Detection of Infectious Hematopoietic Necrosis Virus Using Cell Culture.

Nonlethal sampling techniques have previously been evaluated for detection of a variety of viral salmonid pathogens. However, many of these studies have used molecular assays in lieu of widely accepted cell culture techniques to evaluate the sampled tissues. Samples were collected from female steelhead Oncorhynchus mykiss broodstock using three potential nonlethal sampling methods (mucus/skin scrape, pectoral fin clip, and gill tissue biopsy) and evaluated for the presence of infectious hematopoietic necrosis virus (IHNV) via cell culture techniques. The results were compared with those from samples collected using a standard lethal sampling method (pooled anterior kidney and spleen tissues) applied to the same fish. Of the three nonlethal sampling techniques that were evaluated, fin clipping was the easiest and least invasive method. Furthermore, fin tissue was as sensitive as or more sensitive than kidney/spleen tissue for detecting IHNV in this population of fish. However, with the exception of gill tissue, the nonlethal samples did not appear to be appropriate surrogates for lethally collected tissues with regard to identifying an active infection in a particular fish. Nevertheless, nonlethal sampling coupled with cell culture appears to be suitable for helping to define the IHNV status of a steelhead population. Received July 27, 2016; accepted December 11, 2016.

Bestrophin-1 influences transepithelial electrical properties and Ca2+ signaling in human retinal pigment epithelium.

PURPOSE: Mutations in BEST1, encoding Bestrophin-1 (Best1), cause Best vitelliform macular dystrophy (BVMD) and other inherited retinal degenerative diseases. Best1 is an integral membrane protein localized to the basolateral plasma membrane of the retinal pigment epithelium (RPE). Data from numerous in vitro and in vivo models have demonstrated that Best1 regulates intracellular Ca2+ levels. Although it is known from in vitro and crystal structure data that Best1 is also a calcium-activated anion channel, evidence for Best1 functioning as a channel in human RPE is lacking. To assess Best1-associated channel activity in the RPE, we examined the transepithelial electrical properties of fetal human RPE (fhRPE) cells, which express endogenous Best1. METHODS: Using adenovirus-mediated gene transfer, we overexpressed Best1 and the BVMD mutant Best1W93C in fhRPE cells and assessed resting transepithelial potential (TEP), transepithelial resistance, short circuit current (Isc), and intracellular Ca2+ levels. Cl- currents were directly measured in transfected HEK293 cells using whole-cell patch clamp. RESULTS: Best1W93C showed ablated Cl- currents and, when co-expressed, suppressed the channel activity of Best1 in HEK293 cells. In fhRPE, overexpression of Best1 increased TEP and Isc, while Best1W93C diminished TEP and Isc. Substitution of Cl- in the bath media resulted in a significant reduction of Isc in monolayers overexpressing Best1, but no significant Isc change in monolayers expressing Best1W93C. We removed Ca2+ as a limit on transepithelial electrical properties by treating cells with ionomycin, and found that changes in Isc and TEP for monolayers expressing Best1 were absent in monolayers expressing Best1W93C. Similarly, inhibition of calcium-activated anion channels with niflumic acid reduced both Isc and TEP of control and Best1 monolayers, but did not notably affect Best1W93C monolayers. Stimulation with extracellular ATP induced an increase in TEP in control monolayers that was greater than that observed in those expressing Best1(W93C). Examination of [Ca2+]i following ATP stimulation demonstrated that the expression of Best1W93C impaired intracellular Ca2+ signaling. CONCLUSIONS: These data indicate that Best1 activity strongly influences electrophysiology and Ca2+ signaling in RPE cells, and that a common BVMD mutation disrupts both of these parameters. Our findings support the hypothesis that Best1 functions as an anion channel in human RPE.

Microbiology for Radiologists: How to Minimize Infection Transmission in the Radiology Department.

The implementation of standardized infection control and prevention practices is increasingly relevant as modern radiology practice evolves into its more clinical role. Current Centers for Disease Control and Prevention, National Institutes of Health, and World Health Organization guidelines for the proper use of personal protective equipment, decontamination of reusable medical equipment, and appropriate management of bloodborne pathogen exposures will be reviewed. Standard precautions apply to all patients at all times and are the mainstay of infection control. Proper hand hygiene includes washing hands with soap and water when exposed to certain infectious particles, such as Clostridium difficile spores, which are not inactivated by alcohol-based hand rubs. The appropriate use of personal protective equipment in accordance with recommendations from the Centers for Disease Control and Prevention includes wearing a surgical mask during lumbar puncture. Because radiologists may perform lumbar punctures for patients with prion disease, it is important to appreciate that incineration is the most effective method of inactivating prion proteins. However, there is currently no consensus recommendation on the decontamination of prion-contaminated reusable items associated with lumbar puncture, and institutional policies should be consulted for directed management. In the event of a needlestick injury, radiology staff must be able to quickly provide appropriate initial management and seek medical attention, including laboratory testing for bloodborne pathogens.

Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ.

RlmJ catalyzes the m(6)A2030 methylation of 23S rRNA during ribosome biogenesis in Escherichia coli. Here, we present crystal structures of RlmJ in apo form, in complex with the cofactor S-adenosyl-methionine and in complex with S-adenosyl-homocysteine plus the substrate analogue adenosine monophosphate (AMP). RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. Binding of cofactor and substrate induces a large shift of the N-terminal motif X tail to make it cover the cofactor binding site and trigger active-site changes in motifs IV and VIII. Adenosine monophosphate binds in a partly accommodated state with the target N6 atom 7 Å away from the sulphur of AdoHcy. The active site of RlmJ with motif IV sequence 164DPPY167 is more similar to DNA m(6)A MTases than to RNA m(6)2A MTases, and structural comparison suggests that RlmJ binds its substrate base similarly to DNA MTases T4Dam and M.TaqI. RlmJ methylates in vitro transcribed 23S rRNA, as well as a minimal substrate corresponding to helix 72, demonstrating independence of previous modifications and tertiary interactions in the RNA substrate. RlmJ displays specificity for adenosine, and mutagenesis experiments demonstrate the critical roles of residues Y4, H6, K18 and D164 in methyl transfer.

Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA.

RlmM (YgdE) catalyzes the S-adenosyl methionine (AdoMet)-dependent 2'O methylation of C2498 in 23S ribosomal RNA (rRNA) of Escherichia coli. Previous experiments have shown that RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain. Here, we demonstrate RlmM methyltransferase (MTase) activity on in vitro transcribed 23S rRNA and its domain V. We have solved crystal structures of E. coli RlmM at 1.9 Å resolution and of an RlmM-AdoMet complex at 2.6 Å resolution. RlmM consists of an N-terminal THUMP domain and a C-terminal catalytic Rossmann-like fold MTase domain in a novel arrangement. The catalytic domain of RlmM is closely related to YiiB, TlyA and fibrillarins, with the second K of the catalytic tetrad KDKE shifted by two residues at the C-terminal end of a beta strand compared with most 2'O MTases. The AdoMet-binding site is open and shallow, suggesting that RNA substrate binding may be required to form a conformation needed for catalysis. A continuous surface of conserved positive charge indicates that RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate.

Informed consent-patients' understanding of risk.

AIMS: The central concept of informed consent is communication of the chance of a successful outcome. The risks and benefits are probabilistic concepts derived from populations; they do not map with any certainty to the individual. We tested patients' comprehension of basic probability concepts that are needed for informed consent. METHODS: Patients (n=478) completed five questions designed to test risk estimates that are relevant to informed consent. The questions posed non-medical scenarios to avoid patients associating them with their clinical care. The questionnaire was in English and was only offered to patients whose nurse felt that they had sufficient English literacy to understand the questions. RESULTS: Out of a possible total of five correct answers, Asian patients scored lowest, and significantly less than Pakeha/Europeans (average total score 2.6±1.7 vs 3.6±1.4, p<0.001, 95% confidence interval 0.5 to 1.38). The total score for Maori/Pasifika was intermediate (3.2±1.4), yet they had the lowest deprivation index. This discordant finding may be due to poorer English literacy among Asian participants. On multiple linear regression, Asian ethnicity and advancing age were the independent predictors of a low score. Socio-economic deprivation decile and sex were not. CONCLUSIONS: When answering questions constructed according to best practice, many (but not all) patients have reasonable risk comprehension. Further improvement could target older patients, those of Asian ethnicity and probably all patients where English is a second language. Liberal use of interpreters is suggested.

The thermodynamic and binding properties of the transferrins as studied by isothermal titration calorimetry.

BACKGROUND: In mammals, serum-transferrins transport iron from the neutral environment of the blood to the cytoplasm by receptor-mediated endocytosis. Extensive in-vitro studies have focused on the thermodynamics and kinetics of Fe(3+) binding to a number of transferrins. However, little attention has been given to the thermodynamic characterization of the interaction of transferrin with its receptor. SCOPE OF REVIEW: Iron-loaded transferrin (Tf) binds with high affinity to the specific transferrin receptor (TfR) on the cell surface. The Tf-TfR complex is then internalized via receptor mediated endocytosis into an endosome where iron is released. Here, we provide an overview of recent studies that have used ITC to quantify the interaction of various metal ions with transferrin and highlight our current understanding of the thermodynamics of the transferrin-transferrin receptor system at physiological pH. GENERAL SIGNIFICANCE: The interaction of the iron-loaded transferrin with the transferrin receptor is a key cellular process that occurs during the normal course of iron metabolism. Understanding the thermodynamics of this interaction is important for iron homeostasis since the physiological requirement of iron must be appropriately maintained to avoid iron-related diseases. MAJOR CONCLUSIONS: The thermodynamic data revealed stoichiometric binding of all tested metal ions to transferrin with very high affinities ranging between 10(17) and 10(22)M(-1). Iron-loaded transferrin (monoferric or diferric) is shown to bind avidly (K~10(7)-10(8)M(-1)) to the receptor at neutral pH with a stoichiometry of one Tf molecule per TfR monomer. Significantly, both the N- and the C-lobe contribute to the binding interaction which is shown to be both enthalpically and entropically driven. This article is part of a Special Issue entitled Transferrins: Molecular mechanisms of iron transport and disorders.

Enhanced efficacy of an attenuated Flavobacterium psychrophilum strain cultured under iron-limited conditions.

An attenuated strain of Flavobacterium psychrophilum (CSF259-93B.17) has shown potential as a vaccine for prevention of bacterial coldwater disease (BCWD) in rainbow trout, Oncorhynchus mykiss (Walbaum). Because BCWD outbreaks can result in high mortality in other salmonid species, specifically coho salmon, Oncorhynchus kisutch (Walbaum), the live-attenuated strain was tested as a vaccine in this species. Additionally, we hypothesized that culture of the vaccine strain under iron-limited conditions would lead to improved protection against BCWD. To test this hypothesis, coho salmon were either injection or immersion immunized with CSF259-93B.17 cultured in iron-replete or iron-limited medium. Resultant antibody titers were low and not significantly different between the two treatments regardless of vaccine delivery method (P > 0.05). Following injection challenge with a virulent F. psychrophilum strain, mortality for injection vaccinated fish was significantly reduced compared to the control but did not differ by treatment (P > 0.05). Relative percent survival (RPS) was high in both treatments (90% in iron-replete, 98% in iron-limited medium). Fish immunized by immersion with CSF259-93B.17 grown in iron-replete medium exhibited lower mortality (29.3%; RPS 46%) when compared to mock immunized fish, but this was not significant. However, mortality was significantly lower in fish immunized with CSF259-93B.17 grown in iron-limited medium (14.7%; RPS 73%) when compared to mock immunized fish. The results demonstrate that the live-attenuated F. psychrophilum strain can confer protection to coho salmon and vaccine efficacy is enhanced by culturing the strain under iron-limited conditions.

Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest.

Bovine peripheral lymph nodes (LNs), including subiliac LNs, have been identified as a potential source of human exposure to Salmonella enterica, when adipose trim containing these nodes is incorporated into ground beef. In order to gain a better understanding of the burden of S. enterica in peripheral LNs of feedlot and cull cattle, a cross-sectional study was undertaken in which 3327 subiliac LNs were collected from cattle at harvest in seven plants, located in three geographically distinct regions of the United States. Samples were collected in three seasons: Fall 2010, Winter/Spring 2011, and Summer/Fall 2011. A convenience sample of 76 LNs per day, 2 days per season (approximately 1 month apart), was collected per plant, from carcasses held in the cooler for no less than 24 h. Every 10(th) carcass half on a rail was sampled, in an attempt to avoid oversampling any single cohort of cattle. Median point estimates of S. enterica contamination were generally low (1.3%); however, median Salmonella prevalence was found to be greater in subiliac LNs of feedlot cattle (11.8%) compared to those of cull cattle (0.65%). Enumeration analysis of a subset of 618 feedlot cattle LNs showed that 67% of those harboring S. enterica (97 of 144) did so at concentrations ranging from <0.1 to 1.8 log10 CFU/g, while 33% carried a higher burden of S. enterica, with levels ranging from 1.9 to >3.8 log10 CFU/g. Serotyping of S. enterica isolated identified 24 serotypes, with the majority being Montevideo (44.0%) and Anatum (24.8%). Antimicrobial susceptibility phenotypes were determined for all isolates, and the majority (86.1%) were pansusceptible; however, multidrug-resistant isolates (8.3%) were also occasionally observed. As Salmonella contained within LNs are protected from carcass interventions, research is needed to define opportunities for mitigating the risk of Salmonella contamination in LNs of apparently healthy cattle.

Rate of onset of dopamine transporter inhibitors assessed with intracranial self-stimulation and in vivo dopamine photometry in rats.

Drug self-administration and intracranial self-stimulation (ICSS) are two preclinical behavioral procedures used to predict abuse potential of drugs, and abuse-related drug effects in both procedures are thought to depend on increased mesolimbic dopamine (DA) signaling. Drug self-administration and ICSS yield concordant metrics of abuse potential across a diverse range of drug mechanisms of action. The "rate of onset," defined as the velocity with which a drug produces its effect once administered, has also been implicated as a determinant of abuse-related drug effects in self-administration procedures, but this variable has not been systematically examined in ICSS. Accordingly, this study compared ICSS effects produced in rats by three DA transporter inhibitors that have different rates of onset (fastest to slowest: cocaine, WIN-35428, RTI-31) and that produced progressively weaker metrics of abuse potential in a drug self-administration procedure in rhesus monkeys. Additionally, in vivo photometry using the fluorescent DA sensor dLight1.1 targeted to the nucleus accumbens (NAc) was used to assess the time course of extracellular DA levels as a neurochemical correlate of behavioral effects. All three compounds produced ICSS facilitation and increased DA levels assessed by dLight. In both procedures, the rank order of onset rate was cocaine > WIN-35428 > RTI-31; however, in contrast to monkey drug self-administration results, maximum effects did not differ across compounds. These results provide additional evidence that drug-induced increases in DA drive ICSS facilitation in rats and illustrate the utility of both ICSS and photometry to evaluate the time course and magnitude of abuse-related drug effects in rats.

3D RNA-scaffolded wireframe origami.

Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.

Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.

There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (TetR) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of TetR E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of TetR E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized TetR E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the TetR strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics. IMPORTANCE Antimicrobial resistance (AMR) is projected to be the cause of >10 million deaths annually by 2050. While efforts to find new potent antibiotics are effective, they are expensive and outpaced by the rate at which new resistant strains emerge. There is desperate need for a rational approach to accelerate the discovery of drugs and drug combinations that effectively clear AMR pathogens and even prevent the emergence of new resistant strains. Using tetracycline-resistant (TetR) Escherichia coli, we demonstrate that gaining resistance is accompanied by loss of fitness, which is restored by compensatory physiological changes. We demonstrate that transcriptional regulators of the compensatory physiologic state are promising drug targets because their disruption increases the susceptibility of TetR E. coli to tetracycline. Thus, we describe a generalizable systems biology approach to identify new vulnerabilities within AMR strains to rationally accelerate the discovery of therapeutics that extend the life span of existing antibiotics.

Clec12a tempers inflammation while restricting expansion of a colitogenic commensal.

Regulation of the microbiota is critical to intestinal health yet the mechanisms employed by innate immunity remain unclear. Here we show that mice deficient in the C-Type-lectin receptor, Clec12a developed severe colitis, which was dependent on the microbiota. Fecal-microbiota-transplantation (FMT) studies into germfree mice revealed a colitogenic microbiota formed within Clec12a -/- mice that was marked by expansion of the gram-positive organism, Faecalibaculum rodentium . Treatment with F. rodentium was sufficient to worsen colitis in wild-type mice. Macrophages within the gut express the highest levels of Clec12a. Cytokine and sequencing analysis in Clec12a -/- macrophages revealed heighten inflammation but marked reduction in genes associated with phagocytosis. Indeed, Clec12a -/- macrophages are impaired in their ability to uptake F. rodentium. Purified Clec12a had higher binding to gram-positive organisms such as F. rodentium . Thus, our data identifies Clec12a as an innate immune surveillance mechanism to control expansion of potentially harmful commensals without overt inflammation.