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1.  Complete Genome Sequences of Four Novel Escherichia coli Bacteriophages Belonging to New Phage Groups 
Genome Announcements  2015;3(4):e00741-15.
Here, we describe the sequencing and genome annotations of a set of four Escherichia coli bacteriophages (phages) belonging to newly discovered groups previously consisting of only a single phage and thus expand our knowledge of these phage groups.
doi:10.1128/genomeA.00741-15
PMCID: PMC4505120  PMID: 26184932
2.  Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity 
PLoS ONE  2015;10(7):e0131814.
Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments.
doi:10.1371/journal.pone.0131814
PMCID: PMC4497681  PMID: 26158674
3.  Molecular Basis of Substrate Recognition and Degradation by Human Presequence Protease 
Structure (London, England : 1993)  2014;22(7):996-1007.
Summary
Human Presequence Protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing a ∼13,300Å3 catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and amyloid-β (Aβ), the latter of which contributes to Alzheimer's disease pathogenesis. Here we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size-exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP.
doi:10.1016/j.str.2014.05.003
PMCID: PMC4128088  PMID: 24931469
Alzheimer's disease; M16 metalloproteases; Mitochondria
4.  A novel ligand-independent peptide inhibitor of TREM-1 suppresses tumor growth in human lung cancer xenografts and prolongs survival of mice with lipopolysaccharide-induced septic shock 
International immunopharmacology  2014;21(1):208-219.
Triggering receptor expressed on myeloid cells-1 (TREM-1) amplifies the inflammatory response and plays a role in cancer and sepsis. Inhibition of TREM-1 by short hairpin RNA (shRNA) in macrophages suppresses cancer cell invasion in vitro. In the clinical setting, high levels of TREM-1 expression on tumor-associated macrophages are associated with cancer recurrence and poor survival of patients with non-small cell lung cancer (NSCLC). TREM-1 upregulation on peritoneal neutrophils has been found in human sepsis patients and in mice with experimental lipopolysaccharide (LPS)-induced septic shock. However, the precise function of TREM-1 and the nature of its ligand are not yet known. In this study, we used the signaling chain homooligomerization (SCHOOL) model of immune signaling to design a novel, ligand-independent peptide-based TREM-1 inhibitor and demonstrated that this peptide specifically silences TREM-1 signaling in vitro and in vivo. Utilizing two human lung tumor xenograft nude mouse models (H292 and A549) and mice with LPS-induced sepsis, we show for the first time that blockade of TREM-1 function using non-toxic and non-immunogenic SCHOOL peptide inhibitors: 1) delays tumor growth in xenograft models of human NSCLC, 2) prolongs survival of mice with LPS-induced septic shock, and 3) substantially decreases cytokine production in vitro and in vivo. In addition, targeted delivery of SCHOOL peptides to macrophages utilizing lipoprotein-mimicking nanoparticles significantly increased peptide half-life and dosage efficacy. Together, the results suggest that ligand-independent modulation of TREM-1 function using small synthetic peptides might be a suitable treatment for sepsis and NSCLC and possibly other types of inflammation-associated disorders.
doi:10.1016/j.intimp.2014.05.001
PMCID: PMC4088342  PMID: 24836682
Macrophage; TREM-1 receptor; SCHOOL model of cell signaling; therapeutic peptides; non-small cell lung cancer; sepsis; nanoparticles; targeted delivery
5.  Widespread tsunami-like waves of 23-27 June in the Mediterranean and Black Seas generated by high-altitude atmospheric forcing 
Scientific Reports  2015;5:11682.
A series of tsunami-like waves of non-seismic origin struck several southern European countries during the period of 23 to 27 June 2014. The event caused considerable damage from Spain to Ukraine. Here, we show that these waves were long-period ocean oscillations known as meteorological tsunamis which are generated by intense small-scale air pressure disturbances. An unique atmospheric synoptic pattern was tracked propagating eastward over the Mediterranean and the Black seas in synchrony with onset times of observed tsunami waves. This pattern favoured generation and propagation of atmospheric gravity waves that induced pronounced tsunami-like waves through the Proudman resonance mechanism. This is the first documented case of a chain of destructive meteorological tsunamis occurring over a distance of thousands of kilometres. Our findings further demonstrate that these events represent potentially dangerous regional phenomena and should be included in tsunami warning systems.
doi:10.1038/srep11682
PMCID: PMC4483776  PMID: 26119833
6.  Polycomb Group Targeting through Different Binding Partners of RING1B C-Terminal Domain 
SUMMARY
RING1B, a Polycomb Group (PcG) protein, binds methylated chromatin through its association with another PcG protein called Polycomb (Pc). However, RING1B can associate with nonmethylated chromatin suggesting an alternate mechanism for RING1B interaction with chromatin. Here, we demonstrate that two proteins with little sequence identity between them, the Pc cbox domain and RYBP, bind the same surface on the C-terminal domain of RING1B (C-RING1B). Pc cbox and RYBP each fold into a nearly identical, intermolecular beta sheet with C-RING1B and a loop structure which are completely different in the two proteins. Both the beta sheet and loop are required for stable binding and transcription repression. Further, a mutation engineered to disrupt binding on the Drosophila dRING1 protein prevents chromatin association and PcG function in vivo. These results suggest that PcG targeting to different chromatin locations relies, in part, on binding partners of C-RING1B that are diverse in sequence and structure.
doi:10.1016/j.str.2010.04.013
PMCID: PMC4445678  PMID: 20696397
7.  Starvation-induced collective behavior in C. elegans 
Scientific Reports  2015;5:10647.
We describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their development and disperse in search for food. In contrast, after two or more days without food, the worms change their behavior—they start to aggregate. The aggregation requires a small amount of ethanol or acetate in the environment. In the case of ethanol, it has to be metabolized, which requires functional alcohol dehydrogenase sodh-1. The resulting acetate is used in de novo fatty acid synthesis, and some of the newly made fatty acids are then derivatized to glycerophosphoethanolamides and released into the surrounding medium. We examined several other Caenorhabditis species and found an apparent correlation between propensity of starved L1s to aggregate and density dependence of their survival in starvation. Aggregation locally concentrates worms and may help the larvae to survive long starvation. This work demonstrates how presence of ethanol or acetate, relatively abundant small molecules in the environment, induces collective behavior in C. elegans associated with different survival strategies.
doi:10.1038/srep10647
PMCID: PMC4445038  PMID: 26013573
8.  Dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of GNNQQNY nanocrystals and amyloid fibrils 
Dynamic nuclear polarization (DNP) utilizes the inherently larger polarization of electrons to enhance the sensitivity of conventional solid-state NMR experiments at low temperature. Recent advances in instrumentation development and sample preparation have transformed this field and have opened up new opportunities for its application to biological systems. Here, we present DNP-enhanced 13C–13C and 15N–13C correlation experiments on GNNQQNY nanocrystals and amyloid fibrils acquired at 9.4 T and 100 K and demonstrate that DNP can be used to obtain assignments and site-specific structural information very efficiently. We investigate the influence of temperature on the resolution, molecular conformation, structural integrity and dynamics in these two systems. In addition, we assess the low-temperature performance of two commonly used solid-state NMR experiments, proton-driven spin diffusion (PDSD) and transferred echo double resonance (TEDOR), and discuss their potential as tools for measurement of structurally relevant distances at low temperature in combination with DNP.
doi:10.1039/c003661g
PMCID: PMC4440577  PMID: 20454733
9.  A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types 
A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals.
doi:10.3389/fmicb.2015.00476
PMCID: PMC4436928  PMID: 26042110
DNA; RNA; extraction; environmental sample; low biomass; modular; intracellular; extracellular
10.  THE IMPACT OF MEASURES OF SOCIOECONOMIC STATUS ON HOSPITAL PROFILING IN NEW YORK CITY 
Background
Current 30-day readmission models used by the Center for Medicare and Medicaid Services for the purpose of hospital-level comparisons lack measures of socioeconomic status (SES). We examined whether the inclusion of a SES measure in 30-day congestive heart failure (CHF) readmission models changed hospital risk standardized readmission rates (RSRR) in New York City (NYC) hospitals.
Methods and Results
Using a Centers for Medicare & Medicaid Services (CMS)-like model we estimated 30-day hospital-level RSRR by adjusting for age, gender and comorbid conditions. Next, we examined how hospital RSRRs changed relative to the New York City mean with inclusion of the Agency for Healthcare Research and Quality (AHRQ) validated SES index score. In a secondary analysis, we examined whether inclusion of the AHRQ SES Index score in 30-day readmission models disproportionately impacted the RSRR of minority-serving hospitals.
Higher AHRQ SES scores, indicators of higher socioeconomic status, were associated with lower odds, 0.99, of 30-day readmission (p< 0.019). The addition of the AHRQ SES index did not change the model’s C statistic (0.63). After adjustment for the AHRQ SES index, one hospital changed status from “worse than the NYC average” to “no different than the NYC average”. After adjustment for the AHRQ SES index, one NYC minority-serving hospital was re-classified from “worse” to “no different than average”.
Conclusions
While patients with higher SES were less likely to be admitted, the impact of SES on readmission was very small. In NYC, inclusion of the AHRQ SES score in a CMS based model did not impact hospital-level profiling based on 30-day readmission.
doi:10.1161/CIRCOUTCOMES.113.000520
PMCID: PMC4072036  PMID: 24823956
Congestive heart failure; readmission; socioeconomic status; CMS profiling
11.  Early NADPH oxidase-2 activation is crucial in phenylephrine-induced hypertrophy of H9c2 cells 
Cellular signalling  2014;26(9):1818-1824.
Reactive oxygen species (ROS) produced by different NADPH oxidases (NOX) play a role in cardiomyocyte hypertrophy induced by different stimuli, such as angiotensin II and pressure overload. However, the role of the specific NOX isoforms in phenylephrine (PE)-induced cardiomyocyte hypertrophy is unknown. Therefore we aimed to determine the involvement of the NOX isoforms NOX1, NOX2 and NOX4 in PE-induced cardiomyocyte hypertrophy. Hereto rat neonatal cardiomyoblasts (H9c2 cells) were incubated with 100 μM PE to induce hypertrophy after 24 and 48 h as determined via cell and nuclear size measurements using digital imaging microscopy, electron microscopy and an automated cell counter. Digital-imaging microscopy further revealed that in contrast to NOX1 and NOX4, NOX2 expression increased significantly up to 4 h after PE stimulation, coinciding and co-localizing with ROS production in the cytoplasm as well as the nucleus. Furthermore, inhibition of NOX-mediated ROS production with apocynin, diphenylene iodonium (DPI) or NOX2 docking sequence (Nox2ds)-tat peptide during these first 4 h of PE stimulation significantly inhibited PE-induced hypertrophy of H9c2 cells, both after 24 and 48 h of PE stimulation. These data show that early NOX2-mediated ROS production is crucial in PE-induced hypertrophy of H9c2 cells.
doi:10.1016/j.cellsig.2014.04.018
PMCID: PMC4406486  PMID: 24794531
Cardiomyocyte hypertrophy; Phenylephrine; NADPH oxidase; NOX2
12.  An opioid-like system regulating feeding behavior in C. elegans 
eLife  null;4:e06683.
Neuropeptides are essential for the regulation of appetite. Here we show that neuropeptides could regulate feeding in mutants that lack neurotransmission from the motor neurons that stimulate feeding muscles. We identified nlp-24 by an RNAi screen of 115 neuropeptide genes, testing whether they affected growth. NLP-24 peptides have a conserved YGGXX sequence, similar to mammalian opioid neuropeptides. In addition, morphine and naloxone respectively stimulated and inhibited feeding in starved worms, but not in worms lacking NPR-17, which encodes a protein with sequence similarity to opioid receptors. Opioid agonists activated heterologously expressed NPR-17, as did at least one NLP-24 peptide. Worms lacking the ASI neurons, which express npr-17, did not response to naloxone. Thus, we suggest that Caenorhabditis elegans has an endogenous opioid system that acts through NPR-17, and that opioids regulate feeding via ASI neurons. Together, these results suggest C. elegans may be the first genetically tractable invertebrate opioid model.
DOI: http://dx.doi.org/10.7554/eLife.06683.001
eLife digest
When and how much an animal eats is controlled by a complex web of signals that are produced by the animal's body and brain. Molecules called opioid neuropeptides are among these signals, and act to control eating in mammals by binding to receptors in the brain and body. These receptors can also bind to similar molecules called opiates (such as morphine); opiates are amongst the oldest drugs used by humans and have diverse effects ranging from pain relief to addiction. While the activities of opiates and opioid neuropeptides have been studied in mammals, relatively little is known about opioid signaling in simpler animals.
The mechanisms behind many biological processes have been investigated using a worm called C. elegans as a model system because it has a simple body plan and its genes can be altered easily. The feeding behavior of C. elegans is no exception. This worm feeds by contracting and relaxing its pharyngeal muscle to move food into its gut. When the worms sense that food is available, this ‘pharyngeal pumping’ is regulated by one type of nerve cell. Slow pharyngeal pumping also continues in starved worms when food is not available, possibly to encourage them to eat new potential sources of food. However, this slow pumping does not require the same type of nerve cell.
Cheong et al. hypothesized that the slow pumping in starved worms might depend on neuropeptide signaling instead, and have now tested this idea using engineered worms that made lower levels of a number of these molecules. The experiments uncovered a molecule called NLP-24 that promotes the slow pharyngeal pumping. This molecule is similar to opioid neuropeptides found in mammals. Worms that made less NLP-24 than normal grew more slowly; this suggests that they had problems feeding. Moreover, the levels of NLP-24 were found to increase in normal worms soon after they were deprived of food. Further experiments revealed the identity of the receptor for this molecule, which is also similar to mammalian opioid receptors.
The discovery that opioid signaling is involved in C. elegans' feeding behavior may well, in future, also help to identify new molecular players involved in opioid signaling. Further studies might also help the search for ways to reduce the problematic side-effects that limit the usefulness of opiate drugs as medicines.
DOI: http://dx.doi.org/10.7554/eLife.06683.002
doi:10.7554/eLife.06683
PMCID: PMC4427864  PMID: 25898004
opioid; feeding regulation; neuropeptide; C. elegans
13.  Electrically Induced Limbic Seizures: Preliminary Findings in a Rodent Model 
In epilepsy, novel pharmacological and nonpharmacological treatment approaches are commonly assessed in model systems of acute motor and often generalized seizures. We developed a rodent model with short-term electrical stimulation of the perforant path resulting in stereotyped limbic seizures. Limbic structures play a major role in human intractable epilepsy. In 10 rats, single electrical 5-second and 20-Hz stimuli to the perforant path reliably produced limbic seizures characterized by resting behavior and subtle motor signs. Electrophysiological recordings from the dentate gyrus demonstrated a seizure pattern with 4-Hz to 5-Hz discharges. Multiple inductions of seizures within 72 hours did not alter behavioral and electrophysiological seizure characteristics. Electrophysiological excitatory and inhibitory parameters assessed by evoked single and paired pulses did not change with increasing number of seizures. We present preliminary findings on a new model of electrically induced limbic seizures of mesiotemporal origin. This model may represent a reliable screening tool for new treatment approaches such as deep brain stimulation.
doi:10.4137/JEN.S23759
PMCID: PMC4376203  PMID: 25861223
deep brain stimulation; dentate gyrus; epilepsy
14.  Examining Pharmacy Workforce Issues in the United States and the United Kingdom 
Objective. To examine available data and actions surrounding current pharmacy workforce issues in the United States and United Kingdom.
Methods. Published pharmacy workforce data from the United States and United Kingdom were gathered from various sources, including PUBMED, Internet search engines, and pharmacy organization websites. Data was collated from additional sources including scientific literature, internal documents, news releases, and policy positions.
Results. The number of colleges and schools of pharmacy has expanded by approximately 50% in both the United States and United Kingdom over the previous decade. In the United States, continued demand for the pharmacy workforce has been forecasted, but this need is based on outdated supply figures and assumptions for economic recovery. In the United Kingdom, workforce modeling has predicted a significant future oversupply of pharmacists, and action within the profession has attempted to address the situation through educational planning and regulation.
Conclusion. Workforce planning is an essential task for sustaining a healthy profession. Recent workforce planning mechanisms in the United Kingdom may provide guidance for renewed efforts within the profession in the United States.
doi:10.5688/ajpe79217
PMCID: PMC4386738  PMID: 25861098
manpower; health workforce; internationality; health policy; pharmacy education
15.  Trait Emotional Intelligence and Personality 
This study investigated if the linkages between trait emotional intelligence (trait EI) and the Five-Factor Model of personality were invariant between men and women. Five English-speaking samples (N = 307-685) of mostly undergraduate students each completed a different measure of the Big Five personality traits and either the full form or short form of the Trait Emotional Intelligence Questionnaire (TEIQue). Across samples, models predicting global TEIQue scores from the Big Five were invariant between genders, with Neuroticism and Extraversion being the strongest trait EI correlates, followed by Conscientiousness, Agreeableness, and Openness. However, there was some evidence indicating that the gender-specific contributions of the Big Five to trait EI vary depending on the personality measure used, being more consistent for women. Discussion focuses on the validity of the TEIQue as a measure of trait EI and its psychometric properties, more generally.
doi:10.1177/0734282914550385
PMCID: PMC4361496  PMID: 25866439
trait emotional intelligence; TEIQue; personality; invariance; gender
16.  Modelling of photo-thermal control of biological cellular oscillators 
We study the transient dynamics of biological oscillators subjected to brief heat pulses. A prospective well-defined experimental system for thermal control of oscillators is the peripheral electroreceptors in paddlefish. Epithelial cells in these receptors show spontaneous voltage oscillations which are known to be temperature sensitive. We use a computational model to predict the effect of brief thermal pulses in this system. In our model thermal stimulation is realized through the light excitation of gold nanoparticles delivered in close proximity to epithelial cells and generating heat due to plasmon resonance. We use an ensemble of modified Morris-Lecar systems to model oscillatory epithelial cells. First, we validate that the model quantitatively reproduces the dynamics of epithelial oscillations in paddlefish electroreceptors, including responses to static and slow temperature changes. Second, we use the model to predict transient responses to short heat pulses generated by the light actuated gold nanoparticles. The model predicts that the epithelial oscillators can be partially synchronized by brief 5 – 15 ms light stimuli resulting in a large-amplitude oscillations of the mean field potential.
doi:10.1140/epjst/e2013-02049-0
PMCID: PMC4326011  PMID: 25685293
17.  Primary gynecologic melanoma: A report of two unusual cases 
Background
Primary ovarian and cervical melanomas are extremely rare tumors with a poor prognosis. Diagnosis requires a high index of suspicion as presentation can mimic benign conditions clinically and other neoplasms histologically.
Cases
A 41 year-old with an adnexal mass underwent surgical staging for a stage IA ovarian melanoma. Imaging revealed a brain metastasis treated with radiation. Subsequent nodal recurrence was treated with immune and targeted therapies. She is alive with disease at 61 months follow-up. A 54 year-old presented after endocervical melanoma was diagnosed with polypectomy. She underwent radical hysterectomy, lymphadenectomy, and adjuvant brachytherapy. Immediate post-treatment imaging revealed widespread liver and pulmonary metastasis, currently being treated with ipilimumab.
Conclusion
Immunohistochemistry can facilitate the diagnosis of gynecologic melanoma, and multidisciplinary treatment is recommended.
Highlights
•Ovarian and cervical melanomas are rare tumors that present diagnostic challenges.•Survival is poor, and multidisciplinary treatment is recommended.•Immunotherapy should be considered in the treatment of gynecologic melanoma.
doi:10.1016/j.gore.2015.01.003
PMCID: PMC4434166  PMID: 26076092
Cervical melanoma; Ovarian melanoma; Immunotherapy; Multidisciplinary treatment
18.  Comparing Quantitative Values of Two Generations of Laser-Assisted Indocyanine Green Dye Angiography Systems: Can We Predict Necrosis? 
Eplasty  2014;14:e44.
Objective: Several devices exist today to assist the intraoperative determination of skin flap perfusion. Laser-Assisted Indocyanine Green Dye Angiography (LAICGA) has been shown to accurately predict mastectomy skin flap necrosis using quantitative perfusion values. The laser properties of the latest LAICGA device (SPY Elite) differ significantly from its predecessor system (SPY 2001), preventing direct translation of previous published data. The purpose of this study was to establish a mathematical relationship of perfusion values between these 2 devices. Methods: Breast reconstruction patients were prospectively enrolled into a clinical trial where skin flap evaluation and excision was based on quantitative SPY Q values previously established in the literature. Initial study patients underwent mastectomy skin flap evaluation using both SPY systems simultaneously. Absolute perfusion unit (APU) values at identical locations on the breast were then compared graphically. Results: 210 data points were identified on the same patients (n = 4) using both SPY systems. A linear relationship (y = 2.9883x + 12.726) was identified with a high level or correlation (R2 = 0.744). Previously published values using SPY 2001 (APU 3.7) provided a value of 23.8 APU on the SPY Elite. In addition, postoperative necrosis in these patients correlated to regions of skin identified with the SPY Elite with APU less than 23.8. Conclusion: Intraoperative comparison of LAICGA systems has provided direct correlation of perfusion values predictive of necrosis that were previously established in the literature. An APU value of 3.7 from the SPY 2001 correlates to a SPY Elite APU value of 23.8.
PMCID: PMC4258931  PMID: 25525483
breast reconstruction; indocyanine green dye; mastectomy skin flap necrosis; quantitative perfusion values; SPY
19.  BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types 
Nucleic Acids Research  2014;43(Database issue):D1163-D1170.
BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.
doi:10.1093/nar/gku1244
PMCID: PMC4383997  PMID: 25477388
20.  Microbial sulfur transformations in sediments from Subglacial Lake Whillans 
Diverse microbial assemblages inhabit subglacial aquatic environments. While few of these environments have been sampled, data reveal that subglacial organisms gain energy for growth from reduced minerals containing nitrogen, iron, and sulfur. Here we investigate the role of microbially mediated sulfur transformations in sediments from Subglacial Lake Whillans (SLW), Antarctica, by examining key genes involved in dissimilatory sulfur oxidation and reduction. The presence of sulfur transformation genes throughout the top 34 cm of SLW sediments changes with depth. SLW surficial sediments were dominated by genes related to known sulfur-oxidizing chemoautotrophs. Sequences encoding the adenosine-5′-phosphosulfate (APS) reductase gene, involved in both dissimilatory sulfate reduction and sulfur oxidation, were present in all samples and clustered into 16 distinct operational taxonomic units. The majority of APS reductase sequences (74%) clustered with known sulfur oxidizers including those within the “Sideroxydans” and Thiobacillus genera. Reverse-acting dissimilatory sulfite reductase (rDSR) and 16S rRNA gene sequences further support dominance of “Sideroxydans” and Thiobacillus phylotypes in the top 2 cm of SLW sediments. The SLW microbial community has the genetic potential for sulfate reduction which is supported by experimentally measured low rates (1.4 pmol cm-3d-1) of biologically mediated sulfate reduction and the presence of APS reductase and DSR gene sequences related to Desulfobacteraceae and Desulfotomaculum. Our results also infer the presence of sulfur oxidation, which can be a significant energetic pathway for chemosynthetic biosynthesis in SLW sediments. The water in SLW ultimately flows into the Ross Sea where intermediates from subglacial sulfur transformations can influence the flux of solutes to the Southern Ocean.
doi:10.3389/fmicb.2014.00594
PMCID: PMC4237127  PMID: 25477865
Antarctic subglacial aquatic environments; geomicrobiology; chemosynthesis; sulfur oxidation; sulfate reduction
21.  Photoluminescence response of colloidal quantum dots on VO2 film across metal to insulator transition 
Nanoscale Research Letters  2014;9(1):612.
We have proposed a method to probe metal to insulator transition in VO2 measuring photoluminescence response of colloidal quantum dots deposited on the VO2 film. In addition to linear luminescence intensity decrease with temperature that is well known for quantum dots, temperature ranges with enhanced photoluminescence changes have been found during phase transition in the oxide. Corresponding temperature derived from luminescence dependence on temperature closely correlates with that from resistance measurement during heating. The supporting reflectance data point out that photoluminescence response mimics a reflectance change in VO2 across metal to insulator transition. Time-resolved photoluminescence study did not reveal any significant change of luminescence lifetime of deposited quantum dots under metal to insulator transition. It is a strong argument in favor of the proposed explanation based on the reflectance data.
PACS
71.30. + h; 73.21.La; 78.47.jd
doi:10.1186/1556-276X-9-612
PMCID: PMC4232974  PMID: 25404877
Metal to insulator transition; Vanadium dioxide; Colloidal quantum dots
22.  A Systematic Review of Infection Rates and Associated Antibiotic Duration in Acellular Dermal Matrix Breast Reconstruction 
Eplasty  2014;14:e42.
Introduction: Reported infection rates in breast reconstruction with acellular dermal matrix (ADM) can exceed 31%. Prophylactic antibiotics remain controversial due to the absence of evidence-based literature. The purpose of this study was to examine published antibiotic regimens and their associated infection rates in this population. Methods: Systematic electronic searches were performed in PubMed, OVID, and the Cochrane databases for studies that reported on prophylactic antibiotic use and infection in patients undergoing ADM breast reconstruction. Two independent authors reviewed studies between 1970 and 2012 for inclusion and data extraction. Results: A total of 863 studies were identified and abstracts reviewed. A total of 24 articles were included, with 2148 patients and 3189 ADM reconstructions. Mean infection rates varied between 0% and 31.25%, with a combined average of 11.59%. When comparing antibiotic protocols of less than 24 hours and more than 24 hours, the average infection rate was 2.48% and 13.21%, respectively. Conclusion: The current literature lacks consensus on the necessary duration for postoperative antibiotic prophylaxis following breast reconstruction. The potential increased risk of infection associated with ADM remains controversial. Because of the lack of supportive evidence, we do not recommend prolonged postoperative antibiotics in ADM breast reconstruction.
Level of Evidence: Therapeutic level III evidence.
PMCID: PMC4233926  PMID: 25525481
breast reconstruction; acellular dermal matrix; ADM; infection; antibiotics
24.  Determination of motility forces on isolated chromosomes with laser tweezers 
Scientific Reports  2014;4:6866.
Quantitative determination of the motility forces of chromosomes during cell division is fundamental to understanding a process that is universal among eukaryotic organisms. Using an optical tweezers system, isolated mammalian chromosomes were held in a 1064 nm laser trap. The minimum force required to move a single chromosome was determined to be ≈0.8–5 pN. The maximum transverse trapping efficiency of the isolated chromosomes was calculated as ≈0.01–0.02. These results confirm theoretical force calculations of ≈0.1–12 pN to move a chromosome on the mitotic or meiotic spindle. The verification of these results was carried out by calibration of the optical tweezers when trapping microspheres with a diameter of 4.5–15 µm in media with 1–7 cP viscosity. The results of the chromosome and microsphere trapping experiments agree with optical models developed to simulate trapping of cylindrical and spherical specimens.
doi:10.1038/srep06866
PMCID: PMC4215326  PMID: 25359514
25.  ImmunoPET Imaging of Renal Cell Carcinoma with 124I- and 89Zr-Labeled Anti-CAIX Monoclonal Antibody cG250 in Mice 
Abstract
Introduction
Monoclonal antibody (mAb) cG250 recognizes carbonic anhydrase IX (CAIX), overexpressed on clear cell renal cell carcinoma (ccRCC). 124I-cG250 is currently under clinical investigation for the detection of ccRCC. However, the 124I label is rapidly excreted from the tumor cells after internalization of the radiolabeled mAb. We hypothesized that labeling cG250 with the residualizing positron emitter 89Zr would lead to higher tumor uptake and more sensitive detection of ccRCC lesions.
Materials and Methods
Nude mice with CAIX-expressing ccRCC xenografts (SK-RC-52 or NU-12) were i.v. injected with 89Zr-cG250 or 124I-cG250. To determine specificity of 89Zr-cG250 uptake in ccRCC, one control group was i.v. injected with 89Zr-MOPC21 (irrelevant mAb). PET images were acquired using a small animal PET camera and the biodistribution of the radiolabeled mAb was determined.
Results
The ccRCC xenografts were clearly visualized after injection of 89Zr-cG250 and 124I-cG250. Tumor uptake of 89Zr-cG250 was significantly higher compared with 124I-cG250 in the NU-12 tumor model (114.7%±25.2% injected dose per gram (%ID/g) vs. 38.2±18.3%ID/g, p=0.029), but in the SK-RC-52 the difference in tumor uptake was not significant (48.7±15.2%ID/g vs. 32.0±22.9%ID/g, p=0.26). SK-RC-52 tumors were not visualized with 89Zr-MOPC21 (tumor uptake 3.0%ID/g). Intraperitoneal SK-RC-52 lesions as small as 7 mm3 were visualized with 89Zr-cG250 PET.
Conclusion
ImmunoPET imaging with cG250 visualized s.c. and i.p. ccRCC lesions in murine models. This confirms the potential of cG250 immunoPET in the diagnosis and (re)staging of ccRCC. PET imaging of ccRCC tumors with 89Zr-cG250 could be more sensitive than 124I-cG250-PET.
doi:10.1089/cbr.2013.1487
PMCID: PMC3741422  PMID: 23697926
124I; 89Zr; cG250; immunoPET

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