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1.  Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds 
Biomaterials  2013;35(2):846-855.
Branched peptides containing histidines and lysines (HK) have been shown to be effective carriers for DNA and siRNA. We anticipate that elucidation of the binding mechanism of HK with siRNA will provide greater insight into the self-assembly and delivery of the HK:siRNA polyplex. Non-covalent bonds between histidine residues and nucleic acids may enhance the stability of siRNA polyplexes. We first compared the polyplex biophysical properties of a branched HK with those of branched asparagines-lysine peptide (NK). Consistent with siRNA silencing experiments, gel electrophoresis demonstrated that the HK siRNA polyplex maintained its integrity with prolonged incubation in serum, whereas siRNA in complex with NK was degraded in a time-dependent manner. Isothermal titration calorimetry of various peptides binding to siRNA at pH 7.3 showed that branched polylysine, interacted with siRNA was initially endothermic, whereas branched HK exhibited an exothermic reaction at initial binding. The exothermic interaction indicates formation of non-ionic bonds between histidines and siRNA; purely electrostatic interaction is entropy-driven and endothermic. To investigate the type of non-ionic bond, we studied the protonation state of imidazole rings of a selectively 15N labeled branched HK by heteronuclear single quantum coherence NMR. The peak of Nδ1-H tautomers of imidazole shifted downfield (in the direction of deprotonation) by 0.5 to 1.0 ppm with addition of siRNA, providing direct evidence that histidines formed hydrogen bonds with siRNA at physiological pH. These results establish that histidine-rich peptides form hydrogen bonds with siRNA, thereby enhancing the stability and biological activity of the polyplex in vitro and in vivo.
doi:10.1016/j.biomaterials.2013.10.019
PMCID: PMC3920840  PMID: 24161165
2.  Multiple HLA Epitopes Contribute to Type 1 Diabetes Susceptibility 
Diabetes  2013;63(1):323-331.
Disease susceptibility for type 1 diabetes is strongly associated with the inheritance of specific HLA alleles. However, conventional allele frequency analysis can miss HLA associations because many alleles are rare. In addition, disparate alleles that have similar peptide-binding sites, or shared epitopes, can be missed. To identify the HLA shared epitopes associated with diabetes, we analyzed high-resolution genotyping for class I and class II loci. The HLA epitopes most strongly associated with susceptibility for disease were DQB1 A57, DQA1 V76, DRB1 H13, and DRB1 K71, whereas DPB1 YD9,57, HLA-B C67, and HLA-C YY9,116 were more weakly associated. The HLA epitopes strongly associated with resistance were DQB1 D57, DQA1 Y80, DRB1 R13, and DRB1 A71. A dominant resistance phenotype was observed for individuals bearing a protective HLA epitope, even in the presence of a susceptibility epitope. In addition, an earlier age of disease onset correlated with significantly greater numbers of susceptibility epitopes and fewer resistance epitopes (P < 0.0001). The prevalence of both DQ and DR susceptibility epitopes was higher in patients than in control subjects and was not exclusively a result of linkage disequilibrium, suggesting that multiple HLA epitopes may work together to increase the risk of developing diabetes.
doi:10.2337/db13-1153
PMCID: PMC3868045  PMID: 24357703
3.  Perineural Dexamethasone to Improve Postoperative Analgesia with Peripheral Nerve Blocks: A Meta-Analysis of Randomized Controlled Trials 
Pain Research and Treatment  2014;2014:179029.
Background. The overall effect of perineural dexamethasone on postoperative analgesia outcomes has yet to be quantified. The main objective of this quantitative review was to evaluate the effect of perineural dexamethasone as a nerve block adjunct on postoperative analgesia outcomes. Methods. A systematic search was performed to identify randomized controlled trials that evaluated the effects of perineural dexamethasone as a block adjunct on postoperative pain outcomes in patients receiving regional anesthesia. Meta-analysis was performed using a random-effect model. Results. Nine randomized trials with 760 subjects were included. The weighted mean difference (99% CI) of the combined effects favored perineural dexamethasone over control for analgesia duration, 473 (264 to 682) minutes, and motor block duration, 500 (154 to 846) minutes. Postoperative opioid consumption was also reduced in the perineural dexamethasone group compared to control, −8.5 (−12.3 to −4.6) mg of IV morphine equivalents. No significant neurological symptoms could have been attributed to the use of perineural dexamethasone. Conclusions. Perineural dexamethasone improves postoperative pain outcomes when given as an adjunct to brachial plexus blocks. There were no reports of persistent nerve injury attributed to perineural administration of the drug.
doi:10.1155/2014/179029
PMCID: PMC4251083  PMID: 25485150
4.  Differences in Nuclear DNA Organization Between Lymphocytes, Hodgkin and Reed–Sternberg Cells Revealed by Structured Illumination Microscopy 
Journal of Cellular Biochemistry  2014;115(8):1441-1448.
Advances in light microscopy have enabled the visualization of DNA in the interphase nucleus with more detail than is visible with conventional light microscopy. The nuclear architecture is assumed to be different in cancer cells compared to normal cells. In this paper we have studied, for the first time, the organization of nuclear DNA and that of DNA-free space in control lymphocytes, Hodgkin cells and Reed–Sternberg cells using 3D structured illumination microscopy (SIM). We have observed detail in these SIM images that was not observed in conventional widefield images. We have measured the size distribution of the DNA structure using granulometry and noted a significant, progressive increase in the amount of sub-micron structures from control lymphocytes to Hodgkin cells to Reed–Sternberg cells. The DNA-free space changes as well; “holes” in the DNA distribution start to appear in the malignant cells. We have studied whether these “holes” are nucleoli by staining for upstream binding factor (UBF), a protein associated with the nucleolus. We have found that the relative UBF content progressively and significantly decreases—or is absent—in the DNA-free space when measured as either the Pearson correlation coefficient with the DNA-free space or as the number of “holes” that contain UBF. Similar differences exist within the population of Reed–Sternberg cells between binucleated and multinucleated cells with four or more subnuclei. To our knowledge, this is the first study that investigates the changes of the nuclear DNA structure in any disease with superresolution light microscopy. J. Cell. Biochem. 115: 1441–1448, 2014. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
doi:10.1002/jcb.24800
PMCID: PMC4231252  PMID: 24590512
STRUCTURED ILLUMINATION MICROSCOPY; NUCLEAR ARCHITECTURE; QUANTITATIVE MICROSCOPY; HODGKIN’S LYMPHOMA
5.  Low temperature delays timing and enhances the cost of nitrogen fixation in the unicellular cyanobacterium Cyanothece 
The ISME Journal  2013;7(11):2105-2115.
Marine nitrogen-fixing cyanobacteria are largely confined to the tropical and subtropical ocean. It has been argued that their global biogeographical distribution reflects the physiologically feasible temperature range at which they can perform nitrogen fixation. In this study we refine this line of argumentation for the globally important group of unicellular diazotrophic cyanobacteria, and pose the following two hypotheses: (i) nitrogen fixation is limited by nitrogenase activity at low temperature and by oxygen diffusion at high temperature, which is manifested by a shift from strong to weak temperature dependence of nitrogenase activity, and (ii) high respiration rates are required to maintain very low levels of oxygen for nitrogenase, which results in enhanced respiratory cost per molecule of fixed nitrogen at low temperature. We tested these hypotheses in laboratory experiments with the unicellular cyanobacterium Cyanothece sp. BG043511. In line with the first hypothesis, the specific growth rate increased strongly with temperature from 18 to 30 °C, but leveled off at higher temperature under nitrogen-fixing conditions. As predicted by the second hypothesis, the respiratory cost of nitrogen fixation and also the cellular C:N ratio rose sharply at temperatures below 21 °C. In addition, we found that low temperature caused a strong delay in the onset of the nocturnal nitrogenase activity, which shortened the remaining nighttime available for nitrogen fixation. Together, these results point at a lower temperature limit for unicellular nitrogen-fixing cyanobacteria, which offers an explanation for their (sub)tropical distribution and suggests expansion of their biogeographical range by global warming.
doi:10.1038/ismej.2013.103
PMCID: PMC3806257  PMID: 23823493
climate change; day–night cycle; nitrogenase; nitrogen fixation; respiration; unicellular cyanobacteria
6.  Resident renal mononuclear phagocytes comprise five discrete populations with distinct phenotypes and functions 
Journal of immunology (Baltimore, Md. : 1950)  2013;191(6):10.4049/jimmunol.1300342.
Recent reports have highlighted greater complexity, plasticity and functional diversity of mononuclear phagocytes (MPCs), including monocytes, macrophages and dendritic cells (DCs), in our organs, than previously understood. The functions and origins of MPCs resident within healthy organs, especially in the kidney, are less well understood, while studies suggest they play roles in disease states distinct from recruited monocytes. We developed an unbiased approach using flow cytometry to analyze MPCs residing in the normal mouse kidney, and identified five discrete subpopulations according to CD11b/CD11c expression as well as F4/80, CD103, CD14, CD16 and CD64 expression. In addition to distinct marker profiles, these subpopulations have different lineages and expression of genes involved in tissue homeostasis, including angiogenesis. Among them, the CD11bint CD11cint F4/80hi subpopulation notably exhibited high capacity to produce a representative anti-inflammatory cytokine, IL-10. Each subpopulation had different degrees of both macrophage (phagocytosis) and DC (antigen presentation) capacities, with a tendency to promote differentiation of regulatory T cells, while two of these showed expression of transcription factors reported to be highly expressed by classical DCs, and proclivity to exit the kidney following stimulation with LPS. In summary, resident kidney MPCs comprise discrete subpopulations, which cannot be simply classified into the conventional entities, and they produce anti-inflammatory and tissue-homeostatic factors to differing degrees.
doi:10.4049/jimmunol.1300342
PMCID: PMC3808972  PMID: 23956422
7.  Mechanisms of Isoform Specific Rap2 Signaling during Enterocytic Brush Border Formation 
PLoS ONE  2014;9(9):e106687.
Brush border formation during polarity establishment of intestinal epithelial cells is uniquely governed by the Rap2A GTPase, despite expression of the other highly similar Rap2 isoforms (Rap2B and Rap2C). We investigated the mechanisms of this remarkable specificity and found that Rap2C is spatially segregated from Rap2A signaling as it is not enriched at the apical membrane after polarization. In contrast, both Rap2A and Rap2B are similarly located at Rab11 positive apical recycling endosomes and inside the brush border. However, although Rap2B localizes similarly it is not equally activated as Rap2A during brush border formation. We reveal that the C-terminal hypervariable region allows selective activation of Rap2A, yet this selectivity does not originate from the known differential lipid modifications of this region. In conclusion, we demonstrate that Rap2 specificity during brush border formation is determined by two distinct mechanisms involving segregated localization and selective activation.
doi:10.1371/journal.pone.0106687
PMCID: PMC4159233  PMID: 25203140
8.  Retrospective analysis of the impact of HPV status and smoking on mucositis in patients with oropharyngeal squamous cell carcinoma treated with concurrent chemotherapy and radiotherapy 
Oral oncology  2014;50(9):869-876.
SUMMARY
Objectives
The standard concurrent radiotherapy and chemotherapy regimens for patients with oropharyngeal cancer are highly toxic. Human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) has recently emerged as a distinct biological and clinical entity with improved response to treatment and prognosis. A tailored therapeutic approach is needed to optimize patient care. The aim of our study was to investigate the impact of HPV and smoking status on early toxicities (primarily mucositis) associated with concurrent chemotherapy and radiotherapy in patients with OPSCC.
Materials and methods
We retrospectively evaluated 72 consecutive patients with OPSCC and known HPV status treated with concurrent radiotherapy and chemotherapy at our institution. Treatment-related toxicities were stratified by smoking and HPV status and compared using univariate and multivariate logistic regression.
Results
HPV-positive patients had a 6.86-fold increase in the risk of having severe, grade 3–4 mucositis. This effect was preserved after adjusting for patient smoking status, nodal stage, radiotherapy technique and radiotherapy maximum dose. Additionally, HPV status had significant effect on the objective weight loss during treatment and at three months after treatment. Consistently, non-smokers had a significant 2.70-fold increase in the risk of developing severe mucositis.
Conclusion
Risk factors for OPSCC modify the incidence of treatment-related early toxicities, with HPV-positive and non-smoking status correlating with increased risk of high grade mucositis and associated outcomes. Retrospective single-institution studies need to be interpreted cautiously. However, this finding is important to consider when designing therapeutic strategies for HPV-positive patients and merits further investigation in prospective clinical trials.
doi:10.1016/j.oraloncology.2014.06.010
PMCID: PMC4148719  PMID: 24998139
Human papillomavirus; Smoking; Oral mucositis; Radiotherapy; Chemotherapy; Squamous cell of head and neck
9.  Androgen Receptor Gene Rearrangements: New Perspectives on Prostate Cancer Progression 
Current drug targets  2013;14(4):441-449.
The androgen receptor (AR) is a master regulator transcription factor in normal and cancerous prostate cells. Canonical AR activation requires binding of androgen ligand to the AR ligand binding domain, translocation to the nucleus, and transcriptional activation of AR target genes. This regulatory axis is targeted for systemic therapy of advanced prostate cancer. However, a new paradigm for AR activation in castration-resistant prostate cancer (CRPC) has emerged wherein alternative splicing of AR mRNA promotes synthesis of constitutively active AR variants that lack the AR ligand binding domain (LBD). Recent work has indicated that structural alteration of the AR gene locus represents a key mechanism by which alterations in AR mRNA splicing arise. In this review, we examine the role of truncated AR variants (ARVs) and their corresponding genomic origins in models of prostate cancer progression, as well as the challenges they pose to the current standard of prostate cancer therapies targeting the AR ligand binding domain. Since ARVs lack the COOH-terminal LBD, the genesis of these AR gene rearrangements and their resulting ARVs provides strong rationale for the pursuit of new avenues of therapeutic intervention targeted at the AR NH2-terminal domain. We further suggest that genomic events leading to ARV expression could act as novel biomarkers of disease progression that may guide the optimal use of current and next-generation AR-targeted therapy.
PMCID: PMC3957184  PMID: 23410127
Androgen Receptor; alternative splicing; castration resistance; genomic rearrangement; prostate cancer
10.  FOXO1 Binds to the TAU5 Motif and Inhibits Constitutively Active Androgen Receptor Splice Variants 
The Prostate  2013;73(10):1017-1027.
BACKGROUND
Aberrant activation of the androgen receptor (AR) is a major factor highly relevant to castration-resistant progression of prostate cancer (PCa). FOXO1, a key downstream effector of PTEN, inhibits androgen-independent activation of the AR. However, the underlying mechanism remains elusive.
METHODS
The inhibitory effect of FOXO1 on full-length and constitutively active splice variants of the AR was examined by luciferase reporter assays and real-time reverse transcription polymerase chain reaction (RT-qPCR). In vitro protein binding assays and western blot analyses were used to determine the regions in FOXO1 and AR responsible for their interaction.
RESULTS
We found that a putative transcription repression domain in the NH2-terminus of FOXO1 is dispensable for FOXO1 inhibition of the AR. In vitro protein binding assays showed that FOXO1 binds to the transcription activation unit 5 (TAU5) motif in the AR NH2-terminal domain (NTD), a region required for recruitment of p160 activators including SRC-1. Ectopic expression of SRC-1 augmented transcriptional activity of some, but not all AR splice variants examined. Forced expression of FOXO1 blocked the effect of SRC-1 on AR variants’ transcriptional activity by decreasing the binding of SRC-1 to the AR NTD. Ectopic expression of FOXO1 inhibited expression of endogenous genes activated primarily by alternatively spliced AR variants in human castration-resistant PCa 22Rv1 cells.
CONCLUSIONS
FOXO1 binds to the TAU5 motif in the AR NTD and inhibits ligand-independent activation of AR splice variants, suggesting the PTEN/FOXO1 pathway as a potential therapeutic target for inhibition of aberrant AR activation and castration-resistant PCa growth.
doi:10.1002/pros.22649
PMCID: PMC3915545  PMID: 23389878
androgen receptor; FOXO1; prostate cancer; PTEN
11.  Androgen receptor splice variants mediate enzalutamide resistance in castration-resistant prostate cancer cell lines 
Cancer research  2012;73(2):483-489.
Persistent androgen receptor (AR) transcriptional activity underlies resistance to AR-targeted therapy and progression to lethal castration resistant prostate cancer (CRPC). Recent success in re-targeting persistent AR activity with next-generation androgen/AR axis inhibitors such as enzalutamide (MDV3100) has validated AR as a master regulator during all stages of disease progression. However, resistance to next-generation AR inhibitors limits therapeutic efficacy for many patients. One emerging mechanism of CRPC progression is AR gene rearrangement, promoting synthesis of constitutively-active truncated AR splice variants (AR-Vs) that lack the AR ligand binding domain. In this study, we demonstrate that cells with AR gene rearrangements expressing both full-length and AR-Vs are androgen-independent and enzalutamide-resistant. However, selective knock-down of AR-V expression inhibited androgen-independent growth and restored responsiveness to androgens and antiandrogens. In heterogeneous cell populations, AR gene rearrangements marked individual AR-V-dependent cells that were resistant to enzalutamide. Gene expression profiling following knock-down of full-length AR or AR-Vs demonstrated that AR-Vs drive resistance to AR-targeted therapy by functioning as constitutive and independent effectors of the androgen/AR transcriptional program. Further, mitotic genes deemed previously to be unique AR-V targets were found to be biphasic targets associated with a proliferative level of signaling output from either AR-Vs or androgen-stimulated AR. Overall, these studies highlight AR-Vs as key mediators of persistent AR signaling and resistance to the current arsenal of conventional and next-generation AR-directed therapies, advancing the concept of AR-Vs as therapeutic targets in advanced disease.
doi:10.1158/0008-5472.CAN-12-3630
PMCID: PMC3549016  PMID: 23117885
androgen receptor; prostate cancer; enzalutamide resistance; truncated AR splice variants; castration-resistant
12.  Multicomponent intervention to reduce daily sedentary time: a randomised controlled trial 
BMJ Open  2013;3(10):e003261.
Objectives
To test the efficacy of a multicomponent technology intervention for reducing daily sedentary time and improving cardiometabolic disease risk among sedentary, overweight university employees.
Design
Blinded, randomised controlled trial.
Setting
A large south-eastern university in the USA.
Participants
49 middle-aged, primarily female, sedentary and overweight adults working in sedentary jobs enrolled in the study. A total of 40 participants completed the study.
Interventions
Participants were randomised to either: (1) an intervention group (N=23; 47.6+9.9 years; 94.1% female; 33.2+4.5 kg/m2); (2) or wait-list control group (N=17; 42.6+8.9 years; 86.9% female; 31.7+4.9 kg/m2). The intervention group received a theory-based, internet-delivered programme, a portable pedal machine at work and a pedometer for 12 weeks. The wait-list control group maintained their behaviours for 12 weeks.
Outcome measures
Primary (sedentary and physical activity behaviour measured objectively through StepWatch) and secondary (heart rate, blood pressure, height, weight, waist circumference, per cent body fat, cardiorespiratory fitness, fasting lipids) outcomes were measured at baseline and postintervention (12 weeks). Exploratory outcomes including intervention compliance and process evaluation measures were also assessed postintervention.
Results
Compared to controls, the intervention group reduced daily sedentary time (mean change (95%CI): −58.7 min/day (−118.4 to 0.99; p<0.01)) after adjusting for baseline values and monitor wear time. Intervention participants logged on to the website 71.3% of all intervention days, used the pedal machine 37.7% of all working intervention days and pedalled an average of 31.1 min/day.
Conclusions
These findings suggest that the intervention was engaging and resulted in reductions in daily sedentary time among full-time sedentary employees. These findings hold public health significance due to the growing number of sedentary jobs and the potential of these technologies in large-scale worksite programmes.
Trial Registration
ClinicalTrials.gov #NCT01371084.
doi:10.1136/bmjopen-2013-003261
PMCID: PMC3808782  PMID: 24141969
sedentary; worksite; technology
13.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography 
Science (New York, N.Y.)  2012;337(6092):362-364.
Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
doi:10.1126/science.1217737
PMCID: PMC3788707  PMID: 22653729
14.  Synthesis, characterization, and antimicrobial activity of silver carbene complexes derived from 4,5,6,7-tetrachlorobenzimidazole against antibiotic resistant bacteria† 
Silver N-heterocyclic carbene complexes have been shown to have great potential as antimicrobial agents, affecting a wide spectrum of both Gram-positive and Gram-negative bacteria. A new series of three silver carbene complexes (SCCs) based on 4,5,6,7-tetrachlorobenzimidazole has been synthesized, characterized, and tested against a panel of clinical strains of bacteria. The imidazolium salts and their precursors were characterized by elemental analysis, mass spectrometry, 1H and 13C NMR spectroscopy, and single crystal X-ray diffraction. The silver carbene complexes, SCC32, SCC33, and SCC34 were characterized by elemental analysis, 1H and 13C NMR spectroscopy, and single crystal X-ray diffraction. These complexes proved highly efficacious with minimum inhibitory concentrations (MICs) ranging from 0.25 to 6 μg mL−1. Overall, the complexes were effective against highly resistant bacteria strains, such as methicillin-resistant Staphylococcus aureus (MRSA), weaponizable bacteria, such as Yersinia pestis, and pathogens found within the lungs of cystic fibrosis patients, such as Pseudomonas aeruginosa, Alcaligenes xylosoxidans, and Burkholderia gladioli. SCC33 and SCC34 also showed clinically relevant activity against a silver-resistant strain of Escherichia coli based on MIC testing.
doi:10.1039/c2dt00055e
PMCID: PMC3703457  PMID: 22402409
15.  Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium 
The ISME Journal  2012;6(7):1367-1377.
Marine cyanobacteria of the genus Acaryochloris are the only known organisms that use chlorophyll d as a photosynthetic pigment. However, based on chemical sediment analyses, chlorophyll d has been recognized to be widespread in oceanic and lacustrine environments. Therefore it is highly relevant to understand the genetic basis for different physiologies and possible niche adaptation in this genus. Here we show that unlike all other known isolates of Acaryochloris, the strain HICR111A, isolated from waters around Heron Island, Great Barrier Reef, possesses a unique genomic region containing all the genes for the structural and enzymatically active proteins of nitrogen fixation and cofactor biosynthesis. Their phylogenetic analysis suggests a close relation to nitrogen fixation genes from certain other marine cyanobacteria. We show that nitrogen fixation in Acaryochloris sp. HICR111A is regulated in a light–dark-dependent fashion. We conclude that nitrogen fixation, one of the most complex physiological traits known in bacteria, might be transferred among oceanic microbes by horizontal gene transfer more often than anticipated so far. Our data show that the two powerful processes of oxygenic photosynthesis and nitrogen fixation co-occur in one and the same cell also in this branch of marine microbes and characterize Acaryochloris as a physiologically versatile inhabitant of an ecological niche, which is primarily driven by the absorption of far-red light.
doi:10.1038/ismej.2011.199
PMCID: PMC3379635  PMID: 22237545
Acaryochloris; chlorophyll d; cyanobacteria; dinitrogen fixation; microbial diversity; nitrogenase
16.  Coastal Microbial Mat Diversity along a Natural Salinity Gradient 
PLoS ONE  2013;8(5):e63166.
The North Sea coast of the Dutch barrier island of Schiermonnikoog is covered by microbial mats that initiate a succession of plant communities that eventually results in the development of a densely vegetated salt marsh. The North Sea beach has a natural elevation running from the low water mark to the dunes resulting in gradients of environmental factors perpendicular to the beach. These gradients are due to the input of seawater at the low water mark and of freshwater from upwelling groundwater at the dunes and rainfall. The result is a natural and dynamic salinity gradient depending on the tide, rainfall and wind. We studied the microbial community composition in thirty three samples taken every ten meters along this natural salinity gradient by using denaturing gradient gel electrophoresis (DGGE) of rRNA gene fragments. We looked at representatives from each Domain of life (Bacteria, Archaea and Eukarya) and with a particular emphasis on Cyanobacteria. Analysis of the DGGE fingerprints together with pigment composition revealed three distinct microbial mat communities, a marine community dominated by diatoms as primary producers, an intermediate brackish community dominated by Cyanobacteria as primary producers and a freshwater community with Cyanobacteria and freshwater green algae.
doi:10.1371/journal.pone.0063166
PMCID: PMC3660559  PMID: 23704895
17.  Amyloid Precursor Protein Is an Autonomous Growth Cone Adhesion Molecule Engaged in Contact Guidance 
PLoS ONE  2013;8(5):e64521.
Amyloid precursor protein (APP), a transmembrane glycoprotein, is well known for its involvement in the pathogenesis of Alzheimer disease of the aging brain, but its normal function is unclear. APP is a prominent component of the adult as well as the developing brain. It is enriched in axonal growth cones (GCs) and has been implicated in cell adhesion and motility. We tested the hypothesis that APP is an extracellular matrix adhesion molecule in experiments that isolated the function of APP from that of well-established adhesion molecules. To this end we plated wild-type, APP-, or β1-integrin (Itgb1)- misexpressing mouse hippocampal neurons on matrices of either laminin, recombinant L1, or synthetic peptides binding specifically to Itgb1 s or APP. We measured GC adhesion, initial axonal outgrowth, and substrate preference on alternating matrix stripes and made the following observations: Substrates of APP-binding peptide alone sustain neurite outgrowth; APP dosage controls GC adhesion to laminin and APP-binding peptide as well as axonal outgrowth in Itgb1− independent manner; and APP directs GCs in contact guidance assays. It follows that APP is an independently operating cell adhesion molecule that affects the GC's phenotype on APP-binding matrices including laminin, and that it is likely to affect axon pathfinding in vivo.
doi:10.1371/journal.pone.0064521
PMCID: PMC3653867  PMID: 23691241
18.  Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia spumigena CCY9414 Based on a Genome-Transcriptome Analysis 
PLoS ONE  2013;8(3):e60224.
Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena also is common in brackish water bodies worldwide, suggesting special adaptation allowing it to thrive at moderate salinities. A draft genome analysis of N. spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in length on which genes for 5,294 proteins were annotated. A subsequent strand-specific transcriptome analysis identified more than 6,000 putative transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led us to predict 764 non-coding RNAs, among them 70 copies of a possible retrotransposon and several potential RNA regulators, some of which are also present in other N2-fixing cyanobacteria. Approximately 4% of the total coding capacity is devoted to the production of secondary metabolites, among them the potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin. The transcriptional complexity associated with genes involved in nitrogen fixation and heterocyst differentiation is considerably smaller compared to other Nostocales. In contrast, sophisticated systems exist for the uptake and assimilation of iron and phosphorus compounds, for the synthesis of compatible solutes, and for the formation of gas vesicles, required for the active control of buoyancy. Hence, the annotation and interpretation of this sequence provides a vast array of clues into the genomic underpinnings of the physiology of this cyanobacterium and indicates in particular a competitive edge of N. spumigena in nutrient-limited brackish water ecosystems.
doi:10.1371/journal.pone.0060224
PMCID: PMC3610870  PMID: 23555932
19.  The Role of Nitrogen Fixation in Cyanobacterial Bloom Toxicity in a Temperate, Eutrophic Lake 
PLoS ONE  2013;8(2):e56103.
Toxic cyanobacterial blooms threaten freshwaters worldwide but have proven difficult to predict because the mechanisms of bloom formation and toxin production are unknown, especially on weekly time scales. Water quality management continues to focus on aggregated metrics, such as chlorophyll and total nutrients, which may not be sufficient to explain complex community changes and functions such as toxin production. For example, nitrogen (N) speciation and cycling play an important role, on daily time scales, in shaping cyanobacterial communities because declining N has been shown to select for N fixers. In addition, subsequent N pulses from N2 fixation may stimulate and sustain toxic cyanobacterial growth. Herein, we describe how rapid early summer declines in N followed by bursts of N fixation have shaped cyanobacterial communities in a eutrophic lake (Lake Mendota, Wisconsin, USA), possibly driving toxic Microcystis blooms throughout the growing season. On weekly time scales in 2010 and 2011, we monitored the cyanobacterial community in a eutrophic lake using the phycocyanin intergenic spacer (PC-IGS) region to determine population dynamics. In parallel, we measured microcystin concentrations, N2 fixation rates, and potential environmental drivers that contribute to structuring the community. In both years, cyanobacterial community change was strongly correlated with dissolved inorganic nitrogen (DIN) concentrations, and Aphanizomenon and Microcystis alternated dominance throughout the pre-toxic, toxic, and post-toxic phases of the lake. Microcystin concentrations increased a few days after the first significant N2 fixation rates were observed. Then, following large early summer N2 fixation events, Microcystis increased and became most abundant. Maximum microcystin concentrations coincided with Microcystis dominance. In both years, DIN concentrations dropped again in late summer, and N2 fixation rates and Aphanizomenon abundance increased before the lake mixed in the fall. Estimated N inputs from N2 fixation were large enough to supplement, or even support, the toxic Microcystis blooms.
doi:10.1371/journal.pone.0056103
PMCID: PMC3566065  PMID: 23405255
21.  Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing 
The ISME Journal  2011;5(11):1701-1712.
Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.
doi:10.1038/ismej.2011.52
PMCID: PMC3197164  PMID: 21544102
microbial diversity; microbial mats; 16S tag sequencing
22.  Search Query Data to Monitor Interest in Behavior Change: Application for Public Health 
PLoS ONE  2012;7(10):e48158.
There is a need for effective interventions and policies that target the leading preventable causes of death in the U.S. (e.g., smoking, overweight/obesity, physical inactivity). Such efforts could be aided by the use of publicly available, real-time search query data that illustrate times and locations of high and low public interest in behaviors related to preventable causes of death.
Objectives
This study explored patterns of search query activity for the terms ‘weight’, ‘diet’, ‘fitness’, and ‘smoking’ using Google Insights for Search.
Methods
Search activity for ‘weight’, ‘diet’, ‘fitness’, and ‘smoking’ conducted within the United States via Google between January 4th, 2004 (first date data was available) and November 28th, 2011 (date of data download and analysis) were analyzed. Using a generalized linear model, we explored the effects of time (month) on mean relative search volume for all four terms.
Results
Models suggest a significant effect of month on mean search volume for all four terms. Search activity for all four terms was highest in January with observable declines throughout the remainder of the year.
Conclusions
These findings demonstrate discernable temporal patterns of search activity for four areas of behavior change. These findings could be used to inform the timing, location and messaging of interventions, campaigns and policies targeting these behaviors.
doi:10.1371/journal.pone.0048158
PMCID: PMC3479111  PMID: 23110198
24.  Association of Coronary Wall Shear Stress With Atherosclerotic Plaque Burden, Composition, and Distribution in Patients With Coronary Artery Disease 
Background
Extremes of wall shear stress (WSS) have been associated with plaque progression and transformation, which has raised interest in the clinical assessment of WSS. We hypothesized that calculated coronary WSS is predicted only partially by luminal geometry and that WSS is related to plaque composition.
Methods and Results
Twenty‐seven patients with coronary artery disease underwent virtual histology intravascular ultrasound and Doppler velocity measurement for computational fluid dynamics modeling for WSS calculation in each virtual histology intravascular ultrasound segment (N=3581 segments). We assessed the association of WSS with plaque burden and distribution and with plaque composition. WSS remained relatively constant across the lower 3 quartiles of plaque burden (P=0.08) but increased in the highest quartile of plaque burden (P<0.001). Segments distal to lesions or within bifurcations were more likely to have low WSS (P<0.001). However, the majority of segments distal to lesions (80%) and within bifurcations (89%) did not exhibit low WSS. After adjustment for plaque burden, there was a negative association between WSS and percent necrotic core and calcium. For every 10 dynes/cm2 increase in WSS, percent necrotic core decreased by 17% (P=0.01), and percent dense calcium decreased by 17% (P<0.001). There was no significant association between WSS and percent of fibrous or fibrofatty plaque components (P=NS).
Conclusions
In patients with coronary artery disease: (1) Luminal geometry predicts calculated WSS only partially, which suggests that detailed computational techniques must be used to calculate WSS. (2) Low WSS is associated with plaque necrotic core and calcium, independent of plaque burden, which suggests a link between WSS and coronary plaque phenotype. (J Am Heart Assoc. 2012;1:e002543 doi: 10.1161/JAHA.112.002543.)
doi:10.1161/JAHA.112.002543
PMCID: PMC3487351  PMID: 23130168
atherosclerosis; coronary arteries; computational fluid dynamics; ultrasonography, intravascular; histology, virtual; wall shear stress
25.  Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans 
PLoS Genetics  2012;8(7):e1002702.
RNA interference (RNAi)–related pathways affect gene activity by sequence-specific recruitment of Ago proteins to mRNA target molecules. The sequence specificity of this process stems from small RNA (sRNA) co-factors bound by the Ago protein. Stability of sRNA molecules in some pathways is in part regulated by Hen1-mediated methylation of their 3′ ends. Here we describe the effects of the Caenorhabditis elegans HEN1 RNA–methyl-transferase homolog, HENN-1, on the different RNAi pathways in this nematode. We reveal differential effects of HENN-1 on the two pathways that are known to employ methylated sRNA molecules: the 26G and 21U pathways. Surprisingly, in the germline, stability of 21U RNAs, the C. elegans piRNAs, is only mildly affected by loss of methylation; and introduction of artificial 21U target RNA does not further destabilize non-methylated 21U RNAs. In contrast, most 26G RNAs display reduced stability and respond to loss of HENN-1 by displaying increased 3′-uridylation frequencies. Within the 26G RNA class, we find that specifically ERGO-1–bound 26G RNAs are modified by HENN-1, while ALG-3/ALG-4–bound 26G RNAs are not. Global gene expression analysis of henn-1 mutants reveals mild effects, including down-regulation of many germline-expressed genes. Our data suggest that, apart from direct effects of reduced 26G RNA levels of henn-1 on gene expression, most effects on global gene expression are indirect. These studies further refine our understanding of endogenous RNAi in C. elegans and the roles for Hen1 like enzymes in these pathways.
Author Summary
Small RNAs (sRNAs) have been shown to be potent regulators of gene expression in many different systems. They act by providing sequence specificity to Argonaute (Ago) proteins that in turn affect the expression and/or stability of mRNAs, or affect chromatin structures through recognition of nascent transcripts. Stability of sRNAs can be regulated by methylation of their 3′ end. This modification prevents addition of uridine residues that can destabilize the sRNA. The enzyme that catalyzes the methylation of sRNAs has been identified in Arabidopsis: HEN1. We describe studies on the C. elegans homolog of Hen1, henn-1. Our findings show that HENN-1 protein does not stably associate with the Ago proteins binding methylated sRNAs, but that HENN-1 does localize to subcellular regions known to host these factors. We find that the two known methylated sRNA species in C. elegans (21U and 26G) respond differently to loss of henn-1. While HENN-1 is required for 26G RNA stability in the germline, it has limited impact on 21U RNAs. In addition, we demonstrate that only ERGO-1–bound 26G RNAs are methylated, while those bound by ALG-3/4, are not. Our findings further refine the general understanding of 21U and 26G RNA pathways and identify two separable effects of HENN-1 on these RNAi–related mechanisms.
doi:10.1371/journal.pgen.1002702
PMCID: PMC3400576  PMID: 22829772

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