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1.  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.
PMCID: PMC4326011
2.  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
3.  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.
PMCID: PMC4237127  PMID: 25477865
Antarctic subglacial aquatic environments; geomicrobiology; chemosynthesis; sulfur oxidation; sulfate reduction
4.  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.
71.30. + h; 73.21.La; 78.47.jd
PMCID: PMC4232974  PMID: 25404877
Metal to insulator transition; Vanadium dioxide; Colloidal quantum dots
5.  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
7.  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.
PMCID: PMC4215326  PMID: 25359514
8.  ImmunoPET Imaging of Renal Cell Carcinoma with 124I- and 89Zr-Labeled Anti-CAIX Monoclonal Antibody cG250 in Mice 
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.
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.
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.
PMCID: PMC3741422  PMID: 23697926
124I; 89Zr; cG250; immunoPET
9.  Regional variations in MR relaxation of hip joint cartilage in subjects with and without femoralacetabular impingement☆,☆☆ 
Magnetic resonance imaging  2013;31(7):1129-1136.
The objective of this study was to analyze regional variations of magnetic resonance (MR) relaxation times (T1ρ and T2) in hip joint cartilage of healthy volunteers and subjects with femoral acetabular impingement (FAI). Morphological and quantitative images of the hip joints of 12 healthy volunteers and 9 FAI patients were obtained using a 3 T MR scanner. Both femoral and acetabular cartilage layers in each joint were semi-automatically segmented on sagittal 3D high-resolution spoiled gradient echo (SPGR) images. These segmented regions of interest (ROIs) were automatically divided radially into twelve equal sub-regions (300 intervals) based on the fitted center of the femur head. The mean value of T1ρ/T2 was calculated in each subregion after superimposing the divided cartilage contours on the MR relaxation (T1ρ/T2) maps to quantify the relaxation times. T1ρ and T2 relaxation times of the femoral cartilage were significantly higher in FAI subjects compared to healthy controls (39.9 ± 3.3 msec in FAI vs. 35.4 ± 2.3 msec in controls for T1ρ (P = 0.0020); 33.9 ± 3.1 msec in FAI vs. 31.1 ± 1.7 msec in controls for T2 (P = 0.0160)). Sub-regional analysis showed significantly different T1ρ and T2 relaxation times in the anterior-superior region (R9) of the hip joint cartilage between subjects with FAI and healthy subjects, suggesting possible regional differences in cartilage matrix composition between these two groups. Receiver operating characteristic (ROC) analysis showed that subregional analysis in femoral cartilage was more sensitive in discriminating FAI joint cartilage from that of healthy joints than global analysis of the whole region (T1ρ: area under the curve (AUC) = 0.981, P = 0.0001 for R9 sub-region; AUC = 0.901, P = 0.002 for whole region; T2: AUC = 0.976, P = 0.0005 for R9 sub-region; AUC = 0.808, P = 0.0124 for whole region). The results of this study demonstrated regional variations in hip cartilage composition using MR relaxation times (T1ρ and T2) and suggested that analysis based on local regions was more sensitive than global measures in subjects with and without FAI.
PMCID: PMC3729918  PMID: 23684960
MRI; Hip; Cartilage; T1ρ and T2; Femoral-acetabular impingement
10.  Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides 
BMC Genomics  2014;15(1):730.
The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data.
The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles.
Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-730) contains supplementary material, which is available to authorized users.
PMCID: PMC4158056  PMID: 25164283
Comparative transcriptomics; Module preservation; Gene-protein expression conservation; Rhodobacter capsulatus; Rhodobacter sphaeroides
11.  Genetic and molecular basis of drug resistance and species-specific drug action in Schistosome parasites 
Science (New York, N.Y.)  2013;342(6164):1385-1389.
Oxamniquine resistance evolved in the human blood fluke (Schistosoma mansoni) in Brazil in the 1970s. We crossed parental parasites differing ~500-fold in drug response, determined drug sensitivity and marker segregation in clonally-derived F2s, and identified a single QTL (LOD=31) on chromosome 6. A sulfotransferase was identified as the causative gene using RNAi knockdown and biochemical complementation assays and we subsequently demonstrated independent origins of loss-of-function mutations in field-derived and laboratory-selected resistant parasites. These results demonstrate the utility of linkage mapping in a human helminth parasite, while crystallographic analyses of protein-drug interactions illuminate the mode of drug action and provide a framework for rational design of oxamniquine derivatives that kill both S. mansoni and S. haematobium, the two species responsible for >99% of schistosomiasis cases worldwide.
PMCID: PMC4136436  PMID: 24263136
12.  High-resolution solid-state NMR structure of Alanyl-Prolyl-Glycine 
We present a de novo high-resolution structure of the peptide Alanyl-Prolyl-Glycine using a combination of sensitive solid-state NMR techniques that each yield precise structural constraints. High-quality 13C–13C distance constraints are extracted by fitting rotational resonance width (R2W) experiments using Multimode Multipole Floquet Theory and experimental chemical shift anisotropy (CSA) orientations. In this strategy, a structure is first calculated using DANTE-REDOR and torsion angle measurements and the resulting relative CSA orientations are used as an input parameter in the 13C–13C distance calculations. Finally, a refined structure is calculated using all the constraints. We investigate the effect of different structural constraints on structure quality, as determined by comparison to the crystal structure and also self-consistency of the calculated structures. Inclusion of all or subsets of these constraints into CNS calculations resulted in high-quality structures (0.02 Å backbone RMSD using all 11 constraints).
PMCID: PMC4133121  PMID: 19596601
SSNMR; Structural determination
13.  Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1 
Nucleic Acids Research  2014;42(16):10845-10855.
The enzymatic processing of cellular RNA molecules requires selective recognition of unique chemical and topological features. The unusual 2′,5′-phosphodiester linkages in RNA lariats produced by the spliceosome must be hydrolyzed by the intron debranching enzyme (Dbr1) before they can be metabolized or processed into essential cellular factors, such as snoRNA and miRNA. Dbr1 is also involved in the propagation of retrotransposons and retroviruses, although the precise role played by the enzyme in these processes is poorly understood. Here, we report the first structures of Dbr1 alone and in complex with several synthetic RNA compounds that mimic the branchpoint in lariat RNA. The structures, together with functional data on Dbr1 variants, reveal the molecular basis for 2′,5′-phosphodiester recognition and explain why the enzyme lacks activity toward 3′,5′-phosphodiester linkages. The findings illuminate structure/function relationships in a unique enzyme that is central to eukaryotic RNA metabolism and set the stage for the rational design of inhibitors that may represent novel therapeutic agents to treat retroviral infections and neurodegenerative disease.
PMCID: PMC4176325  PMID: 25123664
14.  Outcomes analysis of an alternative formulation of PEGylated liposomal doxorubicin in recurrent epithelial ovarian carcinoma during the drug shortage era 
OncoTargets and therapy  2014;7:1409-1413.
In response to the critical shortage of Doxil®, the US Food and Drug Administration (FDA) allowed temporary importation of non-FDA-approved second-generation liposomal doxorubicin, Lipo-Dox®. Lipo-Dox utilizes a different liposomal particle than Doxil and demonstrates different pharmacokinetic properties. Its use has never been evaluated in a North American population. The objective of this study was to evaluate the efficacy and tolerability of Lipo-Dox at Magee-Womens Hospital, University of Pittsburgh Medical Center, for patients with recurrent epithelial ovarian cancer who were treated during the Doxil shortage.
Patients treated with Lipo-Dox from January 2012 to December 2012 were identified retrospectively. Disease response was defined radiographically by RECIST (Response Evaluation Criteria in Solid Tumors) or biochemically by CA-125 level if measurable disease was not present. Survival was defined from the start date of Lipo-Dox until the date of progression or death. Toxicity was assessed by the Gynecologic Oncology Group common toxicity criteria.
Eighteen patients with recurrent epithelial ovarian cancer who received Lipo-Dox were identified. These patients had a median of three prior treatment regimens. The median number of Lipo-Dox cycles given was 3.5 (range 1–8). No patients had a complete or partial response. Two patients had stable disease over a mean follow-up of 144.5 days. Fourteen patients had progressive disease, with a median time to progression of 82 days. Progression was based on CA-125 in four patients and RECIST in the remainder. Nine patients died from the disease.
Although this represents a small, pretreated population, there were no clinical responses to Lipo-Dox, raising the question as to whether it is an equivalent substitute for Doxil. Further evaluation is needed, but if confirmed, these findings raise concerns regarding the use of current stocks of Lipo-Dox, as well as the prudence of managing future drug shortages with pharmacologically similar, but clinically untested drugs.
PMCID: PMC4133030  PMID: 25143745
recurrent ovarian carcinoma; liposomal doxorubicin; drug shortage
15.  Macrophage PTEN Regulates Expression and Secretion of Arginase I Modulating Innate and Adaptive Immune Responses 
The activation of innate immune cells triggers numerous intracellular signaling pathways, which require tight control to mount an adequate immune response. The PI3K signaling pathway is intricately involved in innate immunity, and its activation dampens the expression and release of proinflammatory cytokines in myeloid cells. These signaling processes are strictly regulated by the PI3K antagonist, the lipid phosphatase, PTEN, a known tumor suppressor. Importantly, PTEN is responsible for the elevated production of cytokines such as IL-6 in response to TLR agonists, and deletion of PTEN results in diminished inflammatory responses. However, the mechanisms by which PI3K negatively regulates TLR signaling are only partially resolved. We observed that Arginase I expression and secretion were markedly induced by PTEN deletion, suggesting PTEN−/− macrophages were alternatively activated. This was mediated by increased expression and activation of the transcription factors C/EBPβ and STAT3. Genetic and pharmacologic experimental approaches in vitro, as well as in vivo autoimmunity models, provide convincing evidence that PI3K/PTEN-regulated extracellular Arginase I acts as a paracrine regulator of inflammation and immunity.
PMCID: PMC4120896  PMID: 25015834
16.  Resolution and polarization distribution in cryogenic DNP/MAS experiments 
This contribution addresses four potential misconceptions associated with high-resolution dynamic nuclear polarization/magic angle spinning (DNP/MAS) experiments. First, spectral resolution is not generally compromised at the cryogenic temperatures at which DNP experiments are performed. As we demonstrate at a modest field of 9 T (380 MHz 1H), 1 ppm linewidths are observed in DNP/MAS spectra of a membrane protein in its native lipid bilayer, and <0.4 ppm linewidths are reported in a crystalline peptide at 85 K. Second, we address the concerns about paramagnetic broadening in DNP/MAS spectra of proteins by demonstrating that the exogenous radical polarizing agents utilized for DNP are distributed in the sample in such a manner as to avoid paramagnetic broadening and thus maintain full spectral resolution. Third, the enhanced polarization is not localized around the polarizing agent, but rather is effectively and uniformly dispersed throughout the sample, even in the case of membrane proteins. Fourth, the distribution of polarization from the electron spins mediated via spin diffusion between 1H–1H strongly dipolar coupled spins is so rapid that shorter magnetization recovery periods between signal averaging transients can be utilized in DNP/MAS experiments than in typical experiments performed at ambient temperature.
PMCID: PMC4085575  PMID: 20454732
17.  Associations between the Antioxidant Network and Emotional Intelligence: A Preliminary Study 
PLoS ONE  2014;9(7):e101247.
Emotional intelligence (EI) can be broadly defined as the ability to cope with environmental demands. In the scientific research, however, there is not a univocal precise definition of EI and recent articles have underlined the necessity to explore its biological basis to advance understanding of the construct. The aim of study was to investigate if the antioxidant network may be associated with typical-performance or trait EI.
The study group consisted of 50 women (age, M = 25.10, SD = 3.87). Super Oxide Dismutase (SOD), Catalase (CAT), Glutathione Reductase (GR), and Glutathione Peroxidase (GPx) activities were evaluated on proteins extracted from Peripheral Blood Mononuclear Cells. Participants completed the Italian version of the EQ-i (Bar-On, 1997) as a measure of trait EI.
We observed positive and significant correlations between some biological variables and EQ-i scores, and a significant predictive effect of CAT activity when controlling for related biological variables, age, and smoking.
Our preliminary study suggests that the antioxidant network may constitute some of trait EI's biological basis. In particular, CAT and the SOD/CAT ratio could be two biological variables involved in some specific components of EI.
PMCID: PMC4077755  PMID: 24983620
18.  An unexpected copper catalyzed ‘reduction’ of an arylazide to amine through the formation of a nitrene intermediate 
Tetrahedron  2013;69(25):5079-5085.
Azido nitrobenzoxadiazole (NBD) was observed to undergo a ‘reduction’ reaction in the absence of an obvious reducing agent, leading to amine formation. In the presence of an excess amount of DMSO, a sulfoxide conjugate was also formed. The ratio of these two products was both temperature- and solvent-dependent, with the addition of water significantly enhancing the ratio of the ‘reduction’ product. Two intermediates of the azido-NBD reaction in DMSO were trapped and characterized by low-temperature EPR spectroscopy. One was an organic free radical (S=1/2) and another was a triplet nitrene (S=1) species. A mechanism was proposed based on the characterized free radical and triplet intermediates.
PMCID: PMC3752911  PMID: 23997313
NBD; Azide; Reduction; Nitrene; EPR
19.  Safety and feasibility of nucleus accumbens stimulation in five patients with epilepsy 
Journal of Neurology  2014;261(8):1477-1484.
In five adult patients with intractable partial epilepsy, safety and feasibility of chronic bilateral electrical stimulation of the nucleus accumbens (NAC) were assessed, also providing initial indications of therapeutic efficacy. Concurrent medication remained unchanged. In this phase 1 trial, clinical outcome parameters of interest were Quality of Life in Epilepsy questionnaire (QOLIE-31-P), Beck Depression Inventory, Mini International Neuropsychiatric Interview, neuropsychological testing, and Liverpool Seizure Severity Scale. Those data were obtained after 6 months of NAC stimulation and compared to the equivalent assessments made directly before implantation of electrodes. Additionally, monthly frequencies of simple partial seizures, complex partial seizures (CPS), and generalised tonic–clonic seizures (GTCS) were assessed during 3 months before electrode implantation and at the end of 6-month NAC stimulation. Proportion of responders, i.e. ≥50 % reduction in frequency of disabling seizures (sum of CPS and GTCS), was calculated. Main findings were unchanged psychiatric and neuropsychological assessment and a significant decrease in seizure severity (p = 0.043). QOLIE-31-P total score trended towards improvement (p = 0.068). Two out of five participants were responders. The median reduction in frequency of disabling seizures was 37.5 %. In summary, we provide initial evidence for safety and feasibility of chronic electrical stimulation of the NAC in patients with intractable partial epilepsy, as indicated by largely unchanged neurocognitive function and psychiatric comorbidity. Even though our data are underpowered to reliably assess efficacy, the significant decrease in seizure severity provides an initial indication of antiictal efficacy of NAC stimulation. This calls for larger and at best randomised trials to further elucidate efficacy of NAC stimulation in patients with pharmacologically intractable epilepsy.
PMCID: PMC4119256  PMID: 24801491
Deep brain stimulation; Neuropsychology; Psychiatry; Quality of life; Seizure frequency; Seizure severity
20.  Structure of the Polycomb Group protein PCGF1 (NSPC1) in complex with BCOR reveals basis for binding selectivity of PCGF homologs 
Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6) are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes. Here we identify a protein interaction domain in BCL6 co-repressor, BCOR, which binds the ubiquitin-like RAWUL domain of PCGF1 (NSPC1) and PCGF3 but not of PCGF2 (MEL18) or PCGF4 (BMI1). Because of the selective binding, we have named this domain PCGF Ub-like fold Discriminator (PUFD). The structure of BCOR PUFD bound to PCGF1 reveals 1. that PUFD binds to the same surfaces as observed for a different Polycomb Group RAWUL domain and 2. the ability of PUFD to discriminate among RAWULs stems from the identity of specific residues within these interaction surfaces. These data are the first to show the molecular basis for determining the binding preference for a PCGF homolog, which ultimately helps determine the identity of the larger PRC1-like assembly.
PMCID: PMC4003909  PMID: 23523425
21.  Dynamic Nuclear Polarization Study of Inhibitor Binding to the M218–60 Proton Transporter from Influenza A 
Biochemistry  2013;52(16):2774-2782.
We demonstrate the use of dynamic nuclear polarization (DNP) to elucidate ligand binding to a membrane protein using dipolar recoupling magic angle spinning (MAS) NMR. In particular, we detect drug binding in the proton transporter M218–60 from influenza A using recoupling experiments at room temperature and with cryogenic DNP. The results indicate that the pore binding site of rimantadine is correlated with previously reported widespread chemical shift changes, suggesting functional binding in the pore. Futhermore, the 15N labeled ammonium of rimantadine was observed near A30 13Cβ and G34 13Cα suggesting a possible hydrogen bond to A30 Carbonyl. Cryogenic DNP was required to observe the weaker external binding site(s) in a ZF-TEDOR spectrum. This approach is generally applicable, particularly for weakly bound ligands, in which case the application of MAS NMR dipolar recoupling requires the low temperatures to quench dynamic exchange processes. For the fully protonated samples investigated, we observed DNP signal enhancements of ~10 at 400 MHz using only 4–6 mM of the polarizing agent TOTAPOL. At 600 MHz and with DNP, we measured a distance between the drug and the protein to a precision of 0.2 Å.
PMCID: PMC3646523  PMID: 23480101
NMR; dynamic nuclear polarization; M2; influenza; inhibitor binding; solid state NMR; magic angle spinning; dipolar recoupling
22.  Impact of stepwise hyperventilation on cerebral tissue oxygen saturation in anesthetized patients: a mechanistic study 
While the decrease in blood carbon dioxide (CO2) secondary to hyperventilation is generally accepted to play a major role in the decrease of cerebral tissue oxygen saturation (SctO2), it remains unclear if the associated systemic hemodynamic changes are also accountable.
Twenty-six patients (American Society of Anesthesiologists I–II) undergoing nonneurosurgical procedures were anesthetized with either propofol-remifentanil (n = 13) or sevoflurane (n = 13). During a stable intraoperative period, ventilation was adjusted stepwise from hypoventilation to hyper-ventilation to achieve a progressive change in end-tidal CO2 (ETCO2) from 55 to 25 mmHg. Minute ventilation, SctO2, ETCO2, mean arterial pressure (MAP), and cardiac output (CO) were recorded.
Hyperventilation led to a SctO2 decrease from 78 ± 4% to 69 ± 5% (Δ = −9 ± 4%, P < 0.001) in the propofol-remifentanil group and from 81 ± 5% to 71 ± 7% (Δ = −10 ± 3%, P < 0.001) in the sevoflurane group. The decreases in SctO2 were not statistically different between these two groups (P = 0.5). SctO2 correlated significantly with ETCO2 in both groups (P < 0.001). SctO2 also correlated significantly with MAP (P < 0.001) and CO (P < 0.001) during propofol-remifentanil, but not sevoflurane (P = 0.4 and 0.5), anesthesia.
The main mechanism responsible for the hyperventilation-induced decrease in SctO2 is hypocapnia during both propofol-remifentanil and sevoflurane anesthesia. Hyperventilation-associated increase in MAP and decrease in CO during propofol-remifentanil, but not sevoflurane, anesthesia may also contribute to the decrease in SctO2 but to a much smaller degree.
PMCID: PMC3992996  PMID: 23278596
23.  The Structure of the Flavoprotein Tryptophan-2-Monooxygenase, a Key Enzyme in the Formation of Galls in Plants† 
Biochemistry  2013;52(15):2620-2626.
The flavoprotein tryptophan 2-monooxygenase catalyzes the oxidative decarboxylation of tryptophan to yield indole-3-acetamide. This is the initial step in the biosynthesis of the plant growth hormone indole-acetic-acid by bacterial pathogens that cause crown gall and related diseases. The structure of the enzyme from Pseudomonas savastanoi has been determined by X-ray diffraction methods to a resolution of 1.95 Å. The overall structure of the protein shows that it has the same fold as the monoamine oxidase family of flavoproteins, with the greatest similarities to the L-amino acid oxidases. The location of bound indole-3-acetamide in the active site enables identification of residues responsible for substrate binding and specificity. Two residues in the enzyme are conserved in all members of the monoamine oxidase family, Lys365 and Trp466. The K365M mutation decreases the kcat and kcat/KTrp values by 60,000 and 2 million-fold, respectively. The deuterium kinetic isotope effect increases to 3.2, consistent with carbon-hydrogen bond cleavage becoming rate-limiting in the mutant enzyme. The W466F mutation decreases the kcat value less than 2-fold and the kcat/KTrp value only 5-fold, while the W466M mutation results in enzyme lacking flavin and detectable activity. This is consistent with a role for Trp466 in maintaining the structure of the flavin binding site in the more conserved FAD domain.
PMCID: PMC3635830  PMID: 23521653
24.  Transglutaminase and Polyamination of Tubulin: Posttranslational Modification for Stabilizing Axonal Microtubules 
Neuron  2013;78(1):109-123.
Neuronal microtubules support intracellular transport, facilitate axon growth, and form a basis for neuronal morphology. While microtubules in non-neuronal cells are depolymerized by cold, Ca2+ or antimitotic drugs, neuronal microtubules are unusually stable. Such stability is important for normal axon growth and maintenance, while hyperstability may compromise neuronal function in aging and degeneration. Though mechanisms for stability were unclear, studies suggested that stable microtubules contain biochemically distinct tubulins that are more basic than conventional tubulins. Transglutaminase-catalyzed posttranslational incorporation of polyamines is one of the few modifications of intracellular proteins that add positive charges. Here we show that neuronal tubulin can be polyaminated by transglutaminase. Endogenous brain transglutaminase-catalyzed polyaminated tubulins have the biochemical characteristics of neuronal stable microtubules. Inhibiting polyamine synthesis or transglutaminase activity significantly decreases microtubule stability in vitro and in vivo. Together, this suggests that transglutaminase-catalyzed polyamination of tubulins stabilizes neuronal microtubules essential for unique neuronal structures and functions.
PMCID: PMC3627183  PMID: 23583110
Tubulin; Transglutaminase; Polyamine; Microtubule; Axon; Neuron; Stable Microtubules; Polyamination; Spermine; Spermidine; Putrescine
25.  Circulating cell-free methylated DNA and lactate dehydrogenase release in colorectal cancer 
BMC Cancer  2014;14:245.
Hypermethylation of DNA is an epigenetic alteration commonly found in colorectal cancer (CRC) and can also be detected in blood samples of cancer patients. Methylation of the genes helicase-like transcription factor (HLTF) and hyperplastic polyposis 1 (HPP1) have been proposed as prognostic, and neurogenin 1 (NEUROG1) as diagnostic biomarker. However the underlying mechanisms leading to the release of these genes are unclear. This study aimed at examining the possible correlation of the presence of methylated genes NEUROG1, HLTF and HPP1 in serum with tissue breakdown as a possible mechanism using serum lactate dehydrogenase (LDH) as a surrogate marker. Additionally the prognostic impact of these markers was examined.
Pretherapeutic serum samples from 259 patients from all cancer stages were analyzed. Presence of hypermethylation of the genes HLTF, HPP1, and NEUROG1 was examined using methylation-specific quantitative PCR (MethyLight). LDH was determined using an UV kinetic test.
Hypermethylation of HLTF and HPP1 was detected significantly more often in patients with elevated LDH levels (32% vs. 12% [p = 0.0005], and 68% vs. 11% [p < 0.0001], respectively). Also, higher LDH values correlated with a higher percentage of a fully methylated reference in a linear fashion (Spearman correlation coefficient 0.18 for HLTF [p = 0.004]; 0.49 [p < .0001] for HPP1). No correlation between methylation of NEUROG1 and LDH was found in this study. Concerning the clinical characteristics, high levels of LDH as well as methylation of HLTF and HPP1 were significantly associated with larger and more advanced stages of CRC. Accordingly, these three markers were correlated with significantly shorter survival in the overall population. Moreover, all three identified patients with a worse prognosis in the subgroup of stage IV patients.
We were able to provide evidence that methylation of HLTF and especially HPP1 detected in serum is strongly correlated with cell death in CRC using LDH as surrogate marker. Additionally, we found that prognostic information is given by both HLTF and HPP1 as well as LDH. In sum, determining the methylation of HLTF and HPP1 in serum might be useful in order to identify patients with more aggressive tumors.
PMCID: PMC4021086  PMID: 24708595
Colorectal cancer; Dna methylation; Hltf; Hpp1; Neurog1; Ldh

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