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1.  Molecular determinants of Ca2+ sensitivity at the intersubunit interface of the BK channel gating ring 
Scientific Reports  2018;8:509.
The large-conductance calcium-activated K+ (BK) channel contains two intracellular tandem Ca2+-sensing RCK domains (RCK1 and RCK2), which tetramerize into a Ca2+ gating ring that regulates channel opening by conformational expansion in response to Ca2+ binding. Interestingly, the gating ring’s intersubunit assembly interface harbors the RCK2 Ca2+-binding site, known as the Ca2+ bowl. The gating ring’s assembly interface is made in part by intersubunit coordination of a Ca2+ ion between the Ca2+ bowl and an RCK1 Asn residue, N449, and by apparent intersubunit electrostatic interactions between E955 in RCK2 and R786 and R790 in the RCK2 of the adjacent subunit. To understand the role of the intersubunit assembly interface in Ca2+ gating, we performed mutational analyses of these putative interacting residues in human BK channels. We found that N449, despite its role in Ca2+ coordination, does not set the channel’s Ca2+ sensitivity, whereas E955 is a determinant of Ca2+ sensitivity, likely through intersubunit electrostatic interactions. Our findings provide evidence that the intersubunit assembly interface contains molecular determinants of Ca2+-sensitivity in BK channels.
doi:10.1038/s41598-017-19029-8
PMCID: PMC5765161  PMID: 29323236
2.  Anti-Inflammatory Activity of Babassu Oil and Development of a Microemulsion System for Topical Delivery 
Babassu oil extraction is the main income source in nut breakers communities in northeast of Brazil. Among these communities, babassu oil is used for cooking but also medically to treat skin wounds and inflammation, and vulvovaginitis. This study aimed to evaluate the anti-inflammatory activity of babassu oil and develop a microemulsion system with babassu oil for topical delivery. Topical anti-inflammatory activity was evaluated in mice ear edema using PMA, arachidonic acid, ethyl phenylpropiolate, phenol, and capsaicin as phlogistic agents. A microemulsion system was successfully developed using a Span® 80/Kolliphor® EL ratio of 6 : 4 as the surfactant system (S), propylene glycol and water (3 : 1) as the aqueous phase (A), and babassu oil as the oil phase (O), and analyzed through conductivity, SAXS, DSC, TEM, and rheological assays. Babassu oil and lauric acid showed anti-inflammatory activity in mice ear edema, through inhibition of eicosanoid pathway and bioactive amines. The developed formulation (39% A, 12.2% O, and 48.8% S) was classified as a bicontinuous to o/w transition microemulsion that showed a Newtonian profile. The topical anti-inflammatory activity of microemulsified babassu oil was markedly increased. A new delivery system of babassu microemulsion droplet clusters was designed to enhance the therapeutic efficacy of vegetable oil.
doi:10.1155/2017/3647801
PMCID: PMC5753019
3.  Bread formulated with guava powder was enriched in phenolic and aroma compounds, and was highly acceptable by consumers 
Journal of Food Science and Technology  2016;53(12):4168-4178.
Guava powder (GP) was used as source of aroma and phenolic compounds to fortify wheat bread 10% (GB10) and 20% (GB20), substituting for wheat flour. Phenolic compounds, antioxidant capacity, volatile compounds profile, and sensory acceptability of control bread (CB; without GP) and guava breads (GB) were evaluated. Incorporation of GP increased roughly 2-to-3-fold the phenolic compounds contents of bread. Ten phenolic compounds were identified in GB20, and quercetin-3-O-rutinoside was the major compound, while in CB, ferulic acid was the major among the six phenolic compounds in CB. Bread making seemed to promote the release of phenolic compounds from structural components. Breads incorporated with GP presented a richer volatile profile than CB, especially due to the presence of terpenes. GB improved aroma profile of bread. GP added aroma compounds and phenolic antioxidants, and seemed to be an interesting approach to enhance bread bioactivity and acceptability.
Electronic supplementary material
The online version of this article (doi:10.1007/s13197-016-2396-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s13197-016-2396-4
PMCID: PMC5223251  PMID: 28115757
Psidium guajava; Bread making; Antioxidant capacity; Sensory evaluation; Volatile compounds; Functional food
4.  Differential Metabolism of a Two-Carbon Substrate by Members of the Paracoccidioides Genus 
The genus Paracoccidioides comprises known fungal pathogens of humans and can be isolated from different infection sites. Metabolic peculiarities in different members of the Paracoccidioides led us to perform proteomic studies in the presence of the two-carbon molecule acetate, which predominates in the nutrient-poor environment of the phagosome. To investigate the expression rates of proteins of different members of Paracoccidioides, including one isolate of P. lutzii (Pb01) and three isolates of P. brasiliensis (Pb03, Pb339, and PbEPM83), using sodium acetate as a carbon source, proteins were quantified using label-free and data-independent liquid chromatography-mass spectrometry. Protein profiles of the isolates were statistically analyzed, revealing proteins that were differentially expressed when the fungus was cultivated in a non-preferential carbon source rather than glucose. A total of 1,160, 1,211, 1,280, and 1,462 proteins were reproducibly identified and relatively quantified in P. lutzii and the P. brasiliensis isolates Pb03, Pb339, and PbEPM83, respectively. Notably, 526, 435, 744, and 747 proteins were differentially expressed among P. lutzii and the P. brasiliensis isolates Pb03, Pb339, and PbEPM83, respectively, with a fold-change equal to or higher than 1.5. This analysis revealed that reorganization of metabolism occurred through the induction of proteins related to gluconeogenesis, glyoxylic/glyoxylate cycle, response to stress, and degradation of amino acids in the four isolates. The following differences were observed among the isolates: higher increases in the expression levels of proteins belonging to the TCA and respiratory chain in PbEPM83 and Pb01; increase in ethanol production in Pb01; utilization of cell wall components for gluconeogenesis in Pb03 and PbEPM83; and increased β-oxidation and methylcitrate cycle proteins in Pb01and PbEPM83. Proteomic profiles indicated that the four isolates reorganized their metabolism in different manners to use acetate as a carbon source.
doi:10.3389/fmicb.2017.02308
PMCID: PMC5711815
Paracoccidioides spp.; proteomic; two-carbon source; sodium acetate; metabolism
5.  Knowledge-based prediction of protein backbone conformation using a structural alphabet 
PLoS ONE  2017;12(11):e0186215.
Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Blocks, is composed of 16 standard 5-residues long structural prototypes. This form of analyzing proteins involves drafting its structure as a string of Protein Blocks. Predicting the local structure of a protein in terms of protein blocks is the general objective of this work. A new approach, PB-kPRED is proposed towards this aim. It involves (i) organizing the structural knowledge in the form of a database of pentapeptide fragments extracted from all protein structures in the PDB and (ii) applying a knowledge-based algorithm that does not rely on any secondary structure predictions and/or sequence alignment profiles, to scan this database and predict most probable backbone conformations for the protein local structures. Though PB-kPRED uses the structural information from homologues in preference, if available. The predictions were evaluated rigorously on 15,544 query proteins representing a non-redundant subset of the PDB filtered at 30% sequence identity cut-off. We have shown that the kPRED method was able to achieve mean accuracies ranging from 40.8% to 66.3% depending on the availability of homologues. The impact of the different strategies for scanning the database on the prediction was evaluated and is discussed. Our results highlight the usefulness of the method in the context of proteins without any known structural homologues. A scoring function that gives a good estimate of the accuracy of prediction was further developed. This score estimates very well the accuracy of the algorithm (R2 of 0.82). An online version of the tool is provided freely for non-commercial usage at http://www.bo-protscience.fr/kpred/.
doi:10.1371/journal.pone.0186215
PMCID: PMC5697859  PMID: 29161266
6.  PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks 
PeerJ  2017;5:e4013.
This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.
doi:10.7717/peerj.4013
PMCID: PMC5700758
Protein blocks; Deformability; Python; Protein; Structure; Structural alphabet
7.  Localizing sites of disease in patients with rising PSA up to 1 ng/mL following prostatectomy: how much information can conventional imaging provide? 
Urologic oncology  2016;34(11):482.e5-482.e10.
Purpose
Accurate identification of the source of a detectable serum PSA in the postprostatectomy setting is a major challenge amongst the urologic community. The aim of this study was to assess positivity rates of imaging examinations performed in patients with early PSA rise after prostatectomy; and to summarize the management strategies adopted in this clinical scenario.
Methods
IRB-approved retrospective study of 142 post-prostatectomy patients with PSA rise up to 1 ng/mL who underwent evaluation with combination of multiparametric pelvic MRI +/− whole-body or bone MRI, bone scintigraphy (BS), CT chest-abdomen-pelvis (CT-CAP), FDG-PET/ CT and/or NaF-PET/CT at a single tertiary cancer center. Imaging results were summarized per modality and compared to pathology findings.
Results
Pelvic MRI was positive in 15/142 (11%) patients (14 patients with local recurrence in the surgical bed and 1 patient with pelvic osseous metastases). Ten of these 15 patients underwent additional imaging exams; none revealed positive findings. Of the 127 patients with negative pelvic MRI, 54 (43%) underwent additional imaging exams; only 1/54 had positive findings (false positive T8 lesion on BS and FDG-PET/CT-biopsy negative for cancer). 12/16 patients with positive imaging findings and 75/126 (60%) patients with negative imaging received treatment (radiation, hormones and/or chemotherapy).
Conclusion
conventional imaging identified sites of disease, almost always in the form of local recurrence, in a minority of patients with early PSA rise post-prostatectomy.
doi:10.1016/j.urolonc.2016.05.026
PMCID: PMC5097681  PMID: 27346339
Bone scan; CT; MRI; PET; prostate cancer; recurrence
8.  Anatomical and functional correlation in Susac syndrome: multimodal imaging assessment 
Background
Susac’s syndrome (SuS) is an uncommon disease characterized by retinal microangiopathy that may be assessed more accurately with optical coherence tomography angiography (OCTA), a new imaging technique which provides a retinal microvasculature map. The purpose of this case report is to describe the multimodal imaging findings of SuS correlating OCTA with functional tests.
Case presentation
Retrospective review of one case with clinical and imaging evidence of SuS. Color fundus photograph, fluorescein angiography (FA), OCTA, microperimetry (MP) and visual field (VF) tests were analyzed at the time of presentation and at 1- and 6-month visit following initiation of treatment. The study patient underwent standard treatment for SuS. The patient age was 31 year-old and the baseline visual acuity was 20/60 and 20/20 in the right and left eyes, respectively. At presentation, FA showed branch retinal arterial occlusion within the macular area of the right eye and vascular leakage in the periphery of the left eye. OCTA demonstrated areas of superficial and deep retinal vascular plexuses hypoperfusion in both eyes. The OCTA segmentations in the outer retina and choriocapillaris were normal. The low VF and MP sensitivity signals precisely corresponded to the topography of decreased vascular perfusion seen on the OCTA density map in both eyes. Six months after specific SuS therapy, retinal vascular perfusion showed partial improvement in both eyes.
Conclusion
OCTA may demonstrate superficial and deep retinal vascular non-perfusion without choriocapillary vasculature changes in SuS. This anatomical information given by OCTA corresponded to points of low sensitivity on functional tests represented by VF and MP.
doi:10.1186/s40942-017-0092-9
PMCID: PMC5641998
Microperimetry; Optical coherence tomography angiography; Retinal artery occlusion; Susac syndrome; Visual field testing
9.  Assessment of regional left ventricular systolic function by strain imaging echocardiography in phenotypically normal and abnormal Maine coon cats tested for the A31P mutation in the MYBPC3 gene 
Myocardial dysfunction occurs in cats with hypertrophic cardiomyopathy (HCM), but little is known about the early stages of the disease. Strain imaging echocardiography is a method that enables the quantitative assessment of myocardial function and deformity, allowing the characterization of systolic dysfunction. The objective of this study was to assess systolic function using strain imaging echocardiography in Maine coon cats genetically tested for the A31P mutation in the MYBPC3 gene, with and without ventricular hypertrophy. For this purpose, 57 Maine coon cats of both genders, with an unknown status regarding the mutation at inclusion, were included prospectively and evaluated by conventional and strain imaging echocardiography. Comparisons were made among cats without hypertrophy (n = 45), suspect cats (n = 7), and cats with hypertrophic cardiomyopathy (n = 5), and also between the heterozygous for the mutation group (n = 26) and the negative for the mutation group (n = 28). Finally, in the group of phenotypically normal cats, heterozygous cats carrying the mutation were compared to cats without the mutation. Strain values were compared among the groups (blinded prospective study). While echocardiography demonstrated normal contractility, strain values (middle of the septum) were lower in HCM cats. Strain values (base of anterior wall of the left ventricle) were lower in heterozygous than in negative cats, even before hypertrophy. Negative correlation was observed between some values of myocardial strain and thickness. While strain imaging echocardiography was able to detect systolic abnormalities, despite apparent normality on conventional echocardiography, it was not able to identify cats that carry the A31P mutation in the MYBPC3 gene. Strain imaging echocardiography could be a useful tool, however, for detecting systolic alterations in HCM cats with an apparently normal systolic function or for detecting alterations in normal carriers of the MYBPC3 gene mutation.
PMCID: PMC5370540  PMID: 28408782
10.  Dysfunctional gaze processing in bipolar disorder 
NeuroImage : Clinical  2017;16:545-556.
Gaze conveys emotional information, and humans present sensitivity to its direction from the earliest days of life. Bipolar disorder is a disease characterized by fluctuating states of emotional and cognitive dysregulation. To explore the role of attentional control on face processing in bipolar patients (BP) we used gaze direction as an emotion modulation parameter in a two-back Working Memory (WM) task while high-density EEG data were acquired. Since gaze direction influences emotional attributions to faces with neutral expressions as well, we presented neutral faces with direct and averted gaze. Nineteen euthymic BP and a sample of age- and gender-matched controls were examined.
In BP we observed diminished P200 and augmented P300 evoked responses, differentially modulated by non-repeated or repeated faces, as well as by gaze direction. BP showed a reduced P200 amplitude, significantly stronger for faces with direct gaze than averted gaze. Source localization of P200 indicated decreased activity in sensory-motor regions and frontal areas suggestive of abnormal affective processing of neutral faces.
The present study provides neurophysiological evidence for abnormal gaze processing in BP and suggests dysfunctional processing of direct eye contact as a prominent characteristic of bipolar disorder.
Highlights
•This ERP study identified abnormalities in gaze processing in bipolar patients.•We observed functional anomalies in the P200 and P300 evoked responses.•BP showed a strong suppression of the P200 for faces with direct gaze.•Source localization indicated decreased activity in sensory-motor regions.
doi:10.1016/j.nicl.2017.09.006
PMCID: PMC5608173
Bipolar disorder; Gaze processing; Face recognition; Memory; ERP; EEG source imaging
11.  In silico analysis of Glanzmann variants of Calf-1 domain of αIIbβ3 integrin revealed dynamic allosteric effect 
Scientific Reports  2017;7:8001.
Integrin αIIbβ3 mediates platelet aggregation and thrombus formation. In a rare hereditary bleeding disorder, Glanzmann thrombasthenia (GT), αIIbβ3 expression / function are impaired. The impact of deleterious missense mutations on the complex structure remains unclear. Long independent molecular dynamics (MD) simulations were performed for 7 GT variants and reference structure of the Calf-1 domain of αIIb. Simulations were analysed using a structural alphabet to describe local protein conformations. Common and flexible regions as well as deformable zones were observed in all the structures. The most flexible region of Calf-1 (with highest B-factor) is rather a rigid region encompassed into two deformable zones. Each mutated structure barely showed any modifications at the mutation sites while distant conformational changes were observed. These unexpected results question the relationship between molecular dynamics and allostery; and the role of these long-range effects in the impaired αIIbβ3 expression. This method is aimed at studying all αIIbβ3 sub-domains and impact of missense mutations at local and global structural level.
doi:10.1038/s41598-017-08408-w
PMCID: PMC5556033  PMID: 28808266
12.  Maternal PTSD and corresponding neural activity mediate effects of child exposure to violence on child PTSD symptoms 
PLoS ONE  2017;12(8):e0181066.
The aim of this study was to examine the relationship of maternal interpersonal violence-related posttraumatic stress disorder (IPV-PTSD), associated neural activity in response to mother-child relational stimuli, and child psychopathology indicators at child ages 12–42 months and one year later. The study tested the hypothesis that decreased maternal neural activity in regions that subserve emotion regulation would be associated with child symptoms associated with emotional dysregulation at both time points. Functional magnetic resonance imaging of 42 mothers with or without violence-exposure and associated IPV-PTSD were assessed. Their child’s life-events and symptoms/behaviors indicative of high-risk subsequent PTSD diagnosis on a maternal-report questionnaire were measured one year later. Maternal IPV-PTSD severity was significantly associated with decreased ventromedial prefrontal cortex (vmPFC) activation in response to mother-child relational stimuli. Maternal IPV-PTSD severity and decreased vmPFC activation were then significantly associated with a child attachment disturbance at 12–42 months and symptoms/behaviors one year later, that were correlated with emotional dysregulation and risk for child PTSD. Maternal IPV-PTSD and child exposure to IPV were both predictive of child PTSD symptoms with maternal IPV-PTSD likely mediating the effects of child IPV exposure on child PTSD symptoms. These findings suggest that maternal IPV-PTSD severity and associated decreased vmPFC activity in response to mother-child relational stimuli are predictors of child psychopathology by age 12–42 months and one-year later. Significant findings in this paper may well be useful in understanding how maternal top-down cortico-limbic dysregulation promotes intergenerational transmission of IPV and related psychopathology and, thus should be targeted in treatment.
doi:10.1371/journal.pone.0181066
PMCID: PMC5540394  PMID: 28767657
13.  Dibutyltin Compounds Effects on PPARγ/RXRα Activity, Adipogenesis, and Inflammation in Mammalians Cells 
Organotins are a group of chemical compounds that have a tin atom covalently bound to one or more organic groups. The best-studied organotin is tributyltin chloride, which is an environmental pollutant and an endocrine disruptor. Tributyltin chloride has been shown to bind to PPARγ/RXRα and induces adipogenesis in different mammalian cells. However, there are few studies with other organotin compounds, such as dibutyltins. The aim of this study was to investigate the effect of dibutyltins diacetate, dichloride, dilaurate, and maleate on the transcriptional activity of the nuclear PPARγ and RXRα receptors, and on adipogenesis and inflammation. Analogous to tributyltin chloride, in reporter gene assay using HeLa cells, we observed that dibutyltins diacetate, dichloride, dilaurate, and maleate are partial agonists of PPARγ. Unlike tributyltin chloride, which is a full agonist of RXRα, dibutyltins dichloride and dilaurate are partial RXRα agonists. Additionally, the introduction of the C285S mutation, which disrupts tributyltin chloride binding to PPARγ, abrogated the dibutyltin agonistic activity. In 3T3-L1 preadipocytes, all dibutyltin induced adipogenesis, although the effect was less pronounced than that of rosiglitazone and tributyltin chloride. This adipogenic effect was confirmed by the expression of adipogenic markers Fabp4, Adipoq, and Glut4. Exposure of 3T3-L1 cells with dibutyltin in the presence of T0070907, a specific PPARγ antagonist, reduced fat accumulation, suggesting that adipogenic effect occurs through PPARγ. Furthermore, dibutyltins dichloride, dilaurate, and maleate inhibited the expression of proinflammatory genes in 3T3-L1 cells, such as Vcam1, Dcn, Fn1, S100a8, and Lgals9. Additionally, in RAW 264.7 macrophages, tributyltin chloride and dibutyltin dilaurate reduced LPS-stimulated TNFα expression. Our findings indicate that dibutyltins diacetate, dichloride, dilaurate, and maleate are PPARγ partial agonists and that dibutyltins dichloride and dilaurate are also partial RXRα agonists. Furthermore, dibutyltins induce adipogenesis in a PPARγ-dependent manner and repress inflammatory genes in 3T3-L1 and RAW 264.7 cells. Although dibutyltins display some partial PPARγ/RXRα agonistic effects, the translation of cell-based results assays into in vivo effects on inflammation and insulin resistance is not entirely known. Nevertheless, further studies are necessary to address their effects in different periods of life and to elucidate the actions of organostanic compounds in whole-body context.
doi:10.3389/fphar.2017.00507
PMCID: PMC5539189
tributyltin; dibutyltin; peroxisome proliferator activated receptor gamma; adipogenesis; proinflammatory genes
14.  In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping 
BMC Genomics  2017;18:423.
Background
Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs.
Results
Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp.
Conclusions
For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-017-3805-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-017-3805-4
PMCID: PMC5450071  PMID: 28558696
Phaseolus vulgaris L; Diversity arrays technology; Diversity analysis; Linkage disequilibrium; Loci under selection
16.  Stable high-level expression of factor VIII in Chinese hamster ovary cells in improved elongation factor-1 alpha-based system 
BMC Biotechnology  2017;17:33.
Background
Recombinant factor VIII (FVIII), used for haemophilia A therapy, is one of the most challenging among the therapeutic proteins produced in heterologous expression systems. Deletion variant of FVIII, in which the entire domain B is replaced by a short linker peptide, was approved for medical use. Efficacy and safety of this FVIII deletion variant are similar to full-length FVIII preparations while the level of production in CHO cells is substantially higher.
Typical levels of productivity for CHO cell lines producing deletion variant FVIII-BDD SQ, described elsewhere, are 0.5–2 IU/ml, corresponding to the concentration of FVIII of about 0.2 μg/ml. Using standard vectors based on the cytomegalovirus promoter (CMV) and the dihydrofolate reductase cDNA we have previously obtained the cell line secreting 0.5 IU/ml of FVIII-BDD, which roughly corresponds to the previously published data.
Results
An expression system based on CHO genomic sequences including CHO-EEF1A promoter and Epstein-Barr virus terminal repeat fragment allowed us to achieve 80-fold increase in the production level as compared with the conventional expression system based on the CMV promoter.
Immediately after the primary selection FVIII -producing cells secreted 5–10 IU/ml of FVIII-BDD, and after multi-stage methotrexate-driven amplification a stable clonal line 11A4H was selected, secreting 39 IU/ml of FVIII-BDD in the simple batch culturing conditions, which considerably exceeds known indicators for industrial producers of this protein. In contrast to other FVIII-BDD producing lines 11A4H accumulates low proportion of the secreted FVIII on the membrane. Its productivity may be further increased approximately two-fold by adding sodium butyrate and butylated hydroxyanisol to the culture medium.
A five-stage purification process for the factor VIII was employed. It allowed isolation of the intact FVIII-BDD as was confirmed by mass spectrometry. Purified FVIII-BDD has a specific activity of 11,000 IU/mg, similar to known recombinant FVIII drugs.
Conclusions
The recombinant FVIII-BDD was produced in CHO cells without addition of any animal-derived materials, purified and characterized. Novel genetic constructions for the expression of heterologous proteins combined with optimized cultivation method allowed to obtain the secretion level of biologically active recombinant FVIII increased by almost ten times as compared with the previously published analogues.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-017-0353-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-017-0353-6
PMCID: PMC5366130  PMID: 28340620
CHO cells; High level expression; Stable cell line generation; Factor VIII
17.  Differential Role of G Protein-Coupled Receptor Kinase 5 in Physiological Versus Pathological Cardiac Hypertrophy 
Circulation research  2015;117(12):1001-1012.
Rationale
G protein-coupled receptor (GPCR) kinases (GRKs) are dynamic regulators of cellular signaling. GRK5 is highly expressed within myocardium and is up-regulated in heart failure (HF). Although GRK5 is a critical regulator of cardiac GPCR signaling, recent data has uncovered non-canonical activity of GRK5 within nuclei that plays a key role in pathological hypertrophy. Targeted cardiac elevation of GRK5 in mice leads to exaggerated hypertrophy and early HF after transverse aortic constriction (TAC) due to GRK5 nuclear accumulation.
Objective
In this study we investigated the role of GRK5 in physiological, swimming induced hypertrophy (SIH).
Methods and Results
Cardiac-specific GRK5 transgenic mice (TgGRK5) and non-transgenic littermate control (NLC) mice were subjected to a 21-day high intensity swim protocol (or no swim sham controls). SIH and specific molecular and genetic indices of physiological hypertrophy were assessed including nuclear localization of GRK5 and compared to TAC.
Unlike after TAC, swim-trained TgGRK5 and NLC mice exhibited similar increases in cardiac growth. Mechanistically, SIH did not lead to GRK5 nuclear accumulation, which was confirmed in vitro as insulin-like growth factor-1, a known mediator of physiological hypertrophy, was unable to induce GRK5 nuclear translocation in myocytes. We found specific patterns of altered gene expression between TAC and SIH with GRK5 overexpression. Further, SIH in post-TAC TgGRK5 mice was able to preserve cardiac function.
Conclusions
These data suggest that while nuclear-localized GRK5 is a pathological mediator after stress, this non-canonical nuclear activity of GRK5 is not induced during physiological hypertrophy.
doi:10.1161/CIRCRESAHA.115.306961
PMCID: PMC4825669  PMID: 26515328
Exercise; hypertrophy; heart failure; Cell Signaling/Signal Transduction; Genetically altered and Transgenic Models
21.  Extension of the classical classification of β-turns 
Scientific Reports  2016;6:33191.
The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3rd of β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3 and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years.
doi:10.1038/srep33191
PMCID: PMC5024104  PMID: 27627963
22.  Elucidating Protein Involvement in the Stabilization of the Biogenic Silver Nanoparticles 
Silver nanoparticles (AgNPs) have been broadly used as antibacterial and antiviral agents. Further, interests for green AgNP synthesis have increased in recent years and several results for AgNP biological synthesis have been reported using bacteria, fungi and plant extracts. The understanding of the role and nature of fungal proteins, their interaction with AgNPs and the subsequent stabilization of nanosilver is yet to be deeply investigated. Therefore, in an attempt to better understand biogenic AgNP stabilization with the extracellular fungal proteins and to describe these supramolecular interactions between proteins and silver nanoparticles, AgNPs, produced extracellularly by Aspergillus tubingensis—isolated as an endophytic fungus from Rizophora mangle—were characterized in order to study their physical characteristics, identify the involved proteins, and shed light into the interactions among protein-NPs by several techniques. AgNPs of around 35 nm in diameter as measured by TEM and a positive zeta potential of +8.48 mV were obtained. These AgNPs exhibited a surface plasmon resonance (SPR) band at 440 nm, indicating the nanoparticles formation, and another band at 280 nm, attributed to the electronic excitations in tryptophan, tyrosine, and/or phenylalanine residues in fungal proteins. Fungal proteins were covalently bounded to the AgNPs, mainly through S–Ag bonds due to cysteine residues (HS–) and with few N–Ag bonds from H2N– groups, as verified by Raman spectroscopy. Observed supramolecular interactions also occur by electrostatic and other protein–protein interactions. Furthermore, proteins that remain free on AgNP surface may perform hydrogen bonds with other proteins or water increasing thus the capping layer around the AgNPs and consequently expanding the hydrodynamic diameter of the particles (~264 nm, measured by DLS). FTIR results enabled us to state that proteins adsorbed to the AgNPs did not suffer relevant secondary structure alteration upon their physical interaction with the AgNPs or when covalently bonded to them. Eight proteins in the AgNP dispersion were identified by mass spectrometry analyses. All these proteins are involved in metabolic pathways of the fungus and are important for carbon, phosphorous and nitrogen uptake, and for the fungal growth. Thereby, important proteins for fungi are also involved in the formation and stabilization of the biogenic AgNPs.
Electronic supplementary material
The online version of this article (doi:10.1186/s11671-016-1538-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s11671-016-1538-y
PMCID: PMC4927534  PMID: 27356560
Biogenic silver nanoparticles (AgNPs); Capping proteins; Aspergillus tubingensis
23.  ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles 
Scientific Reports  2016;6:28268.
Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation —with Protein Blocks—, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the ‘Hard’ category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/.
doi:10.1038/srep28268
PMCID: PMC4913311  PMID: 27319297
24.  Measurement of the centrality dependence of the charged-particle pseudorapidity distribution in proton–lead collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s_{_\text {NN}}} = 5.02$$\end{document}sNN=5.02 TeV with the ATLAS detector 
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The centrality dependence of the mean charged-particle multiplicity as a function of pseudorapidity is measured in approximately 1 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu $$\end{document}μb\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{-1}$$\end{document}-1 of proton–lead collisions at a nucleon–nucleon centre-of-mass energy of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s_{_\text {NN}}} = 5.02$$\end{document}sNN=5.02 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {TeV}$$\end{document}TeV using the ATLAS detector at the Large Hadron Collider. Charged particles with absolute pseudorapidity less than 2.7 are reconstructed using the ATLAS pixel detector. The collision centrality is characterised by the total transverse energy measured in the Pb-going direction of the forward calorimeter. The charged-particle pseudorapidity distributions are found to vary strongly with centrality, with an increasing asymmetry between the proton-going and Pb-going directions as the collisions become more central. Three different estimations of the number of nucleons participating in the collision have been carried out using the Glauber model as well as two Glauber–Gribov inspired extensions to the Glauber model. Charged-particle multiplicities per participant pair are found to vary differently for these three models, highlighting the importance of including colour fluctuations in nucleon–nucleon collisions in the modelling of the initial state of collisions.
doi:10.1140/epjc/s10052-016-4002-3
PMCID: PMC5312138
25.  AN ARTERIAL BASED COMPLEXITY (ABC) SCORING SYSTEM TO ASSESS THE MORBIDITY PROFILE OF PARTIAL NEPHRECTOMY 
European urology  2015;69(1):72-79.
Background
Tumor characteristics affect surgical complexity and outcomes of partial nephrectomy (PN).
Objective
To develop an Arterial Based Complexity (ABC) scoring system to predict morbidity of PN.
Design, Setting, and Participants
Four readers independently scored contrast-enhanced computed tomography images of 179 patients who underwent PN.
Intervention
Renal cortical masses were categorized by the order of vessels needed to be transected/dissected during PN. Scores of 1, 2, 3S, or 3H were assigned to tumors requiring transection of interlobular and arcuate arteries, interlobar arteries, segmental arteries, or in close proximity of the renal hilum, respectively during PN.
Outcome Measurements and Statistical Analysis
Interobserver variability was assessed with kappa values and percentage of exact matches between each pairwise combination of readers. Linear regression was used to evaluate the association between reference scores and ischemia time, estimated blood loss, and estimated glomerular filtration rates (eGFR) at 6 wk and 6 mo after surgery adjusted for baseline eGFR. Fisher’s exact test was used to test for differences in risk of urinary fistula formation by reference category assignment.
Results and Limitations
Pairwise comparisons of readers’ score assignments were significantly correlated (all p <0.0001); average kappa = 0.545 across all reader pairs. The average proportion of exact matches was 69%. Linear regression between the complexity score system and surgical outcomes showed significant associations between reference category assignments and ischemia time (p <0.0001) and estimated blood loss (p = 0.049). Fisher’s exact test showed a significant difference in risk of urinary fistula formation with higher reference category assignments (p = 0.028). Limitations include use of a single institutional cohort to evaluate our system.
Conclusions
The ABC scoring system for PN is intuitive, easy to use, and demonstrated good correlation with perioperative morbidity.
Patient Summary
The ABC scoring system is novel anatomy-reproducible tool developed to help patients and doctors understand the complexity of renal masses and predict the outcomes of kidney surgery.
doi:10.1016/j.eururo.2015.08.008
PMCID: PMC4826765  PMID: 26298208
kidney neoplasms; nephrometry; observer variation; outcome assessment; partial nephrectomy

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