Assessment of Biotransformed Silica Nanoparticle on Blood Glucose Level in Human: An In Vitro Investigation.

Diabetes has affected nearly half a billion people worldwide. According to current guidelines, glycemic control is essential to mitigate diabetic complications. The antihyperglycemic effects of various chemically synthesized nanoparticles have been reported in animal models. However, their impact on humans has not been previously reported. This study was conducted to biosynthesize and assess the antihyperglycemic property of silica nanoparticles (SiO2-NPs) since they are non-toxic and biocompatible. SiO2-NPs biosynthesized using the endophytic fungus Fusarium oxysporum. In this collaborative study, 26 people, either hyperglycemic or euglycemic, diagnosed at the Endocrinology Outpatients, according to the American Diabetes Association, USA, were recruited. Silica nanoparticles were characterized and assessed for in vitro antihyperglycemic property using blood samples. Particle size distribution based on TEM images confirms that the average size of silica nanoparticle is 25 nm and is monodispersed in nature. The XRD pattern shows that only one broad peak at 2θ = 220 corresponds to the plane (101) of silica nanoparticles. UV Visible spectra show the λmax at 270 nm, peaks in FTIR at 1536 cm-1, 1640 cm-1, and 3420 cm-1 for the protein cap. The mean blood glucose was 120.2 mg/dL in the 'SiO2-NP untreated' group and decreased to 97.24 mg/dL in the 'SiO2-NP treated' group. A paired t-test (P-value < 0.0001) indicates a strong relationship between antihyperglycemia and silica NP. In our study, it has been observed that the biosynthesized silica nanoparticles using the endophytic fungus Fusarium oxysporum show antihyperglycemic property in vitro.

Single nucleotide variants of receptor for advanced glycation end-products (AGER) gene: is it a new opening in the risk assessment of diabetic retinopathy?-a review.

BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes. There is strong evidence suggesting that DR has an inheritable component. The interaction between advanced glycation end products (AGEs) and their receptor is integral in the pathogenesis of diabetic retinopathy and its various complications, retinopathy being one of them. OVERVIEW AND METHODOLOGY: This review discusses the existing literature on the association between single nucleotide variants (SNV) of AGER gene and the risk of DR. It also discusses the current understanding of the AGE-AGER pathway in diabetic retinopathy. Through our article we have tried to consolidate all the available information about these SNVs associated with diabetic retinopathy in a succinct tabular form. Additionally, a current understanding of the AGE-AGER interaction and its deleterious effects on the cells of the retina has been discussed in detail to provide comprehensive information about the topic to the reader. A literature review was performed on PubMed, Cochrane Library, and Google Scholar for studies to find existing literature on the association between AGER gene SNVs and the risk, progression and severity of developing DR. This article will encourage scientific communication and discussion about possibly devising genetic markers for an important cause of blindness both in developed and developing countries, i.e., diabetic retinopathy. RESULT: Based on genetic studies done in Indian and Chinese population G82S(rs2070600) was positively associated with Diabetic Retinopathy. Patients of diabetic retinopathy in Caucasian population had -T374A(rs1800624) polymorphism. + 20T/A was found to be associated with the disease in a study done in UK. Association with G1704T(rs184003) was seen in Chinese and Malaysian population. A Chinese study found its association with CYB242T. -T429C(rs1800625) SNV was not associated with DR in any of the studies. G2245A(rs55640627) was positively associated with the disease process in Malaysian population. It was not associated in Malaysian and Chinese population. Promoter variant rs1051993 has also been found to a susceptible SNV in the Chinese population. CONCLUSION: While providing a comprehensive review of the existing information, we would like to emphasize on a large, multi-centric, trial with a much larger and varied population base to definitely determine these single nucleotide variants predisposing diabetic individuals.

Di-(2-ethylhexyl) phthalate triggers DNA methyltransferase 1 expression resulting in elevated CpG-methylation and enrichment of MECP2 in the p21 promoter in vitro.

Leaching of the plastic constituents leading to their chronic exposure to humans is a major concern for our environmental and occupational health. Our previous and other numerous studies have demonstrated that environmental chemicals like di (2-Ethylhexyl)-phthalate (DEHP) could pose a risk towards the epigenetic mechanisms. Yet, the mechanisms underlying its possible epigenotoxicity are poorly understood. We aimed to assess the impact of DEHP exposure to the human breast cancer cells (MCF-7) and resultant changes in DNA methylation regulators ultimately altering the expression of the cell cycle regulator p21 as a model gene. The MCF-7 cells were exposed to environmentally relevant concentrations (50-500 nM) for 24 h. The results showed that DEHP was proliferative towards the MCF-7 cells while it induced global DNA hypermethylation with selective upregulation of DNMT1 and MECP2. In addition, DEHP significantly reduced p53 protein and its enrichment to the DNMT1 promoter binding site, while elevating SP1 and E2F1 transcription factor levels, stimulating their binding to the promoter DNA. Coincidently, increased DNMT1 level was highly associated with loss of p21 expression and increased cyclin D1 levels. Importantly, the p21, but not cyclin D1 promoter CpG-dinucleotides were hypermethylated after exposure to 500 nM DEHP for 24 h. Furthermore, it was observed that DEHP significantly enriched DNMT1 and MECP2 to the p21 promoter to induce DNA methylation-based epigenetic silencing of p21, resulting in increased cell proliferation. Our results suggest DEHP could potentially induce the epigenetic alterations that might increase the risk of breast cancer, given that the underlying mechanisms should be fully elucidated.

Draft Genome Sequences of 72 Isolates from All Four Species of Shigella.

Shigella is a genus of Gram-negative enteric pathogenic bacteria which has four species, Shigella dysenteriae, S. flexneri, S. boydii, and S. sonnei. Shigella species are clinically important bacteria because they cause shigellosis or dysentery. Here we report the genome sequences of 72 Shigella isolates from these four species.

Presence of quantum correlations results in a nonvanishing ergotropic gap.

The paradigm of extracting work from an isolated quantum system through a cyclic Hamiltonian process is a topic of immense research interest. The optimal work extracted under such a process is termed ergotropy [Europhys. Lett. 67, 565 (2004)]. Here, in a multiparty scenario, we consider only a class of such cyclic processes that can be implemented locally, giving rise to the concept of local ergotropy. Eventually, the presence of quantum correlations results in a nonvanishing thermodynamic quantity called an ergotropic gap, measured by the difference between global and local ergotropy. However, the converse does not hold in general, i.e., its nonzero value does not necessarily imply the presence of quantum correlations. For arbitrary multiparty states, we quantify this gap. We also evaluate the difference between maximum global and local extractable work for arbitrary states when the system is no longer isolated but put in contact with a bath of the same local temperature.

Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.

MOTIVATION: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. RESULTS: Thick rat brain sections (100-300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni's L-measure. Coifman's harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. AVAILABILITY AND IMPLEMENTATION: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors CONTACT: broysam@central.uh.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Efficient Degumming of Rice Bran Oil by Immobilized PLA1 from Thermomyces lanuginosus.

Phospholipase A1 (PLA1) immobilized in calcium alginate can effectively overcome the mass transfer resistance at the lipid-water interface making more room for the enzyme to separate itself from the products of reaction and to bind with the next available molecule at the interface. The reaction of an immobilized PLA1 hydrolase from Thermomyces lanuginosus was comparatively faster than of its free form. The rate of phospholipid hydrolysis by PLA1 was studied in calcium-rich and calcium-depleted environments; and the extent of phosphorus removed from the crude rice bran oil as well as the amount of free fatty acids produced during the reaction were used as indices for analysing the rate of enzymatic hydrolysis under standard conditions of pH, temperature, time of incubation and agitation. The immobilized PLA1 was found to be superior in removing phosphorus in the presence of 10 mM bivalent calcium ions in a solution. As compared to a maximum of 72.52% phosphorus removed by 0.01 kg of free enzyme per kg of oil, the same amount of immobilized PLA1 removed phosphorus from oil by 94.12% under the same experimental conditions (pH=6, 60 °C, 1-hour incubation). Both the free PLA1 and its immobilized form had shown extended rates of hydrolysis in a calcium-rich environment. The mass fractions of free fatty acids produced by the free enzyme and by its immobilized form were 14.9 and 14.16%, respectively, under the above experimental conditions. The removal of phosphorus from oil was accompanied by a significant reduction in colour and restoration of iodine value to the desired level.

Catheter-free discharge on first postoperative day after bipolar transurethral resection of prostate: clinical outcomes of 100 cases.

OBJECTIVES: Our center has adopted a protocol for catheter-free first postoperative day discharge after bipolar transurethral resection of the prostate. We present the immediate, 1-month and 6-month outcomes of our first 100 cases following this protocol. METHODS: All bipolar transurethral resection of the prostate patients followed the protocol regardless of indications and background comorbid conditions. Bladder irrigation was stopped in the evening after transurethral resection of the prostate, and the catheter was removed at 06.00 hours. All patients were discharged on the first postoperative day. They were reviewed at 1 month and 6 months with the International Prostate Symptom Score and uroflowmetry. RESULTS: The mean age of the study population was 70.8 years. A total of 40 patients had urinary retention and were on an indwelling catheter before transurethral resection of the prostate. A total of 14 patients had other surgeries in the same setting as the transurethral resection of the prostate. The mean resection weight was 32.7 g. The mean irrigation time and catheter time were 4.2 h and 15.0 h, respectively. The improvement in terms of International Prostate Symptom Score, quality of life score, peak flow rate and post-void residual volume was comparable with those reported in the literature for bipolar transurethral resection of the prostate. Similarly, early and late complication rates also compared favorably with the literature. The perioperative cost was significantly reduced. CONCLUSIONS: Catheter-free first postoperative day discharge after bipolar transurethral resection of the prostate is safe with good clinical outcomes and cost savings.

Genetic analysis of the roles of agaA, agaI, and agaS genes in the N-acetyl-D-galactosamine and D-galactosamine catabolic pathways in Escherichia coli strains O157:H7 and C.

BACKGROUND: The catabolic pathways of N-acetyl-D-galactosamine (Aga) and D-galactosamine (Gam) in E. coli were proposed from bioinformatic analysis of the aga/gam regulon in E. coli K-12 and later from studies using E. coli C. Of the thirteen genes in this cluster, the roles of agaA, agaI, and agaS predicted to code for Aga-6-P-deacetylase, Gam-6-P deaminase/isomerase, and ketose-aldolase isomerase, respectively, have not been experimentally tested. Here we study their roles in Aga and Gam utilization in E. coli O157:H7 and in E. coli C. RESULTS: Knockout mutants in agaA, agaI, and agaS were constructed to test their roles in Aga and Gam utilization. Knockout mutants in the N-acetylglucosamine (GlcNAc) pathway genes nagA and nagB coding for GlcNAc-6-P deacetylase and glucosamine-6-P deaminase/isomerase, respectively, and double knockout mutants ΔagaA ΔnagA and ∆agaI ∆nagB were also constructed to investigate if there is any interplay of these enzymes between the Aga/Gam and the GlcNAc pathways. It is shown that Aga utilization was unaffected in ΔagaA mutants but ΔagaA ΔnagA mutants were blocked in Aga and GlcNAc utilization. E. coli C ΔnagA could not grow on GlcNAc but could grow when the aga/gam regulon was constitutively expressed. Complementation of ΔagaA ΔnagA mutants with either agaA or nagA resulted in growth on both Aga and GlcNAc. It was also found that ΔagaI, ΔnagB, and ∆agaI ΔnagB mutants were unaffected in utilization of Aga and Gam. Importantly, ΔagaS mutants were blocked in Aga and Gam utilization. Expression analysis of relevant genes in these strains with different genetic backgrounds by real time RT-PCR supported these observations. CONCLUSIONS: Aga utilization was not affected in ΔagaA mutants because nagA was expressed and substituted for agaA. Complementation of ΔagaA ΔnagA mutants with either agaA or nagA also showed that both agaA and nagA can substitute for each other. The ∆agaI, ∆nagB, and ∆agaI ∆nagB mutants were not affected in Aga and Gam utilization indicating that neither agaI nor nagB is involved in the deamination and isomerization of Gam-6-P. We propose that agaS codes for Gam-6-P deaminase/isomerase in the Aga/Gam pathway.

Automated Reconstruction of Neural Trees Using Front Re-initialization.

This paper proposes a greedy algorithm for automated reconstruction of neural arbors from light microscopy stacks of images. The algorithm is based on the minimum cost path method. While the minimum cost path, obtained using the Fast Marching Method, results in a trace with the least cumulative cost between the start and the end points, it is not sufficient for the reconstruction of neural trees. This is because sections of the minimum cost path can erroneously travel through the image background with undetectable detriment to the cumulative cost. To circumvent this problem we propose an algorithm that grows a neural tree from a specified root by iteratively re-initializing the Fast Marching fronts. The speed image used in the Fast Marching Method is generated by computing the average outward flux of the gradient vector flow field. Each iteration of the algorithm produces a candidate extension by allowing the front to travel a specified distance and then tracking from the farthest point of the front back to the tree. Robust likelihood ratio test is used to evaluate the quality of the candidate extension by comparing voxel intensities along the extension to those in the foreground and the background. The qualified extensions are appended to the current tree, the front is re-initialized, and Fast Marching is continued until the stopping criterion is met. To evaluate the performance of the algorithm we reconstructed 6 stacks of two-photon microscopy images and compared the results to the ground truth reconstructions by using the DIADEM metric. The average comparison score was 0.82 out of 1.0, which is on par with the performance achieved by expert manual tracers.

Automated kymograph analysis for profiling axonal transport of secretory granules.

This paper describes an automated method to profile the velocity patterns of small organelles (BDNF granules) being transported along a selected section of axon of a cultured neuron imaged by time-lapse fluorescence microscopy. Instead of directly detecting the granules as in conventional tracking, the proposed method starts by generating a two-dimensional spatio-temporal map (kymograph) of the granule traffic along an axon segment. Temporal sharpening during the kymograph creation helps to highlight granule movements while suppressing clutter due to stationary granules. A voting algorithm defined over orientation distribution functions is used to refine the locations and velocities of the granules. The refined kymograph is analyzed using an algorithm inspired from the minimum set cover framework to generate multiple motion trajectories of granule transport paths. The proposed method is computationally efficient, robust to significant levels of noise and clutter, and can be used to capture and quantify trends in transport patterns quickly and accurately. When evaluated on a collection of image sequences, the proposed method was found to detect granule movement events with 94% recall rate and 82% precision compared to a time-consuming manual analysis. Further, we present a study to evaluate the efficacy of velocity profiling by analyzing the impact of oxidative stress on granule transport in which the fully automated analysis correctly reproduced the biological conclusion generated by manual analysis.

A multistage system for the automated detection of epileptic seizures in neonatal electroencephalography.

This paper describes the design and test results of a three-stage automated system for neonatal EEG seizure detection. Stage I of the system is the initial detection stage and identifies overlapping 5-second segments of suspected seizure activity in each EEG channel. In stage II, the detected segments from stage I are spatiotemporally clustered to produce multichannel candidate seizures. In stage III, the candidate seizures are processed further using measures of quality and context-based rules to eliminate false candidates. False candidates because of artifacts and commonly occurring EEG background patterns such as bifrontal delta activity are also rejected. Seizures at least 10 seconds in duration are considered for reporting results. The testing data consisted of recordings of 28 seizure subjects (34 hours of data) and 48 nonseizure subjects (87 hours of data) obtained in the neonatal intensive care unit. The data were not edited to remove artifacts and were identical in every way to data normally processed visually. The system was able to detect seizures of widely varying morphology with an average detection sensitivity of almost 80% and a subject sensitivity of 96%, in comparison with a team of clinical neurophysiologists who had scored the same recordings. The average false detection rate obtained in nonseizure subjects was 0.74 per hour.

Investigation of regulation of FtsZ assembly by SulA and development of a model for FtsZ polymerization.

In Escherichia coli FtsZ organizes into a cytoskeletal ring structure, the Z ring, which effects cell division. FtsZ is a GTPase, but the free energy of GTP hydrolysis does not appear to be used for generation of the constriction force, leaving open the question of the function of the GTPase activity of FtsZ. Here we study the mechanism by which SulA, an inhibitor of FtsZ induced during the SOS response, inhibits FtsZ function. We studied the effects of SulA on the in vitro activities of FtsZ, on Z rings in vivo, and on a kinetic model for FtsZ polymerization in silico. We found that the binding of SulA to FtsZ is necessary but not sufficient for inhibition of polymerization, since the assembly of FtsZ polymers in the absence of the GTPase activity was not inhibited by SulA. We developed a new model for FtsZ polymerization that accounts for the cooperativity of FtsZ and could account for cooperativity observed in other linear polymers. When SulA was included in the kinetic scheme, simulations revealed that SulA with strong affinity for FtsZ delayed, but did not prevent, the assembly of polymers when they were not hydrolyzing GTP. Furthermore, the simulations indicated that SulA controls the assembly of FtsZ by binding to a polymerization-competent form of the FtsZ molecule and preventing it from participating in assembly. In vivo stoichiometry of the disruption of Z rings by SulA suggests that FtsZ may undergo two cooperative transitions in forming the Z ring.

Altered utilization of N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak.

In silico analyses of previously sequenced strains of Escherichia coli O157:H7, EDL933 and Sakai, localized the gene cluster for the utilization of N-acetyl-D-galactosamine (Aga) and D-galactosamine (Gam). This gene cluster encodes the Aga phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) and other catabolic enzymes responsible for transport and catabolism of Aga. As the complete coding sequences for enzyme IIA (EIIA)(Aga/Gam), EIIB(Aga), EIIC(Aga), and EIID(Aga) of the Aga PTS are present, E. coli O157:H7 strains normally are able to utilize Aga as a sole carbon source. The Gam PTS complex, in contrast, lacks EIIC(Gam), and consequently, E. coli O157:H7 strains cannot utilize Gam. Phenotypic analyses of 120 independent isolates of E. coli O157:H7 from our culture collection revealed that the overwhelming majority (118/120) displayed the expected Aga+ Gam- phenotype. Yet, when 194 individual isolates, derived from a 2006 spinach-associated E. coli O157:H7 outbreak, were analyzed, all (194/194) displayed an Aga- Gam- phenotype. Comparison of aga/gam sequences from two spinach isolates with those of EDL933 and Sakai revealed a single nucleotide change (G:C-->A:T) in the agaF gene in the spinach-associated isolates. The base substitution in agaF, which encodes EIIA(Aga/Gam) of the PTS, changes a conserved glycine residue to serine (Gly91Ser). Pyrosequencing of this region showed that all spinach-associated E. coli O157:H7 isolates harbored this same G:C-->A:T substitution. Notably, when agaF+ was cloned into an expression vector and transformed into six spinach isolates, all (6/6) were able to grow on Aga, thus demonstrating that the Gly91Ser substitution underlies the Aga- phenotype in these isolates.

Detection of pseudosinusoidal epileptic seizure segments in the neonatal EEG by cascading a rule-based algorithm with a neural network.

This paper presents an approach to detect epileptic seizure segments in the neonatal electroencephalogram (EEG) by characterizing the spectral features of the EEG waveform using a rule-based algorithm cascaded with a neural network. A rule-based algorithm screens out short segments of pseudosinusoidal EEG patterns as epileptic based on features in the power spectrum. The output of the rule-based algorithm is used to train and compare the performance of conventional feedforward neural networks and quantum neural networks. The results indicate that the trained neural networks, cascaded with the rule-based algorithm, improved the performance of the rule-based algorithm acting by itself. The evaluation of the proposed cascaded scheme for the detection of pseudosinusoidal seizure segments reveals its potential as a building block of the automated seizure detection system under development.

Exploring genotypic and phenotypic diversity of microbes using microarray approaches.

Application of genome-scale analysis like DNA microarray technology has revolutionized multiple scientific disciplines. Herein, a next generation of DNA microarrays, a DNA tiling approach that allows high throughput sampling of genomes with single-nucleotide precision, is described. As methods revealing a genomic scale examination of cellular phenotypes offer keen insights for genomic analyses, a high throughput system for whole cell phenotyping is similarly detailed. The merit of these technologies in discriminating pathogenic and commensal strains of microbes is emphasized using the microbe, Escherichia coli, as an example. Deployment of microarray strategies to assess closely-related microbial strains should help address diversity of organisms in their feral settings.

Molecular applications for identifying microbial pathogens in the post-9/11 era.

Rapid advances in molecular and optical technologies over the past 10 years have dramatically impacted the way biologic research is conducted today. Examples include microarrays, capillary sequencing, optical mapping and real-time sequencing (Pyrosequencing). These technologies are capable of rapidly delivering massive amounts of genetic information and are becoming routine mainstays of many laboratories. Fortunately, advances in scientific computing have provided the enormous computing power necessary to analyze these enormous data sets. The application of molecular technologies should prove useful to the burgeoning field of microbial forensics. In the post-9/11 era, when securing America's food supply is a major endeavor, the need for rapid identification of microbes that accidentally or intentionally find their way into foods is apparent. The principle that distinguishes a microbial forensic investigation from a molecular epidemiology study is that a biocrime has been committed. If proper attribution is to be attained, a link must be made between a particular microbe in the food and the perpetrator who placed it there. Therefore, the techniques used must be able to discriminate individual isolates of a particular microbe. A battery of techniques in development for distinguishing individual isolates of particular foodborne pathogens is discussed.