Geometry-induced asymmetric diffusion

Past work has shown that ions can pass through a membrane more readily in one direction than the other. We demonstrate here in a model and an experiment that for a mixture of small and large particles such asymmetric diffusion can arise solely from an asymmetry in the geometry of the pores of the membrane. Our deterministic simulation considers a two-dimensional gas of elastic disks of two sizes diffusing through a membrane, and our laboratory experiment examines the diffusion of glass beads of two sizes through a metal membrane. In both experiment and simulation, the membrane is permeable only to the smaller particles, and the asymmetric pores lead to an asymmetry in the diffusion rates of these particles. The presence of even a small percentage of large particles can clog a membrane, preventing passage of the small particles in one direction while permitting free flow of the small particles in the other direction. The purely geometric kinetic constraints may play a role in common biological contexts such as membrane ion channels.Comment: published with minuscule change

Urine peptidomic biomarkers for diagnosis of patients with systematic lupus erythematosus

Background: Systematic lupus erythematosus (SLE) is characterized with various complications which can cause serious organ damage in the human body. Despite the significant improvements in disease management of SLE patients, the non-invasive diagnosis is entirely missing. In this study, we used urinary peptidomic biomarkers for early diagnosis of disease onset to improve patient risk stratification, vital for effective drug treatment. Methods: Urine samples from patients with SLE, lupus nephritis (LN) and healthy controls (HCs) were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS) for state-of-the-art biomarker discovery. Results: A biomarker panel made up of 65 urinary peptides was developed that accurately discriminated SLE without renal involvement from HC patients. The performance of the SLE-specific panel was validated in a multicentric independent cohort consisting of patients without SLE but with different renal disease and LN. This resulted in an area under the receiver operating characteristic (ROC) curve (AUC) of 0.80 (p < 0.0001, 95% confidence interval (CI) 0.65–0.90) corresponding to a sensitivity and a specificity of 83% and 73%, respectively. Based on the end terminal amino acid sequences of the biomarker peptides, an in silico methodology was used to identify the proteases that were up or down-regulated. This identified matrix metalloproteinases (MMPs) as being mainly responsible for the peptides fragmentation. Conclusions: A laboratory-based urine test was successfully established for early diagnosis of SLE patients. Our approach determined the activity of several proteases and provided novel molecular information that could potentially influence treatment efficacy

Pelaksanaan Fungsi Aparat Pengawas Intern Pemerintah (Apip) Untuk Menunjang Tingkat Kewajaran Laporan Keuangan Pemerintah Kota Manado

Internal Audit is the whole process of audit activities, the Review, evaluation, monitoring and supervisory activities other against the implementation of tasks and functions of the organization in order to provide reasonable assurance that the activities have been carried out in accordance with the benchmarks that have been set effectively and efficiently for the benefit of the leadership to Realize good governance.Accountability and transparency in the new government could be achieved if all levels of leadership controlling activities on the overall activities in their respective agencies . Internal control system ( SPI ) is a process that is integral to the actions and activities carried out continuously by the management and all employees to provide reasonable assurance on the achievement of organizational goals through effective and efficient , the reliability of financial reporting , the safeguarding of state assets, and compliance with legislation. To strengthen and support the effectiveness of internal control over the SPI made ​​implementation of tasks and functions of government agencies including state audits carried out by the internal control official Government ( APIP ) .The auditor\u27s responsibility to detect fraud or irregularity embodied in the planning and execution to obtain reasonable assurance about whether the financial statements have been prepared in accordance with established standards.The purpose of this study was to analyze the functions of Government Internal Supervisory Apparatus (APIP) / Internal Auditor in supporting reasonable levels of Local Government Finance Report Manado City. Respondents were selected are few skilled examiner at the office of the Inspectorate of Manado. Approach Using Qualitative methods Ethnography.APIP functions that work well to prevent fraud , to produce valuable output to be input to the external auditor , the executive and the legislature to improve financial management and accountability in the area of ​​the future . Eksternal Auditor may use the results from the monitoring APIP mainly reviews the financial statements of the government , supporting the management of local government in implementing the recommendations and improvements Internal control system . APIP professional and independent encourage increased transparency and accountability in financial management to improve the fairness of the financial statements

Correlation studies of open and closed states fluctuations in an ion channel: Analysis of ion current through a large conductance locust potassium channel

Ion current fluctuations occurring within open and closed states of large conductance locust potassium channel (BK channel) were investigated for the existence of correlation. Both time series, extracted from the ion current signal, were studied by the autocorrelation function (AFA) and the detrended fluctuation analysis (DFA) methods. The persistent character of the short- and middle-range correlations of time series is shown by the slow decay of the autocorrelation function. The DFA exponent $\alpha$ is significantly larger than 0.5. The existence of strongly-persistent long-range correlations was detected only for closed-states fluctuations, with $\alpha=0.98\pm0.02$. The long-range correlation of the BK channel action is therefore determined by the character of closed states. The main outcome of this study is that the memory effect is present not only between successive conducting states of the channel but also independently within the open and closed states themselves. As the ion current fluctuations give information about the dynamics of the channel protein, our results point to the correlated character of the protein movement regardless whether the channel is in its open or closed state.Comment: 12 pages, 5 figures; to be published in Phys. Rev.

Rectification in synthetic conical nanopores: a one-dimensional Poisson-Nernst-Planck modeling

Ion transport in biological and synthetic nanochannels is characterized by phenomena such as ion current fluctuations and rectification. Recently, it has been demonstrated that nanofabricated synthetic pores can mimic transport properties of biological ion channels [P. Yu. Apel, {\it et al.}, Nucl. Instr. Meth. B {\bf 184}, 337 (2001); Z. Siwy, {\it et al.}, Europhys. Lett. {\bf 60}, 349 (2002)]. Here, the ion current rectification is studied within a reduced 1D Poisson-Nernst-Planck (PNP) model of synthetic nanopores. A conical channel of a few $\mathrm{nm}$ to a few hundred of nm in diameter, and of few $\mu$m long is considered in the limit where the channel length considerably exceeds the Debye screening length. The rigid channel wall is assumed to be weakly charged. A one-dimensional reduction of the three-dimensional problem in terms of corresponding entropic effects is put forward. The ion transport is described by the non-equilibrium steady-state solution of the 1D Poisson-Nernst-Planck system within a singular perturbation treatment. An analytic formula for the approximate rectification current in the lowest order perturbation theory is derived. A detailed comparison between numerical results and the singular perturbation theory is presented. The crucial importance of the asymmetry in the potential jumps at the pore ends on the rectification effect is demonstrated. This so constructed 1D theory is shown to describe well the experimental data in the regime of small-to-moderate electric currents.Comment: 27 pages, 7 figure

Proteomics as a quality control tool of pharmaceutical probiotic bacterial lysate products

Probiotic bacteria have a wide range of applications in veterinary and human therapeutics. Inactivated probiotics are complex samples and quality control (QC) should measure as many molecular features as possible. Capillary electrophoresis coupled to mass spectrometry (CE/MS) has been used as a multidimensional and high throughput method for the identification and validation of biomarkers of disease in complex biological samples such as biofluids. In this study we evaluate the suitability of CE/MS to measure the consistency of different lots of the probiotic formulation Pro-Symbioflor which is a bacterial lysate of heat-inactivated Escherichia coli and Enterococcus faecalis. Over 5000 peptides were detected by CE/MS in 5 different lots of the bacterial lysate and in a sample of culture medium. 71 to 75% of the total peptide content was identical in all lots. This percentage increased to 87–89% when allowing the absence of a peptide in one of the 5 samples. These results, based on over 2000 peptides, suggest high similarity of the 5 different lots. Sequence analysis identified peptides of both E. coli and E. faecalis and peptides originating from the culture medium, thus confirming the presence of the strains in the formulation. Ontology analysis suggested that the majority of the peptides identified for E. coli originated from the cell membrane or the fimbrium, while peptides identified for E. faecalis were enriched for peptides originating from the cytoplasm. The bacterial lysate peptides as a whole are recognised as highly conserved molecular patterns by the innate immune system as microbe associated molecular pattern (MAMP). Sequence analysis also identified the presence of soybean, yeast and casein protein fragments that are part of the formulation of the culture medium. In conclusion CE/MS seems an appropriate QC tool to analyze complex biological products such as inactivated probiotic formulations and allows determining the similarity between lots

Voltage-controlled current loops with nanofluidic diodes electrically coupled to solid state capacitors

[EN] We describe experimentally and theoretically voltage-controlled current loops obtained with nanofluidic diodes immersed in aqueous salt solutions. The coupling of these soft matter diodes with conventional electronic elements such as capacitors permits simple equivalent circuits which show electrical properties reminiscent of a resistor with memory. Different conductance levels can be reproducibly achieved under a wide range of experimental conditions (input voltage amplitudes and frequencies, load capacitances, electrolyte concentrations, and single pore and multipore membranes) by electrically coupling two types of passive components: the nanopores (ionics) and the capacitors (electronics). Remarkably, these electrical characteristics do not result from slow ionic redistributions within the nanopores, which should be difficult to control and would give only small conductance changes, but arise from the robust collective response of equivalent circuits. Coupling nanoscale diodes with conventional electronic elements allows interconverting ionic and electronic currents, which should be useful for electrochemical signal processing and energy conversion based on charge transport.Support from the Ministry of Economic Affairs and Competitiveness and FEDER (project MAT2015-65011-P), the Generalitat Valenciana (project Prometeo/GV/0069 for Groups of Excellence). M. A, S. N. and W. E acknowledge the funding from the Hessen State Ministry of Higher Education, Research and the Arts, Germany, in the frame of LOEWE project iNAPO. Z. S. acknowledges the funding from the National Science Foundation (CHE 1306058).Ramirez Hoyos, P.; Gómez Lozano, V.; Cervera, J.; Nasir, S.; Ali, M.; Ensinger, W.; Siwy, Z.... (2016). Voltage-controlled current loops with nanofluidic diodes electrically coupled to solid state capacitors. RSC Advances. 6(60):54742-54746. https://doi.org/10.1039/c6ra08277gS5474254746660Fologea, D., Krueger, E., Mazur, Y. I., Stith, C., Okuyama, Y., Henry, R., & Salamo, G. J. (2011). Bi-stability, hysteresis, and memory of voltage-gated lysenin channels. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1808(12), 2933-2939. doi:10.1016/j.bbamem.2011.09.005Pustovoit, M. A., Berezhkovskii, A. M., & Bezrukov, S. M. (2006). Analytical theory of hysteresis in ion channels: Two-state model. The Journal of Chemical Physics, 125(19), 194907. doi:10.1063/1.2364898Ramirez, P., Cervera, J., Ali, M., Ensinger, W., & Mafe, S. (2014). Logic Functions with Stimuli-Responsive Single Nanopores. ChemElectroChem, 1(4), 698-705. doi:10.1002/celc.201300255Martin, C. R., & Siwy, Z. S. (2007). CHEMISTRY: Learning Nature’s Way: Biosensing with Synthetic Nanopores. Science, 317(5836), 331-332. doi:10.1126/science.1146126Hou, X., & Jiang, L. (2009). Learning from Nature: Building Bio-Inspired Smart Nanochannels. ACS Nano, 3(11), 3339-3342. doi:10.1021/nn901402bZhang, H., Tian, Y., & Jiang, L. (2016). Fundamental studies and practical applications of bio-inspired smart solid-state nanopores and nanochannels. Nano Today, 11(1), 61-81. doi:10.1016/j.nantod.2015.11.001Chun, H., & Chung, T. D. (2015). Iontronics. Annual Review of Analytical Chemistry, 8(1), 441-462. doi:10.1146/annurev-anchem-071114-040202Tagliazucchi, M., & Szleifer, I. (2015). Transport mechanisms in nanopores and nanochannels: can we mimic nature? Materials Today, 18(3), 131-142. doi:10.1016/j.mattod.2014.10.020Misra, N., Martinez, J. A., Huang, S.-C. J., Wang, Y., Stroeve, P., Grigoropoulos, C. P., & Noy, A. (2009). Bioelectronic silicon nanowire devices using functional membrane proteins. Proceedings of the National Academy of Sciences, 106(33), 13780-13784. doi:10.1073/pnas.0904850106Senapati, S., Basuray, S., Slouka, Z., Cheng, L.-J., & Chang, H.-C. (2011). A Nanomembrane-Based Nucleic Acid Sensing Platform for Portable Diagnostics. Topics in Current Chemistry, 153-169. doi:10.1007/128_2011_142Haywood, D. G., Saha-Shah, A., Baker, L. A., & Jacobson, S. C. (2014). Fundamental Studies of Nanofluidics: Nanopores, Nanochannels, and Nanopipets. Analytical Chemistry, 87(1), 172-187. doi:10.1021/ac504180hPérez-Mitta, G., Tuninetti, J. S., Knoll, W., Trautmann, C., Toimil-Molares, M. E., & Azzaroni, O. (2015). Polydopamine Meets Solid-State Nanopores: A Bioinspired Integrative Surface Chemistry Approach To Tailor the Functional Properties of Nanofluidic Diodes. Journal of the American Chemical Society, 137(18), 6011-6017. doi:10.1021/jacs.5b01638Ali, M., Nasir, S., Ramirez, P., Ahmed, I., Nguyen, Q. H., Fruk, L., … Ensinger, W. (2011). Optical Gating of Photosensitive Synthetic Ion Channels. Advanced Functional Materials, 22(2), 390-396. doi:10.1002/adfm.201102146Ali, M., Nasir, S., Ramirez, P., Cervera, J., Mafe, S., & Ensinger, W. (2013). Carbohydrate-Mediated Biomolecular Recognition and Gating of Synthetic Ion Channels. The Journal of Physical Chemistry C, 117(35), 18234-18242. doi:10.1021/jp4054555Ali, M., Ahmed, I., Nasir, S., Ramirez, P., Niemeyer, C. M., Mafe, S., & Ensinger, W. (2015). Ionic Transport through Chemically Functionalized Hydrogen Peroxide-Sensitive Asymmetric Nanopores. ACS Applied Materials & Interfaces, 7(35), 19541-19545. doi:10.1021/acsami.5b06015Albrecht, T. (2011). How to Understand and Interpret Current Flow in Nanopore/Electrode Devices. ACS Nano, 5(8), 6714-6725. doi:10.1021/nn202253zLemay, S. G. (2009). Nanopore-Based Biosensors: The Interface between Ionics and Electronics. ACS Nano, 3(4), 775-779. doi:10.1021/nn900336jGomez, V., Ramirez, P., Cervera, J., Nasir, S., Ali, M., Ensinger, W., & Mafe, S. (2015). Charging a Capacitor from an External Fluctuating Potential using a Single Conical Nanopore. Scientific Reports, 5(1). doi:10.1038/srep09501Ramirez, P., Gomez, V., Cervera, J., Nasir, S., Ali, M., Ensinger, W., & Mafe, S. (2015). Energy conversion from external fluctuating signals based on asymmetric nanopores. Nano Energy, 16, 375-382. doi:10.1016/j.nanoen.2015.07.013Tybrandt, K., Forchheimer, R., & Berggren, M. (2012). Logic gates based on ion transistors. Nature Communications, 3(1). doi:10.1038/ncomms1869Apel, P. (2001). Track etching technique in membrane technology. Radiation Measurements, 34(1-6), 559-566. doi:10.1016/s1350-4487(01)00228-1Cervera, J., Schiedt, B., Neumann, R., Mafé, S., & Ramírez, P. (2006). Ionic conduction, rectification, and selectivity in single conical nanopores. The Journal of Chemical Physics, 124(10), 104706. doi:10.1063/1.2179797Ali, M., Ramirez, P., Mafé, S., Neumann, R., & Ensinger, W. (2009). A pH-Tunable Nanofluidic Diode with a Broad Range of Rectifying Properties. ACS Nano, 3(3), 603-608. doi:10.1021/nn900039fRamirez, P., Gomez, V., Verdia-Baguena, C., Nasir, S., Ali, M., Ensinger, W., & Mafe, S. (2016). Designing voltage multipliers with nanofluidic diodes immersed in aqueous salt solutions. Physical Chemistry Chemical Physics, 18(5), 3995-3999. doi:10.1039/c5cp07203dWang, D., Kvetny, M., Liu, J., Brown, W., Li, Y., & Wang, G. (2012). Transmembrane Potential across Single Conical Nanopores and Resulting Memristive and Memcapacitive Ion Transport. Journal of the American Chemical Society, 134(8), 3651-3654. doi:10.1021/ja211142eMomotenko, D., & Girault, H. H. (2011). Scan-Rate-Dependent Ion Current Rectification and Rectification Inversion in Charged Conical Nanopores. Journal of the American Chemical Society, 133(37), 14496-14499. doi:10.1021/ja2048368Zhang, A., & Lieber, C. M. (2015). Nano-Bioelectronics. Chemical Reviews, 116(1), 215-257. doi:10.1021/acs.chemrev.5b0060

Principles of Small-Molecule Transport through Synthetic Nanopores

Synthetic nanopores made from DNA replicate the key biological processes of transporting molecular cargo across lipid bilayers. Understanding transport across the confined lumen of the nanopores is of fundamental interest and of relevance to their rational design for biotechnological applications. Here we reveal the transport principles of organic molecules through DNA nanopores by synergistically combining experiments and computer simulations. Using a highly parallel nanostructured platform, we synchronously measure the kinetic flux across hundreds of individual pores to obtain rate constants. The single-channel transport kinetics are close to the theoretical maximum, while selectivity is determined by the interplay of cargo charge and size, the pores' sterics and electrostatics, and the composition of the surrounding lipid bilayer. The narrow distribution of transport rates implies a high structural homogeneity of DNA nanopores. The molecular passageway through the nanopore is elucidated via coarse-grained constant-velocity steered molecular dynamics simulations. The ensemble simulations pinpoint with high resolution and statistical validity the selectivity filter within the channel lumen and determine the energetic factors governing transport. Our findings on these synthetic pores' structure-function relationship will serve to guide their rational engineering to tailor transport selectivity for cell biological research, sensing, and drug delivery

Local solid-state modification of nanopore surface charges

The last decade, nanopores have emerged as a new and interesting tool for the study of biological macromolecules like proteins and DNA. While biological pores, especially alpha-hemolysin, have been promising for the detection of DNA, their poor chemical stability limits their use. For this reason, researchers are trying to mimic their behaviour using more stable, solid-state nanopores. The most successful tools to fabricate such nanopores use high energy electron or ions beams to drill or reshape holes in very thin membranes. While the resolution of these methods can be very good, they require tools that are not commonly available and tend to damage and charge the nanopore surface. In this work, we show nanopores that have been fabricated using standard micromachning techniques together with EBID, and present a simple model that is used to estimate the surface charge. The results show that EBID with a silicon oxide precursor can be used to tune the nanopore surface and that the surface charge is stable over a wide range of concentrations.Comment: 10 pages, 6 figure

Exact formula for currents in strongly pumped diffusive systems

We analyze a generic model of mesoscopic machines driven by the nonadiabatic variation of external parameters. We derive a formula for the probability current; as a consequence we obtain a no-pumping theorem for cyclic processes satisfying detailed balance and demonstrate that the rectification of current requires broken spatial symmetry.Comment: 10 pages, accepted for publication in the Journal of Statistical Physic