Elementary simulation of tethered Brownian motion

We describe a simple numerical simulation, suitable for an undergraduate project (or graduate problem set), of the Brownian motion of a particle in a Hooke-law potential well. Understanding this physical situation is a practical necessity in many experimental contexts, for instance in single molecule biophysics; and its simulation helps the student to appreciate the dynamical character of thermal equilibrium. We show that the simulation succeeds in capturing behavior seen in experimental data on tethered particle motion.Comment: Submitted to American Journal of Physic

Effect of a biological additive on nitrogen losses from pig slurry during storage

Additives applied to animal manure slurries can affect the chemical composition and the biological processes of slurries during storage, with possible improvement of their management and reduction of environmental problems. Some new formulations are marketed claiming a nitrogen (N) removal effect due to denitrification, with the consequence of a reduced N content in the manure after storage. This study evaluated the effects of one of these commercial additives (BACTYcomplex) on slurry characteristics and N losses at a commercial piggery. The additive was applied to four different sectors of the piggery, each with an independent under-floor slurry pit; four other sectors served as controls without treatment. Pits were emptied every 4 wk, and the manure was analyzed for total and ammonia-N and total and volatile solids. Slurry samples from the last month of the on-farm assessment were removed and stored thermostatically in vessels external to the piggery. A subsample of slurry that was treated with the additive at the piggery was treated with an additional dose of additive at the beginning of long-term storage. The additive did not change the composition of the slurry during in-house storage (4 wk duration). During the 155 d of external thermostatic storage, the total solids content of treated slurry was reduced by 18% compared with control slurry, but the N content and composition of treated slurry was unaffected. The additive had a positive effect in accelerating the stabilization of the slurry but did not modify N losses

Chronic Central Serous Chorioretinopathy with Pigment Epithelium Detachment Treated with Sildenafil: A Case Report

Central serous chorioretinopathy (CSCR) is a retinal disease that may be complicated by the development of serous retinal pigment epithelial detachment (PED). The exact molecular mechanisms of CSCR have remained uncertain as well as there is no effective medical therapy. Herein, we describe a case of a 43-year-old male suffering from chronic CSCR with PED and visual acuity reduction (20/40) that showed improvement in visual acuity (20/25) and metamorphopsia 2 weeks after daily intake of 20 mg sildenafil tablets. Optical coherence tomography (OCT) scan showed resolution of PED with residual degeneration of the photoreceptor inner and outer segment layer and retinal pigmented epithelium. The patient continued treatment with sildenafil 20 mg for 2 months. Six months after the discontinuation of therapy, visual acuity was maintained, with absence of PED at OCT. Our case supports the hypothesis that phosphodiesterase type 5 (PDE-5) inhibitors may be an alternative in the treatment of patients with CSCR, alone or combined with other medications

Mixed mucus-secreting and oncocytic carcinoma of the thyroid - Pathologic, histochemical, immunohistochemical, and ultrastructural study of a case

We report a carcinoma that is, to the best of our knowledge, the first case of a mixed mucus-secreting and oncocytic carcinoma of the thyroid. We also describe the histochemical, immunohistochemical, and ultrastructural features of this tumor. A 59-year-old man complaining of severe bone pain and weight loss underwent clinical and radiologic investigations. The studies revealed a nodule in the left thyroid lobe that was "cold" by (131)I scintiscan and multiple lytic lesions of the skeleton that showed increased uptake by (99m)Tc-Sestamibi scintiscan. Left hemithyroidectomy was performed and the surgical specimen contained a well-circumscribed nodule of 3 cm in the greatest diameter. Light microscopy showed an oncocytic carcinoma with an area of glandular and papillary proliferation of mucin-producing cells. A double histochemical approach (Alcian blue-periodic acid-Schiff and Alcian blue-high-iron diamine) combined with ultrastructural investigation confirmed the presence of true mucus, ruling out the presence of breakdown products of thyroglobulin. Ultrastructural and immunohistochemical studies, together with clinical findings, excluded a possible metastatic origin of the mucin-producing componen

Effect of short range order on electronic and magnetic properties of disordered Co based alloys

We here study electronic structure and magnetic properties of disordered CoPd and CoPt alloys using Augmented Space Recursion technique coupled with the tight-binding linearized muffin tin orbital (TB-LMTO) method. Effect of short range ordering present in disordered phase of alloys on electronic and magnetic properties has been discussed. We present results for magnetic moments, Curie temperatures and electronic band energies with varying degrees of short range order for different concentrations of Co and try to understand and compare the magnetic properties and ordering phenomena in these systems.Comment: 15 pages,17 postscript figures,uses own style file

Global climate change and tree nutrition: effects of elevated CO2 and temperature

Although tree nutrition has not been the primary focus of large climate change experiments on trees, we are beginning to understand its links to elevated atmospheric CO2 and temperature changes. This review focuses on the major nutrients, namely N and P, and deals with the effects of climate change on the processes that alter their cycling and availability. Current knowledge regarding biotic and abiotic agents of weathering, mobilization and immobilization of these elements will be discussed. To date, controlled environment studies have identified possible effects of climate change on tree nutrition. Only some of these findings, however, were verified in ecosystem scale experiments. Moreover, to be able to predict future effects of climate change on tree nutrition at this scale, we need to progress from studying effects of single factors to analysing interactions between factors such as elevated CO2, temperature or water availability

Tethered Particle Motion as a Diagnostic of DNA Tether Length

The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping

DNA Looping Kinetics Analyzed Using Diffusive Hidden Markov Model

Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this method is used to measure rate constants of DNA loop formation and breakdown mediated by repressor protein that binds to the DNA. We report a new technique for measuring these rates using a modified hidden Markov analysis that directly incorporates the diffusive motion of the bead, which is an inherent complication of tethered particle motion because it occurs on a time scale between the sampling frequency and the looping time. We compare looping lifetimes found with our method, which are consistent over a range of sampling frequencies, to those obtained via the traditional threshold-crossing analysis, which vary depending on how the raw data are filtered in the time domain. Our method does not involve such filtering, and so can detect short-lived looping events and sudden changes in looping behavior.Comment: 3 page pdf including 3 figures corrections: 2nd page, 1st column, values of diffusion coefficient, spring constant and the decay time were typed incorrectly. No conlcusions were affecte

A farm-scale pilot plant for biohydrogen and biomethane production by two-stage fermentation

Hydrogen is considered one of the possible main energy carriers for the future, thanks to its unique environmental properties. Indeed, its energy content (120 MJ/kg) can be exploited virtually without emitting any exhaust in the atmosphere except for water. Renewable production of hydrogen can be obtained through common biological processes on which relies anaerobic digestion, a well-established technology in use at farm-scale for treating different biomass and residues. Despite two-stage hydrogen and methane producing fermentation is a simple variant of the traditional anaerobic digestion, it is a relatively new approach mainly studied at laboratory scale. It is based on biomass fermentation in two separate, seuqential stages, each maintaining conditions optimized to promote specific bacterial consortia: in the first acidophilic reactorhydrogen is produced production, while volatile fatty acids-rich effluent is sent to the second reactor where traditional methane rich biogas production is accomplished. A two-stage pilot-scale plant was designed, manufactured and installed at the experimental farm of the University of Milano and operated using a biomass mixture of livestock effluents mixed with sugar/starch-rich residues (rotten fruits and potatoes and expired fruit juices), afeedstock mixture based on waste biomasses directly available in the rural area where plant is installed. The hydrogenic and the methanogenic reactors, both CSTR type, had a total volume of 0.7m3 and 3.8 m3 respectively, and were operated in thermophilic conditions (55 2 °C) without any external pH control, and were fully automated. After a brief description of the requirements of the system, this contribution gives a detailed description of its components and of engineering solutions to the problems encountered during the plant realization and start-up. The paper also discusses the results obtained in a first experimental run which lead to production in the range of previous laboratory results, with a typical hydrogen and methane specific productivity of 2.2 and 0.5 Nm3/m3reactor per day, in the first and second stage of the plant respectively. At our best knowledge, this plant is one of the very first prototypes producing biohydrogen at farm scale, and it represents a distributed, small scale demonstration to obtain hydrogen from renewable waste-sources