-Classifying prion and prion-like phenomena

The universe of prion and prion-like phenomena has expanded significantly in the past several years. Here, we overview the challenges in classifying this data informatically, given that terms such as “prion-like”, “prion-related” or “prion-forming” do not have a stable meaning in the scientific literature. We examine the spectrum of proteins that have been described in the literature as forming prions, and discuss how “prion” can have a range of meaning, with a strict definition being for demonstration of infection with in vitro-derived recombinant prions. We suggest that although prion/prion-like phenomena can largely be apportioned into a small number of broad groups dependent on the type of transmissibility evidence for them, as new phenomena are discovered in the coming years, a detailed ontological approach might be necessary that allows for subtle definition of different “flavors” of prion / prion-like phenomena.     

The Kinetics of Osmotic Transport through Pores of Molecular Dimensions

This paper presents a theoretical analysis of the kinetics of osmotic transport across a semipermeable membrane. There is a thermodynamic connection between the rate of flow under a hydrostatic pressure difference and the rate of flow due to a difference in solute concentration on the two sides. One might therefore attempt to calculate the osmotic transport coefficient by applying Poiseuille's equation to the flow produced by a difference in hydrostatic pressure. Such a procedure is, however, inappropriate if the pores in the membrane are too small to allow molecules to “overtake.” It then becomes necessary to perform a statistical calculation of the transport coefficient, and such a calculation is described in this paper. The resulting expression for the number of solvent molecules passing through a pore per second is J = m D₁ δn₁/l² where m is the number of solvent molecules in the pore, l is the length of the pore, D₁ is the self-diffusion coefficient of the solute, and δn₁ the difference in solvent mole fraction on the two sides of the membrane. This equation is used for estimating the number of pores per unit area of the squid axon membrane; the result is 6 × 10⁹ pores/cm².     

The role of abscisic Acid in cross-adaptation of tobacco plants

Tobacco plants (Nicotiana rustica L.) pre-exposed to leaf dehydration, mineral deprivation, salination, or BO₃³⁻ toxicity exhibited increased resistance to subzero temperature and to reduced oxygen in the root medium. The stressed plants all showed an elevated content of leaf abscisic acid. Upon transfer of mineral deprived and salinated plants to prestress conditions, a decline in leaf abscisic acid content to prestress levels took place together with a loss of the increased resistance to subzero temperature and to deprivation of root oxygen. Treatment with abscisic acid by direct application to the leaves or by addition to the root medium improved leaf resistance to subzero temperature and to deprivation of root oxygen. A common hormone-regulation mechanism involving abscisic acid is suggested for this phenomenon of “cross-adaptation” by which a given stress confers increased resistance to other, apparently unrelated stresses.     

Analysis of coupled intra- and extraluminal flows for single and multiple capillaries

Matched asymptotic expansions are used to study a model of the coupled fluid flow in the capillaries and tissue of the microcirculation. These capillaries are long, narrow cylindrical tubes embedded in a uniform tissue space. The capillary, or intraluminal, flow is assumed to be that of an incompressible Navier-Stokes fluid wherein colloids are represented as dilute solute; the extraluminal flow in the tissue is according to Darcy's law. Central to this fluid exchange is the boundary condition on the fluid radial velocity at the semipermeable wall of the capillary. This boundary condition, involving the local hydrostatic and colloidal osmotic pressures in both the capillary and the tissue, together with the radial gradient of the tissue hydrostatic pressure, couples the intra- and extraluminal flow fields. With this model we investigate the relationship between transport properties, hydrostatic pressures, and flow exchange for a single capillary, and describe the fluid transport in the tissue space produced by an array of such capillaries.     

A mixture theory model of fluid and solute transport in the microvasculature of normal and malignant tissues. I. Theory

In order to better understand the mechanisms governing transport of drugs, nanoparticle-based treatments, and therapeutic biomolecules, and the role of the various physiological parameters, a number of mathematical models have previously been proposed. The limitations of the existing transport models indicate the need for a comprehensive model that includes transport in the vessel lumen, the vessel wall, and the interstitial space and considers the effects of the solute concentration on fluid flow. In this study, a general model to describe the transient distribution of fluid and multiple solutes at the microvascular level was developed using mixture theory. The model captures the experimentally observed dependence of the hydraulic permeability coefficient of the capillary wall on the concentration of solutes present in the capillary wall and the surrounding tissue. Additionally, the model demonstrates that transport phenomena across the capillary wall and in the interstitium are related to the solute concentration as well as the hydrostatic pressure. The model is used in a companion paper to examine fluid and solute transport for the simplified case of an axisymmetric geometry with no solid deformation or interconversion of mass.     

Transport of Water and Solutes across Maize Roots Modified by Puncturing the Endodermis (Further Evidence for the Composite Transport Model of the Root)

The effects of puncturing the endodermis of young maize roots (Zea mays L.) on their transport properties were measured using the root pressure probe. Small holes with a diameter of 18 to 60 [mu]m were created 70 to 90 mm from the tips of the roots by pushing fine glass tubes radially into them. Such wounds injured about 10-2 to 10-3% of the total surface area of the endodermis, which, in these hydroponically grown roots, had developed a Casparian band but no suberin lamellae. The small injury to the endodermis caused the original root pressure, which varied from 0.08 to 0.19 MPa, to decrease rapidly (half-time = 10-100 s) and substantially to a new steady-state value between 0.02 and 0.07 MPa. The radial hydraulic conductivity (Lpr) of control (uninjured) roots determined using hydrostatic pressure gradients as driving forces was larger by a factor of 10 than that determined using osmotic gradients (averages: Lpr [hydrostatic] = 2.7 x 10-7 m s-1 MPa-1; Lpr [osmotic] = 2.2 x 10-8 m s-1 MPa-1; osmotic solute: NaCl). Puncturing the endodermis did not result in measurable increases in hydraulic conductivities measured by either method. Thus, the endodermis was not rate-limiting root Lpr: apparently the hydraulic resistance of roots was more evenly distributed over the entire root tissue. However, puncturing the endodermis did substantially change the reflection ([sigma]sr) and permeability (Psr) coefficients of roots for NaCl, indicating that the endodermis represented a considerable barrier to the flow of nutrient ions. Values of [sigma]sr decreased from 0.64 to 0.41 (average) and Psr increased by a factor of 2.6, i.e. from 3.8 x 10-9 to 10.1 x 10.-9 m s-1(average). The roots recovered from puncturing after a time and regained root pressure. Measurable increases in root pressure became apparent as soon as 0.5 to 1 h after puncturing, and original or higher root pressures were attained 1.5 to 20 h after injury. However, after recovery roots often did not maintain a stable root pressure, and no further osmotic experiments could be performed with them. The Casparian band of the endodermis is discontinuous at the root tip, where the endodermis has not yet matured, and at sites of developing lateral roots. Measurements of the cross-sectional area of the apoplasmic bypass at the root tip yielded an area of 0.031% of the total surface area of the endodermis. An additional 0.049% was associated with lateral root primordia. These areas are larger than the artificial bypasses created by wounding in this study and may provide pathways for a "natural bypass flow" of water and solutes across the intact root. If there were such a pathway, either in these areas or across the Casparian band itself, roots would have to be treated as a system composed of two parallel pathways (a cell-to-cell and an apoplasmic path). It is demonstrated that this "composite transport model of the root" allows integration of several transport properties of roots that are otherwise difficult to understand, namely (a) the differences between osmotic and hydrostatic water flow, (b) the dependence of root hydraulic resistance on the driving force or water flow across the root, and (c) low reflection coefficients of roots.     

Nitrate-regulated growth and cytokinin responses in seminal roots of barley

The influence of nitrate availability on growth of seminal roots, and root cytokinin levels, was studied in barley (Hordeum vulgare L. cv Golf). Nitrate was continuously supplied to initially N-starved seedlings at relative addition rates (RA) of 0.03 to 0.21 per day (standard cultures) or at RA 0.09 per day in split root cultures with the nitrate additions distributed in ratios of 100:0 or 80:20 to the two subroots. Data were collected both during a phase of acclimation (first 10 days of N additions) and in the acclimated stage (>10 days after onset of N additions). Limitation of whole-plant growth was observed at RA <0.15 per day. The lateral root frequency increased with RA in plants of equal chronological age. However, the lateral root frequency was related to root size rather than to RA; roots of uneven age but having comparable total root lengths also had comparable lateral root frequencies. Growth of individual subroots in split root systems during acclimation was proportional to the fraction of the total N addition that was fed to the root. All subroots had comparable relative growth rates in acclimated plants, and their lateral root frequency correlated with total root length in the same manner as in standard cultures. Onset of N additions in a 80:20 split root culture resulted in doublings of zeatin riboside (ZR) levels in shoots and in the “80” root, whereas the response of the “20” root was small. No effect of perturbed nitrate availability on xylem translocation of ZR was observed. The ZR levels remained higher in the “80” root during acclimation but returned to the level of the “20” root after acclimation. Root cytokinin levels and xylem translocation in acclimated standard cultures were unaffected by RA in the lower range but increased at high RA. Arguments for involvement of cytokinins in the nitrate-regulated growth response are discussed.     

Source-sink coupling in young barley plants and control of phloem loading

Phloem loading of carbohydrate within a mature exporting leaf of a barley seedling is shown to respond quickly to a change in the temperature of the root and the shoot meristem. This is interpreted as a close coupling between source supply and sink demand for carbohydrate, through the hydrostatic pressure gradient linking source and sink generated by the solute concentration within the sieve tubes. This interpretation was tested by using anoxia to alter solute concentration within the sieve tubes of one region of a leaf while observing phloem loading in an adjacent region. Responses to anoxia could not be explained by the above model, suggesting that either this model is incorrect or other signalling pathways are involved. There is evidence in the literature for coarse control of phloem loading but no evidence was found of fine control by solute content of the loaded sieve elements.     

Do soil depth and plant community composition interact to modify the resistance and resilience of grassland ecosystem functioning to drought?

While the effect of drought on plant communities and their associated ecosystem functions is well studied, little research has considered how responses are modified by soil depth and depth heterogeneity. We conducted a mesocosm study comprising shallow and deep soils, and variable and uniform soil depths, and two levels of plant community composition, and exposed them to a simulated drought to test for interactive effects of these treatments on the resilience of carbon dioxide fluxes, plant functional traits, and soil chemical properties. We tested the hypotheses that: (a) shallow and variable depth soils lead to increased resistance and resilience of ecosystem functions to drought due to more exploitative plant trait strategies; (b) plant communities associated with intensively managed high fertility soils, will have more exploitative root traits than extensively managed, lower fertility plant communities. These traits will be associated with higher resistance and resilience to drought and may interact with soil depth and depth heterogeneity to amplify the effects on ecosystem functions. Our results showed that while there were strong soil depth/heterogeneity effects on plant‐driven carbon fluxes, it did not affect resistance or resilience to drought, and there were no treatment effects on plant‐available carbon or nitrogen. We did observe a significant increase in exploitative root traits in shallow and variable soils relative to deep and uniform, which may have resulted in a compensation effect which led to the similar drought responses. Plant community compositions representative of intensive management were more drought resilient than more diverse “extensive” communities irrespective of soil depth or soil depth heterogeneity. In intensively managed plant communities, root traits were more representative of exploitative strategies. Taken together, our results suggest that reorganization of root traits in response to soil depth could buffer drought effects on ecosystem functions.     

Water transport in maize roots : measurement of hydraulic conductivity, solute permeability, and of reflection coefficients of excised roots using the root pressure probe

A root pressure probe has been used to measure the root pressure (P_r) exerted by excised main roots of young maize plants (Zea Mays L.). Defined gradients of hydrostatic and osmotic pressure could be set up between root xylem and medium to induce radial water flows across the root cylinder in both directions. The hydraulic conductivity of the root (Lp_r) was evaluated from root pressure relaxations. When permeating solutes were added to the medium, biphasic root pressure relaxations were observed with water and solute phases and root pressure minima (maxima) which allowed the estimation of permeability (P_Sr) and reflection coefficients (σ_sr) of roots. Reflection coefficients were: ethanol, 0.27; mannitol, 0.74; sucrose, 0.54; PEG 1000, 0.82; NaCl, 0.64; KNO₃, 0.67, and permeability coefficients (in 10⁻⁸ meters per second): ethanol, 4.7; sucrose, 1.6; and NaCl, 5.7. Lp_r was very different for osmotic and hydrostatic gradients. For hydrostatic gradients Lp_r was 1·10⁻⁷ meters per second per megapascal, whereas in osmotic experiments the hydraulic conductivity was found to be an order of magnitude lower. For hydrostatic gradients, the exosmotic Lp_r was about 15% larger than the endosmotic, whereas in osmotic experiments the polarity in the water movement was reversed. These results either suggest effects of unstirred layers at the osmotic barrier in the root, an asymmetrical barrier, and/or mechanical effects. Measurements of the hydraulic conductivity of individual root cortex cells revealed an Lp similar to Lp_r (hydrostatic). It is concluded that, in the presence of external hydrostatic gradients, water moves primarily in the apoplast, whereas in the presence of osmotic gradients this component is much smaller in relation to the cell-to-cell component (symplasmic plus transcellular transport).     

Water and solute transport along developing maize roots

Hydraulic and osmotic properties were measured along developing maize (Zea mays L.) roots at distances between 15 and 465 mm from the root tip to quantify the effects of changes in root structure on the radial and longitudinal movement of water and solutes (ions). Root development generated regions of different hydraulic and osmotic properties. Close to the root tip, passive solute permeability (root permeability coefficient, P_sr) was high and selectivity (root reflection coefficient, _sr) low, indicative of an imperfect semipermeable root structure. Within the apical 100–150 mm, P_sr decreased by an order of magnitude and _sr increased significantly. Root hydraulic conductivity (Lp_r) depended on the nature of the force (hydrostatic and osmotic). Osmotic Lp_r was smaller by an order of magnitude than hydrostatic Lp_r and decreased with increasing distance from the root tip. Throughout the root, responses in turgor of cortical cells and late metaxylem to step changes in xylem pressure applied to the base of excised roots were measured at high spatial resolution. The resulting profiles of radial and longitudinal propagation of pressure showed that the endodermis had become the major hydraulic barrier in older parts of the root, i.e. at distances from the apex ä 150 mm. Other than at the endodermis, no significant radial hydraulic resistance could be detected. The results permit a detailed analysis of the root's composite structure which is important for its function in collecting and translocating water and nutrients.Abbreviations and Symbols CPP cell pressure probe - IT root segments with intact tips; - Lp_r root hydraulic conductivity - Lp_rh hydrostatic hydraulic conductivity of root - Lp_ro osmotic hydraulic conductivity of root - P_app hydrostatic pressure applied to cut end of root - P_c cell turgor - P_{c, cor} turgor of cortical cell - P_c,xyl turgor of late metaxylem vessel - P_ro stationary root pressure - P_r0,seal stationary root pressure of sealed root segment - P_sr solute permeability coefficient of root - RPP root pressure probe - TR root segments with tip removed - _sr reflection coefficient of root Dedicated to Professor Andreas Sievers on the occasion of his retirement     

Single-Cell Microbiology: Tools, Technologies, and Applications

The field of microbiology has traditionally been concerned with and focused on studies at the population level. Information on how cells respond to their environment, interact with each other, or undergo complex processes such as cellular differentiation or gene expression has been obtained mostly by inference from population-level data. Individual microorganisms, even those in supposedly “clonal” populations, may differ widely from each other in terms of their genetic composition, physiology, biochemistry, or behavior. This genetic and phenotypic heterogeneity has important practical consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. New appreciation of the importance of cellular heterogeneity, coupled with recent advances in technology, has driven the development of new tools and techniques for the study of individual microbial cells. Because observations made at the single-cell level are not subject to the “averaging” effects characteristic of bulk-phase, population-level methods, they offer the unique capacity to observe discrete microbiological phenomena unavailable using traditional approaches. As a result, scientists have been able to characterize microorganisms, their activities, and their interactions at unprecedented levels of detail.     

Interaction between Osmotic- and Pressure-induced Water Flow in Plant Roots

When the pressure gradient across a root alters, there is often an apparent change in the permeability of the root to water. Fiscus (Plant Physiol. 1975. 55: 917-922) has suggested that this can be explained by a simple two-compartment model which takes into account rates of solute uptake into the xylem. A method of testing actual data against the Fiscus model is proposed; this shows that in some cases the apparent changes in permeability cannot be explained by the model. The model is not adequate to predict the amounts of solute reaching the xylem by passive drag: a three-compartment model would be more realistic.     

Bortezomib Resistance Can Be Reversed by Induced Expression of Plasma Cell Maturation Markers in a Mouse In Vitro Model of Multiple Myeloma

Multiple myeloma (MM), the second most common hematopoietic malignancy, remains an incurable plasma cell (PC) neoplasm. While the proteasome inhibitor, bortezomib (Bz) has increased patient survival, resistance represents a major treatment obstacle as most patients ultimately relapse becoming refractory to additional Bz therapy. Current tests fail to detect emerging resistance; by the time patients acquire resistance, their prognosis is often poor. To establish immunophenotypic signatures that predict Bz sensitivity, we utilized Bz-sensitive and -resistant cell lines derived from tumors of the Bcl-X_L/Myc mouse model of PC malignancy. We identified significantly reduced expression of two markers (CD93, CD69) in “acquired” (Bz-selected) resistant cells. Using this phenotypic signature, we isolated a subpopulation of cells from a drug-naïve, Bz-sensitive culture that displayed “innate” resistance to Bz. Although these genes were identified as biomarkers, they may indicate a mechanism for Bz-resistance through the loss of PC maturation which may be induced and/or selected by Bz. Significantly, induction of PC maturation in both “acquired” and “innate” resistant cells restored Bz sensitivity suggesting a novel therapeutic approach for reversing Bz resistance in refractory MM.     

Modeling spatial–temporal operations with context-dependent associative memories

We organize our behavior and store structured information with many procedures that require the coding of spatial and temporal order in specific neural modules. In the simplest cases, spatial and temporal relations are condensed in prepositions like “below” and “above”, “behind” and “in front of”, or “before” and “after”, etc. Neural operators lie beneath these words, sharing some similarities with logical gates that compute spatial and temporal asymmetric relations. We show how these operators can be modeled by means of neural matrix memories acting on Kronecker tensor products of vectors. The complexity of these memories is further enhanced by their ability to store episodes unfolding in space and time. How does the brain scale up from the raw plasticity of contingent episodic memories to the apparent stable connectivity of large neural networks? We clarify this transition by analyzing a model that flexibly codes episodic spatial and temporal structures into contextual markers capable of linking different memory modules.     

Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry

Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N₂ bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N₂ bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N₂ sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, “semi-unfolded” ↔ “native” ↔ “globally unfolded” → “aggregated”. This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS.     

Proposed Classification of Auriculotemporal Nerve,Based on the Root System

The topography of the auriculotemporal nerve (ATN) root system is the main criterion of this nerve classification. Previous publications indicate that ATN may have between one and five roots. Most common is a one- or two-root variant of the nerve structure. The problem of many publications is the inconsistency of nomenclature which concerns the terms “roots”, “connecting branches”, or “branches” that are used to identify the same structures. This study was performed on 80 specimens (40 adults and 40 fetuses) to propose a classification based on: (i) the number of roots, (ii) way of root division, and (iii) configuration of interradicular fibers that form the ATN trunk. This new classification is a remedy for inconsistency of nomenclature of ATN in the infratemporal fossa. This classification system has proven beneficial when organizing all ATN variants described in previous studies and could become a helpful tool for surgeons and dentists. Examination of ATN from the infratemporal fossa of fetuses (the youngest was at 18 weeks gestational age) showed that, at that stage, the nerve is fully developed.     

Analysis of time hierarchy in plant cell volume changes

A simple model of plant cell volume changes is presented. It is based on Kedem-Katchalsky equations for water and solute transport and on linear approximation of the dependence of intracellular hydrostatic pressure on the cell volume. Active transport of solute is also included. The time hierarchy within the system is analyzed by appropriate normalization of variables and by the assessment of the numerical values of model coefficients. The dynamics of the system comprises a slow process of solute exchange and a fast process of water transport. This explains the wellknown biphasic response of the cell volume to a sudden change in external conditions. An approximation of equations describing the system behaviour on the basis of the Tikhonov's theorem is proposed. The approximative solution is compared with the exact numerical solution of the original equations. The approximation is very good under physiological conditions, but it ceases to hold when the solute permeability of the cell membrane increases causing the breakdown of the entire time hierarchy within the system.     

A Stored Charge Model for the Sodium Channel

A new model is proposed to account for the apparent conductance changes of the sodium, or early, channel in nerve fiber membranes. In this model it is assumed that the channels are gated at the interior side of the membrane and are resistively limited at the exterior side by sodium selective barriers of high resistance to ion flow. Under resting conditions the closed channels accumulate a store of sodium ions, dependent on the exterior sodium concentration. With the application of a depolarizing clamp the interior gates open allowing the stored ions to discharge into the interior low sodium concentration solution. In this model the initial rise in the early current results from the opening of more and more gates in response to the depolarizing clamp. The subsequent fall in the early current results from the “capacitative” discharge of the opened channels, limited by the high resistive barrier at the exterior end. Upon repolarization, the gates reclose and sodium ions reaccumulate in the channels from the high concentration external solution, but at a slow rate determined by the resistive barrier. Preliminary tests of this model, using a number of simplifying assumptions, show that it has the ability to account, at least semiquantitatively, for the major characteristics of the experimental clamp results.