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Death of dopaminergic (DAergic) neurons in the substantia nigra pars compacta of the human brain is the characteristic pathological feature of Parkinson's disease (PD). On exposure to neurotoxicants, Drosophila too exhibits mobility defects and diminished levels of brain dopamine. In the fly model of sporadic PD, our laboratory has demonstrated that there is no loss of DAergic neuronal number, however, a significant reduction in fluorescence intensity (FI) of secondary antibodies that target the primary antibody-anti-tyrosine hydroxylase (TH). Here, we present a sensitive, economical, and repeatable assay to characterize neurodegeneration based on the quantification of FI of the secondary antibody. As the intensity of fluorescence correlates with the amount of TH synthesis, its reduction under PD conditions denotes the depletion in the TH synthesis, suggesting DAergic neuronal dysfunction. Reduction in TH protein synthesis is further confirmed through Bio-Rad Stain-Free Western Blotting. Quantification of brain DA and its metabolites (DOPAC and HVA) using HPLC-ECD further demonstrated the depleted DA level and altered DA metabolism as evident from enhanced DA turnover rate. Together all these PD marker studies suggest that FI quantification is a refined and sensitive method to understand the early stages of DAergic neurodegeneration. FI quantification is performed using ZEN 2012 SP2, a licensed software from Carl Zeiss, Germany. This method will be of good use to biologists, as it with few modifications, can also be implemented to characterize the extent of degeneration of different cell types. Unlike the expensive and cumbersome confocal microscopy, the present method using fluorescence microscopy will be a feasible option for fund-constrained neurobiology laboratories in developing countries., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Ayajuddin, Chaurasia, Das, Modi, Phom, Koza and Yenisetti.)

Sexual dysfunction (SD) is one of the most common non-motor symptoms of Parkinson's disease (PD) and remains the most neglected, under-reported, and under-recognized aspect of PD. Studies have shown that Dopamine (DA) in the hypothalamus plays a role in regulating sexual behavior. But the detailed mechanism of SD in PD is not known. Drosophila melanogaster shares several genes and signaling pathways with humans which makes it an ideal model for the study of a neurodegenerative disorder such as PD. Courtship behavior of Drosophila is one such behavior that is closely related to human sexual behavior and so plays an important role in understanding sexual behavior in diseased conditions as well. In the present study, a sporadic SD model of PD using Drosophila was developed and SD phenotype was observed based on abnormalities in courtship behavior markers. The Drosophila SD model was developed in such a way that at the window of neurotoxin paraquat (PQ) treatment [PQ is considered a crucial risk factor for PD due to its structural similarity with 1-methyl-4-phenyl pyridinium (MPP+), the active form of PD-inducing agent, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)], it does not exhibit mobility defects but shows SD. The whole brain tyrosine hydroxylase immunostaining showed no observable dopaminergic (DAergic) degeneration (number of DA neurons and fluorescence intensity of fluorescently labeled secondary antibodies that target anti-TH primary antibody) of the SD model. Similarly, there was no significant depletion of brain DA and its metabolite levels (HVA and DOPAC) as determined using HPLC-ECD (High-Performance Liquid Chromatography using Electrochemical Detector). The present study illustrates that the traits associated with courtship and sexual activity provide sensitive markers at the earlier stage of PD onset. This PQ-induced SD fly model throws an opportunity to decipher the molecular basis of SD under PD conditions and to screen nutraceuticals/potential therapeutic molecules to rescue SD phenotype and further to DAergic neuroprotection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Koza, Ayajuddin, Das, Chaurasia, Phom and Yenisetti.)

Parkinson's disease (PD) affects almost 1% of the population worldwide over the age of 50 years. Exposure to environmental toxins like paraquat and rotenone is a risk factor for sporadic PD which constitutes 95% of total cases. Herbicide rotenone has been shown to cause Parkinsonian symptoms in multiple animal models. Drosophila is an excellent model organism for studying neurodegenerative diseases (NDD) including PD. The aging process is characterized by differential expression of genes during different life stages. Hence it is necessary to develop life-stage-matched animal models for late-onset human disease(s) such as PD. Such animal models are critical for understanding the pathophysiology of age-related disease progression and important to understand if a genotropic drug/nutraceutical can be effective during late stages. With this idea, we developed an adult life stage-specific (health and transition phase, during which late-onset NDDs such as PD sets in) rotenone-mediated Drosophila model of idiopathic PD. Drosophila is susceptible to rotenone in dose-time dependent manner. Rotenone-mediated fly model of sporadic PD exhibits mobility defects (independent of mortality), inhibited mitochondrial complex I activity, dopaminergic (DAergic) neuronal dysfunction (no loss of DAergic neuronal number; however, reduction in rate-limiting enzyme tyrosine hydroxylase (TH) synthesis), and alteration in levels of dopamine (DA) and its metabolites; 3,4-Dihydroxyphenylacetic acid (DOPAC) and Homovanilic acid (HVA) in brain-specific fashion. These PD-linked behaviors and brain-specific phenotypes denote the robustness of the present fly model of PD. This novel model will be of great help to decipher life stage-specific genetic targets of small molecule mediated DAergic neuroprotection; understanding of which is critical for formulating therapeutic strategies for PD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ayajuddin, Phom, Koza, Modi, Das, Chaurasia, Thepa, Jamir, Neikha and Yenisetti.)

We study site percolation on lattices confined to a semi-infinite strip. For triangular and square lattices we find that the probability that a cluster touches the three sides of such a system at the percolation threshold has a continuous limit of 1/2 and argue that this limit is universal for planar systems. This value is also expected to hold for finite systems for any self-matching lattice. We attribute this result to the asymptotic symmetry of the separation lines between alternating spanning clusters of occupied and unoccupied sites formed on the original and matching lattice, respectively.

Random sequential adsorption (RSA) is a standard method of modeling adsorption of large molecules at the liquid-solid interface. Several studies have recently conjectured that in the RSA of rectangular needles, or k-mers, on a square lattice, percolation is impossible if the needles are sufficiently long (k of order of several thousand). We refute these claims and present rigorous proof that in any jammed configuration of nonoverlapping, fixed-length, horizontal, or vertical needles on a square lattice, all clusters are percolating clusters.

Velocity distribution functions link the micro- and macro-level theories of fluid flow through porous media. Here we study them for the fluid absolute velocity and its longitudinal and lateral components relative to the macroscopic flow direction in a model of a random porous medium. We claim that all distributions follow the power-exponential law controlled by an exponent γ and a shift parameter u_{0} and examine how these parameters depend on the porosity. We find that γ has a universal value 1/2 at the percolation threshold and grows with the porosity, but never exceeds 2.

Models of porous media are often applied to relatively small systems, which leads not only to system-size-dependent results, but also to phenomena that would be absent in larger systems. Here we investigate one such finite-size effect: anisotropy of the permeability tensor. We show that a nonzero angle between the external body force and macroscopic flux vector exists in three-dimensional periodic models of sizes commonly used in computer simulations and propose a criterion, based on the ratio of the system size to the grain size, for this phenomenon to be relevant or negligible. The finite-size anisotropy of the porous matrix induces a pressure gradient perpendicular to the axis of a porous duct and we analyze how this effect scales with the system and grain sizes. We also analyze how the size of the representative elementary volume (REV) for anisotropy compares with the REV for permeability.

Tortuosity (T) is a parameter describing an average elongation of fluid streamlines in a porous medium as compared to free flow. In this paper several methods of calculating this quantity from lengths of individual streamlines are compared and their weak and strong features are discussed. An alternative method is proposed, which enables one to calculate T directly from the fluid velocity field, without the need of determining streamlines, which greatly simplifies determination of tortuosity in complex geometries, including those found in experiments or three-dimensional computer models. Based on numerical results obtained with this method, (a) a relation between the hydraulic tortuosity of an isotropic fibrous medium and the porosity is proposed, (b) a relation between the divergence rate of T with the system size at percolation porosity and the scaling of the most probable traveling length at bond percolation is found, and (c) a range of porosities for which the shape factor is constant is identified.

Gamma-H2AX foci are sensitive and specific indicator for the induction of DNA double-strand breaks (DSBs) and an immunocytochemical assay with antibodies recognizing gamma-H2AX has become the gold standard for the detection of this type of DNA lesion. Quantification of gamma-H2AX foci can be achieved by various methods such as Western blotting, flow cytometry, visual analysis and computational analysis with a fluorescence microscope. The best sensitivity is achieved by computer analysis. Since no freeware programme for the analysis of gamma-H2AX foci exists for a PC platform, the aim of our study was to develop a simple and user-friendly public-domain software. The algorithm applied in our programme allows determination of the number of foci in a single cell, a focus intensity per cell, as well as a cell intensity. Its graphical user interface is based on a GTK+ library and the whole application can be run under a variety of operating systems, including MS Windows and Linux. The programme called FociCounter is publicly available at http://focicounter.sourceforge.net. Application of the programme was tested by analysing gamma-H2AX foci in CHO and MO59K cells irradiated in vitro with X-rays and validated by comparing the results obtained with the outcome of automated image analysis and flow cytometry., (Copyright © 2009 Elsevier B.V. All rights reserved.)

Anisotropy of the permeability tensor in statistically uniform porous media of sizes used in typical computer simulations is studied. Although such systems are assumed to be isotropic by default, we show that de facto their anisotropic permeability can give rise to significant changes in transport parameters such as permeability and tortuosity. The main parameter controlling the anisotropy is a/L , being the ratio of the obstacle to system size. Distribution of the angle alpha between the external force and the volumetric fluid stream is found to be approximately normal, and the standard deviation of alpha is found to decay with the system size as (a/L);{d/2} , where d is the space dimensionality. These properties can be used to estimate both anisotropy-related statistical errors in large-scale simulations and the size of the representative elementary volume. For porous media types studied here, the anisotropy effect becomes negligible only if a/L < or = 0.01 . This constraint was apparently violated in many previous computer simulations that need now to be recalculated.

We study numerically the tortuosity-porosity relation in a microscopic model of a porous medium arranged as a collection of freely overlapping squares. It is demonstrated that the finite-size, slow relaxation and discretization errors, which were ignored in previous studies, may cause significant underestimation of tortuosity. The simple tortuosity calculation method proposed here eliminates the need for using complicated, weighted averages. The numerical results presented here are in good agreement with an empirical relation between tortuosity (T) and porosity (varphi) given by T-1 proportional, variantlnvarphi , that was found by others experimentally in granule packings and sediments. This relation can be also written as T-1 proportional, variantRSvarphi with R and S denoting the hydraulic radius of granules and the specific surface area, respectively. Applicability of these relations appears to be restricted to porous systems of randomly distributed obstacles of equal shape and size.

We examine properties of a reaction front that forms in irreversible reaction-diffusion systems with concentration-dependent diffusivities. We study two different models of such systems and find that in the limit of a vanishingly small diffusivity of the reaction product, the reaction front dynamics enters a separate universality class, with the front width asymptotically tending to a constant value, and the reaction rate at the reaction front center diminishing with time t as t(-1/2). This behavior can be also observed in systems with nonvanishing (but small) diffusivity of the reaction product at intermediate times.

The single-cell gel electrophoresis, also known as the comet assay, has gained wide-spread popularity as a simple and reliable method to measure genotoxic and cytotoxic effects of physical and chemical agents as well as kinetics of DNA repair. Cells are generally stained with fluorescent dyes. The analysis of comets--damaged cells which form a typical comet-shaped pattern--is greatly facilitated by the use of a computer image-analysis program. Although several image-analysis programs are available commercially, they are expensive and their source codes are not provided. For Macintosh computers a cost-free public domain macro is available on the Internet. No ready for use, cost-free program exists for the PC platform. We have, therefore, developed such a public domain program under the GNU license for PC computers. The program is called CASP and can be run on a variety of hardware and software platforms. Its practical merit was tested on human lymphocytes exposed to gamma-rays and found to yield reproducible results. The binaries for Windows 95 and Linux, together with the source code can be obtained from: http://www.casp.of.pl.

We study long-time properties of reversible reaction-diffusion systems of type A+B<-->C by means of the perturbation expansion in powers of 1/t (inverse of time). For the case of equal diffusion coefficients we present exact formulas for the asymptotic forms of reactant concentrations and a complete, recursive expression for an arbitrary term of the expansions. Taking an appropriate limit we show that by studying reversible reactions one can obtain "singular" solutions typical of irreversible reactions.

We consider a particle diffusing in a one-dimensional periodic lattice with arbitrary transition rates between nearest-neighbor sites. We show rigorously that the ratio of the drift velocity V to the diffusion coefficient D has the upper bound 2N/d, where N is the number of nodes in an elementary cell and d denotes its length. Applying this result to a model of a molecular motor introduced by Fisher and Kolomeisky [Proc. Natl. Acad. Sci. USA 96, 6597 (1999)] we show that the so called Einstein force, which sets the lower bound for the force exerted by a molecular motor, is bounded from above by 2k(B)TN/d irrespective of the actual values of the jump rates between internal states of the motor.