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Molecular evolution of pathogenic bacteria based on rrsA gene
Aravind Setti,T A Phazna Devi,Smita C Pawar,G Rajesh
Journal of Medical and Allied Sciences , 2012,
Abstract: Evolution of pathogens in prokaryotic bacteria was studied by 16srRNA genes. In this study rrsA genes of 45 bacteria were considered, which includes pathogens, non-pathogens and out-group bacteria. We considered non-pathogenic bacteria, for each class in bacterial classification, to support the pathogenic evolution. In this investigation, aligned nucleotide sequences of rrsA genes were used for Phylogenetic analysis and they have been clustered precisely. Maximum Likelihood (ML) and Maximum Parsimony (MP) methods were employed for the molecular evolution of pathogenic bacteria. The best-fit substitution model with the lowest Bayesian Information Criterion scores is considered to describe the substitution pattern the best, and non-uniformity of evolutionary rates among sites were modeled by using a discrete Gamma distribution. Nearest Neighbor Interchange (NNI) heuristic method was used to generate the tree for ML and Close Neighbor Interchange (CNI) on random trees search methods for MP. Further both the phylogenetic trees were statistically evaluated for accuracy by bootstrap value. Transition and transversion ratio of the rrsA genes have been estimated for the mutation frequency over the evolution by Maximum Composite Likelihood (MCL) bias and ML bias. Combined pathogenic and non pathogenic bacteria analysis reflected the clear diversity of bacteria over time and agrees with morphological and cytological data. These molecular evolution results should be useful to study the evolution pattern of pathogenic bacteria.
Finite Element Modeling of Stress Strain Curve and Micro Stress and Micro Strain Distributions of Titanium Alloys— A Review  [PDF]
Gangi Setti Srinivasu, Narasimha Rao Raja
Journal of Minerals and Materials Characterization and Engineering (JMMCE) , 2012, DOI: 10.4236/jmmce.2012.1110094
Abstract: Most of the alloys like titanium, steel, brass, copper, etc., are used in engineering applications like automobile, aero- space, marine etc., consist of two or more phases. If a material consists of two or more phases or components it is very difficult to predict the properties like mechanical and other properties based on simple laws such as rule of mixtures. Titanium alloys are capable of producing different microstructures when it subjected to heat treatments, so much of money and time are squandering to study the effect of microstructure on mechanical properties of titanium alloys. This squandering can be reduced with the help of modeling and optimization techniques. There are many modeling tech- niques like Finite element method, Mat lab, Mathematical modeling etc. are available. But Finite element method is widely used for prediction because of capable of producing distributions of stresses and strains at any different loads. From the literature it is observed that there is a good agreement between the calculated and measured stress strain curves. This review paper describes the effect of volume fraction and grain size of alpha phase on the stress strain curve of the titanium alloys. It also can predict the effect of strength ratio on stress strain curve by using FEM. This informa- tion will be of great use in designing and selecting the titanium alloys for various engineering applications.
Caustics, Cold Flows, and Annual Modulation
Aravind Natarajan
Advances in Astronomy , 2011, DOI: 10.1155/2011/285346
Abstract: We discuss the formation of dark matter caustics, and their possible detection by future dark matter experiments. The annual modulation expected in the recoil rate measured by a dark matter detector is discussed. We consider the example of dark matter particles with a Maxwell-Boltzmann velocity distribution modified by a cold stream due to a nearby caustic. It is shown that the effect of the caustic flow is potentially detectable, even when the density enhancement due to the caustic is small. This makes the annual modulation effect an excellent probe of inner caustics. We also show that the phase of the annual modulation at low recoil energies does not constrain the particle mass unless the velocity distribution of particles in the solar neighborhood is known. 1. Introduction Caustics of light have been known since ancient times. The rainbow is a common example of a light caustic that forms when the family of refracted light rays is projected on to the plane of the sky. Another common example is the heart-shaped, or nephroid pattern seen on the bottom of a polished coffee cup. Thus caustics of light are regions where the light intensity is very large. Caustics have well-defined physical properties. The light intensity on the inner (concave) side of the rainbow varies like the inverse of the square root of distance from the rainbow. However, when the rainbow is approached from the outside (convex) side, the light intensity remains small until the rainbow is reached, at which point it shoots up abruptly. The coffee cup caustic is shown in Figure 1. The caustic is the envelope of the family of reflected light rays, that is, the curve tangent to all members of the family of rays. There are two qualitatively distinct regions separated by the caustic: one with three rays at each point and the other with one ray at each point. Consider the point . Near this point, the light intensity varies ~ when measured along , and ~ when measured along . The intensity at the point is double the intensity at the point for small . Near the smooth curve and far from the point , the light intensity only varies in the region with 3 rays at each point, like the inverse square root of the distance from the smooth curve. As long as one is far from the boundary between the two regions, a small change in position results in only a small change in light intensity. However, close to the boundary, a small change in position leads to a very large change in light intensity. Figure 1: Light rays reflected by a polished metal ring or the inner surface of a reflective coffee cup. The
Opening Pandora's Box: making biological discoveries through computational data exploration
L Aravind
Biology Direct , 2007, DOI: 10.1186/1745-6150-2-29
Abstract: The essential philosophy of this new movement within biology – computational biology – has been the use of computational methods to explore repositories of biological information to make new scientific discoveries. An early example of the success of these methods was the identification of the helix-turn-helix domain as a determinant of DNA-protein interaction [1]. This allowed the prediction of diverse bacterial and eukaryotic transcription factors, and resulted in testable hypotheses regarding the functions of key developmental regulators and oncogenes [2,3]. Ever since, computational investigations have resulted in discovery of new protein domains and prediction of their biochemical roles [4], discovery of new RNAs [5], identification of subcellular targeting signals in proteins [6] and prediction of transcription factor binding sites [7]. Application of such methodologies has also been at the heart of genomics – being central to the interpretation of genome sequences. Most remarkably it has allowed us to reconstruct the biology of diverse life forms, such as the syphilis pathogen [8], the malarial parasite [9] or the diverse uncultivable microorganisms [10], which were never too amenable to classical experimentation. The successes of genomics have also spawned whole assemblies of new forms of high-throughput data. These include genome-scale collations of data pertaining to gene expression, protein-protein interactions, genetic interactions and intra-population genomic polymorphisms. By adding a new layer of contextual information to that contained in sequences and structures of biomolecules these new datasets greatly add to the power of the computational discovery process.The principal idea behind announcing the Discovery Notes section of Biology Direct is to augment the process of discovery in light of the unprecedented accumulation of biological data. The articles submitted to this section aim to occupy a specific niche in the already rich menagerie of publicat
WIMP annihilation in caustics
Natarajan, Aravind
High Energy Physics - Phenomenology , 2007, DOI: 10.1103/PhysRevD.75.123514
Abstract: The continuous infall of dark matter with low velocity dispersion from all directions in a galactic halo leads to the formation of caustics which are very small scale ($\sim$parsec) high density structures. If the dark matter is made up of SUSY neutralinos, the annihilation of these particles produces a characteristic spectrum of gamma rays which in principle, could be detected. The annihilation signal at different energy bands is computed and compared with the expected gamma ray background.
Nucleus management with irrigating vectis
Srinivasan Aravind
Indian Journal of Ophthalmology , 2009,
Abstract: The main objective in modern cataract surgery is to achieve a better unaided visual acuity with rapid post-surgical recovery and minimal surgery-related complications. Early visual rehabilitation and better unaided vision can be achieved only by reducing the incision size. In manual small incision cataract surgery (MSICS), incision is between 5.5 to 7 mm. Once the nucleus is prolapsed into the anterior chamber, it can be extracted through the tunnel. Nucleus extraction with an irrigating vectis is a very simple technique, which combines mechanical and hydrostatic forces to express out the nucleus. This technique is time-tested with good results and more than 95% of nuclei in MSICS are extracted in this way offering all the merits of phacoemulsification with the added benefits of having wider applicability, better safety, shorter learning curve and lower cost.
Staining of palatal torus secondary to long term minocycline therapy
Buddula Aravind
Journal of the Indian Society of Periodontology , 2009,
Abstract: Minocycline and other tetracycline analogs are well known to cause discoloring of alveolar bone, teeth and other tissues. The present case reports palatine torus discoloring, in a 91-year-old patient, after long term minocycline therapy. The patient was presented with staining of the palatal torus resulting from prior minocycline use for three-and-a-half years. The diagnosis of minocycline staining of palatal torus was done during a routine hygiene examination. The patient was informed that the bluish appearance of the palatal torus was the result of long term minocycline use. The patient was not willing to discontinue the antibiotic and was not concerned about the appearance. The clinician should inform patients on long term minocycline therapy about the possible side effects of staining of the alveolar bone, teeth and other soft tissue.
A case report of metastatic adenocarcinoma of the gingiva
Buddula Aravind
Journal of the Indian Society of Periodontology , 2009,
Abstract: Localized gingival enlargement is often associated with specific systemic medication, abscess formation, trauma or reactive lesions. Scant literature is available reporting enlargement of gingiva due the metastasis of adenocarcinoma from lung. The case report presents a unique case of an adenocarcinoma in the lung metastasizing to the buccal and lingual interdental papillae of teeth numbering 34 and 35. A 72-year-old female was referred to the Mayo Clinic with a recent diagnosis of metastatic stage IV adenocarcinoma of the left lung presented with an abnormal mass located on the left posterior buccal keratinized tissue adjacent to teeth numbering 34-35. Biopsy of the lesion was performed for CK7, CK20, TTF-1 and p63. The tumor cells were positive for CK7 and TTF-1, and weakly positive for p63 suggesting a diagnosis of adenocarcinoma. The periodontist may be in the unique position to be the first oral health care provider to evaluate any biopsy suspicious intra-oral lesions.
Gene flow and biological conflict systems in the origin and evolution of eukaryotes
L. Aravind
Frontiers in Cellular and Infection Microbiology , 2012, DOI: 10.3389/fcimb.2012.00089
Abstract: The endosymbiotic origin of eukaryotes brought together two disparate genomes in the cell. Additionally, eukaryotic natural history has included other endosymbiotic events, phagotrophic consumption of organisms, and intimate interactions with viruses and endoparasites. These phenomena facilitated large-scale lateral gene transfer and biological conflicts. We synthesize information from nearly two decades of genomics to illustrate how the interplay between lateral gene transfer and biological conflicts has impacted the emergence of new adaptations in eukaryotes. Using apicomplexans as example, we illustrate how lateral transfer from animals has contributed to unique parasite-host interfaces comprised of adhesion- and O-linked glycosylation-related domains. Adaptations, emerging due to intense selection for diversity in the molecular participants in organismal and genomic conflicts, being dispersed by lateral transfer, were subsequently exapted for eukaryote-specific innovations. We illustrate this using examples relating to eukaryotic chromatin, RNAi and RNA-processing systems, signaling pathways, apoptosis and immunity. We highlight the major contributions from catalytic domains of bacterial toxin systems to the origin of signaling enzymes (e.g., ADP-ribosylation and small molecule messenger synthesis), mutagenic enzymes for immune receptor diversification and RNA-processing. Similarly, we discuss contributions of bacterial antibiotic/siderophore synthesis systems and intra-genomic and intra-cellular selfish elements (e.g., restriction-modification, mobile elements and lysogenic phages) in the emergence of chromatin remodeling/modifying enzymes and RNA-based regulation. We develop the concept that biological conflict systems served as evolutionary “nurseries” for innovations in the protein world, which were delivered to eukaryotes via lateral gene flow to spur key evolutionary innovations all the way from nucleogenesis to lineage-specific adaptations.
Taylor-Goldstein equation and stability
Aravind Banerjee
Physics , 2005,
Abstract: Taylor-Goldstein equation (TGE) governs the stability of a shear-flow of an inviscid fluid of variable density. It is investigated here from a rigorous geometrical point of view using a canonical class of its transformations. Rayleigh's point of inflection criterion and Fjortoft's condition of instability of a homogenous shear-flow have been generalized here so that only the profile carrying the point of inflection is modified by the variation of density. This fulfils a persistent expectation in the literature. A pair of bounds exists such that in any unstable flow the flow-curvature (a function of flow-layers) exceeds the upper bound at some flow-layer and falls below the lower bound at a higher layer. This is the main result proved here. Bounds are obtained on the growth rate and the wave numbers of unstable modes, in fulfillment of longstanding predictions of Howard. A result of Drazin and Howard on the boundedness of the wave numbers is generalized to TGE. The results above hold if the local Richardson number does not exceed 1/4 anywhere in the flow, otherwise a weakening of the conditions necessary for instability is seen. Conditions for the propagation of neutrally stable waves and bounds on the phase speeds of destabilizing waves are obtained. It is also shown that the set of complex wave velocities of normal modes of an arbitrary flow is bounded. Fundamental solutions of TGE are obtained and their smoothness is examined. Finally sufficient conditions for instability are suggested.
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