BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

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Properties Of Concrete

Microbial carbonate precipitation in construction materials: A review

Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.

The Selective Value of Bacterial Shape

Use of microorganism to improve the strength of cement mortar

Microbial modified mortar or concrete has become an important area of research for high-performance construction materials. This study investigates the effects of incorporating a facultative anaerobic hot spring bacterium on the microstructure of a cement–sand mortar. Environmental scanning electron microscopic (ESEM) views and image analysis (IA) of the bacteria modified mortar (thin-section) showed significant textural differences with respect to the control (without bacteria) samples. X-ray diffraction (XRD) study confirmed the formation of new phases of silicates (Gehlenite) within the matrix of such mortar material, which causes an improvement in the strength of the material. Electron probe microstructure analysis (EPMA) suggested that the bacterial treatment promoted uniform distribution of silicate phases and increased the calcium/silicon ratio within CSH gel of the matrices. The bacterium is found to leach a novel protein, which is capable of isolating silica from its source. The addition of such isolated protein, instead of the bacteria, into mortar also improves the strength of mortar.

Microbial activity on the microstructure of bacteria modified mortar

In the biosphere, bacteria can function as geo-chemical agents, promoting the dispersion, fractionation and/or concentration of materials. Microbial mineral precipitation is resulted from metabolic activities of microorganisms. Based on this biomineralogy concept, an attempt has been made to develop bioconcrete material incorporating of an enrichment culture of thermophilic and anaerobic bacteria within cement-sand mortar/concrete. The results showed a significant increase in compressive strength of both cement-sand mortar and concrete due to the development of filler material within the pores of cement sand matrix. Maximum strength was observed at concentration 10(5)cell/ml of water used in mortar/concrete. Addition of Escherichia coil or media composition on mortar showed no such improvement in strength.

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Development of bioconcrete material using an enrichment culture of novel thermophilic anaerobic bacteria.

Bioremediase a unique protein from a novel bacterium BKH1, ushering a new hope in concrete technology

A silver–silica nano composite based geopolymer mortar has been developed by simple adsorption of silver in a suitable amount of a colloidal silica suspension for anti-bacterial property development. The silver nanoparticles (3–7 nm) were attached on the surface of 20–50 nm sized silica nanoparticles. The silver–silica nano-composite was characterized by Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) and energy dispersive X-ray spectral analysis. Mechanical strength, durability and mechanistic anti-bacterial activity of the silver–silica nano composite modified geopolymer mortar (GMAg–Si) were investigated and compared to nano silica modified geopolymer mortar (GMSi) and control cement mortar (CM). To accesses the anti-microbial efficacy of the samples, 99% mortality for Gram positive and Gram negative bacteria was calculated. Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) values were determined from batch cultures. The addition of 6% (w/w) of the silver–silica nano composite in the geopolymer mortar cured at ambient temperature shows substantial improvement in mechanical strength, durability and anti-bacterial property. Reactive Oxygen Species (ROS) generation and cell wall rupture as observed from fluorescence microscopy and Field Emission Scanning Electron Microscopy (FESEM) may be possible reasons behind the anti-bacterial efficacy of silver–silica nano composite modified geopolymer mortar.

Brajadulal Chattopadhyay

Papers

Use of microorganism to improve the strength of cement mortar

Microbial activity on the microstructure of bacteria modified mortar

Development of bioconcrete material using an enrichment culture of novel thermophilic anaerobic bacteria.

Bioremediase a unique protein from a novel bacterium BKH1, ushering a new hope in concrete technology

Anti-microbial efficiency of nano silver–silica modified geopolymer mortar for eco-friendly green construction technology