A stain-free detection system for electrophoresis

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2001.Includes bibliographical references.In this thesis, a novel stain free detection system for slab gel electrophoresis is examined. Currently, stained techniques are used to identify electrophoretic bands in gels. The stains utilized in these methods involve health risks since they are mutagenic. Also stains like EtBr are intercalating agents meaning they wedge themselves into the grooves of DNA and stay there. Since this includes a physical contact the stains remain in the DNA at the end of the experiment. This makes further use DNA very difficult. The stains need to be removed by chemical techniques which are timewise very costly. Also these operations are very inefficient, retrieve rates are very low which leads to waste of most of the analyte. The specific method we addressed aims to eliminate the use of any kind of stains and therefore inherently increase the end product efficiency. The method introduces the absorption method as the means of detection. The physical law governing the absorption technique is the Beer-Lambert Law. The Beer-Lambert Law defines the linear relation, which correlates absorption value to the analyte concentration, path length of the light and wavelength-dependent absorptivity coefficient. Although the proposed method is intended to apply to all kind of different analytes, to achieve primary goals and prove the feasibility of the method, as the first step detection of DNA molecules are targeted. Hence absorption pattern at a wavelength of 254 nm (which is characteristic absorption peak for DNA) is examined. After the method is proven to work robustly, it will be extended to all kind of different analytes. The unique approach used in the proposed detection system is the use of a scanning technique incorporated with absorption technique utilizing a high QE (Quantum efficiency) CCD camera as the detector. Experiments have been performed to determine the only unknown parameter -wavelength-dependent absorptivity coefficient a([gamma])- in the Beer-Lambert Law. The value of a([gamma]) is dependent on the wavelength and also on the transmission media. In our case wavelength of interest is 254 nm and the specific transmission media is agarose gel with 0.8% concentration. Each lane in the agarose gel is scanned under UV light and transmittance values at 254 nm are recorded as a function of position. The recorded data are processed to see the absorption pattern along the lane. The drop in the signal indicates the existence of a DNA band. Experiments have been performed on three different agarose gels, which are 4 mm thick, and with 0.8% concentration. The value of wavelength-dependent absorptivity coefficient a([gamma]) was determined within an error margin. The resolution of the method was found to be 4 ng/[mu]l.by Namik Kemal Yilmaz.S.M

UNERTAN SYNDROME: A CASE SERIES DEMONSTRTAING HUMAN DEVOLUTION

A large family with six individuals exhibiting the Unertan syndrome (UTS) was identified residing in southern Turkey. All of the individuals had mental impairments and walked on all four extremities. The intra-familial marriages suggested that the UTS is an autosomal recessive disorder. The inferior portions of the cerebellum and vermis were absent as evidenced by MRI and CT scans. The height and head circumference of those affected were within normal ranges. Barany’s test suggested normal vestibular system function. The subjects could not name objects or their close relatives. The males (n = 4) could understand simple questions, answering them with only one or two sounds. The females (n = 2) were superior to the males with respect to language skills and walking, suggesting an association between walking and speaking abilities. One male exhibited three walking patterns at the same time: quadripedal, tiptoe, and scissor walking. Another male used two walking styles: quadripedal and toe-walking. It is emphasized that there are important differences between the UTS and the disequilibrium syndrome (DES). It is suggested that the inability to walk upright in those affected with the UTS may be best explained by a disturbance in lateral-balance mechanisms. An interruption of locomotor development during the transition from quadripedality to bipedality may result in habitual walking on all four extremities and is normal in some children. Since quadripedal gait is an ancestral trait, individuals with the UTS, exhibiting a manifestation of reverse evolution in humans, may be considered an experiment of nature, useful in understanding the mechanisms underlying the transition from quadripedality to bipedality during human evolution. The proposed mutant gene or gene pool playing a role in human quadrupedality may also be responsible for human bipedality at the same time. Herein there is no intent to insult or injure, rather this report is an endeavor to better understand human beings

Path planning of AUVs for adaptive sampling

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, February 2006.Includes bibliographical references (p. 235-244).This thesis develops new methods for path planning of Autonomous Underwater Vehicles for adaptive sampling. The problem is approached in an optimization framework and two methods are developed to solve it based on Mixed Integer Programming (MIP). The first method is predicated on network-flow ideas and is shown to have similarities to the Selective Traveling Salesman Problem. An important classification of the set of path-planning problems to be solved is the number of days that are involved in the complete sampling mission. Intrinsic limitations of the first network-flow-based method limit it to single day adaptive sampling missions. The second method emerged by taking into consideration the limitations of the first method and is based on a general MIP formulation. It is a more powerful formulation as it can handle multiple-day adaptive sampling missions, it is scalable as it can address the multiple vehicle case with ease, and it is more easily extensible to cover unforeseen situations that might arise as adaptive sampling concepts and needs evolve. The second formulation also allowed solution of auxiliary problems, required to determine suitable initial conditions for the main method. The method is applied to various test problems including evaluation of performance issues.(cont.) A real-world problem is also solved by the second method taking two different approaches. The first approach (static approach) involves a three-day-long adaptive sampling mission using the uncertainty information available on the first day. The second approach (dynamic approach) involves updating of the uncertainty information for each day using data assimilation features of the Harvard Ocean Prediction System and the Error Subspace Statistical Estimation system. The dynamic method is illustrative of how path planning for adaptive sampling fits into modern dynamic data driven oceanography. The results from the dynamic approach show that the uncertainty of the forecast decreases and becomes confined to a smaller region, indicating the strength of the method.by Namik Kemal Yilmaz.Ph.D

Petrogenesis of Late Cretaceous Adakitic Magmatism in the Istanbul Zone (Cavusbasi Granodiorite, NW Turkey)

The Cavusbasi granodiorite intrudes Ordovician sedimentary rocks in the western part of the Istanbul Zone (NW Turkey). The intrusion is made up mainly of granodiorite, and subordinate tonalite and quartz diorite, and has a granular texture and some special mixing textures such as antirapakivi, blade-shaped biotite, acicular apatite, spongy cellular dissolution/melting plagioclase textures. The main mafic minerals are hornblende and biotite. U-Pb in-situ dating of zircons from two samples via SHRIMP yielded weighted age values of similar to 68 Ma, suggesting emplacement during the Late Cretaceous. Geochemically the Cavusbasi granodiorite resembles adakites with high Sr/Y and La/Yb ratios, low Y and HREE contents and no Eu anomaly. It contains 63.4 (wt%) >SiO2, and is I-type, metaluminous, middle-K calc-alkaline. These adakitic rocks have high values of MgO (0.77-2.56 wt%), Mg# (45.3-59.3) and LILE (e.g., Rb, K, Ba, Sr). Initial epsilon Nd and Sr-87/Sr-86 values are 3.2-3.7 and 0.7035-0.7036, respectively. Based on the continuing subduction along the Izmir-Ankara and Intra-Pontide Neo-Tethyan oceanic domains and depleted Sr-Nd isotopic signatures, we suggest that the adakitic magmas may be derived from the partial melting of an oceanic slab under amphibole-eclogite facies conditions