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Communication: Multiple atomistic force fields in a single enhanced sampling simulation. - The Journal of chemical physics
The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.
Strategies for enhancing the speed and integration of microchip genetic amplification. - Electrophoresis
In this work, we explore the use of methods that allow a significant acceleration of genetic analysis within microchips fabricated from low thermal conductivity materials such as glass or polymers. Although these materials are highly suitable for integrating a number of genetic analysis techniques onto lab-on-a-chip devices, their low thermal conductivity limits the rate at which heat can be transferred and hence lowers the speed of thermal cycling. However, short thermal cycling times are the key to bringing PCR to clinical point-of-care applications. Although shrinking the PCR reaction chamber volume can increase the speed of thermal cycling, this strategy is not always suitable, particularly when dealing with clinical samples with low analyte concentrations. In the present work, we combine two alternate strategies for decreasing the time required to perform PCR: implementing a heat sink and optimizing the PCR protocol. First, the heat sink substantially reduces the thermal resistance opposing heat dissipation into the ambient environment, and eliminates the parasitic thermal capacitance of the regions in the microchip that do not require heating. The low thermal conductivity of glass is used to our advantage to design the heat-sink placement to achieve fast thermal transitions while maintaining low power consumption. Second, we explore the application of two-stage PCR to provide a further reduction in the time required to perform genetic amplification by merging the annealing and extension stages of the commonly used three-stage PCR approach. In combination, we reduce the time required to perform thermal cycling by roughly a factor of 3 while improving the temperature control.
Elemental analysis using micro laser-induced breakdown spectroscopy (microLIBS) in a microfluidic platform. - Optics express
We present here a non-labeled, elemental analysis detection technique that is suitable for microfluidic chips, and demonstrate its applicability with the sensitive detection of sodium (Na). Spectroscopy performed on small volumes of liquids can be used to provide a true representation of the composition of the isolated fluid. Performing this using low power instrumentation integrated with a microfluidic platform makes it potentially feasible to develop a portable system. For this we present a simple approach to isolating minute amounts of fluid from bulk fluid within a microfluidic chip. The chip itself contains a patterned thin film resistive element that super-heats the sample in tens of microseconds, creating a micro-bubble that extrudes a micro-droplet from the microchip. For simplicity a non-valved microchip is used here as it is highly compatible to a continuous flow-based fluidic system suitable for continuous sampling of the fluid composition. We believe such a nonlabeled detection technique within a microfluidic system has wide applicability in elemental analysis. This is the first demonstration of laser-induced breakdown spectroscopy (LIBS) as a detection technology in conjunction with microfluidics, and represents first steps towards realizing a portable lower power LIBS-based detection system.
Electrically controlled microvalves to integrate microchip polymerase chain reaction and capillary electrophoresis. - Lab on a chip
Microvalves are key in realizing portable miniaturized diagnostic platforms. We present a scalable microvalve that integrates well with standard lab on a chip (LOC) implementations, yet which requires essentially no external infrastructure for its operation. This electrically controlled, phase-change microvalve is used to integrate genetic amplification and analysis via capillary electrophoresis--the basis of many diagnostics. The microvalve is actuated using a polymer (polyethylene glycol, PEG) that exhibits a large volumetric change between its solid and liquid phases. Both the phase change of the PEG and the genetic amplification via polymerase chain reaction (PCR) are thermally controlled using thin film resistive elements that are patterned using standard microfabrication methods. By contrast with many other valve technologies, these microvalves and their control interface scale down in size readily. The novelty here lies in the use of fully integrated microvalves that require only electrical connections to realize a portable and inexpensive genetic analysis platform.
Percutaneously inserted central catheter for total parenteral nutrition in neonates: complications rates related to upper versus lower extremity insertion. - Pediatrics
The objective of this study was to compare the complication rates of upper versus lower extremity percutaneously inserted central catheters used for total parenteral nutrition in neonates.During a 48-month study period, 396 neonates were identified as having had percutaneously inserted central venous catheters. A total of 370 catheters were inserted from the upper and 107 from the lower extremity. Data retrieved and analyzed were birth weight, gestational age, age at placement, duration in place, duration of total parenteral nutrition, type of infusates, catheter-related bloodstream infection, phlebitis, leakage, occlusion, necrotizing enterocolitis, intraventricular hemorrhage, serum creatinine, liver function tests, and length of hospitalization.The median birth weight and gestational age were 940 g and 28 weeks. The rate of catheter-related bloodstream infection was 11.6% for the upper and 9.3% in the lower extremity catheters. The most common organism was coagulase-negative Staphylococcus for both upper and lower extremity catheters and significantly higher with catheters from the upper extremity. Lower extremity catheters were in place longer, and the time from insertion to complication was also longer. The rate of cholestasis was higher for the upper extremity catheters. Multiple regression analysis showed that the most significant contributor to cholestasis was duration of time the catheters were in place and the duration of total parenteral nutrition administration. Receiver operating characteristics curve demonstrated higher sensitivity for duration of catheters in predicting cholestasis with duration of total parenteral nutrition being more specific.Lower extremity percutaneously inserted central venous catheters had lower rates of catheter-related bloodstream infection, longer time to first complication, and lower cholestasis despite longer duration of total parenteral nutrition. When possible, lower extremity inserted catheters should be used for the administration of total parenteral nutrition.
Dynamic temperature measurement in microfluidic devices using thermochromic liquid crystals. - Lab on a chip
Thermochromic liquid crystals (TLCs) are used to explore the temperature transients during thermal cycling for microchip-based polymerase chain reaction (PCR). By analyzing the reflected spectra of the TLCs over time, temperature vs. time trajectories were extracted and overshoots/undershoots were estimated. To our knowledge, this is the first report of TLC-based dynamic temperature measurements in a microfluidic device for all PCR temperature stages.
An inexpensive and portable microchip-based platform for integrated RT-PCR and capillary electrophoresis. - The Analyst
We present an inexpensive, portable and integrated microfluidic instrument that is optimized to perform genetic amplification and analysis on a single sample. Biochemical reactions and analytical separations for genetic analysis are performed within tri-layered glass-PDMS microchips. The microchip itself consists of integrated pneumatically-actuated valves and pumps for fluid handling, a thin-film resistive element that acts simultaneously as a heater and a temperature sensor, and channels for capillary electrophoresis (CE). The platform is comprised of high voltage circuitry, an optical assembly consisting of a laser diode and a charged coupled device (CCD) camera, circuitry for thermal control, and mini-pumps to generate vacuum/pressure to operate the on-chip diaphragm-based pumps and valves. Using this microchip and instrument, we demonstrate an integration of reverse transcription (RT), polymerase chain reaction (PCR), and capillary electrophoresis (CE). The novelty of this system lies in the cost-effective integration of microfluidics, optics, and electronics to realize a fully portable and inexpensive system (on the order of $1000 in component costs) for performing both genetic amplification and analysis - the basis of many medical diagnostics. We believe that this combination of portability, cost-effectiveness and performance will enable more accessible healthcare.
A comparative study of the effect of refining on physical and electrokinetic properties of various cellulosic fibres. - Bioresource technology
The aim of this work was to study the influence of refining on various pulp properties such as freeness, specific surface area, specific volume, surface charge, total charge and elastic modulus. The results indicated that specific surface area of the pulps increased with increased refining, and at the same freeness level the pine pulp exhibited higher surface charge, surface area, and specific volume than the eucalyptus pulps. Also, the eucalypt pulps were much easier to beat than the pine pulps. The total fibre charge, as determined by conductometric titrations, was not affected by refining. However, the surface charge, as determined by titrations with poly-DADMAC, increased with refining. Increasing the specific surface area by refining resulted in a higher fibre surface charge and better fibre-fibre bonding. The change of the fibre surface charge during refining could be monitored using the FTIR characteristic bands within 1700-1300cm(-1).
Effect of refining on pulp surface charge accessible to polydadmac and FTIR characteristic bands of high yield kraft fibres. - Bioresource technology
Studies were carried out to determine the surface charge and total charge of refined softwood high yield kraft pulps at different levels by titration methods. The results showed that the surface charge was highly dependent on the degree of refining. However, the total fibre charge was not affected by refining. The change of the fibre surface charge during refining monitored using ATR-FTIR characteristic bands was within 1700-1300 cm(-1). Reliable PLS1 calibration models could be established to correlate the FTIR spectral data and the surface charge of the refined pulps.
The role of cis-acting sequences governing catabolite repression control of lacS expression in the archaeon Sulfolobus solfataricus. - Genetics
The archaeon Sulfolobus solfataricus uses a catabolite repression-like system to control production of several glycoside hydrolases. To better understand this regulatory system, studies of the regulation of expression of the beta-glycosidase gene (lacS) were conducted. Expression of lacS varies in response to medium composition and to mutations at an unlinked gene called car. Despite gene overlap, expression of the lacS promoter proximal gene, SSO3017, exhibited coregulation but not cotranscription with lacS. Measurements of mRNA half-life excluded differential stability as a factor in lacS regulation. Chromosomal repositioning by homologous recombination of a lacS deletion series clarified critical cis-acting sequences required for lacS regulation. lacS repositioned at amyA exhibited increased lacS expression and compromised the response to medium composition independently of lacS 5' flanking sequence composition. In contrast, regulation of lacS by the car mutation was dependent on sequences upstream of the archaeal TATA box. Expression of a promoter fusion between lacS and the car-independent malA promoter integrated either at amyA or at the natural lacS locus was insensitive to the allelic state of car. In contrast, the promoter fusion retained a response to medium composition only at the lacS locus. These results indicate that car acts at the lacS promoter and that the response to medium composition involves locus-specific sequences exclusive of those present 5' to lacS or within the lacS transcription unit.Copyright 2004 Genetics Society of America
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