In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine

Widespread use of the chlorotriazine herbicide, atrazine, has led to serious environmental and human health consequences. Current methods of detecting atrazine contamination are neither rapid nor cost-effective. In this work, atrazine-specific single-stranded DNA (ssDNA) molecular recognition elements (MRE) were isolated. We utilized a stringent Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology that placed the greatest emphasis on what the MRE should not bind to. After twelve rounds of SELEX, an atrazine-specific MRE with high affinity was obtained. The equilibrium dissociation constant (K_d) of the ssDNA sequence is 0.62 ± 0.21 nM. It also has significant selectivity for atrazine over atrazine metabolites and other pesticides found in environmentally similar locations and concentrations. Furthermore, we have detected environmentally relevant atrazine concentrations in river water using this MRE. The strong affinity and selectivity of the selected atrazine-specific ssDNA validated the stringent SELEX methodology and identified a MRE that will be useful for rapid atrazine detection in environmental samples.     

Mechanical damage to Gram-negative bacteria by surface plating with the Drigalski-spatula technique

Colony counting by spreading bacterial suspensions on plating media by various techniques is of general concern. Comparative studies between hand plating (Drigalski-spatula technique) for different time intervals and spiral plating resulted in significant differences in colony counts. Lower counts of Gram-negative bacteria were obtained by using hand plating for more than 10 s, compared with short time hand plating (5 s) or spiral plating. Colony counting of Gram-positive bacteria showed no differences between both techniques. Further characterisation of Escherichia coli cells spread with the Drigalski-spatula technique by electron microscopy revealed a large number of damaged cells compared to control samples. The data clearly shows that the mechanical forces during hand plating are sufficient to damage E. coli cells.     

Accelerating Machine-Learning Algorithms on FPGAs using Pattern-Based Decomposition

Machine-learning algorithms are employed in a wide variety of applications to extract useful information from data sets, and many are known to suffer from super-linear increases in computational time with increasing data size and number of signals being processed (data dimension). Certain principal machine-learning algorithms are commonly found embedded in larger detection, estimation, or classification operations. Three such principal algorithms are the Parzen window-based, non-parametric estimation of Probability Density Functions (PDFs), K-means clustering and correlation. Because they form an integral part of numerous machine-learning applications, fast and efficient execution of these algorithms is extremely desirable. FPGA-based reconfigurable computing (RC) has been successfully used to accelerate computationally intensive problems in a wide variety of scientific domains to achieve speedup over traditional software implementations. However, this potential benefit is quite often not fully realized because creating efficient FPGA designs is generally carried out in a laborious, case-specific manner requiring a great amount of redundant time and effort. In this paper, an approach using pattern-based decomposition for algorithm acceleration on FPGAs is proposed that offers significant increases in productivity via design reusability. Using this approach, we design, analyze, and implement a multi-dimensional PDF estimation algorithm using Gaussian kernels on FPGAs. First, the algorithm’s amenability to a hardware paradigm and expected speedups are predicted. After implementation, actual speedup and performance metrics are compared to the predictions, showing speedup on the order of 20× over a 3.2 GHz processor. Multi-core architectures are developed to further improve performance by scaling the design. Portability of the hardware design across multiple FPGA platforms is also analyzed. After implementing the PDF algorithm, the value of pattern-based decomposition to support reuse is demonstrated by rapid development of the K-means and correlation algorithms.     

Microscale exoglycosidase processing and lectin capture of glycans with phospholipid assisted capillary electrophoresis separations

Capillary electrophoresis separations of glycans labeled with 1-aminopyrene-3,6,8-trisulfonic acid were achieved with separation efficiencies ranging from 480,000 to 640,000 theoretical plates in a 60.2 cm, 25 μm inner diameter fused silica capillary. Under these separation conditions, the coefficient of variation in peak area is 10%, and if labeling efficiency is estimated at 100%, the limit of detection is 15 fM. The capillary electrophoresis method incorporated phospholipid additives to enhance the separation of glycans with slight differences in hydrodynamic volume. In addition, the phospholipid additives supported the integration of the lectin concanavalin A as well as the enzymes α1-2,3 mannosidase or β1-4 galactosidase to provide structural and compositional information about the glycans subject to separation. The use of in-capillary cleavage of terminal glycan residues with exoglycosidases offers a number of advantages over benchtop enzymatic sequencing, including reduced consumption of analyte, as well as enzyme. These methods were used to evaluate glycans derived from the glycoproteins α1-acid glycoprotein, fetuin, and ribonuclease B, as well as from glycoproteins collected from MCF7 cells.     

PDZ-domain-mediated interaction of the Eph-related receptor tyrosine kinase EphB3 and the ras-binding protein AF6 depends on the kinase activity of the receptor

Eph-related receptor tyrosine kinases (RTKs) have been implicated in intercellular communication during embryonic development. To elucidate their signal transduction pathways, we applied the yeast two-hybrid system. We could demonstrate that the carboxyl termini of the Eph-related RTKs EphA7, EphB2, EphB3, EphB5, and EphB6 interact with the PDZ domain of the ras-binding protein AF6. A mutational analysis revealed that six C-terminal residues of the receptors are involved in binding to the PDZ domain of AF6 in a sequence-specific fashion. Moreover, this PDZ domain also interacts with C-terminal sequences derived from other transmembrane receptors such as neurexins and the Notch ligand Jagged. In contrast to the association of EphB3 to the PDZ domain of AF6, the interaction with full-length AF6 clearly depends on the kinase activity of EphB3, suggesting a regulated mechanism for the PDZ-domain-mediated interaction. These data gave rise to the idea that the binding of AF6 to EphB3 occurs in a cooperative fashion because of synergistic effects involving different epitopes of both proteins. Moreover, in NIH 3T3 and NG108 cells endogenous AF6 is phosphorylated specifically by EphB3 and EphB2 in a ligand-dependent fashion. Our observations add the PDZ domain to the group of conserved protein modules such as Src-homology-2 (SH2) and phosphotyrosine-binding (PTB) domains that regulate signal transduction through their ability to mediate the interaction with RTKs.     

A mesoscopic ballistic electron mixer with efficient frequencyconversion at radio frequency

The voltage-current characteristic of a four-terminal mesoscopic cross is grossly nonlinear, exhibiting two clear regions of negative differential resistance (NDR). This behavior is potentially useful in millimeter wave detectors since these small devices have very low parasitic capacitance and great sensitivity. The device exploits a planar GaAs technology which lends itself to integrated systems. We have exploited one of the NDR regions (at a current of only 1.9 μA) to carry out frequency conversion. At low frequency we observed efficient frequency doubling, with the second harmonic exceeding the fundamental by up to 10 dB at the output. We have also operated the device at radio frequency (5 MHz) and demonstrated both asynchronous and heterodyne amplitude demodulation. The effect of DC current bias was examined and it was shown that biasing the device close to the NDR gave the optimum frequency conversion. A conversion loss in the heterodyne mixer circuit of 3 dB was achieved     

The Adult Attachment Interview and self-reports of attachment style: An empirical rapprochement.

Although 10 studies have been published on the empirical overlap of the Adult Attachment Interview (AAI) and measures of self-reported attachment style, results in this literature have been inconsistently interpreted in narrative reviews. This report was designed as a rapprochement of the AAI and attachment style literatures and includes 3 studies. Study 1 (combined N = 961) is a meta-analytic review showing that by J. Cohen's (1992) criteria (mean r = .09), the association between AAI security and attachment style dimensions is trivial to small. Study 2 (N = 160) confirms meta-analytic results with state-of-the-art assessments of attachment security and also examines attachment dimensions in relation to the Big 5 personality traits. Finally, Study 3 is an investigation of 50 engaged couples that shows that developmental and social psychological measures of attachment security predict somewhat distinct--though theoretically anticipated--aspects of functioning in adult relationships. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Guidelines for the treatment of cytomegalovirus diseases in patients with AIDS in the era of potent antiretroviral therapy: recommendations of an international panel. International AIDS Society-USA

OBJECTIVE: To provide recommendations for the treatment of acquired immunodeficiency syndrome-related cytomegalovirus (CMV) end-organ diseases, including retinitis, colitis, pneumonitis, and neurologic diseases. PARTICIPANTS: A 17-member panel of physicians with expertise in clinical and virological research and inpatient care in the field of CMV diseases. EVIDENCE: Available clinical and virological study results. Recommendations are rated according to the quality and strength of available evidence. Recommendations were limited to the treatment of CMV diseases; prophylaxis recommendations are not included. PROCESS: The panel was convened in February 1997 and met regularly through November 1997. Subgroups of the panel summarized and presented available information on specific topics to the full panel; recommendations and ratings were determined by group consensus. CONCLUSIONS: Although the epidemiological features of CMV diseases are changing in the setting of potent, combination antiretroviral therapy, continued attention must be paid to CMV diseases in patients infected with the human immunodeficiency virus to prevent irreversible endorgan dysfunction. The initial and maintenance treatment of CMV retinitis must be individualized based on the characteristics of the lesions, including location and extent, specific patient factors, and characteristics of available therapies among others. Management of relapse or refractory retinitis must be likewise individualized. Ophthalmologic screening for patients at high risk for retinitis or who have a prior diagnosis of extraretinal disease is recommended. Recommendations for gastrointestinal, pulmonary, and neurologic manifestations are included.     

Comparative analysis of breast cancer contamination in mobilized and nonmobilized hematopoietic grafts

We report a case of an 18-month-old female who presented with three supernumerary upper limbs of varying lengths on the right side. Each limb had a proximal, middle, and distal segment, and an intercalated elbow and wrist joint. A single digit was present in the superior limb, three digits in the middle limb, and two digits in the caudal-most limb. Right plagiocephaly, congenital torticollis, scoliosis involving the upper and mid thoracic region, and a hypoplastic right pectoralis major were the other abnormal features noted. Radiography showed two scapulae, humerus, a single forearm bone in each limb, and rudimentary metacarpals and phalanges. Limb duplication may rarely be encountered in parasitic conjoined twins. The role of mutagens, drugs, cellular contributions, and morphogens in the growth and differentiation of limbs has been studied in animals. It is rather difficult to deduce the time of action of the factors responsible for such a malformation.