High Throughput Primer Walking of cDNA Clones

Primer walking of cloned DNA is a standard research tool. It has been used in the past to determine the sequence of individual clones of interest. With the expansion of DNA sequencing capacity the need to be able to walk larger numbers of clones has become necessary. Our laboratory is a mid-sized genomics facility. In conjunction with the Advanced Biomedical Computing Center (ABCC) we have developed methods for automating the primer selection, DNA sequencing, contig assembly and sequence analysis for clones arrayed in microtiter format. This approach has allowed us to walk 475 clones (five microtiter plates) selected from a cDNA library.     

Single-Threaded vs. Multithreaded: Where Should We Focus?

Today, with the increasing popularity of multicore processors, one approach to optimizing the processor's performance is to reduce the execution times of individual applications running on each core by designing and implementing more powerful cores. Another approach, which is the polar opposite of the first, optimizes the processor's performance by running a larger number of applications on a correspondingly larger number of cores, albeit simpler ones. The difference between these two approaches is that the former focuses on reducing the latency of individual applications or threads (it optimizes the processor's single-threaded performance), whereas the latter focuses on reducing the latency of the applications' threads taken as a group (it optimizes the processor's multithreaded performance). The panel, from the 2007 Workshop on Computer Architecture Research Directions, discusses the relevant issues.     

Intermittent Phenomena in Switched Systems With High Coupling Strengths

In this paper, one kind of intermittency generated by a discontinuous system is studied. Although this system, which is composed of two switched subsystems coupled with a high strength, is nonsmooth, the mechanism of this kind of intermittency can be analyzed with several explicit relations between the intermittency characteristics and the system control parameters. In particular, estimates of "steady-state" values of the system (in the laminar phases) and a critical value for this intermittency can be derived, which are helpful in relevant control systems design. Moreover, some power laws for the observed intermittency are obtained and discussed     

Pyrolysis of tertiarybutylphosphine at low pressure

The pyrolysis of tertiarybutylphosphine (TBP) has been studied in the low pressure conditions used for chemical beam epitaxy (CBE). The pyrolysis studies were carried out in low pressure reactors of two different configurations, one of which is a cracker cell designed for use in a CBE system. The reaction products were studied using a quadrupole mass spectrometer. The products observed are accounted for by a reaction mechanism involving homolysis of the parent TBP molecule to produce PH₂ and C₄H₉ radicals. These undergo subsequent reactions to form the stable products C₄H₈, PH₃ and H₂, with smaller amounts of P and P₂ being produced. The production of the sub-hydride PH₂ using this cracker cell design indicates that the use of partially cracked TBP may be a promising technique for reducing the amount of carbon incorporated into the growing epitaxial layer.     

COAEs and SSOAEs in adults with increased age

OBJECTIVE: The purpose of this study was to compare click-evoked otoacoustic emissions (COAEs) of subjects having similar auditory thresholds but different age ranges. It is well known that elevated hearing thresholds are common with increasing age and that deterioration of outer hair cells is often noted in cases of hearing loss due to increased age. It has also been reported that evoked otoacoustic emissions (EOAEs) decrease with increased age. However, there is still some question whether changes in EOAEs with aging are associated with the increased hearing threshold or whether there is some additional effect of aging that enfluences EOAEs. DESIGN: COAE input/output functions and synchronized spontaneous OAEs (SSOAEs) were measured in two groups of subjects having similar auditory thresholds, one ranging in age from 19 to 29 yr, the other ranging in age from 40 to 61 yr. Mixed-model ANOVAs were performed to determine whether there were any statistically significant differences in COAEs based on age group. RESULTS: There were no statistically significant differences in COAE level or COAE threshold between age groups. Significant differences in COAEs were found for subjects based on whether they had measurable SSOAEs, regardless of age. CONCLUSIONS: Age does not significantly reduce COAE level nor increase COAE threshold. Other factors, such as presence of SSOAEs and hearing loss, undoubtedly have more influence on COAEs than the factor of age.     

Selective interference with class I major histocompatibility complex presentation of the major immediate-early protein following infection with human cytomegalovirus

Responses of cytotoxic T-cells (Tc) to human cytomegalovirus (CMV) represent the predominant mechanism by which hosts resist CMV infection. The CMV major immediate-early protein (IE) is present throughout the virus replicative cycle. Studies were performed to determine whether Tc specific for IE effectively lyse CMV-infected targets and are thus capable of providing protective immunity against infection. After in vitro stimulation of peripheral blood mononuclear cells with CMV-infected autologous fibroblasts, Tc specific for IE were not readily detectable in CMV-reactive polyclonal Tc lines. However, after stimulation of peripheral blood mononuclear cells with cells selectively expressing IE, weak but detectable IE-specific Tc responses were observed. The frequency of IE-specific Tc clones derived from cultures stimulated with IE-expressing cells was 50 to 100 times lower than the frequency of Tc clones specific for other CMV proteins isolated from cultures stimulated with CMV-infected cells. All of the IE-specific Tc clones, which efficiently lysed targets selectively expressing IE, demonstrated minimal lysis of CMV-infected fibroblasts, despite abundant IE expression in these target cells. In contrast to these results with IE, other viral proteins were efficiently presented during all phases of CMV infection. These data suggest that CMV has evolved a unique mechanism for selectively limiting the presentation of the potentially immunogenic IE protein, which may preclude IE-specific Tc from providing protective immunity to CMV infection.