Structure of a rare non-standard sequence k-turn bound by L7Ae protein

Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates

A video display interface for the LORAN-C navigation receiver development system

A microprocessor-based development system was designed and fabricated for prototype test of navigation receiver designs. During use of this system in the development of low-cost LORAN-C receiver/processor concepts, the limitations of the integral KIM-1 display were severely felt. It was to augment this numerical display that the video character display was produced. The circuit design presented meets the need for a flexible-format display capable of driving a small standard video monitor with only minimal demands upon microprocessor memory and MPU cycles

A microcomputer-based low-cost Omega navigation system

The application of a low cost, commercially available microcomputer as the navigation processor for a simplified OMEGA navigation system is an area of current research. The interface of a low cost front end OMEGA sensor is described and an example of the phase processing software and navigation routines is given. Emphasis is placed on the description of results obtained with the software version of the OMEGA burst filter known as the memory aided phase locked loop

Estimation of tunnel blockage from wall pressure signatures: A review and data correlation

A method is described for estimating low speed wind tunnel blockage, including model volume, bubble separation and viscous wake effects. A tunnel-centerline, source/sink distribution is derived from measured wall pressure signatures using fast algorithms to solve the inverse problem in three dimensions. Blockage may then be computed throughout the test volume. Correlations using scaled models or tests in two tunnels were made in all cases. In many cases model reference area exceeded 10% of the tunnel cross-sectional area. Good correlations were obtained regarding model surface pressures, lift drag and pitching moment. It is shown that blockage-induced velocity variations across the test section are relatively unimportant but axial gradients should be considered when model size is determined

Simulation analysis of a microcomputer-based, low-cost Omega navigation system

The current status of research on a proposed micro-computer-based, low-cost Omega Navigation System (ONS) is described. The design approach emphasizes minimum hardware, maximum software, and the use of a low-cost, commercially-available microcomputer. Currently under investigation is the implementation of a low-cost navigation processor and its interface with an omega sensor to complete the hardware-based ONS. Sensor processor functions are simulated to determine how many of the sensor processor functions can be handled by innovative software. An input data base of live Omega ground and flight test data was created. The Omega sensor and microcomputer interface modules used to collect the data are functionally described. Automatic synchronization to the Omega transmission pattern is described as an example of the algorithms developed using this data base

The k-junction motif in RNA structure

The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. The k-junction exhibits all the key features of an N1-class k-turn, including the standard cross-strand hydrogen bonds. The third helix of the junction is coaxially aligned with the C (canonical) helix, while the k-turn loop forms the turn into the NC (non-canonical) helix. Analysis of ligand binding by ITC and global folding by gel electrophoresis demonstrates the importance of the k-turn nucleotides. Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn

Laterality of Eye Use by Bottlenose (Tursiops truncatus) and Rough-toothed (Steno bredanensis) Dolphins While Viewing Predictable and Unpredictable Stimuli

Laterality of eye use has been increasingly studied in cetaceans. Research supports that many cetacean species keep prey on the right side while feeding and preferentially view unfamiliar objects with the right eye. In contrast, the left eye has been used more by calves while in close proximity to their mothers. Despite some discrepancies across and within species, laterality of eye use generally indicates functional specialization of brain hemispheres in cetaceans. The present study aimed to examine laterality of eye use in bottlenose dolphins (Tursiops truncatus) and rough-toothed dolphins (Steno bredanensis) under managed care. Subjects were video-recorded through an underwater window while viewing two different stimuli, one predictable and static and the other unpredictable and moving. Bottlenose dolphins displayed an overall right-eye preference, especially while viewing the unpredictable, moving stimulus. Rough-toothed dolphins did not display eye preference while viewing stimuli. No significant correlations between degree of laterality and behavioral interest in the stimuli were found. Only for bottlenose dolphins were the degree of laterality and curiosity ratings correlated. This study extends research on cetacean lateralization to a species not extensively examined and to stimuli that varied in movement and degree of predictability. Further research is needed to make conclusions regarding lateralization in cetaceans

A preliminary study towards the construction of Carboxypeptidase Y - Legumin gene fusions to facilitate an analysis of protein sorting in yeast

In an attempt to isolate and clone the promotor and preprosequence of the yeast vacuolar protease carboxypeptidase Y, three, PRC-1-derived, Bsc I - Bam HI restriction fragments were ligated into a vector plasmid (pKS(^+)) and separately transformed into E. coli. Preliminary screening and restriction analysis suggested that one transformant (pCPYF3), contained the desired sequences. However, more detailed restriction analyses and ultimately DNA sequencing of the cloned insert, subsequently showed this not to be so. A reappraisal of the data indicated the likely location of the desired PRCl fragment in a different set of transformants (pCPYF2). Screening of these transformants however, yielded an inconclusive result. Legumin encoding cDNA sequences were successfully cloned into pKS(^+). Exonuclease III/mung bean nuclease deletion of both the PRCl and leg A derived sequences was performed in order to edit both genes in preparation for the construction of a PRCl-leg A gene fusion

Acoustic Management of Library Fishbowls

The purpose of this project is to aid the Cal Poly Robert E. Kennedy library in modifying the “fishbowl” study spaces to more effectively maintain the desirable sound that is generated within the fishbowls while avoiding the entrance and exit of excess noise to and from the fishbowls. A collaboration between the Materials Engineering Department and the Architecture Department provided the combined expertise needed to design, test, and install a prototype acoustic treatment in fishbowl 216-R in consultation with the Cal Poly Library as the voice of the customer. The fishbowl’s undesirable acoustic properties can be attributed to the hard surfaces within the fishbowl and the large air gap between the top of the walls of the fishbowl and the ceiling of the room. Working with industry standard sound measurement equipment and noise pollution expertise provided by Dr. Tracy Thatcher of the Environmental Engineering Department, wool felt was chosen and found to be a material satisfactory in improving fishbowl sound quality. The felt reduced reverberation within the fishbowl by about 0.1 seconds. With the help of the Architecture Department, the wool felt was incorporated into a fishbowl to provide both an acoustically effective and aesthetically pleasing treatment. The prototype acoustic treatment will be installed in fishbowl 216-R during finals week of the Spring 2017 quarter

Bringing Oversight Review in Line with Online Research

The purpose of an oversight structure or institution is to protect human subjects from research that would pose unacceptable dangers or deny human rights. Review boards provide an independent assessment of research proposals. This additional level of scrutiny is meant to provide an additional level of protection for human subjects. However, oversight of human subject research, as currently carried out in the bureaucratic, rule-based, clinically-biased American system, is too cumbersome with regard to online research. In addition, it is not conducive to the training of ethical Internet researchers. Internet research differs from traditional human subject research in many ways, and the oversight rules governing traditional research do not easily relate to the complexities of conducting research online. Online researchers do not oppose the foundational principles of non-maleficence (avoiding harm) and autonomy, nor do they reject the ideals of informed consent and confidentiality, nevertheless, they face practical dilemmas in attempting to follow these principles and apply these ideals in the various Internet domains. The current oversight system is ill-equipped to assist. A conservative response to this problem of fit might entail adjustments to the oversight system that, in the case of the American system, would entail modifications to the Common Rule and Institutional Review Boards (IRBs). I will argue in this paper, instead, that re-structuring is needed to allow more oversight authority for Internet researchers. I will utilize Consequentialism and Virtue Ethics in making this case