Introduction to new series

Peer reviewedPublisher PD

Comprehensive Detection of Genes Causing a Phenotype using Phenotype Sequencing and Pathway Analysis

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. In this paper we combine an experimental design for multiple independent detections of the genetic causes of a phenotype, with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome

Broughton Archipelago Clam Terrace Survey : final report

During a 1995 aerial video survey of the coastline of Johnstone Strait, an unusual shoreline feature was noted and termed “clam terraces” (inset) because of the terrace-type morphology and the apparent association with high clam productivity on the sandflats. Typical alongshore lengths of the terrace ridges are 20-50m, and across-shore widths are typically 20-40m. An area with an especially high density of clam terraces was noted in the Broughton Archipelago, between Broughton and Gilford Islands of southeastern Queen Charlotte Strait. Clam terraces in this area were inventoried from the aerial video imagery to quantify their distribution. The terraces accounted for over 14 km of shoreline and 365 clam terraces were documented. A three-day field survey by a coastal geomorphologist, archeologist and marine biologist was conducted to document the features and determine their origin. Nine clam terraces were surveyed. The field observations confirmed that: the ridges are comprised of boulder/cobblesized material, ridge crests are typically in the range of 1-1.5m above chart datum, sandflats are comprised almost entirely of shell fragments (barnacles and clams) and sandflats have very high shellfish production. There are an abundance of shell middens in the area (over 175) suggesting that the shellfish associated with the terraces were an important food source of aboriginal peoples. The origin of the ridges is unknown; they appear to be a relict feature in that they are not actively being modified by present-day processes. The ridges may be a relict sea-ice feature, although the mechanics of ridge formation is uncertain. Sand accumulates behind the ridge because the supply rate of the shell fragments exceeds the dispersal rate in these low energy environments. The high density areas of clam terraces correspond to high density areas of shell middens, and it is probable that the clam terraces were subjected to some degree of modification by aboriginal shellfish gatherers over the thousands of years of occupation in the region. (Document contains 39 pages

A Survey to Select Area Headings to be Included in a Handbook for School Administrators to Administer Departments of Vocational Agriculture in South Dakota

In this study the writer is attempting to find a few of the problems that confront the teacher of agriculture and the superintendent. It is believed that the constant moving and shifting of vocational agricultural instructors from our smaller high schools can be somewhat relieved through a study of this particular type. In a study by Clarke, a former vocational agricultural in South Dakota, it appears that, although salary was the primary problem, there were also other problems that caused vocational agricultural instructors to leave the profession. One of these problems was the lack of cooperation on the part of the administration. Most of the problems that arise stem from misunderstandings. Therefore, an attempt at eliminating these misunderstandings should be made. This study was prompted by the fact that the writer’s first two years of teaching experience were under a superintendent who for the first time experienced having a vocational agricultural department in his school system. It was further prompted by other agricultural instructors who expressed their feelings about working in systems where misunderstandings existed. The writer immediately asked, “Why can’t we clear up these unfortunate misunderstandings? Why can’t we show the vocational agricultural instructor the superintendent’s problems, and the superintendent how the vocational agricultural instructor operates?” However, the main purpose of this paper is an introduction to a handbook to be written at some later date when sufficient material has become accumulated and other studies have been initiated that will make it feasible

Pocket Rocket: A 1U+ Propulsion System Design To Enhance CubeSat Capabilities

The research presented provides an overview of a 1U+ form factor propulsion system design developed for the Cal Poly CubeSat Laboratory (CPCL). This design utilizes a Radiofrequency Electrothermal Thruster (RFET) called Pocket Rocket that can generate 9.30 m/s of delta-V with argon, and 20.2 ± 3 m/s of delta-V with xenon. Due to the demand for advanced mission capabilities in the CubeSat form factor, a need for micro-propulsion systems that can generate between 1 – 1500 m/s of delta-V are necessary. By 2019, Pocket Rocket had been developed to a Technology Readiness Level (TRL) of 5 and ground tested in a 1U CubeSat form factor that incorporated propellant storage, pressure regulation, RF power and thruster control, as well as two Pocket Rocket thrusters under vacuum, and showcased a thrust of 2.4 mN at a required 10 Wdc of power with Argon propellant. The design focused on ground testing of the thruster and did not incorporate all necessary components for operation of the thruster. Therefore in 2020, a 1U+ Propulsion Module that incorporates Pocket Rocket, the RF amplification PCB, a propellant tank, propellant regulation and delivery, as well as a DC-RF conversion with a PIB, that are all attached to a 2U customer CubeSat for a 3U+ overall form factor. This design was created to increase the TRL level of Pocket Rocket from 5 to 8 by demonstrating drag compensation in a 400 km orbit with a delta-V of 20 ± 3 m/s in the flight configuration. The 1U+ Propulsion Module design included interface and requirements definition, assembly instructions, Concept of Operations (ConOps), as well as structural and thermal analysis of the system. The 1U+ design enhances the capabilities of Pocket Rocket in a 1U+ form factor propulsion system and increases future mission capabilities as well as propulsion system heritage for the CPCL

The ecological role of beavers (Castor canadensis) in a Southwestern desert stream

The ecological impact of beavers on a stream in the southwestern United States was investigated to determine if beavers have impact on community and ecosystem level processes in a manner similar to what has been documented in more mesic regions. Specifically, my goals were to determine: (1) whether beaver pond densities differ in an arid Mojave Desert system from densities reported for those of more mesic regions, (2) what riparian plant species beaver are foraging on most frequently in this system, and (3) to determine if beaver ponds alter the system retention of nitrogen, a nutrient that often limits primary production in streams of the western United States; The spatial prevalence of beaver ponds along Meadow Valley Wash, a perennial stream in southeast Nevada, was determined by surveying 31.5 kilometers of the stream\u27s length. At the ecosystem level, stream nitrogen retention was measured. (Abstract shortened by UMI.)

Attorneys as State Actors: A State Action Model and Argument for Holding SLAPP-Plaintiffs\u27 Attorneys Liable under 42 U.S.C. 1983

Strategic Litigation Against Public Participation ( SLAPP ) is a recently identified genre of intimidation suit that menaces citizen activism on matters of public concern. The problem with SLAPPs is that their success is not contingent on victory in court; they begin achieving their purpose the moment suit is filed. This Note reviews SLAPPs and defenses and deterrents to SLAPPs. It proposes an additional deterrent to SLAPPs: applying 42 U.S.C. § 1983 to SLAPP-plaintiffs\u27 attorneys. Because section 1983 requires deprivation of civil rights under color of law, this Note explores whether and when attorneys are state actors and proposes a model to harmonize the United States Supreme Court\u27s cases on that subject. Under certain circumstances, attorneys are state actors who can be liable under section 1983