Life Sciences Commons^™

Genomic Testing And Method R Variance Components Theory Of Dairy Cattle, Joseph Dewey Coleman

Dairy Science

Abstract

The objective of this study is to determine the change in reliability from non genomic evaluations or Parent Averages to genomic evaluations. Due to recent industry popularity of genomic evaluations the California Polytechnic University, San Luis Obispo, decided to participate in the genetic movement of the dairy cattle industry. Genomic evaluations of both Holstein and Jersey cows at the Cal Poly dairy were chosen based on genetic superiority in order to possibly generate more income for the dairy and increase the herd’s popularity. Leading genomic companies such as Pfizer Animal Health, and GenSeek made genomic evaluation of the Cal …

Ear Length As A Diagnostic Character For Identifying Species Of Kangaroo Rats, Daniel W. Ziebron

Biological Sciences

The following study examines the use of ear length as a diagnostic field character for differentiating between species of Kangaroo rats in San Luis Obispo County. Data was taken from a study of Kangaroo rats in the Guadalupe-Nipomo Dunes National Wildlife Refuge, as well as various collections under the supervision of Francis X. Villablanca, Ph. D. and California Polytechnic State University, San Luis Obispo. An ANOVA was used to compare subspecies within Dipodomys heermanni and t-tests were used to compare ear lengths between Dipodomys heermanni and Dipodomys venustus. The analysis shows a statistically significant difference and supports the hypothesis …

Safety Hazard Analysis And Corrective Measures For Koot Dairy, Billy Koot

Dairy Science

The objective of the study was to determine any potential safety hazards at Koot Dairy in order to prevent injuries and lawsuits. A hazard walkthrough was performed with employees to help discover hazards and determine the correctible actions that must take place. A farm safety checklist was used to assess some of the most common dairy hazards and to ensure law compliance. The checklist included many potential areas of hazard—first aid and emergency, power and electrical, farm equipment and machinery, farm chemicals, fuel tanks, confined spaces, environment, and workplace policies. After implementing the checklist, it was clear as to what …

Dna Collection With Performagene Nasal Swabs: Quantity, Quality, And Cost Effectiveness, Robert Kamper

Dairy Science

The objective was to determine the quality and quantity of DNA collected via nasal swab in Holstein and Jersey cows compared to the time taken to collect the samples through a person inexperienced with the Performagene™ LIVESTOCK product. DNA was collected from 100 cows at the California Polytechnic State University San Luis Obispo Dairy. Holsteins (n=47) and Jerseys (n=53) were collected and samples were shipped to Iowa State University where DNA was extracted by Dr. Jim Reecy’s lab. Results were compiled into a spreadsheet based on DNA quantity in ng/ul, and protein to DNA ratios (A260/A280). Extracted DNA was sent …

Effect Of Cnv Of Production Related Genes On Expression Of Production Traits In Dairy Cattle, Tyler Kamper

Dairy Science

The objective of this project was to determine if copy number variation (CNV) at specific genes related to BST had an effect on milk production. Hair samples from 1000 fresh heifers from Maddox Dairy in Riverdale, CA were sent to Geneseek, a Neogen Company for DNA extraction and processing. The DNA was processed using the BovineSNP50 BeadChip and the data were loaded into the GenomeStudio software. The data were manipulated in GenomeStudio to estimate the CNV at each single nucleotide polymorphism (SNP) of which a vast majority was two. The SNPs with a copy number of two were excluded and …

Science & The Senses: Perceptions & Deceptions, William D. Stansfield

Biological Sciences

Science requires the acquisition and analysis of empirical (sense-derived) data. Given the same physical objects or phenomena, the sense organs of all people do not respond equally to these stimuli, nor do their minds interpret sensory signals identically. Therefore, teachers should develop lectures on human sensory systems that include some common examples of sensory limitations, variations, deficiencies, malfunctions, and diseases (as discussed herein) because they have important implications for conducting scientific investigations, science education, and introspection that are seldom included in biology textbooks. Students need to be made aware of the human tendency to self deception in order to avoid …

Potential For Barn Owl As Rodent Biological Control In Central California Vineyards, Hannah Tillmann

Biological Sciences

The pocket gopher (Thomomys bottae) and voles (Microtus spp.) cause significant economic damage to vineyards. In response, many growers have taken steps to attract Barn Owls (Tyto alba) to their properties to help keep these rodent populations in check. This research project investigated Barn Owl consumption of pocket gophers and voles in Central California vineyards in order to assess the efficiency of this integrated pest management strategy. I collected a total of 715 owl pellets from five vineyard locations in Templeton and Paso Robles, California over an eight-month period during nesting and post-fledging seasons. I …

Fishing Top Predators Indirectly Affects Condition And Reproduction In A Reef-Fish Community, S.M. Walsh, S.L. Hamilton, Bi. Ruttenberg, M.K. Donovan, S.A. Sandin

Biological Sciences

To examine the indirect effects of fishing on energy allocation in non-target prey species, condition and reproductive potential were measured for five representative species (two-spot red snapper Lutjanus bohar, arc-eye hawkfish Paracirrhites arcatus, blackbar devil Plectroglyphidodon dickii, bicolour chromis Chromis margaritifer and whitecheek surgeonfish Acanthurus nigricans) from three reef-fish communities with different levels of fishing and predator abundance in the northern Line Islands, central Pacific Ocean. Predator abundance differed by five to seven-fold among islands, and despite no clear differences in prey abundance, differences in prey condition and reproductive potential among islands were found. Body condition …

Design, Acnd Construction Of A Portable Artificial Insemination Chute, Chris Herrera

BioResource and Agricultural Engineering

This senior project report discusses the design, construction, and evaluation of a portable artificial insemination chute for the use of the Cal Poly Beef Department. The design was based on the suggested modifications from operators of several other chutes currently in use.

The main areas considered for the design were; Ergonomics, cattle safety, factors effecting maximum breeding conception rates, and Portability.

The breeding chute proved superior over traditional chutes in a variety of ways. Improvement occurred in the areas of consideration as follows, user operation was simplified, animal stress was decreased, and maximum breeding efficiency was obtained.

The Proteomic Response Of Sea Squirts (Genus Ciona Congeners) To Hyposalinity Stress, James S. Koman

Master's Theses

The ascidian species Ciona savignyi and C. intestinalis are invasive species but show interspecific differences in their population response to hypo-saline stress associated with heavy winter-run off events that are predicted to become more frequent due to climate change. Despite an almost world-wide distribution, C. intestinalis seems to be more susceptible to hypo-saline stress than the geographically more limited C. savignyi. Given that the genomes of both species are fully sequenced, we were able to compare their proteomic response to both acute and chronic salinity to characterize the mechanisms that are responsible for setting tolerance limits to hyposaline conditions …

Effects Of Chainring Type (Circular Vs. Rotor Q-Ring) On 1km Time Trial Performance Over Six Weeks In Competitive Cyclists And Triathletes, Christiane R. O'Hara, Robert D. Clark, Todd A. Hagobian, Karen Mcgaughey

Kinesiology and Public Health

The purpose of this study was to examine the effects of chainring type (circular vs. the non- circular Rotor Q-Ring) on performance during a 1km time trial and physiological responses over a six week period. Eight competitive male cyclists and triathletes were pre-tested using the original circular chainring. Graded submaximal exercise tests were followed by the 1km time trial with subjects using their own racing bicycle. The circular chainrings were then removed and replaced with Rotor Q-Rings during the intervention period. Subjects trained and raced with this alteration to their bicycles and repeated the submaximal and 1km performance tests for …

Socio-Economic Position And Lower Dietary Moderation Among Chinese Immigrant Women In The Usa, Marilyn Tseng, Carolyn Y. Fang

Kinesiology and Public Health

Objective: To examine associations of education and occupation, as indicators of socio-economic position (SEP), with dietary intake and diet quality in a sample of Chinese immigrant women.

Design: Cross-sectional. Data collection included four days of dietary recalls and information on education and current occupation for participants and their spouses.

Setting: Philadelphia, PA, USA.

Subjects: Chinese immigrant women (n 423) recruited from October 2005 to April 2008.

Results: In multivariate models, both higher education level and occupation category were significantly associated with higher energy density and intake of energy and sugar. Education was additionally associated with intake of sugar-sweetened beverages …

Bovine Viral Diarrhea In Dairy And Beef Cattle, William Tyler Stevenson

Dairy Science

The objective of the literature review was to understand the nature and characteristics of BVD within dairy and beef herds. The paper reviewed important aspects of the disease that are relevant and practical to producers. The ideas and opinions presented in the paper were a result of compilation and review of the current literature focused on BVD. Some particular areas of focus were general information about the disease, costs and effects, pathophysiology, virology, transmission, prevention and testing. Information provided throughout the paper attempts to link practices that producers may adopt or modify in order to minimize effects of the disease. …

Proposal To Implement A Surveillance System At The Cal Poly Dairy, Madelyn Cobb

Dairy Science

The objective of this project is to determine how to implement a cost effective and efficient surveillance system at the Cal Poly Dairy. This system would help monitor labor, feed, and cows while increasing the biosecurity, accountability, and efficiency throughout the Cal Poly Dairy. To make this determination, I researched different types of products and the equipment necessary that will meet the needs of the dairy currently and for future projects. A list of specifications was created that help guide the search for appropriate companies and products for this project. Talking to surveillance experts also helped create a better sense …

Vitamin D Sub-Set Analysis From The Flash Study, Megan Bishop, Laura Hall, Ann Mcdermott, Aydin Nazmi

Master's Theses

Vitamin D is important to the health of college students. The objective of our study was to measure sun exposure, skin pigmentation, vitamin D intake, and serum 25-hydroxyvitamin D (25[OH]D) in a subset of participants from The Following the Longitudinal Aspects of Student Health (FLASH) Study to determine the best predictors of 25(OH)D status. Participants were college-aged freshman who had their blood drawn in spring (Visit 1) and fall 2010 (Visit 2) at California Polytechnic State University (Cal Poly), San Luis Obispo, CA. (35.3°N). Vitamin D intake was measured using a 28-day food frequency recall questionnaire (specific to vitamin D …

Comparing The Demographics Of Two Steelhead Populations And Their Habitat Characteristics, Eileen Ann Baglivio

Master's Theses

Currently, little is known about the demographics of the Oncorhynchus mykiss irideus, or steelhead trout, populations in San Luis Obispo County. Specifically, demographic information including length, age, and condition when first leaving a watershed for the open ocean is lacking. This thesis takes a closer look at a biological and environmental data collected by the California Department of Fish and Game Central Coast Steelhead and Coho Salmon project under the direction of Associate Biologist Jennifer Nelson. The main goal of this thesis is to analyze demographic and habitat data from the steelhead populations of two northern San Luis Obispo …

The Chicken Challenge – What Contemporary Studies Of Fowl Mean For Science And Ethics, Carolynn L. Smith, Jane Johnson

Between the Species

Studies with captive fowl have revealed that they possess greater cognitive capacities than previously thought. We now know that fowl have sophisticated cognitive and communicative skills, which had hitherto been associated only with certain primates. Several theories have been advanced to explain the evolution of such complex behavior. Central to these theories is the enlargement of the brain in species with greater mental capacities. Fowl present us with a conundrum, however, because they show the behaviors anticipated by the theories but do not have the expected changes in the brain. Consequently fowl present two challenges of interest to us here. …

Who Will Create The Iphone Equivalent In Dairy Foods?, Phillip S. Tong

Dairy Science

No abstract provided.

Dobzhansky's Dictum: An Object Lesson For Critical Thinking, William D. Stansfield

Biological Sciences

A creationist has called Dobzhansky's dictum a myth. Discussion of this debate could be used as an object lesson for critical thinking.

Spontaneous Multiscale Phase Separation Within Fluorinated Xerogel Coatings For Fouling-Release Surfaces, Anastasiya Sokolova, Joseph J. Bailey, Grant T. Waltz, Lenora H. Brewer, John A. Finlay, Jill Fornalik, Dean Wendt, Maureen E. Callow, James A. Callow, Frank V. Bright, Michael R. Detty

Biological Sciences

Four-component xerogel films consisting of 1 mole-% n-octadecyltrimethoxysilane (C18) and 50 mole-% tetraethoxysilane (TEOS) in combination with 1–24 mole-% tridecafluoro-1,1,2,2-tetrahydrooctyltriethoxysilane (TDF) and 25–48 mole-% n-octyltriethoxysilane (C8) and a 1:49:50 mole-% C18/TDF/TEOS were prepared. Settlement of barnacle cyprids and removal of juvenile barnacles, settlement of zoospores of the alga Ulva linza, and strength of attachment of 7-day sporelings (young plants) of Ulva were compared amongst the xerogel formulations. Several of the xerogel formulations were comparable to poly(dimethylsiloxane) elastomer with respect to removal of juvenile barnacles and removal of sporeling biomass. The 1:4:45:50 and 1:14:35:50 C18/TDF/C8/TEOS xerogels displayed some phase …

Camera Survey Of Wildlife Corridors Adjacent To Highway 101, Grace K. Mannell, Chelsea E. Rose

Natural Resources Management and Environmental Sciences

Driving poses a significant threat to safety for both humans and wildlife. Along highway 101 in San Luis Obispo, California, is a stretch of roadway that is exceptionally deadly to mammals such as deer and bears. Roadkill counts and motion-activated cameras have been utilized along this route in a previous study (Perrine and Snyder, 2011) to assist Caltrans in setting up wildlife barriers. We sought to continue this research using remote motion-sensing cameras to monitor wildlife during winter and spring of 2011. We set up cameras at five previously monitored locations that had already been determined to host heavy wildlife …

Evaluation Of Bio-Optical Inversion Of Spectral Irradiance Measured From An Autonomous Underwater Vehicle, Mark A. Moline, Ian Robbins, Brian Zelenke, W. Scott Pegau, Hemantha Wijesekera

Biological Sciences

Autonomous underwater vehicles (AUVs) can map water conditions at high spatial (horizontal and vertical) and temporal resolution, including under cloudy conditions when satellite and airborne remote sensing are not feasible. As part of the RADYO program, we deployed a passive radiometer on an AUV in the Santa Barbara Channel and off the coast of Hawaii to apply existing bio-optical algorithms for characterizing the optical constituents of coastal seawater (i.e., dissolved organic material, algal biomass, and other particles). The spectral differences between attenuation coefficients were computed from ratios of downwelling irradiance measured at depth and used to provide estimates of the …

Can Vertical Migrations Of Dinoflagellates Explain Observed Bioluminescence Patterns During An Upwelling Event In Monterey Bay, California?, Igor Shulman, Bradley Penta, Mark A. Moline, Steven H.D. Haddock, Stephanie Anderson, Matthew J. Oliver, Peter Sakalaukus

Biological Sciences

Extensive AUVs surveys showed that during the development of upwelling, bioluminescent dinoflagellates from the northern part of the Monterey Bay, California (called the upwelling shadow area), were able to avoid advection by southward flowing currents along the entrance to the Bay, while non-bioluminescent phytoplankton were advected by currents. It is known that vertical swimming of dinoflagellates to deeper layers helps them avoid losses due to advection. In the present paper, we investigate if modeling dinoflagellates’ vertical swimming can explain the observed dinoflagellates’ ability to avoid advection during the upwelling development. The dynamics of a dinoflagellate population is modeled with the …

Fully Enclosed Microfluidic Paper-Based Analytical Devices, Kevin M. Schilling, Anna L. Lepore, Jason A. Kurian, Andres W. Martinez

Chemistry and Biochemistry

This article introduces fully enclosed microfluidic paper-based analytical devices (microPADs) fabricated by printing toner on the top and bottom of the devices using a laser printer. Enclosing paper-based microfluidic channels protects the channels from contamination, contains and protects reagents stored on the device, contains fluids within the channels so that microPADs can be handled and operated more easily, and reduces evaporation of solutions from the channels. These benefits extend the capabilities of microPADs for applications as low-cost point-of-care diagnostic devices.

Sirtuin-Induced Protein Deacetylation Affects The Heat Shock Response In Blue Mussel Congeners (Mytilus), M. Beam, M. Zuzow, L. Tomanek

Biological Sciences

The warm-adapted Mediterranean blue mussel species Mytilus galloprovincialis invaded southern California during the last century and has since replaced the cold-adapted native M. trossulus from its southern range, possibly due to climate change. Based on previous proteomic analyses, we hypothesized that the more heat-sensitive M. trossulus switches from NADH-producing metabolic pathways that may generate reactive oxygen species (ROS) to NADPH-producing pathways that are able to scavenge ROS during severe heat stress (32°C). We further linked these changes to the activity of the mitochondrial NAD-dependent deacetylase, sirtuin-5, which has been shown to regulate many metabolic pathways. To test the latter hypothesis, …

The Proteomic Response To Acute Heat Stress After Acclimation To Fluctuating Temperatures In The Eurythermal Porcelain Crab, Petrolisthes Cinctipes, Michael A. Garland, Holland Elder, David A. Hurt, Jonathon H. Stillman, Lars Tomanek

Biological Sciences

The porcelain crab Petrolisthes cinctipes inhabits the high intertidal along the Pacific coast between British Columbia and central California and is an emerging model organism to study the effects of environmental stress. In its habitat it experiences not only variability in average temperature but also variability in temperature fluctuations. To investigate the effect of temperature fluctuations, we characterized the heat shock response at 30°C for 6 h by acclimating individuals to three different acclimation treatments: 10°C, 10-20°C (4 h), and 10-30°C (4 h) on a daily basis for one month. We dissected claw muscle and separated proteins by 2D gel …

Experimentally Altered Navigational Demands Induce Changes In The Cortical Forebrain Of Free-Ranging Northern Pacific Rattlesnakes (Crotalus O. Oreganus), Matthew L. Holding, Julius A. Frazier, Emily N. Taylor, Christine R. Strand

Biological Sciences

The hippocampus of birds and mammals plays a crucial role in spatial memory and navigation. The hippocampus exhibits plasticity in adulthood in response to diverse environmental factors associated with spatial demands placed on an animal. The medial and dorsal cortices of the telencephalon of squamate reptiles have been implicated as functional homologues to the hippocampus. This study sought to experimentally manipulate the navigational demands placed on free-ranging northern Pacific rattlesnakes (Crotalus o. oreganus) to provide direct evidence of the relationship between spatial demands and neuroplasticity in the cortical telencephalon of the squamate brain. Adult male rattlesnakes were radio-tracked for 2 …

The Proteomic Response Of Mytilus Californianus To Acute Oxidative Stress In The Presence Of A Sirtuin Inhibitor, H. Chilton, J. Mier, M. Zuzow, L. Tomanek

Biological Sciences

The ribbed mussel (Mytilus californianus) occurs in the in the rocky intertidal zone along the Pacific coast of North America where it experiences greatly varying environmental conditions in terms of temperature and hypoxia, stressors that are known to induce oxidative stress. It has been hypothesized that while under acute heat stress, related Mytilus congeners undergo a shift in redox potential through the reduction of NADH fueled respiration pathways to the production of the reducing agent NADPH as a potential defensive mechanism against the production of reactive oxygen species. In addition, it has been hypothesized that sirtuins (a family …

Proteomic Responses Of Mytilus Congeners To Hypo-Saline Stress, M. Z. Zuzow, L. Serafini, L. Hitt, J. Valenzuela, L. Tomanek

Biological Sciences

The invading Mediterranean blue mussel species Mytilus galloprovincialis requires higher salinity levels than the more hypo-saline tolerant and native M.trossulus,which it replaced from its southern range in California, possibly due to climate change.It is also the warm-adapted congener.Hypo-salinity,due to an increase in extreme precipitation events,has been hypothesized to limit the expansion of the invader.By comparing the proteomic responses of the congeners to acute hypo-saline stress we were trying to identify the interspecific differences that set limits to hypo-saline stress and assess their contribution to the range shifts.We exposed mussels to acute hypo-saline(100%, 85% and 70% salinity)stress for 4h followed …

Proteomic Analysis Of Hyposalinity Stress In The Ascidian Species Ciona Savignyi And C. Intestinalis, James S. Koman, Lars Tomanek

Biological Sciences

The ascidian species Ciona savignyi and C. intestinalis are invasive species but show interspecific differences in their population response to hypo-saline stress associated with heavy winter-run off events that are predicted to become more frequent due to climate change. Despite an almost world-wide distribution, C. intestinalis seems to be more susceptible to hypo-saline stress than the geographically more limited C. savignyi. Given that the genomes of both species are fully sequenced, we were able to compare their proteomic response to both acute and chronic salinity to characterize the mechanisms that are responsible for setting tolerance limits to hyposaline conditions …