Life Sciences Commons^™

Agriculture In A Water Scarce World, Allison Roberts, Amjad Assi, Bassel Daher, Men Li

Student Papers in Public Policy

According to the McKinsey report (2009), the world is facing a water scarcity challenge where agriculture is its predominant consumer. It accounts for approximately 3100 billion m³, or 71 percent of global water withdrawals today, and is expected to increase to 4500 billion m³ by 2030. This increase is due to a number of factors: growing population and the ever growing necessity to cater for its food needs, economic growth, the variability of precipitation trends and increase in global temperatures. In addition to the increase in water scarcity, the agricultural sector faces an enormous challenge of producing almost ...

The Obesity Epidemic, Lenka Kollar, Evienne Epifano, Molly Mckneight, Jeff Miskovich, Heather Moore

Student Papers in Public Policy

The incidence of chronic, noncommunicable diseases, such as heart disease, is increasing at an alarming rate on the global scale. The growing prevalence of overweight and obesity have led to an upsurge in cases of diabetes and other obesity-related diseases. About 18 million people die every year from heart disease, of which diabetes and obesity are major predisposing factors. Worldwide, more than 1.1 billion adults are overweight, 312 million of which are obese. The number of children that are overweight or obese is also growing (Hossain, Parvez et al.). Obesity, and the associated diseases, has become a worldwide epidemic ...

Dynamic Nucleosome Organization At Hox Promoters During Zebrafish Embryogenesis, Steven Weicksel, Jia Xu, Charles G. Sagerstrom

University of Massachusetts Medical School Faculty Publications

Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR) at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements) as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors). However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome must undergo a broad reprogramming event upon fusion of sperm and oocyte. Using four stages of early embryonic ...

Food Security And State: Policy Considerations For The Contemporary Food Crisis, Mangala Subramaniam, Christopher Bunka

Global Policy Research Institute (GPRI) Policy Briefs

In 1996, The World Food Summit (WFS) set a target to eradicate hunger in all countries and an immediate goal to half the number of undernourished people by 2015. Backed by the United Nations (UN), international organizations launched a global effort with the intent of achieving food security for all people. A variety of approaches were employed, including the distribution of food aid and farming supplies, skills training in agricultural development, funding for country-specific research, and legal counsel for states. Despite international efforts, over a decade later the number of undernourished was calculated to have risen by nearly 60 million ...

Measuring The Impacts Of Agricultural Input Subsidies In Sub-Saharan Africa: Evidence From Malawi's Farm Input Subsidy Program, Gerald E. Shively, Jacob Ricker-Gilbert

Global Policy Research Institute (GPRI) Policy Briefs

Malawi, a small, land-locked country in south Eastern Africa has been at the forefront of the recent push to reestablish subsidies as a way of boosting agricultural production and improving food security, especially among the poor. Its programs have been widely observed, scrutinized, and emulated. This policy brief examines Malawi’s Farm Input Subsidy Program (FISP) and distills a set of key research findings drawn from research conducted recently at Purdue University.

Impact Of Hydraulic Fracturing On Ground And Surface Water Resources, Reyna Schenck

Natural Resources Management and Environmental Sciences

The following study examines hydraulic fracturing operations in the United States in relation to groundwater contamination, withdrawals of freshwater resources, and jurisdictional authority over the activity with the purpose of producing objective analysis of research findings. With a growing population and increasing energy needs, hydraulic fracturing is expanding across the nation, as is public concern over the risks to freshwater resources. Because of the difficulty in identifying non-point sources of water pollution, a lack of legitimate water samples representing baseline conditions, and incomplete lists of chemical additives used, study results are often inconclusive as to the correlation between hydraulic fracturing ...

A Floristic Analysis And Comparison Of Plant Communities In Harlan County, Nebraska, Naomi D. Hastings, Steven J. Rothenberger

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Historically, the Republican River Valley in Harlan County, Nebraska, has been extensively explored, but the county flora has continually been under-represented and has been found to lack records for plants that are considered common. During the 2009 growing season, a taxonomic study and comparison of 3 different sites in Harlan County was made. Site #1 was pastureland and Sites #2 and #3 were both riparian, located on the north side of the Republican River. Collections were pressed, dried, identified, and deposited in the University of Nebraska at Kearney Herbarium (NEBK). Forty-eight new county records were verified, in­cluding cutleaf-cucumber (Cyclanthera ...

Creation Of A Pamphlet On Young Tree Care, John G. Sanchez

Horticulture and Crop Science

No abstract provided.

Effects Of Post-Castration Interval Length On Recovery Of Epididymal Sperm Of Canine And Equine Sperm, Jordan Escobar

Animal Science

No abstract provided.

Cal Poly Goat Program, Lauren Christensen

Animal Science

The Cal Poly Goat Program was established in the Summer of 2012 to provide vegetation management services on the Cal Poly campus and to allow students to gain hands on experience with goats. Student interest in adding goats as an additional species in the Animal Science Department spurred the realization and development of the program. The department also experienced demand for goats to use for vegetation management at the animal units and around various facilities on campus. The Goat Program integrates Cal Poly’s hands-on, ‘Learn by Doing’ philosophy with sustainable management practices to serve the needs of students as ...

Pesticide Regulation Differences Of The U.S., Chile, And Mexico On Imported Berries, Kayla Felicia Gardener

Agribusiness

Growing consumer demand for knowledge in the area of food safety and producer accountability on what is applied to fresh produce is resulting in a greater need for transparency in the industry. Additionally, the demand for safe, fresh produce year round has led to extensive international trade and consumers to wonder if imported produce is of the same quality of that in produced in the U.S. The study analyzes the differences and similarities between pesticide application tolerance standards, and labels for applied use on berries produced in the U.S., Mexico, and Chile. This is done by reviewing tolerance ...

Functional Analysis Of Transcription Factor Binding Sites In Human Promoters, Troy W. Whitfield, Jie Wang, Patrick J. Collins, E. Christopher Partridge, Shelley Force Aldred, Nathan D. Trinklein, Richard M. Myers, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1.

RESULTS: In each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall ...

Understanding Transcriptional Regulation By Integrative Analysis Of Transcription Factor Binding Data, Chao Cheng, Roger Alexander, Rengqiang Min, Jing Leng, Kevin Y. Yip, Joel Rozowsky, Koon-Kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, Carrie A. Davis, Piero Carninci, Timo Lassman, Thomas R. Gingeras, Roderic Guigo, Ewan Birney, Zhiping Weng, Michael Snyder, Mark B. Gerstein

Program in Bioinformatics and Integrative Biology Publications and Presentations

Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study transcriptional regulation by TFs. Our results reveal a notable difference in the prediction accuracy of expression levels of transcription start sites (TSSs) captured by different technologies and RNA extraction protocols. In general, the expression levels of TSSs with high CpG content are more predictable than those with low CpG content. For genes with alternative TSSs, the expression levels of downstream TSSs are more predictable than those ...

Sequence Features And Chromatin Structure Around The Genomic Regions Bound By 119 Human Transcription Factors, Jie Wang, Jiali Zhuang, Sowmya Iyer, Xinying Lin, Troy W. Whitfield, Melissa C. Greven, Brian G. Pierce, Xianjun Dong, Anshul Kundaje, Yong Cheng, Oliver J. Rando, Ewan Birney, Richard M. Myers, William S. Noble, Michael Snyder, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion. We frequently detected secondary motifs in addition to the canonical motifs of the TFs, indicating tethered binding and cobinding between multiple TFs. We observed significant ...

Factorbook.Org: A Wiki-Based Database For Transcription Factor-Binding Data Generated By The Encode Consortium, Jie Wang, Jiali Zhuang, Sowmya Iyer, Xinying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the resulting DNA. As part of the ENCODE project, we have developed a Web-accessible repository accessible at http://factorbook.org. In Wiki format, factorbook is a transcription factor (TF)-centric repository of all ENCODE ChIP-seq datasets ...

Strand-Specific Libraries For High Throughput Rna Sequencing (Rna-Seq) Prepared Without Poly(A) Selection, Zhao Zhang, William E. Theurkauf, Zhiping Weng, Phillip D. Zamore

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs.

DESIGN: Here, we describe a procedure for preparing RNA-Seq libraries from 1 ...

Networking Development By Boolean Logic, Shikui Tu, Thoru Pederson, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Eric Davidson at Caltech has spent several decades investigating the molecular basis of animal development using the sea urchin embryo as an experimental system ( 1) (,) ( 2) although his scholarship extends to all of embryology as embodied in several editions of his landmark book. ( 3) In recent years his laboratory has become a leading force in constructing gene regulatory networks (GRNs) operating in sea urchin development. ( 4) This axis of his work has its roots in this laboratory's cDNA cloning of an actin mRNA from the sea urchin embryo (for the timeline see ref. 1)-one of the first eukaryotic ...

Managing Soil Microbial Communities With Organic Amendments To Promote Soil Aggregate Formation And Plant Health, Shawn T. Lucas

Theses and Dissertations--Plant and Soil Sciences

The effects of managing soil with organic amendments were examined with respect to soil microbial community dynamics, macroaggregate formation, and plant physio-genetic responses. The objective was to examine the possibility of managing soil microbial communities via soil management, such that the microbial community would provide agronomic benefits. In part one of this research, effects of three amendments (hairy vetch residue, manure, compost) on soil chemical and microbial properties were examined relative to formation of large macroaggregates in three different soils. Vetch and manure promoted fungal proliferation (measured via two biomarkers: fatty acid methyl ester 18:2ω6c and ergosterol) and also ...

Polychlorinated Biphenyl Ligands Of The Aryl Hydrocarbon Receptor Promote Adipocyte-Mediated Diabetes, Nicki A. Baker

Theses and Dissertations--Nutritional Sciences

Numerous epidemiology studies suggest a correlation between exposures to polychlorinated biphenyls (PCBs) and the development and severity of type 2 diabetes (T2D); however, mechanisms remain largely unknown. Previous studies demonstrated that PCBs that are ligands of the aryl hydrocarbon receptor (AhR) promote the expression of proinflammatory cytokines, including tumor necrosis factor-α (TNF-α), that are linked to insulin resistance in adipocytes. To explore potential mechanisms linking PCB exposures to diabetes, we developed a mouse model of glucose and insulin intolerance induced by acute and chronic exposures to PCB-77. We hypothesized that PCB ligands of AhR result in adipocyte-specific elevations in TNF-α ...

Economic Optimization And Precision Agriculture: A Carbon Footprint Story, Rachael M. Brown

Theses and Dissertations--Agricultural Economics

This thesis examines the economic and environmental impacts that precision agriculture technologies (PATs) can have on the carbon footprint of a grain farm. An analysis is offered using two manuscripts. The first examines the impacts of three PATs and compares the findings to a conventional farming method. It was found that all three PATs investigated showed a potential Pareto improvement over conventional farming. The second manuscript expanded the model used previously to in order to develop a process to construct a carbon efficient frontier (CEF). The model employed examined uniform and variable rate technologies. In addition to the CEF, a ...