Cloning and Characterization of the Promoter for the Ovarian-Specific Inhibin Alpha Gene Form Zebrafish (Danio rerio)

Inducible cAMP Early Repressor (ICER) is an important regulator of folliculogenesis as it regulates the nuclear response to gonadotropins in ovarian tissue. Studies in mice demonstrated a 3.0 kb region of the alpha inhibin (INHa) promoter is a site of transcriptional activation in response to follicle-stimulating hormone (FSH). The purpose of this study was to isolate and construct an ICER transgene and characterize the putative 3.0 kb promoter region of the ovarian-specific INHa gene in Danio rerio (zebrafish). The sequences for ICER and the INHa promoter in zebrafish were identified using BLAST searches with the known sequences from mouse and chicken. The putative sequences were subsequently isolated and amplified using RT-PCR and PCR. Successful isolation and amplification was confirmed with restriction enzyme mapping and DNA sequencing. ICER was cloned into pFLAG-CMV-2 plasmid to create the FLAG-dr- ICER Iy transgene construct. Expression of FLAG-ICER protein was confirmed by Western blot after transfection into HEK293T human kidney cells. The INHa promoter was cloned into a pGL3-Basic luciferase expression vector for characterization studies. The transgene containing the INHa promoter was transfected into AB9 zebrafish tailfm cells and embryonic PAC2 zebrafish cells. Transfection experiments in AB9 and PAC2 cells demonstrated promoter induction by follicle-stimulating hormone (FSH) and repression of promoter activity by luteinizing hormone (LH)

Operationalizing Embeddedness for Sustainability in Local and Regional Food Systems

Agricultural systems are deeply embedded in social processes and the institutions that govern them. Measuring these processes and understanding the extent of that embeddedness is critical to crafting policy for sustainable agricultural systems. The bulk of measurement in sustainability research, however, focuses on economic and environmental indicators such as farm profitability and water quality. Since policy is most often aimed at what is measured, it tends to focus on issues like price, production, and market access. And while those are important, policies aimed at social issues such as community reciprocity are often outside the scope of policy design. The gap between social measurement and policy is not for lack of care; the importance of social dynamics is well known. Yet due to the difficulty of measuring complex social systems— How does one measure values?—more straightforward economic and environmental measures dominate research and policy. When social systems are measured, as, for example, with the social capital or sustainable livelihoods frameworks, they often do so using economic methodologies and indicators. Such economic-based social indicators are important but focus heavily on outcomes such as poverty or profitability. Accordingly, the complex social processes that lead to such outcomes such as culture, heritage, tradition or generational dynamics are often overlooked. These policy and methodological difficulties present a problem: measurements import the theoretical framing of their intellectual development. Economic methodologies are largely rooted in an atomistic theory of human behavior in which individuals are selfishly motivated by economic gains. While individuals do seek economic success, they are also motivated by social connection, reciprocity, values, and culture. The institutions governing these social processes and the degree to which individuals and businesses are embedded in society are incredibly important, yet poorly understood and measured. This paper outlines a theoretical framing for understanding these complex social processes and develops a methodology for measuring social embeddedness in local and regional agricultural systems. Coined by sociologist Karl Polanyi, embeddedness is the extent to which economic systems like markets are governed by non-economic systems such as culture and social cohesion. While markets and their price and output components are well understood and widely measured, the non-economic institutions like culture and values that support and govern markets have tended to be seen as non-measurable. This has important policy implications for rural agriculture. Accordingly, this paper develops a tool for measuring the social embeddedness of producers and consumers in ten agricultural sectors in Vermont that can be replicated across New England. The tool uses a Likert scale survey designed to understand the degree to which producers and consumers are motivated by self-interest—what we call Instrumentalism—and the extent to which they are market-oriented—what we call Marketness. Survey responses are analyzed using a Factor Analysis to generate Instrumentalism and Marketness scores for each survey respondent on a scale of -1 to 1. The Embeddedness Type Matrix consists of a vertical Instrumentalism axis and a horizontal Marketness axis that together create four quadrants that represent different types of embeddedness: embedded, underembedded, disembedded, and overembedded. Individual consumers and producers are plotted on the matrix based upon their respective Instrumentalism and Marketness scores and yield an embeddedness type given their quadrant. Plotting all producers and consumers of a particular industry on the Embeddedness Type Matrix provides an understanding of the motivations, values, actions, and interactions of the individuals in that industry. This paper provides researchers and policy makers in Vermont and New England with a tool to understand and measure the social aspect of agricultural sustainability in multiple industries. This approach allows for the design of policy aimed at aspects of the food system outside of price, production, and market access alone

Indications of Potential Toxic/Mutagenic Effects of World Trade Center Dust on Human Lung Cell Cultures

Problem statement: Respiratory complications have been linked with exposure to dust particulates after the tragedy of September 11th, 2001 at the World Trade Center (WTC) site. Approach: The purpose of these experiments was to investigate the extent of cellular damage resulting from WTC dust exposure. Results: This research project was conducted with human lung fibroblast cells exposed to WTC dust. To determine if cell proliferation levels were affected, cultured cells were exposed to WTC dust at various concentrations in simulated physiological stress environments via decreased serum levels. Results indicated that cell proliferation levels decreased as WTC dust concentrations increased. This pattern persisted regardless of serum level. The serum concentrations used were 10% Fetal Bovine Serum (FBS), which represented a non-stressed system, with 2.5 and 1% FBS concentrations used to simulate stressed environments. Assessment for apoptosis, programmed cell death, resulted in higher than baseline levels in cells exposed to WTC dust in both MRC-5 and WI-38 human lung fibroblasts. Conclusion/Recommendations: In summary, results showed that exposure to WTC dust led to decreased cell proliferation and increased apoptosis levels. These findings evidence need for future research regarding mutagenic properties of World Trade Center dust

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu

Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

Abstract Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. We now analyze genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and perform replication among 456,893 European participants. Common alleles on chromosome Xq23 are strongly associated with reduced total cholesterol, LDL cholesterol, and triglycerides (min P = 8.5 × 10−72), with similar effects for males and females. Chromosome Xq23 lipid-lowering alleles are associated with reduced odds for CHD among 42,545 cases and 591,247 controls (P = 1.7 × 10−4), and reduced odds for diabetes mellitus type 2 among 54,095 cases and 573,885 controls (P = 1.4 × 10−5). Although we observe an association with increased BMI, waist-to-hip ratio adjusted for BMI is reduced, bioimpedance analyses indicate increased gluteofemoral fat, and abdominal MRI analyses indicate reduced visceral adiposity. Co-localization analyses strongly correlate increased CHRDL1 gene expression, particularly in adipose tissue, with reduced concentrations of blood lipids