Protecting the Constitutional Rights of Minority Youth on Rikers Island

In 2014, the United States Attorney’s Office for the Southern District of New York released a report on their investigation into the patterns and practices of treatment of adolescent inmates on Rikers Island, finding systemic defects that result in the pervasive violation of the adolescent inmates’ constitutional rights. Ninety-five percent of the adolescent population on Rikers is Black or Latino. New York is uniquely harsh with its treatment of 16- and 17-year-olds, as it and North Carolina are the only states to set the minimum age of criminal responsibility at 16. Over seventy-five percent of youth on Rikers Island are awaiting trial and have not been convicted of a crime. The prevalence of the unconstitutional conduct on Rikers Island is attributable, in large part, to the lack of accountability among Department of Corrections (DOC) staff members on Rikers Island, which results in a code of silence. To effectively deal with the pervasive pattern and practice of conduct on the part of DOC staff that violates adolescent inmates on Rikers Island’s constitutional rights, it is crucial to understand the differences between adolescents and adults and the power of the DOC staff union. This Note posits that in order to create meaningful reform and protect the constitutional rights of adolescent inmates, the cut-off age for criminal responsibility should be raised so that 16- and 17-year-olds fall under the jurisdiction of the Family Court and are not placed on Rikers Island. Additionally, the portion of the Administrative Code requiring all uniformed DOC ranks to be filled by promotion from within the uniformed force must be amended to obstruct the code of silence and prevent violence against inmates. Without such measures, the abuses against minority youth on Rikers Island will persist

The Ethnic Bildungsroman

This thesis will compare coming-of-age narratives by writers from three different ethnic groups, Mexican American, Native American, and Asian American: The House on Mango Street by Sandra Cisneros; The Absolutely True Diary of a Part-time Indian by Sherman Alexie; and American Born Chinese by Gene Luen Yang. The purpose of this study is to analyze three coming-of-age novels using the definition of bildungsroman as an analytic tool. This analysis will enable me to determine the existence and characteristics of the ethnic bildungsroman and how it differs from the original genre. For modern teenagers growing into adulthood and dealing with completely different issues from those faced by traditional bildungsroman protagonists, a new genre such as ethnic bildungsroman is necessary. The ethnic teens face additional challenges, such as dual identity, financial instability, stereotypes, and racism. Not only do the ethnic protagonists succeed and build connections, but they also come back to the community and try to inspire others as well.M.A

Altered Ecosystem Nitrogen Dynamics as a Consequence of Land Cover Change in Tallgrass Prairie

ABSTRACT.-Inre cent decades, substantial areas of North American tallgrass prairie have been lost to the establishment and expansion of woodlands and forests, including those dominated by eastern redcedar (Juniperus virginiana). This shift in dominant plant life form, from C4 grasses to coniferous trees, may be accompanied by changes in productivity, standing stocks of biomass and nutrients and biogeochemical cycles. The goal of this study was to quantify and compare major pools and fluxes of nitrogen in recently established (5 80 y) redcedar forests and adjacent native grasslands. Three former grassland sites in the Flint Hills region of Kansas that developed closed-canopy redcedar forests in the recent past were paired with adjacent grassland sites on similar soil type and topographic position (n = 3 sites/land cover type), and selected soil and plant nitrogen pools and fluxes were measured in replicate plots (n = 6/site) along transects in each forest or grassland site over a 20-mo period. We found few significant differences in median soil inorganic N pools or net N mineralization rates between the forest and grassland sites, though there was a trend for greater concentrations of inorganic N in grassland sites on most sample dates, and cumulative growing season net N mineralization averaged 15% less in forest sites (14.3 kg N-ha-1\u27yr-1) than in grassland sites (16.9 kg N-ha-\u27.yr-1). Mean aboveground plant productivity of forest sites (9162 kg ha-1 yr-1) was about 2.5X greater than that of comparable grasslands (similar soils and topographic position), in spite of similar levels of soil N availability. This resulted in an ecosystem-level nitrogen use efficiency (ANPP:litterfall N) in forests that was more than double that of the grasslands they replaced. Additional changes in N cycling associated with redcedar forest development included large accumulations of N in aboveground biomass and transfer to the forest floor via litterfall; redcedar aboveground biomass contained 617 kg N/ ha, forest floor litter N was 253 kg N/ha, and litterfall N flux was 41 kg ha-l\u27yr-1. These are substantial increases in aboveground biomass N accumulation, surface litter N inputs, and surface litter N accumulation compared to the native grasslands characteristic of this region. These fundamental shifts in ecosystem patterns and processes have the potential to alter regional biogeochemistry and both nitrogen and carbon storage throughout areas of the eastern Central Plains where coverage of redcedars is increasing

Cdc53p acts in concert with Cdc4p and Cdc34p to control the G1 to S phase transition and identifies a conserved family of proteins

Regulation of cell cycle progression occurs in part through the targeted degradation of both activating and inhibitory subunits of the cyclin-dependent kinases. During G1, CDC4, encoding a WD-40 repeat protein, and CDC34, encoding a ubiquitin-conjugating enzyme, are involved in the destruction of these regulators. Here we describe evidence indicating that CDC53 also is involved in this process. Mutations in CDC53 cause a phenotype indistinguishable from those of cdc4 and cdc34 mutations, numerous genetic interactions are seen between these genes, and the encoded proteins are found physically associated in vivo. Cdc53p defines a large family of proteins found in yeasts, nematodes, and humans whose molecular functions are uncharacterized. These results suggest a role for this family of proteins in regulating cell cycle proliferation through protein degradation

The role of ecotypic variation and the environment on biomass and nitrogen in a dominant prairie grass

Citation: Mendola, M. L., Baer, S. G., Johnson, L. C., & Maricle, B. R. (2015). The role of ecotypic variation and the environment on biomass and nitrogen in a dominant prairie grass. Ecology, 96(9), 2433-2445. doi:10.1890/14-1492.1Knowledge of the relative strength of evolution and the environment on a phenotype is required to predict species responses to environmental change and decide where to source plant material for ecological restoration. This information is critically needed for dominant species that largely determine the productivity of the central U.S. grassland. We established a reciprocal common garden experiment across a longitudinal gradient to test whether ecotypic variation interacts with the environment to affect growth and nitrogen (N) storage in a dominant grass. We predicted plant growth would increase from west to east, corresponding with increasing precipitation, but differentially among ecotypes due to local adaptation in all ecotypes and a greater range of growth response in ecotypes originating from west to east. We quantified aboveground biomass, root biomass, belowground net primary production (BNPP), root C:N ratio, and N storage in roots of three ecotypes of Andropogon gerardii collected from and reciprocally planted in central Kansas, eastern Kansas, and southern Illinois. Only the ecotype from the most mesic region (southern Illinois) exhibited more growth from west to east. There was evidence for local adaptation in the southern Illinois ecotype by means of the local vs. foreign contrast within a site and the home vs. away contrast when growth in southern Illinois was compared to the most distant site in central Kansas. Root biomass of the eastern Kansas ecotype was higher at home than at either away site. The ecotype from the driest region, central Kansas, exhibited the least response across the environmental gradient, resulting in a positive relationship between the range of biomass response and precipitation in ecotype region of origin. Across all sites, ecotypes varied in root C: N ratio (highest in the driest-origin ecotype) and N storage in roots (highest in the most mesic-origin ecotype). The low and limited range of biomass, higher C: N ratio of roots, and lower N storage in the central Kansas ecotype relative to the southern Illinois ecotype suggests that introducing ecotypes of A. gerardii from much drier regions into highly mesic prairie would reduce productivity and alter belowground ecosystem processes under a wide range of conditions

Plant Community Response to Regional Sources of Dominant Grasses in Grasslands Restored Across a Longitudinal Gradient

Restorations in the light of climate change will need to take into account whether or not sources of the dominant plants are adapted to the future conditions at a site. In addition, the effect of these dominants, especially if sourced from outside the local area, on the assembling plant community needs assessment. We investigated how different ecotypes of the tallgrass prairie dominants Andropogon gerardii and Sorghastrum nutans affect assembling prairie communities. Four reciprocal common garden experiments were established across a longitudinal climate gradient characterized by a decrease in aridity in western Kansas (COLBY), central Kansas (HAYS), eastern Kansas (MANHATTAN), and southern Illinois (CARBONDALE). At each site, plots were seeded with ecotypes of A. gerardii and S. nutans sourced from central Kansas (CKS), eastern Kansas (EKS), southern Illinois (SIL), or a mix of all three regional ecotypes (MIX). All plots were also seeded with the same suite of seven subordinate species. Species composition was measured during the fourth year of restoration. The greatest variation between communities occurred at HAYS and CARBONDALE between plots seeded with CKS and SIL ecotypes. At these sites, plots seeded with the local source had the lowest diversity and cover of nondominant species. Compositional variation between plots seeded with different dominant grass ecotypes was found exclusively at CARBONDALE between CKS and SIL plots. Differences between locally seeded plots and plots seeded with a MIX of dominant grass ecotypes were contingent upon site. At CARBONDALE, MIX seeded plots had higher diversity than SIL ecotype plots. Our results indicate that across a wide geographic precipitation gradient, limited but important differences in community assembly occur in restorations established with different ecotypes of the dominant grasses. However, our results also support the use of mixtures of nonlocal ecotypes of dominant grasses in restorations without risk to the assembling plant community. Future studies need to determine the potential for out- breeding effects among seed sources in mixed stands

Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

Plant response to climate depends on a species’ adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, and wet ecotypes originating from western KS to Illinois that span 500–1,200 mm rainfall/year. We aimed to answer: (a) What is the relative role of genetic constraints and phenotypic plasticity in controlling phenotypes? (b) When planted in the homesite, is there a trait syndrome for each ecotype? (c) How are genotypes and phenotypes structured by climate? and (d) What are implications of these results for response to climate change and use of ecotypes for restoration? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. Considering ecotype traits in homesite, the dry ecotype was characterized by reduced canopy area and diameter, short plants, and low vegetative biomass and putatively adapted to water limitation. The wet ecotype was robust, tall with high biomass, and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. Ecotype differentiation was supported by random forest classification and PCA. We detected genetic differentiation and outlier genes associated with primarily precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration

Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

Citation: Raithel, S., Johnson, L., Galliart, M., Brown, S., Shelton, J., Herndon, N., & Bello, N. M. (2016). Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii. Bmc Genomics, 17, 16. doi:10.1186/s12864-016-2442-7Background: Differential expression (DE) analysis of RNA-seq data still poses inferential challenges, such as handling of transcripts characterized by low expression levels. In this study, we use a plasmode-based approach to assess the relative performance of alternative inferential strategies on RNA-seq transcripts, with special emphasis on transcripts characterized by a small number of read counts, so-called low-count transcripts, as motivated by an ecological application in prairie grasses. Big bluestem (Andropogon gerardii) is a wide-ranging dominant prairie grass of ecological and agricultural importance to the US Midwest while edaphic subspecies sand bluestem (A. gerardii ssp. Hallii) grows exclusively on sand dunes. Relative to big bluestem, sand bluestem exhibits qualitative phenotypic divergence consistent with enhanced drought tolerance, plausibly associated with transcripts of low expression levels. Our dataset consists of RNA-seq read counts for 25,582 transcripts (60 % of which are classified as low-count) collected from leaf tissue of individual plants of big bluestem (n = 4) and sand bluestem (n = 4). Focused on low-count transcripts, we compare alternative ad-hoc data filtering techniques commonly used in RNA-seq pipelines and assess the inferential performance of recently developed statistical methods for DE analysis, namely DESeq2 and edgeR robust. These methods attempt to overcome the inherently noisy behavior of low-count transcripts by either shrinkage or differential weighting of observations, respectively. Results: Both DE methods seemed to properly control family-wise type 1 error on low-count transcripts, whereas edgeR robust showed greater power and DESeq2 showed greater precision and accuracy. However, specification of the degree of freedom parameter under edgeR robust had a non-trivial impact on inference and should be handled carefully. When properly specified, both DE methods showed overall promising inferential performance on low-count transcripts, suggesting that ad-hoc data filtering steps at arbitrary expression thresholds may be unnecessary. A note of caution is in order regarding the approximate nature of DE tests under both methods. Conclusions: Practical recommendations for DE inference are provided when low-count RNA-seq transcripts are of interest, as is the case in the comparison of subspecies of bluestem grasses. Insights from this study may also be relevant to other applications focused on transcripts of low expression levels

Genetic and environmental influences on stomates of big bluestem (Andropogon gerardii)

Big bluestem (Andropogon gerardii) is a dominant C4 prairie grass that has wide distribution and several genetically distinct ecotypes. Many of the ecotypic adaptations are related to water availability in the native environment. Stomates facilitate photosynthetic gas exchange and regulate water loss from the plant. As such, stomatal size and density represent possible adaptations to conserve water. We hypothesized drought-tolerant ecotypes of big bluestem would have fewer or smaller stomates compared to more mesic ecotypes. Five ecotypes of big bluestem were planted in four common gardens from western Kansas to southern Illinois, USA to determine genetic and environmental influences on stomates. Leaves of all ecotypes of A. gerardii were largely hypostomatous and genetics was a greater influence than environment for stomatal size and density. The drought-tolerant Sand bluestem had larger stomates on abaxial surfaces of leaves, but a lower density compared to most other ecotypes. The most mesic Illinois ecotype and the Kaw cultivar had the greatest density of stomates on abaxial surfaces of leaves. Sand Bluestem had a greater density of stomates on adaxial surfaces of leaves compared to all other ecotypes. Gas exchange measures followed patterns of stomate distribution, where abaxial CO2 uptake rates were greater than adaxial CO2 uptake rates, although differences between leaf surfaces was more pronounced in stomatal density than in CO2 uptake. There were minor differences in size and density of stomates among sites that corresponded with precipitation, although these differences were minor, illustrating the genetic underpinnings of stomates in big bluestem. There is a genetic predisposition for drought-tolerant ecotypes to have fewer stomates, illustrating an evolutionary adaptation to drought tolerance in an important prairie species