Reconnaissance surveying of Bechevin Bay, AK using satellite-derived bathymetry

Recently, a remote sensing study has been conducted over Bechevin Bay Channel, Alaska as part of a collaboration project between NOAA and the U.S. Coast Guard (USCG). The goal of the study to develop a procedure to prioritize survey areas and plan the annual deployment of Aids to Navigation (AtoN) along the channel. Bechevin Bay is considered a priority for marine surveying because it constitutes the easternmost passage through the Aleutians from the Bering Sea to the Gulf of Alaska. The channel is located in a mud flat area, where every winter the passage is closed due to ice cover. As a result, the path of the channel may change after sea ice has melted. Because of the geographic location of Bechevin Bay, many resources are required in order to conduct an annual survey to map the channel’s path. The surveys are typically conducted by the USCG buoy tenders using small boats and reconnaissance-style single beam lines. This paper presents the use of single-image satellite-derived bathymetry (SDB) as an economic alternative approach. The study compares the performance using different band ratios. Datasets that were used in the study included Landsat 8 and WorldView 2 (WV-2) imagery

Public or private religiosity: which Is protective for adolescent substance use and by what pathways?

While it is well understood that adolescent religiosity is associated with the use and abuse of licit and illicit substances, few studies have revealed the pathways through which religiosity buffers youth against involvement in such behavior. The aim of this study is to examine the complexity of the relationships between religiosity, sensation seeking, injunctive norms, and adolescent substance use. Using a national sample of adolescents (N = 18,614), negative binomial regression and path analysis were used to examine the various components of the relationship between religiosity and the use of cigarettes, alcohol, and marijuana. Results indicate that private religiosity moderates the relationship between key risk factors and substance use. Public and private religiosity were associated with tolerant injunctive substance use norms which, in turn, were associated with substance use. Implications for research and theory related to religiosity and adolescent substance use are discussed

Organization and Expression of a Cluster of Drosophila Cuticle Genes

A 50 kb DNA segment of the Drosophila genome has been cloned and characterized. This segment lies at chromosomal location 44D and contains two small gene families. One family is comprised of four related cuticle genes clustered within 7.9 kb of DNA. The four genes encode four of the five major third instar larval cuticle proteins. These cuticle genes are coordinately expressed in the integument of third instar larvae, and they are not abundantly expressed in other developmental stages. A fifth cuticle-like gene lies within this gene cluster. It is judged to be a pseudogene, because several features of its structure and the absence of transcripts suggest that it is nonfunctional. Sequence comparisons indicate it arose by an unequal crossing over event involving two closely related and adjacent cuticle genes. Eleven kb away from the cuticle gene cluster lies another gene family. This family is comprised of three genes that are 55-60% homologous in DNA sequence and clustered within 8 kb of DNA. The three genes are expressed together in larval stages and adults but show a different pattern of developmental expression from the third instar larval cuticle protein genes. Thus two small gene families can lie adjacent on the chromosome and exhibit different patterns of developmental expression, even though individual genes within a clustered family are coordinately expressed. Additionally, a Drosophila strain has been studied which fails to synthesize one of the cuticle proteins. A molecular characterization of this strain is reported, which includes the finding of a transposable element in the promoter region of the unexpressed gene.</p

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

BACKGROUND: The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing. We therefore devised integrated tDNA expression profiling, a method that combines RNAPIII mapping with biotin-capture of nascent tRNAs. We apply this method to the study of dynamic tRNA gene regulation during macrophage development and further integrate these data with high-resolution maps of 3D chromatin structure. RESULTS: Integrated tDNA expression profiling reveals domain-level and loop-based organization of tRNA gene transcription during cellular differentiation. tRNA genes connected by DNA loops, which are proximal to CTCF binding sites and expressed at elevated levels compared to non-loop tDNAs, change coordinately with tDNAs and protein-coding genes at distal ends of interactions mapped by in situ Hi-C. We find that downregulated tRNA genes are specifically marked by enhanced promoter-proximal binding of MAF1, a transcriptional repressor of RNAPIII activity, altogether revealing multiple levels of tDNA regulation during cellular differentiation. CONCLUSIONS: We present evidence of both local and coordinated long-range regulation of human tDNA expression, suggesting the location and organization of tRNA genes contribute to dynamic tDNA activity during macrophage development

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression(1). The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community

H3K56me3 is a novel, conserved heterochromatic mark that largely but not completely overlaps with H3K9me3 in both regulation and localization.

Histone lysine (K) methylation has been shown to play a fundamental role in modulating chromatin architecture and regulation of gene expression. Here we report on the identification of histone H3K56, located at the pivotal, nucleosome DNA entry/exit point, as a novel methylation site that is evolutionary conserved. We identify trimethylation of H3K56 (H3K56me3) as a modification that is present during all cell cycle phases, with the exception of S-phase, where it is underrepresented on chromatin. H3K56me3 is a novel heterochromatin mark, since it is enriched at pericentromeres but not telomeres and is thereby similar, but not identical, to the localization of H3K9me3 and H4K20me3. Possibly due to H3 sequence similarities, Suv39h enzymes, responsible for trimethylation of H3K9, also affect methylation of H3K56. Similarly, we demonstrate that trimethylation of H3K56 is removed by members of the JMJD2 family of demethylases that also target H3K9me3. Furthermore, we identify and characterize mouse mJmjd2E and its human homolog hKDM4L as novel, functionally active enzymes that catalyze the removal of two methyl groups from trimethylated H3K9 and K56. H3K56me3 is also found in C. elegans, where it co-localizes with H3K9me3 in most, but not all, tissues. Taken together, our findings raise interesting questions regarding how methylation of H3K9 and H3K56 is regulated in different organisms and their functional roles in heterochromatin formation and/or maintenance

Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association

Transcription factors (TFs) are fundamental controllers of cellular regulation that function in a complex and combinatorial manner. Accurate identification of a transcription factor's targets is essential to understanding the role that factors play in disease biology. However, due to a high false positive rate, identifying coherent functional target sets is difficult. We have created an improved mapping of targets by integrating ChIP-Seq data with 423 functional modules derived from 9,395 human expression experiments. We identified 5,002 TF-module relationships, significantly improved TF target prediction, and found 30 high-confidence TF-TF associations, of which 14 are known. Importantly, we also connected TFs to diseases through these functional modules and identified 3,859 significant TF-disease relationships. As an example, we found a link between MEF2A and Crohn's disease, which we validated in an independent expression dataset. These results show the power of combining expression data and ChIP-Seq data to remove noise and better extract the associations between TFs, functional modules, and disease

Tree Mortality following Prescribed Fire and a Storm Surge Event in Slash Pine (Pinus elliottii var. densa) Forests in the Florida Keys, USA

In fire-dependent forests, managers are interested in predicting the consequences of prescribed burning on postfire tree mortality. We examined the effects of prescribed fire on tree mortality in Florida Keys pine forests, using a factorial design with understory type, season, and year of burn as factors. We also used logistic regression to model the effects of burn season, fire severity, and tree dimensions on individual tree mortality. Despite limited statistical power due to problems in carrying out the full suite of planned experimental burns, associations with tree and fire variables were observed. Post-fire pine tree mortality was negatively correlated with tree size and positively correlated with char height and percent crown scorch. Unlike post-fire mortality, tree mortality associated with storm surge from Hurricane Wilma was greater in the large size classes. Due to their influence on population structure and fuel dynamics, the size-selective mortality patterns following fire and storm surge have practical importance for using fire as a management tool in Florida Keys pinelands in the future, particularly when the threats to their continued existence from tropical storms and sea level rise are expected to increase

Mapping and Assessing Fire Damage on Broadleaved Forest Communities in Big Cypress National Preserve

Within Big Cypress National Preserve (BICY), oak-dominated forests and woodlands as well as tropical and temperate hardwood hammocks are integral components of the landscape and are biodiversity hotpots for both flora and fauna. These broadleaved forest communities serve as refugia for many of the Preserve’s wildlife species during prolonged flooding and fires. However, both prolonged flooding and severe fires, which are important and necessary disturbance vectors within this landscape, can have deleterious effects on these forested communities. This is particularly true in the case of fires, which under extreme conditions associated with drought and elevated fuel loads, can burn through these forested communities consuming litter and understory vegetation and top killing most, if not all, of the trees present