scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development.

The Drosophila larval ventral nerve cord (VNC) shares many similarities with the spinal cord of vertebrates and has emerged as a major model for understanding the development and function of motor systems. Here, we use high-quality scRNA-seq, validated by anatomical identification, to create a comprehensive census of larval VNC cell types. We show that the neural lineages that comprise the adult VNC are already defined, but quiescent, at the larval stage.

Establishing the relationship between wildfire smoke and performance metrics on finished beef cattle in Western Rangelands.

Identifying causal relationships is complicated. Researchers usually overlook causality behind relationships which can generate misleading associations. Herein, we carefully examine the parametric relationship and causality between wildfire smoke exposure and animal performance and behavior metrics over a period of 2 yr in Reno, Nevada.

Single-Cell RNA Sequencing Analysis of the Drosophila Larval Ventral Cord.

Drosophila provides a powerful genetic system and an excellent model to study the development and function of the nervous system. The fly's small brain and complex behavior has been instrumental in mapping neuronal circuits and elucidating the neural basis of behavior. The fast pace of fly development and the wealth of genetic tools has enabled systematic studies on cell differentiation and fate specification, and has uncovered strategies for axon guidance and targeting.

Assembly and Exploration of a Single Cell Atlas of the Drosophila Larval Ventral Cord. Identification of Rare Cell Types.

Single-cell RNA sequencing provides a new approach to an old problem: how to study cellular diversity in complex biological systems. This powerful tool has been instrumental in profiling different cell types and investigating, at the single-cell level, cell states, functions, and responses. However, mining these data requires new analytical and statistical methods for high-dimensional analyses that must be customized and adapted to specific goals.

Ultraconserved Non-coding DNA Within Diptera and Hymenoptera.

This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking developmental genes to homologous sequences in and Many of the conserved sequence blocks (CSBs) that constitute -regulatory DNA, recognized by alignment protocols, are also conserved in and Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito algorithm, we have also identified uCSBs shared among distantly related mosquito species.

Databases and Web Sites for Neurogenetics.

The goal of neurogenetics is an understanding of the genetic basis of brain structure and function. Neurogenetics deals with multiple areas of investigation, including the genetic basis of neural induction, patterning, cell fate specification, neuron maturation, axonal and dendritic organization, synapse function, neural information processing, and learning and behavior. This appendix provides links to databases and other Web sites used by neurobiologists for discovery of information about genes and cellular networks involved in neural development and neuron function.

Mutational analysis of a Drosophila neuroblast enhancer governing nubbin expression during CNS development.

While developmental studies of Drosophila neural stem cell lineages have identified transcription factors (TFs) important to cell identity decisions, currently only an incomplete understanding exists of the cis-regulatory elements that control the dynamic expression of these TFs. Our previous studies have identified multiple enhancers that regulate the POU-domain TF paralogs nubbin and pdm-2 genes. Evolutionary comparative analysis of these enhancers reveals that they each contain multiple conserved sequence blocks (CSBs) that span TF DNA-binding sites for known regulators of neuroblast (NB) gene expression in addition to novel sequences.

Structure and cis-regulatory analysis of a Drosophila grainyhead neuroblast enhancer.

Evolutionary analysis of cis-regulatory DNA reveals that enhancers consist of clusters of conserved sequence blocks (CSBs) that are made up of both unique and repeated sequence elements. This study seeks to address the basis for spatial and temporal regulation of neuroblas. A search for temporally restricted CNS NB enhancers identified one within the transcription factor grainyhead (grh) gene locus.

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.

Background: Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging.

Food and Dietary Supplement Package Labeling-Guidance from FDA's Warning Letters and Title 21 of the Code of Federal Regulations.

Package labels for foods and dietary supplements must conform with Title 21 of the Code of Federal Regulations. This review provides guidance for the content and format of labels, including for the Nutrient Facts panel and Supplement Facts panel, and for drafting structure/function claims, health claims, and nutrient content claims. Also provided is guidance on how to refrain from drafting disease claims.

cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers.

Background: One of the major challenges in developmental biology is to understand the regulatory events that generate neuronal diversity. During Drosophila embryonic neural lineage development, cellular temporal identity is established in part by a transcription factor (TF) regulatory network that mediates a cascade of cellular identity decisions. Two of the regulators essential to this network are the POU-domain TFs Nubbin and Pdm-2, encoded by adjacent genes collectively known as pdm.

Making Drosophila lineage-restricted drivers via patterned recombination in neuroblasts.

The Drosophila cerebrum originates from about 100 neuroblasts per hemisphere, with each neuroblast producing a characteristic set of neurons. Neurons from a neuroblast are often so diverse that many neuron types remain unexplored. We developed new genetic tools that target neuroblasts and their diverse descendants, increasing our ability to study fly brain structure and development.

Drosophila intermediate neural progenitors produce lineage-dependent related series of diverse neurons.

Drosophila type II neuroblasts (NBs), like mammalian neural stem cells, deposit neurons through intermediate neural progenitors (INPs) that can each produce a series of neurons. Both type II NBs and INPs exhibit age-dependent expression of various transcription factors, potentially specifying an array of diverse neurons by combinatorial temporal patterning. Not knowing which mature neurons are made by specific INPs, however, conceals the actual variety of neuron types and limits further molecular studies.

Cis-regulatory complexity within a large non-coding region in the Drosophila genome.

Analysis of cis-regulatory enhancers has revealed that they consist of clustered blocks of highly conserved sequences. Although most characterized enhancers reside near their target genes, a growing number of studies have shown that enhancers located over 50 kb from their minimal promoter(s) are required for appropriate gene expression and many of these 'long-range' enhancers are found in genomic regions that are devoid of identified exons. To gain insight into the complexity of Drosophila cis-regulatory sequences within exon-poor regions, we have undertaken an evolutionary analysis of 39 of these regions located throughout the genome.

Isolation and characterization of Staphylococcus aureus strains from a Paso del Norte dairy.

The primary purpose of this study was to determine if methicillin-resistant Staphylococcus aureus (MRSA) strains could be identified in the milk of dairy cattle in a Paso del Norte region dairy of the United States. Using physiological and PCR-based identification schemes, a total of 40 Staph. aureus strains were isolated from 29 raw milk samples of 133 total samples analyzed.

The cis-regulatory dynamics of the Drosophila CNS determinant castor are controlled by multiple sub-pattern enhancers.

In the developing CNS, unique functional identities among neurons and glia are, in part, established as a result of successive transitions in gene expression programs within neural precursor cells. One of the temporal-identity windows within Drosophila CNS neural precursor cells or neuroblasts (NBs) is marked by the expression of a zinc-finger transcription factor (TF) gene, castor (cas). Our analysis of cis-regulatory DNA within a cas loss-of-function rescue fragment has identified seven enhancers that independently activate reporter transgene expression in specific sub-patterns of the wild-type embryonic cas gene expression domain.

Analysis of inland crude oil spill threats, vulnerabilities, and emergency response in the midwest United States.

Although coastal oil spills tend to be highly publicized, crude oil spills in the United States affect inland areas relatively often. Spills to inland areas often affect sensitive environments and can have greater impacts to health and welfare than spills to coastal areas. For these reasons, the authors investigated inland crude oil spill threats, vulnerabilities, and emergency response in the midwestern U.

Identification of cis-Regulatory Elements in the dmyc Gene of Drosophila Melanogaster.

Myc is a crucial regulator of growth and proliferation during animal development. Many signals and transcription factors lead to changes in the expression levels of Drosophila myc, yet no clear model exists to explain the complexity of its regulation at the level of transcription. In this study we used Drosophila genetic tools to track the dmyc cis-regulatory elements.

Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.

Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs.

Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome.

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis.

Summary: Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects.

Functional analysis of conserved sequences within a temporally restricted neural precursor cell enhancer.

Many of the key regulators of Drosophila CNS neural identity are expressed in defined temporal orders during neuroblast (NB) lineage development. To begin to understand the structural and functional complexity of enhancers that regulate ordered NB gene expression programs, we have undertaken the mutational analysis of the temporally restricted nerfin-1 NB enhancer. Our previous studies have localized the enhancer to a region just proximal to the nerfin-1 transcription start site.

Self-selected or mandated, open access increases citation impact for higher quality research.

Background: Articles whose authors have supplemented subscription-based access to the publisher's version by self-archiving their own final draft to make it accessible free for all on the web ("Open Access", OA) are cited significantly more than articles in the same journal and year that have not been made OA. Some have suggested that this "OA Advantage" may not be causal but just a self-selection bias, because authors preferentially make higher-quality articles OA. To test this we compared self-selective self-archiving with mandatory self-archiving for a sample of 27,197 articles published 2002-2006 in 1,984 journals.

Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development.

We have identified clusters of conserved sequences constituting discrete modular enhancers within the Drosophilanerfin-1 locus. nerfin-1 encodes a Zn-finger transcription factor that directs pioneer interneuron axon guidance. nerfin-1 mRNA is detected in many early delaminating neuroblasts, ganglion mother cells and transiently in nascent neurons.

Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria.

Background: Acquisition of virulence factors and antibiotic resistance by many clinically important bacteria can be traced to horizontal gene transfer (HGT) between related or evolutionarily distant microflora. Comparative genomic analysis has become an important tool for identifying HGT DNA in emerging pathogens. We have adapted the multi-genome alignment tool EvoPrinter to facilitate discovery of HGT DNA sequences within bacterial genomes and within their mobile genetic elements.