Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies.

Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures.

Justifying the need for a recovery related surveillance system: Exploratory focused interviews.

Background And Aims: No recovery related surveillance system exists but given the evidence of effectiveness and growing supply, a house- and resident- level recovery house (RH) surveillance system could be beneficial for data collection on recovery support service (RSS) engagement, and retention; for improved standardization of RH programs and services; and for identification of outcomes associated with long-term recovery.

Methods: This study aimed to explore current data collection practices at the resident- and house- level through qualitative focus interviews of RH representatives. The 13 RH interviews were scheduled with 16 RH representative respondents.

Mutation of two intronic nucleotides alters RNA structure and dynamics inhibiting MBNL1 and RBFOX1 regulated splicing of the Insulin Receptor.

Alternative splicing (AS) of Exon 11 of the Insulin Receptor ( ) is highly regulated and disrupted in several human disorders. To better understand exon 11 AS regulation, splicing activity of an exon 11 minigene reporter was measured across a gradient of the AS regulator muscleblind-like 1 protein (MBNL1). The RNA-binding protein Fox-1 (RBFOX1) was added to determine its impact on MBNL1-regulated splicing.

Alternative Splicing Outcomes Across an RNA-Binding Protein Concentration Gradient.

Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs). The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development.

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids.

Economically viable production of cellulosic biofuels requires operation at high solids loadings-on the order of 15 wt%. To this end we characterize Nature's ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L.

Histone acetyltransferase inhibition rescues differentiation of emerin-deficient myogenic progenitors.

Introduction: Emery-Dreifuss muscular dystrophy (EDMD) is a disease characterized by skeletal muscle wasting, major tendon contractures, and cardiac conduction defects. Mutations in the gene encoding emerin cause EDMD1. Our previous studies suggested that emerin activation of histone deacetylase 3 (HDAC3) to reduce histone 4-lysine 5 (H4K5) acetylation (ac) is important for myogenic differentiation.

Understanding lipopolysaccharide aggregation and its influence on activation of Factor C.

The quantification of lipopolysaccharide (LPS) shed by bacteria within aqueous samples is typically performed by binding LPS to a protein called Factor C within a lysate prepared from the blood of horseshoe crabs (Limulus amebocyte lysate (LAL)). How the state of aggregation of LPS impacts Factor C activation, however, is not understood, particularly in the presence of select salts and non-ionic surfactants that are commonly incorporated into pharmaceutical formulations. To address this open question, herein we report on the aggregation status of LPS in aqueous solution, characterized using angle-dependent static and dynamic light scattering with and without chelating salts and polysorbate surfactants, and its correlation with activation of Factor C.

Spatiotemporal Dynamics of Molecular Messaging in Bacterial Co-Cultures Studied by Multimodal Chemical Imaging.

Microbial community behavior is coupled to a set of genetically-regulated chemical signals that correlate with cell density - the quorum sensing (QS) system - and there is growing appreciation that the QS-regulated behavior of bacteria is chemically, spatially, and temporally complex. In addition, while it has been known for some time that different species use different QS networks, we are beginning to appreciate that different strains of the same bacterial species also differ in their QS networks. Here we combine mass spectrometric imaging (MSI) and confocal Raman microscopy (CRM) approaches to investigate co-cultures involving different strains (FRD1 and PAO1C) of the same species () as well as those involving different species ( and ).

Optically Guided Single Cell Mass Spectrometry of Rat Dorsal Root Ganglia to Profile Lipids, Peptides and Proteins.

The mammalian dorsal root ganglia (DRG) are located on the dorsal roots of the spinal nerves and contain cell bodies of primary sensory neurons. DRG cells have been classified into subpopulations based on their size, morphology, intracellular markers, response to stimuli, and neuropeptides. To understand the connections between DRG chemical heterogeneity and cellular function, we performed optically guided, high-throughput single cell profiling using sequential matrix-assisted laser desorption/ionization mass spectrometry (MS) to detect lipids, peptides, and several proteins in individual DRG cells.

MAPK signaling pathways and HDAC3 activity are disrupted during differentiation of emerin-null myogenic progenitor cells.

Mutations in the gene encoding emerin cause Emery-Dreifuss muscular dystrophy (EDMD). Emerin is an integral inner nuclear membrane protein and a component of the nuclear lamina. EDMD is characterized by skeletal muscle wasting, cardiac conduction defects and tendon contractures.

Single stimulus learning in zebrafish larvae.

Learning about a moving visual stimulus was examined in zebrafish larvae using an automated imaging system and a t1-t2 design. In three experiments, zebrafish larvae were exposed to one of two inputs at t1 (either a gray bouncing disk or an identical but stationary disk) followed by a common test at t2 (the gray bouncing disk). Using 7days post-fertilization (dpf) larvae and 12 stimulus exposures, Experiment 1 established that these different treatments produced differential responding to the moving disk during testing.

Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants.

Extremely low birth weight (ELBW) infants have high morbidity and mortality, frequently due to invasive infections from bacteria, fungi, and viruses. The microbial communities present in the gastrointestinal tracts of preterm infants may serve as a reservoir for invasive organisms and remain poorly characterized. We used deep pyrosequencing to examine the gut-associated microbiome of 11 ELBW infants in the first postnatal month, with a first time determination of the eukaryote microbiota such as fungi and nematodes, including bacteria and viruses that have not been previously described.