Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation.

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities.

Natural Attenuation of Nonionic Surfactants Used in Hydraulic Fracturing Fluids: Degradation Rates, Pathways, and Mechanisms.

Hydraulic fracturing fluids are injected into shales to extend fracture networks that enhance oil and natural gas production from unconventional reservoirs. Here we evaluated the biodegradability of three widely used nonionic polyglycol ether surfactants (alkyl ethoxylates (AEOs), nonylphenol ethoxylates (NPEOs), and polypropylene glycols (PPGs)) that function as weatherizers, emulsifiers, wetting agents, and corrosion inhibitors in injected fluids. Under anaerobic conditions, we observed complete removal of AEOs and NPEOs from solution within 3 weeks regardless of whether surfactants were part of a chemical mixture or amended as individual additives.

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome.

Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS.

The Microbial Ecosystem Distinguishes Chronically Diseased Tissue from Adjacent Tissue in the Sigmoid Colon of Chronic, Recurrent Diverticulitis Patients.

Diverticular disease is commonly associated with the older population in the United States. As individual's age, diverticulae, or herniation of the mucosa through the colonic wall, develop. In 10-25% of individuals, the diverticulae become inflamed, resulting in diverticulitis.

NOD2 Genetic Variants Predispose One of Two Familial Adenomatous Polyposis Siblings to Pouchitis Through Microbiome Dysbiosis.

Background And Aims: Individuals with familial adenomatous polyposis (FAP) may undergo a total proctocolectomy with ileal pouch-anal anastomosis (IPAA) to surgically treat their disease. Inflammation of the ileal pouch, termed pouchitis, is uncommon in FAP patients but prevalent in patients who received IPAA for ulcerative colitis, a type of inflammatory bowel disease (IBD).

Methods And Results: We report on two FAP siblings, living in the same household, who underwent IPAA surgery within one week of each other.

Evaluating expected outcomes of acid remediation in an intensively mined Appalachian watershed.

Assessments of watershed-based restoration efforts are rare but are essential for the science of stream restoration to advance. We conducted a watershed scale assessment of Abram Creek before and after implementation of a watershed-based plan designed to maximize ecological recovery from acid mine drainage (AMD) impairment. We surveyed water chemistry, physical habitat, benthic macroinvertebrates, and fish community structure in three stream types: AMD-impacted (14 streams), AMD-treated (13 streams), and unimpaired reference (4 streams).

Body Image Models among Low-income African American Mothers and Daughters in the Southeast United States.

Obesity among low-income African American women has been studied using the concepts of both satisfaction and acceptance. The satisfaction frame suggests greater satisfaction with their bodies than their white counterparts, irrespective of size. The acceptance frame suggests that alternative aesthetics serve as resistance against intersectional marginalization.

Ecology of ontogenetic body-mass scaling of gill surface area in a freshwater crustacean.

Several studies have documented ecological effects on intraspecific and interspecific body-size scaling of metabolic rate. However, little is known about how various ecological factors may affect the scaling of respiratory structures supporting oxygen uptake for metabolism. To our knowledge, our study is the first to provide evidence for ecological effects on the scaling of a respiratory structure among conspecific populations of any animal.

Draft Genome Sequence of Type Strain Fl-0169.

We report here the draft genome sequence of the type strain Fl-0169, a member of the complex (MAC). Fl-0169 was isolated from a patient in Italy and is highly similar to strains of isolated in Ireland, although Fl-0169 possesses unique virulence genes.

Dynamics of the human gut microbiome in inflammatory bowel disease.

Inflammatory bowel disease (IBD) is characterized by flares of inflammation with a periodic need for increased medication and sometimes even surgery. The aetiology of IBD is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD subtypes, including ulcerative colitis, colonic Crohn's disease and ileal Crohn's disease.

ZnT2-Mediated Zinc Import Into Paneth Cell Granules Is Necessary for Coordinated Secretion and Paneth Cell Function in Mice.

Background & Aims: Defects in Paneth cell (PC) function are associated with microbial dysbiosis and intestinal inflammation. PC granules contain antimicrobial peptides, cytokines, and substantial stores of zinc (Zn). We hypothesized that Zn, transported into the granule through the Zn transporter (ZnT)2, is critical for signature PC functions.

Population genomics reveals high gene flow in grass rockfish (Sebastes rastrelliger).

Variation at the genomic level is important for understanding a species' demographic and phylogenetic history, in addition to identifying candidate regions that may be under selection and important to local adaptation. We used restriction-site associated DNA (RAD) sequencing to sample single nucleotide polymorphisms (SNPs) from the grass rockfish genome (Sebastes rastrelliger) to assess range-wide patterns of population structure and test for signatures of selection (i.e.

APOE gene and neuropsychiatric disorders and endophenotypes: A comprehensive review.

The Apolipoprotein E (APOE) gene is one of the main candidates in neuropsychiatric genetics, with hundreds of studies carried out in order to explore the possible role of polymorphisms in the APOE gene in a large number of neurological diseases, psychiatric disorders, and related endophenotypes. In the current article, we provide a comprehensive review of the structural and functional aspects of the APOE gene and its relationship with brain disorders. Evidence from genome-wide association studies and meta-analyses shows that the APOE gene has been significantly associated with several neurodegenerative disorders.

Fracked ecology: Response of aquatic trophic structure and mercury biomagnification dynamics in the Marcellus Shale Formation.

Unconventional natural gas development and hydraulic fracturing practices (fracking) are increasing worldwide due to global energy demands. Research has only recently begun to assess fracking impacts to surrounding environments, and very little research is aimed at determining effects on aquatic biodiversity and contaminant biomagnification. Twenty-seven remotely-located streams in Pennsylvania's Marcellus Shale basin were sampled during June and July of 2012 and 2013.

Interplay between Vacuum-Grown Monolayers of Alkylphosphonic Acids and the Performance of Organic Transistors Based on Dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene.

Monolayers of six alkylphosphonic acids ranging from C8 to C18 were prepared by vacuum evaporation and incorporated into low-voltage organic field-effect transistors based on dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene (DNTT). Similar to solution-assembled monolayers, the molecular order for vacuum-deposited monolayers improved with increasing length of the aliphatic tail. At the same time, Fourier transform infrared (FTIR) measurements suggested lower molecular coverage for longer phosphonic acids.

An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies.

A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy.

A Simple Approach to Manipulate Dissolved Oxygen for Animal Behavior Observations.

The ability to manipulate dissolved oxygen (DO) in a laboratory setting has significant application to investigate a number of ecological and organismal behavior questions. The protocol described here provides a simple, reproducible, and controlled method to manipulate DO to study behavioral response in aquatic organisms resulting from hypoxic and anoxic conditions. While performing degasification of water with nitrogen is commonly used in laboratory settings, no explicit method for ecological (aquatic) application exists in the literature, and this protocol is the first to describe a protocol to degasify water to observe organismal response.

Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor.

Granules enriched with anammox bacteria are essential in enhancing the treatment of ammonia-rich wastewater, but little is known about how anammox bacteria grow and multiply inside granules. Here, we combined metatranscriptomics, quantitative PCR and 16S rRNA gene sequencing to study the changes in community composition, metabolic gene content and gene expression in a granular anammox reactor with the objective of understanding the molecular mechanism of anammox growth and multiplication that led to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass.

Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study.

This study sought to characterize the bacterial and fungal microbiota changes associated with Clostridium difficile infection (CDI) among inpatients with diarrhea, in order to further explain the pathogenesis of this infection as well as to potentially guide new CDI therapies. Twenty-four inpatients with diarrhea were enrolled, 12 of whom had CDI. Each patient underwent stool testing for CDI prior to being treated with difficile-directed antibiotics, when appropriate.

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy.

Unlabelled: Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy.

Loss of Nicastrin from Oligodendrocytes Results in Hypomyelination and Schizophrenia with Compulsive Behavior.

The biological underpinnings and the pathological lesions of psychiatric disorders are centuries-old questions that have yet to be understood. Recent studies suggest that schizophrenia and related disorders likely have their origins in perturbed neurodevelopment and can result from a large number of common genetic variants or multiple, individually rare genetic alterations. It is thus conceivable that key neurodevelopmental pathways underline the various genetic changes and the still unknown pathological lesions in schizophrenia.

Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes.

Fish have evolved a variety of sex-determining (SD) systems including male heterogamy (XY), female heterogamy (ZW) and environmental SD. Little is known about SD mechanisms of Sebastes rockfishes, a highly speciose genus of importance to evolutionary and conservation biology. Here, we characterize the sex determination system in the sympatrically distributed sister species Sebastes chrysomelas and Sebastes carnatus.

Fingerprinting two metal contaminants in streams with Cu isotopes near the Dexing Mine, China.

Transition metal isotope signatures are becoming useful for fingerprinting sources in surface waters. This study explored the use of Cu isotope values to trace dissolved metal contaminants in stream water throughout a watershed affected by mining by-products of the Dexing Mine, the largest porphyry Cu operation in Asia. Cu isotope values of stream water were compared to potential mineral sources of Cu in the mining operation, and to proximity to the known Cu sources.

Extracellular Recording of Light Responses from Optic Nerve Fibers and the Caudal Photoreceptor in the Crayfish.

Few laboratory exercises have been developed using the crayfish as a model for teaching how neural processing is done by sensory organs that detect light stimuli. This article describes the dissection procedures and methods for conducting extracellular recording from light responses of both the optic nerve fibers found in the animal's eyestalk and from the caudal photoreceptor located in the ventral nerve cord. Instruction for ADInstruments' data acquisition system is also featured for the data collection and analysis of responses.

Electronic cigarette solutions and resultant aerosol profiles.

Electronic cigarettes (e-cigarettes) are growing in popularity exponentially. Despite their ever-growing acceptance, their aerosol has not been fully characterized. The current study focused on evaluating e-cigarette solutions and their resultant aerosol for potential differences.