Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

B553: Consumer Packages for Maine Mcintosh Apples

Three kinds of consumer packages for apples were developed for testing in the 1955-56 marketing season. In developing these packages, the authors modified the jumble-pack, polyethylene package in a way that would protect the fruit from most of the bruising and still maintain almost complete visibility of the fruit. One consumer package developed was a long narrow polyethylene bag, another was a polyethylene bag with a divider insert, and the third package had a cell partition placed in a similar plastic bag. All three packages were well accepted by consumers in the Portland market.https://digitalcommons.library.umaine.edu/aes_bulletin/1085/thumbnail.jp

Effect of Long-Duration Spaceflight on Postural Control During Self-Generated Perturbations

This report is the first systematic evaluation of the effects of prolonged weightlessness on the bipedal postural control processes during self-generated perturbations produced by voluntary upper limb movements. Spaceflight impacts humans in a variety of ways, one of which is compromised postflight postural control. We examined the neuromuscular activation characteristics and center of pressure motion (COP) associated with arm movement of eight subjects who experienced long duration spaceflight (3-6 months) aboard the Mir space station. Surface electromyography (EMG), arm acceleration, and COP motion were collected while astronauts performed rapid unilateral shoulder flexions prior to and after spaceflight. Subjects displayed compromised postural control after flight as evidenced by modified peak-to-peak COP anterior-posterior and medio-lateral motion and COP pathlength relative to preflight values. These changes were associated with disrupted neuromuscular activation characteristics, particularly after the completion of arm acceleration (i.e. when subjects were attempting to maintain their upright posture). These findings suggest that although the subjects were able to assemble coordination modes that enabled them to generate rapid arm movements, the subtle control necessary to maintain bipedal equilibrium evident in their preflight performance is compromised after long duration spaceflight

Role of interferon‐γ and inflammatory monocytes in driving colonic inflammation during acute Clostridium difficile infection in mice

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136491/1/imm12700.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136491/2/imm12700_am.pd

The enrichment of an alkaliphilic biofilm consortia capable of the anaerobic degradation of isosaccharinic acid from cellulosic materials incubated within an anthropogenic, hyperalkaline environment.

Anthropogenic hyper-alkaline sites provide an environment that is analogous to proposed cementitious geological disposal facilities (GDF) for radioactive waste. Under anoxic, alkaline conditions cellulosic wastes will hydrolyse to a range of cellulose degradation products (CDP) dominated by isosaccharinic acids (ISA). In order to investigate the potential for microbial activity in a cementitious GDF, cellulose samples were incubated in the alkaline (∼pH 12), anaerobic zone of a lime kiln waste site. Following retrieval, these samples had undergone partial alkaline hydrolysis and were colonised by a Clostridia dominated biofilm community, where hydrogenotrophic, alkaliphilic methanogens were also present. When these samples were used to establish an alkaline CDP fed microcosm, the community shifted away from Clostridia, methanogens became undetectable and a flocculate community dominated by Alishewanella sp. established. These flocs were composed of bacteria embedded in polysaccharides and protein stabilised by extracellular DNA. This community was able to degrade all forms of ISA with >60% of the carbon flow being channelled into extracellular polymeric substance (EPS) production. This study demonstrated that alkaliphilic microbial communities can degrade the CDP associated with some radioactive waste disposal concepts at pH 11. These communities divert significant amounts of degradable carbon to EPS formation, suggesting that EPS has a central role in the protection of these communities from hyper-alkaline conditions

Methods for Linking Community Views to Measureable Outcomes in a Youth Violence Prevention Program

Background: All parties in community–academic partnerships have a vested interest prevention program success. Markers of success that reflect community’s experiences of programmatic prevention success are not always measurable, but critically speak to community-defined needs. Objective: The purpose of this manuscript was to (1) describe our systematic process for linking locally relevant community views (community-defined indicators) to measurable outcomes in the context of a youth violence prevention program and (2) discuss lessons learned, next steps, and recommendations for others trying to replicate a similar process. Methods: A research team composed of both academic and community researchers conducted a systematic process of matching community-defined indicators of youth violence prevention programmatic success to standardized youth survey items being administered in the course of a program evaluation. The research team of three community partners and five academic partners considered 43 community-defined indicators and 208 items from the youth surveys being utilized within the context of a community-based aggression prevention program. At the end of the matching process, 92 youth survey items were identified and agreed upon as potential matches to 11 of the community-defined indicators. Conclusions: We applied rigorous action steps to match community-defined indicators to survey data collected in the youth violence prevention intervention. We learned important lessons that inform recommendations for others interested in such endeavors. The process used to derive and assess community-defined indicators of success emphasized the principles of community-based participatory research (CBPR) and use of existing and available data to reduce participant burden

Interleukin‐22 and CD160 play additive roles in the host mucosal response to Clostridium difficile infection in mice

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110834/1/imm12414.pd

TransitFit: an exoplanet transit fitting package for multi-telescope datasets and its application to WASP-127~b, WASP-91~b, and WASP-126~b

We present TransitFit, an open-source Python~3 package designed to fit exoplanetary transit light-curves for transmission spectroscopy studies (Available at https://github.com/joshjchayes/TransitFit and https://github.com/spearnet/TransitFit, with documentation at https://transitfit.readthedocs.io/). TransitFit employs nested sampling to offer efficient and robust multi-epoch, multi-wavelength fitting of transit data obtained from one or more telescopes. TransitFit allows per-telescope detrending to be performed simultaneously with parameter fitting, including the use of user-supplied detrending alogorithms. Host limb darkening can be fitted either independently ("uncoupled") for each filter or combined ("coupled") using prior conditioning from the PHOENIX stellar atmosphere models. For this TransitFit uses the Limb Darkening Toolkit (LDTk) together with filter profiles, including user-supplied filter profiles. We demonstrate the application of TransitFit in three different contexts. First, we model SPEARNET broadband optical data of the low-density hot-Neptune WASP-127~b. The data were obtained from a globally-distributed network of 0.5m--2.4m telescopes. We find clear improvement in our broadband results using the coupled mode over uncoupled mode, when compared against the higher spectral resolution GTC/OSIRIS transmission spectrum obtained by Chen et al. (2018). Using TransitFit, we fit 26 transit observations by TESS to recover improved ephemerides of the hot-Jupiter WASP-91~b and a transit depth determined to a precision of 170~ppm. Finally, we use TransitFit to conduct an investigation into the contested presence of TTV signatures in WASP-126~b using 126 transits observed by TESS, concluding that there is no statistically significant evidence for such signatures from observations spanning 31 TESS sectors.Comment: 14 pages, 5 figures, 5 tables, submitted to MNRAS. Temporary data address at https://cdsarc.u-strasbg.fr/ftp/vizier.submit/wasp-127b/ (Final address to be included in accepted paper