Context-specific synthetic T cell promoters from assembled transcriptional elements.

Genetic engineering of human lymphocytes for therapeutic applications is constrained by a lack of transgene transcriptional control, resulting in a compromised therapeutic index. Incomplete understanding of transcriptional logic limits the rational design of contextually responsive genetic modules1. Here, we juxtaposed rationally curated transcriptional response element (TRE) oligonucleotides by random concatemerization to generate a library from which we selected context-specific inducible synthetic promoters (iSynPros).

Sleep Measurement Using Wrist-Worn Accelerometer Data Compared with Polysomnography.

This study determined if using alternative sleep onset (SO) definitions impacted accelerometer-derived sleep estimates compared with polysomnography (PSG). Nineteen participants (48%F) completed a 48 h visit in a home simulation laboratory. Sleep characteristics were calculated from the second night by PSG and a wrist-worn ActiGraph GT3X+ (AG).

Prevalence of Field-Collected House Flies and Stable Flies With Bacteria Displaying Cefotaxime and Multidrug Resistance.

Antibiotic use in livestock accounts for 80% of total antibiotic use in the United States and has been described as the driver for resistance evolution and spread. As clinical infections with multidrug-resistant pathogens are rapidly rising, there remains a missing link between agricultural antibiotic use and its impact on human health. In this study, two species of filth flies from a livestock operation were collected over the course of 11 mo: house flies Musca domestica (L.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Quadriceps Lipid Content Has Sex-Specific Associations With Whole-Muscle, Cellular, and Molecular Contractile Function in Older Adults.

Increased adiposity is associated with reduced skeletal muscle function in older adults, but the mechanisms underlying this relationship remain unclear. To explore whether skeletal muscle properties track with adiposity, whole-muscle, cellular, and molecular function were examined in relation to adiposity measured at various anatomical levels in healthy older (60-80 years) men and women. Although women had greater absolute and relative body and thigh fat than men, quadriceps muscle attenuation, an index of intramuscular lipid content, was similar between sexes.

Time of day, but not sleep restriction, affects markers of hemostasis following heavy exercise.

We sought to determine the effects of sleep restriction on markers of hemostasis the morning after an exercise session. Seven subjects performed evening exercise followed by an exercise session the next morning, both with and without sleep restriction. Evening exercise included a 20-min submaximal cycling trial (10 min at 50% maximal power (W), 10 min at 60% W), a 3-km cycling time trial, 60 min of cycling intervals, and 3 sets of leg press.

Structure/property comparisons of chemistries based on renewable 1,3-propanediol and petroleum-derived alkylene oxides.

Structure/property comparisons were made of chemistries based on renewable 1,3-propanediol (PDO)- versus petroleum-based alkylene oxides as well as comparisons of the respective polyethers, emulsifiers, and cosmetic formulations based on these feedstocks. Green Chemistry Principles were applied in the manufacture of polyethylene glycol (PEG)-free renewable PDO-based oligomers and PDO-based fatty acid ester emulsifiers. Sustainable cosmetic products formulated with renewable PDO-based emulsifiers gave equivalent performance in sensory and moisturization evaluations compared to those formulated with the petroleum-derived PEG-based emulsifiers.

One night of sleep restriction following heavy exercise impairs 3-km cycling time-trial performance in the morning.

The goal of this project was to examine the influence of a single night of sleep restriction following heavy exercise on cycling time-trial (TT) performance and skeletal muscle function in the morning. Seven recreational cyclists (age, 24 ± 7 years; peak oxygen consumption, 62 ± 4 mL·kg·min) completed 2 phases, each comprising evening (EX1) and next-morning (EX2) exercise sessions. EX1 and EX2 were separated by an assigned sleep condition: a full night of rest (CON; 7.

Geography and Location Are the Primary Drivers of Office Microbiome Composition.

In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices.

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.

The number of samples in high-throughput comparative "omics" studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards.

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

Background: Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians.

Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis.

Inflammatory bowel diseases (IBD) are associated with functional inhibition of epithelial Na+/H+ exchange. In mice, a selective disruption of NHE3 (Slc9a3), a major apical Na+/H+ exchanger, also promotes IBD-like symptoms and gut microbial dysbiosis. We hypothesized that disruption of Na+/H+ exchange is necessary for the development of dysbiosis, which promotes an exacerbated mucosal inflammatory response.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Background: Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately.

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention.

Background: Intestinal microbiota influences the progression of colitis-associated colorectal cancer. With diet being a key determinant of the gut microbial ecology, dietary interventions are an attractive avenue for the prevention of colitis-associated colorectal cancer. Curcumin is the most active constituent of the ground rhizome of the Curcuma longa plant, which has been demonstrated to have anti-inflammatory, antioxidative, and antiproliferative properties.

Temporal variability is a personalized feature of the human microbiome.

Background: It is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults.

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis.

Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility.

Copy neutral segments with allelic homozygosity, also known as regions of homozygosity (ROHs), are frequently identified in cases interrogated by oligonucleotide single-nucleotide polymorphism (oligo-SNP) microarrays. Presence of ROHs may be because of parental relatedness, chromosomal recombination or rearrangements and provides important clues regarding ancestral homozygosity, consanguinity or uniparental disomy. In this study of 14 574 consecutive cases, 832 (6%) were found to harbor one or more ROHs over 10 Mb, of which 651 cases (78%) had multiple ROHs, likely because of identity by descent (IBD), and 181 cases (22%) with ROHs involving a single chromosome.

Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

Infants in Neonatal Intensive Care Units (NICUs) are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs) in the spread of infections.

Acidomonas methanolica-associated necrotizing lymphadenitis in a patient with chronic granulomatous disease.

Purpose: Adenitis for which no causative organism can be isolated is a common occurrence in patients with chronic granulomatous disease (CGD). Here we identify Acidomonas methanolica as a pathogen associated with adenitis in a patient with CGD.

Methods: The causative pathogen was obtained after prolonged incubation of an excised lymph node in thioglycolate broth.

Urban trees and the risk of poor birth outcomes.

This paper investigated whether greater tree-canopy cover is associated with reduced risk of poor birth outcomes in Portland, Oregon. Residential addresses were geocoded and linked to classified-aerial imagery to calculate tree-canopy cover in 50, 100, and 200 m buffers around each home in our sample (n=5696). Detailed data on maternal characteristics and additional neighborhood variables were obtained from birth certificates and tax records.

Skin moisturization by hydrogenated polyisobutene--quantitative and visual evaluation.

Hydrogenated polyisobutene (HP) is used in topically applied cosmetic/personal care formulations as an emollient that leaves a pleasing skin feel when applied, and rubbed in after application. This effect, although distinguishable to the user, is difficult to define and quantify. Recognizing that some of the physical properties of HP such as film formation and wear resistance may contribute, in certain mechanisms, to skin moisturization, we designed a short-term pilot study to follow changes in skin moisturization.