The relationship between depressive symptoms and coping style on asthma outcomes in older adults.

Objective: To examine the impact of coping styles in older adults with asthma on the prospective relationship between depressive symptoms and asthma outcomes, and how their perceptions of social support influenced their coping styles.

Methods: Adults 60 and over with asthma were recruited and interviewed about their experiences of asthma, depression, and other psychosocial factors over three time points (Baseline, 6-month, and 12-month visits). Structural equation models examined the mediating roles of coping styles in the relationship between depressive symptoms (assessed by BDI-II) and asthma outcomes (i.

Under-perception of airflow limitation, self-efficacy, and beliefs in older adults with asthma.

Objective: Under-perception of airflow limitation is more common in older adults with asthma and may lead to under-reporting of asthma symptoms. Asthma management self-efficacy is linked with better asthma control and quality of life (QoL). We sought to examine asthma and medication beliefs as a mediator in the relationship between both under-perception and self-efficacy with asthma outcomes.

The relationship between social support, self-efficacy, and asthma outcomes in older adults.

Objective: There has been a call for research examining factors that influence asthma outcomes in older adults because of the notable disparities observed in this age group. Social support and self-efficacy are resources that factor into asthma outcomes. The current study aimed to examine the relationship between these resources (independently and jointly) and asthma control and quality of life.

Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers.

Manipulation of the gut microbiota via fecal microbiota transplantation (FMT) has shown clinical promise in diseases such as recurrent Clostridioides difficile infection (rCDI). However, the variable nature of this approach makes it challenging to describe the relationship between fecal strain colonization, corresponding microbiota changes, and clinical efficacy. Live biotherapeutic products (LBPs) consisting of defined consortia of clonal bacterial isolates have been proposed as an alternative therapeutic class because of their promising preclinical results and safety profile.

Reduced asthma morbidity during COVID-19 in minority children: is medication adherence a reason?

Objectives: Asthma control improved during the COVID-19 pandemic. This study examined objectively measured medication adherence, asthma morbidity and quality of life (QoL) outcomes in Black and Latinx children by month for January-June 2019 (pre-COVID) compared to January-June 2020 (including first peak of COVID).

Methods: Secondary analyses of 94 children with asthma (ages 10-17 years, 64% Latinx, 36% Black) and their caregivers assigned to the comparison group of a longitudinal RCT intervention trial.

Depressive Symptoms and Overperception of Airflow Obstruction in Older Adults With Asthma.

Objective: Older adults are at increased risk for depression and poor asthma outcomes. We examined whether depressive symptoms are associated with overperception of airflow obstruction and a pattern of worse asthma control, but not pulmonary function.

Methods: We recruited a cohort of adults with asthma 60 years and older in East Harlem and the Bronx, New York.

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.

Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane.

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

Following publication of the original article [1], the authors would like to highlight the following two corrections.

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

Background: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.

Results: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers.

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications.

Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample.

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples.

Determining the cause of recurrent Clostridium difficile infection using whole genome sequencing.

Understanding the contribution of relapse and reinfection to recurrent Clostridium difficile infection (CDI) has implications for therapy and infection prevention, respectively. We used whole genome sequencing to determine the relation of C. difficile strains isolated from patients with recurrent CDI at an academic medical center in the United States.

Circular dichroism (CD) analyses of protein-protein interactions.

Circular dichroism (CD) spectroscopy is a useful technique for studying protein-protein interactions in solution. CD in the far ultraviolet region (178-260 nm) arises from the amides of the protein backbone and is sensitive to the conformation of the protein. Thus, CD can determine whether there are changes in the conformation of proteins when they interact.

Structural and protein interaction effects of hypertrophic and dilated cardiomyopathic mutations in alpha-tropomyosin.

The potential alterations to structure and associations with thin filament proteins caused by the dilated cardiomyopathy (DCM) associated tropomyosin (Tm) mutants E40K and E54K, and the hypertrophic cardiomyopathy (HCM) associated Tm mutants E62Q and L185R, were investigated. In order to ascertain what the cause of the known functional effects may be, structural and protein-protein interaction studies were conducted utilizing actomyosin ATPase activity measurements and spectroscopy. In actomyosin ATPase measurements, both HCM mutants and the DCM mutant E54K caused increases in Ca(2+)-induced maximal ATPase activities, while E40K caused a decrease.

Imaging late complications of cholecystectomy.

Objective: To review the imaging findings in late complications of cholecystectomy.

Conclusions: Late postcholecystectomy complications include papillary stenosis, choledocholithiasis, biliary stricture, remnant gallbladder, and dropped gallstones. Such complications can cause substantial morbidity, and knowledge of the imaging appearances can facilitate expeditious diagnosis and treatment.

Pharmacogenomic biomarkers in dermatologic drugs.

Biomarkers are becoming increasingly important when considering the efficacy, toxicology, mechanism of action, and risk of adverse events in certain drugs. As availability of bio-genomic information increases, more treatments can be tailored to specific individuals, with a net effect of improved health outcomes. Many dermatology drugs have pharmacogenomic information on their labels.

Evaluating the adequacy of fluid resuscitation in patients with septic shock: controversies and future directions.

Fluid resuscitation is a cornerstone in the treatment of severe sepsis and septic shock. However, there is little evidence to guide clinicians in its administration. Current guidelines recommend targeting fluid therapy based on measurements of cardiac filling pressures, such as central venous pressure.

Characterization of an actively linearized ultrabroadband chirped laser with a fiber-laser optical frequency comb.

The optical frequency sweep of an actively linearized, ultrabroadband, chirped laser source is characterized through optical heterodyne detection against a fiber-laser frequency comb. Frequency sweeps were measured over approximately 5 THz bandwidths from 1530 nm to 1570 nm. The dominant deviation from linearity resulted from the nonzero dispersion of the fiber delay used as a reference for the sweep linearization.

Structure of the N terminus of a nonmuscle alpha-tropomyosin in complex with the C terminus: implications for actin binding.

Tropomyosin is a coiled-coil actin binding protein that stabilizes the filament, protects it from severing, and cooperatively regulates actin's interaction with myosin. Depending on the first coding exon, tropomyosins are low molecular weight (LMW), found in the cytoskeleton and predominant in transformed cells, or high molecular weight (HMW), found in muscle and nonmuscle cells. The N- and C-terminal ends form a complex that allows tropomyosin to associate N terminus-to-C terminus along the actin filament.

Molecular basis of tropomyosin binding to tropomodulin, an actin-capping protein.

The tropomodulin (Tmod) family of proteins that cap the pointed, slow-growing end of actin filaments require tropomyosin (TM) for optimal function. Earlier studies identified two regions in Tmod1 that bind the N terminus of TM, though the ability of different isoforms to bind the two sites is controversial. We used model peptides to determine the affinity and define the specificity of the highly conserved N termini of three short, non-muscle TMs (alpha, gamma, delta-TM) for the two Tmod1 binding sites using circular dichroism spectroscopy, native gel electrophoresis, and chemical crosslinking.

Tropomyosin regulates elongation by formin at the fast-growing end of the actin filament.

The balance between dynamic and stable actin filaments is essential for the regulation of cellular functions including the determination of cell shape and polarity, cell migration, and cytokinesis. Proteins that regulate polymerization at the filament ends and filament stability confer specificity to actin filament structure and cellular function. The dynamics of the barbed, fast-growing end of the filament are controlled in space and time by both positive and negative regulators of actin polymerization.

Effects of estradiol and 4-hydroxytamoxifen on the conformation, thermal stability, and DNA recognition of estrogen receptor beta.

Estrogen receptors (ERalpha and ERbeta) are ligand-activated transcription factors. We examined the effects of estradiol (E2), 4-hydroxytamoxifen (HT), and the estrogen response element (ERE) on the helical content and thermal unfolding of ERbeta. A circular dichroism (CD) spectrum of ERbeta showed changes at 210 and 222 nm that were due to the presence of E2, which is indicative of partial unfolding.

Analysis of the kinetics of folding of proteins and peptides using circular dichroism.

Circular dichroism (CD) is a useful spectroscopic technique for studying the secondary structure, folding and binding properties of proteins. This protocol covers how to use the intrinsic circular dichroic properties of proteins to follow their folding and unfolding as a function of time. Included are methods of obtaining data and for analyzing the folding and unfolding data to determine the rate constants and the order of the folding and unfolding reactions.