Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis

Abstract Background The study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray technology. However, current applications of microarrays are mostly limited to single species studies. The purpose of this study is to develop a method to separate one species, Escherichia coli as an example, from mixed-species communities for transcriptome analysis. Results E. coli cells were separated from a dual-species (E. coli and Stenotrophomonas maltophilia) community using immuno-magnetic separation (IMS). High recovery rates of E. coli were achieved. The purity of E. coli cells was as high as 95.0% separated from suspended mixtures consisting of 1.1 - 71.3% E. coli, and as high as 96.0% separated from biofilms with 8.1% E. coli cells. Biofilms were pre-dispersed into single-cell suspensions. The reagent RNAlater (Ambion, Austin, TX) was used during biofilm dispersion and IMS to preserve the transcriptome of E. coli. A microarray study and quantitative PCR confirmed that very few E. coli genes (only about eight out of 4,289 ORFs) exhibited a significant change in expression during dispersion and separation, indicating that transcriptional profiles of E. coli were well preserved. Conclusions A method based on immuno-magnetic separation (IMS) and application of RNAlater was developed to separate a bacterial species, E. coli as an example, from mixed-species communities while preserving its transcriptome. The method combined with cDNA microarray analysis should be very useful to study species interactions in mixed-species communities.http://deepblue.lib.umich.edu/bitstream/2027.42/112838/1/12866_2011_Article_1346.pd

Bayesian Network Expansion Identifies New ROS and Biofilm Regulators

Signaling and regulatory pathways that guide gene expression have only been partially defined for most organisms. However, given the increasing number of microarray measurements, it may be possible to reconstruct such pathways and uncover missing connections directly from experimental data. Using a compendium of microarray gene expression data obtained from Escherichia coli, we constructed a series of Bayesian network models for the reactive oxygen species (ROS) pathway as defined by EcoCyc. A consensus Bayesian network model was generated using those networks sharing the top recovered score. This microarray-based network only partially agreed with the known ROS pathway curated from the literature and databases. A top network was then expanded to predict genes that could enhance the Bayesian network model using an algorithm we termed ‘BN+1’. This expansion procedure predicted many stress-related genes (e.g., dusB and uspE), and their possible interactions with other ROS pathway genes. A term enrichment method discovered that biofilm-associated microarray data usually contained high expression levels of both uspE and gadX. The predicted involvement of gene uspE in the ROS pathway and interactions between uspE and gadX were confirmed experimentally using E. coli reporter strains. Genes gadX and uspE showed a feedback relationship in regulating each other's expression. Both genes were verified to regulate biofilm formation through gene knockout experiments. These data suggest that the BN+1 expansion method can faithfully uncover hidden or unknown genes for a selected pathway with significant biological roles. The presently reported BN+1 expansion method is a generalized approach applicable to the characterization and expansion of other biological pathways and living systems

Ultrasonic metamaterials with negative modulus

The emergence of artificially designed subwavelength electromagnetic materials, denoted metamaterials1, 2, 3, 4, 5, 6, 7, 8, 9, 10, has significantly broadened the range of material responses found in nature. However, the acoustic analogue to electromagnetic metamaterials has, so far, not been investigated. We report a new class of ultrasonic metamaterials consisting of an array of subwavelength Helmholtz resonators with designed acoustic inductance and capacitance. These materials have an effective dynamic modulus with negative values near the resonance frequency. As a result, these ultrasonic metamaterials can convey acoustic waves with a group velocity antiparallel to phase velocity, as observed experimentally. On the basis of homogenized-media theory, we calculated the dispersion and transmission, which agrees well with experiments near 30 kHz. As the negative dynamic modulus leads to a richness of surface states with very large wavevectors, this new class of acoustic metamaterials may offer interesting applications, such as acoustic negative refraction and superlensing below the diffraction limit

A combined amplicon approach to nematode polyparasitism occurring in captive wild animals in southern China

Abstract Background Gastrointestinal tract (GIT) nematodes prefer to live in the intestines of wild animals, causing damage and even death, and posing a zoonotic risk. The polyparasitism of GIT nematodes results in the complex dynamics of the nematode communities that occur naturally in wild animals. However, the nematode community in captive wild animals is poorly understood. Methods We combined  microscopic examination and amplicon sequencing for community diversity. Results We characterized GIT nematode assemblages to one order, one family, four genera, and ten species, in 512 fecal samples of 121 species from captive wild animals in southern China. The positive rate of GIT nematodes was 20.7% (106/512), including 42.3% (11/26) in reptiles, 26.5% (39/147) in herbivores, 25.0% (25/100) in non-human primates, 20.0% (5/25) in omnivores, 12.2% (9/74) in carnivores, and 12.1% (17/140) in avians. The dominant nematodes were Haemonchus contortus in herbivores and Trichuris species in primates. The nematode communities of arboreal primates differed from their terrestrial counterparts, reflecting both host phylogeny and ecological constraints. Soil-transmitted Strongyloides species were widespread throughout the herbivore, primate, avian, and carnivore communities, and tended to infect omnivorous primates and terrestrial herbivores. In addition, new Trichuris and Heterakis species were found in the nematode communities of captive porcupines and peafowls. Conclusion This study highlights the variation in the composition of the GIT nematode community and strengthens the attention to the harms induced by zoonotic nematodes and co-infective nematodes with low species richness. Graphical Abstrac

Additional file 1: Figure S1. of Molluscicidal activity and mechanism of toxicity of a novel salicylanilide ester derivative against Biomphalaria species

The high resolution mass spectra analysis of salicylanilidate. (TIFF 1218 kb

Potential Factors for Psychological Symptoms at Three Months in Patients with Young Ischemic Stroke

Objective. Psychological status plays a vital role in the recovery in young ischemic stroke patients. However, few reports on the psychological symptoms in Chinese young ischemic stroke patients have been published. In the present study, we aimed to outline the psychological status of young ischemic stroke patients and its risk factors at three months after their stroke. Methods. 364 patients with young ischemic stroke and 384 age-matched healthy controls were consecutively recruited from our study hospitals of the mainland of China between June 2018 and November 2020. Social demographic and clinical data were collected from all enrolled participants in the acute stage of their stroke, and their psychological variables were assessed via the Symptom Checklist 90 Revised (SCL-90-R) at three-month timepoint after their stroke. Multivariable logistic regression analyses were run to identify the independent factors for psychological variables in patients. Results. Compared with healthy controls, patients with young ischemic stroke had significantly higher total score of SCL-90-R and all subscale total scores (p<0.01 or 0.05). 22.3% (81/364 cases) in young ischemic stroke patients had psychological abnormalities. Compared with young ischemic stroke patients without psychological symptoms (n=283), patients with psychological symptoms (n=81) had higher rate of married status (p=0.03), rate of hypertension (p=0.01), infarct size (p=0.01), and the family dysfunction (p<0.01). Multivariate logistic regression analyses revealed that the family dysfunction (odds ratio [OR], 2.50, 95% confidence interval [CI]: 1.71 to 3.54, p<0.01), having hypertension (OR, 3.27, 95% CI: 1.92 to 4.27, p=0.02), and ≥20mm3 infarct size (OR, 2.39, 95% CI: 1.53 to 3.45, p<0.01) were independent factors for having psychological abnormalities in patients with young ischemic stroke at three months after their stroke. Single (OR, 1.23, 95% CI: 1.03 to 1.54, p=0.01), poor family function (OR, 1.21, 95% CI: 1.05 to 1.45, p=0.03), and ≥20mm3 infarct size (OR, 1.74, 95% CI: 1.14 to 3.13, p=0.02) were independent factors for having depression in patents with psychological symptoms. The family dysfunction (OR, 2.32, 95% CI: 1.51 to 2.80, p<0.01) and hypertension (OR, 2.41, 95% CI: 1.54 to 3.46, p=0.03) were independent factors for emerging somatization and anxiety in patients with psychological symptoms, respectively. Conclusions. At three months after their stroke, young ischemic stroke patients had psychological problems and risk factors for developing them