Genotype-by-environment interactions govern fitness changes associated with adaptive mutations in two-component response systems

Introduction: Two-component response systems (TCRS) are the main mechanism by which prokaryotes acclimate to changing environments. These systems are composed of a membrane bound histidine kinase (HK) that senses external signals and a response regulator (RR) that activates transcription of response genes. Despite their known role in acclimation, little is known about the role TCRS play in environmental adaptation. Several experimental evolution studies have shown the acquisition of mutations in TCRS during adaptation, therefore here we set out to characterize the adaptive mechanism resulting from these mutations and evaluate whether single nucleotide changes in one gene could induce variable genotype-by-environment (GxE) interactions. Methods: To do this, we assessed fitness changes and differential gene expression for four adaptive mutations in cusS, the gene that encodes the HK CusS, acquired by Escherichia coli during silver adaptation. Results: Fitness assays showed that as the environment changed, each mutant displayed a unique fitness profile with greatest fitness in the original selection environment. RNAseq then indicated that, in ± silver nitrate, each mutant induces a primary response that upregulates cusS, its RR cusR, and constitutively expresses the target response genes cusCFBA. This then induces a secondary response via differential expression of genes regulated by the CusR through TCRS crosstalk. Finally, each mutant undergoes fitness tuning through unique tertiary responses that result in gene expression patterns specific for the genotype, the environment and optimized for the original selection conditions. Discussion: This three-step response shows that different mutations in a single gene leads to individualized phenotypes governed by unique GxE interactions that not only contribute to transcriptional divergence but also to phenotypic plasticity.

Reporting off-target effects of recombinant engineering using the pORTMAGE system

pORTMAGE recombineering is a simple technique for incorporation of novel point mutations into bacterial genomes that eliminates off-target effects. Here we inserted point mutations into the cusS gene from Escherichia coli, then, using Illumina sequencing, report genetic variants in all mutant strains. Several off-site mutations were found at high frequency. Low frequency mutations also show high heterogeneity. This means that it is essential for studies to report all off-target effects and acknowledge the effect that this may have on resultant phenotypes.

Long-Term Recovery of the Adaptive Immune System in Rhesus Macaques After Total Body Irradiation

PURPOSE

Ionizing radiation causes acute damage to hematopoietic and immune cells, but the long-term immunologic consequences of irradiation are poorly understood. We therefore performed a prospective study of the delayed immune effects of radiation using a rhesus macaque model.

METHODS AND MATERIALS

Ten macaques received 4 Gy high-energy x-ray total body irradiation (TBI) and 6 control animals received sham irradiation. TBI caused transient lymphopenia that resolved over several weeks. Once white blood cell counts recovered, flow cytometry was used to immunophenotype the circulating adaptive immune cell populations 4, 9, and 21 months after TBI. Data were fit using a mixed-effects model to determine age-dependent, radiation-dependent, and interacting effects. T cell receptor (TCR) sequencing and quantification of TCR Excision Circles were used to determine relative contributions of thymopoiesis and peripheral expansion to T cell repopulation. Two years after TBI, the cohort was vaccinated with a 23-valent pneumococcal polysaccharide vaccine and a tetravalent influenza hemagglutinin vaccine.

RESULTS

Aging, but not TBI, led to significant changes in the frequencies of dendritic cells, CD4 and CD8 T cells, and B cells. However, irradiated animals exhibited increased frequencies of central memory T cells and decreased frequencies of naïve T cells. These consequences of irradiation were time-dependent and more prolonged in the CD8 T cell population. Irradiation led to transient increases in CD8+ T cell TCR Excision Circles and had no significant effect on TCR sequence entropy, indicating T cell recovery was partially mediated by thymopoiesis. Animals that were irradiated and then vaccinated showed normal immunoglobulin G binding and influenza neutralization titers in response to the 4 protein antigens but weaker immunoglobulin G binding titers to 10 of the 23 polysaccharide antigens.

CONCLUSIONS

These findings indicate that TBI causes subtle but long-lasting immune defects that are evident years after recovery from lymphopenia.

Respiratory rate during acute asthma

Asthmatic patients hyperventilate during acute attacks, but controversy persists as to whether they breathe rapidly, deeply or both. We monitored respiratory rate under the three following conditions: (1) asthma treated in the emergency room; (2) airways obstruction provoked by methacholine inhalation; and (3) airways obstruction provoked by exercise. In 47 acutely ill asthmatic patients, respiratory rate was higher than in 42 nonasthmatic control patients in the emergency room. Pretreatment respiratory rate correlated with peak expiratory flow rate and forced expired volume in one second. In 17 asthmatic patients and 16 healthy volunteers, breathing pattern was monitored by respiratory inductance plethysmography. Methacholine inhalation and exercise provoked significant airways obstruction in asthmatic patients but not in control subjects. In asthmatic patients, minute ventilation and tidal volume increased above that of control subjects following methacholine and exercise, but the rate was no higher than in control subjects. We conclude that the respiratory rate is increased in naturally occurring asthma, but not when acute airways obstruction is induced transiently in the laboratory. In the former setting, the respiratory rate is correlated with spirometric measures of airflow obstruction, but the weakness of the correlation does not allow the respiratory rate to be used as a substitute for spirometry.

Use of the interview in admissions

A description of one method of dealing with nonacademic information from applicants seeking acceptance into a physical therapy curriculum is presented. The strengths of this admission process are interviewer training sessions, use of simulated interviews presented by videotape, subsequent discussion of ratings, specific criteria to support interview ratings, and an arbitration procedure. Attempts were made to increase the objectivity of the interview through frequent meetings of the admission committee to decide on the areas of the interview and specific criteria on which to rate each area. In the areas of weighting factors, training of interviewers, development of specific interview criteria, arbitration procedure, and the use of the computer printout, this admission process could be easily adapted to other allied health programs. Details of the interview are discussed.

Mock clinic. An approach to clinical education

This paper presents a new clinical education experience initiated at the University of Wisconsin-La Crosse. A Mock Clinic was developed that simulates a real-life physical therapy department: students adopt roles of both physical therapist and patient. Each student is student-therapist and student-patient at least once each session. At the beginning of each session, the student-therapist selects a patient treatment card (containing instructions submitted by academic and clinical faculty members) and a faculty supervisor discusses the role of the patient with the student-patient to assist him in accurately displaying signs and symptoms. The student-therapist alos meets with the faculty supervisor to review the patient and the approach. The student-therapist then "evaluates" and "treats" the student-patient. A group discussion concludes each session. Mock Clinic is a role-playing experience that provides the opportunity for students to see themselves in clinical situations and enables them to learn without involving real clients. Strengths and weaknesses of Mock Clinic identified by all participants are discussed.

Enhancement of tumor growth in allogeneic mice following impairment of macrophage function

Teratoma 402 AX is an embryo-like tumor cell line originally derived from the testicles of strain 129/J mice. This teratocarcinoma grows well in males and pregnant females but poorly in virgin females when given in small doses. Induction of growth of this tumor is syngeneic and allogeneic virgin females was achieved by modification of macrophage function by antimacrophage serum. Tumor-bearing animals of both sexes, whether treated with antimacrophage serum or normal rabbit serum, produce antitumor antibodies of the IgM, IgA, IgG, IgG, and IgG classes. These antibodies are bound to the tumor cell surface and are not cytotoxic to the target cell in the presence of rabbit or guinea pig complement.