Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology

Organisms cope with physiological stressors through acclimatizing mechanisms in the short-term and adaptive mechanisms over evolutionary timescales. During adaptation to an environmental or genetic perturbation, beneficial mutations can generate numerous physiological changes: some will be novel with respect to prior physiological states, while others might either restore acclimatizing responses to a wild-type state, reinforce them further, or leave them unchanged. We examined the interplay of acclimatizing and adaptive responses at the level of global gene expression in Methylobacterium extorquens AM1 engineered with a novel central metabolism. Replacing central metabolism with a distinct, foreign pathway resulted in much slower growth than wild-type. After 600 generations of adaptation, however, eight replicate populations founded from this engineered ancestor had improved up to 2.5-fold. A comparison of global gene expression in wild-type, engineered, and all eight evolved strains revealed that the vast majority of changes during physiological adaptation effectively restored acclimatizing processes to wild-type expression states. On average, 93% of expression perturbations from the engineered strain were restored, with 70% of these occurring in perfect parallel across all eight replicate populations. Novel changes were common but typically restricted to one or a few lineages, and reinforcing changes were quite rare. Despite this, cases in which expression was novel or reinforced in parallel were enriched for loci harboring beneficial mutations. One case of parallel, reinforced changes was the pntAB transhydrogenase that uses NADH to reduce $NADP^+$ to NADPH. We show that PntAB activity was highly correlated with the restoration of NAD(H) and NADP(H) pools perturbed in the engineered strain to wild-type levels, and with improved growth. These results suggest that much of the evolved response to genetic perturbation was a consequence rather than a cause of adaptation and that physiology avoided “reinventing the wheel” by restoring acclimatizing processes to the pre-stressed state.Organismic and Evolutionary Biolog

Memory B cells and CD8⁺ lymphocytes do not control seasonal influenza A virus replication after homologous re-challenge of rhesus macaques.

This study sought to define the role of memory lymphocytes in the protection from homologous influenza A virus re-challenge in rhesus macaques. Depleting monoclonal antibodies (mAb) were administered to the animals prior to their second experimental inoculation with a human seasonal influenza A virus strain. Treatment with either anti-CD8α or anti-CD20 mAbs prior to re-challenge had minimal effect on influenza A virus replication. Thus, in non-human primates with pre-existing anti-influenza A antibodies, memory B cells and CD8α⁺ T cells do not contribute to the control of virus replication after re-challenge with a homologous strain of influenza A virus

A cross-sectional study of predatory publishing emails received by career development grant awardees

OBJECTIVE: To investigate the scope of academic spam emails (ASEs) among career development grant awardees and the factors associated with the amount of time spent addressing them. DESIGN: A cross-sectional survey of career development grant investigators via an anonymous online survey was conducted. In addition to demographic and professional information, we asked investigators to report the number of ASEs received each day, how they determined whether these emails were spam and time they spent per day addressing them. We used bivariate analysis to assess factors associated with the amount of time spent on ASEs. SETTING: An online survey sent via email on three separate occasions between November and December 2016. PARTICIPANTS: All National Institutes of Health career development awardees funded in the 2015 fiscal year. MAIN OUTCOME MEASURES: Factors associated with the amount of time spent addressing ASEs. RESULTS: A total of 3492 surveys were emailed, of which 206 (5.9%) were returned as undeliverable and 96 (2.7%) reported an out-of-office message; our overall response rate was 22.3% (n=733). All respondents reported receiving ASEs, with the majority (54.4%) receiving between 1 and 10 per day and spending between 1 and 10 min each day evaluating them. The amount of time respondents reported spending on ASEs was associated with the number of peer-reviewed journal articles authored (p<0.001), a history of publishing in open access format (p<0.01), the total number of ASEs received (p<0.001) and a feeling of having missed opportunities due to ignoring these emails (p=0.04). CONCLUSIONS: ASEs are a common distraction for career development grantees that may impact faculty productivity. There is an urgent need to mitigate this growing problem

Synthesis And Characterization Of (pyNO−)2GaCl: A Redox-Active Gallium Complex

We report the synthesis of a gallium complex incorporating redox-active pyridyl nitroxide ligands. The (pyNO−)2GaCl complex was prepared in 85% yield via a salt metathesis route and was characterized by 1H and 13C NMR spectroscopies, X-ray diffraction, and theory. UV–Vis absorption spectroscopy and electrochemistry were used to access the optical and electrochemical properties of the complex, respectively. Our discussion focuses primarily on a comparison of the gallium complex to the corresponding aluminum derivative and shows that although the complexes are very similar, small differences in the electronic structure of the complexes can be correlated to the identity of the metal

Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

Background: A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or “domestication” of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 (“AM1”) has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own “Modern” stock of AM1 to a sample archived at a culture stock center shortly after the strain’s discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means. Results: Using whole-genome re-sequencing, we identified some 29 mutations – including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains. Conclusions: These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts

Reply to 'Letter to Editor by Finsterer J and Zarrouk-Mahjoub S : Phenotypic manifestations of the m.8969G > A variant'

Peer reviewe

RNA Decay and RNA Silencing in Plants: Competition or Collaboration?

Initiation of RNA polymerase II transcription signals the beginning of a series of physically and functionally coupled pre-mRNA processing events that transform an RNA transcript into a highly structured, mature ribonucleoprotein complex. With such a complexity of co-transcriptional processes comes the need to identify and degrade improperly processed transcripts. Quality control of mRNA expression primarily involves exonucleolytic degradation of aberrant RNAs. RNA silencing, on the other hand, tends to be viewed separately as a pathway that primarily functions in regulating endogenous gene expression and in genome defense against transposons and viruses. Here, we review current knowledge of these pathways as they exist in plants and draw parallels to similar pathways in other eukaryotes. We then highlight some unexplored overlaps that exist between the RNA silencing and RNA decay pathways of plants, as evidenced by their shared RNA substrates and shared genetic requirements

Simulations of the Dipole-Dipole Interaction Between Two Spatially Separated Groups of Rydberg Atoms

The dipole-dipole interaction among ultracold Rydberg atoms is simulated. We examine a general interaction scheme in which two atoms excited to the x and x(\u27) states are converted to y and y(\u27) states via a Förster resonance. The atoms are arranged in two spatially separated groups, each consisting of only one species of atom. We monitor the state mixing by recording the fraction of atoms excited to the y(\u27) state as the distance between the two groups is varied. With zero detuning a many-body effect that relies on always resonant interactions causes the state mixing to have a finite range. When the detuning is greater than zero, another many-body effect causes a peak in the state mixing when the two groups of atoms are some distance away from each other. To obtain these results it is necessary to include multiple atoms and solve the full many-body wave function. These simulation results are supported by recent experimental evidence. These many-body effects, combined with appropriate spatial arrangement of the atoms, could be useful in controlling the energy exchange among the atoms

Simulations of the Dipole-Dipole Interaction Between Two Spatially Separated Groups of Rydberg Atoms

The dipole-dipole interaction among ultracold Rydberg atoms is simulated. We examine a general interaction scheme in which two atoms excited to the x and x(\u27) states are converted to y and y(\u27) states via a Förster resonance. The atoms are arranged in two spatially separated groups, each consisting of only one species of atom. We monitor the state mixing by recording the fraction of atoms excited to the y(\u27) state as the distance between the two groups is varied. With zero detuning a many-body effect that relies on always resonant interactions causes the state mixing to have a finite range. When the detuning is greater than zero, another many-body effect causes a peak in the state mixing when the two groups of atoms are some distance away from each other. To obtain these results it is necessary to include multiple atoms and solve the full many-body wave function. These simulation results are supported by recent experimental evidence. These many-body effects, combined with appropriate spatial arrangement of the atoms, could be useful in controlling the energy exchange among the atoms