scholarly journals Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Erik M Quandt ◽  
Jimmy Gollihar ◽  
Zachary D Blount ◽  
Andrew D Ellington ◽  
George Georgiou ◽  
...  
Keyword(s):  
Citrate Synthase ◽  
Fine Tuning ◽  
Ecological Niches ◽  
Glta Gene ◽  
Evolutionary Changes ◽  
Before And After ◽  
Evolution Experiment ◽  
History Of ◽  
Second Wave

Evolutionary innovations that enable organisms to colonize new ecological niches are rare compared to gradual evolutionary changes in existing traits. We discovered that key mutations in the gltA gene, which encodes citrate synthase (CS), occurred both before and after Escherichia coli gained the ability to grow aerobically on citrate (Cit+ phenotype) during the Lenski long-term evolution experiment. The first gltA mutation, which increases CS activity by disrupting NADH-inhibition of this enzyme, is beneficial for growth on the acetate and contributed to preserving the rudimentary Cit+ trait from extinction when it first evolved. However, after Cit+ was refined by further mutations, this potentiating gltA mutation became deleterious to fitness. A second wave of beneficial gltA mutations then evolved that reduced CS activity to below the ancestral level. Thus, dynamic reorganization of central metabolism made colonizing this new nutrient niche contingent on both co-opting and overcoming a history of prior adaptation.

Priming-Induced Shift in Synaptic Plasticity in the Rat Hippocampus

1999 ◽  
Vol 82 (4) ◽  
pp. 2024-2028 ◽  
Author(s):  
Hongyan Wang ◽  
John J. Wagner
Keyword(s):  
Synaptic Plasticity ◽  
Hippocampal Slices ◽  
Long Term Potentiation ◽  
Crossover Point ◽  
Term Potentiation ◽  
Before And After ◽  
History Of ◽  
The Brain ◽  
Dependent Mechanism

The activity history of a given neuron has been suggested to influence its future responses to synaptic input in one prominent model of experience-dependent synaptic plasticity proposed by Bienenstock, Cooper, and Munro (BCM theory). Because plasticity of synaptic plasticity (i.e., metaplasticity) is similar in concept to aspects of the BCM proposal, we have tested the possibility that a form of metaplasticity induced by a priming stimulation protocol might exhibit BCM-like characteristics. CA1 field excitatory postsynaptic potentials (EPSPs) obtained from rat hippocampal slices were used to monitor synaptic responses before and after conditioning stimuli (3–100 Hz) of the Schaffer collateral inputs. A substantial rightward shift (>5-fold) in the frequency threshold between long-term depression (LTD) and long-term potentiation (LTP) was observed <1 h after priming. This change in the LTD/P crossover point occurred at both primed and unprimed synaptic pathways. These results provide new support for the existence of a rapid, heterosynaptic, experience-dependent mechanism that is capable of modifying the synaptic plasticity phenomena that are commonly proposed to be important for developmental and learning/memory processes in the brain.

scholarly journals Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Bing Li ◽  
Wei-Min Wu ◽  
David B. Watson ◽  
Erick Cardenas ◽  
Yuanqing Chao ◽  
...  
Keyword(s):  
Network Analysis ◽  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Ecological Niches ◽  
Content Type ◽  
Oak Ridge ◽  
Α Diversity ◽  
Before And After

ABSTRACTA site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilizedin situthrough intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A pairedttest indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion.Castellaniellahad the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing generaGeothrix,Desulfovibrio,Ferribacterium, andGeobacterdecreased significantly, whereas the denitrifyingAcidovoraxabundance increased significantly after groundwater invasion. Additionally, seven genera, i.e.,Castellaniella,Ignavibacterium,Simplicispira,Rhizomicrobium,AcidobacteriaGp1,AcidobacteriaGp14, andAcidobacteriaGp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCEHigh-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.

scholarly journals Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

2015 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Richard E. Lenski ◽  
Jeffrey E. Barrick
Keyword(s):  
Escherichia Coli ◽  
Frequency Dependence ◽  
Evolutionary Dynamics ◽  
Selective Sweeps ◽  
Clonal Interference ◽  
Beneficial Mutations ◽  
Frequency Dependent ◽  
Evolution Experiment ◽  
History Of

Twelve replicate populations of Escherichia coli have been evolving in the laboratory for more than 25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara???1. By tracking 42 known mutations in these samples, we reconstructed the history of this population???s genotypic evolution over this period. The evolutionary dynamics of Ara???1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, we found that two clades coexisted for over 6000 generations before one drove the other extinct. In that time, at least nine mutations arose in the clade that prevailed. We found evidence that the clades evolved a frequency-dependent interaction, which prevented the competitive exclusion of either clade, but which eventually collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone.

scholarly journals Antiepileptic pharmacotherapy is the leading factor in the induced pathomorphosis of epilepsy

2018 ◽  
Vol 10 (2) ◽  
pp. 59-73
Author(s):  
M. G. Amirkhanian
Keyword(s):  
Focal Epilepsy ◽  
Rational Approach ◽  
Chi Square ◽  
Antiepileptic Therapy ◽  
Evolutionary Changes ◽  
G 21 ◽  
Chi Square Test ◽  
History Of

Aim– to elucidate the role of antiepileptic pharmacotherapy in pathomorphosis of focal epilepsy in adult patients.Materials and methods. We examined 91 patients with focal epilepsy (main group, G); among them, 37 (41%) men (M) and 54 (59%) women (W). At the time of the first visit, 82 (90%) of  them [33 (89%) M and 49 (91%) W] were under antiepileptic therapy. The age of patients ranged  from 18 to 78 years (average 37.5 years). The debut of epilepsy was observed at the ages from 4  to 71 years. The duration of the disease ranged from 1 to 52 years, with the average of 16.1 years. All patients were then followed up for 1 to 2.5 years. Clinical and neurological examinations were  conducted in all patients; laboratory and instrumental diagnostic tests were used if indicated. The  medical history of patients was analyzed from the onset of epilepsy; if needed, new therapies were  prescribed or the existing therapies were modified. The therapeutic efficacy was assessed  using the data from the daily-seizures diary. The differences between the groups were tested for  their significance using the Chi-square test or the exact Fisher test if there were less than five  observations in the group. Results.Only 47 (52%) patients of group G [21 (57%) M and 26 (48%) W] received an antiepileptic therapy from the debut of the disease; the therapy was then adjusted in 41 (45%)  cases [19 (51%) M and 22 (41%) W (р>0.05)]. Of the 82 patients receiving therapy at the time of  examination, 37 (45%) received the basic, 20 (24%) – the updated, and 24 (29%) – a  combination of the basic and updated AED; in about 2% of cases, a combination with the 1st  generation drugs was prescribed. Monotherapy was used in 45 (55%), and polytherapy – in 37  (45%) patients. Of the 19 patients taking KBZ as the starting monotherapy, 10 (52%) received the drug in the non-prolonged form, twice a day. Relapse after long-term remission (12 months or  more) in 80% of cases was associated with changes in the AED regimen. Side effects were  observed in 43 (52%) patients under the treatment [15 (45%) M and 28 (57%) W]. Among those,  who underwent MRI examination, structural epileptogenic changes were detected in 37 (54%)  patients [21 (72%) M and 16 (40%) W (p<0.05)]. Comorbidity and the associated co-therapy were detected in 88% M and 90% W who were >50 years old.Conclusion. Antiepileptic pharmacotherapy is a leading factor that induces evolutionary changes in the clinical and neurophysiological picture of epilepsy. With a timely and rational approach, the  use of AED allows for creating favorable development of pathomorphosis of the disease. Full  patients awareness of the AED therapeutic regimens and the associated risks may increases the  compliance, reduce the risk of decompensation and improve the prognosis of epilepsy.

scholarly journals New historical data for long-term swordfish ecological studies in the Mediterranean Sea

2021 ◽  
Vol 13 (12) ◽  
pp. 5867-5877
Author(s):  
Brian R. MacKenzie ◽  
Teresa Romeo ◽  
Piero Addis ◽  
Pietro Battaglia ◽  
Pierpaolo Consoli ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Fishery Management ◽  
Data Availability ◽  
Knowledge Based ◽  
Time Period ◽  
Before And After ◽  
Trap Fishery ◽  
History Of ◽  
The Mediterranean

Abstract. Management of marine fisheries and ecosystems is constrained by knowledge based on datasets with limited temporal coverage. Many populations and ecosystems were perturbed long before scientific investigations began. This situation is particularly acute for the largest and commercially most valuable species. We hypothesized that historical trap fishery records for bluefin tuna (Thunnus thynnus Linnaeus, 1758) could contain catch data and information for other, bycatch species, such as swordfish (Xiphias gladius Linnaeus, 1758). This species has a long history of exploitation and is presently overexploited, yet indicators of its status (biomass) used in fishery management only start in 1950. Here we examine historical fishery records and logbooks from some of these traps and recovered ca. 110 years of bycatch data (1896–2010). These previously neglected, but now recovered, data include catch dates and amounts in numbers and/or weights (including individual weights) for the time period before and after major expansion of swordfish fisheries in the Mediterranean Sea. New historical datasets such as these could help understand how human activities and natural variability interact to affect the long-term dynamics of this species. The datasets are online and available with open access via three DOIs, as described in the “Data availability” section of the article.

scholarly journals Knowledge and perception of COVID-19 pandemic. Before-and-after online community survey.

2020 ◽  
Author(s):  
Wojciech Nazar ◽  
Julia Leszkowicz ◽  
Agata Pieńkowska ◽  
Michał Brzeziński ◽  
Agnieszka Szlagatys-Sidorkiewicz ◽  
...  
Keyword(s):  
Online Community ◽  
Medical Professionals ◽  
Second Phase ◽  
School Students ◽  
Online Questionnaire ◽  
Chi Square ◽  
Before And After ◽  
Second Wave ◽  
Management Issues

Abstract Background COVID-19 pandemic impacts many communities worldwide. In this study the Poles' knowledge about COVID-19 as well as people’s behaviours, attitudes and fears during the pandemic were assessed. Changes in these between the outset of the pandemic and the imposition of the strictest lockdown measures in Poland were investigated.Methods Physicians, nurses, students of medicine-oriented faculties, non-medical professionals, students of non-medicine-oriented faculties and secondary school students were surveyed by an anonymous online questionnaire two times: at the onset of the pandemic and in the second week of the strictest lockdown. Statistical analyses were performed using non-parametric tests – Pearson Chi Square, Kruskal-Wallis tests.Results In total 2618 responses were collected. At the beginning people knew that the respiratory system was attacked (97.9%); correctly identified the major symptoms of COVID-19 (95.0%) and ways to prevent infection: hand washing (99.8%), covering mouth (85.9%) and the need to call sanitary-epidemiological services if one experienced COVID-19-like symptoms (92.1%).The biggest changes between the first and second phase of the study concerned behaviours: more people wearing facial masks (+37.5%) and staying at home (+66.1%). Respondents in the second wave of the survey were also more scared of the pandemic (+19.6%), economic crisis (+64.1%), and worried about their families (+26.5%). However, they were less afraid of the quarantine (lockdown) (-18.2%). Nurses and physicians were the most worried groups.Conclusions The study showed that even at the outset of the pandemic Polish population had a good initial knowledge about symptoms, transmission, and preventive behaviours regarding COVID-19. People revealed more short-term concerns, such as the worries about coping with quarantine and isolation. After a month, the knowledge and the concerns among the respondents changed. A shift towards long-term pandemic management issues was observed. Respondents reported to experience more fears concerning the pandemic in general, as well as economic and healthcare crises. Medical professionals reported higher level of fear of the pandemic than other groups included in this study. This study uses before-and-after approach which highlights the changes in people’s knowledge and perception of the COVID-19 pandemic during the pandemic’s progression.

scholarly journals New historical data for long-term swordfish ecological studies in the Mediterranean Sea

2021 ◽  
Author(s):  
Brian R. MacKenzie ◽  
Teresa Romeo ◽  
Piero Addis ◽  
Pietro Battaglia ◽  
Pierpaolo Consoli ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Fishery Management ◽  
Scientific Investigations ◽  
Knowledge Based ◽  
Time Period ◽  
Before And After ◽  
Trap Fishery ◽  
History Of ◽  
The Mediterranean

Abstract. Management of marine fisheries and ecosystems is constrained by knowledge based on datasets with limited temporal coverage. Many populations and ecosystems have been perturbed long before scientific investigations have begun. This situation is particularly acute for the largest and commercially most valuable species. We hypothesized that historical trap fishery records for bluefin tuna, Thunnus thynnus, could contain catch data and information for other, bycatch species, such as swordfish, Xiphias gladius. This species has a long history of exploitation and is presently overexploited, yet indicators of its status (biomass) used in fishery management only start in 1950. Here we examine historical fishery records and logbooks from some of these traps and recovered ca. 110 years of bycatch data (1896–2010). These previously-neglected, but now recovered, data include catch dates and amounts in numbers and/or weights (including individual weights) for the time period before and after major expansion of swordfish fisheries in the Mediterranean Sea. New historical datasets such as these could help understand how human activities and natural variability interact to affect long-term dynamics of this species.

scholarly journals Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

2016 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Philip J. Hatcher ◽  
Anna G. Green ◽  
Barry L. Williams ◽  
Debora S. Marks ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Positive Selection ◽  
Long Term Evolution ◽  
Fine Tuning ◽  
Adaptive Mutations ◽  
E Coli ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Core Genes

AbstractBacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that are fast evolving in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. We identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to fine-tune protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to the long sweep of its evolution in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.Competing Interests StatementWe, the authors, declare that we have no conflicts of interest.

Do Vaccinated People Reduce Their Precautionary Behaviours? A Test on a British Cohort

2021 ◽  
Author(s):  
Olivier Desrichard ◽  
Lisa Moussaoui ◽  
Nana Ofosu
Keyword(s):  
Vaccination Status ◽  
Drop Out ◽  
Before And After ◽  
History Of ◽  
Massive Change

Abstract Background.There is a risk that people vaccinated against COVID-19 will drop out or reduce their behaviours (i.e. a phenomenon of risk homeostasis). Our aim is to assess the occurrence of this effect in a cohort of UK participants who were interviewed 141 days before and 161 days after the start of the vaccination programme.Methods.Of the 7651 people who could be followed up before and after the start of the programme and whose vaccination status was known, 178 had not received any injection and 583 were more or less advanced in the process (one vs. two doses since less vs. more than 14 days). The frequency of 14 precautionary behaviours was assessed at both times of measurement, as well as potential covariates (gender, age, comorbidities and history of COVID-19).Findings.Controlling for covariates, we found no decrease in precautionary behaviours, including among vaccinated individuals, regardless of how far along they were in the process.Interpretation.The results observed in this sample show that a massive change in behaviour among vaccinated individuals does not threaten the fight against the COVID-19 pandemic. The pressure to adopt precautionary behaviours remains strong and probably prevents the emergence of a risk homeostasis effect. Nevertheless, communication on the importance of precautionary behaviour should be maintained so that it does not regress in the long term.

A history of lignite coal mining and reclamation practices in Lusatia, eastern Germany

2012 ◽  
Vol 92 (1) ◽  
pp. 53-66 ◽  
Author(s):  
Julia Krümmelbein ◽  
Oliver Bens ◽  
Thomas Raab ◽  
M. Anne Naeth
Keyword(s):  
Coal Mining ◽  
Lignite Mining ◽  
Eastern Germany ◽  
Mining Areas ◽  
Before And After ◽  
History Of ◽  
Lignite Coal ◽  
The 19Th Century ◽  
Physical And Chemical

Krümmelbein, J., Bens, O., Raab, T. and Naeth, M. A. 2012. A history of lignite coal mining and reclamation practices in Lusatia, eastern Germany. Can. J. Soil Sci. 92: 53–66. Germany is the world's leading lignite coal producer. The region surrounding the towns of Cottbus and Senftenberg in Lusatia, Eastern Germany, is one of the largest mining areas in Germany, and has economically been strongly dependent on lignite mining and lignite processing industries since the middle of the 19th century. We introduce the area, give a brief historical overview of lignite mining techniques and concentrate on post-mining recultivation (reclamation) to agricultural and forestry dominated landscapes. An overview of the physical and chemical limitations for reclamation of the Tertiary and Quaternary substrates due to their natural composition and the technical processes of mine site construction is provided. We introduce some recultivation practices and end with a display of land uses before and after mining and an outlook on the future use of the reclaimed landscape. This review serves as a defined perspective on long-term coal mine reclamation from which to address global similarities and contrasts.

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