Fixation probabilities for the Moran process in evolutionary games with two strategies: graph shapes and large population asymptotics

This paper is based on the complete classification of evolutionary scenarios for the Moran process with two strategies given by Taylor et al. (Bull Math Biol 66(6):1621–1644, 2004. https://doi.org/10.1016/j.bulm.2004.03.004). Their classification is based on whether each strategy is a Nash equilibrium and whether the fixation probability for a single individual of each strategy is larger or smaller than its value for neutral evolution. We improve on this analysis by showing that each evolutionary scenario is characterized by a definite graph shape for the fixation probability function. A second class of results deals with the behavior of the fixation probability when the population size tends to infinity. We develop asymptotic formulae that approximate the fixation probability in this limit and conclude that some of the evolutionary scenarios cannot exist when the population size is large.

     

Broadening the concept of glycoconjugates: glycoRNA and ubiquitinylated lipopolysaccharide

Glycoconjugate Journal - Two recent papers ( https://doi.org/10.1016/j.cell.2021.04.023 and https://doi.org/10.1038/s41586-021-03566-4 ) extend the definition of glycoconjugates to new classes of...     

The Virtues of Theory: How Some Academics Succeeded – Big Time – in Reaching Non-Academic Audiences

ABSTRACT

This is a short essay stimulated by Why Anthropologists Don’t Reach the Public: A Rumination on Books of Thomas Hylland Eriksen, by Gordon Mathews (DOI: https://doi.org/10.1080/00664677.2018.1502074).     

The following two articles for this Special Issue were previously published and can be found in their respective issues online

Reactive oxygen species signaling in primordial germ cell development in Drosophila embryos (58:6) https://doi.org/10.1002/dvg.23362 Generation of B6‐Ddx4 ^{em1(CreERT2)Utr}, a novel CreERT2 knock‐in line, for germ cell lineage by CRISPR /Cas9 (58:7) https://doi.org/10.1002/dvg.23367     

Species notions that combine phylogenetic trees and phenotypic partitions

A recent paper (Manceau and Lambert in bioRxiv, 2017. https://doi.org/10.1101/075580) developed a novel approach for describing two well-defined notions of ‘species’ based on a phylogenetic tree and a phenotypic partition. In this paper, we explore some further combinatorial properties of this approach and describe an extension that allows an arbitrary number of phenotypic partitions to be combined with a phylogenetic tree for these two species notions.

     

Restraining reactive oxygen species in Listeria monocytogenes promotes the apoptosis of glial cells

Objectives: Listeria monocytogenes is a facultative anaerobic foodborne pathogen that can traverse the blood–brain barrier and cause brain infection. L. monocytogenes infection induces host cell apoptosis in several cell types. In this study, we investigated the apoptosis of human glioma cell line U251 invaded by L. monocytogenes and evaluated the function of bacterial reactive oxygen species (ROS) during infection.

Methods: Bacterial ROS level was reduced by carrying out treatment with N-acetyl cysteine (NAC) and diphenyleneiodonium chloride (DPI). After infection, the apoptosis of U251 cells was examined by flow cytometry assay and propidium iodide staining.

Results: DPI and NAC efficiently decreased ROS level in L. monocytogenes without affecting bacterial growth. Moreover, the apoptosis of glial cells was enhanced upon invasion of DPI- and NAC-pretreated L. monocytogenes.

Discussion: Results indicate that the apoptosis of glial cells can be induced by L. monocytogenes, and that the inhibition of bacterial ROS increases the apoptosis of host cells.     

Cover Picture: Biotechnology Journal 9/2016

This regular issue of BTJ includes articles on bioprocess engineering and biochemical engineering. Also it contains two special articles to the topic ‘Eukaryotic Synthetic Biology’. The cover shows mouse embryonic stem cells proliferating in a microfluidic culture device capable of monitoring specific oxygen uptake rates in real time. Monitoring occurs without disruption of the cell culture and label‐free. Image is provided by Alexandre Super, Nicolas Jaccard, Marco Paulo Cardoso Marques, Rhys Jarred Macown, Lewis D. Griffin, Farlan Singh Veraitch and Nicolas Szita authors of ‘Real‐time monitoring of specific oxygen uptake rates of embryonic stem cells in a microfluidic cell culture device’ ( http://dx.doi.org/10.1002/biot.201500479 ).     

RETRACTED ARTICLE: A review of 45 candidate genes: Association of single nucleotide polymorphism to schizophrenia Risk

The following article has been retracted from publication in the Taylor & Francis journal New Genetics and Society. I. Priya, S. Sharma, I. Sharma, R. Mahajan and N. Kapoor, A review of 45 candidate genes: association of single nucleotide polymorphism to schizophrenia risk, New Genetics and Society https://doi.org/10.1080/14636778.2018.1481740. Version of Record published online 13 July 2018.

The editorial office of the journal inadvertently processed the paper through the online submission system without proper peer review or requisite checks. This has now been remedied and the journal and publishers apologise to the authors that this occurred. Journal processes and checks have now been reviewed and updated so that all best efforts are made to ensure this does not occur again.

© Taylor & Francis/Journal owner     

Differential expression of circulating vascular cell adhesion molecule-1 in subjects with coronary artery disease and cardiac syndrome X without known diabetes mellitus

Context: Inflammation is one of the mechanisms underlying cardiac syndrome X (CSX).

Objectives: Few studies have compared the expression of inflammatory or adhesion molecules between coronary artery disease (CAD) versus CSX.

Materials and methods: Ninety-two CSX and 145 CAD subjects without known diabetes mellitus underwent coronary angiogram for angina.

Results: Vascular cell adhesion molecule (VCAM)-1 (median, 507 versus 431?ng/ml, p?=?0.001) was significantly higher in the CAD group. In the binary regression, VCAM-1 was a significant differential factor for CAD versus CSX.

Discussion and conclusion: Adhesion molecules might be implicated in the differential expression of macro versus microvascular coronary disease.

Trial registration number: NCT01198730 at https://clinicaltrials.gov     

Immunogenicity of Novel Mumps Vaccine Candidates Generated by Genetic Modification

Mumps is a highly contagious human disease, characterized by lateral or bilateral nonsuppurative swelling of the parotid glands and neurological complications that can result in aseptic meningitis or encephalitis. A mumps vaccination program implemented since the 1960s reduced mumps incidence by more than 99% and kept the mumps case numbers as low as hundreds of cases per year in the United States before 2006. However, a large mumps outbreak occurred in vaccinated populations in 2006 and again in 2009 in the United States, raising concerns about the efficacy of the vaccination program. Previously, we have shown that clinical isolate-based recombinant mumps viruses lacking expression of either the V protein (rMuVΔV) or the SH protein (rMuVΔSH) are attenuated in a neurovirulence test using newborn rat brains (P. Xu et al., Virology 417:126–136, 2011, http://dx.doi.org/10.1016/j.virol.2011.05.003; P. Xu et al., J. Virol. 86:1768–1776, 2012, http://dx.doi.org/10.1128/JVI.06019-11) and may be good candidates for vaccine development. In this study, we examined immunity induced by rMuVΔSH and rMuVΔV in mice. Furthermore, we generated recombinant mumps viruses lacking expression of both the V protein and the SH protein (rMuVΔSHΔV). Analysis of rMuVΔSHΔV indicated that it was stable in tissue culture cell lines. Importantly, rMuVΔSHΔV was immunogenic in mice, indicating that it is a promising candidate for mumps vaccine development.     

Micromechanical study of the load transfer in a polycaprolactone–collagen hybrid scaffold when subjected to unconfined and confined compression

Scaffolds are used in diverse tissue engineering applications as hosts for cell proliferation and extracellular matrix formation. One of the most used tissue engineering materials is collagen, which is well known to be a natural biomaterial, also frequently used as cell substrate, given its natural abundance and intrinsic biocompatibility. This study aims to evaluate how the macroscopic biomechanical stimuli applied on a construct made of polycaprolactone scaffold embedded in a collagen substrate translate into microscopic stimuli at the cell level. Eight poro-hyperelastic finite element models of 3D printed hybrid scaffolds from the same batch were created, along with an equivalent model of the idealized geometry of that scaffold. When applying an 8% confined compression at the macroscopic level, local fluid flow of up to 20 \(\upmu \)m/s and octahedral strain levels mostly under 20% were calculated in the collagen substrate. Conversely unconfined compression induced fluid flow of up to 10 \(\upmu \)m/s and octahedral strain from 10 to 35%. No relevant differences were found amongst the scaffold-specific models. Following the mechanoregulation theory based on Prendergast et al. (J Biomech 30:539–548, 1997.  https://doi.org/10.1016/S0021-9290(96)00140-6), those results suggest that mainly cartilage or fibrous tissue formation would be expected to occur under unconfined or confined compression, respectively. This in silico study helps to quantify the microscopic stimuli that are present within the collagen substrate and that will affect cell response under in vitro bioreactor mechanical stimulation or even after implantation.     

Ichnology Picture

Ichnology Picture

All authors

Ronald K. Pickerill

https://doi.org/10.1080/10420940600739823

Published online:

26 January 2007

(See Color Plate V)     

13.

Mechanisms involved in the development of diabetic retinopathy induced by oxidative stress     

David Calderón Guzman  Ernestina Hernández García  Armando Valenzuela Peraza  Diego Zamora de la Cruz  Monica Punzo Soto 《Redox report : communications in free radical research》2017,22(1):10-16

Background: Diabetic retinopathy (DR) is one of the main complications in patients with diabetes and has been the leading cause of visual loss since 1990. Oxidative stress is a biological process resulting from excessive production of reactive oxygen species (ROS). This process contributes to the development of many diseases and disease complications. ROS interact with various cellular components to induce cell injury. Fortunately, there is an antioxidan t system that protects organisms against ROS. Indeed, when ROS exceed antioxidant capacity, the resulting cell injury can cause diverse physiological and pathological changes that could lead to a disease like DR.

Objective: This paper reviews the possible mechanisms of common and novel biomarkers involved in the development of DR and explores how these biomarkers could be used to monitor the damage induced by oxidative stress in DR, which is a significant complication in people with diabetes.

Conclusion: The poor control of glucemy in pacients with DB has been shown contribute to the development of complications in eyes as DR.     

14.

Presence of Siderophores on Grape Marc Aerated Compost Tea     

F. Diánez  M. Santos  M. de Cara  J. C. Tello 《Geomicrobiology journal》2013,30(5):323-331

Please click here to view a statement of retraction concerning this article.     

15.

Gender-dependent differences of mitochondrial function and oxidative stress in rat skeletal muscle at rest and after exercise training     

Firas Farhat  Aline Amérand  Bernard Simon  Nathalie Guegueniat 《Redox report : communications in free radical research》2017,22(6):508-514

Objective: This study investigated gender-dependent differences of mitochondrial function and sensitivity to in vitro ROS exposure in rat skeletal muscle at rest and after exercise training.

Methods: Wistar rats underwent running training for 6 weeks. In vitro measurements of hydroxyl radical production, oxygen consumption (under basal and maximal respiration conditions) and ATP production were made on permeabilized fibers. Mitochondrial function was examined after exposure and non-exposure to an in vitro generator system of reactive oxygen species (ROS). Antioxidant enzyme activities and malondialdehyde (MDA) content were also determined.

Results: Compared with sedentary males, females showed a greater resistance of mitochondrial function (oxygen consumption and ATP production) to ROS exposure, and lower MDA content and antioxidant enzyme activities. The training protocol had more beneficial effects in males than females with regard to ROS production and oxidative stress. In contrast to male rats, the susceptibility of mitochondrial function to ROS exposure in trained females was unchanged.

Discussion: Exercise training improves mitochondrial function oxidative capacities in both male and female rats, but is more pronounced in males as a result of different mechanisms. The resistance of mitochondrial function to in vitro oxidative stress exposure and the antioxidant responses are gender- and training-dependent, and may be related to the protective effects of estrogen.     

16.

Song learning in Varied Tits Poecile varia: sensitive period and the effects of night-sleep     

Jiangxia Yin  Tingting Xu  Zhiwei Zhang  Donglai Li  Paul Racey 《Bird Study》2018,65(1):84-91

Capsule: Varied Tits Poecile varia learned vocalizations in the first few weeks of their life. Night-sleep affected the development of vocal learning in Varied Tits.

Aims: We aimed to quantify the sensitive period of song learning and to examine the effects of sleep on song development in Varied Tits, an endemic forest songbird in East Asia.

Methods: Song development in Varied Tits was investigated in the first 90 days following hatching. The effect of night-sleep on birdsong learning was examined by analysing and comparing the song structure in the evening and the next morning.

Results: We found that most individuals began to sing a subsong from 15 days of age and acquired mature song at about 53 days. The sensitive period of song learning in Varied Tits was from 25 to 53 days after hatching. There were significant and positive correlations between maximum frequency and vocal changes before and after night-sleep.

Conclusion: Our findings uncover the timings and processes of song development, and highlight the importance of the sensitive period in birdsong development in wild birds.     

17.

Standardization in synthetic biology: an engineering discipline coming of age     

Thomas Decoene  Brecht De Paepe  Jo Maertens  Pieter Coussement  Gert Peters  Sofie L. De Maeseneire 《Critical reviews in biotechnology》2018,38(5):647-656

Background: Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited.

Purpose: In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed.

Conclusion: Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.     

18.

Downregulation of IDH2 exacerbates H2O2-mediated cell death and hypertrophy     

Hyeong Jun Ku 《Redox report : communications in free radical research》2017,22(1):35-41

Objectives: Reactive oxygen species-mediated cell death contributes to the pathophysiology of cardiovascular disease and myocardial dysfunction. We recently showed that mitochondrial NADP⁺-dependent isocitrate dehydrogenase (IDH2) functions as an antioxidant and anti-apoptotic protein by supplying NADPH to antioxidant systems.

Methods: In the present study, we demonstrated that H₂O₂-induced apoptosis and hypertrophy of H9c2 cardiomyoblasts was markedly exacerbated by small interfering RNA (siRNA) specific for IDH2.

Results: Attenuated IDH2 expression resulted in the modulation of cellular and mitochondrial redox status, mitochondrial function, and cellular oxidative damage. MitoTEMPO, a mitochondria-targeted antioxidant, efficiently suppressed increased caspase-3 activity, increased cell size, and depletion of cellular GSH levels in IDH2 siRNA-transfected cells that were treated with H₂O₂.

Discussion: These results indicated that the disruption of cellular redox balance might be responsible for the enhanced H₂O₂-induced apoptosis and hypertrophy of cultured cardiomyocytes by the attenuated IDH2 expression.     

19.

Searching the literature for proteins facilitates the identification of biological processes,if advanced methods of analysis are linked: a case study on microgravity-caused changes in cells     

Johann Bauer  Markus Bussen  Petra Wise  Markus Wehland  Sabine Schneider  Daniela Grimm 《Expert review of proteomics》2016,13(7):697-705

Background: More than one hundred reports were published about the characterization of cells from malignant and healthy tissues, as well as of endothelial cells and stem cells exposed to microgravity conditions.

Methods: We retrieved publications about microgravity related studies on each type of cells, extracted the proteins mentioned therein and analyzed them aiming to identify biological processes affected by microgravity culture conditions.

Results: The analysis revealed 66 different biological processes, 19 of them were always detected when papers about the four types of cells were analyzed.

Conclusion: Since a response to the removal of gravity is common to the different cell types, some of the 19 biological processes could play a role in cellular adaption to microgravity. Applying computer programs, to extract and analyze proteins and genes mentioned in publications becomes essential for scientists interested to get an overview of the rapidly growing fields of gravitational biology and space medicine.     

20.

P-gp expression levels in the erythrocytes of brown trout: a new tool for aquatic sentinel biomarker development     

Emeline Valton  Ivan Wawrzyniak  Christian Amblard  Bruno Combourieu  Marie-Laure Bayle  François Desmolles 《Biomarkers》2017,22(6):566-574

     

Mechanisms involved in the development of diabetic retinopathy induced by oxidative stress

Background: Diabetic retinopathy (DR) is one of the main complications in patients with diabetes and has been the leading cause of visual loss since 1990. Oxidative stress is a biological process resulting from excessive production of reactive oxygen species (ROS). This process contributes to the development of many diseases and disease complications. ROS interact with various cellular components to induce cell injury. Fortunately, there is an antioxidan t system that protects organisms against ROS. Indeed, when ROS exceed antioxidant capacity, the resulting cell injury can cause diverse physiological and pathological changes that could lead to a disease like DR.

Objective: This paper reviews the possible mechanisms of common and novel biomarkers involved in the development of DR and explores how these biomarkers could be used to monitor the damage induced by oxidative stress in DR, which is a significant complication in people with diabetes.

Conclusion: The poor control of glucemy in pacients with DB has been shown contribute to the development of complications in eyes as DR.     

Presence of Siderophores on Grape Marc Aerated Compost Tea

Please click here to view a statement of retraction concerning this article.     

Gender-dependent differences of mitochondrial function and oxidative stress in rat skeletal muscle at rest and after exercise training

Objective: This study investigated gender-dependent differences of mitochondrial function and sensitivity to in vitro ROS exposure in rat skeletal muscle at rest and after exercise training.

Methods: Wistar rats underwent running training for 6 weeks. In vitro measurements of hydroxyl radical production, oxygen consumption (under basal and maximal respiration conditions) and ATP production were made on permeabilized fibers. Mitochondrial function was examined after exposure and non-exposure to an in vitro generator system of reactive oxygen species (ROS). Antioxidant enzyme activities and malondialdehyde (MDA) content were also determined.

Results: Compared with sedentary males, females showed a greater resistance of mitochondrial function (oxygen consumption and ATP production) to ROS exposure, and lower MDA content and antioxidant enzyme activities. The training protocol had more beneficial effects in males than females with regard to ROS production and oxidative stress. In contrast to male rats, the susceptibility of mitochondrial function to ROS exposure in trained females was unchanged.

Discussion: Exercise training improves mitochondrial function oxidative capacities in both male and female rats, but is more pronounced in males as a result of different mechanisms. The resistance of mitochondrial function to in vitro oxidative stress exposure and the antioxidant responses are gender- and training-dependent, and may be related to the protective effects of estrogen.     

Song learning in Varied Tits Poecile varia: sensitive period and the effects of night-sleep

Capsule: Varied Tits Poecile varia learned vocalizations in the first few weeks of their life. Night-sleep affected the development of vocal learning in Varied Tits.

Aims: We aimed to quantify the sensitive period of song learning and to examine the effects of sleep on song development in Varied Tits, an endemic forest songbird in East Asia.

Methods: Song development in Varied Tits was investigated in the first 90 days following hatching. The effect of night-sleep on birdsong learning was examined by analysing and comparing the song structure in the evening and the next morning.

Results: We found that most individuals began to sing a subsong from 15 days of age and acquired mature song at about 53 days. The sensitive period of song learning in Varied Tits was from 25 to 53 days after hatching. There were significant and positive correlations between maximum frequency and vocal changes before and after night-sleep.

Conclusion: Our findings uncover the timings and processes of song development, and highlight the importance of the sensitive period in birdsong development in wild birds.     

Standardization in synthetic biology: an engineering discipline coming of age

Background: Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited.

Purpose: In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed.

Conclusion: Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.     

Downregulation of IDH2 exacerbates H2O2-mediated cell death and hypertrophy

Objectives: Reactive oxygen species-mediated cell death contributes to the pathophysiology of cardiovascular disease and myocardial dysfunction. We recently showed that mitochondrial NADP⁺-dependent isocitrate dehydrogenase (IDH2) functions as an antioxidant and anti-apoptotic protein by supplying NADPH to antioxidant systems.

Methods: In the present study, we demonstrated that H₂O₂-induced apoptosis and hypertrophy of H9c2 cardiomyoblasts was markedly exacerbated by small interfering RNA (siRNA) specific for IDH2.

Results: Attenuated IDH2 expression resulted in the modulation of cellular and mitochondrial redox status, mitochondrial function, and cellular oxidative damage. MitoTEMPO, a mitochondria-targeted antioxidant, efficiently suppressed increased caspase-3 activity, increased cell size, and depletion of cellular GSH levels in IDH2 siRNA-transfected cells that were treated with H₂O₂.

Discussion: These results indicated that the disruption of cellular redox balance might be responsible for the enhanced H₂O₂-induced apoptosis and hypertrophy of cultured cardiomyocytes by the attenuated IDH2 expression.     

Searching the literature for proteins facilitates the identification of biological processes,if advanced methods of analysis are linked: a case study on microgravity-caused changes in cells

Background: More than one hundred reports were published about the characterization of cells from malignant and healthy tissues, as well as of endothelial cells and stem cells exposed to microgravity conditions.

Methods: We retrieved publications about microgravity related studies on each type of cells, extracted the proteins mentioned therein and analyzed them aiming to identify biological processes affected by microgravity culture conditions.

Results: The analysis revealed 66 different biological processes, 19 of them were always detected when papers about the four types of cells were analyzed.

Conclusion: Since a response to the removal of gravity is common to the different cell types, some of the 19 biological processes could play a role in cellular adaption to microgravity. Applying computer programs, to extract and analyze proteins and genes mentioned in publications becomes essential for scientists interested to get an overview of the rapidly growing fields of gravitational biology and space medicine.