The dynamical Matryoshka model: 1. Incoherent neutron scattering functions for lipid dynamics in bilayers

Fluid lipid bilayers are the building blocks of biological membranes. Although there is a large amount of experimental data using incoherent quasi-elastic neutron scattering (QENS) techniques to study membranes, very little theoretical works have been developed to study the local dynamics of membranes. The main objective of this work is to build a theoretical framework to study and describe the local dynamics of lipids and derive analytical expressions of intermediate scattering functions (ISF) for QENS. As results, we developed the dynamical Matryoshka model which describes the local dynamics of lipid molecules in membrane layers as a nested hierarchical convolution of three motional processes: (i) individual motions described by the vibrational motions of H-atoms; (ii) internal motions including movements of the lipid backbone, head groups and tails, and (iii) molecule movements of the lipid molecule as a whole. The analytical expressions of the ISF associated with these movements are all derived. For use in analyzing the QENS experimental data, we also derived an analytical expression for the aggregate ISF of the Matryoshka model which involves an elastic term plus three inelastic terms of well-separated time scales and whose amplitudes and rates are functions of the lipid motions. And as an illustrative application, we used the aggregated ISF to analyze the experimental QENS data on a lipid sample of multilamellar bilayers of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine). It is clear from this analysis that the dynamical Matryoshka model describes very well the experimental data and allow extracting the dynamical parameters of the studied system.     

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.

     

Exploring potential induction of grapevine (Vitis spp.) root phenolic compounds by ring nematodes,Mesocriconema xenoplax

This paper explored the fixed point results for the mappings satisfying generalized weak contractive conditions in a complete partially ordered b-metric space. These contractions are some variations of the work done by the authors (Mituku et al. in BMC Res Notes 13:537. https://doi.org/10.1186/s13104-020-05354-1 , 2020; Seshagiri et al. in BMC Res Notes 13:451. https://doi.org/10.1186/s13104-020-05273-1 , 2020, BMC Res Notes 14:390. https://doi.org/10.1186/s13104-021-05801-7 , 2021, BMC Res Notes 14:263. https://doi.org/10.1186/s13104-021-05649-x , 2021) in the same context. To validate the results a few examples are provided. The aim of this work is to prove some fixed point results of the self mappings in ordered b-metric space satisfying variant generalized weak contraction conditions. These results generalize some known results in the provided literature.     

Occam’s razor revisited: guenon species morphology supports evidence for an African influence in Bronze Age Aegean fresco primate iconography from Akrotiri,Thera

Primates - In a recent exchange, Pareja et al. (Primates 61: 159–168, 2020a; Primates 61: 767–774, 2020b) and Urbani and Youlatos (Primates, https://doi.org/10.1007/s10329-020-00825-2 ,...     

Cover Picture: Biotechnology Journal 2/2010

Cover illustration Focus: Transgenic Crops. This issue of BTJ highlights two articles about transgenic crops. Erlendsson et al. show for the first time that barley can be used as a green factory for growth factors (pp. 163–171); Herman et al. use a transclinic medicine model to access the safety of transgenic crops (pp. 172–182); Image © PhotoDisc/Getty Images. http://dx.doi.org/10.1002/biot.200900111 ; http://dx.doi.org/10.1002/biot.200900217 .     

Commentary on Coram et al. (2021) on the use of Facebook to understand marine mammal stranding issues in Southeast Asia

We reviewed Coram et al. (Biodivers Conserv 30:2341–2359, 2021, https://doi.org/10.1007/s10531-021-02196-6), a paper that highlights the use of social media data to understand marine litter and marine mammals in Southeast Asia. While we commend its intent, we find that the methodology used and conclusions drawn portray an incomplete and inaccurate perception of how strandings, stranding response, and analysis of stranding data have been conducted in the region. By focusing on investigative results revealed by a very limited search of one social media platform (Facebook), using only English keywords, and insufficient ground-truthing, Coram et al. (2021) have, unintentionally, given the perception that Southeast Asian scientists have not conducted even the bare minimum of investigation required to better understand the issue of marine litter and its impact on marine mammals. In this commentary we provide a more accurate account of strandings research in Asia and include recommendations to improve future studies using social media to assess conservation issues.

     

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.

     

Performance evaluation of a novel conceptual bioprocess for clinically-required mass production of hematopoietic cells

Objective

The novel engineered bioprocess, which was designed and modeled to provide the clinically relevant cell numbers for different therapies in our previous work (Kaleybar et al. Food Bioprod Process 122:254–268, https://doi.org/10.1016/j.fbp.2020.04.012, 2020), was evaluated by using U937 as hematopoietic model cells.

Results

The culture system showed a 30-fold expansion of U937 cells in one-step during a 10-day culture period. The cell growth profile, the substrate and oxygen consumptions, and byproduct formations were all in agreement with the model predications during 7 days. The cell proliferation decrease after 7 days was attributed to optional oxygen limiting condition in the last days of culture. The bioreactor culture system revealed also a slight enhancement of lactate dehydrogenase (LDH) production as compared to the 2D conventional culture system, indicating the low impact of shear stress on cellular damage in the dynamic system.

Conclusions

The results demonstrated that the conceptual bioprocess for suspended stem cell production has a great potential in practice although additional experiments are required to improve the system.

     

The dynamical Matryoshka model: 2. Modeling of local lipid dynamics at the sub-nanosecond timescale in phospholipid membranes

Biological membranes are generally formed by lipids and proteins. Often, the membrane properties are studied through model membranes formed by phospholipids only. They are molecules composed by a hydrophilic head group and hydrophobic tails, which can present a panoply of various motions, including small localized movements of a few atoms up to the diffusion of the whole lipid or collective motions of many of them. In the past, efforts were made to measure these motions experimentally by incoherent neutron scattering and to quantify them, but with upcoming modern neutron sources and instruments, such models can now be improved. In the present work, we expose a quantitative and exhaustive study of lipid dynamics on DMPC and DMPG membranes, using the Matryoshka model recently developed by our group. The model is confronted here to experimental data collected on two different membrane samples, at three temperatures and two instruments. Despite such complexity, the model describes reliably the data and permits to extract a series of parameters. The results compare also very well to other values found in the literature.     

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...     

Beyond immunomodulation: The regenerative role for regulatory T cells in central nervous system remyelination

Central nervous system regeneration after injury can occur in the form of remyelination, the reinstatement of myelin around axons which restores axon health and function. However, remyelination often fails in chronic neurological diseases, such as progressive multiple sclerosis. The lack of currently approved pro-remyelination therapies highlights the need to elucidate the cellular and molecular mechanisms underpinning this regenerative process. Whereas some T lymphocyte subsets such as Th1 and Th17 are implicated in inducing myelin injury, a recent study by Dombrowski et al. reveals a novel role for regulatory T cells (T_regs) in directly driving remyelination, independent of immunomodulation (Nat Neurosci doi: 10.1038/nn.4528 2017)(Dombrowski et al., 2017). This study is summarized in this Bits and Bytes.     

The role of vascular endothelial protein tyrosine phosphatase on nitric oxide synthase function in diabetes: from molecular biology to the clinic

Endothelial nitric oxide synthase (eNOS) and receptor-type vascular endothelial protein tyrosine phosphatase (VE-PTP) are one of the majors signaling pathways related to endothelial health in diabetes. Several reports have shown that the inhibition of VE-PTP can lead the nitric oxide production, although repeated studies showed that VE-PTP regulated the eNOS exclusive at Ser1177 in indirect-manner. A recent, exciting paper (Siragusa et al. in Cardiovasc Res, 2020. https://doi.org/10.1093/cvr/cvaa213), showing that VE-PTP regulates eNOS in a direct-manner, dephosphorylating eNOS at Tyr81 and indirect at Ser1177 and the effects of a VE-PTP inhibitor, AKB-9778, in the blood pressure from diabetic patients.     

Cover Picture: Biotechnology Journal 3/2014

This “regular” issue of Biotechnology Journal gathers the state‐of‐the‐art in biotechnology, including articles on CHO cells, plant biotechnology and tissue engineering. The cover image shows immunohistochemical staining of tissue sections using antibodies recognizing different target proteins (www.proteinatlas.org) and is provided by Sophia Hober et al., authors of “Antibody performance in western blot applications is context‐dependent” (http://dx.doi.org/10.1002/biot.201300341)     

The ATM protein: The importance of being active

The ataxia telangiectasia mutated (ATM) protein kinase regulates the cellular response to deoxyribonucleic acid (DNA) double-strand breaks by phosphorylating numerous players in the extensive DNA damage response network. Two papers in this issue (Daniel et al. 2012. J. Cell Biol. http://dx.doi.org/10.1083/jcb201204035; Yamamoto et al. 2012. J. Cell Biol. http://dx.doi.org/10.1083/jcb201204098) strikingly show that, in mice, the presence of a catalytically inactive version of ATM is embryonically lethal. This is surprising because mice completely lacking ATM have a much more moderate phenotype. The findings impact on basic cancer research and cancer therapeutics.     

Retracted: Bisindole‐oxadiazole hybrids,T3P mediated® ‐synthesis and appraisal of their apoptotic,antimetastatic and computational Bcl‐2 binding potential

Retraction: Kamath PR, Joseph MM, Ajees AA, et al. Bisindole‐oxadiazole hybrids, T3P mediated synthesis and appraisal of their apoptotic, antimetastatic and computational Bcl‐2 binding potential. J Biochem Mol Toxicol . 2017;31:e21962. https://doi.org/10.1002/jbt.21962 The above article from the Journal of Biochemical and Molecular Toxicology , published online on 19 July 2017 in Wiley Online Library ( https://onlinelibrary.wiley.com/doi/abs/10.1002/jbt.21962 ) and in Volume 31, Issue 11, has been retracted by agreement of the Journal Editor‐in‐Chief, Dr Hari Bhat, and Wiley Periodicals, Inc. The retraction has been agreed due to the absence of access to the original data needed to answer questions about the reliability of some of the findings presented in the paper.     

Scaffold-free cell-based systems

Cover illustration Scaffold-free cell-based systems. This issue of BTJ, edited by Umut Gurkan (Harvard Medical School, MA, USA) and Feng Xu (Xi' an Jiaotong University, China) highlights several applications of scaffold-free systems such as cell therapies for tissue regeneration, in vitro functional tissue and disease models for drug sensitivity testing, cell-based biosensors, and drug delivery. Cover image: Confocal image of a microtissue generated from human colorectal carcinoma cell line, HCT-116, stained for integrin, 1 (green), cytoskeleton (red) and nuclei (blue). Image: Irina Agarkova (InSphero AG, Zurich, Switzerland). See the article by Drewitz et al., http://dx.doi.org/10.1002/biot.201100290     

Photoacoustic and photothermal cytometry using photoswitchable proteins and nanoparticles with ultrasharp resonances

In the article by E. I. Galanzha et al. (doi: http://dx.doi.org/10.1002/jbio.201300140 ), published in J. Biophotonics 8, 81–93 (2015), the Conflict of Interest statement is missing. This erratum is published to correct this.     

Comments on “a framework for assessing readiness for tiger reintroductions”

We comment on five aspects of Gray et al.’s (Biodivers Conserv,  https://doi.org/10.1007/s10531-017-1365-1, 2017a) framework for assessing the readiness of sites for tiger reintroductions. Clarifications in numbers of tigers, available habitat and prey requirements indicate that more land and additional recovery of preferred prey species will be critical for a successful reintroduction. A focus on threat assessments and mitigations will be more important than a focus on site management tools. Local attitudes and levels of poaching require more attention than in the current assessment, as they are likely to be major obstacles to successful large carnivore reintroductions in Asia. Given the limited resources for rangewide tiger conservation, the value of such long-term initiatives must be weighed relative to the urgent need to recover and secure existing tiger populations before they also become extinct.     

A commentary on the paper: ‘Evaluation of spice and herb as phytoderived selective modulators of human retinaldehyde dehydrogenases using a simple in vitro method’

It is commonly known that aldehyde dehydrogenases (ALDHs) are a promising therapeutic target in many diseases. Bui et al.—the authors of the paper I am discussing here (Biosci Rep (2021) 41(5): BSR20210491 https://doi.org/10.1042/BSR20210491)—point that there is a lack of research on the use of spices and herbs as the sources of naturally occurring modulators of ALDH activity. In order to carry out this type of research, the authors prepared ethanolic extracts of 22 spices and herbs. The main objective of the study was to investigate retinaldehyde dehydrogenases (RALDHs), of which retinal is the main substrate and ALDH2, the mitochondrial isoform, having acetaldehyde as the main substrate.The obtained results indicated that the tested extracts exhibited differential regulatory effects on RALDHs/ALDH2 and some of them showed a potential selective inhibition of the activity of RALDHs.     

Commentary on: Screening of immunosuppressive cells from colorectal adenocarcinoma and identification of prognostic markers

Colorectal adenocarcinoma (COAD) is one subtype of colorectal carcinoma (CRC), whose development is associated with genetics, inappropriate immune response, and environmental factors. Although significant advances have been made in the treatment of COAD, the mortality rate remains high. It is a pressing need to explore novel therapeutic targets of COAD. Available evidence indicated that immune cell infiltration was correlated with cancer prognosis. To reveal the roles of immune cells in the COAD prognosis, a study published in Bioscience Reports by Li et al. (Bioscience Reports (2021) 41, https://doi.org/10.1042/BSR20203496) analyzed data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset. It demonstrated a beneficial effect of Th17 cells in COAD prognosis. In addition, six hub genes (KRT23, ULBP2, ASRGL1, SERPINA1, SCIN, and SLC28A2) were identified to correlate with Th17 cells and COAD prognosis, suggesting one new therapy strategy and some predictive biomarkers of COAD. These findings reported by Li et al. may pave one way to explore the molecular mechanism of COAD further.