Heme metabolism in nonerythroid cells.

Heme is an iron-containing prosthetic group necessary for the function of several proteins termed "hemoproteins." Erythrocytes contain most of the body's heme in the form of hemoglobin and contain high concentrations of free heme. In nonerythroid cells, where cytosolic heme concentrations are 2 to 3 orders of magnitude lower, heme plays an essential and often overlooked role in a variety of cellular processes. Indeed, hemoproteins are found in almost every subcellular compartment and are integral in cellular operations such as oxidative phosphorylation, amino acid metabolism, xenobiotic metabolism, and transcriptional regulation. Growing evidence reveals the participation of heme in dynamic processes such as circadian rhythms, NO signaling, and the modulation of enzyme activity. This dynamic view of heme biology uncovers exciting possibilities as to how hemoproteins may participate in a range of physiologic systems. Here, we discuss how heme is regulated at the level of its synthesis, availability, redox state, transport, and degradation and highlight the implications for cellular function and whole organism physiology.

Segmentation strategy of de novo designed four-helical bundles expands protein oligomerization modalities for cell regulation.

Protein-protein interactions govern most biological processes. New protein assemblies can be introduced through the fusion of selected proteins with di/oligomerization domains, which interact specifically with their partners but not with other cellular proteins. While four-helical bundle proteins (4HB) have typically been assembled from two segments, each comprising two helices, here we show that they can be efficiently segmented in various ways, expanding the number of combinations generated from a single 4HB. We implement a segmentation strategy of 4HB to design two-, three-, or four-chain combinations for the recruitment of multiple protein components. Different segmentations provide new insight into the role of individual helices for 4HB assembly. We evaluate 4HB segmentations for potential use in mammalian cells for the reconstitution of a protein reporter, transcriptional activation, and inducible 4HB assembly. Furthermore, the implementation of trimerization is demonstrated as a modular chimeric antigen receptor for the recognition of multiple cancer antigens.

Did you forget your cell sex? An update on the inclusion of sex as a variable in AJP-Cell Physiology.

"I don't know the question, but sex is definitely the answer!," was a Woody Allen quote cited by Fuller and Insel in an Editorial Comment in 2013 on the importance of cell sex in submissions to AJP-Cell Physiology, and in biomedical research in general. The notion that cell sex is important is axiomatic in studies on prostate cancer (LnCAP) or placental physiology (BeWo). Indeed, most researchers are aware that HeLa cells are female cervical derived, and CHO are female hamster ovary cells, yet beyond those well-known examples, it would be fair to assume that the sex of cells derived from kidney, lung, or liver, for example, is given cursory, if any thought. In the end, what possible impact could the presence or absence of a Y chromosome have on protein trafficking in a nonreproductive tissue, such as a pancreatic ß cell? However, this approach to cell, and indeed organismal physiology, seems to be in conflict with accumulating data, that show that far from being irrelevant, genes expressed off sex chromosomes have a broad-ranging impact on cells as diverse as neurons and renal cells. Moreover, it is also the policy of AJP-Cell Physiology that the source of all cells used (species, sex, etc.) should be clearly indicated when submitting an article for publication (https://journals.physiology.org/author-info.manuscript-composition). In 2013, we wrote a review examining how faithfully such requirements were adhered to in submissions to Cell Physiology. Nearly a decade later, it seems fitting to revisit the topic and ask if any improvements have been made in the description of cells and cell lines used in publications submitted to AJP-Cell Physiology.

Emergence of behaviour in a self-organized living matter network.

What is the origin of behaviour? Although typically associated with a nervous system, simple organisms also show complex behaviours. Among them, the slime mold Physarum polycephalum, a giant single cell, is ideally suited to study emergence of behaviour. Here, we show how locomotion and morphological adaptation behaviour emerge from self-organized patterns of rhythmic contractions of the actomyosin lining of the tubes making up the network-shaped organism. We quantify the spatio-temporal contraction dynamics by decomposing experimentally recorded contraction patterns into spatial contraction modes. Notably, we find a continuous spectrum of modes, as opposed to a few dominant modes. Our data suggests that the continuous spectrum of modes allows for dynamic transitions between a plethora of specific behaviours with transitions marked by highly irregular contraction states. By mapping specific behaviours to states of active contractions, we provide the basis to understand behaviour's complexity as a function of biomechanical dynamics.

Optimal transport analysis reveals trajectories in steady-state systems.

Understanding how cells change their identity and behaviour in living systems is an important question in many fields of biology. The problem of inferring cell trajectories from single-cell measurements has been a major topic in the single-cell analysis community, with different methods developed for equilibrium and non-equilibrium systems (e.g. haematopoeisis vs. embryonic development). We show that optimal transport analysis, a technique originally designed for analysing time-courses, may also be applied to infer cellular trajectories from a single snapshot of a population in equilibrium. Therefore, optimal transport provides a unified approach to inferring trajectories that is applicable to both stationary and non-stationary systems. Our method, StationaryOT, is mathematically motivated in a natural way from the hypothesis of a Waddington's epigenetic landscape. We implement StationaryOT as a software package and demonstrate its efficacy in applications to simulated data as well as single-cell data from Arabidopsis thaliana root development.

Cell physiology and molecular mechanism of anion transport by erythrocyte band 3/AE1.

The major transmembrane protein of the red blood cell, known as band 3, AE1, and SLC4A1, has two main functions: 1) catalysis of Cl-/[Formula: see text] exchange, one of the steps in CO2 excretion, and 2) anchoring the membrane skeleton. This review summarizes the 150-year history of research on red cell anion transport and band 3 as an experimental system for studying membrane protein structure and ion transport mechanisms. Important early findings were that red cell Cl- transport is a tightly coupled 1:1 exchange and band 3 is labeled by stilbenesulfonate derivatives that inhibit anion transport. Biochemical studies showed that the protein is dimeric or tetrameric (paired dimers) and that there is one stilbenedisulfonate binding site per subunit of the dimer. Transport kinetics and inhibitor characteristics supported the idea that the transporter acts by an alternating access mechanism with intrinsic asymmetry. The sequence of band 3 cDNA provided a framework for detailed study of protein topology and amino acid residues important for transport. The identification of genetic variants produced insights into the roles of band 3 in red cell abnormalities and distal renal tubular acidosis. The publication of the membrane domain crystal structure made it possible to propose concrete molecular models of transport. Future research directions include improving our understanding of the transport mechanism at the molecular level and of the integrative relationships among band 3, hemoglobin, carbonic anhydrase, and gradients (both transmembrane and subcellular) of [Formula: see text], Cl-, O2, CO2, pH, and nitric oxide (NO) metabolites during pulmonary and systemic capillary gas exchange.

Membrane-Mediated Activity of Local Anesthetics.

The activity of local anesthetics (LAs) has been attributed to the inhibition of ion channels, causing anesthesia. However, there is a growing body of research showing that LAs act on a wide range of receptors and channel proteins far beyond simple analgesia. The current concept of ligand recognition may no longer explain the multitude of protein targets influenced by LAs. We hypothesize that LAs can cause anesthesia without directly binding to the receptor proteins just by changing the physical properties of the lipid bilayer surrounding these proteins and ion channels based on LAs' amphiphilicity. It is possible that LAs act in one of the following ways: They 1) dissolve raft-like membrane microdomains, 2) impede nerve impulse propagation by lowering the lipid phase transition temperature, or 3) modulate the lateral pressure profile of the lipid bilayer. This could also explain the numerous additional effects of LAs besides anesthesia. Furthermore, the concepts of membrane-mediated activity and binding to ion channels do not have to exclude each other. If we were to consider LA as the middle part of a continuum between unspecific membrane-mediated activity on one end and highly specific ligand binding on the other end, we could describe LA as the link between the unspecific action of general anesthetics and toxins with their highly specific receptor binding. This comprehensive membrane-mediated model offers a fresh perspective to clinical and pharmaceutical research and therapeutic applications of local anesthetics. SIGNIFICANCE STATEMENT: Local anesthetics, according to the World Health Organization, belong to the most important drugs available to mankind. Their rediscovery as therapeutics and not only anesthetics marks a milestone in global pain therapy. The membrane-mediated mechanism of action proposed in this review can explain their puzzling variety of target proteins and their thus far inexplicable therapeutic effects. The new concept presented here places LAs on a continuum of structures and molecular mechanisms in between small general anesthetics and the more complex molecular toxins.

Metabolic limits on classical information processing by biological cells.

Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.

Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance.

From time immemorial, humans have exploited plants as a source of food and medicines. The World Health Organization (WHO) has recorded 21,000 plants with medicinal value out of 300,000 species available worldwide. The promising modern "multi-omics" platforms and tools have been proven as functional platforms able to endow us with comprehensive knowledge of the proteome, genome, transcriptome, and metabolome of medicinal plant systems so as to reveal the novel connected genetic (gene) pathways, proteins, regulator sequences and secondary metabolite (molecule) biosynthetic pathways of various drug and protein molecules from a variety of plants with therapeutic significance. This review paper endeavors to abridge the contemporary advancements in research areas of multi-omics and the information involved in decoding its prospective relevance to the utilization of plants with medicinal value in the present global scenario. The crosstalk of medicinal plants with genomics, transcriptomics, proteomics, and metabolomics approaches will be discussed.

Nanobiomechanical behavior of Fe3O4@SiO2and Fe3O4@SiO2-NH2nanoparticles over HeLa cells interfaces.

In this work, we studied the impact of magnetic nanoparticles (MNPs) interactions with HeLa cells when they are exposed to high frequency alternating magnetic field (AMF). Specifically, we measured the nanobiomechanical properties of cell interfaces by using atomic force microscopy (AFM). Magnetite (Fe3O4) MNPs were synthesized by coprecipitation and encapsulated with silica (SiO2): Fe3O4@SiO2and functionalized with amino groups (-NH2): Fe3O4@SiO2-NH2, by sonochemical processing. HeLa cells were incubated with or without MNPs, and then exposed to AMF at 37 °C. A biomechanical analysis was then performed through AFM, providing the Young's modulus and stiffness of the cells. The statistical analysis (p < 0.001) showed that AMF application or MNPs interaction modified the biomechanical behavior of the cell interfaces. Interestingly, the most significant difference was found for HeLa cells incubated with Fe3O4@SiO2-NH2and exposed to AMF, showing that the local heat of these MNPs modified their elasticity and stiffness.

High shear resistance of insect cells: the basis for substantial improvements in cell culture process design.

Multicellular organisms cultivated in continuous stirred tank reactors (CSTRs) are more sensitive to environmental conditions in the suspension culture than microbial cells. The hypothesis, that stirring induced shear stress is the main problem, persists, although it has been shown that these cells are not so sensitive to shear. As these results are largely based on Chinese Hamster Ovary (CHO) cell experiments the question remains if similar behavior is valid for insect cells with a higher specific oxygen demand. The requirement of higher oxygen transfer rates is associated with higher shear forces in the process. Consequently, we focused on the shear resistance of insect cells, using CHO cells as reference system. We applied a microfluidic device that allowed defined variations in shear rates. Both cell lines displayed high resistance to shear rates up to 8.73 × 105 s-1. Based on these results we used microbial CSTRs, operated at high revolution speeds and low aeration rates and found no negative impact on cell viability. Further, this cultivation approach led to substantially reduced gas flow rates, gas bubble and foam formation, while addition of pure oxygen was no longer necessary. Therefore, this study contributes to the development of more robust insect cell culture processes.

Oxytocin Signaling Pathway: From Cell Biology to Clinical Implications.

BACKGROUND: In addition to the well-known role played in lactation and parturition, Oxytocin (OT) and OT receptor (OTR) are involved in many other aspects such as the control of maternal and social behavior, the regulation of the growth of the neocortex, the maintenance of blood supply to the cortex, the stimulation of limbic olfactory area to mother-infant recognition bond, and the modulation of the autonomic nervous system via the vagal pathway. Moreover, OT and OTR show antiinflammatory, anti-oxidant, anti-pain, anti-diabetic, anti-dyslipidemic and anti-atherogenic effects. OBJECTIVE: The aim of this narrative review is to summarize the main data coming from the literature dealing with the role of OT and OTR in physiology and pathologic conditions focusing on the most relevant aspects. METHODS: Appropriate keywords and MeSH terms were identified and searched in Pubmed. Finally, references of original articles and reviews were examined. RESULTS: We report the most significant and updated data on the role played by OT and OTR in physiology and different clinical contexts. CONCLUSION: Emerging evidence indicates the involvement of OT system in several pathophysiological mechanisms influencing brain anatomy, cognition, language, sense of safety and trust and maternal behavior, with the possible use of exogenous administered OT in the treatment of specific neuropsychiatric conditions. Furthermore, it modulates pancreatic ß-cell responsiveness and lipid metabolism leading to possible therapeutic use in diabetic and dyslipidemic patients and for limiting and even reversing atherosclerotic lesions.

CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing.

Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.

Cellular Dynamics of Transition Metal Exchange on Proteins: A Challenge but a Bonanza for Coordination Chemistry.

Transition metals interact with a large proportion of the proteome in all forms of life, and they play mandatory and irreplaceable roles. The dynamics of ligand binding to ions of transition metals falls within the realm of Coordination Chemistry, and it provides the basic principles controlling traffic, regulation, and use of metals in cells. Yet, the cellular environment stands out against the conditions prevailing in the test tube when studying metal ions and their interactions with various ligands. Indeed, the complex and often changing cellular environment stimulates fast metal-ligand exchange that mostly escapes presently available probing methods. Reducing the complexity of the problem with purified proteins or in model organisms, although useful, is not free from pitfalls and misleading results. These problems arise mainly from the absence of the biosynthetic machinery and accessory proteins or chaperones dealing with metal / metal groups in cells. Even cells struggle with metal selectivity, as they do not have a metal-directed quality control system for metalloproteins, and serendipitous metal binding is probably not exceptional. The issue of metal exchange in biology is reviewed with particular reference to iron and illustrating examples in patho-physiology, regulation, nutrition, and toxicity.

PyOIF: Computational tool for modelling of multi-cell flows in complex geometries.

A user ready, well documented software package PyOIF contains an implementation of a robust validated computational model for cell flow modelling. The software is capable of simulating processes involving biological cells immersed in a fluid. The examples of such processes are flows in microfluidic channels with numerous applications such as cell sorting, rare cell isolation or flow fractionation. Besides the typical usage of such computational model in the design process of microfluidic devices, PyOIF has been used in the computer-aided discovery involving mechanical properties of cell membranes. With this software, single cell, many cell, as well as dense cell suspensions can be simulated. Many cell simulations include cell-cell interactions and analyse their effect on the cells. PyOIF can be used to test the influence of mechanical properties of the membrane in flows and in membrane-membrane interactions. Dense suspensions may be used to study the effect of cell volume fraction on macroscopic phenomena such as cell-free layer, apparent suspension viscosity or cell degradation. The PyOIF module is based on the official ESPResSo distribution with few modifications and is available under the terms of the GNU General Public Licence. PyOIF is based on Python objects representing the cells and on the C++ computational core for fluid and interaction dynamics. The source code is freely available at GitHub repository, runs natively under Linux and MacOS and can be used in Windows Subsystem for Linux. The communication among PyOIF users and developers is maintained using active mailing lists. This work provides a basic background to the underlying computational models and to the implementation of interactions within this framework. We provide the prospective PyOIF users with a practical example of simulation script with reference to our publicly available User Guide.

Cell-cell interfaces as specialized compartments directing cell function.

Cell-cell interfaces are found throughout multicellular organisms, from transient interactions between motile immune cells to long-lived cell-cell contacts in epithelia. Studies of immune cell interactions, epithelial cell barriers, neuronal contacts and sites of cell-cell fusion have identified a core set of features shared by cell-cell interfaces that critically control their function. Data from diverse cell types also show that cells actively and passively regulate the localization, strength, duration and cytoskeletal coupling of receptor interactions governing cell-cell signalling and physical connections between cells, indicating that cell-cell interfaces have a unique membrane organization that emerges from local molecular and cellular mechanics. In this Review, we discuss recent findings that support the emerging view of cell-cell interfaces as specialized compartments that biophysically constrain the arrangement and activity of their protein, lipid and glycan components. We also review how these biophysical features of cell-cell interfaces allow cells to respond with high selectivity and sensitivity to multiple inputs, serving as the basis for wide-ranging cellular functions. Finally, we consider how the unique properties of cell-cell interfaces present opportunities for therapeutic intervention.

Unraveling spatial cellular pattern by computational tissue shuffling.

Cell biology relies largely on reproducible visual observations. Unlike cell culture, tissues are heterogeneous, making difficult the collection of biological replicates that would spotlight a precise location. In consequence, there is no standard approach for estimating the statistical significance of an observed pattern in a tissue sample. Here, we introduce SET (for Synthesis of Epithelial Tissue), a method that can accurately reconstruct the cell tessellation formed by an epithelium in a microscopy image as well as thousands of alternative synthetic tessellations made of the exact same cells. SET can build an accurate null distribution to statistically test if any local pattern is necessarily the result of a process, or if it could be explained by chance in the given context. We provide examples in various tissues where visible, and invisible, cell and subcellular patterns are unraveled in a statistically significant manner using a single image and without any parameter settings.