Biological Communication Systems Research Articles

3,4-Ethylenedioxythiophene Hydrogels: Relating Structure and Charge Transport in Supramolecular Gels.

Ionic charge transport is a ubiquitous language of communication in biological systems. As such, bioengineering is in constant need of innovative, soft, and biocompatible materials that facilitate ionic conduction. Low molecular weight gelators (LMWGs) are complex self-assembled materials that have received increasing attention in recent years. Beyond their biocompatible, self-healing, and stimuli responsive facets, LMWGs can be viewed as a "solid" electrolyte solution. In this work, we investigate 3,4-ethylenedioxythiophene (EDOT) as a capping group for a small peptide library, which we use as a system to understand the relationship between modes of assembly and charge transport in supramolecular gels. Through a combination of techniques including small-angle neutron scattering (SANS), NMR-based Van't Hoff analysis, atomic force microscopy (AFM), rheology, four-point probe, and electrochemical impedance spectroscopy (EIS), we found that modifications to the peptide sequence result in distinct assembly pathways, thermodynamic parameters, mechanical properties, and ionic conductivities. Four-point probe conductivity measurements and electrochemical impedance spectroscopy suggest that ionic conductivity is approximately doubled by programmable gel assemblies with hollow cylinder morphologies relative to gels containing solid fibers or a control electrolyte. More broadly, it is hoped this work will serve as a platform for those working on charge transport of aqueous soft materials in general.

Emerging Microfluidic Tools for Simultaneous Exosomes and Cargo Biosensing in Liquid Biopsy: New Integrated Miniaturized FFF-Assisted Approach for Colon Cancer Diagnosis

The early-stage diagnosis of cancer is a crucial clinical need. The inadequacies of surgery tissue biopsy have prompted a transition to a less invasive profiling of molecular biomarkers from biofluids, known as liquid biopsy. Exosomes are phospholipid bilayer vesicles present in many biofluids with a biologically active cargo, being responsible for cell-to-cell communication in biological systems. An increase in their excretion and changes in their cargo are potential diagnostic biomarkers for an array of diseases, including cancer, and they constitute a promising analyte for liquid biopsy. The number of exosomes released, the morphological properties, the membrane composition, and their content are highly related to the physiological and pathological states. The main analytical challenge to establishing liquid biopsy in clinical practice is the development of biosensors able to detect intact exosomes concentration and simultaneously analyze specific membrane biomarkers and those contained in their cargo. Before analysis, exosomes also need to be isolated from biological fluids. Microfluidic systems can address several issues present in conventional methods (i.e., ultracentrifugation, size-exclusion chromatography, ultrafiltration, and immunoaffinity capture), which are time-consuming and require a relatively high amount of sample; in addition, they can be easily integrated with biosensing systems. A critical review of emerging microfluidic-based devices for integrated biosensing approaches and following the major analytical need for accurate diagnostics is presented here. The design of a new miniaturized biosensing system is also reported. A device based on hollow-fiber flow field-flow fractionation followed by luminescence-based immunoassay is applied to isolate intact exosomes and characterize their cargo as a proof of concept for colon cancer diagnosis.

Extracellular vesicles - on the cusp of a new language in the biological sciences.

Extracellular vesicles (EVs) play a key role both in physiological balance and homeostasis and in disease processes through their ability to participate in intercellular signaling and communication. An ever-expanding knowledge pool and a myriad of functional properties ascribed to EVs point to a new language of communication in biological systems that has opened a path for the discovery and implementation of novel diagnostic applications. EVs originate in the endosomal network and via non-random shedding from the plasma membrane by mechanisms that allow the packaging of functional cargoes, including proteins, lipids, and genetic materials. Deciphering the molecular mechanisms that govern packaging, secretion and targeted delivery of extracellular vesicle-borne cargo will be required to establish EVs as important signaling entities, especially when ascribing functional properties to a heterogeneous population of vesicles. Several molecular cascades operate within the endosomal network and at the plasma membrane that recognize and segregate cargos as a prelude to vesicle budding and release. EVs are transferred between cells and operate as vehicles in biological fluids within tissues and within the microenvironment where they are responsible for short- and long-range targeted information. In this review, we focus on the remarkable capacity of EVs to establish a dialogue between cells and within tissues, often operating in parallel to the endocrine system, we highlight selected examples of past and recent studies on the functions of EVs in health and disease.

Towards Generalizing the Information Theory for Neural Communication.

Neuroscience extensively uses the information theory to describe neural communication, among others, to calculate the amount of information transferred in neural communication and to attempt the cracking of its coding. There are fierce debates on how information is represented in the brain and during transmission inside the brain. The neural information theory attempts to use the assumptions of electronic communication; despite the experimental evidence that the neural spikes carry information on non-discrete states, they have shallow communication speed, and the spikes’ timing precision matters. Furthermore, in biology, the communication channel is active, which enforces an additional power bandwidth limitation to the neural information transfer. The paper revises the notions needed to describe information transfer in technical and biological communication systems. It argues that biology uses Shannon’s idea outside of its range of validity and introduces an adequate interpretation of information. In addition, the presented time-aware approach to the information theory reveals pieces of evidence for the role of processes (as opposed to states) in neural operations. The generalized information theory describes both kinds of communication, and the classic theory is the particular case of the generalized theory.

Saturating Receiver and Receptor Competition in Synaptic DMC: Deterministic and Statistical Signal Models.

Synaptic communication is based on a biological Molecular Communication (MC) system which may serve as a blueprint for the design of synthetic MC systems. However, the physical modeling of synaptic MC is complicated by the possible saturation of the molecular receiver caused by the competition of neurotransmitters (NTs) for postsynaptic receptors. Receiver saturation renders the system behavior nonlinear in the number of released NTs and is commonly neglected in existing analytical models. Furthermore, due to the ligands' competition for receptors (and vice versa), the individual binding events at the molecular receiver are in general not statistically independent and the commonly used binomial model for the statistics of the received signal does not apply. Hence, in this work, we propose a novel deterministic model for receptor saturation in terms of a state-space description based on an eigenfunction expansion of Fick's diffusion equation. The presented solution is numerically stable and computationally efficient. Employing the proposed deterministic model, we show that saturation at the molecular receiver effectively reduces the peak-value of the expected received signal and accelerates the clearance of NTs as compared to the case when receptor occupancy is neglected. We further derive a statistical model for the received signal in terms of the hypergeometric distribution which accounts for the competition of NTs for receptors and the competition of receptors for NTs. The proposed statistical model reveals how the signal statistics are shaped by the number of released NTs, the number of receptors, and the binding kinetics of the receptors, respectively, in the presence of competition. In particular, we show that the impact of these parameters on the signal variance is qualitatively different depending on the relative numbers of NTs and receptors. Finally, the accuracy of the proposed deterministic and statistical models is verified by particle-based computer simulations.

Earth's Amphibious Transformation: Tange Kenzo, Buckminster Fuller, and marine urbanization in global environmental thought (1950s–present)

AbstractClimate change and rising sea levels, which threaten many Asian and other coastal cities, have returned the question of adaptation to unstable marine surfaces to the global discussions about urbanization, as was illustrated by a recent United Nations (UN) roundtable. As de facto counterproposals to hydroelectric dams and similar regional development projects, floating or elevated structures reject land reclamation and terrestrialization processes. Consequently, the rapidly growing number of offshore structures, which often constitute unconventional settlements, have contributed to an amphibious transformation of Earth's surface in the course of the twentieth and early twenty-first centuries. This amphibious transformation meant that both terrestrial and aquatic places have turned into human habitats. This article asks how and why today's leading environmental-political strand in large-scale marine urbanization emerged from the waters of Tokyo Bay. It investigates Japanese star architect Tange Kenzō's ‘Plan for Tokyo 1960’ (1961) and world-renowned American designer R. Buckminster Fuller's floating design called ‘Tetrahedronal City’ (1966). Emphasizing the important role that Asian cities have played in shaping global urbanization ideas and practices, Tokyo Bay became a node in the global cybernetics revolution that moved urban design into the information age. Tange's and Fuller's evolution-inspired cybernetic designs used the post-war communication technology revolution to replicate, through artificial communication networks, the biological communication systems that enable organisms to interact with their environments. Applying communication technology to recreate, in floating or elevated structures, the biological processes of growth, adaptation, mobility, and autonomy became the central environmental-political strand for large-scale marine urbanization and reducing its ecological footprint.

Harmonic Progression in Bioinformatics and Recurrent Series in Inherited Biostructures

The article is devoted to the study of new approaches to the development of mathematical models in genetic biomechanics, which studies the structural relationships of the genetic coding system with genetically inherited biological forms. More specifically, we are talking about models based on the recurrent harmonic progression whose connection with the information sequences of DNA molecules in the genomes of higher and lower organisms was recently revealed. In particular, the article describes previously unknown connections of the function of natural logarithms with the structures of the molecular genetic system, which allow modelling the main psychophysical logarithmic law by Weber-Fechner and also many other logarithmic structures in genetically inherited biological systems. In physics, the harmonic progression is traditionally considered, first of all, as related to standing waves in resonators. Our results are correlated with Frohlich’s vibration-resonant theory about collective quantum effects and long-range communication in biological systems.

Is BCH Code Useful to DNA Classification as an Alignment-Free Method?

Similarities between biological and digital communication systems have been investigated since biology also uses a discrete alphabet to represent and transmit information. The genetic information of an organism is encoded in DNA molecules by units called bases. However, there is no a definitive model and the question as what error-correcting code underlies DNA sequences remains an open problem. Recent works show that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as BCH codes. We propose improvements regarding the code construction process that resulted in a novel algorithm for searching BCH codes whose codeword differ from a given DNA sequence (mapped to finite field $\mathbb {F}_{4}$ ) in up to only one symbol. The most important improvement is to replace brute force decoding with syndrome decoding. In this sense, based on a statistical analysis, we verify whether in a collection of sequences with the same taxonomic rank there is a code that identifies most of these sequences, called dominant code. Furthermore, we check whether the dominant code can provides a biological information to DNA classification being an alignment-free method. Finally, we show that the probability of a DNA sequences with odd-length $n$ be identified by a BCH code tends to analytical probability of the same code identifying a random vector.

The meaning of non-classical estrogen receptors and peroxisome proliferator-activated receptor for boar Leydig cell of immature testis

Communication in biological systems involves diverse-types of cell-cell interaction including cross-talk between receptors expressed by the target cells. Recently, novel sort of estrogen receptors (G protein - coupled estrogen receptor; GPER and estrogen-related receptor; ERR) that signal directly via estrogen binding and/or via mutual interaction-regulated estrogen signaling were reported in various organs including testis. Peroxisome proliferator - activated receptor (PPAR) is responsible for maintaining of lipid homeostasis that is critical for sex steroid production in the testis. Here, we investigated the role of interaction between GPER, ERRβ and PPARγ in steroidogenic Leydig cells of immature boar testis. Testicular fragments cultured ex vivo were treated with GPER or PPARγ antagonists. Then, cell ultrastructure, expression and localization of GPER, ERRβ, PPARγ together with the molecular receptor mechanism, through cyclic AMP and Raf/Ras/extracellular signal activated kinases (ERK), in the control of cholesterol concentration and estrogen production by Leydig cells were studied. In the ultrastructure of antagonist-treated Leydig cells, mitochondria were not branched and not bifurcated as they were found in control. Additionally, in PPARγ-blocked Leydig cells changes in the number of lipid droplets were revealed. Independent of used antagonist, western blot revealed decreased co-expression of GPER, ERRβ, PPARγ with exception of increased expression of ERRβ after PPARγ blockage. Immunohistochemistry confirmed presence of all receptors partially located in the nucleus or cytoplasm of Leydig cells of both control and treated testes. Changes in receptor expression, decreased cholesterol and increased estradiol tissue concentrations occurred through decreased cAMP level (with exception after GPER blockage) as well as Raf/Ras/ERK pathway expression. These all findings indicate that GPER-ERRβ-PPARγ interaction exists in immature boar testis and regulates Leydig cell function. Further detailed studies and considerations on GPER-ERRβ-PPARγ as possible diagnosis/therapy target in disturbances of testis steroidogenic function are needed.

Using chemical language to shape future marine health

“Infochemicals” (information‐conveying chemicals) dominate much of the underwater communication in biological systems. They influence the movement and behavior of organisms, the ecological interactions between and across populations, and the trophic structure of marine food webs. However, relative to their terrestrial equivalents, the wider ecological and economic importance of marine infochemicals remains understudied and a concerted, cross‐disciplinary effort is needed to reveal the full potential of marine chemical ecology. We highlight current challenges with specific examples and suggest how research on the chemical ecology of marine organisms could provide opportunities for implementing new management solutions for future “blue growth” (the sustainable use of ocean resources) and maintaining healthy marine ecosystems.

Genetic Expression in Biological Systems: A Digital Communication Perspective

The transcription and translation of Deoxyribonucleic Acid (DNA) involve the processing of genetic information (adenine, thymine, guanine, and cytosine), which can be interpreted as the processing of discrete signals. Additionally, the proper transmission and reception of proteins can be understood with typical theories of digital communication systems. Thus, concepts as routing, error control, and Shannon’s theorem may be the equivalence to determine a target organ, the maturation in the primary transcript molecule of Ribonucleic Acid (RNA) messenger, and the regulation of gene expression (that defines the development of multicellular organisms), respectively. Due to the high performance of transmitting information shown by typical digital communication systems, modeling the analogies between biological communication systems and digital communication systems as mentioned above may allow overcoming the challenges that biological systems face and having more efficient treatment of lethal diseases such as cancer.

Preliminary soundscape observations from a Colombian humpback whale breeding ground before port construction

The Gulf of Tribuga in the Colombian Pacific is still relatively undisturbed. No road access between villages nor from major urban areas exists. Small boats and walking beaches at low tide serve as the main transportation conduits. In this breeding ground for humpback whale Stock G, small-scale artisanal and shrimp fisheries and whale-watching activities support the livelihood of local communities but may already interfere with biological communication systems. Once a proposed international port is built anthropogenic pressure is expected to increase. Baseline information is key to understand the Gulf's current acoustic state and to document the best approximation of its practically pristine state. An ecological Acoustic Recorder (EAR, Oceanwide Science Institute) was deployed between the largest town (about 2000 residents) and the southern boundary of the Utria National Park marine reserve from October to December, 2018. Also, opportunistic over-the-side recordings from July to September, 2018, provided point surveys at a greater spatial resolution during peak humpback whale breeding season. Results include the first acoustic catalogue of the area and a preliminary understanding of important bandwidths for future monitoring and current contributions of small vessels to the soundscape.The Gulf of Tribuga in the Colombian Pacific is still relatively undisturbed. No road access between villages nor from major urban areas exists. Small boats and walking beaches at low tide serve as the main transportation conduits. In this breeding ground for humpback whale Stock G, small-scale artisanal and shrimp fisheries and whale-watching activities support the livelihood of local communities but may already interfere with biological communication systems. Once a proposed international port is built anthropogenic pressure is expected to increase. Baseline information is key to understand the Gulf's current acoustic state and to document the best approximation of its practically pristine state. An ecological Acoustic Recorder (EAR, Oceanwide Science Institute) was deployed between the largest town (about 2000 residents) and the southern boundary of the Utria National Park marine reserve from October to December, 2018. Also, opportunistic over-the-side recordings from July to September, 2018, provided ...

Brain Computer Interface for Neurodegenerative Person Using Electroencephalogram

Brain–computer interface (BCI) connects the outside world, in real time and in a natural way, like biological communication system. It facilitates the communication link from the brain to the external world by converting brain thoughts in to control commands to control the external devices, such as wheelchair, keyboard mouse, and other home appliances. Measuring the electrical brain activity by placing electrodes over scalp is called electroencephalogram (EEG). By combining these two techniques, we are able to create EEG-based BCI. In this paper, we use band power and radial basis function to analyze the signal for four mentally composed tasks to design four states BCI for a neurodegenerative person using EEG. Online study was conducted to analyze the performance of the wheelchair for a neurodegenerative person. The result shows that an overall average classification accuracy of 92.50% and individual tasks with an average classification of 95%, 87.50%, 92.50%, and 95.00% were achieved for the four tasks. The result proves that control commands generated from the EEG signal have the bcapacity to control the intelligent systems.

Spectral Characterization of Three-Electron Two-Center (3e-2c) Bonds of Gaseous CH3S∴S(H)CH3 and (CH3SH)2+ and Enhancement of the 3e-2c Bond upon Protonation.

The three-electron two-center (3e-2c) bond plays an important role in structures and electron communication in biological systems involving cationic sulfur compounds. Although the nature of 3e-2c bonds and their theoretical formalism have attracted great interest, direct spectral identifications of 3e-2c-bound molecules are scarce. We observed the infrared spectra of the weakly 3e-2c-bound CH3S∴S(H)CH3 and the strongly 3e-2c-bound (CH3SH)2+ in a supersonic jet using infrared (IR) dissociation with vacuum-ultraviolet photoionization and time-of-flight detection. Protonation of CH3S∴S(H)CH3 to form [CH3(H)S∴S(H)CH3]+ significantly enhances the 3e-2c bond, characterized by a large red shift of the SH-stretching band with enhanced IR intensity, shortening of the calculated S-S distance from 3.00 to 2.86 Å, and a dissociation energy increased from ∼23 to 162 kJ mol-1.

Plasma exosomes as novel biomarker for the early diagnosis of gastric cancer.

Exosomes are lipid bilayer vesicles of endocytic origin ranging from 30 to 100 nm in size, and contain various nucleic acid molecules such as DNA, mRNA, miRNA, lncRNA and multiple proteins, which could be transferred into target cells. Recent study indicated that exosomes as information carriers between cells has introduced us to a new previously unknown biological communication system. Increasing evidences show that exosomes play a crucial role in gastric cancer because they are potential to influence normal cellular physiology and promote various states of the cancer. In this review, we focus on the latest findings on exosomes in the plasma of gastric cancer patients, mainly summarizing the functions of miRNAs, lncRNAs and multiple proteins in diagnosis, prognosis, and in establishing treatment regimens against gastric cancer. Furtherly, potential functions of exosomes as novel diagnostic biomarkers for gastric cancer are discussed extensively. Exosomes are believed to be a non-invasive disease biomarker with a dual capability to provide insights into the early diagnosis for gastric cancer.

Signalling under Uncertainty: Interpretative Alignment without a Common Prior

Communication involves a great deal of uncertainty. Prima facie, it is therefore surprising that biological communication systems—from cellular to human—exhibit a high degree of ambiguity and often leave its resolution to contextual cues. This puzzle deepens once we consider that contextual information may diverge between individuals. In the following we lay out a model of ambiguous communication in iterated interactions between subjectively rational agents lacking a common contextual prior. We argue ambiguity’s justification to lie in endowing interlocutors with means to flexibly adapt language use to each other and the context of their interaction to serve their communicative preferences. Linguistic alignment is shown to play an important role in this process; it foments convergence of contextual expectations and thereby leads to agreeing use and interpretation of ambiguous messages. We conclude that ambiguity is ecologically rational when (i) interlocutors’ (beliefs about) contextual expectations are generally in line or (ii) they interact multiple times in an informative context, enabling for the alignment of their expectations. In light of these results meaning multiplicity can be understood as an opportunistic outcome enabled and shaped by linguistic adaptation and contextual information. 1. Meaning Multiplicity in Communication2. Ambiguous Signalling through Pragmatic Inference 2.1. Preliminaries2.2. Signalling behaviour2.3. Communicative success2.4. Iterated interactions3. Predictions for Single and Iterated Interactions 3.1. Simulations3.2. Exploration and past experience3.3. Preemptive adaptation4. Discussion5. ConclusionAppendix

Exosomes carrying immunoinhibitory proteins and their role in cancer.

Recent emergence of exosomes as information carriers between cells has introduced us to a new previously unknown biological communication system. Multi-directional cross-talk mediated by exosomes carrying proteins, lipids and nucleic acids between normal cells, cells harbouring a pathogen or cancer and immune cells has been instrumental in determining outcomes of physiological as well as pathological conditions. Exosomes play a key role in the broad spectrum of human diseases. In cancer, tumour-derived exosomes carry multiple immunoinhibitory signals, disable anti-tumour immune effector cells and promote tumour escape from immune control. Exosomes delivering negative signals to immune cells in cancer, viral infections, autoimmune or other diseases may interfere with therapy and influence outcome. Exosomes can activate tissue cells to produce inhibitory factors and thus can suppress the host immune responses indirectly. Exosomes also promise to be non-invasive disease biomarkers with a dual capability to provide insights into immune dysfunction as well as disease progression and outcome.

Nano-Communication Propagation Channel Model Using Flow and Diffusion

Inspired by biological communication systems, nano-communication in particular molecular communication has been proposed as a viable scheme to communicate between nano-sized devices separated by a very short distance. Here, molecules are released by the transmitter into the medium, which are then sensed by the receiver .Thus, this has necessitated the research on the potential applications of nanotechnology in a wide range of nano-networking areas. Nano-networking is a new type of networking which can also be applied to the communication theory. In this paper, a well justified channel propagation model for flow-based nano-characteristic communication channel is considered. The signal propagation model based on the advection and diffusion processes is analyzed. Furthermore, a sound mathematical justification for the linearity and time-variance properties of flow and diffusion based nano-communication channel model is investigated.

Evaluation and modeling of HIV based on communication theory in biological systems

Some forms of communication are used in biological systems such as HIV transmission in human beings. In this paper, we plan to get a unique insight into biological communication systems generally through the analogy between HIV infection and electrical communication system. The model established in this paper can be used to test and simulate various communication systems since it provides researchers with an opportunity. We interpret biological communication systems by using telecommunications exemplification from a layered communication protocol developed before and use the model to indicate HIV spreading. We also implement a simulation of HIV infection based on the layered communication protocol to predict the development of this disease and the results prove the validity of the model.

What is duality of patterning, anyway?

AbstractThe notion of duality of patterning (henceforth DoP), at least for readers of this special issue, is probably most closely associated with Charles F. Hockett's project of identifying the ‘design features’ of language in order to characterise the ways in which human language is unique among biological communication systems (Hockett 1958: chapter 64; Hockett 1960; Hockett and Ascher 1964). Roughly speaking, DoP refers to the fact that the meaningful units of language – words or morphemes – are made up of meaningless units – phonemes or features – whose only function is to distinguish the meaningful units from one another. Stated this way, the idea seems quite straightforward, and to have it explicitly stated as a property of language seems a useful insight. In fact, though, of all the design features discussed by Hockett, DoP seems to have engendered the most confusion. The idea that meaningful units are composed of meaningless ones seems simple enough, but many complications arise when we look more closely. The goal of this short paper is to document some of the complications and perhaps alleviate some of the confusion.