Biochemical Environment Research Articles

Coupling Microfluidic Platforms, Microfabrication, and Tissue Engineered Scaffolds to Investigate Tumor Cells Mechanobiology.

The tumor microenvironment (TME) is composed of dynamic and complex networks composed of matrix substrates, extracellular matrix (ECM), non-malignant cells, and tumor cells. The TME is in constant evolution during the disease progression, most notably through gradual stiffening of the stroma. Within the tumor, increased ECM stiffness drives tumor growth and metastatic events. However, classic in vitro strategies to study the TME in cancer lack the complexity to fully replicate the TME. The quest to understand how the mechanical, geometrical, and biochemical environment of cells impacts their behavior and fate has been a major force driving the recent development of new technologies in cell biology research. Despite rapid advances in this field, many challenges remain in order to bridge the gap between the classical culture dish and the biological reality of actual tissue. Microfabrication coupled with microfluidic approaches aim to engineer the actual complexity of the TME. Moreover, TME bioengineering allows artificial modulations with single or multiple cues to study different phenomena occurring in vivo. Some innovative cutting-edge tools and new microfluidic approaches could have an important impact on the fields of biology and medicine by bringing deeper understanding of the TME, cell behavior, and drug effects.

A chemo-mechanical model for osmo-inelastic effects in the annulus fibrosus.

The annulus fibrosus exhibits complex osmotic and inelastic effects responsible for unusual transversal behavior with a Poisson's ratio higher than 0.5 in fibers plane and negative (i.e., auxetic) in lamellae plane. In this paper, we present a new chemo-mechanical approach for the intrinsic osmo-inelastic response of the annulus fibrosus in relation to the microstructure of the layered reinforced soft tissue, the biochemical environment and the mechanical loading conditions. The constitutive model introduces the coupling between the deformation-induced inelastic stress in the tangled extracellular matrix and the stress-free swelling due to internal fluid content variation by osmosis. The proposed formulation is implemented into a finite element code, and numerical simulations on annulus specimens, including explicitly lamellae and interlamellar zones, are presented. To illustrate the capability of the approach to capture experimental observations quantitatively, the simulated results are compared to experimental results obtained by monitoring the full-field strain in annulus specimens using digital image correlation method. Some material constants are found by matching the free swelling in a water bath with different salt concentrations, and others are found by matching tensile results in terms of loading-unloading stress-stretch curve and transversal behavior. The constitutive model is found to successfully capture the variations in osmolarity and strain-rate conditions (both statistically significant, p < 0.05) on the intrinsic response and the auxeticity. The stress/strain patterns in the model simulation provide valuable insights into the role of the interlamellar zone in the osmo-inelastic mechanisms.

Reaction Systems and Synchronous Digital Circuits.

A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause–effect relationships in biochemical environments. Biochemical processes in this framework are seen to interact with each other by producing the ingredients enabling and/or inhibiting other reactions. They can also be influenced by the environment seen as a systematic driver of the processes through the ingredients brought into the cellular environment. In this paper, the first attempt is made to implement reaction systems in the hardware. We first show a tight relation between reaction systems and synchronous digital circuits, generally used for digital electronics design. We describe the algorithms allowing us to translate one model to the other one, while keeping the same behavior and similar size. We also develop a compiler translating a reaction systems description into hardware circuit description using field-programming gate arrays (FPGA) technology, leading to high performance, hardware-based simulations of reaction systems. This work also opens a novel interesting perspective of analyzing the behavior of biological systems using established industrial tools from electronic circuits design.

Resilient Graphene Ultrathin Flat Lens in Aerospace, Chemical, and Biological Harsh Environments.

The development of ultrathin flat lenses has revolutionized the lens technologies and holds great promise for miniaturizing the conventional lens system in integrated photonic applications. In certain applications, the lenses are required to operate in harsh and/or extreme environments, for example aerospace, chemical, and biological environments. Under such circumstances, it is critical that the ultrathin flat lenses can be resilient and preserve their outstanding performance. However, the majority of the demonstrated ultrathin flat lenses are based on metal or semiconductor materials that have poor chemical, thermal, and UV stability, which limit their applications. Herein, we experimentally demonstrate a graphene ultrathin flat lens that can be applied in harsh environments for different applications, including a low Earth orbit space environment, strong corrosive chemical environments (pH = 0 and pH = 14), and biochemical environment. The graphene lenses have extraordinary environmental stability and can maintain a high level of structural integrity and outstanding focusing performance under different test conditions. Thus, it opens tremendous practical application opportunities for ultrathin flat lenses.

Hydrogenase-Like Electrocatalytic Activation and Inactivation Mechanism by Three-Dimensional Binderless Molecular Catalyst

In response to issues raised by modern energy challenges, molecular electrocatalysis is currently attracting a lot of attention to the tailoring of “model” catalysts, notably understanding the mechanisms and kinetic and thermodynamic parameters that occur during a catalytic reaction. In this regard, nature offers extremely efficient enzymes called hydrogenases. These enzymes that catalyze the reversible interconversions between H2 and H+ at high turnover rates are inactivated by O2. This inactivation yields odd cyclic voltammetric responses originating from a chemical inactivation–redox activation process (IAP). Although IAP has been extensively studied for hydrogenases, their catalytic mechanism is not fully understood because of the intricate but necessary electrical wiring, desorption, and complex biochemical environment required. Here, we report a unique example of IAP based on a nonenzymatic catalyst prepared by mixing rhodium-porphyrinic catalyst and an interconnected multiwalled carbon nanotubes matrix which presents an excellent and stable electron transfer. We combined organic synthesis, electrochemistry, mathematical models, and density functional theory calculations to uncover the molecular IAP at the catalytic metallic site. We present a mechanistic analysis of the noncatalytic and catalytic responses exhibited by this complex, enabling a comprehensive understanding of the thermodynamic and kinetic parameters that govern the IAP. These stepwise studies support a mechanism for glucose oxidation that proceeds most likely through an EC′CE scheme with catalytic steps similar to the ones reported for NiFe hydrogenases. The overall mechanism of the molecular IAP was detailed on the basis of our experimentally validated models and compared to NiFe hydrogenase IAP. Our findings offer novel perspectives to design finely optimized catalysts by eliminating the inactivation phenomena.

Intramolecular isotopic evidence for bacterial oxidation of propane in subsurface natural gas reservoirs

Microbial anaerobic oxidation of hydrocarbons is a key process potentially involved in a myriad of geological and biochemical environments yet has remained notoriously difficult to identify and quantify in natural environments. We performed position-specific carbon isotope analysis of propane from cracking and incubation experiments. Anaerobic bacterial oxidation of propane leads to a pronounced and previously unidentified 13C enrichment in the central position of propane, which contrasts with the isotope signature associated with the thermogenic process. This distinctive signature allows the detection and quantification of anaerobic oxidation of hydrocarbons in diverse natural gas reservoirs and suggests that this process may be more widespread than previously thought. Position-specific isotope analysis can elucidate the fate of natural gas hydrocarbons and provide insight into a major but previously cryptic process controlling the biogeochemical cycling of globally significant greenhouse gases.

Impact of Gut Dysbiosis on Neurohormonal Pathways in Chronic Kidney Disease.

Chronic kidney disease (CKD) is a worldwide major health problem. Traditional risk factors for CKD are hypertension, obesity, and diabetes mellitus. Recent studies have identified gut dysbiosis as a novel risk factor for the progression CKD and its complications. Dysbiosis can worsen systemic inflammation, which plays an important role in the progression of CKD and its complications such as cardiovascular diseases. In this review, we discuss the beneficial effects of the normal gut microbiota, and then elaborate on how alterations in the biochemical environment of the gastrointestinal tract in CKD can affect gut microbiota. External factors such as dietary restrictions, medications, and dialysis further promote dysbiosis. We discuss the impact of an altered gut microbiota on neuroendocrine pathways such as the hypothalamus–pituitary–adrenal axis, the production of neurotransmitters and neuroactive compounds, tryptophan metabolism, and the cholinergic anti-inflammatory pathway. Finally, therapeutic strategies including diet modification, intestinal alpha-glucosidase inhibitors, prebiotics, probiotics and synbiotics are reviewed.

Follicular fluid progesterone concentration is associated with fertilization outcome after IVF: a systematic review and meta-analysis.

Follicular fluid is a key biochemical environment for oocyte development. The potential effect of follicular progesterone level on successful fertilization is a subject of debate, and so the aim of this study was to provide a summary of the currently available evidence on the association between follicular fluid progesterone level and fertilization outcome. To do so, a systematic review and a meta-analysis were performed, with the literature searches being conducted in three databases (PubMed, Embase and the Cochrane Library) to identify all relevant studies published up to 19 August 2017. Data were available from 13 studies (four intracytoplasmic sperm injection [ICSI] and nine conventional IVF) and 1009 individually aspirated follicular fluid samples were included in the analysis. The progesterone levels in follicular fluid were significantly higher in normal fertilization than in failed fertilization, both in conventional IVF (33% difference, P<0.001) and ICSI (34% difference, P=0.004). Although these data show that fertilized oocytes are derived from follicles with higher levels of progesterone, the results must be interpreted with caution, because of various progesterone measurement methods and different treatment protocols and it is too early to state that follicular fluid progesterone level could be considered as a marker for oocyte quality.

Therapeutic Effect of Agmatine on Neurological Disease: Focus on Ion Channels and Receptors.

The central nervous system (CNS) is the most injury-prone part of the mammalian body. Any acute or chronic, central or peripheral neurological disorder is related to abnormal biochemical and electrical signals in the brain cells. As a result, ion channels and receptors that are abundant in the nervous system and control the electrical and biochemical environment of the CNS play a vital role in neurological disease. The N-methyl-D-aspartate receptor, 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl) propanoic acid receptor, kainate receptor, acetylcholine receptor, serotonin receptor, α2-adrenoreceptor, and acid-sensing ion channels are among the major channels and receptors known to be key components of pathophysiological events in the CNS. The primary amine agmatine, a neuromodulator synthesized in the brain by decarboxylation of L-arginine, can regulate ion channel cascades and receptors that are related to the major CNS disorders. In our previous studies, we established that agmatine was related to the regulation of cell differentiation, nitric oxide synthesis, and murine brain endothelial cell migration, relief of chronic pain, cerebral edema, and apoptotic cell death in experimental CNS disorders. In this review, we will focus on the pathophysiological aspects of the neurological disorders regulated by these ion channels and receptors, and their interaction with agmatine in CNS injury.

Life history shapes variation in egg composition in the blue tit Cyanistes caeruleus

Maternal investment directly shapes early developmental conditions and therefore has long-term fitness consequences for the offspring. In oviparous species prenatal maternal investment is fixed at the time of laying. To ensure the best survival chances for most of their offspring, females must equip their eggs with the resources required to perform well under various circumstances, yet the actual mechanisms remain unknown. Here we describe the blue tit egg albumen and yolk proteomes and evaluate their potential to mediate maternal effects. We show that variation in egg composition (proteins, lipids, carotenoids) primarily depends on laying order and female age. Egg proteomic profiles are mainly driven by laying order, and investment in the egg proteome is functionally biased among eggs. Our results suggest that maternal effects on egg composition result from both passive and active (partly compensatory) mechanisms, and that variation in egg composition creates diverse biochemical environments for embryonic development.

The application of atomic force microscopy for viruses and protein shells: Imaging and spectroscopy.

Atomic force microscopy (AFM) probes surface-adsorbed samples at the nanoscale by using a sharp stylus of nanometric size located at the end of a micro-cantilever. This technique can also work in a liquid environment and offers unique possibilities to study individual protein assemblies, such as viruses, under conditions that resemble their natural liquid milieu. Here, I show how AFM can be used to explore the topography of viruses and protein cages, including that of structures lacking a well-defined symmetry. AFM is not limited for imaging and allows the manipulation of individual viruses with force spectroscopy approaches, such as single indentation and mechanical fatigue assays. These pushing experiments deform the protein cages to obtain their mechanical information and can be used to monitor the structural changes induced by maturation or the exposure to different biochemical environments, such as pH variation. We discuss how studying capsid rupture and self-healing events offers insight into virus uncoating pathways. On the other hand, pulling tests can provide information about the virus-host interaction established between the viral fibers and the cell membrane.

Problems of Physical Rehabilitation of Patients Suffering Type I Diabetesand Abdominal Obesity

Type I diabetes mellitus is endocrine pathology, which is increasingly detected in young people, usually at the age of 35 years. Diabetes is often combined with an increase in cholesterol in the blood, a decrease in the functions of the thyroid gland and adrenal glands, metabolic disorders, heart diseases, gout, osteochondrosis, obesity, exacerbations in the respiratory system. Often there are pinpoint hemorrhages associated with vascular rupture, including in the vascular system of the eye. Because of the slow flow of protein synthesis processes, the processes of regeneration of damaged tissue are significantly delayed. The patient develops asthenia, depression and many other phenomena. In the intestine, the fermentation of excess carbohydrates is activated and its biochemical environment changes, which leads to suppression of intestinal flora and decay of proteins. It is clear that properly selected physical activities can contribute to this reduction in body weight, improve metabolic processes, and help prevent cardiovascular disease. Daily exercise helps to strengthen the human body, develop muscle corset and reduce subcutaneous fat in diabetes and abdominal obesity. Properly selected physical activity improves the susceptibility of insulin receptors, while reducing the glucose level in the blood. Regular moderate muscular activity helps patients to reduce the dose of insulin, adjust the diet and reduce body weight. Particularly useful in this regard is circular training, which is able to have a number of effects in the patient's body: improves the functioning of the cardiovascular system; accelerates metabolism; burns subcutaneous fat.

Mechanical-Chemical Coupling in Temporomandibular Joint Disc

This paper reports an experimental investigation based on vibrational spectroscopy of biological materials by a new custom-made device allowing simultaneously applying tensile load with changes within a controlled chemical environment. The response of the molecular structures of Temporomandibular Joint (TMJ) discs under simulated daily mechanical stimulations was characterized by stress-strain analysis and Raman spectra. The results show that changes in the biochemical environment around tissue (associated to common disorders) led to significant modifications to its mechanical properties. The molecular response to stress was then fully characterized by a combination of molecular mapping followed by statistical analysis via Principal Component Analysis resulting in the identification of the phenylalanine-aromatic amino acids as a significant and major mechanical-chemical effector of TMJ discs. The coupled tensile machine and vibrational spectroscopy approach enabling in-situ molecular studies proves to be a powerful technique for biological material characterization and tissue engineering.

Optofluidics: the interaction between light and flowing liquids in integrated devices

Optofluidics is a rising technology that combines microfluidics and optics. Its goal is to manipulate light and flowing liquids on the micro/nanoscale and exploiting their interaction in optofluidic chips. The fluid flow in the on-chip devices is reconfigurable, non-uniform and usually transports substances being analyzed, offering a new idea in the accurate manipulation of lights and biochemical samples. In this paper, we summarized the light modulation in heterogeneous media by unique fluid dynamic properties such as molecular diffusion, heat conduction, centrifugation effect, light-matter interaction and others. By understanding the novel phenomena due to the interaction of light and flowing liquids, quantities of tunable and reconfigurable optofluidic devices such as waveguides, lenses, and lasers are introduced. Those novel applications bring us firm conviction that optofluidics would provide better solutions to high-efficient and high-quality lab-on-chip systems in terms of biochemical analysis and environment monitoring.

A Synthetic Signal Varied Weight Indicator in Bacteria

Biomolecular computing devices always work in a complex biochemical environment. The weight which shows the importance degree of a specific signal may vary in different environments because it may be influenced by other signals even in the absence of direct interaction. To measure a signal accurately, several biomolecular computing devices always need to be used to detect environmental factors. This study describes a novel method to determine the varied weight of a specific signal in different environments using the differential expression of a gene to avoid using several biomolecular computing devices. We constructed and verified a signal varied weight indicator (SVWI) in the bacterium Escherichia coli using the lac operon, Ptet promoter system, and the clustered regularly interspaced short palindromic repeats/DNase-dead Cpf1 system. The SVWI could indicate the varied weight of an isopropyl $\beta $ -d-thiogalactoside signal in three states: existing, non-existing, and existing with another signal of anhydrotetracycline, based on the controllable differential expression of the lacZ gene. It could also be used to indicate three different kinds of environments. The quantitative reverse transcription polymerase chain reaction, which is a traditionally used method to detect gene expression levels, was used to detect the results. The experimental results in the wet lab showed that SVWI can implement the expected functions. The SVWI has great potential in the application of biomedical, biocomputing, biosensors, and environmental monitoring. It will also inspire further research on the construction of biomolecular computing devices using controllable differential gene expression.

Kinases: Understanding Their Role in HIV Infection.

Antiviral drugs currently on the market primarily target proteins encoded by specific viruses. The drawback of these drugs is that they lack antiviral mechanisms that account for resistance or viral mutation. Thus, there is a pressing need for researchers to explore and investigate new therapeutic agents with other antiviral strategies. Viruses such as the human immunodeficiency virus (HIV) alter canonical signaling pathways to create a favorable biochemical environment for infectivity. We used Qiagen Ingenuity Pathway Analysis (IPA) software to review the function of several cellular kinases and the resulting perturbed signaling pathways during HIV infection such as NF-κB signaling. These host cellular kinases such as ADK, PKR, MAP3K11 are involved during HIV infection at various stages of the life cycle. Additionally IPA analysis indicated that these modified host cellular kinases are known to have interactions with each other especially AKT1, a serine/threonine kinase involved in multiple pathways. We present a list of cellular host kinases and other proteins that interact with these kinases. This approach to understanding the relationship between HIV infection and kinase activity may introduce new drug targets to arrest HIV infectivity.

Biomimetic polycaprolactone-chitosan nanofibrous substrate influenced cell cycle and ECM secretion affect cellular uptake of nanoclusters

Biomimetic cell culture substrates are developed as an alternative to the conventional substrates. They provide necessary biochemical and biophysical cues to the cells from their surrounding environment for their optimal growth, behaviour and physiology. Changes in physiology of cells growing on biomimetic substrate can essentially affect results of in vitro biological experiments such as drug cytotoxicity, nanoparticle internalization or signalling pathways. As majority of ECM proteins are fibrous in nature, nanofibrous scaffolds have more biomimicking properties. Therefore, in this study, we developed ECM mimicking polycaprolactone-chitosan nanofiber substrate and evaluated its effect on cell morphology, proliferation, cell cycle and ECM production. Further, cellular uptake of BSA-AuNCs has been assessed on conventional and biomimetic substrate in order to demonstrate the effect of these events on cellular properties. It was observed that the cells that were grown for 15 days on the nanofibers, had majority of cells in the proliferative phase of cell cycle compared to TCPS. Moreover, these cells showed extensive collagen and fibronectin production. Due to these conditions C3H10T1/2 cells displayed higher cell internalization of BSA-AuNCs. Overall, this study indicates that the nano-topographical and biochemical environment could alter the cell proliferative behaviour and ECM production, which affects the cell internalization of BSA-AuNCs. Also, PCL-chitosan nanofibrous substrate could be a better alternative to TCPS for cell culture studies.

Chemical Approaches to Dynamically Modulate the Properties of Synthetic Matrices.

As knowledge about the dynamic nature of tissues within the human body has increased, the need for cell culture models that mimic the properties of these dynamic microenvironments has grown. Hydrogels are useful platforms for investigating cellular responses to microenvironment cues in disease and regeneration processes and recently have been designed to contain dynamic bonds to regulate the mechanical and biochemical properties of the matrix in three-dimensional cell culture applications. In this Viewpoint, we highlight recent advances in developing hydrogels with dynamic properties for modeling aspects of human tissues, providing control over the properties of the synthetic matrix on multiple length and time scales, and their application for understanding or directing cell response. We conclude by discussing how orthogonal chemistries can be utilized to design dynamic hydrogel platforms for controlling both the mechanical and biochemical environment, affording opportunities to investigate more complex questions associated with disease progression and tissue regeneration.

Spatially structured cell populations process multiple sensory signals in parallel in intact vascular endothelium.

Blood flow, blood clotting, angiogenesis, vascular permeability, and vascular remodeling are each controlled by a large number of variable, noisy, and interacting chemical inputs to the vascular endothelium. The endothelium processes the entirety of the chemical composition to which the cardiovascular system is exposed, carrying out sophisticated computations that determine physiological output. Processing this enormous quantity of information is a major challenge facing the endothelium. We analyzed the responses of hundreds of endothelial cells to carbachol (CCh) and adenosine triphosphate (ATP) and found that the endothelium segregates the responses to these two distinct components of the chemical environment into separate streams of complementary information that are processed in parallel. Sensitivities to CCh and ATP mapped to different clusters of cells, and each agonist generated distinct signal patterns. The distinct signals were features of agonist activation rather than properties of the cells themselves. When there was more than one stimulus present, the cells communicated and combined inputs to generate new distinct signals that were nonlinear combinations of the inputs. Our results demonstrate that the endothelium is a structured, collaborative sensory network that simplifies the complex environment using separate cell clusters that are sensitive to distinct aspects of the overall biochemical environment and interactively compute signals from diverse but interrelated chemical inputs. These features enable the endothelium to selectively process separate signals and perform multiple computations in an environment that is noisy and variable.

PH-Regulated supramolecular chirality of phenylalanine-based hydrogels

To achieve desired physicochemical and biochemical activities of optically active molecules at targetted sites in biological systems, tuning of chiral sense by varying internal conditions (e.g., pH) is of utmost importance. However, it has been a challenge to gain the balance of non-covalent interactions required for chiral transformations merely by deviations in biochemical environment. Herein, pH-controlled chirality of supramolecular nanostructures obtained from coassembly of phenylalanine-derived gelator and achiral cationic polyacrylamide has successfully been achieved. Specifically, any changes in the pH remarkably influence the chirality of these nanostructures. For instance, coassembled hydrogels possessing l-enantiomer provide right-handed nanostructures at pH < 7; whereas at pH ≥ 7, handedness of nanostructures switches to the left-handed nanostructures. Moreover, viscoelastic properties and twist pitch were also regulated under the influence of pH change. This study may provide a methodology to control chirality by simply varying biochemical conditions, which points toward its potential to be used in biological systems as a key to gain preferential chiral sense in different sites of living systems.