Search

Background Brucellosis, as a serious zoonotic infectious disease, has been recognized as a re-emerging disease in the developing countries worldwide. In china, the incidence of brucellosis is increasing each year, seriously threatening the health of humans as well as animal populations. Despite a quite number of diagnostic methods currently being used for brucellosis, innovative technologies are still needed for its rapid and accurate diagnosis, especially in area where traditional diagnostic is unavailable. Methodology/Principal findings In this study, a total of 22 B cell linear epitopes were predicted from five Brucella outer membrane proteins (OMPs) using an immunoinformatic approach. These epitopes were then chemically synthesized, and with the method of indirect ELISA (iELISA), each of them displayed a certain degree of capability in identifying human brucellosis positive sera. Subsequently, a fusion protein consisting of the 22 predicted epitopes was prokaryotically expressed and used as diagnostic antigen in a newly established brucellosis testing method, nano-ZnO modified paper-based ELISA (nano-p-ELISA). According to the verifying test using a collection of sera collected from brucellosis and non-brucellosis patients, the sensitivity and specificity of multiepitope based nano-p-ELISA were 92.38% and 98.35% respectively. The positive predictive value was 98.26% and the negative predictive value was 91.67%. The multiepitope based fusion protein also displayed significantly higher specificity than Brucella lipopolysaccharide (LPS) antigen. Conclusions B cell epitopes are important candidates for serologically testing brucellosis. Multiepitope fusion protein based nano-p-ELISA displayed significantly sensitivity and specificity compared to Brucella LPS antigen. The strategy applied in this study will be helpful to develop rapid and accurate diagnostic method for brucellosis in human as well as animal populations., Author summary Brucellosis is one of the most important zoonosis in the world and has caused tremendous economic losses in agriculture and animal husbandry in many countries. Developing rapid, sensitive and specific diagnostic methods is very important for early detection and treatment of brucellosis patients. In this study, a novel diagnostic technique, nano-ZnO modified paper ELISA, was established. The antigen used in this technique was a fusion protein containing multiple B cell epitopes, which were predicted from Brucella major outer membrane proteins such as Bp26, Omp31, Omp16, Omp2b and Omp25. Comparing to traditional LPS antigen, this multiepitope based antigen displayed considerably higher sensitivity and higher specificity in laboratory. With the strategy described in this paper, more efficient epitopes and protein antigen can be identified in the future. Currently, LPS antigen is only prepared from live Brucella, while protein antigen can be produced in large quantities in prokaryotic expression system. In addition to nano-p-ELISA, this protein antigen can also be used for development other methods such as fluorescent polarization assay (FPA) and immunochromatographic assay (ICA) to meet the varied demand for brucellosis testing.

The breakthrough potentials of research papers can be explained by their boundary-spanning qualities. Here, for the first time, we apply the structural variation analysis (SVA) model and its affiliated metrics to investigate the extent to which such qualities characterize a group of Nobel Prize winning papers. We find that these papers share remarkable boundary-spanning traits, marked by exceptional abilities to connect disparate and topically-diverse clusters of research papers. Further, their publications exert structural variations on the scale that significantly alters the betweenness centrality distributions of existing intellectual space. Overall, SVA not only provides a set of leading indicators for describing future Nobel Prize winning papers, but also broadens our understanding of the similar prize-winning properties that may have been overlooked among other regular publications., 27 pages, 8 figures, 9 tables. Submitted to Frontiers in Research Metrics and Analytics

Membrane contact sites (MCSs) are defined as regions where two organelles are closely apposed, and most MCSs associated with each other via protein-protein or protein-lipid interactions. A number of key molecular machinery systems participate in mediating substance exchange and signal transduction, both of which are essential processes in terms of cellular physiology and pathophysiology. The endoplasmic reticulum (ER) is the largest reticulum network within the cell and has extensive communication with other cellular organelles, including the plasma membrane (PM), mitochondria, Golgi, endosomes and lipid droplets (LDs). The contacts and reactions between them are largely mediated by various protein tethers and lipids. Ions, lipids and even proteins can be transported between the ER and neighboring organelles or recruited to the contact site to exert their functions. This review focuses on the key molecules involved in the formation of different contact sites as well as their biological functions.

The involvement of non-coding RNAs (ncRNAs) in cellular physiology and disease pathogenesis is becoming increasingly relevant in recent years specifically in cancer research. Breast cancer (BC) has become a health concern and accounts for most of the cancer-related incidences and mortalities reported amongst females. In spite of the presence of promising tools for BC therapy, the mortality rate of metastatic BC cases is still high. Therefore, the genomic exploration of the BC subtype and the use of ncRNAs for possible regulation is pivotal. The expression and prognostic values of AURKA gene were assessed by Oncomine, GEPIA, KM-plotter, and bc-GenExMiner v4.4, respectively. Associated proteins and functional enrichment were evaluated by Cytoscape and DAVID databases. Additionally, molecular docking approach was employed to investigate the regulatory role of hsa-miR-32-3p assisted argonaute (AGO) protein of AURKA gene in BC. AURKA gene was highly expressed in patients with BC relative to normal counterpart and significantly correlated with poor survival. The docking result suggested that AURKA could be regulated by hsa-miR-32-3p as confirmed by the reported binding energy and specific interactions. The study gives some insights into role of AURKA and its regulation by microRNAs through AGO protein. It also provides exciting opportunities for cancer therapeutic intervention.

Motivation Accurate annotation of protein functions is fundamental for understanding molecular and cellular physiology. Data-driven methods hold promise for systematically deriving rules underlying the relationship between protein structure and function. However, the choice of protein structural representation is critical. Pre-defined biochemical features emphasize certain aspects of protein properties while ignoring others, and therefore may fail to capture critical information in complex protein sites. Results In this paper, we present a general framework that applies 3D convolutional neural networks (3DCNNs) to structure-based protein functional site detection. The framework can extract task-dependent features automatically from the raw atom distributions. We benchmarked our method against other methods and demonstrate better or comparable performance for site detection. Our deep 3DCNNs achieved an average recall of 0.955 at a precision threshold of 0.99 on PROSITE families, detected 98.89 and 92.88% of nitric oxide synthase and TRYPSIN-like enzyme sites in Catalytic Site Atlas, and showed good performance on challenging cases where sequence motifs are absent but a function is known to exist. Finally, we inspected the individual contributions of each atom to the classification decisions and show that our models successfully recapitulate known 3D features within protein functional sites. Availability and implementation The 3DCNN models described in this paper are available at https://simtk.org/projects/fscnn. Supplementary information Supplementary data are available at Bioinformatics online.

TRPM3 is a non-selective cation channel that is activated by neural steroids such as pregnenolone sulfate, nifedipine, and clotrimazole. Despite the number of TRPM3 variants, few reports have described functional analyses of these different TRPM3 types. Here we identified a new TRPM variant from mouse dorsal root ganglion, termed TRPM3γ3. We classified TRPM3γ3 and another known variant (variant 6) into the γ subtype, and analyzed the TRPM3γ variants. mRNA expression of TRPM3γ was higher than that of TRPM3α variants in the mouse dorsal root ganglion. In Ca2+-imaging of HEK293 cells expressing either the TRPM3γ variants or TRPM3α2, increases in cytosolic Ca2+ concentrations ([Ca2+]i) induced by pregnenolone sulfate or nifedipine were smaller in cells expressing the TRPM3γ variants compared to those expressing TRPM3α2. On the other hand, co-expression of TRPM3γ variants had no effect on [Ca2+]i increases induced by pregnenolone sulfate or nifedipine treatment of HEK293 cells expressing TRPM3α2. In Xenopus oocytes, small responses of TRPM3γ variants to chemical agonists compared to TRPM3α2 were also observed. Interestingly, Xenopus oocytes expressing TRPM3α2 displayed heat-evoked currents with clear thresholds of about 40 °C that were larger than those evoked in oocytes expressing TRPM3γ variants. Overall, these findings indicate that TRPM3γ variants have low channel activity compared to TRPM3α. Electronic supplementary material The online version of this article (10.1007/s12576-019-00677-6) contains supplementary material, which is available to authorized users.

The homeobox-containing gene Csx/Nkx2.5 codes several cardiac transcription factors and plays a critical role in early cardiogenesis. We investigated the effect of Csx/Nkx2.5 on the expression of cardiac ion channels using P19-derived cardiomyocytes. P19CL6 cells and P19CL6 cells with Csx/Nkx2.5 overexpression (P19CL6-Csx cells) were induced to differentiate into cardiomyocytes by treatment with dimethyl sulfoxide. Action potentials and membrane currents were measured by whole cell patch clamp at different differentiation stage: the early stage (1–5 days after beating had begun) and the late stage (10–15 days after beating). Expression of Csx/Nkx2.5 mRNA was increased as the differentiation stages advanced in both P19CL6 and P19CL6-Csx cells. In action potential configuration, maximal diastolic potentials in P19CL6-Csx cells exhibited more hyperpolarized potential (‒ 64.2 mV) than those in P19CL6 cells (‒ 54.8 mV,p +channels expressed during the early stage, the transient-outward K+channel was most predominant. By overexpression of Csx/Nkx2.5, developmental decrease in the transient-outward K+channel was suppressed. Homeobox-containing gene Csx/Nkx2.5 modifies the amount of distinct ionic channels, during differentiation periods, predominantly changing the expression of the transient-outward K+channel.

Pathophysiological functions of chloride intracellular channel protein 3 (CLIC3) in human gastric cancer have been unclear. In the tissue microarray analysis using 107 gastric cancer specimens, CLIC3 expression was negatively correlated with pathological tumor depth, and the patients with lower expression of CLIC3 exhibited poorer prognosis. CLIC3 was expressed in the plasma membrane of cancer cells in the tissue. CLIC3 expression was also found in a human gastric cancer cell line (MKN7). In whole-cell patch-clamp recordings of the cells expressing CLIC3, NPPB-sensitive outwardly rectifying Cl− currents were observed. Cell proliferation was significantly accelerated by knockdown of CLIC3 in MKN7 cells. On the other hand, the proliferation was attenuated by exogenous CLIC3 expression in human gastric cancer cells (KATOIII and NUGC-4) in which endogenous CLIC3 expression is negligible. Our results suggest that CLIC3 functions as a Cl− channel in the plasma membrane of gastric cancer cells and that decreased expression of CLIC3 results in unfavorable prognosis of gastric cancer patients.

International audience; Antibiotics are often considered as weapons conferring a competitive advantage to their producers in their ecological niche. However, since these molecules are produced in specific environmental conditions, notably phosphate limitation that triggers a specific metabolic state, they are likely to play important roles in the physiology of the producing bacteria that have been overlooked. Our recent experimental data as well as careful analysis of the scientific literature led us to propose that, in conditions of moderate to severe phosphate limitation—conditions known to generate energetic stress—antibiotics play crucial roles in the regulation of the energetic metabolism of the producing bacteria. A novel classification of antibiotics into types I, II, and III, based on the nature of the targets of these molecules and on their impact on the cellular physiology, is proposed. Type I antibiotics are known to target cellular membranes, inducing energy spilling and cell lysis of a fraction of the population to provide nutrients, and especially phosphate, to the surviving population. Type II antibiotics inhibit respiration through different strategies, to reduce ATP generation in conditions of low phosphate availability. Lastly, Type III antibiotics that are known to inhibit ATP consuming anabolic processes contribute to ATP saving in conditions of phosphate starvation.

Pulmonary vein (PV) cardiomyocytes have the potential to generate spontaneous activity, in contrast to working myocytes of atria. Different electrophysiological properties underlie the potential automaticity of PV cardiomyocytes, one being the hyperpolarization-activated inward current (Ih), which facilitates the slow diastolic depolarization. In the present study, we examined pharmacological characteristics of the Ih of PV cardiomyocytes in rat, guinea pig and rabbit. The results showed that guinea pig and rat PV cardiomyocytes possessed sizeable amplitudes of the Ih, and the Ih of guinea pig was suppressed by Cs+, a blocker of the hyperpolarization-activated cation current. However, the Ih of rat was not suppressed by Cs+, but by Cd2+, a blocker of the Cl− current. The current density of the Ih of rabbit PV cardiomyocytes was significantly smaller than those of other species. This suggests that the ion channels that carry the Ih of PV cardiomyocytes differ among the animal species.

Exercise has been reported to induce autophagy. We hypothesized that exercise preconditioning (EP)-related autophagy in cardiomyocytes could be attributed to intermittent ischemia–hypoxia, allowing the heart to be protected for subsequent high-intensity exercise (HE). We applied approaches, chromotrope-2R brilliant green (C-2R BG) staining and plasma cTnI levels measuring, to characterize two periods of cardioprotection after EP: early EP (EEP) and late EP (LEP). Further addressing the relationship between ischemia–hypoxia and autophagy, key proteins, Beclin1, LC3, Cathepsin D, and p62, were determined by immunohistochemical staining, western blotting, and by their adjacent slices with C-2R BG. Results indicated that exercise-induced ischemia–hypoxia is a key factor in Beclin1-dependent autophagy. High-intensity exercise was associated with the impairment of autophagy due to high levels of LC3II and unchanged levels of p62, intermittent ischemia–hypoxia by EP itself plays a key role in autophagy, which resulted in more favorable cellular effects during EEP-cardioprotection compared to LEP.

Experiments on animal hearts (rat, rabbit, guinea pig, etc.) have demonstrated that mechano-calcium feedback (MCF) and mechano-electric feedback (MEF) are very important for myocardial self-regulation because they adjust the cardiomyocyte contractile function to various mechanical loads and to mechanical interactions between heterogeneous myocardial segments in the ventricle walls. In in vitro experiments on these animals, MCF and MEF manifested themselves in several basic classical phenomena (e.g., load dependence, length dependence of isometric twitches, etc.), and in the respective responses of calcium transients and action potentials. However, it is extremely difficult to study simultaneously the electrical, calcium, and mechanical activities of the human heart muscle in vitro. Mathematical modeling is a useful tool for exploring these phenomena. We have developed a novel model to describe electromechanical coupling and mechano-electric feedbacks in the human cardiomyocyte. It combines the 'ten Tusscher-Panfilov' electrophysiological model of the human cardiomyocyte with our module of myocardium mechanical activity taken from the 'Ekaterinburg-Oxford' model and adjusted to human data. Using it, we simulated isometric and afterloaded twitches and effects of MCF and MEF on excitation-contraction coupling. MCF and MEF were found to affect significantly the duration of the calcium transient and action potential in the human cardiomyocyte model in response to both smaller afterloads as compared to bigger ones and various mechanical interventions applied during isometric and afterloaded twitches. © 2020 The Author(s). Russian Foundation for Basic Research, RFBR: 18‑01‑00059 The work was carried out within the framework of the IIP UrB RAS themes (Nos. AAAA‑A18‑118020590031‑8, AAAA‑A18‑118020590134‑6) and was supported by RFBR (18‑01‑00059) and by Act 211 Government of the Russian Federation, contract No. 02.A03.21.0006.

// Yuzo Yamazato 1, * , Atsushi Shiozaki 1, * , Daisuke Ichikawa 1, 2 , Toshiyuki Kosuga 1 , Katsutoshi Shoda 1 , Tomohiro Arita 1 , Hirotaka Konishi 1 , Shuhei Komatsu 1 , Takeshi Kubota 1 , Hitoshi Fujiwara 1 , Kazuma Okamoto 1 , Mitsuo Kishimoto 3 , Eiichi Konishi 3 , Yoshinori Marunaka 4, 5 and Eigo Otsuji 1 1 Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan 2 Department of Gastrointestinal, Breast & Endocrine Surgery, Faculty of Medicine, University of Yamanashi, Chuo, 409-3898, Japan 3 Department of Pathology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan 4 Departments of Molecular Cell Physiology and Bio-Ionomics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan 5 Japan Institute for Food Education and Health, St. Agnes’ University, Kyoto, 602-8013, Japan * These authors have contributed equally to this work Correspondence to: Atsushi Shiozaki, email: shiozaki@koto.kpu-m.ac.jp Keywords: AQP1(aquaporin 1); esophageal squamous cell carcinoma; apoptosis; death receptor signaling; cellular physiology Received: January 22, 2018 Accepted: June 19, 2018 Published: July 06, 2018 ABSTRACT Aquaporin 1 (AQP1) is a membrane protein whose main function is to transfer water across cellular membranes. Recent studies have described important roles for AQP1 in epithelial carcinogenesis and tumor behavior. The objectives of the present study were to investigate the role of AQP1 in the regulation of genes involved in tumor progression and the clinicopathological significance of its expression in esophageal squamous cell carcinoma (ESCC). An immunohistochemical analysis was performed on 50 primary tumor samples underwent esophagectomy. AQP1 was primarily located in the cytoplasm and/or the nuclear membrane of carcinoma cells. The 5-year survival rate of patients with the “cytoplasm dominant” expression of AQP1 (47.1%) was significantly lower than other patients (83.2%). The depletion of AQP1 using siRNA induced apoptosis in TE5 and TE15 cells. The results of microarray analysis revealed that Death receptor signaling pathway-related genes were changed in AQP1-depleted TE5 cells. In conclusion, the results of the present study suggested that the cytoplasm dominant expression of AQP1 is related to a poor prognosis in patients with ESCC, and that it activates tumor progression by affecting Death receptor signaling pathway. These results provide insights into the role of AQP1 as a mediator of and/or a biomarker for ESCC.

Hypotonic solutions can cause painful sensations in nasal and ocular mucosa through molecular mechanisms that are not entirely understood. We clarified the ability of human TRPA1 (hTRPA1) to respond to physical stimulus, and evaluated the response of hTRPA1 to cell swelling under hypotonic conditions. Using a Ca2+-imaging method, we found that modulation of AITC-induced hTRPA1 activity occurred under hypotonic conditions. Moreover, cell swelling in hypotonic conditions evoked single-channel activation of hTRPA1 in a cell-attached mode when the patch pipette was attached after cell swelling under hypotonic conditions, but not before swelling. Single-channel currents activated by cell swelling were also inhibited by a known hTRPA1 blocker. Since pre-application of thapsigargin or pretreatment with the calcium chelator BAPTA did not affect the single-channel activation induced by cell swelling, changes in intracellular calcium concentrations are likely not related to hTRPA1 activation induced by physical stimuli.

Cellular compartmentalization of biochemical processes in eukaryotic cells is critical for many functions including shuttling of reducing equivalents across membranes. Although coordination of metabolic flux between different organelles is vital for cell physiology, its impact on tumor cell survival is not well understood. By using an integrative approach, we have dissected the role of the key metabolic enzymes Malate dehydrogenases (MDH1 and MDH2) to the survival of Non-small Cell Lung Carcinomas. Here, we report that while both the MDH1 (cytosolic) and the MDH2 (mitochondrial) enzymes display elevated levels in patients compared to normal counterparts, only high expression of MDH1 is associated with poor prognosis. We further show that the MDH1 enzymatic activity is significantly higher in NSCLC cells than that of MDH2. Accordingly, genetic depletion of MDH1 leads to significantly higher toxicity than depletion of MDH2. These findings provide molecular insights into the metabolic characteristics of the malate isoenzymes and mark MDH1 as a potential therapeutic target in these tumors.

Orexin-A and -B, and ghrelin are potent orexigenic peptides. The effects of ACT462206, a novel dual orexin receptor antagonist (DORA), on ghrelin-induced feeding were examined in adult male Wistar rats. Hyperphagia induced by the intracerebroventricular (icv) administration of ghrelin was significantly suppressed for at least 2 h by pretreatment with icv administration of DORA. A marked increase was observed in the number of neurons showing Fos immunoreactivity in the paraventricular nucleus, arcuate nucleus and lateral hypothalamic area (LHA), 90 min after icv administration of ghrelin. Pretreatment with DORA significantly decreased the number of Fos-immunoreactive (IR) neurons; however, Fos immunoreactivity remained significantly increased. Double-immunostaining for Fos and orexin-A showed that many orexin-A-IR neurons in the LHA coexisted with Fos immunoreactivity after icv administration of ghrelin, but their number was reduced significantly by DORA pretreatment. These results suggest that centrally administered ghrelin may activate the orexinergic and non-orexinergic pathways responsible for the regulation of feeding.

Circadian clocks regulate much of behavior and physiology, but the mechanisms by which they do so remain poorly understood. While cyclic gene expression is thought to underlie metabolic rhythms, little is known about cycles in cellular physiology. We found that Drosophila insulin-producing cells (IPCs), which are located in the pars intercerebralis and lack an autonomous circadian clock, are functionally connected to the central circadian clock circuit via DN1 neurons. Insulin mediates circadian output by regulating the rhythmic expression of a metabolic gene (sxe2) in the fat body. Patch clamp electrophysiology reveals that IPCs display circadian clock-regulated daily rhythms in firing event frequency and bursting proportion under light:dark conditions. The activity of IPCs and the rhythmic expression of sxe2 are additionally regulated by feeding, as demonstrated by night feeding-induced changes in IPC firing characteristics and sxe2 levels in the fat body. These findings indicate circuit-level regulation of metabolism by clock cells in Drosophila and support a role for the pars intercerebralis in integrating circadian control of behavior and physiology.

Glucose-stimulated insulin secretion (GSIS) by pancreatic β cells is biphasic. However, the physiological significance of biphasic GSIS and its relationship to diabetes are not yet fully understood. This study demonstrated that impaired first-phase GSIS follows fasting, leading to increased blood glucose levels and brain glucose distribution in humans. Animal experiments to determine a possible network between the brain and β cells revealed that fasting-dependent hyperactivation of AMP-activated protein kinase in the hypothalamus inhibited first-phase GSIS by stimulating the α-adrenergic pancreatic nerve. Furthermore, abnormal excitability of this brain-β cell neural axis was involved in diabetes-related impairment of first-phase GSIS in diabetic animals. Finally, pancreatic denervation improved first-phase GSIS and glucose tolerance and ameliorated severe diabetes by preventing β cell loss in diabetic animals. These results indicate that impaired first-phase GSIS is critical for brain distribution of dietary glucose after fasting. Furthermore, β cells in individuals with diabetes mistakenly sense that they are under conditions that mimic prolonged fasting. The present study provides additional insight into both β cell physiology and the pathogenesis of β cell dysfunction in type 2 diabetes., Highlights • Fasting-induced hypothalamic AMPK activation inhibited first-phase GSIS by stimulating the α-adrenergic nerve. • The brain-pancreas neural axis was involved in β cell dysfunction and glucose intolerance in diabetes. • Pancreatic denervation improved first-phase GSIS, glucose tolerance and β cell survival in type 2 diabetic animals. Glucose-stimulated insulin secretion (GSIS) from pancreatic β cells is biphasic. Furthermore, first-phase GSIS is inhibited in type 2 diabetes. This study revealed that fasting reduced first-phase GSIS by signaling via the brain-pancreatic β cell neural axis, which is essential for maintaining glucose supply to the brain at re-feeding after fasting. Abnormal excitability of this neural axis was also associated with impaired first-phase GSIS in type 2 diabetes. Surgical pancreatic denervation improved diabetes in an animal study. The present data reveal that diabetic β cells exist under conditions that mimic starvation and provide a therapeutic potency of pancreatic denervation against diabetes., Graphical Abstract Image 2

Abnormal loading of a joint's ligamentous capsule causes pain by activating the capsule's nociceptive afferent fibers, which reside in the capsule's collagenous matrix alongside fibroblast-like synoviocytes (FLS) and transmit pain to the dorsal root ganglia (DRG). This study integrated FLS into a DRG-collagen gel model to better mimic the anatomy and physiology of human joint capsules; using this new model, the effect of FLS on multiscale biomechanics and cell physiology under load was investigated. Primary FLS cells were co-cultured with DRGs at low or high concentrations, to simulate variable anatomical FLS densities, and failed in tension. Given their roles in collagen degradation and nociception, matrix-metalloproteinase (MMP-1) and neuronal expression of the neurotransmitter substance P were probed after gel failure. The amount of FLS did not alter (p > 0.3) the gel failure force, displacement, or stiffness. FLS doubled regional strains at both low (p

Brain slices have been the workhorse for many neuroscience labs since the pioneering work of Henry McIlwain in the 1950s. Their utility is undisputed and their acceptance as appropriate models for the central nervous system is widespread, if not universal. However, the skeleton in the closet is that ATP levels in brain slices are lower than those found in vivo, which may have important implications for cellular physiology and plasticity. Far from this being a disadvantage, the ATP-impoverished slice can serve as a useful and experimentally-tractable surrogate for the injured brain, which experiences similar depletion of cellular ATP. We have shown that the restoration of cellular ATP in brain slices to in vivo values is possible with a simple combination of d-ribose and adenine (RibAde), two substrates for ATP synthesis. Restoration of ATP in slices to physiological levels has implications for synaptic transmission and plasticity, whilst in the injured brain in vivo RibAde shows encouraging positive results. Given that ribose, adenine, and a third compound, allopurinol, are all separately in use in man, their combined application after acute brain injury, in accelerating ATP synthesis and increasing the reservoir of the neuroprotective metabolite, adenosine, may help reduce the morbidity associated with stroke and traumatic brain injury.\ud \ud

The system (PTTRS) formed by typical 2-Cys peroxiredoxins (Prx), thioredoxin (Trx), Trx reductase (TrxR), and sulfiredoxin (Srx) is central in antioxidant protection and redox signaling in the cytoplasm of eukaryotic cells. Understanding how the PTTRS integrates these functions requires tracing phenotypes to molecular properties, which is non-trivial. Here we analyze this problem based on a model that captures the PTTRS’ conserved features. We have mapped the conditions that generate each distinct response to H2O2 supply rates (vsup), and estimated the parameters for thirteen human cell types and for Saccharomyces cerevisiae. The resulting composition-to-phenotype map yielded the following experimentally testable predictions. The PTTRS permits many distinct responses including ultra-sensitivity and hysteresis. However, nearly all tumor cell lines showed a similar response characterized by limited Trx-S- depletion and a substantial but self-limited gradual accumulation of hyperoxidized Prx at high vsup. This similarity ensues from strong correlations between the TrxR, Srx and Prx activities over cell lines, which contribute to maintain the Prx-SS reduction capacity in slight excess over the maximal steady state Prx-SS production. In turn, in erythrocytes, hepatocytes and HepG2 cells high vsup depletes Trx-S- and oxidizes Prx mainly to Prx-SS. In all nucleated human cells the Prx-SS reduction capacity defined a threshold separating two different regimes. At sub-threshold vsup the cytoplasmic H2O2 concentration is determined by Prx, nM-range and spatially localized, whereas at supra-threshold vsup it is determined by much less active alternative sinks and μM-range throughout the cytoplasm. The yeast shows a distinct response where the Prx Tsa1 accumulates in sulfenate form at high vsup. This is mainly due to an exceptional stability of Tsa1's sulfenate. The implications of these findings for thiol redox regulation and cell physiology are discussed. All estimates were thoroughly documented and provided, together with analytical approximations for system properties, as a resource for quantitative redox biology., Graphical abstract fx1, Highlights • A simple model maps cells’ protein composition to responses to H2O2 supply. • Most human cell lines are predicted to show a similar response to H2O2. • This similarity is due to protein concentrations being correlated over cell lines. • The yeast is predicted to show a response that is distinct from human cells’. • Capacity for PrxSS reduction sets a threshold separating distinct signaling regimes.

The MC1R gene plays a crucial role in pigmentation synthesis. Loss-of-function MC1R variants, which impair protein function, are associated with red hair color (RHC) phenotype and increased skin cancer risk. Cultured cutaneous cells bearing loss-of-function MC1R variants show a distinct gene expression profile compared to wild-type MC1R cultured cutaneous cells. We analysed the gene signature associated with RHC co-cultured melanocytes and keratinocytes by Protein-Protein interaction (PPI) network analysis to identify genes related with non-functional MC1R variants. From two detected networks, we selected 23 nodes as hub genes based on topological parameters. Differential expression of hub genes was then evaluated in healthy skin biopsies from RHC and black hair color (BHC) individuals. We also compared gene expression in melanoma tumors from individuals with RHC versus BHC. Gene expression in normal skin from RHC cutaneous cells showed dysregulation in 8 out of 23 hub genes (CLN3, ATG10, WIPI2, SNX2, GABARAPL2, YWHA, PCNA and GBAS). Hub genes did not differ between melanoma tumors in RHC versus BHC individuals. The study suggests that healthy skin cells from RHC individuals present a constitutive genomic deregulation associated with the red hair phenotype and identify novel genes involved in melanocyte biology.

Dietary fiber intake is linked to a reduced risk of colon cancer. This effect may in part be due to butyrate, the fermentation product of fiber in the colon. Butyrate is a short-chain fatty acid that acts as a histone deacetylase inhibitor (HDACi). Butyrate induces apoptosis and represses clonal growth of colorectal cancer (CRC) cells, in a manner dependent upon the hyperactivation of Wnt /beta-catenin signaling. While fiber has been linked to CRC prevention, in vitro studies on the action of butyrate have used CRC cell lines, instead of cells representative of earlier stages of colonic neoplasia, which are the likely target of butyrate-mediated preventive activity. The LT97 cell line is derived from a microadenoma, the earliest stage of colonic neoplasia from which cells can be isolated. We characterized LT97 cells with respect to effects of butyrate on Wnt signaling and apoptosis, and we determined whether modulation of CREB binding protein (CBP)/p300 activity influences the ability of butyrate to induce Wnt activity and apoptosis. We report that in LT97 cells, butyrate induces apoptosis, strongly upregulates Wnt signaling, and the upregulation of Wnt signaling is dependent upon CBP/p300 activity. In addition, findings from overexpression experiments suggest differences between CBP and p300 in their ability to influence Wnt signaling in LT97 cells; p300, but not CBP, stimulates basal Wnt activity. We also evaluated differences in gene expression between early stage LT97 cells and late stage metastatic SW620 CRC cells that exhibit markedly different cellular phenotypes. The comparative gene expression analyses revealed differences that may impact neoplastic progression and the sensitivity to the effects of butyrate. The findings have implications for the prevention of CRC by fiber/butyrate.

The cellulose binding domain (CBD) of cellulase binding to cellulosic materials is the initiation of a synergistic action on the enzymatic hydrolysis of the most abundant renewable biomass resources in nature. The binding of the CBD domain to cellulosic substrates generally relies on the interaction between the aromatic amino acids structurally located on the flat face of the CBD domain and the glucose rings of cellulose. In this study, we found the CBD domain of a newly cloned Penicillium crustosum endoglucanase EGL1, which was phylogenetically related to Aspergillus, Fusarium and Rhizopus, and divergent from the well-characterized Trichoderma reeseis cellulase CBD domain, contain two conserved aromatic amino acid-rich regions, Y451-Y452 and Y477-Y478-Y479, among which three amino acids Y451, Y477, and Y478 structurally sited on a flat face of this domain. Cellulose binding assays with green fluorescence protein as the marker, adsorption isotherm assays and an isothermal titration calorimetry assays revealed that although these three amino acids participated in this process, the Y451-Y452 appears to contribute more to the cellulose binding than Y477-Y478-Y479. Further glycine scanning mutagenesis and structural modelling revealed that the binding between CBD domain and cellulosic materials might be multi-amino-acids that participated in this process. The flexible poly-glucose molecule could contact Y451, Y477, and Y478 which form the contacting flat face of CBD domain as the typical model, some other amino acids in or outside the flat face might also participate in the interaction. Thus, it is possible that the conserved Y451-Y452 of CBD might have a higher chance of contacting the cellulosic substrates, contributing more to the affinity of CBD than the other amino acids.

Endo-s-1,4-glucanase AkEG21 belonging to glycosyl hydrolase family 45 (GHF45) is the most abundant cellulase in the digestive fluid of sea hare (Aplysia kurodai). The specific activity of this 21-kDa enzyme is considerably lower than those of other endo s-1,4-glucanases in the digestive fluid of A. kurodai, therefore its role in whole cellulose hydrolysis by sea hare is still uncertain. Although AkEG21 has a catalytic domain without a cellulose binding domain, it demonstrated stable binding to cellulose fibers, similar to that of fungal cellobiohydrolase (CBH) 1 and CBH 2, which is strongly inhibited by cellohexaose, suggesting the involvement of the catalytic site in cellulose binding. Cellulose-bound AkEG21 hydrolyzed cellulose to cellobiose, cellotriose and cellotetraose, but could not digest an external substrate, azo-carboxymethyl cellulose. Cellulose hydrolysis was considerably stimulated by the synergistic action of cellulose-bound AkEG21 and AkEG45, another s-1,4-endoglucanase present in the digestive fluid of sea hare; however no synergy in carboxymethylcellulose hydrolysis was observed. When AkEG21 was removed from the digestive fluid by immunoprecipitation, the cellulose hydrolyzing activity of the fluid was significantly reduced, indicating a critical role of AkEG21 in cellulose hydrolysis by A. kurodai. These findings suggest that AkEG21 is a processive endoglucanase functionally equivalent to the CBH, which provides a CBH-independent mechanism for the mollusk to digest seaweed cellulose to glucose.

Mutations in the WNT/beta-catenin pathway are responsible for initiating the majority of colorectal cancers (CRCs). We have previously shown that hyperactivation of this signaling by histone deacetylase inhibitors (HDACis) such as butyrate, a fermentation product of dietary fiber, promotes CRC cell apoptosis. The extent of association between beta-catenin and the transcriptional coactivator CREB-binding protein (CBP) influences WNT/catenin signaling and, therefore, colonic cell physiology. CBP functions as a histone acetylase (HAT); therefore, we hypothesized that the modulation of WNT/catenin activity by CBP modifies the ability of the HDACi butyrate to hyperinduce WNT signaling and apoptosis in CRC cells. Our findings indicate that CBP affects the hyperinduction of WNT activity by butyrate. ICG-001, which specifically blocks association between CBP and beta-catenin, abrogates the butyrate-triggered increase in the number of CRC cells with high levels of WNT/catenin signaling. Combination treatment of CRC cells with ICG-001 and butyrate results in cell type-specific effects on apoptosis. Further, both butyrate and ICG-001 repress CRC cell proliferation, with additive effects in suppressing cell growth. Our study strongly suggests that ICG-001-like agents would be effective against butyrate/HDACi-resistant CRC cells. Therefore, ICG-001-like agents may represent an important therapeutic option for CRCs that exhibit low-fold hyperactivation of WNT activity and apoptosis in the presence of HDACis. The findings generated from this study may lead to approaches that utilize modulation of CBP activity to facilitate CRC therapeutic or chemopreventive strategies.

// Florian Alonso 1, * , Sonia Domingos-Pereira 2, * , Loic Le Gal 1 , Laurent Derre 2 , Paolo Meda 3 , Patrice Jichlinski 2 , Denise Nardelli-Haefliger 2, # , Jacques-Antoine Haefliger 1, # 1 Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland 2 Department of Urology, Lausanne University Hospital, Lausanne, Switzerland 3 Department of Cell Physiology and Metabolism, University of Geneva, Medical Center, Geneva, Switzerland * Contributed equally to this work as first authors # Contributed equally to this work as senior authors Correspondence to: Jacques-Antoine Haefliger, e-mail: Jacques-Antoine.Haefliger@chuv.ch Keywords: cell-cell communication, connexins, angiogenesis, tumors, transgenic mice Received: October 19, 2015 Accepted: January 29, 2016 Published: February 13, 2016 ABSTRACT Endothelial connexin40 (Cx40) contributes to regulate the structure and function of vessels. We have examined whether the protein also modulates the altered growth of vessels in tumor models established in control mice (WT), mice lacking Cx40 (Cx40–/–), and mice expressing the protein solely in endothelial cells (Tie2-Cx40). Tumoral angiogenesis and growth were reduced, whereas vessel perfusion, smooth muscle cell (SMC) coverage and animal survival were increased in Cx40–/– but not Tie2-Cx40 mice, revealing a critical involvement of endothelial Cx40 in transformed tissues independently of the hypertensive status of Cx40–/– mice. As a result, Cx40–/– mice bearing tumors survived significantly longer than corresponding controls, including after a cytotoxic administration. Comparable observations were made in WT mice injected with a peptide targeting Cx40, supporting the Cx40 involvement. This involvement was further confirmed in the absence of Cx40 or by peptide-inhibition of this connexin in aorta-sprouting, matrigel plug and SMC migration assays, and associated with a decreased expression of the phosphorylated form of endothelial nitric oxide synthase. The data identify Cx40 as a potential novel target in cancer treatment.

Replicative cellular senescence was discovered some 50 years ago. The phenotypes of senescent cells have been investigated extensively in cell culture, and found to affect essentially all aspects of cellular physiology. The relevance of cellular senescence in the context of age-associated pathologies as well as normal aging is a topic of active and ongoing interest. Considerable effort has been devoted to biomarker discovery to enable the microscopic detection of single senescent cells in tissues. One characteristic of senescent cells documented very early in cell culture studies was an increase in cell size and total protein content, but whether this occurs in vivo is not known. A limiting factor for studies of protein content and localization has been the lack of suitable fluorescence microscopy tools. We have developed an easy and flexible method, based on the merocyanine dye known as NanoOrange, to visualize and quantitatively measure total protein levels by high resolution fluorescence microscopy. NanoOrange staining can be combined with antibody-based immunofluorescence, thus providing both specific target and total protein information in the same specimen. These methods are optimally combined with automated image analysis platforms for high throughput analysis. We document here increasing protein content and density in nuclei of senescent human and mouse fibroblasts in vitro, and in liver nuclei of aged mice in vivo. Additionally, in aged liver nuclei NanoOrange revealed protein-dense foci that colocalize with centromeric heterochromatin.

Previous investigations suggested that lamin A/C gene (LMNA) mutations, which cause a variety of human diseases including muscular dystrophies and cardiomyopathies, alter the nuclear mechanical properties. We hypothesized that biomechanical changes may extend beyond the nucleus. Combining atomic force microscopy (AFM), molecular and cellular biology, we studied the biomechanical properties of cardiomyocytes expressing the cardiomyopathy LMNA D192G mutation, and attempted rescue through the subsequent introduction of wild-type LMNA. Neonatal rat ventricular myocytes (NRVMs) were infected with adenoviral vectors carrying either human LMNA wild-type or D192G gene. LMNA protein expression was confirmed up to day 6 by western blot. Live-cell AFM force-deformation curves from day 1 through day 6 showed that the nuclei of NRVMs expressing LMNA D192G displayed increased stiffness compared to both uninfected and wild-type expressing cells, with a peak at 48 hours (3-fold increase in nuclear Young modulus, p

Aneuploidy, defined as an alteration in chromosome number that is not a multiple of the haploid complement, severely affects cellular physiology. Changes in chromosome number lead to imbalances in cellular protein composition, thus disrupting cellular processes and causing proteins to misfold and aggregate. We recently reported that in mammalian cells protein aggregates are readily encapsulated within autophagosomes but are not degraded by lysosomes. This leads to a lysosomal stress response in which the transcription factor TFEB induces expression of factors needed for macroautophagy-mediated protein degradation. Our studies uncover lysosomal degradation defects as a feature of the aneuploid state, and a role for the transcription factor TFEB in the response thereto. Keywords: aneuploidy; autophagy; cancer; proteotoxicity; TFEB

Angiogenesis is the process by which new blood vessels sprout from existing blood vessels, enabling new vascular elements to be added to an existing vasculature. This review discusses our investigations into the role of cell-matrix mechanics in the mechanical regulation of angiogenesis. The experimental aspects of the research are based on in vitro experiments using an organ culture model of sprouting angiogenesis with the goal of developing new treatments and techniques to either promote or inhibit angiogenic outgrowth, depending on the application. Computational simulations were performed to simulate angiogenic growth coupled to matrix deformation, and live two-photon microscopy was used to obtain insight into the dynamic mechanical interaction between angiogenic neovessels and the extracellular matrix. In these studies, we characterized how angiogenic neovessels remodel the extracellular matrix (ECM) and how properties of the matrix such as density and boundary conditions influence vascular growth and alignment. Angiogenic neovessels extensively deform and remodel the matrix through a combination of applied traction, proteolytic activity, and generation of new cell-matrix adhesions. The angiogenic phenotype within endothelial cells is promoted by ECM deformation and remodeling. Sensitivity analysis using our finite element model of angiogenesis suggests that cell-generated traction during growth is the most important parameter controlling the deformation of the matrix and, therefore, angiogenic growth and remodeling. Live two-photon imaging has also revealed numerous neovessel behaviors during angiogenesis that are poorly understood such as episodic growth/regression, neovessel colocation, and anastomosis. Our research demonstrates that the topology of a resulting vascular network can be manipulated directly by modifying the mechanical interaction between angiogenic neovessels and the matrix.

Deregulated WNT/catenin pathway, usually resulting from mutations in the adenomatous polyposis coli and beta-catenin genes, drives colorectal tumorigenesis. Dietary fiber has been shown to have a protective role against colorectal cancer (CRC). We have previously demonstrated that the histone deacetylase inhibitor (HDACi) butyrate, a fermentation product of dietary fiber, induces WNT/catenin hyperactivation, which promotes CRC cell apoptosis. Therefore, the ability of butyrate to induce WNT hyperactivation and thus promote CRC cell apoptosis may in part explain the preventive function of fiber against CRC. The association between beta-catenin and the transcriptional coactivator p300 may influence WNT/catenin signaling and, therefore, colonic cell physiology. p300 functions as a histone acetylase (HAT); therefore, the modulation of WNT/catenin activity by p300 may influence the ability of the HDACi butyrate to hyperinduce WNT signaling and apoptosis in CRC cells. Our findings indicate that p300 affects the hyperinduction of WNT activity by butyrate. Knockdown of p300 levels represses butyrate-mediated WNT/catenin activity; but still allows for butyrate-mediated apoptosis. Overexpression of p300 stimulates basal and butyrate-induced WNT signaling in some, but not all, CRC cell lines. We also evaluate the role of p300 in therapeutic approaches that target CBP. The small molecule ICG-001, in clinical trial, is a specific inhibitor of CBP-mediated WNT signaling, and previous studies have suggested that p300 is required for the activity of ICG-001. However, we report that ICG-001 maintains full activity against CBP-mediated WNT signaling in p300-deficient cell lines, including the butyrate-resistance line HCT-R. In addition, our findings evaluating combinatorial treatment of ICG-001 and butyrate in HCT-R cells may have important therapeutic implications for the treatment of butyrate-resistant CRCs.

The biogenic methylation of inorganic, divalent mercury (Hg(II)) by methylating microorganisms leads to formation and bioaccumulation of monomethyl mercury (MeHg) in the environment and can cause severe damage to ecosystems and human health. Diverse microorganisms carry the gene sequence hgcAB and are able to methylate Hg(II) intracellularly. The interplay of biological, chemical and physical parameters is driving mercury (Hg) transformation by microorganisms. The chemical speciation of Hg(II) with thiol compounds, both with dissolved low molecular mass (LMM) thiols and thiols present on microbial membrane surfaces, is one key factor for Hg availability and transformation. In this work the role of thiol compounds with respect to Hg speciation, uptake and transformation was studied by the iron-reducing model organisms Geobacter sulfurreducens. The turnover of dissolved thiols and the role of outer and inner membrane thiols was studied with novel experimental strategies. In Paper I and II the formation of thiol compounds was studied under varying nutrient conditions. It was shown that the formation of LMM-thiol compounds was impacted by divalent iron, Fe(II). Furthermore, we showed the turnover of the small LMM-thiol cysteine to the branched LMM-thiol penicillamine, which was further amplified by the addition of exogenous cysteine or nutrients. This turnover of small to branched LMM-thiols impacted the Hg(II) speciation in methylation assays and the relative contribution between cysteine and penicillamine was important for Hg(II) availability, uptake and methylation. In addition, the partition of Hg(II) between the cell-adsorbed and dissolved phase was shifted towards the latter at higher LMM-thiol concentrations. Nutrient concentrations impacted cell physiology due to a shift to an active metabolism and a faster metabolization of LMM-thiols. We concluded that the interplay between thiol metabolism, Hg(II) speciation and cell physiology are key parameters for Hg(II) methylation by G. sulfurreducens. In Paper III The outer and inner membrane was characterized independently by two X-ray absorption spectroscopy techniques. The determination of the Hg speciation by both X-ray absorption spectroscopy techniques showed coherent results for both the outer and inner membrane of G. sulfurreducens. The concentration of thiol membrane groups was higher on the inner compared to the outer membrane. The differences between the outer and inner membrane suggested that thiol concentration and Hg coordination environment likely impact the Hg(II) internalization. The role of membrane thiols for Hg(II) uptake and transformation was further investigated in Paper IV by selectively blocking these functional groups. Partitioning and uptake of Hg was not affected by blocking the outer and inner membrane thiols of whole cell and spheroplast samples, respectively. However, the Hg(II) methylation was decreased by blocking thiols at the outer membrane, but no effect was observed by blocking thiols at the inner membrane. Blocking of membrane surface thiols changed the physiology in whole cells but not in spheroplasts. This result suggested weaknesses of the applied blocking approach. In addition, Hg(II) reduction was studied on the outer and inner membrane and showed the formation of liquid and gaseous elemental Hg, Hg(0), in Paper III and IV, respectively. Overall, this work showed the central role of dissolved and cell-associated thiol compounds for Hg(II) uptake and the transformation reactions. Herby, concentration, compositions and distribution of thiols are crucial and impact the Hg(II) speciation, partitioning, uptake and availability for Hg(II) methylation and reduction. In addition, cell physiology is impacting the methylation potential and the turnover of LMM-thiol compounds. The role of membrane surface thiols for Hg(II) uptake was not fully identified, however such thiols were for the first time characterized selectively for the outer and inner membrane by X-ray absorption spectroscopy.

Inorganic polyphosphate (PolyP) is a biological polymer that plays important roles in the cell physiology of both prokaryotic and eukaryotic organisms. Among the available methods for PolyP localization and quantification, a 4',6-diamidino-2-phenylindole(DAPI)-based assay has been used for visualization of PolyP-rich organelles. Due to differences in DAPI permeability to different compartments and/or PolyP retention after fixation, a general protocol for DAPI-PolyP staining has not yet been established. Here, we tested different protocols for DAPI-PolyP detection in a range of samples with different levels of DAPI permeability, including subcellular fractions, free-living cells and cryosections of fixed tissues. Subcellular fractions of PolyP-rich organelles yielded DAPI-PolyP fluorescence, although those with a complex external layer usually required longer incubation times, previous aldehyde fixation and/or detergent permeabilization. DAPI-PolyP was also detected in cryosections of OCT-embedded tissues analyzed by multi-photon microscopy. In addition, a semi-quantitative fluorimetric analysis of DAPI-stained fractions showed PolyP mobilization in a similar fashion to what has been demonstrated with the use of enzyme-based quantitative protocols. Taken together, our results support the use of DAPI for both PolyP visualization and quantification, although specific steps are suggested as a general guideline for DAPI-PolyP staining in biological samples with different degrees of DAPI and PolyP permeability.

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

Early embryonic rodent ventricular cells exhibit spontaneous action potential (AP), which disappears in later developmental stages. Here, we used 3 mathematical models—the Kyoto, Ten Tusscher–Panfilov, and Luo–Rudy models—to present an overview of the functional landscape of developmental changes in embryonic ventricular cells. We switched the relative current densities of 9 ionic components in the Kyoto model, and 160 of 512 representative combinations were predicted to result in regular spontaneous APs, in which the quantitative changes in Na+ current (INa) and funny current (If) made large contributions to a wide range of basic cycle lengths. In all three models, the increase in inward rectifier current (IK1) before the disappearance of If was predicted to result in abnormally high intracellular Ca2+ concentrations. Thus, we demonstrated that the developmental changes in APs were well represented, as INa increased before the disappearance of If, followed by a 10-fold increase in IK1. Electronic supplementary material The online version of this article (doi:10.1007/s12576-013-0271-x) contains supplementary material, which is available to authorized users.

Rapid lowering of the solution temperature (rapid cooling, RC) from 24 to 3°C within 3 s releases considerable amounts of Ca(2+) from the sarcoplasmic reticulum (SR) in mammalian cardiac muscles. In this study, we investigated the intracellular mechanism of RC-induced Ca(2+) release, especially the role of Ca(2+), in ferret ventricular muscle. Saponin-treated skinned trabeculae were placed in a glass capillary, and the amount of Ca(2+) released from the SR by RC and caffeine (50 mM) was measured with fluo-3. It was estimated that in the presence of ATP about 45% of the Ca(2+) content in the SR was released by RC. The amount of SR Ca(2+) released by RC was unchanged by the replacement of ATP by AMP-PCP (a non-hydrolysable ATP analogue and agonist for the ryanodine receptor but not for the Ca(2+) pump of SR), suggesting that the suppression of the Ca(2+) pump of SR at low temperature might not be a major mechanism in RC-induced Ca(2+) release. The free Ca(2+) concentration of the solution used for triggering RC-induced Ca(2+) release was estimated to be only about 20 nM with fluo-3 or aequorin. When this solution was applied to the preparation at 3°C, only a small amount of Ca(2+) was released from SR presumably by the Ca(2+)-induced Ca(2+) release (CICR) mechanism. Thus, in mammalian cardiac muscles, RC releases a part of the (50%) stored Ca(2+) contained in the SR, and the mechanism of RC-induced Ca(2+) release may differ from that of CICR, which is thought to play a role in frog skeletal muscle fibres that express ryanodine receptors of different types.

This paper is a literature review about electromagnetic field’s effects on cells, tissues and new treatment modalities. We have compiled the papers which have been published in well qualited journals in the last 5 years as two authors. This review’s aim is to be a resource for experimental studies about electricity’s effects on cell biology and pathophysiology. As a result of literature review, we found that especially extremely low electric frequency and intermediate frequency fields have very important pathophysiological effects. We have mentioned about four important expressions on this subject; electroporation, electrofusion, electrochemotherapy, gene electrotransference. Two different new treatment approaches have been developed by use of these two important frequency waves. First is tumor treating fields and the other is pulsed electric fields. Most studies in literature have been done with extremely low frequency and pulsed electric fields. In terms of diseases, most studies are about glioblastoma and melanoma., {"references":["1)Pasachoff, (2015) The history of electromagnetic theory through the lives of its founders,N. Metascience, 24: 233. https://doi.org/10.1007/s11016-014-9982-8","2)Kazamel M1, Warren PP2, (2017)History of electromyography and nerve conduction studies:A tribute to the founding fathers. J Clin Neurosci. 2017 Sep;43:54-60. doi: 10.1016/j.jocn.2017.05.018.","3)W. Ragsdale, A triz. Yan Wang and Clifton (2019), Cephalopod Nervous System Organization Subject: Invertebrate Neuroscience, DOI: 10.1093/acrefore/9780190264086.013.181","4)Chrysafides SM, Sharma S. (2019) Physiology, Resting Potential. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2019 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK538338/","5)Giladi, Rosa S, Voloshin, (December 2015) Mitotic Spindle Disruption by Alternating Electric Fields Leads to Improper Chromosome Segregation and Mitotic Catastrophe in Cancer Cells https://doi.org/10.1038/srep1804610.1038/srep18046 https://www.nature.com/articles/srep18046#supplementary-information","6)Song, K., Im, S. H., Yoon, Y. J., Kim, H. M., Lee, H. J., & Park, G. S. (2018). A 60 Hz uniform electromagnetic field promotes human cell proliferation by decreasing intracellular reactive oxygen species levels. PloS one, 13(7), e0199753. doi:10.1371/journal.pone.0199753","7)Crespi, C. M., Vergara, X. P., Hooper, C., Oksuzyan, S., Wu, S., Cockburn, M., & Kheifets, L. (2016). Childhood leukaemia and distance from power lines in California: a population-based case-control study. British journal of cancer, 115(1), 122–128. doi:10.1038/bjc.2016.142","8)Fenga, C. (2016). Occupational exposure and risk of breast cancer . Biomedical Reports, 4, 282-292. https://doi.org/10.3892/br.2016.575","9) Panagopoulos D, Johansson, Carlo, (2015) Polarization: A Key Difference between Man-made and Natural Electromagnetic Fields, in regard to Biological Activity, Scientific Reports, 14914 https://doi.org/10.1038/srep14914","10)Burri, S. H., Gondi, V., Brown, P. D., & Mehta, M. P. (2018). The Evolving Role of Tumor Treating Fields in Managing Glioblastoma: Guide for Oncologists. American journal of clinical oncology, 41(2), 191–196. doi:10.1097/COC.0000000000000395","11)Trusheim, J., Dunbar, E., Battiste, J., Iwamoto, F., Mohile, N., Damek, D., … Connelly, J. (2017). A state-of-the-art review and guidelines for tumor treating fields treatment planning and patient follow-up in glioblastoma. CNS oncology, 6(1), 29–43. doi:10.2217/cns-2016-0032","12)Varani, K., Vincenzi, F., Ravani, A., Pasquini, S., Merighi, S., Gessi, S., … Cadossi, R. (2017). Adenosine Receptors as a Biological Pathway for the Anti-Inflammatory and Beneficial Effects of Low Frequency Low Energy Pulsed Electromagnetic Fields. Mediators of inflammation, 2017, 2740963. doi:10.1155/2017/2740963","13)Manser, M., Sater, M. R., Schmid, C. D., Noreen, F., Murbach, M., Kuster, N., … Schär, P. (2017). ELF-MF exposure affects the robustness of epigenetic programming during granulopoiesis. Scientific reports, 7, 43345. doi:10.1038/srep43345","14)Vincenzi, F., Targa, M., Corciulo, C., Gessi, S., Merighi, S., Setti, S., … Varani, K. (2013). Pulsed electromagnetic fields increased the anti-inflammatory effect of A₂A and A₃ adenosine receptors in human T/C-28a2 chondrocytes and hFOB 1.19 osteoblasts. PloS one, 8(5), e65561. doi:10.1371/journal.pone.0065561","15) Watson, T. C., Obiang, P., Torres-Herraez, A., Watilliaux, A., Coulon, P., Rochefort, C., & Rondi-Reig, L. (2019). Anatomical and physiological foundations of cerebello-hippocampal interaction. eLife, 8, e41896. doi:10.7554/eLife.41896","16) Du, E; Qiang, Yuhao; Liu, Jia. (2018.) \"Erythrocyte Membrane Failure by Electromechanical Stress.\" Appl. Sci. 8, no. 2: 174.","17)Zhang, Y., Dong, F., Liu, Z., Guo, J., Zhang, J., & Fang, J. (2018). Nanosecond pulsed electric fields promoting the proliferation of porcine iliac endothelial cells: An in vitro study. PloS one, 13(5), e0196688. doi:10.1371/journal.pone.0196688","18) Grys, M., Madeja, Z., & Korohoda, W. (2017). Avoiding the side effects of electric current pulse application to electroporated cells in disposable small volume cuvettes assures good cell survival. Cellular & molecular biology letters, 22, 1. doi:10.1186/s11658-016-0030-0","19)Muratori, C., Pakhomov, A. G., Heller, L., Casciola, M., Gianulis, E., Grigoryev, Pakhomova, O. N. (2017). Electrosensitization Increases Antitumor Effectiveness of Nanosecond Pulsed Electric Fields In Vivo. Technology in cancer research & treatment, 16(6), 1533034617712397. Advance online publication. doi:10.1177/1533034617712397","20)Steuer, A., Wolff, C. M., von Woedtke, T., Weltmann, K. D., & Kolb, J. F. (2018). Cell stimulation versus cell death induced by sequential treatments with pulsed electric fields and cold atmospheric pressure plasma. PloS one, 13(10), e0204916. doi:10.1371/journal.pone.0204916","21)Hummos, A., & Nair, S. S. (2017). An integrative model of the intrinsic hippocampal theta rhythm. PloS one, 12(8), e0182648. doi:10.1371/journal.pone.0182648","22)Iwasa, K., & Reddi, A. H. (2018). Pulsed Electromagnetic Fields and Tissue Engineering of the Joints. Tissue engineering. Part B, Reviews, 24(2), 144–154. doi:10.1089/ten.TEB.2017.0294","23)Dorsey, B. M., Cass, C. L., Cedeño, D. L., Vallejo, R., & Jones, M. A. (2018). Effects of Specific Electric Field Stimulation on the Release and Activity of Secreted Acid Phosphatases from Leishmania tarentolae and Implications for Therapy. Pathogens (Basel, Switzerland), 7(4), 77. doi:10.3390/pathogens7040077","24)Beebe S.J. (2015) Considering effects of nanosecond pulsed electric fields on proteins Bioelectrochemistry, 103 , pp. 52-59.","25)Rosazza, C., Meglic, S. H., Zumbusch, A., Rols, M. P., & Miklavcic, D. (2016). Gene Electrotransfer: A Mechanistic Perspective. Current gene therapy, 16(2), 98–129. doi:10.2174/1566523216666160331130040","26)Morotomi-Yano K., Akiyama H., Yano K.-I. (2014) Different involvement of extracellular calcium in two modes of cell death induced by nanosecond pulsed electric fields, Archives of Biochemistry and Biophysics, 555-556 , pp. 47-54.","27)Hanna, H., Andre, F. M., & Mir, L. M. (2017). Electrical control of calcium oscillations in mesenchymal stem cells using microsecond pulsed electric fields. Stem cell research & therapy, 8(1), 91. doi:10.1186/s13287-017-0536-z","28)Borys P. (2012). On the biophysics of cathodal galvanotaxis in rat prostate cancer cells: Poisson-Nernst-Planck equation approach. European biophysics journal : EBJ, 41(6), 527–534. doi:10.1007/s00249-012-0807-7","29)Steuer, A., Wolff, C. M., von Woedtke, T., Weltmann, K. D., & Kolb, J. F. (2018). Cell stimulation versus cell death induced by sequential treatments with pulsed electric fields and cold atmospheric pressure plasma. PloS one, 13(10), e0204916. doi:10.1371/journal.pone.0204916","30)Hanna, H., Denzi, A., Liberti, M., André, F. M., & Mir, L. M. (2017). Electropermeabilization of Inner and Outer Cell Membranes with Microsecond Pulsed Electric Fields: Quantitative Study with Calcium Ions. Scientific reports, 7(1), 13079. doi:10.1038/s41598-017-12960-w","31)Zhu, P., & Zhu, J. (2017). Tumor treating fields: a novel and effective therapy for glioblastoma: mechanism, efficacy, safety and future perspectives. Chinese Clinical Oncology, 6(4). doi:10.21037/cco.v6i4.16215","32)Mrugala MM, Engelhard HH, Dinh Tran D, et al. (2014) Clinical practice experience with NovoTTF-100A™ system for glioblastoma: The Patient Registry Dataset (PRiDe). Semin Oncol ; 41 Suppl 6:S4.","33)Hottinger, A. F., Pacheco, P., & Stupp, R. (2016). Tumor treating fields: a novel treatment modality and its use in brain tumors. Neuro-oncology, 18(10), 1338–1349. doi:10.1093/neuonc/now182","34)Carr, L., Bardet, S. M., Burke, R. C., Arnaud-Cormos, D., Leveque, P., & O'Connor, R. P. (2017). Calcium-independent disruption of microtubule dynamics by nanosecond pulsed electric fields in U87 human glioblastoma cells. Scientific reports, 7, 41267. doi:10.1038/srep41267","35)Berzingi, S., Newman, M., & Yu, H. G. (2016). Altering bioelectricity on inhibition of human breast cancer cells. Cancer cell international, 16, 72. doi:10.1186/s12935-016-0348-8","36) Pakhomova, O. N., Gregory, B. W., Semenov, I., & Pakhomov, A. G. (2013). Two modes of cell death caused by exposure to nanosecond pulsed electric field. PloS one, 8(7), e70278. doi:10.1371/journal.pone.0070278","37) Yung-Shin, (2017), Studying Electrotaxis in Microfluidic Devices, Sensors, 17(9), 2048; https://doi.org/10.3390/s17092048,","38)Huang, Y. J., Hoffmann, G., Wheeler, B., Schiapparelli, P., Quinones-Hinojosa, A., & Searson, P. (2016). Cellular microenvironment modulates the galvanotaxis of brain tumor initiating cells. Scientific reports, 6, 21583. doi:10.1038/srep21583","39)Huang, Y. J., Schiapparelli, P., Kozielski, K., Green, J., Lavell, E., Guerrero-Cazares, H., … Searson, P. (2017). Electrophoresis of cell membrane heparan sulfate regulates galvanotaxis in glial cells. Journal of cell science, 130(15), 2459–2467. doi:10.1242/jcs.203752","40) Staresinic, B., Jesenko, T., Kamensek, U., Krog Frandsen, S., Sersa, G., Gehl, J., & Cemazar, M. (2018). Effect of calcium electroporation on tumour vasculature. Scientific reports, 8(1), 9412. doi:10.1038/s41598-018-27728-z","41)Kıvrak, E. G., Yurt, K. K., Kaplan, A. A., Alkan, I., & Altun, G. (2017). Effects of electromagnetic fields exposure on the antioxidant defense system. Journal of microscopy and ultrastructure, 5(4), 167–176. doi:10.1016/j.jmau.2017.07.003","42)Kim, E. H., Song, H. S., Yoo, S. H., & Yoon, M. (2016). Tumor treating fields inhibit glioblastoma cell migration, invasion and angiogenesis. Oncotarget, 7(40), 65125–65136. doi:10.18632/oncotarget.11372","43) Wichtowski, M., & Murawa, D. (2018). Electrochemotherapy in the treatment of melanoma. Contemporary Oncology/Współczesna Onkologia, 22(1), 8-13. https://doi.org/10.5114/wo.2018.74387","44)Bian, S., Zhou, Y., Hu, Y., Cheng, J., Chen, X., Xu, Y., & Liu, P. (2017). High-throughput in situ cell electroporation microsystem for parallel delivery of single guide RNAs into mammalian cells. Scientific reports, 7, 42512. doi:10.1038/srep42512","45)Shi, J., Ma, Y., Zhu, J., Chen, Y., Sun, Y., Yao, Y., … Xie, J. (2018). A Review on Electroporation-Based Intracellular Delivery. Molecules (Basel, Switzerland), 23(11), 3044. doi:10.3390/molecules23113044","46)Probst, U., Fuhrmann, I., Beyer, L., & Wiggermann, P. (2018). Electrochemotherapy as a New Modality in Interventional Oncology: A Review. Technology in cancer research & treatment, 17, 1533033818785329. doi:10.1177/1533033818785329","47)Sersa, G., Teissie, J., Cemazar, M., Signori, E., Kamensek, U., Marshall, G., & Miklavcic, D. (2015). Electrochemotherapy of tumors as in situ vaccination boosted by immunogene electrotransfer. Cancer immunology, immunotherapy : CII, 64(10), 1315–1327. doi:10.1007/s00262-015-1724-2","48) Trontelj, K., Usaj, M., & Miklavcic, D. (2010). Cell electrofusion visualized with fluorescence microscopy. Journal of visualized experiments : JoVE, (41), 1991. doi:10.3791/1991","49) Rosazza, C., Meglic, S. H., Zumbusch, A., Rols, M. P., & Miklavcic, D. (2016). Gene Electrotransfer: A Mechanistic Perspective. Current gene therapy, 16(2), 98–129. doi:10.2174/1566523216666160331130040","50)Znidar, K., Bosnjak, M., Semenova, N., Pakhomova, O., Heller, L., & Cemazar, M. (2018). Tumor cell death after electrotransfer of plasmid DNA is associated with cytosolic DNA sensor upregulation. Oncotarget, 9(27), 18665–18681. doi:10.18632/oncotarget.24816","51)Lesueur, L. L., Mir, L. M., & André, F. M. (2016). Overcoming the Specific Toxicity of Large Plasmids Electrotransfer in Primary Cells In Vitro. Molecular therapy. Nucleic acids, 5(3), e291. doi:10.1038/mtna.2016.4"]}

Striatal oscillatory activity is associated with movement, reward, and decision-making, and observed in several interacting frequency bands. Local field potential recordings in rodent striatum show dopamine- and reward-dependent transitions between two states: a “spontaneous” state involving β (∼15-30 Hz) and low γ (∼40-60 Hz), and a state involving θ (∼4-8 Hz) and high γ (∼60-100 Hz) in response to dopaminergic agonism and reward. The mechanisms underlying these rhythmic dynamics, their interactions, and their functional consequences are not well understood. In this paper, we propose a biophysical model of striatal microcircuits that comprehensively describes the generation and interaction of these rhythms, as well as their modulation by dopamine. Building on previous modeling and experimental work suggesting that striatal projection neurons (SPNs) are capable of generating β oscillations, we show that networks of striatal fast-spiking interneurons (FSIs) are capable of generating δ/θ (ie, 2 to 6 Hz) and γ rhythms. Under simulated low dopaminergic tone our model FSI network produces low γ band oscillations, while under high dopaminergic tone the FSI network produces high γ band activity nested within a δ/θ oscillation. SPN networks produce β rhythms in both conditions, but under high dopaminergic tone, this β oscillation is interrupted by δ/θ-periodic bursts of γ-frequency FSI inhibition. Thus, in the high dopamine state, packets of FSI γ and SPN β alternate at a δ/θ timescale. In addition to a mechanistic explanation for previously observed rhythmic interactions and transitions, our model suggests a hypothesis as to how the relationship between dopamine and rhythmicity impacts motor function. We hypothesize that high dopamine-induced periodic FSI γ-rhythmic inhibition enables switching between β-rhythmic SPN cell assemblies representing the currently active motor program, and thus that dopamine facilitates movement in part by allowing for rapid, periodic shifts in motor program execution., Author summary Striatal oscillatory activity is associated with movement, reward, and decision-making, and observed in several interacting frequency bands. The mechanisms underlying these rhythmic dynamics, their interactions, and their functional consequences are not well understood. In this paper, we propose a biophysical model of striatal microcircuits that comprehensively describes the generation and interaction of striatal rhythms, as well as their modulation by dopamine. Our model suggests a hypothesis as to how the relationship between dopamine and rhythmicity impacts the function of the motor system, enabling rapid, periodic shifts in motor program execution.

As antimicrobial resistance increases, it is crucial to develop new treatment strategies to counter the emerging threat. In this paper, we consider combination therapies involving conventional antibiotics and debridement, coupled with a novel anti-adhesion therapy, and their use in the treatment of antimicrobial resistant burn wound infections. Our models predict that anti-adhesion–antibiotic–debridement combination therapies can eliminate a bacterial infection in cases where each treatment in isolation would fail. Antibiotics are assumed to have a bactericidal mode of action, killing bacteria, while debridement involves physically cleaning a wound (e.g. with a cloth); removing free bacteria. Anti-adhesion therapy can take a number of forms. Here we consider adhesion inhibitors consisting of polystyrene microbeads chemically coupled to a protein known as multivalent adhesion molecule 7, an adhesin which mediates the initial stages of attachment of many bacterial species to host cells. Adhesion inhibitors competitively inhibit bacteria from binding to host cells, thus rendering them susceptible to removal through debridement. An ordinary differential equation model is developed and the antibiotic-related parameters are fitted against new in vitro data gathered for the present study. The model is used to predict treatment outcomes and to suggest optimal treatment strategies. Our model predicts that anti-adhesion and antibiotic therapies will combine synergistically, producing a combined effect which is often greater than the sum of their individual effects, and that anti-adhesion–antibiotic–debridement combination therapy will be more effective than any of the treatment strategies used in isolation. Further, the use of inhibitors significantly reduces the minimum dose of antibiotics required to eliminate an infection, reducing the chances that bacteria will develop increased resistance. Lastly, we use our model to suggest treatment regimens capable of eliminating bacterial infections within clinically relevant timescales., Author summary Since the development of the first antibiotics, bacteria have utilised and developed resistance mechanisms, helping them to avoid being eliminated and to survive within a host. Traditionally, the solution to this problem has been to treat with multiple antibiotics, switching to a new type when the one currently in use proves ineffective. However, the development of antibiotics has slowed significantly in the past two decades, while multi-drug resistant strains, otherwise known as ‘super bugs’, are on the rise. In answer to this challenge, alternative approaches, such as anti-adhesion therapy, are being developed as a complement or alternative to traditional antimicrobials. In this paper we formulate and analyse a mathematical model of a combination therapy, applied in the context of an infected burn wound, bringing together antibiotics, anti-adhesion therapy and debridement (the physical cleaning of a wound). We use our models to make sense of how these treatments interact to combat a bacterial infection, to predict treatment outcomes for a range of strategies and to suggest optimal treatment regimens. It is hoped that this study will guide future experimental and clinical research, helping biomedical researchers to identify the most promising approaches to treatment.

The preventive activity of dietary fiber against colorectal cancer (CRC) may be in part mediated by the fermentation product of fiber, butyrate, a histone deacetylase inhibitor (HDACi) that induces CRC cell growth arrest and apoptosis. This action of butyrate, and other HDACis, is in part due to the hyperactivation of the deregulated Wnt activity found in the relevant CRC cell lines. The histone acetylases CBP and p300 interact with beta-catenin; and the relative levels of CBP-Wnt vs. p300-Wnt activity influences CRC cell physiology. It has previously been observed that there are cell type-specific differences in how cotreatment with butyrate and ICG-001, an agent that blocks CBP-Wnt activity allowing for p300-Wnt activity, affects CRC cell physiology. These differences may have clinical significance in dealing with treatment of CRC patients with ICG-001-like agents. Sam68 is a factor differentially expressed in cancer cells, with higher expression in cancer cell lines that have cancer stem cell (CSC)-like properties. Sam68 expression sensitizes cancer cells to ICG-001 treatment, as ICG-001 enhances nuclear localization of Sam68, where binding between Sam68 and CBP diminishes CBP-beta-catenin binding and thus CBP-Wnt activity. Pygo2 is a chromatin effector involved with Wnt signaling that is differentially acetylated by CBP and p300; thus CBP-mediated acetylation localized Pygo2 to the nucleus where it functions in transcriptional activation, while p300-mediated acetylation localizes Pygo2 to the cytoplasm. This paper proposes the hypothesis that Sam68 and Pygo2 are responsible for cell type-specific response of CRC cell lines cotreated with ICG-001 and butyrate as well as other HDACis. Further, experiments are proposed to evaluate this hypothesis and consider possible expected results that could be obtained from such studies.

Wood is the most important, industrially used renewable resource on the planet, but the aging mechanism of biopolymers on cell walls is poorly understood. Adhesion properties are of critical importance for wood and many other lignocellulosic materials. We used atomic force microscopy and defined the jump-off force ratio in the retract force-displacement curve to study the adhesion force phenomenon and the effects of heat treatments. Here, we identified two sigmoidal curves describing the shift of the adhesion force and the jump-off force ratio: the first curve was attributed to the movement of extractives and the second to the degradation of the hemicellulose-lignin matrix. We confirmed the hypothesis formulated in this paper by the cell wall surface topography, the analysis of the treated samples by Fourier transform infrared spectroscopy, and the analysis of volatiles during heating by headspace gas chromatography-mass spectrometry.

Astrocytes occupy a vast area within the central nervous system (CNS). Despite their abundance, the functional role of astrocytes in vivo has only begun to be uncovered. Astrocytes were typically thought to be involved in pathophysiological states. However, recent studies have shown that astrocytes are actively involved in cell signaling in normal physiological states; manipulating various aspects of astrocytic cell signaling in vivo has revealed that astrocytes are key players in controlling healthy behavior in the absence of pathophysiology. Unfortunately, the study of astrocyte function is often limited by the number of approaches available due to our lack of understanding of cell physiology. This review summarizes recent studies in which altered astrocyte signaling capacity resulted in dramatic changes in behavior. We not only discuss the methodologies available to manipulate astrocytes but also provide insights into the behavioral roles of astrocytes in the CNS., Animal behavior: Starring roles for star-shaped cells Genetic studies provide increased evidence that astrocytes, star-shaped cells in the central nervous system, play important roles affecting behavior in mammals. Although they are just as abundant as neurons, astrocytes are not excited by electrical signals. For this reason they have traditionally been regarded simply as ‘support cells’ for neurons, but recent evidence suggests that they can significantly modulate neuron signals. A review paper by Keebum Park and Sung Joong Lee at Seoul National University in South Korea highlights improved methods for monitoring the signaling processes related to astrocytes, which manifest most notably through sharp changes in calcium levels. Several studies have used genetic knockout mice, designer drugs and light-sensitive proteins to change astrocyte activity, affecting a diverse range of behaviors including sleeping and feeding patterns, memory formation, depression and obsessive compulsive disorder.

A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets, aided by cell shape changes at the cellular-level. Changes in cell shape must be studied in the context of cell-polarised biomechanical processes within the epithelial sheet. In epithelia with highly curved surfaces, finding single-cell alignment along a biological axis can be difficult to automate in silico. We present ‘Origami’, a MATLAB-based image analysis pipeline to compute direction-variant cell shape features along the epithelial apico-basal axis. Our automated method accurately computed direction vectors denoting the apico-basal axis in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia., Author summary During embryonic development, two-dimensional epithelial sheets bend and fold into complex three-dimensional structures–like paper in the origami art form. The genetic and biomechanical processes driving epithelial folding can be polarised in the epithelium, leading to asymmetric shape changes at the single cell level. Defects in such epithelial shaping have been linked to many developmental anomalies and diseases. It is, therefore, important not only to quantify shape change at the single cell level, but also to orientate these asymmetrical changes along an epithelial axis of polarity when studying morphogenetic processes. Origami is a MATLAB-based software that has been developed to automatically extract such single-cell asymmetrical shape features along the epithelial apico-basal axis from fluorescence microscopy images of folding epithelia. Origami provides a solution to computing directional vectors along the epithelial apico-basal axis followed by extracting direction-variant shape features of each segmented cell. It is generally applicable to epithelial structures regardless of complexity or direction of folding and is robust to imaging conditions. As proof of concept, Origami successfully differentiated between different cell shape signatures in highly curved structures at different developmental timepoints in the zebrafish inner ear.

Several studies have suggested that free d-Asp has a crucial role in N-methyl d-Asp receptor-mediated neurotransmission playing very important functions in physiological and pathological processes. This paper describes the development of an analytical procedure for the direct and simultaneous determination of free d-Asp, l-Asp and N-methyl d-Asp in specimens of different mouse brain tissues using chiral LC-MS/MS in Multiple Reaction Monitoring scan mode. After comparing three procedures and different buffers and extraction solvents, a simple preparation procedure was selected the analytes of extraction. The method was validated by analyzing l-Asp, d-Asp and N-methyl d-Asp recovery at different spiked concentrations (50, 100 and 200 pg/μl) yielding satisfactory recoveries (75-110%), and good repeatability. Limits of detection (LOD) resulted to be 0.52 pg/μl for d-Asp, 0.46 pg/μl for l-Asp and 0.54 pg/μl for NMDA, respectively. Limits of quantification (LOQ) were 1.57 pg/μl for d-Asp, 1.41 pg/μl for l-Asp and 1.64 pg/μl for NMDA, respectively. Different concentration levels were used for constructing the calibration curves which showed good linearity. The validated method was then successfully applied to the simultaneous detection of d-Asp, l-Asp and NMDA in mouse brain tissues. The concurrent, sensitive, fast, and reproducible measurement of these metabolites in brain tissues will be useful to correlate the amount of free d-Asp with relevant neurological processes, making the LC-MS/MS MRM method well suited, not only for research work but also for clinical analyses. Several studies have suggested that free D-Asp has a crucial role in N-methyl D-Asp receptor-mediated neurotransmission playing very important functions in physiological and pathological processes. This paper describes the development of an analytical procedure for the direct and simultaneous determination of free D-Asp, L-Asp and N-methyl D-Asp in specimens of different mouse brain tissues using chiral LC-MS/MS in Multiple Reaction Monitoring scan mode. After comparing three procedures and different buffers and extraction solvents, a simple preparation procedure was selected the analytes of extraction. The method was validated by analyzing L-Asp, D-Asp and N-methyl D-Asp recovery at different spiked concentrations (50, 100 and 200 pg/μl) yielding satisfactory recoveries (75-110%), and good repeatability. Limits of detection (LOD) resulted to be 0.52 pg/μl for D-Asp, 0.46 pg/μl for L-Asp and 0.54 pg/μl for NMDA, respectively. Limits of quantification (LOQ) were 1.57 pg/μl for D-Asp, 1.41 pg/μl for L-Asp and 1.64 pg/μl for NMDA, respectively. Different concentration levels were used for constructing the calibration curves which showed good linearity. The validated method was then successfully applied to the simultaneous detection of D-Asp, L-Asp and NMDA in mouse brain tissues. The concurrent, sensitive, fast, and reproducible measurement of these metabolites in brain tissues will be useful to correlate the amount of free D-Asp with relevant neurological processes, making the LC-MS/MS MRM method well suited, not only for research work but also for clinical analyses.

Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation., This paper presents IVEN (Internal Versus External Neighbourhood), a new user-interactive tool for the quantitative description of cell environment and organismal architecture, and uses it to reveal how changes in embryo architecture relate to changes in cell neighbourhood, identifying nuanced effects of FGF treatment on embryo morphology.

International audience; Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery.To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the ªxyl-docº cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.

Extracellular vesicles (EVs), including exosomes, are emerging as important carriers of signals in normal and pathological physiology. As EVs are a long-range communication or signaling modality—just like hormones are—the field of endocrinology is uniquely poised to offer insight into their functional biology and regulation. EVs are membrane-bound particles secreted by many different cell types and can have local or systemic effects, being transported in body fluids. They express transmembrane proteins, some of which are shared between EVs and some being specific to the tissue of origin, that can interact with target cells directly (much like hormones can). They also contain cargo within them that includes DNA, RNA, miRNA, and various metabolites. They can fuse with target cells to empty their cargo and alter their target cell physiology in this way also. Similar to the endocrine system, the EV system is likely to be under homeostatic control, making the regulation of their biogenesis and secretion important aspects to study. In this review, we briefly highlight select examples of how EVs are implicated in normal physiology and disease states. We also discuss what is known about their biogenesis and regulation of secretion. We hope that this paper inspires the endocrinology field to use our collective expertise to explore these new multimodal “hormones.”

Background Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle that maintain the cell size within a range from generation to generation. Such control mechanisms introduce substantial variabilities to important properties of the cell cycle such as growth and division. To quantitatively study the effect of such variability in progression through cell cycle, detailed stochastic models are required. Results In this paper, a new hybrid stochastic model is proposed to study the effect of molecular noise and size control mechanism on the variabilities in cell cycle of the budding yeast Saccharomyces cerevisiae. The proposed model provides an accurate, yet computationally efficient approach for simulation of an intricate system by integrating the deterministic and stochastic simulation schemes. The developed hybrid stochastic model can successfully capture several key features of the cell cycle observed in experimental data. In particular, the proposed model: 1) confirms that the majority of noise in size control stems from low copy numbers of transcripts in the G1 phase, 2) identifies the size and time regulation modules in the size control mechanism, and 3) conforms with phenotypes of early G1 mutants in exquisite detail. Conclusions Hybrid stochastic modeling approach can be used to provide quantitative descriptions for stochastic properties of the cell cycle within a computationally efficient framework. Published version