Search

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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.

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.

The study of plant cell physiology is currently experiencing a profound transformation. Novel techniques allow dynamic in vivo imaging with subcellular resolution, covering a rapidly growing range of plant cell physiology. Several basic biological questions that have been inaccessible by the traditional combination of biochemical, physiological and cell biological approaches now see major progress. Instead of grinding up tissues, destroying their organisation, or describing cell- and tissue structure, without a measure for its function, novel imaging approaches can provide the critical link between localisation, function and dynamics. Thanks to a fast growing collection of available fluorescent protein variants and sensors, along with innovative new microscopy technologies and quantitative analysis tools, a wide range of plant biology can now be studied in vivo, including cell morphology & migration, protein localization, topology & movement, protein-protein interaction, organelle dynamics, as well as ion, ROS & redox dynamics. Within the cell, genetic targeting of fluorescent protein probes to different organelles and subcellular locations has started to reveal the stringently compartmentalized nature of cell physiology and its sophisticated spatiotemporal regulation in response to environmental stimuli. Most importantly, such cellular processes can be monitored in their natural 3D context, even in complex tissues and organs – a condition not easily met in studies on mammalian cells. Recent new insights into plant cell physiology by functional imaging have been largely driven by technological developments, such as the design of novel sensors, innovative microscopy & imaging techniques and the quantitative analysis of complex image data. Rapid further advances are expected which will require close interdisciplinary interaction of plant biologists with chemists, physicists, mathematicians and computer scientists. High-throughput approaches will become increasingly important, to fill genomic data with ‘life’ on the scale of cell physiology. If the vast body of information generated in the -omics era is to generate actual mechanistic understanding of how the live plant cell works, functional imaging has enormous potential to adopt the role of a versatile standard tool across plant biology and crop breeding. We welcome original research papers, methodological papers, reviews and mini reviews, with particular attention to contributions in which novel imaging techniques enhance our understanding of plant cell physiology and permits to answer questions that cannot be easily addressed with other techniques.

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.

reply: In our recent paper (2) we reported on the effects of fatty acids on trophoblast cellular signaling and amino acid transport activity in vitro. As with any other cell culture experiments, we are aware that this is an artificial environment on multiple levels. No matter how well designed the experiment, cell cultures in and of themselves cannot completely reproduce in vivo physiological conditions. However, despite their inherent limitations, cell culture experiments do provide an important tool for studying cell physiology. In vivo, cells are exposed to a multitude of effectors at variable concentrations and we concur with Dr. Keelan (1) that it is important to study effectors in combination. However, a problem arises with respect to which effectors should be included. For example, when studying effects of fatty acids on trophoblast cell function, should all effectors known to affect mTOR signaling and amino acid transport be included in the cell culture media for the experiment to be considered valid? By analogy, in studies of insulin effects on cell function, do all known effectors impinging on the insulin signaling pathway (adiponectin, leptin, and cytokines, just to mention a few) have to be included for the experiment to be physiologically relevant? If so, Dr. Keelan's argument invalidates most of the published studies in cell physiology. We believe that a reductionist approach in which single effector molecules are studied remains valid and we disagree with the argument that fatty acids should only be studied in combination. We reported that, in the presence of oleic acid, the effects of docosahexaenoic acid (DHA) alone were no longer predominant. Dr. Keelan suggests that this finding should be interpreted that DHA responses were an in vitro artifact. However, such an interpretation fails to appreciate that DHA counteracted the observed effects of oleic acid alone. Clearly, both DHA and oleic acid have the capacity to influence trophoblast signaling and function, both in isolation and when combined. In our paper we demonstrate that DHA reduces the activity of the amino transporters System A and System L in cultured primary human trophoblast cells. In a separate study following pregnant women supplemented with DHA, we found that placental DHA levels measured at term inversely correlated with System A and System L amino acid transport capacity (3). Such data from clinical samples strongly support the assertion that the reported in vitro effects are physiologically relevant and not an experimental artifact. As already discussed in our paper, we believe that these results merit further exploration of the effects of fatty acids on trophoblast function, both singularly and in combination.

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.

Sir, we read with considerable interest the recent paper on Establishment of clonal cell lines of taste buds from a p53−/− mouse tongue by Sako et al. 2011. Sako et al. reported establishment of 11 clonal taste cell lines isolated from a tongue of a p53-deficient mouse at Day 12 and investigated the expression of markers of epithelial and taste bud cells. However, we feel the paper lacks critical information needed to support their conclusion that these are “taste buds” or to replicate their results. First, the authors did not report how many days they were able to culture and maintain the cells. Second, although they mentioned that they obtained 11 different clones of taste buds from a p53 −/− mouse tongue, they did not provide any details about how they defined and characterized these clones. Third, and most importantly, Sako et al. did not demonstrate whether or not their cultured taste cells were responsive to tastant stimuli. We believe that without calcium imaging and/or electrophysiological data, it would be difficult to claim these are physiologically mature taste cells. Fourth, in Material and Methods, they mentioned the use of CD-1 mice and the preparation of tongue tissue from CD-1 mice, however, there were no results demonstrating comparable immunostaining in CD-1 mice tongue. Finally, the phrase “clonal cell lines of taste buds” is not accurate. The entire taste bud is not replicated, even if we accept the data provided suggesting several cell types may be present. A taste bud requires a specific polarized structure and configuration, which is clearly not the output of this method. It is well known that cell culture techniques can be a valuable approach to advance our knowledge and understanding of the molecular structure and cellular physiology of taste cells and the processes of proliferation, differentiation, and regeneration. Several groups, including ours, have been interested in the development and establishment of taste cell culture models. Most attempts to culture taste cells have reported limited viability, with cells typically not lasting beyond 3–5 d (Spielman et al. 1989; Kishi et al. 2001; Ruiz et al. 2001; Stone et al. 2002). We recently reported successfully, for the first time, a method for the establishment of long-term primary cultures of rodent taste cells (Ozdener et al. 2006) and of human fungiform taste cells that have molecular and physiological properties consistent with both developing and mature taste cells (Ozdener et al. 2011). We would like to consider the work of Sato et al. as a valuable extension of this effort, but unfortunately feel that the manuscript as published lacks adequate experimental detail and results to justify that conclusion. M. H. Ozdener (*) Monell Chemical Senses Center, Philadelphia, PA 19104, USA e-mail: hozdener@yahoo.com

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.”

Although multiple microscopic techniques have been applied to horticultural research, few studies of individual organelles in living fruit cells have been reported to date. In this paper, we established an efficient system for the transient transformation of citrus fruits using an Agrobacterium-mediated method. Kumquat (Fortunella crassifolia Swingle) was used; it exhibits higher transformation efficiency than all citrus fruits that have been tested and a prolonged-expression window. Fruits were transformed with fluorescent reporters, and confocal microscopy and live-cell imaging were used to study their localization and dynamics. Moreover, various pH sensors targeting different subcellular compartments were expressed, and the local pH environments in cells from different plant tissues were compared. The results indicated that vacuoles are most likely the main organelles that contribute to the low pH of citrus fruits. In summary, our method is effective for studying various membrane trafficking events, protein localization, and cell physiology in fruit and can provide new insight into fruit biology research.

The recognition and classification of White Blood Cell (WBC) play a remarkable role in blood-related diseases (i.e., leukemia, infections) diagnosis. For the highly similar morphology of different WBC subtypes, it is too confused to classify the WBC effectively and accurately for visual observation of blood cell smears. This paper proposes a Deep Convolutional Neural Network (DCNN) with feature fusion strategies, named WBC-AMNet, for automatically classifying WBC subtypes based on focalized attention mechanism. To obtain more localized attention of CNN, the fusion features of the first and the last convolutional layer are extracted by focalized attention mechanism combining Squeeze-and-Excitation (SE) and Gather-Excite (GE) modules. The new method performs successfully in classifying monocytes, neutrophils, lymphocytes, and eosinophils on the complex background with an overall accuracy of 95.66%, better than that of general CNNs. The multi-classification accuracy of WBC-AMNet with the background segmentation is over 98% in all cases. In addition, Gradient-weighted Class Activation Mapping (Grad-CAM) is employed to visualize the attention heatmaps of different feature maps.

Learning rules by which cell shape impacts cell function would enable control of cell physiology and fate in medical applications, particularly, on the interface of cells and material of the implants. We defined the phenotypic response of human bone marrow-derived mesenchymal stem cells (hMSCs) to 2176 randomly generated surface topographies by probing basic functions such as migration, proliferation, protein synthesis, apoptosis, and differentiation using quantitative image analysis. Clustering the surfaces into 28 archetypical cell shapes, we found a very strict correlation between cell shape and physiological response and selected seven cell shapes to describe the molecular mechanism leading to phenotypic diversity. Transcriptomics analysis revealed a tight link between cell shape, molecular signatures, and phenotype. For instance, proliferation is strongly reduced in cells with limited spreading, resulting in down-regulation of genes involved in the G2/M cycle and subsequent quiescence, whereas cells with large filopodia are related to activation of early response genes and inhibition of the osteogenic process. In this paper we were aiming to identify a universal set of genes that regulate the material-induced phenotypical response of human mesenchymal stem cells. This will allow designing implants that can actively regulate cellular, molecular signalling through cell shape. Here we are proposing an approach to tackle this question.

Our common knowledge on oxidative stress has evolved substantially over the years, being focused mostly on the fundamental chemical reactions and the most relevant chemical species involved in human pathophysiology of oxidative stress-associated diseases. Thus, reactive oxygen species and reactive nitrogen species (ROS and RNS) were identified as key players in initiating, mediating, and regulating the cellular and biochemical complexity of oxidative stress either as physiological (acting pro-hormetic) or as pathogenic (causing destructive vicious circles) processes. The papers published in this particular Special Issue of Cells show an impressive range on the pathophysiological relevance of ROS and RNS, including the relevance of second messengers of free radicals like 4-hydroxynonenal, allowing us to assume that the future will reveal even more detailed mechanisms of their positive and negative effects that might improve the monitoring of major modern diseases, and aid the development of advanced integrative biomedical treatments.

Autophagy is a process of degradation of macromolecules in the cytoplasm, particularly proteins of a long half-life, as well as whole organelles, in eukaryotic cells. Lysosomes play crucial roles during this degradation. Autophagy is a phylogenetically old, and evolutionarily conserved phenomenon which occurs in all eukaryotic cells. It can be found in yeast Saccharomyces cerevisiae, insect Drosophila melanogaster, and mammals, including humans. Its high importance for cell physiology has been recognized, and in fact, dysfunctions causing impaired autophagy are associated with many severe disorders, including cancer and metabolic brain diseases. The types and molecular mechanisms of autophagy have been reviewed recently by others, and in this paper they will be summarized only briefly. Regulatory networks controlling the autophagy process are usually described as negative regulations. In contrast, here, we focus on different ways by which autophagy can be stimulated. In fact, activation of this process by different factors or processes can be considered as a therapeutic strategy in metabolic neurodegenerative diseases. These aspects are reviewed and discussed in this article.

Despite abundant measurements of bacterial growth rate, cell size, and protein content, we lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we estimate the basic requirements and physical constraints on steady-state growth by considering key processes in cellular physiology across a collection of Escherichia coli proteomic data covering ≈4,000 proteins and 36 growth rates. Our analysis suggests that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates; specific processes do not limit growth rate or dictate cell size. We present a model of proteomic regulation as a function of nutrient supply that reconciles observed interdependences between protein synthesis, cell size, and growth rate and propose that a theoretical inability to parallelize ribosomal synthesis places a firm limit on the achievable growth rate. A record of this paper’s transparent peer review process is included in the supplemental information.

The seven members of the tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of intracellular proteins were originally discovered and characterized as signaling adaptor molecules coupled to the cytoplasmic regions of receptors of the TNF-R superfamily. Functionally, TRAFs act both as a scaffold and/or enzymatic proteins to regulate activation of mitogen-activated protein kinases (MAPKs) and transcription factors of nuclear factor-κB family (NF-κB). Given the wide variety of stimuli intracellularly conveyed by TRAF proteins, they are physiologically involved in multiple biological processes, including embryonic development, tissue homeostasis, and regulation of innate and adaptive immune responses. In the last few years, it has become increasingly evident the involvement of TRAF7, the last member of the TRAF family to be discovered, in the genesis and progression of several human cancers, placing TRAF7 in the spotlight as a novel tumor suppressor protein. In this paper, we review and discuss the literature recently produced on this subject. J. Cell. Physiol. 232: 1233-1238, 2017. © 2016 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.

The subset of pro-inflammatory B cells, called late memory, tissue-like or double negative (DN), accumulates in the blood of elderly individuals. Here we show that DN B cells do not proliferate and do not make antibodies to influenza antigens, but they secrete antibodies with autoimmune reactivity, in agreement with their membrane phenotype (CD95+CD21-CD11c+) and their spontaneous expression of the transcription factor T-bet. These cells also increase in the blood of individuals with obesity and autoimmune diseases, but causative mechanisms and signaling pathways involved are known only in part. In the present paper we compare frequencies and metabolic requirements of these cells in the blood of healthy individuals of different ages and in the blood and the subcutaneous adipose tissue (SAT) of individuals with obesity. Results show that DN B cells from young individuals have minimal metabolic requirements, DN B cells from elderly and obese individuals utilize higher amounts of glucose to perform autoimmune antibody production and enroll in aerobic glycolysis to support their function. DN B cells from the SAT have the highest metabolic requirements as they activate oxidative phosphorylation, aerobic glycolysis and fatty acid oxidation. DN B cells from the SAT also show the highest levels of ROS and the highest levels of phosphorylated AMPK (5’-AMP activated kinase) and Sestrin 1, both able to mitigate stress and cell death. This metabolic advantage drives DN B cell survival and function (secretion of autoimmune antibodies).

The conduction of electrical signals through cardiac tissue is essential for maintaining the function of the heart, and conduction abnormalities are known to potentially lead to life-threatening arrhythmias. The properties of cardiac conduction have therefore been the topic of intense study for decades, but a number of questions related to the mechanisms of conduction still remain unresolved. In this paper, we demonstrate how the so-called EMI model may be used to study some of these open questions. In the EMI model, the extracellular space, the cell membrane, the intracellular space and the cell connections are all represented as separate parts of the computational domain, and the model therefore allows for study of local properties that are hard to represent in the classical homogenized bidomain or monodomain models commonly used to study cardiac conduction. We conclude that a non-uniform sodium channel distribution increases the conduction velocity and decreases the time delays over gap junctions of reduced coupling in the EMI model simulations. We also present a theoretical optimal cell length with respect to conduction velocity and consider the possibility of ephaptic coupling (i.e. cell-to-cell coupling through the extracellular potential) acting as an alternative or supporting mechanism to gap junction coupling. We conclude that for a non-uniform distribution of sodium channels and a sufficiently small intercellular distance, ephaptic coupling can influence the dynamics of the sodium channels and potentially provide cell-to-cell coupling when the gap junction connection is absent., Author summary The electrochemical wave traversing the heart during every beat is essential for cardiac pumping function and supply of blood to the body. Understanding the stability of this wave is crucial to understanding how lethal arrhythmias are generated. Despite this importance, our knowledge of the physical determinants of wave propagation are still evolving. One particular challenge has been the lack of accurate mathematical models of conduction at the cellular level. Because cardiac muscle is an electrical syncytium, in which direct charge transfer between cells drives wave propagation, classical bidomain and monodomain tissue models employ a homogenized approximation of this process. This approximation is not valid at the length scale of single cells, and prevents any analysis of how cellular structures impact cardiac conduction. Instead, so-called microdomain models must be used for these questions. Here we utilize a recently developed modelling framework that is well suited to represent small collections of cells. By applying this framework, we show that concentration of sodium channels at the longitudinal borders of myocytes accelerates cardiac conduction. We also demonstrate that when juxtaposed cells are sufficiently close, this non-uniform distribution induces large ephaptic currents, which contribute to intercellular coupling.

Flip-flop of lipids of the lipid bilayer (LBL) constituting the plasma membrane (PM) plays a crucial role in a myriad of events ranging from cellular signaling and regulation of cell shapes to cell homeostasis, membrane asymmetry, phagocytosis, and cell apoptosis. While extensive research has been conducted to probe the lipid flip flop of planar lipid bilayers (LBLs), less is known regarding lipid flip-flop for highly curved, nanoscopic LBL systems despite the vast importance of membrane curvature in defining the morphology of cells and organelles and in maintaining a variety of cellular functions, enabling trafficking, and recruiting and localizing shape-responsive proteins. In this paper, we conduct molecular dynamics (MD) simulations to study the energetics, structure, and configuration of a lipid molecule undergoing flip-flop and desorption in a highly curved LBL, represented as a nanoparticle-supported lipid bilayer (NPSLBL) system. We compare our findings against those of a planar substrate supported lipid bilayer (PSSLBL). Our MD simulation results reveal that despite the vast differences in the curvature and other curvature-dictated properties (e.g., lipid packing fraction, difference in the number of lipids between inner and outer leaflets, etc.) between the NPSLBL and the PSSLBL, the energetics of lipid flip-flop and lipid desorption as well as the configuration of the lipid molecule undergoing lipid flip-flop are very similar for the NPSLBL and the PSSLBL. In other words, our results establish that the curvature of the LBL plays an insignificant role in lipid flip-flop and desorption.

In this study, we established a dynamic micromodel of urinary tract infection to analyze the impact of UT-segment-specific urinary outflow on the persistence of E. coli colonization. We found that the adherence of Dr+ E. coli to bladder T24 transitional cells and type IV collagen is maximal at lowest shear stress and is reduced by any increase in flow velocity. The analyzed adherence was effective in the whole spectrum of physiological shear stress and was almost irreversible over the entire range of generated shear force. Once Dr+ E. coli bound to host cells or collagen, they did not detach even in the presence of elevated shear stress or of chloramphenicol, a competitive inhibitor of binding. Investigating the role of epithelial surface architecture, we showed that the presence of budding cells–a model microarchitectural obstacle–promotes colonization of the urinary tract by E. coli. We report a previously undescribed phenomenon of epithelial cell “rolling-shedding” colonization, in which the detached epithelial cells reattach to the underlying cell line through a layer of adherent Dr+ E. coli. This rolling-shedding colonization progressed continuously due to “refilling” induced by the flow-perturbing obstacle. The shear stress of fluid containing free-floating bacteria fueled the rolling, while providing an uninterrupted supply of new bacteria to be trapped by the rolling cell. The progressive rolling allows for transfer of briefly attached bacteria onto the underlying monolayer in a repeating cascading event., Author summary Uropathogenic E. coli (UPEC) equipped with Dr fimbriae are associated with recurrent and chronic urinary tract infections (UTIs). The fimbriae assembled by the chaperone-usher pathway provide strong host-specific adherence which is, however, strongly modulated by the dynamically changing urine flow in the urinary tract (UT). In this paper, we use a dynamic in vitro micro-model of UTI to analyze the UT segment-specific impact of urinary outflow on the persistence and spread of Dr+ E. coli during host colonization. We conclude that the adhesive envelope formed by Dr fimbriae promotes strong and irreversible multivalent adherence of Dr+ E. coli to host receptors under flow conditions. We also observed that budding host cells–a model of any form of epithelial roughness, including carcinogenesis or physical injuries–facilitate the adherence of bacteria at flow conditions typically found in the UT, and our numerical simulations provided a mechanistic explanation for this effect. Finally, we combined the results to propose a rolling-shedding-refilling colonization model that shows how the wash off of detached colonized host cells may provoke a massive spread of UPEC. Our findings shed new light on UTI development and may be instrumental in the development of novel therapeutics.

Chromosome mis-segregation leads to aneuploidy, a condition in which cells harbor an imbalanced chromosome number. Several lines of evidence strongly indicate that aneuploidy triggers genome instability, ultimately generating cells with complex karyotypes that arrest their proliferation. Isolation and characterization of cells harboring complex karyotypes are crucial to study the impact of an imbalanced chromosome number on cell physiology. To date, no methods have been established to reliably isolate such aneuploid cells. This paper provides a protocol for the enrichment and analysis of aneuploid cells with complex karyotypes utilizing standard, inexpensive tissue culture techniques. This protocol can be used to analyze several features of aneuploid cells with complex karyotypes including their induced senescence-associated secretory phenotype, pro-inflammatory properties, and ability to interact with immune cells. Because cancer cells often harbor imbalances in chromosome number, it is crucial to decipher how aneuploidy impacts cell physiology in normal cells, with the ultimate goal of uncovering both its pro- and anti-tumorigenic effects.

The continuous development of high electrical equipment towards high power output requires better heat dissipation performance of internal insulation structure. It challenges the traditional paper-based insulating materials, with poor thermal conductivity. Introducing thermally conductive and electrically insulating filler into cellulose-based insulating material can enhance heat conduction performance. This work provided a method to prepare thermally conductive and electrically insulating BN/cellulosic fibre composites. And the thermal conductivity of the composites was remarkably increased via grafting APTES and adding dual-sized fillers. The thermal conductivity of the composite reached 0.682 W/(m•k) that increased by 387% with h-BN loading of 41.08 wt%. Simultaneously, BN fillers improved the insulating properties of the resultant composites. The dielectric constant, breaking strength of and volume resistivity of the composites reached 4.75, 9.2 kV/mm-1 and 4.72×10(14) Ω•m, respectively. The resultant insulating material which has better heat conduction property may have a vast potential for future development in electrical equipment.

Rho-GTPases are master regulators of polarity establishment and cell morphology. Positive feedback enables concentration of Rho-GTPases into clusters at the cell cortex, from where they regulate the cytoskeleton. Different cell types reproducibly generate either one (e.g. the front of a migrating cell) or several clusters (e.g. the multiple dendrites of a neuron), but the mechanistic basis for unipolar or multipolar outcomes is unclear. The design principles of Rho-GTPase circuits are captured by two-component reaction-diffusion models based on conserved aspects of Rho-GTPase biochemistry. Some such models display rapid winner-takes-all competition between clusters, yielding a unipolar outcome. Other models allow prolonged co-existence of clusters. We investigate the behavior of a simple class of models and show that while the timescale of competition varies enormously depending on model parameters, a single factor explains a large majority of this variation. The dominant factor concerns the degree to which the maximal active GTPase concentration in a cluster approaches a “saturation point” determined by model parameters. We suggest that both saturation and the effect of saturation on competition reflect fundamental properties of the Rho-GTPase polarity machinery, regardless of the specific feedback mechanism, which predict whether the system will generate unipolar or multipolar outcomes., Author summary Cell morphology is a critical determinant of cell function, and the conserved Rho-family GTPases (Cdc42, Rac, Rho, or Rop in plants) are key regulators of cell morphology. Rho-GTPases self-organize by concentrating into clusters at the cortex, and several mathematical models have been proposed that capture the essential features of such pattern formation. However, it has been unclear how such systems reliably generate either a single cluster (unipolar outcome) or multiple clusters (multipolar outcome). In this paper, we show that a broad class of models for Rho-GTPase polarization all exhibit the ability to switch between a regime in which rapid winner-takes-all competition between clusters yields unipolar outcomes and a regime in which competition is so slow that multipolar outcomes occur at biologically relevant timescales. We find that the switch in model behavior follows a surprisingly simple rule, and elucidate the fundamental principles that underpin that rule. Our theoretical study explains how the same biochemical system can robustly yield unipolar or multipolar outcomes, and makes experimentally testable predictions.

Reactive oxygen species (ROS) initially considered as only damaging agents in living organisms further were found to play positive roles also. This paper describes ROS homeostasis, principles of their investigation and technical approaches to investigate ROS-related processes. Especial attention is paid to complications related to experimental documentation of these processes, their diversity, spatiotemporal distribution, relationships with physiological state of the organisms. Imbalance between ROS generation and elimination in favor of the first with certain consequences for cell physiology has been called "oxidative stress". Although almost 30years passed since the first definition of oxidative stress was introduced by Helmut Sies, to date we have no accepted classification of oxidative stress. In order to fill up this gape here classification of oxidative stress based on its intensity is proposed. Due to that oxidative stress may be classified as basal oxidative stress (BOS), low intensity oxidative stress (LOS), intermediate intensity oxidative stress (IOS), and high intensity oxidative stress (HOS). Another classification of potential interest may differentiate three categories such as mild oxidative stress (MOS), temperate oxidative stress (TOS), and finally severe (strong) oxidative stress (SOS). Perspective directions of investigations in the field include development of sophisticated classification of oxidative stresses, accurate identification of cellular ROS targets and their arranged responses to ROS influence, real in situ functions and operation of so-called "antioxidants", intracellular spatiotemporal distribution and effects of ROS, deciphering of molecular mechanisms responsible for cellular response to ROS attacks, and ROS involvement in realization of normal cellular functions in cellular homeostasis.

Ion channels are tightly involved in various aspects of cell physiology, including cell signaling, proliferation, motility, endo- and exo-cytosis. They may be involved in toxin production and release by marine dinoflagellates, as well as harmful algal bloom proliferation. So far, the patch-clamp technique, which is the most powerful method to study the activity of ion channels, has not been applied to dinoflagellate cells, due to their complex cellulose-containing cell coverings. In this paper, we describe a new approach to overcome this problem, based on the preparation of spheroplasts from armored bloom-forming dinoflagellate Prorocentrum minimum. We treated the cells of P. minimum with a cellulose synthesis inhibitor, 2,6-dichlorobenzonitrile (DCB), and found out that it could also induce ecdysis and arrest cell shape maintenance in these microalgae. Treatment with 100–250 µM DCB led to an acceptable 10% yield of P. minimum spheroplasts and was independent of the incubation time in the range of 1–5 days. We show that such spheroplasts are suitable for patch-clamping in the cell-attached mode and can form 1–10 GOhm patch contact with a glass micropipette, allowing recording of ion channel activity. The first single-channel recordings of dinoflagellate ion channels are presented.

Tailored therapy aims to cure cancer patients effectively and safely, based on the complex interactions between patients' genomic features, disease pathology and drug metabolism. Thus, the continual increase in scientific literature drives the need for efficient methods of data mining to improve the extraction of useful information from texts based on patients' genomic features. An important application of text mining to tailored therapy in cancer encompasses the use of mutations and cancer fusion genes as moieties that change patients' cellular networks to develop cancer, and also affect drug metabolism. Fusion proteins, which are derived from the slippage of two parental genes, are produced in cancer by chromosomal aberrations and trans-splicing. Given that the two parental proteins for predicted fusion proteins are known, we used our previously developed method for identifying chimeric protein–protein interactions (ChiPPIs) associated with the fusion proteins. Here, we present a validation approach that receives fusion proteins of interest, predicts their cellular network alterations by ChiPPI and validates them by our new method, ProtFus, using an online literature search. This process resulted in a set of 358 fusion proteins and their corresponding protein interactions, as a training set for a Naïve Bayes classifier, to identify predicted fusion proteins that have reliable evidence in the literature and that were confirmed experimentally. Next, for a test group of 1817 fusion proteins, we were able to identify from the literature 2908 PPIs in total, across 18 cancer types. The described method, ProtFus, can be used for screening the literature to identify unique cases of fusion proteins and their PPIs, as means of studying alterations of protein networks in cancers. Availability: http://protfus.md.biu.ac.il/, Author summary Tailored therapy aims to cure cancer patients in a fully personal way. Thus, the continual increase in scientific information and, particularly, in published literature, drives the need for efficient methods of data mining to find unique personal genomic features and their connections. Fusion proteins, which are derived from the slippage of two parental genes or chromosomal translocations, are frequently drivers of cancers. We used our previously developed method for identifying chimeric protein–protein interactions (ChiPPIs) for multiple fusion proteins. In this paper, we present a validation approach, ProtFus, which receives fusion proteins of interest, predicts their cellular network alterations by ChiPPI and validates them by online literature searches. This process resulted in a set of 358 fusion proteins and their corresponding protein interactions, as training set. Next, for a test set of 1817 fusion proteins, we were able to identify 2908 previously published PPIs across 18 different cancer types. The described method can be used for screening the literature to identify unique cases of fusion proteins and their PPI networks, as means of studying alterations of protein networks for personalized approaches in cancers.

Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance (including product titer or rate) under suboptimal metabolism and complex bioprocess conditions. On the other hand, machine learning, complementary to metabolic modeling necessitates large amounts of data. Building such a database for metabolic engineering designs requires significant manpower and is prone to human errors and bias. We propose an approach to integrate data-driven methods with genome scale metabolic model for assessment of microbial bio-production (yield, titer and rate). Using engineered E. coli as an example, we manually extracted and curated a data set comprising about 1200 experimentally realized cell factories from ~100 papers. We furthermore augmented the key design features (e.g., genetic modifications and bioprocess variables) extracted from literature with additional features derived from running the genome-scale metabolic model iML1515 simulations with constraints that match the experimental data. Then, data augmentation and ensemble learning (e.g., support vector machines, gradient boosted trees, and neural networks in a stacked regressor model) are employed to alleviate the challenges of sparse, non-standardized, and incomplete data sets, while multiple correspondence analysis/principal component analysis are used to rank influential factors on bio-production. The hybrid framework demonstrates a reasonably high cross-validation accuracy for prediction of E.coli factory performance metrics under presumed bioprocess and pathway conditions (Pearson correlation coefficients between 0.8 and 0.93 on new data not seen by the model).

Cell intercalation is a highly directed cell rearrangement that is essential for animal morphogenesis. As such, intercalation requires orchestration of cell polarity across the plane of the tissue. CDC-42 is a Rho family GTPase with key functions in cell polarity, yet its role during epithelial intercalation has not been established because its roles early in embryogenesis have historically made it difficult to study. To circumvent these early requirements, in this paper we use tissue-specific and conditional loss-of-function approaches to identify a role for CDC-42 during intercalation of the Caenorhabditis elegans dorsal embryonic epidermis. CDC-42 activity is enriched in the medial tips of intercalating cells, which extend as cells migrate past one another. Moreover, CDC-42 is involved in both the efficient formation and orientation of cell tips during cell rearrangement. Using conditional loss-of-function we also show that the PAR complex functions in tip formation and orientation. Additionally, we find that the sole C. elegans Eph receptor, VAB-1, functions during this process in an Ephrin-independent manner. Using epistasis analysis, we find that vab-1 lies in the same genetic pathway as cdc-42 and is responsible for polarizing CDC-42 activity to the medial tip. Together, these data establish a previously uncharacterized role for polarized CDC-42, in conjunction with PAR-6, PAR-3 and an Eph receptor, during epithelial intercalation., Author Summary As embryos develop, tissues must change shape to establish an animal’s form. One key form-shaping movement, cell intercalation, often occurs when a tissue elongates in a preferred direction. How cells in epithelial sheets can intercalate while maintaining tissue integrity is not well understood. Here we use the dorsal epidermis in embryos of the nematode worm, C. elegans, to study cell intercalation. As cells begin to intercalate, they form highly polarized tips that lead their migration. While some mechanisms that polarize intercalating cells have been established in other systems, our work identifies a new role for CDC-42—a highly conserved, highly regulated protein that controls the actin cytoskeleton. We previously established that a related protein, Rac, is involved in tip extension during dorsal intercalation. CDC-42 also contributes to this process in addition to helping orient the extending tip. CDC-42 appears to work in conjunction with two other known cell polarity proteins, PAR-3 and PAR-6, and the cell surface receptor, VAB-1. Our work identifies a novel pathway involving proteins conserved from worms to humans that regulates a ubiquitous process during animal development.