Can mathematics explain the evolution of human language?

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer science-based formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language.

Can mathematics explain the evolution of human language?

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer science-based formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language.

A multivariate model of ErbB network composition predicts ovarian cancer cell response to canertinib

Identifying the optimal treatment strategy for cancer is an important challenge, particularly for complex diseases like epithelial ovarian cancer (EOC) that are prone to recurrence. In this study we developed a quantitative, multivariate model to predict the extent of ovarian cancer cell death following treatment with an ErbB inhibitor (canertinib, CI-1033). A partial least squares regression model related the levels of ErbB receptors and ligands at the time of treatment to sensitivity to CI-1033. In this way, the model mimics the clinical problem by incorporating only information that would be available at the time of drug treatment. The full model was able to fit the training set data and was predictive. Model analysis demonstrated the importance of including both ligand and receptor levels in this approach, consistent with reports of the role of ErbB autocrine loops in EOC. A reduced multi-protein model was able to predict CI-1033 sensitivity of six distinct EOC cell lines derived from the three subtypes of EOC, suggesting that quantitatively characterizing the ErbB network could be used to broadly predict EOC response to CI-1033. Ultimately, this systems biology approach examining multiple proteins has the potential to uncover multivariate functions to identify subsets of tumors that are most likely to respond to a targeted therapy.

Clinical significance of histone deacetylases 1, 2, 3, and 7: HDAC2 is an independent predictor of survival in HCC

Histone deacetylases (HDAC) are responsible for the transcriptional control of genes through chromatin remodeling and control tumor suppressor genes. In several tumors, their expression has been linked to clinicopathological factors and patient survival. This study investigates HDACs 1, 2, 3, and 7 expressions in hepatocellular carcinoma (HCC) and their correlation with clinical data and patient survival. Tissue microarrays of 170 surgically resected primary HCCs and adjacent uninvolved tissue were evaluated immunohistochemically for the expression of HDACs 1, 2, 3, 7, and Ki-67 and were analyzed with respect to clinicopathological data and patient survival. HDACs 1, 2, 3, and Ki-67 were expressed significantly higher in cancer cells compared to normal tissue (HDAC1: p = 0.034, HDACs 2 and 3 and Ki-67: p < 0.001), while HDAC7 expression did not differ between HCC and non-cancerous liver tissue. In tumor tissue HDACs 1-3 expression levels showed high concordance with each other, Ki-67 and tumor grade (p < 0.001). High HDAC2 expression was associated with poor survival in low-grade and early-stage tumors (p < 0.05). The expression of the HDACs 1, 2, and 3 (but not HDAC7) isoenzymes correlates with clinicopathological factors, and HDAC2 expression has an impact on patient survival.

Drosophila phagocytosis - still many unknowns under the surface

In mammals, phagocytosis coordinates host defence on two levels: It acts both as an effector of the innate immunity, as well as an initiator of the adaptive immunity. The fruit fly Drosophila melanogaster (D. melanogaster) lacks the adaptive immune response, and the role of Drosophila plasmatocytes, cells that resemble phagocytosing mammalian macrophages, is limited to innate immune responses. During the past years, several studies have shed light on the role of phagocytosis in the Drosophila host defence. At least in some infection models, the systemic production of potent antimicrobial peptides (AMPs) does not completely compensate for the need for cellular immune responses. As a model, Drosophila offers powerful tools for studying phagocytosis including, large-scale RNA interference (RNAi) based in vitro screens that can be combined with classical Drosophila genetics. These kinds of approaches have led to important discoveries related especially to microbial recognition by Drosophila plasmatocytes. Events following initial recognition, however, have remained more elusive. This review summarizes the current knowledge on Drosophila phagocytosis focusing on the most recent advancements in the field, and highlighting the benefits the Drosophila system has to offer for research on phagocytosis.

Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis

Chlamydia trachomatis, an obligate intracellular bacterium, is a highly prevalent human pathogen. Hydroxamic-acid-based matrix metalloprotease inhibitors can effectively inhibit the pathogen both in vitro and in vivo, and have exhibited therapeutic potential. Here, we provide genome sequencing data indicating that peptide deformylase (PDF) is the sole target of the inhibitors in this organism. We further report molecular mechanisms that control chlamydial PDF (cPDF) expression and inhibition efficiency. In particular, we identify the σ⁶⁶-dependent promoter that controls cPDF gene expression and demonstrate that point mutations in this promoter lead to resistance by increasing cPDF transcription. Furthermore, we show that substitution of two amino acids near the active site of the enzyme alters enzyme kinetics and protein stability.

Azithromycin decreases MMP-9 expression in the airways of lung transplant recipients

The neomacrolide antibiotic azithromycin is known to have an anti-inflammatory effect and is increasingly being used in the treatment of chronic inflammatory pulmonary diseases. We investigated whether azithromycin influenced matrix remodeling. Matrix metalloproteinase (MMP)-9 protein levels were measured by ELISA in bronchoalveolar lavaga fluid in 10 stable patients and in 10 lung transplant patients suffering from nCLAD/NRAD. MMP-9 was measured via ELISA before and after 3 to 6 months of azithromycin therapy. We further elaborated on the role of MMP-9 by performing gelatin-zymography and gelatinolytic activity assays. Differential and total cell counts on BAL were performed in all cases. The nCLAD/NRAD patients showed higher airway neutrophilia (p<0.0001), ELISA MMP-9 (p<0.0001), zymography proMMP-9 (p<0.0001), activated MMP-9 (p=0.0003) and gelatinolytic activity (p=0.0002) compared to the control group. Airway neutrophilia in the nCLAD/NRAD group significantly decreased after 3-6 months of treatment with azithromycin (p=0.0020). This was associated with a decrease in ELISA MMP-9 levels (p=0.0059), in activated MMP-9 shown on zymography (p=0.016) and in gelatinolytic activity (p=0.031). Remarkably, proMMP-9 levels were not altered by azithromycin. Although azithromycin significantly reduced ELISA MMP-9 levels and gelatinolytic activity in transplant patients, these levels remained higher compared to control patients (p=0.0011 and p=0.043). Neutrophil counts, activated MMP-9 and gelatinolytic activity levels in nCLAD/NRAD decreased after azithromycin treatment, but some remained elevated compared to control patients. This illustrates that treatment with azithromycin did not completely restore chronic inflammation in the airways and suggested that preventive therapy may yield added value to curative therapy.

Clinical significance of histone deacetylases 1, 2, 3, and 7: HDAC2 is an independent predictor of survival in HCC

Histone deacetylases (HDAC) are responsible for the transcriptional control of genes through chromatin remodeling and control tumor suppressor genes. In several tumors, their expression has been linked to clinicopathological factors and patient survival. This study investigates HDACs 1, 2, 3, and 7 expressions in hepatocellular carcinoma (HCC) and their correlation with clinical data and patient survival. Tissue microarrays of 170 surgically resected primary HCCs and adjacent uninvolved tissue were evaluated immunohistochemically for the expression of HDACs 1, 2, 3, 7, and Ki-67 and were analyzed with respect to clinicopathological data and patient survival. HDACs 1, 2, 3, and Ki-67 were expressed significantly higher in cancer cells compared to normal tissue (HDAC1: p = 0.034, HDACs 2 and 3 and Ki-67: p < 0.001), while HDAC7 expression did not differ between HCC and non-cancerous liver tissue. In tumor tissue HDACs 1-3 expression levels showed high concordance with each other, Ki-67 and tumor grade (p < 0.001). High HDAC2 expression was associated with poor survival in low-grade and early-stage tumors (p < 0.05). The expression of the HDACs 1, 2, and 3 (but not HDAC7) isoenzymes correlates with clinicopathological factors, and HDAC2 expression has an impact on patient survival.

Natural haemozoin modulates matrix metalloproteinases and induces morphological changes in human microvascular endothelium

Severe malaria, including cerebral malaria (CM), is characterized by the sequestration of parasitized erythrocytes in the microvessels after cytoadherence to endothelial cells. Products of parasite origin, such as haemozoin (HZ), contribute to the pathogenesis of severe malaria by interfering with host inflammatory response. In human monocytes, HZ enhanced the levels of matrix metalloproteinase-9 (MMP-9), a protease involved in neuroinflammation. Here the effects of HZ on the regulation of MMPs by the human microvascular endothelial cell line HMEC-1 were investigated. Cells treated with natural (n)HZ appeared elongated instead of polygonal, and formed microtubule-like vessels on synthetic basement membrane. nHZ enhanced total gelatinolytic activity by inducing proMMP-9 and MMP-9 without affecting basal MMP-2. The level of the endogenous tissue inhibitor of MMP-9 (TIMP-1) was not altered by nHZ, while TIMP-2, the MMP-2 inhibitor, was enhanced. Additionally, nHZ induced MMP-1 and MMP-3, two enzymes sequentially involved in collagenolysis and proMMP-9 proteolytic activation. Lipid-free HZ did not reproduce nHZ effects. Present data suggest that the lipid moiety of HZ alters the MMP/TIMP balances and promotes the proteolytic activation of proMMP-9 in HMEC-1, thereby enhancing total gelatinolytic activity, cell activation and inflammation. These findings might help understanding the mechanisms of blood brain barrier damage during CM.

Interaction of plasma membrane Ca(2+)-ATPase isoform 4 with calcineurin A: implications for catecholamine secretion by PC12 cells

PMCA1-4 isoforms have been recently recognised as regulators of various signalling pathways in mammalian cells. PMCAs were found to interact with calcineurin A in an isoform specific manner. In this study we focus on the interaction of calcineurin A with PMCA4 and its effect on catecholamine secretion in PC12 cells with reduced PMCA2 or PMCA3 content. Reduction of synthesis of PMCA2 or PMCA3 led to upregulation of PMCA4 manifested by preferential interaction of PMCA4 with calcineurin A. On the other hand, we observed a significant reduction of dopamine secretion, which did not correspond with an increased [Ca(2+)](c). This result indicates that the interaction of PMCA4 with calcineurin A plays a regulatory role in the signalling during catecholamine secretion.

Ikaros in hematopoiesis and leukemia

Ikaros is a gene whose activity is essential for normal hematopoiesis. Ikaros acts as a master regulator of lymphoid and myeloid development as well as a tumor suppressor. In cells, Ikaros regulates gene expression via chromatin remodeling. During the past 15 years tremendous advances have been made in understanding the role of Ikaros in hematopoiesis and leukemogenesis. In this Topic Highlights series of reviews, several groups of international experts in this field summarize the experimental data that is shaping the emerging picture of Ikaros function at the biochemical and cellular levels. The articles provide detailed analyses of recent scientific advancements and present models that will serve as a basis for future studies aimed at developing a better understanding of normal hematopoiesis and hematological malignancies and at accelerating the application of this knowledge in clinical practice.

Protective Action of Neurotrophic Factors and Estrogen against Oxidative Stress-Mediated Neurodegeneration

Oxidative stress is involved in the pathogenesis of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. Low levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS) are important for maintenance of neuronal function, though elevated levels lead to neuronal cell death. A complex series of events including excitotoxicity, Ca(2+) overload, and mitochondrial dysfunction contributes to oxidative stress-mediated neurodegeneration. As expected, many antioxidants like phytochemicals and vitamins are known to reduce oxidative toxicity. Additionally, growing evidence indicates that neurotrophic factors such as brain-derived neurotrophic factor (BDNF) and estrogens significantly prevent neuronal damage caused by oxidative stress. Here, we review and discuss recent studies addressing the protective mechanisms of neurotrophic factors and estrogen within this system.

Inhibiting the mTOR pathway synergistically enhances cytotoxicity in ovarian cancer cells induced by etoposide through upregulation of c-Jun

PURPOSE

The mTOR pathway is thought to be a central regulator of proliferation and survival of cells. Rapamycin and its analogs are undergoing clinical trials in patients with epithelial ovarian cancer. This study aimed to assess the potential to use rapamycin and anticancer agents in combination for first- and second-line chemotherapy to treat ovarian cancer.

EXPERIMENTAL DESIGN

We used six ovarian serous adenocarcinoma cell lines (KF, KOC-2S, SHIN-3, SK-OV-3, TU-OS-3, and TU-OS-4) in this study. We treated the cells with rapamycin and anticancer agents, then assessed cell viability, apoptosis, and the expression of protein in apoptotic pathways and molecules downstream of the mTOR signaling pathways. We also investigated the effect of these drug combinations on survival in nude mouse xenograft models.

RESULTS

Synergistic effects were observed in five cell lines from the combination of etoposide and rapamycin. However, we observed antagonistic effects when rapamycin was combined with gemcitabine, cisplatin, or paclitaxel on more than two cell lines. Rapamycin dramatically enhanced apoptosis induced by etoposide and the expression of cleaved caspase 9. This effect was associated with upregulation of phosphorylated c-Jun and downregulation of Bcl-xL. The synergistic interaction of rapamycin and etoposide was lower when the c-Jun pathway was suppressed by a c-Jun N-terminal kinase inhibitor (SP600125). Finally, treating nude mice with rapamycin and etoposide significantly prolonged survival in the model mice with ovarian cancer xenografts.

CONCLUSIONS

Chemotherapy with rapamycin and etoposide combined is worth exploring as a treatment modality for women with epithelial ovarian cancer.

Myelodysplastic syndrome and histone deacetylase inhibitors: "to be or not to be acetylated"?

Myelodysplastic syndrome (MDS) represents a heterogeneous group of diseases with clonal proliferation, bone marrow failure and increasing risk of transformation into an acute myeloid leukaemia. Structured guidelines are developed for selective therapy based on prognostic subgroups, age, and performance status. Although many driving forces of disease phenotype and biology are described, the complete and possibly interacting pathogenetic pathways still remain unclear. Epigenetic investigations of cancer and haematologic diseases like MDS give new insights into the pathogenesis of this complex disease. Modifications of DNA or histones via methylation or acetylation lead to gene silencing and altered physiology relevant for MDS. First clinical trials give evidence that patients with MDS could benefit from epigenetic treatment with, for example, DNA methyl transferase inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi). Nevertheless, many issues of HDACi remain incompletely understood and pose clinical and translational challenges. In this paper, major aspects of MDS, MDS-associated epigenetics and the potential use of HDACi are discussed.

Evidence for covert baculovirus infections in a Spodoptera exigua laboratory culture

A laboratory culture of Spodoptera exigua was examined to assess covert (latent or persistent) baculovirus infections and spontaneous disease outbreaks. Two nucleopolyhedrovirus (NPV) species were found to be reactivated from a covert state in a laboratory culture of S. exigua to fully lethal forms. These were identified as S. exigua multinucleopolyhedrovirus (SeMNPV) and Mamestra brassicae NPV (MbNPV) using restriction enzyme analysis of purified viral DNA. Sequence data derived from both overtly and covertly virus-infected insects revealed highly conserved sequences for lef-8, lef-9 and polyhedrin gene sequence (98–100 % nucleotide identity to SeMNPV published sequence). By monitoring spontaneous overt infections and quantifying viral DNA (by quantitative-PCR) in asymptomatic individuals over two generations we identified fluctuating trends in viral DNA levels from covert SeMNPV and MbNPV within an S. exigua host population. Virus levels per insect life stage ranged from 3.51±0.101×105 to 0.29±0.036 pg (detection limit at 0.06 pg). Bioassays performed with this culture of larvae showed a differential susceptibility to SeMNPV-like or MbNPV-like viruses, with SeMNPV superinfections being extremely virulent. The data presented has broad implications relating to our understanding of transmission patterns of baculovirus in the environment and the role of covert infections in host–pathogen interaction dynamics.

Plasma membrane calcium ATPases and cancer

The plasma membrane calcium ATPases (PMCAs) are vital regulators of basal Ca(2+) and shape the nature of intracellular free Ca(2+) transients after cellular stimuli and are thus regulators of a plethora of cellular processes. Studies spanning many years have identified that at least some cancers are associated with a remodeling of PMCA isoform expression. This alteration in Ca(2+) efflux capacity may have a variety of consequences including reduced sensitivity to apoptosis and increases in the responsiveness of cancer cells to proliferative stimuli. In this review we provide an overview of studies focused on PMCAs in the context of cancer. We discuss how the remodeling of PMCA expression could provide a survival and/or growth advantage to cancer cells, as well as the potential of pharmacological agents that target specific PMCA isoforms to be novel therapies for the treatment of cancer.

The emerging role of autophagy in alcoholic liver disease

Autophagy is a highly conserved intracellular catabolic pathway that degrades cellular long-lived proteins and organelles. Autophagy is normally activated in response to nutrient deprivation and other stresses as a cell survival mechanism. Accumulating evidence indicates that autophagy plays a critical role in liver pathophysiology, in addition to maintaining hepatic energy and nutrient balance. Alcohol consumption causes hepatic metabolic changes, oxidative stress, accumulation of lipid droplets and damaged mitochondria; all of these can be regulated by autophagy. This review summarizes the recent findings about the role and mechanisms of autophagy in alcoholic liver disease (ALD), and the possible intervention for treating ALD by modulating autophagy.

Protease expression by microorganisms and its relevance to crucial physiological/pathological events

The treatment of infections caused by fungi and trypanosomatids is difficult due to the eukaryotic nature of these microbial cells, which are similar in several biochemical and genetic aspects to host cells. Aggravating this scenario, very few antifungal and anti-trypanosomatidal agents are in clinical use and, therefore, therapy is limited by drug safety considerations and their narrow spectrum of activity, efficacy and resistance. The search for new bioactive agents against fungi and trypanosomatids has been expanded because progress in biochemistry and molecular biology has led to a better understanding of important and essential pathways in these microorganisms including nutrition, growth, proliferation, signaling, differentiation and death. In this context, proteolytic enzymes produced by these eukaryotic microorganisms are appointed and, in some cases, proven to be excellent targets for searching novel natural and/or synthetic pharmacological compounds, in order to cure or prevent invasive fungal/trypanosomatid diseases. With this task in mind, our research group and others have focused on aspartic-type proteases, since the activity of this class of hydrolytic enzymes is directly implicated in several facets of basic biological processes of both fungal and trypanosomatid cells as well as due to the participation in numerous events of interaction between these microorganisms and host structures. In the present paper, a concise revision of the beneficial effects of aspartic protease inhibitors, with emphasis on the aspartic protease inhibitors used in the anti-human immunodeficiency virus therapy, will be presented and discussed using our experience with the following microbial models: the yeast Candida albicans, the filamentous fungus Fonsecaea pedrosoi and the protozoan trypanosomatid Leishmania amazonensis.

Roles of sphingosine 1-phosphate on tumorigenesis

Sphingosine 1-phosphate (S1P) is a bioactive sphingolipid with a variety of biological activities. It is generated from the conversion of ceramide to sphingosine by ceramidase and the subsequent conversion of sphingosine to S1P, which is catalyzed by sphingosine kinases. Through increasing its intracellular levels by sphingolipid metabolism and binding to its cell surface receptors, S1P regulates several physiological and pathological processes, including cell proliferation, migration, angiogenesis and autophagy. These processes are responsible for tumor growth, metastasis and invasion and promote tumor survival. Since ceramide and S1P have distinct functions in regulating in cell fate decision, the balance between the ceramide/sphingosine/S1P rheostat becomes a potent therapeutic target for cancer cells. Herein, we summarize our current understanding of S1P signaling on tumorigenesis and its potential as a target for cancer therapy.

Tumor-suppressive sphingosine-1-phosphate receptor-2 counteracting tumor-promoting sphingosine-1-phosphate receptor-1 and sphingosine kinase 1 - Jekyll Hidden behind Hyde

Sphingosine-1-phosphate (S1P) is a plasma lipid mediator with multiple roles in mammalian development, physiology and pathophysiology. It is constitutively produced mostly by erythrocytes by the action of sphingosine kinase 1 (SphK1), resulting in high (∼0.5 micromolar) steady-state plasma S1P content and steep S1P concentration gradient imposed between plasma/lymph/tissue interstitial fluid. S1P is also locally produced by activated platelets and tumor cells, in the latter case SphK1 is a downstream target of activated Ras mutant and hypoxia, and is frequently upregulated especially in advanced stages of tumors. Most if not all of the S1P actions in vertebrates are mediated through evolutionarily conserved G protein-coupled S1P receptor family. Ubiquitously expressed mammalian subtypes S1PR1, S1PR2 and S1PR3 mediate pleiotropic actions of S1P in diverse cell types, through coupling to distinctive repertoire of heterotrimeric G proteins. S1PR1 and S1PR3 mediate directed cell migration toward S1P through coupling to G(i) and activating Rac, a Rho family small G protein essential for cell migration. Indeed, S1PR1 expressed in lymphocytes directs their egress from lymph nodes into lymph and recirculation, serving as the target for downregulation by the immunosuppressant FTY720 (fingolimod). S1PR1 in endothelial cells plays an essential role in vascular maturation in embryonic stage, and mediates angiogenic and vascular protective roles of S1P which include eNOS activation and maintenance of barrier integrity. It is likely that S1PR1 and SphK1 expressed in host endothelial cells and tumor cells act in concert in a paracrine loop to contribute to tumor angiogenesis, tumor invasion and progression. In sharp contrast, S1PR2 mediates S1P inhibition of Rac at the site downstream of G(12/13)-mediated Rho activation, thus identified as the first G protein-coupled receptor that negatively regulates Rac and cell migration. S1PR2 could also mediate inhibition of Akt and cell proliferation/survival signaling via Rho-ROCK-PTEN pathway. S1PR2 expressed in tumor cells mediates inhibition of cell migration and invasion in vitro and metastasis in vivo. Moreover, S1PR2 expressed in host endothelial cells and tumor-infiltrating myeloid cells in concert mediates potent inhibition of tumor angiogenesis and tumor growth in vivo, with inhibition of VEGF expression and MMP9 activity. These recent findings provide further basis for S1P receptor subtype-specific, novel therapeutic tactics for individualized treatment of patients with cancer.

To stay or to leave: Stem cells and progenitor cells navigating the S1P gradient

Most hematopoietic stem progenitor cells (HSPCs) reside in bone marrow (BM), but a small amount of HSPCs have been found to circulate between BM and tissues through blood and lymph. Several lines of evidence suggest that sphingosine-1-phosphate (S1P) gradient triggers HSPC egression to blood circulation after mobilization from BM stem cell niches. Stem cells also visit certain tissues. After a temporary 36 h short stay in local tissues, HSPCs go to lymph in response to S1P gradient between lymph and tissue and eventually enter the blood circulation. S1P also has a role in the guidance of the primitive HSPCs homing to BM in vivo, as S1P analogue FTY720 treatment can improve HSPC BM homing and engraftment. In stress conditions, various stem cells or progenitor cells can be attracted to local injured tissues and participate in local tissue cell differentiation and tissue rebuilding through modulation the expression level of S1P(1), S1P(2) or S1P(3) receptors. Hence, S1P is important for stem cells circulation in blood system to accomplish its role in body surveillance and injury recovery.

Muscle atrophy induced by SOD1G93A expression does not involve the activation of caspase in the absence of denervation

Background

The most remarkable feature of skeletal muscle is the capacity to adapt its morphological, biochemical and molecular properties in response to several factors. Nonetheless, under pathological conditions, skeletal muscle loses its adaptability, leading to atrophy or wasting. Several signals might function as physiopathological triggers of muscle atrophy. However, the specific mechanisms underlying the atrophic phenotype under different pathological conditions remain to be fully elucidated. In this paper, we address the involvement of caspases in the induction of muscle atrophy in experimental models of amyotrophic lateral sclerosis (ALS) expressing the mutant SOD1^G93A transgene either locally or ubiquitously.

Results

We demonstrate that SOD1^G93A-mediated muscle atrophy is independent from caspase activity. In particular, the expression of SOD1^G93A promotes a reduction of the phosphatidylinositol 3-kinase/Akt pathway associated with activation of forkhead box O3. In contrast, the activation of caspases occurs later and is causally linked to motor neuron degeneration, which is associated with exacerbation of the atrophic phenotype and a shift in fiber-type composition.

Conclusion

This study suggests that muscle atrophy induced by the toxic effect of SOD1^G93A is independent from the activation of apoptotic markers and that caspase-mediated apoptosis is a process activated upon muscle denervation.

An outlook on ion signaling and ionome of mycorrhizal symbiosis

The 450-million-year-old interaction between the majority of land plants and mycorrhizal fungi is one of the most ancient, abundant, and ecologically important symbiosis on earth. The early events in the evolution of mycorrhizal symbioses seem to have involved reciprocal genetic changes in ancestral plants and free-living fungi. new data on the mechanism of action of specific signaling molecules and how it influence and is influenced by the membrane ions fluxes and cytoplasm ion oscillations which integrate the symbiotic ionome are improving our understanding of the molecular bases of the mycorrhization process. This mini-review will highlight topics regarding what is known about the ionome and ionic communication in the arbuscular mycorrhizal symbiosis focusing on the signals involved in the development of symbioses. Here we present an overview integrating the available data with the prospects of the research in the field.

The role of microRNA in cardiac excitability

Cardiomyocytes are excitable cells that can generate and propagate excitations; excitability is a fundamental characteristic of these cells, which is reflected by action potential; the changes of transmembrane potential as a function of time; and orchestrated by ion channels, transporters, and cellular proteins. The electrical excitation evoked in muscles must be transformed into mechanical contraction through the so-called excitation-contraction coupling mechanism, and the proper contraction of cardiac muscles then drives pumping of blood to the body circulation. Arrhythmias are electrical disturbances that can result in irregular heart beating with consequent insufficient pumping of blood. Arrhythmias are often lethal, constituting a major cause for cardiac death, particularly sudden cardiac death, in myocardial infarction and heart failure. Recent studies have led to discovery of microRNAs (miRNAs) as a new player in the cardiac excitability by fine-tuning expression of ion channels, transporters, and cellular proteins, which determines the arrhythmogenicity in many conditions. This review article will give a comprehensive summary on the data available in the literature. The basics of cardiac excitability will first be introduced, followed by a brief introduction to the basics of miRNAs. Then, studies on regulation of cardiac excitability by miRNAs will be described and analyzed. Finally, concluding remarks will be provided.

Surveying selenium speciation from soil to cell--forms and transformations

The aim of this review is to present and evaluate the present knowledge of which selenium species are available to the general population in the form of food and common supplements and how these species are metabolized in mammals. The overview of the selenium sources takes a horizontal approach, which encompasses identification of new metabolites in yeast and food of plant and animal origin, whereas the survey of the mammalian metabolism takes a horizontal as well as a vertical approach. The vertical approach encompasses studies on dynamic conversions of selenium compounds within cells, tissues or whole organisms. New and improved sample preparation, separation and detection methods are evaluated from an analytical chemical perspective to cover the progress in horizontal speciation, whereas the analytical methods for the vertical speciation and the interpretations of the results are evaluated from a biological angle as well.

Uniform categorization of biocommunication in bacteria, fungi and plants

This article describes a coherent biocommunication categorization for the kingdoms of bacteria, fungi and plants. The investigation further shows that, besides biotic sign use in trans-, inter- and intraorganismic communication processes, a common trait is interpretation of abiotic influences as indicators to generate an appropriate adaptive behaviour. Far from being mechanistic interactions, communication processes within organisms and between organisms are sign-mediated interactions. Sign-mediated interactions are the precondition for every cooperation and coordination between at least two biological agents such as cells, tissues, organs and organisms. Signs of biocommunicative processes are chemical molecules in most cases. The signs that are used in a great variety of signaling processes follow syntactic (combinatorial), pragmatic (context-dependent) and semantic (content-specific) rules. These three levels of semiotic rules are helpful tools to investigate communication processes throughout all organismic kingdoms. It is not the aim to present the latest empirical data concerning communication in these three kingdoms but to present a unifying perspective that is able to interconnect transdisciplinary research on bacteria, fungi and plants.

Regenerative frontiers in craniofacial reconstruction: grand challenges and opportunities for the mammalian transforming growth factor-β proteins

Science's fascination with bone and its repair processes span for thousands of years since the ancient Greek Hippocrates, the father of Medicine, made the key discovery that bone heals without scarring. Through the centuries, several lucid investigators perceived that the extracellular matrix of bone must be a reservoir of differentiating and morphogenetic factors ultimately responsible for its pronounced healing potential (reviewed in Urist, 1968, 1994; Reddi, 2000; Ripamonti et al., 2006).

Method for lipidomic analysis: p53 expression modulation of sulfatide, ganglioside, and phospholipid composition of U87 MG glioblastoma cells

Lipidomics can complement genomics and proteomics by providing new insight into dynamic changes in biomembranes; however, few reports in the literature have explored, on an organism-wide scale, the functional link between nonenzymatic proteins and cellular lipids. Here, we report changes induced by adenovirus-delivered wild-type p53 gene and chemotherapy of U87 MG glioblastoma cells, a treatment known to trigger apoptosis and cell cycle arrest. We compare polar lipid changes in treated cells and control cells by use of a novel, sensitive method that employs lipid extraction, one-step liquid chromatography separation, high-resolution mass analysis, and Kendrick mass defect analysis. Nano-LC FT-ICR MS and quadrupole linear ion trap MS/MS analysis of polar lipids yields hundreds of unique assignments of glyco- and phospholipids at sub-ppm mass accuracy and high resolving power (m/Deltam50% = 200 000 at m/z 400) at 1 s/scan. MS/MS data confirm molecular structures in many instances. Sulfatides are most highly modulated by wild-type p53 treatment. The treatment also leads to an increase in phospholipids such as phosphatidyl inositols, phosphatidyl serines, phosphatidyl glycerols, and phosphatidyl ethanolamines. An increase in hydroxylated phospholipids is especially noteworthy. Also, a decrease in the longer chain gangliosides, GD1 and GM1b, is observed in wild-type p53 (treated) cells.

Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3

Tissue degradation by the matrix metalloproteinase gelatinase A is pivotal to inflammation and metastases. Recognizing the catalytic importance of substrate-binding exosites outside the catalytic domain, we screened for extracellular substrates using the gelatinase A hemopexin domain as bait in the yeast two-hybrid system. Monocyte chemoattractant protein-3 (MCP-3) was identified as a physiological substrate of gelatinase A. Cleaved MCP-3 binds to CC-chemokine receptors-1, -2, and -3, but no longer induces calcium fluxes or promotes chemotaxis, and instead acts as a general chemokine antagonist that dampens inflammation. This suggests that matrix metalloproteinases are both effectors and regulators of the inflammatory response.

Conservative surgery in the Zollinger-Ellison syndrome

Breast cancer stem cells have been known to contribute immensely to the carcinogenesis of the breast and therapeutic resistance in the clinic. Current studies show that the population of breast cancer stem cells is heterogeneous, involving various cellular markers and regulatory signaling pathways. In addition, different subtypes of breast cancer exhibit distinct subtypes and frequencies of breast cancer stem cells. In this review, we provide an overview of the characteristics of breast cancer stem cells, including their various molecular markers, prominent regulatory signaling, and complex microenvironment. The cellular origins of breast cancer are discussed to understand the heterogeneity and diverse differentiations of stem cells. Importantly, we also outline the recent advances and controversies in the therapeutic implications of breast cancer stem cells in different subtypes of breast cancer.