Dopamine D4 Receptor Agonist Drastically Increases Delta Activity in the Thalamic Nucleus Reuniens: Potential Role in Communication between Prefrontal Cortex and Hippocampus

Network oscillations are essential for all cognitive functions. Oscillatory deficits are well established in psychiatric diseases and are recapitulated in animal models. They are significantly and specifically affected by pharmacological interventions using psychoactive compounds. Dopamine D4 receptor (D4R) activation was shown to enhance gamma rhythm in freely moving rats and to specifically affect slow delta and theta oscillations in the urethane-anesthetized rat model. The goal of this study was to test the effect of D4R activation on slow network oscillations at delta and theta frequencies during wake states, potentially supporting enhanced functional connectivity during dopamine-induced attention and cognitive processing. Network activity was recorded in the prefrontal cortex (PFC), hippocampus (HC) and nucleus reuniens (RE) in control conditions and after injecting the D4R agonist A-412997 (3 and 5 mg/kg; systemic administration). We found that A-412997 elicited a lasting (~40 min) wake state and drastically enhanced narrow-band delta oscillations in the PFC and RE in a dose-dependent manner. It also preferentially enhanced delta synchrony over theta coupling within the PFC-RE-HC circuit, strongly strengthening PFC-RE coupling. Thus, our findings indicate that the D4R may contribute to cognitive processes, at least in part, through acting on wake delta oscillations and that the RE, providing an essential link between the PFC and HC, plays a prominent role in this mechanism.

CLIPB4 Is a Central Node in the Protease Network that Regulates Humoral Immunity in Anopheles gambiae Mosquitoes

Insect humoral immune responses are regulated in part by protease cascades, whose components circulate as zymogens in the hemolymph. In mosquitoes, these cascades consist of clip-domain serine proteases (cSPs) and/or their non-catalytic homologs, which form a complex network, whose molecular make-up is not fully understood. Using a systems biology approach, based on a co-expression network of gene family members that function in melanization and co-immunoprecipitation using the serine protease inhibitor (SRPN)2, a key negative regulator of the melanization response in mosquitoes, we identify the cSP CLIPB4 from the African malaria mosquito Anopheles gambiae as a central node in this protease network. CLIPB4 is tightly co-expressed with SRPN2 and forms protein complexes with SRPN2 in the hemolymph of immune-challenged female mosquitoes. Genetic and biochemical approaches validate our network analysis and show that CLIPB4 is required for melanization and antibacterial immunity, acting as a prophenoloxidase (proPO)-activating protease, which is inhibited by SRPN2. In addition, we provide novel insight into the structural organization of the cSP network in An. gambiae, by demonstrating that CLIPB4 is able to activate proCLIPB8, a cSP upstream of the proPO-activating protease CLIPB9. These data provide the first evidence that, in mosquitoes, cSPs provide branching points in immune protease networks and deliver positive reinforcement in proPO activation cascades.

CLIPB4 is a central node in the protease network that regulates humoral immunity in Anopheles gambiae mosquitoes

Insect humoral immune responses are regulated in part by protease cascades, whose components circulate as zymogens in the hemolymph. In mosquitoes, these cascades consist of clip domain serine proteases (cSPs) and/or their non-catalytic homologs (cSPHs), which form a complex network, whose molecular make-up is not fully understood. Using a systems biology approach, based on a co-expression network of gene family members that function in melanization and co-immunoprecipitation using the serine protease inhibitor (SRPN)2, a key negative regulator of the melanization response in mosquitoes, we identify the cSP CLIPB4 from the African malaria mosquito Anopheles gambiae as a central node in this protease network. CLIPB4 is tightly co-expressed with SRPN2 and forms protein complexes with SRPN2 in the hemolymph of immune-challenged female mosquitoes. Genetic and biochemical approaches validate our network analysis and show that CLIPB4 is required for melanization and antibacterial immunity, acting as a prophenoloxidase (proPO)-activating protease, which is inhibited by SRPN2. In addition, we provide novel insight into the structural organization of the cSP network in An. gambiae, by demonstrating that CLIPB4 is able to activate proCLIPB8, a cSP upstream of the proPO-activating protease CLIPB9. These data provide the first evidence that, in mosquitoes, cSPs provide branching points in immune protease networks and deliver positive reinforcement in proPO activation cascades.

GeCoNet-Tool: a software package for gene co-expression network construction and analysis

BACKGROUND

Network analysis is a powerful tool for studying gene regulation and identifying biological processes associated with gene function. However, constructing gene co-expression networks can be a challenging task, particularly when dealing with a large number of missing values.

RESULTS

We introduce GeCoNet-Tool, an integrated gene co-expression network construction and analysis tool. The tool comprises two main parts: network construction and network analysis. In the network construction part, GeCoNet-Tool offers users various options for processing gene co-expression data derived from diverse technologies. The output of the tool is an edge list with the option of weights associated with each link. In network analysis part, the user can produce a table that includes several network properties such as communities, cores, and centrality measures. With GeCoNet-Tool, users can explore and gain insights into the complex interactions between genes.

Feature learning and network structure from noisy node activity data

In the studies of network structures, much attention has been devoted to developing approaches to reconstruct networks and predict missing links when edge-related information is given. However, such approaches are not applicable when we are only given noisy node activity data with missing values. This work presents an unsupervised learning framework to learn node vectors and construct networks from such node activity data. First, we design a scheme to generate random node sequences from node context sets, which are generated from node activity data. Then, a three-layer neural network is adopted training the node sequences to obtain node vectors, which allow us to construct networks and capture nodes with synergistic roles. Furthermore, we present an entropy-based approach to select the most meaningful neighbors for each node in the resulting network. Finally, the effectiveness of the method is validated through both synthetic and real data.

A global [Formula: see text] gene co-expression network constructed from hundreds of experimental conditions with missing values

BACKGROUND

Gene co-expression networks (GCNs) can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarrays and RNA-sequencing, allow evaluating thousands of gene expression data simultaneously, but these methodologies provide results that cannot be directly compared. Thus, it is complex to analyze co-expression relations between genes, especially when there are missing values arising for experimental reasons. Networks are a helpful tool for studying gene co-expression, where nodes represent genes and edges represent co-expression of pairs of genes.

RESULTS

In this paper, we establish a method for constructing a gene co-expression network for the Anopheles gambiae transcriptome from 257 unique studies obtained with different methodologies and experimental designs. We introduce the sliding threshold approach to select node pairs with high Pearson correlation coefficients. The resulting network, which we name AgGCN1.0, is robust to random removal of conditions and has similar characteristics to small-world and scale-free networks. Analysis of network sub-graphs revealed that the core is largely comprised of genes that encode components of the mitochondrial respiratory chain and the ribosome, while different communities are enriched for genes involved in distinct biological processes.

CONCLUSION

Analysis of the network reveals that both the architecture of the core sub-network and the network communities are based on gene function, supporting the power of the proposed method for GCN construction. Application of network science methodology reveals that the overall network structure is driven to maximize the integration of essential cellular functions, possibly allowing the flexibility to add novel functions.

Layer reconstruction and missing link prediction of a multilayer network with maximum a posteriori estimation

From social networks to biological networks, different types of interactions among the same set of nodes characterize distinct layers, which are termed multilayer networks. Within a multilayer network, some layers, confirmed through different experiments, could be structurally similar and interdependent. In this paper, we propose a maximum a posteriori-based method to study and reconstruct the structure of a target layer in a multilayer network. Nodes within the target layer are characterized by vectors, which are employed to compute edge weights. Further, to detect structurally similar layers, we propose a method for comparing networks based on the eigenvector centrality. Using similar layers, we obtain the parameters of the conjugate prior. With this maximum a posteriori algorithm, we can reconstruct the target layer and predict missing links. We test the method on two real multilayer networks, and the results show that the maximum a posteriori estimation is promising in reconstructing the target layer even when a large number of links is missing.

A "human knockout" model to investigate the influence of the α-actinin-3 protein on exercise-induced mitochondrial adaptations

Research in α-actinin-3 knockout mice suggests a novel role for α-actinin-3 as a mediator of cell signalling. We took advantage of naturally-occurring human “knockouts” (lacking α-actinin-3 protein) to investigate the consequences of α-actinin-3 deficiency on exercise-induced changes in mitochondrial-related genes and proteins, as well as endurance training adaptations. At baseline, we observed a compensatory increase of α-actinin-2 protein in ACTN3 XX (α-actinin-3 deficient; n = 18) vs ACTN3 RR (expressing α-actinin-3; n = 19) participants but no differences between genotypes for markers of aerobic fitness or mitochondrial content and function. There was a main effect of genotype, without an interaction, for RCAN1-4 protein content (a marker of calcineurin activity). However, there was no effect of genotype on exercise-induced expression of genes associated with mitochondrial biogenesis, nor post-training physiological changes. In contrast to results in mice, loss of α-actinin-3 is not associated with higher baseline endurance-related phenotypes, or greater adaptations to endurance exercise training in humans.

Unraveling the discrepancies in size dependence of hardness and thermal stability in crystalline/amorphous nanostructured multilayers: Cu/Cu-Ti vs. Cu/HfO2

Crystalline/amorphous interfaces (CAIs) confer outstanding mechanical properties on crystalline/amorphous nanostructured multilayers (C/ANMs), which are widely used in micro/nanodevices, because their unique interfacial structure possesses high strain compatibility. In this study, Cu/X (X = Cu-Ti, HfO2) C/ANMs with equal layer thicknesses (h) were comparatively investigated in terms of size-dependent hardness (H) and thermal stability to uncover the fundamental difference(s) between Cu/Cu-Ti and Cu/HfO2. It was found that both as-deposited Cu/Cu-Ti and Cu/HfO2 C/ANMs exhibited a maximum hardness at a critical thickness of h ∼30 nm, which was caused by a transition from confined dislocation gliding to dislocation transmission across the interface. Specifically, the Cu/Cu-Ti C/ANMs exhibited annealing hardening, whereas the Cu/HfO2 C/ANMs exhibited annealing softening associated with a minimum softening at h ∼ 30 nm, which was closely correlated with their thermal stability. In comparison with monolithic amorphous X thin films, the glassy X nanolayers in the present Cu/X C/ANMs exhibited reduced thermal stability and a trend that smaller sizes led to higher stability. The underlying mechanism of the size-dependent crystallization behavior of X nanolayers is discussed in terms of the constraining effects of the interface. These findings provide deep insights into the design of Cu/metallic-glass and Cu/ceramic-glass C/ANMs with optimal performance.

STAT3 regulates cytokine expression in peripheral blood mononuclear cells from asthma patients

Asthma is a common long term inflammatory disease of the airways. This disease affected millions of people worldwide. Recently, it is demonstrated that signal transducer and activator of transcription 3 (STAT3) plays critical role in asthma occurrence. In the current study, we isolated peripheral blood mononuclear cells (PBMCs) from patients with mild and moderate asthma, and then determined the correlation between STAT3 and cytokine expression. We found that the concentration and mRNA level of cytokines was increased in PBMCs from asthma patients. The concentration and mRNA level of cytokines was altered by the regulation of STAT3 expression and the concentration and mRNA expression level of cytokines was positively correlated with STAT3 activation. Furthermore, phosphorylated STAT3 expression in PBMCs from asthma patients was increased compared with the control. Collectively, this study directly proved that STAT3 was correlated with cytokine expression in PBMCs from asthma patients, providing a potential linkage between STAT3 and pathogenesis of asthma.

Linking genomic reorganization to tumor initiation via the giant cell cycle

To investigate the mechanisms underlying our recent paradoxical finding that mitotically incapacitated and genomically unstable polyploid giant cancer cells (PGCCs) are capable of tumor initiation, we labeled ovarian cancer cells with α-tubulin fused to green fluorescent protein, histone-2B fused to red fluorescent protein and FUCCI (fluorescent ubiquitination cell cycle indicator), and tracked the spatial and time-dependent change in spindle and chromosomal dynamics of PGCCs using live-cell fluorescence time-lapse recording. We found that single-dose (500 nm) treatment with paclitaxel paradoxically initiated endoreplication to form PGCCs after massive cell death. The resulting PGCCs continued self-renewal via endoreplication and further divided by nuclear budding or fragmentation; the small daughter nuclei then acquired cytoplasm, split off from the giant mother cells and acquired competency in mitosis. FUCCI showed that PGCCs divided via truncated endoreplication cell cycle (endocycle or endomitosis). Confocal microscopy showed that PGCCs had pronounced nuclear fragmentation and lacked expression of key mitotic proteins. PGCC-derived daughter cells were capable of long-term proliferation and acquired numerous new genome/chromosome alterations demonstrated by spectral karyotyping. These data prompt us to conceptualize a giant cell cycle composed of four distinct but overlapping phases, initiation, self-renewal, termination and stability. The giant cell cycle may represent a fundamental cellular mechanism to initiate genomic reorganization to generate new tumor-initiating cells in response to chemotherapy-induced stress and contributes to disease relapse.

Recruitment of trimeric proliferating cell nuclear antigen by G1-phase cyclin-dependent kinases following DNA damage with platinum-based antitumour agents

BACKGROUND

In cycling tumour cells, the binary cyclin-dependent kinase Cdk4/cyclin D or Cdk2/cyclin E complex is inhibited by p21 following DNA damage to induce G1 cell-cycle arrest. However, it is not known whether other proteins are also recruited within Cdk complexes, or their role, and this was investigated.

METHODS

Ovarian A2780 tumour cells were exposed to the platinum-based antitumour agent 1R,2R-diaminocyclohexane(trans-diacetato)(dichloro)platinum(IV) (DAP), which preferentially induces G1 arrest in a p21-dependent manner. The Cdk complexes were analysed by gel filtration chromatography, immunoblot and mass spectrometry.

RESULTS

The active forms of Cdk4 and Cdk2 complexes in control tumour cells have a molecular size of ~140 kDa, which increased to ~290 kDa when inhibited following G1 checkpoint activation by DAP. Proteomic analysis identified Cdk, cyclin, p21 and proliferating cell nuclear antigen (PCNA) in the inhibited complex, and biochemical studies provided unequivocal evidence that the increase in ~150 kDa of the inhibited complex is consistent with p21-dependent recruitment of PCNA as a trimer, likely bound to three molecules of p21. Although p21 alone was sufficient to inhibit the Cdk complex, PCNA was critical for stabilising p21.

CONCLUSION

G1 Cdk complexes inhibited by p21 also recruit PCNA, which inhibits degradation and, thereby, prolongs activity of p21 within the complex.

RSK promotes G2/M transition through activating phosphorylation of Cdc25A and Cdc25B

Activation of the mitogen-activated protein kinase (MAPK) cascade in mammalian cell lines positively regulates the G2/M transition. The molecular mechanism underlying this biological phenomenon remains poorly understood. Ribosomal S6 kinase (RSK) is a key downstream element of the MAPK cascade. Our previous studies established roles of RSK2 in Cdc25C activation during progesterone-induced meiotic maturation of Xenopus oocytes. In this study we demonstrate that both recombinant RSK and endogenous RSK in Xenopus egg extracts phosphorylate all three isoforms of human Cdc25 at a conserved motif near the catalytic domain. In human HEK293 and PC-3mm2 cell lines, RSK preferentially phosphorylates Cdc25A and Cdc25B in mitotic cells. Phosphorylation of the RSK sites in these Cdc25 isoforms increases their M-phase-inducing activities. Inhibition of RSK-mediated phosphorylation of Cdc25 inhibits G2/M transition. Moreover, RSK is likely to be more active in mitotic cells than in interphase cells, as evidenced by the phosphorylation status of T359/S363 in RSK. Together, these findings indicate that RSK promotes G2/M transition in mammalian cells through activating phosphorylation of Cdc25A and Cdc25B.

Generation of cancer stem-like cells through the formation of polyploid giant cancer cells

Polyploid giant cancer cells (PGCCs) have been observed by pathologists for over a century. PGCCs contribute to solid tumor heterogeneity, but their functions are largely undefined. Little attention has been given to these cells, largely because PGCCs have been generally thought to originate from repeated failure of mitosis/cytokinesis and have no capacity for long-term survival or proliferation. Here we report our successful purification and culture of PGCCs from human ovarian cancer cell lines and primary ovarian cancer. These cells are highly resistant to oxygen deprivation and could form through endoreduplication or cell fusion, generating regular-sized cancer cells quickly through budding or bursting similar to simple organisms like fungi. They express normal and cancer stem cell markers, they divide asymmetrically and they cycle slowly. They can differentiate into adipose, cartilage and bone. A single PGCC formed cancer spheroids in vitro and generated tumors in immunodeficient mice. These PGCC-derived tumors gained a mesenchymal phenotype with increased expression of cancer stem cell markers CD44 and CD133 and become more resistant to treatment with cisplatin. Taken together, our results reveal that PGCCs represent a resistant form of human cancer using an ancient, evolutionarily conserved mechanism in response to hypoxia stress; they can contribute to the generation of cancer stem-like cells, and also play a fundamental role in regulating tumor heterogeneity, tumor growth and chemoresistance in human cancer.

Upregulation of p27 and its inhibition of CDK2/cyclin E activity following DNA damage by a novel platinum agent are dependent on the expression of p21

The cisplatin analogue 1R,2R-diaminocyclohexane(trans-diacetato)(dichloro)platinum^IV (DAP) is a DNA-damaging agent that will be entering clinical trials for its potent cytotoxic effects against cisplatin-resistant tumour cells. This cytotoxicity may reside in its ability to selectively activate G1-phase checkpoint response by inhibiting CDKs via the p53/p21 pathway. We have now evaluated the role of another CDK inhibitor p27 as a contributor to DAP-mediated inhibition of G1-phase CDK2 activity. Our studies in ovarian A2780 tumour cells demonstrate that p27 levels induced by DAP are comparable to or greater than those seen for p21. The induction of p27 is not through a transcriptional mechanism, but rather is due to a four-fold increase in protein stabilisation through a mechanism dependent on p21. Moreover, DAP-induced p21 promoted the selective increase of p27 in the CDK2 complex, but not in CDK4 complex, and this selective increase contributed to inhibition of the CDK2 kinase activity. The inhibited complex contained either p27 or p21, but not both, with the relative levels of cyclin E associated with p27 and p21 indicating that about 25% of the inhibition of CDK2 activity was due to p27 and 75% due to p21. This study provides the first evidence that p27 upregulation is directly attributable to activation of the p53/p21 pathway by a DNA-damaging agent, and promulgates p53/p21/p27 axis as a significant component of checkpoint response.

Principal component regression analysis with SPSS

The paper introduces all indices of multicollinearity diagnoses, the basic principle of principal component regression and determination of 'best' equation method. The paper uses an example to describe how to do principal component regression analysis with SPSS 10.0: including all calculating processes of the principal component regression and all operations of linear regression, factor analysis, descriptives, compute variable and bivariate correlations procedures in SPSS 10.0. The principal component regression analysis can be used to overcome disturbance of the multicollinearity. The simplified, speeded up and accurate statistical effect is reached through the principal component regression analysis with SPSS.

Bimodal effects of 1R,2R-diaminocyclohexane(trans-diacetato)(dichloro)platinum(IV) on cell cycle checkpoints

1R,2R-Diaminocyclohexane(trans-diacetato)(dichloro)-platinum(IV) (DACH-acetato-Pt) is a novel platinum-based agent that is highly effective against cisplatin-resistant ovarian tumor cells. To probe its cellular mechanism, the effects of DACH-acetato-Pt (0-6.4 microM) on cell cycle checkpoints were examined using the ovarian cancer A2780 cell line as the model system. We found that DACH-acetato-Pt at > or =0.2 microM dramatically inhibited cell growth and induced cell death. At concentrations < or =0.6 microM (low effective concentrations), DACH-acetato-Pt specifically induced G(1) phase arrest by selectively inhibiting cyclin-dependent kinase 4 (Cdk4) and Cdk2 activities. The Cdc2 activity, which regulates G(2)-M phase progression, was unaffected by the drug at these concentrations. At concentrations >0.6 microM (high effective concentrations), DACH-acetato-Pt first transiently inhibited S-phase progression and then blocked cell cycle progression at both G(1) and G(2) phases. These cell cycle effects were associated with sequential inhibitions of Cdk2/cyclin A activity, Cdk4 and Cdk2 activities, and Cdc2 kinase activity. Following the cell cycle effects, both the low and high effective concentrations of DACH-acetato-Pt induced cell death through apoptosis. These results indicate that DACH-acetato-Pt activates multiple cell cycle checkpoints in a bimodal manner and suggest that the cell cycle effects demonstrated in these studies may be linked to its ability to induce apoptosis.

NaCl consumption is attenuated in female KCNE1 null mutant mice

The role of potassium channels in the regulation of NaCl intake has not been investigated previously. One potassium channel, KCNQ1, and its regulator, KCNE1, are expressed in salivary glands and kidneys, and KCNE1 null mutant mice are deficient in KCNQ1 potassium currents. To understand the role of the KCNQ1/KCNE1 channel complex in NaCl taste and intake, we compared the NaCl consumption of KCNE1 +/+ (129/Sv), KCNE1 +/-, and KCNE1 -/- mice using two-bottle intake tests and lick rate tests. Although KCNE1 +/+ and KCNE1 +/- mice exhibited consumption patterns for 75-150 mM NaCl solutions considered typical for 129/Sv mice, the KCNE1 -/- null mutant 129/Sv mice were indifferent to or rejected them. This effect was observed in female mice only, required prior exposure to NaCl solutions, and the extent of rejection was greater after prior exposure to 150 mM NaCl solution than 75 mM NaCl solution. No differences were observed in the avidity for KCl solutions or in lick rates of naive mice for 150 or 300 mM NaCl solutions. These results demonstrate that a single potassium channel gene can influence voluntary NaCl intake. We speculate that disruption of the KCNE1 gene impairs sodium metabolism in female mice drinking high levels of 150 mM NaCl, which causes malaise that becomes associated with NaCl taste, and as a consequence, reduced preference for NaCl.

Tumorhead, a Xenopus gene product that inhibits neural differentiation through regulation of proliferation

Tumorhead (TH) is a novel maternal gene product from Xenopus laevis containing several basic domains and a weak coiled-coil. Overexpression of wild-type TH resulted in increased proliferation of neural plate cells, causing expansion of the neural field followed by neural tube and craniofacial abnormalities. Overexpressed TH protein repressed neural differentiation and neural crest markers, but did not inhibit the neural inducers, pan-neural markers or mesodermal markers. Loss of function by injection of anti-TH antibody inhibited cell proliferation. Our data are consistent with a model in which tumorhead functions in regulating differentiation of the neural tissues but not neural induction or determination through its effect on cell proliferation.