The Inverse G-Wishart Distribution and Variational Message Passing

Message passing on a factor graph is a powerful paradigm for the coding of approximate inference algorithms for arbitrarily graphical large models. The notion of a factor graph fragment allows for compartmentalization of algebra and computer code. We show that the Inverse G-Wishart family of distributions enables fundamental variational message passing factor graph fragments to be expressed elegantly and succinctly. Such fragments arise in models for which approximate inference concerning covariance matrix or variance parameters is made, and are ubiquitous in contemporary statistics and machine learning

Functional compartmentalization of Rad9 and Hus1 reveals diverse assembly of the 9-1-1 complex components during the DNA damage response in Leishmania

The Rad9-Rad1-Hus1 (9-1-1) complex is a key component in the coordination of DNA damage sensing, cell cycle progression and DNA repair pathways in eukaryotic cells. This PCNA-related trimer is loaded onto RPA-coated single stranded DNA and interacts with ATR kinase to mediate effective checkpoint signaling to halt the cell cycle and to promote DNA repair. Beyond these core activities, mounting evidence suggests that a broader range of functions can be provided by 9-1-1 structural diversification. The protozoan parasite Leishmania is an early-branching eukaryote with a remarkably plastic genome, which hints at peculiar genome maintenance mechanisms. Here, we investigated the existence of homologs of the 9-1-1 complex subunits in L. major and found that LmRad9 and LmRad1 associate with chromatin in response to replication stress and form a complex in vivo with LmHus1. Similar to LmHus1, LmRad9 participates in telomere homeostasis and in the response to both replication stress and double strand breaks. However, LmRad9 and LmHus1-deficient cells present markedly opposite phenotypes, which suggest their functional compartmentalization. We show that some of the cellular pool of LmRad9 forms an alternative complex and that some of LmHus1 exists as a monomer. We propose that the diverse assembly of the Leishmania 9-1-1 subunits mediates functional compartmentalization, which has a direct impact on the response to genotoxic stress

Trombin és ischémia együttes hatása a vér-agy-gát sejtjeire = The effects of thrombin and ischemia on the cells of the blood-brain-barrier

A vér-agy-gát (VAG) sejtjeiben, agyi kapilláris endotél sejtekben és asztrocitákban vizsgáltuk trombin és receptorainak kölcsönhatását.. A trombin szignalizáció meghatározott lépéseit tanulmányoztuk, az intracelluláris Ca szint változását és az ERK foszforilációt. Kimutattuk a PAR-1 és PAR-4 thrombin receptorok expresszióját és a két receptor eltérő Ca- ill. ERK szignalizációját. Angiogenezis témában a tumor indukált angiogenezis kvantitativ modeljét dolgoztuk ki. A tumor MVD (mikrovaszkuláris denzitás) csökkenése ill. növekedése általában diagnosztikus paraméterként használt a tumor terápia során. Az általunk kidolgozott kvantitativ angiogenezis model predikciói szerint viszont tumor mikroerek száma, ezek denzitása (MVD, mikrovaszkuláris denzitás) nem feltétlenül áll összhangban a tumor növekedésével. Ez a predikció összhangban van a melanomában publikált kisérleti angiogenezis tapasztalataival. Általánositva, a tumor indukált angiogenezis kezdeti lépéseiben a tumor MVD-n kivül fontos szerepe van az eredeti szöveti környezet mikrovaszkulásris sürüségének, illetve a tumor metabolikus aktivitásának. | Protease activated receptors (PARs) mediate thrombin signaling of brain endothelial cells and thrombin accelerate intracerebral ischemia. We measuered PAR expression, [Ca2+]i and extracellular-signal-regulated kinase (ERK) phosphorylation in brain capillary endothelial cells. Calcium imaging confirmed that the cells responded to PAR-1 and PAR-4 agonist peptide by an elevation of [Ca2+]i , the shape of [Ca2+]i transient was different. Ca2+ entry was required to maintain oscillations. A method to culture brain capillary endothelial cells on glass, covered by Matrigel was worked out.The procedure yields cells that express tight junction proteins ZO-1, claudin-5 and ?-catenin. Glass coverslips covered with Matrigel provide a stable and low background base for microfluorimetric calcium measurements. The transformation of the regular vasculature in normal tissue into a inhomogeneous tumor speci?c capillary network is described. The theoretical model incorporates tumor growth, vessel cooption, neo-vascularization, vessel collapse and cell death.Compartmentalization of the tumor into regions differing in vessel density, diameter and in necrosis is observed in agreement with the vessel morphology found in human melanoma. The model predicts that microvascular density (MVD), regarded as an important diagnostic tool in cancer treatment, does not determine the tempo of tumor progression. Instead it is suggested that the MVD of the original tissue and the metabolic demand of the tumor cell plays the role in tumor growth

Retrograde trafficking of Argonaute 2 acts as a rate-limiting step for de novo miRNP formation on endoplasmic reticulum–attached polysomes in mammalian cells

microRNAs are short regulatory RNAs in metazoan cells. Regulation of miRNA activity and abundance is evident in human cells where availability of target messages can influence miRNA biogenesis by augmenting the Dicer1-dependent processing of precursors to mature microRNAs. Requirement of subcellular compartmentalization of Ago2, the key component of miRNA repression machineries, for the controlled biogenesis of miRNPs is reported here. The process predominantly happens on the polysomes attached with the endoplasmic reticulum for which the subcellular Ago2 trafficking is found to be essential. Mitochondrial tethering of endoplasmic reticulum and its interaction with endosomes controls Ago2 availability. In cells with depolarized mitochondria, miRNA biogenesis gets impaired, which results in lowering of de novo–formed mature miRNA levels and accumulation of miRNA-free Ago2 on endosomes that fails to interact with Dicer1 and to traffic back to endoplasmic reticulum for de novo miRNA loading. Thus, mitochondria by sensing the cellular context regulates Ago2 trafficking at the subcellular level, which acts as a rate-limiting step in miRNA biogenesis process in mammalian cells

Electrical Compartmentalization in Neurons

The dendritic tree of neurons plays an important role in information processing in the brain. While it is thought that dendrites require independent subunits to perform most of their computations, it is still not understood how they compartmentalize into functional subunits. Here, we show how these subunits can be deduced from the properties of dendrites. We devised a formalism that links the dendritic arborization to an impedance-based tree graph and show how the topology of this graph reveals independent subunits. This analysis reveals that cooperativity between synapses decreases slowly with increasing electrical separation and thus that few independent subunits coexist. We nevertheless find that balanced inputs or shunting inhibition can modify this topology and increase the number and size of the subunits in a context-dependent manner. We also find that this dynamic recompartmentalization can enable branch-specific learning of stimulus features. Analysis of dendritic patch-clamp recording experiments confirmed our theoretical predictions.Peer reviewe

Synchronization of Nonlinear Circuits in Dynamic Electrical Networks with General Topologies

Sufficient conditions are derived for global asymptotic synchronization in a system of identical nonlinear electrical circuits coupled through linear time-invariant (LTI) electrical networks. In particular, the conditions we derive apply to settings where: i) the nonlinear circuits are composed of a parallel combination of passive LTI circuit elements and a nonlinear voltage-dependent current source with finite gain; and ii) a collection of these circuits are coupled through either uniform or homogeneous LTI electrical networks. Uniform electrical networks have identical per-unit-length impedances. Homogeneous electrical networks are characterized by having the same effective impedance between any two terminals with the others open circuited. Synchronization in these networks is guaranteed by ensuring the stability of an equivalent coordinate-transformed differential system that emphasizes signal differences. The applicability of the synchronization conditions to this broad class of networks follows from leveraging recent results on structural and spectral properties of Kron reduction---a model-reduction procedure that isolates the interactions of the nonlinear circuits in the network. The validity of the analytical results is demonstrated with simulations in networks of coupled Chua's circuits