Regulatory links between imprinted genes: evolutionary predictions and consequences

Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.     

Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

O-GalNAc-glycosylation is one of the main types of glycosylation in mammalian cells. No consensus recognition sequence for the O-glycosyltransferases is known, making prediction methods necessary to bridge the gap between the large number of known protein sequences and the small number of proteins experimentally investigated with regard to glycosylation status. From O-GLYCBASE a total of 86 mammalian proteins experimentally investigated for in vivo O-GalNAc sites were extracted. Mammalian protein homolog comparisons showed that a glycosylated serine or threonine is less likely to be precisely conserved than a nonglycosylated one. The Protein Data Bank was analyzed for structural information, and 12 glycosylated structures were obtained. All positive sites were found in coil or turn regions. A method for predicting the location for mucin-type glycosylation sites was trained using a neural network approach. The best overall network used as input amino acid composition, averaged surface accessibility predictions together with substitution matrix profile encoding of the sequence. To improve prediction on isolated (single) sites, networks were trained on isolated sites only. The final method combines predictions from the best overall network and the best isolated site network; this prediction method correctly predicted 76% of the glycosylated residues and 93% of the nonglycosylated residues. NetOGlyc 3.1 can predict sites for completely new proteins without losing its performance. The fact that the sites could be predicted from averaged properties together with the fact that glycosylation sites are not precisely conserved indicates that mucin-type glycosylation in most cases is a bulk property and not a very site-specific one. NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc.     

Stress-mediated signaling in PC12 cells - the role of the small heat shock protein,Hsp27, and Akt in protecting cells from heat stress and nerve growth factor withdrawal

We have investigated the role of stress-activated signaling pathways and the small heat shock protein, Hsp27, in protecting PC12 cells from heat shock and nerve growth factor (NGF) withdrawal-induced apoptosis. PC12 cells and a stable cell line overexpressing Hsp27 (HSPC cells) were subjected to heat shock. This resulted in the rapid activation of Akt followed by p38 mitogen-activated protein kinase (MAPK) signaling, with phosphorylation and intracellular translocation of Hsp27 also detectable. Hsp27 was found to form an immunoprecipitable complex with Akt and p38 MAPK in both non-stimulated and heat shocked cells, although after heat shock there was a gradual dissociation of Akt and p38 from the Hsp27. Cells were differentiated with NGF and then subjected to NGF withdrawal, a treatment which results in substantial cell death over 24-72 h. Hsp27 was shown to be protective against this treatment, since HSPC cells which overexpress Hsp27 showed significantly less cell death than the parental PC12 cells. In addition, we observed that phosphorylation of Akt was maintained in HSPC cells subjected to heat shock and NGF withdrawal compared with the parental cells. Taken together, our results suggest that Hsp27 may protect Akt from dephosphorylation and may also act in stabilizing Akt.     

不同水分处理下双接种丛枝菌根真菌和根瘤菌对疏叶骆驼刺生长及氮素转移的影响

以疏叶骆驼刺为研究对象,设定3个水分梯度正常水分(土壤相对含水量(70±5)%)、干旱胁迫(土壤相对含水量(20±5)%)和复水处理(干旱胁迫60天后恢复至正常水分)与四组接种处理(单接种丛枝菌根真菌(AMF)、单接种根瘤菌、双接种AMF+根瘤菌和不接种),分析不同水分条件下双接种丛枝菌根真菌和根瘤菌对疏叶骆驼刺的生长以及供、受体疏叶骆驼刺之间氮素转移的影响。结果表明,正常水分处理时,双接种疏叶骆驼刺的AMF侵染率、地上生物量、地下生物量、总生物量以及氮含量均要高于单接种处理;根瘤数量、最大荧光(Fm)、初始荧光(Fo)、最大光化学效率(Fv/Fm)与单接种处理之间无差异;在遭遇干旱胁迫时,双接种疏叶骆驼刺的AMF侵染率、总生物量、Fv/Fm均小于单接种处理;地上生物量、地下生物量、根瘤数、Fm、Fo以及氮含量与单接种之间无差异。复水后,双接种疏叶骆驼刺的地上生物量、地下生物量、总生物量、根瘤数均优于单接种;AMF侵染率、氮含量低于单接种;Fm、Fo、Fv/Fm均与单接种之间无差异。在氮素转移方面,正常水分时,双接种与单接种的氮素转移率无差异,在遭遇干旱胁迫时,双接种疏叶骆驼刺的氮素转...     

CCN proteins: A centralized communication network

The CCN family of proteins includes six members presently known as CCN1, CCN2, CCN3, CCN4, CCN5 and CCN6. These proteins were originally designated CYR61, CTGF, NOV, and WISP-1, WISP-2, WISP-3. Although these proteins share a significant amount of structural features and a partial identity with other large families of regulatory proteins, they exhibit different biological functions. A critical examination of the progress made over the past two decades, since the first CCN proteins were discovered brings me to the conclusion that most of our present knowledge regarding the functions of these proteins was predicted very early after their discovery. In an effort to point out some of the gaps that prevent us to reach a comprehensive view of the functional interactions between CCN proteins, it is necessary to reconsider carefully data that was already published and put aside, either because the scientific community was not ready to accept them, or because they were not fitting with the « consensus » when they were published. This review article points to avenues that were not attracting the attention that they deserved. However, it is quite obvious that the six members of this unique family of tetra-modular proteins must act in concert, either simultaneously or sequentially, on the same sites or at different times in the life of living organisms. A better understanding of the spatio-temporal regulation of CCN proteins expression requires considering the family as such, not as a set of single proteins related only by their name. As proposed in this review, there is enough convincing pieces of evidence, at the present time, in favor of these proteins playing a role in the coordination of multiple signaling pathways, and constituting a Centralized Communication Network. Deciphering the hierarchy of regulatory circuits involved in this complex system is an important challenge for the near future. In this article, I would like to briefly review the concept of a CCN family of proteins and critically examine the progress made over the past 10 years in the understanding of their biological functions and involvement in both normal and pathological processes.     

Signal transduction pathways in Synechocystis sp. PCC 6803 and biotechnological implications under abiotic stress

Cyanobacteria have developed various response mechanisms in long evolution to sense and adapt to external or internal changes under abiotic stresses. The signal transduction system of a model cyanobacterium Synechocystis sp. PCC 6803 includes mainly two-component signal transduction systems of eukaryotic-type serine/threonine kinases (STKs), on which most have been investigated at present. These two-component systems play a major role in regulating cell activities in cyanobacteria. More and more co-regulation and crosstalk regulations among signal transduction systems had been discovered due to increasing experimental data, and they are of great importance in corresponding to abiotic stresses. However, mechanisms of their functions remain unknown. Nevertheless, the two signal transduction systems function as an integral network for adaption in different abiotic stresses. This review summarizes available knowledge on the signal transduction network in Synechocystis sp. PCC 6803 and biotechnological implications under various stresses, with focuses on the co-regulation and crosstalk regulations among various stress-responding signal transduction systems.     

Neural Coding with Graded Membrane Potential Changes and Spikes

The neural encoding of sensory stimuli is usually investigated for spike responses, although many neurons are known to convey information by graded membrane potential changes. We compare by model simulations how well different dynamical stimuli can be discriminated on the basis of spiking or graded responses. Although a continuously varying membrane potential contains more information than binary spike trains, we find situations where different stimuli can be better discriminated on the basis of spike responses than on the basis of graded responses. Spikes can be superior to graded membrane potential fluctuations if spikes sharpen the temporal structure of neuronal responses by amplifying fast transients of the membrane potential. Such fast membrane potential changes can be induced deterministically by the stimulus or can be due to membrane potential noise that is influenced in its statistical properties by the stimulus. The graded response mode is superior for discrimination between stimuli on a fine time scale.     

Regulation of progenitor cell survival by a novel chromatin remodeling factor during neural tube development

During development, progenitor cell survival is essential for proper tissue functions, but the underlying mechanisms are not fully understood. Here we show that ERCC6L2, a member of the Snf2 family of helicase-like proteins, plays an essential role in the survival of developing chick neural cells. ERCC6L2 expression is induced by the Sonic Hedgehog (Shh) signaling molecule by a mechanism similar to that of the known Shh target genes Ptch1 and Gli1. ERCC6L2 blocks programmed cell death induced by Shh inhibition and this inhibition is independent of neural tube patterning. ERCC6L2 knockdown by siRNA resulted in the aberrant appearance of apoptotic cells. Furthermore, ERCC6L2 cooperates with the Shh signal and plays an essential role in the induction of the anti-apoptotic factor Bcl-2. Taken together, ERCC6L2 acts as a key factor in ensuring the survival of neural progenitor cells.     

Q-NET – a new scholarly network on quantitative wood anatomy

Quantitative wood anatomy (QWA) is a dynamic research approach of increasing interest that can provide answers to a wide range of research questions across different disciplines. However, the lack of common protocols and knowledge gaps hinder the realisation of the full potential of QWA. Therefore, we established the new community-based network Q-NET to provide an open interdisciplinary platform for exchange and research around QWA. Q-NET (https://qwa-net.com) combines an online knowledge and exchange base with virtual workshops. The first two workshops each attracted more than 125 participants from around the world, demonstrating the community's interest in QWA and this virtual way of networking and collaborating. Indeed, virtual networks such as Q-NET could increase the inclusiveness, efficiency and sustainability of scientific collaboration while providing additional training and teaching opportunities for early career scientists, both of which complement in-person conferences and workshops.