Lang, Florian, Gillian L. Busch, Markus Ritter, Harald Volkl, Siegfried Waldegger, Erich Gulbins, and Dieter Haussinger. Functional Significance of Cell Volume Regulatory Mechanisms. Physiol. Rev. ...

Functional Significance of Cell Volume Regulatory Mechanisms

The current status of the use of nanoparticles for photothermal treatments is reviewed in detail. The different families of heating nanoparticles are described paying special attention to the physical mechanisms at the root of the light-to-heat conversion processes. The heating efficiencies and spectral working ranges are listed and compared. The most important results obtained in both in vivo and in vitro nanoparticle assisted photothermal treatments are summarized. The advantages and disadvantages of the different heating nanoparticles are discussed.

Nanoparticles for photothermal therapies.

https://carollee.labs.wisc.edu/Evolution410_Reading/EpigeneticReview2014.pdf

Transgenerational Epigenetic Inheritance: myths and mechanisms

DNA methylation is a defining feature of mammalian cellular identity and essential for normal development 1,2 . Most cell types, except germ cells and pre-implantation embryos 3–5 , display relatively stable DNA methylation patterns with 70–80% of all CpGs being methylated 6 . Despite recent advances we still have a too limited understanding of when, where and how many CpGs participate in genomic regulation. Here we report the in depth analysis of 42 whole genome bisulfite sequencing (WGBS) data sets across 30 diverse human cell and tissue types. We observe dynamic regulation for only 21.8% of autosomal CpGs within a normal developmental context, a majority of which are distal to transcription start sites. These dynamic CpGs co-localize with gene regulatory elements, particularly enhancers and transcription factor binding sites (TFBS), which allow identification of key lineage specific regulators. In addition, differentially methylated

/pdf/charting-a-dynamic-dna-methylation-landscape-of-the-human-5cpngajiox.pdf

Charting a dynamic DNA methylation landscape of the human genome

https://wiki.uio.no/projects/clsi/images/7/74/Assembly_algorithms_for_next-generation_sequencing_data.pdf

Assembly algorithms for next-generation sequencing data.

Vinculin is a cytoskeletal protein believed to be involved in linking microfilaments to the cell membrane. It is a substrate for the Ca(2+)- and phospholipid-dependent protein kinase C. We show here that when human platelets attach and spread on a solid surface, the alpha isoforms of vinculin become phosphorylated at serine and/or threonine residues. Phosphorylation is dependent on adhesion to a surface, since suspended, unattached platelets can produce filopodia but no phosphorylation of vinculin. Phosphorylation is also dependent on actin polymerization, as it does not occur when platelets had been pretreated with cytochalasin B. Most likely, protein kinase C is responsible for the phosphorylation of vinculin, since phosphorylation also occurs when platelets are treated with a phorbol ester, which activates protein kinase C, and is blocked by treatment with a staurosporine derivative which inhibits this enzyme. These results suggest that phosphorylation plays a role in anchoring vinculin at sites of microfilament-membrane interaction.

Phosphorylation of vinculin in human platelets spreading on a solid surface.

Author response: Long-term balancing selection drives evolution of immunity genes in Capsella

Cell surface carbohydrates play an important role in the regulation of neurite outgrowth during neuronal development. We have investigated the actions of the plant lectin concanavalin A (Con A), a carbohydrate-binding protein, on neurite outgrowth from hippocampal pyramidal neurons in primary cell culture. Neurons plated in culture medium containing nanomolar concentrations of Con A have a larger number of primary neurites arising directly from the cell soma than do neurons plated in culture medium alone. Furthermore, Con A causes counterclock-wise turning of neurites in over 70% of the cultured neurons. Both of these effects of Con A are blocked by the hapten sugar α-methyl-d-mannopyranoside, suggesting that they result from the interaction of Con A with a cell surface carbohydrate. Another lectin with a different sugar specificity, wheat germ agglutinin, does not modulate neurite outgrowth. Analysis of neurite outgrowth using video-enhanced microscopy reveals that the counter-clockwise turning is accompanied by directionally biased extension of filopodia from the growth cones of growing neurites. Treatment of the neurons with cytochalasin, which disrupts actin polymerization, eliminates the neurite turning induced by Con A, suggesting that actin microfilaments are involved in directional control of neurite outgrowth. © 1992 John Wiley & Sons, Inc.

Directional control of neurite outgrowth from cultured hippocampal neurons is modulated by the lectin concanavalin A.

The outermost cell layer of plant roots (epidermis) constantly encounters environmental challenges. The epidermal outer plasma membrane domain harbours the PENETRATION3 (PEN3)/ABCG36/PDR8 ATP-binding cassette transporter that confers non-host resistance to several pathogens. Here, we show that the Arabidopsis ENDOPLASMIC RETICULUM-ARRESTED PEN3 (EAP3) BTB/POZ-domain protein specifically mediates PEN3 exit from the endoplasmic reticulum and confers resistance to a root-penetrating fungus, providing prime evidence for BTB/POZ-domain protein-dependent membrane trafficking underlying disease resistance. PEN3 is polarly localized at the outside of the epidermal layer in roots, and is involved in defence against penetrating pathogens. A forward genetic screen identifies a BTB/POZ protein needed for the correct localization and function of PEN3.

/pdf/arabidopsis-btb-poz-protein-dependent-penetration3-1t82tstbfx.pdf

Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility

Pangenome graphs can represent all variation between multiple genomes, but existing methods for constructing them are biased due to reference-guided approaches. In response, we have developed PanGenome Graph Builder (PGGB), a reference-free pipeline for constructing unbi-ased pangenome graphs. PGGB uses all-to-all whole-genome alignments and learned graph embeddings to build and iteratively refine a model in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.

/pdf/building-pangenome-graphs-3vvr8qyb.pdf

Jörg Hagmann

Papers

Phosphorylation of vinculin in human platelets spreading on a solid surface.

Author response: Long-term balancing selection drives evolution of immunity genes in Capsella

Directional control of neurite outgrowth from cultured hippocampal neurons is modulated by the lectin concanavalin A.

Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility

Building pangenome graphs