Introducing BPS Mechanobiology Blogger Rishita Changede

Rishita is a senior research fellow at the Mechanobiology Institute, National University of Singapore (MBI).. Her primary interest is to understand the design principles that allow the cells and organisms to respond appropriately to their diverse physical (geometry and forces) and chemical (biochemical ligands) environment. With her experience in multidisciplinary approaches, she is aspires to address challenging questions to understand nature of cell matrix interaction and the complex signal integration of the varied signals the cell receives within the cell in response to its local environment and tissue maintenance. Understanding these fundamental questions has implications in regeneration and progression of major diseases such as cancer and ageing related diseases. Her postdoctoral studies with Professor  Michael Sheetz, she developed quantitative super resolution imaging based assays to understand the emergent properties of nascent adhesions. Her work showed that these adhesions form on all substrates of as discs of 100nm with about 50 integrins. These cell matrix adhesions are universally laid down as loose aggregates of modular units of densely packed integrins.

With the satellite meeting in this beautiful tropical island, Rishita is hoping to enjoy the perennial summer with excellent scientist from all around the world. Among other things, she recommends a walk around Clare Quay to see the city or Macritchie reservoir for a walk in the tropical rain forests. Feel free to join her along these trips. For the foodies Singapore has lots to offer and feel free to ask her about it and if you ask nicely, she might ‘bring you to the kampong’ as the locals would put it.

She loves nature in every form, understanding it through science, listening to music in it, playing that music, traveling to see it, photographing it, growing it in her house, and perhaps getting bitten by jelly fish along the path…

In addition to the her posts on this blog, and visiting her poster (if you are attending the meeting)  you can follow Rishita’s understanding of this meeting on Twitter @RishitaChangede.

 

 

From the Field—The Rally for Medical Research

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Eric Jakobsson (far right) visits the office of Senator Mark Kirk with to advocate for NIH funding as part of the Rally for Medical Research.  

On September 21 and 22 I attended the Rally for Medical Research in Washington DC, as a representative of the Biophysical Society.  We visited legislators with the request to fund the National Institutes of Health at a $34.1 billion level for the coming fiscal year, a $2 billion increase from the present year, and to argue for sustainable and robust increases for out years to ensure continued momentum in supporting foundational research and translating those results into cures.

The Rally was dramatically unlike other scientific meetings that I go to.  There were some scientists there, like me.  And Ellen Weiss was there from the Biophysical Society staff and staff from other biomedical science organizations.  But we were all there in support of the patients who came to urge their legislators to support NIH.  There were pancreatic cancer survivors, of whom there are far too few.  There were people living with hydrocephalus, who had undergone twenty or more surgeries to maintain appropriate fluid flow in their brains.  A mother of a child with hydrocephalus.  An older man who had received a lung transplant, the only available treatment for pulmonary fibrosis.  A young woman who is at high genetic risk for developing pulmonary fibrosis, because of her family history.  The list goes on and on.  Each story is different, but a common thread connects them.  For each of these diseases, research at the NIH provides a foundation on which to base a reasonable hope for a cure.

The patient whom I got to know best, because the accident of geography led us to the same schedule of office visits, was Ginger.  Ginger is a single mother with a 13 year old daughter.  She has lived for four years with Stage 4 lung cancer, through a series of clinical trials.  We went to Senate offices in the morning and House in the afternoon.  During the afternoon coffee break Ginger was exhausted, having had therapy the previous day and flying in to DC the previous evening.  But in the congressional office she stiffened up and her voice was firm.  She was on a mission.

In the offices I presented myself as a patient, a parent, and a researcher.  As a patient I have benefited from NIH supported research that led to the understanding of the regulation of smooth muscle governing intraocular pressure, and led in turn to the chemical nature of the eye drops that are preserving my sight.  NIH-supported research has also informed the pattern of treatment of my prostate cancer, I am sure to my benefit.  As a parent however, I became tragically aware that there is as yet neither curative nor palliative effective treatment for Frontotemporal Dementia, with the result that my wife and I helplessly watched our son move from happy successful mid-40’s to death in a little over two years.  As a researcher I talked of my hope that the computational work we are now doing on binding affinities of mutated virus coat proteins with complementarily mutated antibody fragments will lead to the ability to rapidly redesign synthetic antibodies to combat evolving pathogenic viruses.senate-group

I believe we may be at a turning point in congressional support for the NIH.  In one office where we received a cool reception last year, this year the member not only expressed support for us but opened up about the health crises that his mother and his wife had encountered.  Every office that I visited seems to finally get the story: The NIH pipeline of basic research, translational research, and clinical research lengthens lives and improves the quality of lives.

It would be great if everybody who reads this would write to your Congressional Representative and your Senators, telling what the NIH has done for which you and your family are grateful, and what you hope the NIH will be able to do in the future if there is enough support.

-Eric Jakobsson

Last Three Days of the Liposomes, Exosomes and Virosomes Meeting … a sunny afternoon off, a couple of thunderstorms and a late night dancing party

ascona2Over the last three days of the liposomes, exosomes and virosomes meeting in the lovely Monte Verita’, Ascona, we had the opportunity to attend a series of very interesting talks and to have just a little bit of fun too. Here is a “brief” summary of the notes Marina and I were taking on the talks (disclaimer: you might find some inaccuracy; spoiler alert: this post is unbelievably very long):

Wolfgang Meier showed how biomimetic polymer and peptide membranes made of amphiphilic block copolymers form nanotubes, vesicle containers, cubic gels and lamellar gels. In particular block copolymer vesicles with a maximum diameter of 100 nm and a thickness of 10.9 nm are thicker and more stable than lipid vesicles. They can be used as a nanoparticle platform for the drug delivery of the hydrophobic anticancer drug doxorubicin and the serine hydroxymethil transferase inhibitor to treat malaria. Interestingly, the insertion of membrane proteins in block copolymer membranes does not affect their activity and function. The lateral mobility of proteins inside the more viscous block copolymer membranes is comparable to the lateral mobility of polymers, which is ten times slower than that of lipids in lipid bilayers. Block copolymers membranes are thicker and more stable than lipid membranes. Mixed block copolymer:DPPC monolayers and bilayers can also be produced with the formation of lipid domains due to the big thickness mismatch between the block copolymer (50 nm) and lipid (3 nm) domains. The insertion of a transmembrane protein in mixed systems occurs in different domains depending on the composition of the system: in systems with DPPC:DPPE, POPC and DOPC in the block copolymer domain, in both domains and in the lipid domain, respectively.

Andreas Kuhn showed different pathways for the membrane insertion of single proteins in bacteria, in particular the stepwise insertion of the Pf3 coat protein involving binding, transmembrane conformation and release. He proposed a two step insertion mechanism for the insertion of a Pf3 coat protein into a lipid bilayer, involving the binding to a groove and a greasy slide of the protein followed by bilayer insertion. He also talked about the purification and reconstitution of YidC protein in liposomes to form proteoliposomes with the cytoplasmisc domain of the protein in the outside or inside of the liposome. Fluorescent labelled Pf3 at the N- and C-terminii added to liposomes and proteoliposomes can be used to investigate protein translocation of single molecules with confocal microscope and fluorescence: fluorescent labelled Pf3 inserts into YidC proteoliposomes but not in liposomes and its C-terminal region is not translocated if labelled.

Sonia Troeira Henriques talked about the interaction of cyclic peptides Kalata B1, which are expressed in plants, with POPC and POPE model membranes. The presence of PE enhances the amount of peptides bound to the lipid bilayer because of a specific binding with PE lipids. She also showed that single lysine mutants have stronger haemolytic and insecticidal activity and the internalisation of the peptide labelled with Alexa and pHRodo fluorescent labels at different temperatures in endosomes. At 4 oC the internalisation is lost because the membrane is more rigid. The presence of the dynamin inhibitor peptide enhances the interaction with PE and internalisation. The insertion of the peptide into the membrane of GUVs is shown by solid state NMR.

Burkhard Bechinger showed how the amphipathic peptide Htt17, the membrane anchor of Huntingtin, which is a more than 3500 aa long protein involved in Huntington’s disease, is associated with POPC and other lipid bilayers through 15N and 2H NMR. He also showed that the extension of this peptide with Q17 forms aggregate only in the presence of vesicles and that the presence of more glutamines induces a faster aggregation leading to the formation of fibers observed in the disease.

Daniel Müller talked about the application of single molecule atomic force microscopy (AFM) to generate high resolution AFM images in biology showing how force distance curve based AFM imaging of biological membranes topography, adhesion and other processes, such as ligand-receptor binding, can be studied. In particular he showed that the folding of the membrane protein LacY, which is present in Escherichia coli inner and outer membranes, can be investigated by its mechanical unfolding from the C-terminus. LacY unfolds via structural segments as shown by force distance spectra, in which the probability of misfolding, unfolding, and folding events can be estimated, the folding probability being higher in the presence of YidC. Free energy profiles show that the misfolding process is associated with a high free energy barrier. Unfolded and extracted LacY cannot self insert into the membrane, while they can in the presence of YidC. Moreover, PE depletion leads to a topological change in LacY. ascona7

Christian Eggeling described how super resolution optical microscopy can be used to study lipid rafts/nanodomains, which are transient and smaller than 200 nm, using fluorescence labelled lipids and fluorescence correlation spectroscopy (FCS) to determine transit times for different areas. STED-FCS can be also employed to measure apparent diffusion coefficients for the lipids and highlight molecular interactions. He also talked about live cell model systems, such as giant plasma membrane vesicles (GPMVs), in which diffusion is not hindered as in cells, and the hopping of lipids proposed by Kusumi.

Phyllis Hanson gave a beautiful overview of the role of ESCRT III in the formation of membrane tubules and in the exocytosis of viral particles from infected cells. She showed us results using electron microscopy, mutational analysis, and simulation of the physical principles of coils to understand the coiling and three dimensional growth of this complex. ESCRT III creates ‘fences’ in the membrane. The diameter and the handedness of the coil varies depending on the proteins forming the complex.

On Wednesday afternoon the organizers let us take a well deserved break🙂 I spent it going to Ascona via the steep stairs of the picture, enjoying as many views of Lake Maggiore as possible and walking around the historical centre for a couple of hours. Then, on my way back my heart realised how steep the stairs were and I met Robert Vácha, a colleague I met at the Biophysical Society Annual Meeting held in Philadelphia three years ago, who was starting his steepest decent, here is an inside joke for computational chemists (sorry I couldn’t resist).. I tried to convince him that I needed to be rescued, but he said that it was good for my health and he was right. Other attendees were more adventurous than me, for example my roommate, Marek Cebecauer, managed to go to Ascona and to hike a nearby mountain in the same day. At dinner I had the pleasure to talk to Karin Norling, who actually worked on the afternoon, and my roommate. After dinner I had a lovely chat with Helen Saibil, who gave a very interesting talk on toxins and pore forming proteins a couple of days before, about her love for Sardinia, its prehistoric nuragic age, an EMBO conference she organized in a beautiful place in my region three years ago and other things … and while looking for the website of that conference I’ve just found out that a thematically related EMBO conference was being held in Sardinia in the same week of the meeting we’ve just attended.

Anne Kenworthy showed how the cooperation of lipids and proteins is involved in the formation of liquid ordered (Lo) membrane domains. In particular she talked about the preferential interaction of cholera AB5 bacterial toxin, CTxB, with Lo domains in a more efficient manner when it is in its pentameric form rather than in its monomeric form. Pentameric CTxB reorganises membrane domain structure in model membranes and plasma membrane blebs affecting their phase behaviour, enhancing raft association and stabilising raft-like domains. She also introduced another interesting property of toxins, such as shiga toxin, which is the ability to induce their own uptake by bending membranes forming tubulations. CTxB tubules have a similar orientation of microtubules in cells. Microtubules and motors like dynein bend the plasma membrane during endocytosis.ascona6

Horst Vogel talked about the structure and function of the pentameric ligand-gated ion channel (pLGIC) 5HT3R, which has the neurotransmitter serotonin, showing its purification, ligand binding and CD spectroscopy studies at different temperatures. The crystal structure of 5HT3R in complex with VHH15 has the neurotransmitter serotonin in its binding site and a 0.45 nm hydrophobic gate at the centre of the transmembrane domain. The structures of 5HT3R in lipid vesicles and bilayers revealed by cryo EM are similar. Molecular dynamics simulations of the ligand associated in the binding site show that hydrophobic residues, such as tyrosine and phenylalanine, undergo a conformational change inducing a cascade of conformational changes that allow the of the transmembrane helical domain letting the water flow into the channel.

Stavroula Sofou explained how the pH can affect the phase separation of lipid bilayers and liposomes (or vesicles) and the roles played by electrostatic repulsion and hydrogen bonding in systems with domains of negatively charged lipids (PS) at neutral pH 7.2-7.4 (in normal cells) and acidic pH 6-6.5 (in cancer cells). She also showed the binding reactivity of uniformly functionalized nanoparticles, how receptor targeting nanoparticles deliver measurable amounts of the antitumoral drug doxorubicin and the pathway of the interaction of liposomes with cancer cells. Drug-loaded liposomes are sticky/active and selective only at the acidic pH of 6, they are not toxic to normal cells expressing the same receptor and their internalisation doesn’t depend on the type of ligand.

Karin Norling talked about the properties and cellular uptake characteristics of liposomes delivering vaccines, showing that liposomes with antigens inside and outside without and with PEG have different activity, the non PEGylated liposomes (150 nm) being more active that the PEGylated ones (200 nm). The in vivo study was performed in a mouse model and the antigen uptake was monitored on dendritic cells surface by means of TIRF microscopy and topographical micropattern to image liposomes. TIRF-based single particle tracking was also used to study interactions between cells and liposomes, showing that the liposome bound antigen is more present on the cell surface.

Anne Spang showed that the communication between organelles happens through transport vesicles via contact sites, allowing the exchange of lipids and ions in the plasma membrane (PM). Processing bodies (P-bodies) full of mRNA generated under different stress conditions might have other subcompartments. Csh3p, which is colocalized in the PM, and Pin2p are cargo proteins that can undergo prion formation. Pin2p is rapidly internalised upon osmotic stress and the mutation of the prion-like domain reduces its retention in the trans Golgi network (TGN), in which a phase separation occurs due to prion-like domain interactions.ascona3

Lukas Tamm talked about the role of cholesterol in the entry of Influenza and Ebola viruses into endosomes through pH mechanisms. He also showed the structure of influenza hemagglutinin monomer, it’s different domains, receptor binding and antigenic sites. He described how structural intermediates in HIV gp41 mediate membrane fusion, the post fusion crystal structure class 1 viral fusion protein having a 6 helix bundle. He also presented the NMR structure of Ebola virus fusion loop at pH 7 (inactive) and pH 5.5 (active) forming a fist structure, in which the double mutation to alanine residues removes completely the activity of the virus. HIV gp41 fusion domain contains alpha helix and beta sheet secondary structure elements, which mediate membrane fusion. The role of CHOL rich domains in HIV entry was also described via TIRF of SM:PS:CHOL and PC:PS 3:1 systems, showing that 50% of the particles bind to Lo/Ld boundaries, 35% to the Lo domains and the remaining to the Ld domains of supported lipid bilayers. Moreover, virosomes with Lo/Ld phases exhibit more fusion, the increase of the domain height mismatch from DLPC to DSPC increases also the fusion due to the reduction of the line tension and the energy gain due to reduction of line tension depends on the size of vesicles and lipid domains.

Sarah Veatch gave a very clear and interesting talk on the study of the phase behaviour of lipid bilayers and vesicle having Lo and Ld phases by means of 2H NMR spectroscopy. She showed what kind of composition fluctuations occur near critical points and how critical fluctuations can be studied with the 2D Ising model in GPMVs. She pointed out that raft domains are small dynamic regions of the lipid membrane and protein-protein interactions occur because proteins like to share the same local lipids. She also showed that the protein CTxB is clustered in certain domains of the PM depending on the type of probe: if a ordered probe is used the Lo domain is enriched in CTxB, while using a disordered probe the protein partitions more in the Ld phase. This analytical approach is going to be used to study the PM heterogeneity of the PM in intact cells. She also presented really interesting results on the anesthetic properties of small compounds, which depend on their structure and how they partition. Specific ligand-gated ion channels can be affected by anesthetics. Ethanol lowers the critical temperature Tc in GPMVs in a quantitative way: the more alcohol the lower Tc. Different alcohols have also the same effect on Tc of GMPVs. These properties of anesthetics are correlated with hydrophobicity and non anesthetics do not lower Tc. A shift in Tc can switch the channel from an inactive to an active state. Ligand-gated ion channels acquire the slow dynamics of membrane fluctuations. She also showed how tadpoles placed in ethanol and put to sleep become less sleepy with the addition of hexadecanol because it raises Tc.

Susan Daniel talked about membrane protein mobility and orientation are conserved in supported lipid bilayers (SLBs) created directly from cell PM blebs. These mammalian cells and GPMVs blebs can be used to study coronavirus, ebola virus and E. coli outer membrane vesicles. She also showed adsorbed blebs on the PM and their fusion and that lipid bilayers containing protein have a fluidity lower than protein free lipid bilayers. The protein mobility can be conserved with PEGylated lipid vesicles to form a cushion, in which protein can diffuse faster. An enzymatic orientation assay can be performed to see how the proteins are oriented. A mixed population of adsorbed blebs with a diameter size under 500 nm and PEG liposomes is used to generate SLBs.

Kelly Lee gave an excellent talk on the visualisation and sequencing of membrane remodelling leading to influenza virus fusion through cryo electron tomography (cryo-ET) tomography. He gave some background on endocytosis and pH triggered membrane fusion by influenza A virus, which contains 350-500 copies of the protein hemagglutinin (HA), and showed how the attachment via HA bridges leads to a significant deformation of the attached liposome. HA coordinates also the formation of dimples and can form extended interfaces with membranes tightly docked consistent with partially dehydrated proximal leaflets co-mingling. When HA is in the periphery of the liposome a trilayer structure, structurally similar to the one reported by the molecular dynamics study by Marrink cited in Marina’s post, is observed. In the presence of fusogenic lipidsNat pH 5.5 intermediates accumulate and if the pH is lowered to 5.25-5 the fusion progresses and more HAs are activated. He also pointed out that hemifusion is a very rare event.

Max Piffoux showed how the monitoring of extracellular vesicles dynamics at the nanoscale can be performed with liquid cell TEM of EVs coated with gold nanoparticles having a 100 nm diameter. The morphological analysis highlights the presence of different sized and shaped EVs in different media/buffers. Dynamics of EVs depends on nanoparticles coating not on their size and the aggregation of gold nanoparticles might be due to PS flip-flop.ascona5

Suzanne Eaton talked about the tissue size, shape, and collective cell behaviour in Drosophila (fruit flies), whose feeding occurs on rotting fruit allowing the uptake of yeast (fungal sterols) and plant (phitosterols) sterols. Yeast and plants have different lipid membrane compositions. She showed that animals fed with yeast lipid extracts have short lives, while plant fed animals live longer because they release less protein Dilp2 and have low systemic insulin signalling. Lipophorin ( Lpp) and Lipid transfer particles (LTP) are proteins that accumulate in the drosophila brain, but LTP is present on specific neurons. In particular two specific neurons recruit LTP only when larvae feed on yeast food, which enhances calcium release in glial cells. Since yeasts are a summer resource, the effect of the winter can be reproduced by performing experiments at 12 C during which drosophila eat more plant food. In another experiment she showed tha yeast-fed flies become uncoordinated at 12 C, while plant fed flies survive at lower temperatures. Moreover, larvae fed with plants survive outside in Dresden in the fall and adults can survive in the winter too. High levels of insulin are good for survival at high T, while flies fed on plants at 12 C have more fluid membranes, which prevent the formation of gel phases.

Matthew Wood gave a very interesting evening lecture on the development of treatments for muscular distrophy disease using RNA splicing. In his introductory slides he showed how the secretion of dystrophin, which is the protein product of the duchenne muscular distrophy locus, can be reduced by modulating splicing with small oligonucleotides to repair genetic defects. He explained that the absence of exons 49 and 50 leads to muscular distrophy and the removal of exon 51and the linking of exons 48 and 52 does not ead to the disease. He also pointed out that oligonucleotides tested in patients have had marginal benefits so far because RNA drugs are large macromolecules very difficult to be delivered and to be bioavailable in the tissue. Then, he showed the next generation of oligonucleotides and a peptide platform technology to synthesise cell penetrating peptides with a solid phase synthesis. In particular he talked about the use of Pip6a, a 22 amino acids arginine rich peptide, to treat spinal muscular atrophy, which is a childhood motoneuron disease due to the missing of exon 7 and whose current invasive treatment involves the drug to be delivered directly to the brain with possible infection risks. The delivery of Pip6a-PMO corrects sMN expression and phenotype in SMA mice, increases the lifetime with a single dose and with a double dose mice live a normal life. The shortening to 12-14 amino acid long peptides has generated other 17 peptides that can be used as drugs. He explained that there are different brain barriers, no barrier, a blood CSF barrier and a blood brain barrier, which form a complex multicellular barrier. Then, he showed how EVs can be used as possible delivery methods, a hypothesis supported by the ability of exosomes to transport mRNA between cells. Their EV engineering strategy involved the presence of the integral exososomal protein Lamp2b and dendritic cells to have rabies virus glycopeptide (RVG) and RNA encapsulation into EVs, in particular single stranded RNA (siRNA) and microRNA. Targeting peptides enhance brain penetration leading to the siRNA drug delivery to mouse cortical neurons. He also talked about the treatment of Parkinson’s disease Lewy bodies and alpha synuclein accumulation with RVG-exosomes. Finally, he described the EV delivery mechanism, intercellular vehicles for RNA delivery and the retro engineering into lipid nanoparticles (LNPs), which are extremely inefficient to deliver siRNA. He showed that in the EV cell uptake most LNPs aggregate on the cell surface with an uptake time of 5 minutes. Exosomes are taken up as single vesicles in all recorded events andore than 80% of EVs are internalised at equilibrium conditions. EV cell uptake is highly polarised and associated with filopodia active regions, which are cortical actin bundles rich domains. EV uptake is facilitated by filopodia showing surfing along and filopodia mediated exosome grabbing; more than 98% uptake events happen at the base of the filopodia. These 80-100 nm Evs make stop-and-go movements along the ER and after kiss and run, dynamic and sampling events are finally sorted to the lysosomes.

On a rainy Thursday night, after dinner, we also had the chance to dance and I ended up dancing (or at least that’s what I was trying to do) very shyly with a playlist that included songs by Michael Jackson, David Bowie and other artists, and we kept drinking and socialising..

Sarah Keller gave the most energetic, enthusiastic and lively talk of the meeting to wake up an audience dealing with sleep deprivation, hangover and other more or less personal problems. At the beginning she showed clearly how at high temperature GUVs display an uniform disordered domain and the appearance of vesicle liquid ordered domains lowering the temperature. The mixing of high and low melting temperatures lipids leads to domains in both membrane leaflets. She also explained how to read a ternary phase diagram with lipids in ternary and binary mixtures phase diagrams and to quantify the strength of the transbilayer coupling between domains in each leaflet. The energy of the transbilayer coupling ranges from 10-8 kT to 0.15-0.5 kT/nm2, the latter values being reported from MD simulations. Lipid bilayers on a solid subtstrate move like tanks, in order to avoid this process GUVs are burst on a solid substrate, which will make a lipid bilayer after a flow of water. Small domains are stuck big domains move hydrodynamic with the shear stress being inversely proportional to the size of domains. Four forces are involved in the process: shear stress, dragging, friction and registration forces. The measured interleaflet coupling parameter of 0.016 makes possible the registration of bigger than 10 nm domains. Finally, she made some pretty reasonable wild speculations on the origins of life by reporting a study of the fatty acids interacting with different RNA bases. Adenine and guanine stick the best to vesicles because these bases bind better to membranes.

Petra Dittrich talked about microfluidic devices to study lipid membrane properties by creating of nL and pL volumes, allowing the fast exchange of fluids and the immobilisation/trapping of cells and vesicles through the fabrication of different sized channels chambers with multilayer soft lithography. A single vesicle can be trapped without its rupture and fluids can be exchanged very quickly (100 ms). She showed the permeation partitioning across membranes containing membrane pore alpha hemolysin, studies of cell penetrating peptides (CPPs) and their permeation across a POPC membrane, and a study of the fusion of membranes by trapping two vesicles and using a modified fusogenic amphipathic peptide derived from influenza virus. She also presented a study of the fusion of membranes by electrical fields, how forces acting on membranes generate deformation making flat vesicles, how small domains fuse to larger domains and Ld domain budding. Finally, she gave an overview of the different applications of microfluidic devices, including cell/vesicle analysis, vesicles in droplets a model to study intracellular compartments, liposome screening platforms used for permeation studies, ligand-receptor binding and hormone-receptor binding.

Wye Khay Fong talked about different lipid phases, in particular bicontinuos cubic and reversed hexagonal phases, can be used as substrates biosensor and have applications to drug delivery. She showed how the cubosome nanostructure controls the drug release in vitro and in vivo with a temperature switch, which can be monitored with kinetics synchrotron SAXS measurements to study external and internal triggered changes in the nanostructure. She also described the lipid digestion on the nanoscale, in particular the milk digestion involving fats that can form different mesophases, and introduced a pharmaceutical milk shake in which invertase catalyses the digestion of the sugar glucose. She also mentioned that hydrolysis leads to phase transitions and drug release.ascona1

Roy Ziblat talked about the building-up of a membrane library for protein-lipid match with a very nice movie and a funny soundtrack. He pointed out that membrane receptors interacting with viruses are not only proteins but are also lipid based ones. He showed affinity profiles of Dengue, Ebola and vesicular stomatite virus for different lipids. He highlighted that liposomes treatment with infected cells is biocompatible, FDA approved and only few micrograms are effective.

Chen-Yu Zhang talked about exosomes sufficiently delivering secreted small RNA to recipient tissues. Initially, he explained some biological functions of microRNA, the use of circulating microRNA as a novel class of biomarker for diseases and the employment of Microvesicles MVs, which are identical to exosomes secreted in the cells, as carriers for microRNA. He also showed how human blood cells and cultured THP-1cells selectively package miRNAs in exosomes and MVs and the biological function of exogenous miRNA-150 in circulation. Secreted microRNA acts as a signalling molecule in mediating intercellular communication and in MVs enhances angiogenesis in cancer cells (enriched in MVs) and hepatic insulin resistance. Plant microRNAs absorbed by mammalians can be packaged into MVs leading to cross kingdom regulation. He pointed out that honeysuckle microRNA, which is not destructed by the boiling process, shuts down the viral activity because of its specific sequence and it can be used to treat viral infection in the fetus.

Gisou van dear Groot gave a very interesting talk on the function and dynamics of protein palmitoylation. Initially, she explained how S-palmitoylation adds hydrophobicity to a protein containing cysteine residues, phosphorylation adds a charge changing the conformation of a protein, affecting its folding and function, and ubiquitination puts a tag on a protein. Then, she talked about the DHHC family of palmitoyltransferases, which are 23 in human genome with 18 out of 23 in the ER and are involved in brain and cancer diseases. She also promoted the website SwissPalm.epfl.ch in which different properties of these enzymes are described. She highlighted that when a protein acquire a lipid within the transmembrane region a conformational change of the transmembrane domain occurs, especially those proteins associated with lipid rafts are affected by palmitoylation and specific lipids are required to modulate the hydrophobic mismatch. The formation of protein complexes and interplay with other post translational modifications can be investigated with tritium labelled or clickable palmitate only the non palmitoylated proteins are labelled.

She also stressed that palmitoylation contributes to the integration of diverse ER functions and it is also involved in intraorganelles contacts. Then, she described calnexin palmitoylation (protein-SH –> proteinS-palmitoyl),cal-SH –> calS-palmitoyl, the presence of two palmitoylation sites and the long time (45 hours) of the dual palmitoylation. The frequency of palmitoylation has a median time very slow of 6 hours due to phosphorylation and the palmitoylation of the second site is cooperative. DHHC6 spans the membrane three times with three cysteines that can be palmitoylated by DHHC16 and undergoes rapid depalmitoylation. Palmitoylation destabilises the enzyme, affects localisation and oligomerization and it is required for activity. The stability of DHHC6 is site dependent and most of the protein is not palmitoylated, only one of the site is active, the presence of three sites protects it from degradation and preserves its activity. PEGylation can be used to check palmitoylation and site occupancy. Finally, she presented the results of a molecular dynamics simulation showing that the palmitoylated cysteines of calnexin are inside the lipid bilayer and they need to be exposed in order to be palmitoylated by the enzyme.

At the end of the meeting Kalina Hristova announced the recipients of two student and two postdoctoral poster awards, which were assigned to Erik Henrich, Georg Krainer, Kirstin Hobiger and Radhakrishnan Panatala.

If you made it to the end of this very long post you are about to read a flashback with my personal comments on the meeting, which actually started for me at Locarno railway station, where I was supposed to meet Marina Ramirez Alvarado. I eventually ended up meeting Kellen Brunaldi, Carmen Domene, Kirstin Hobiger and Marek Cebecauer before having the pleasure of meeting Marina. Initially, she introduced me to Rosalba Kampman, the executive director of the Biophysical Society. Then, I also started seeing the familiar faces of Robert Vácha, Luca Monticelli and Giulia Rossi. I met Luca for the first time at the Biophysical Society Annual Meeting held in Salt Lake City in 2006 and less than two years later we were working in Ilpo Vattulainen’s group, in which Giulia was also working at that time. I had the pleasure to see Giulia giving a very interesting talk at an International Workshop on Biomembranes held in Espoo, Helsinki, a couple of years ago. It was kind of interesting and funny at the same time that we were all clustered in the first poster session. I enjoyed talking to them about different, not always specifically scientific, things, it was really nice seeing both of them again. Then, during my poster presentation and the other days of the meeting at breakfast, lunch and dinner I had the chance to talk to many nice and extremely talented people. Here is a brief list of the interactions we had in a more or less chronological order.ascona4

Marie-Eve Aubin-Tam was the first person interested in the research shown in my poster (maybe she was judging me :)) and in seeing the movies of coarse grained MD simulations reported in it. We also had very interesting more or less scientific conversations over lunch and dinner. Marina, Steven Boxer (the official judge), Carmen, Giulia and Alexander Karabadzhak asked excellent questions about my poster too. The same day I had the pleasure to have lunch with Donald Engelman, who told me he had an Italian postdoc from Sardinia working in his lab in the past, his wife, Daniel Müller, Stefania Mari, Botond Roska, who is also in love with Sardinia, Giulia and Luca. Stefania, Johannes Thoma and Estefania Mulvihill were also interested in molecular dynamics simulations and it was nice talking to them about other things too. I also had very nice conversations with Xiaojun Shi, Kirstin Hobiger, Nikhil Gandasi, Hudson Pace, Jenny Isaksson, Vanessa Carvalho, Radhakrishnan Panatala, Marisa Sarria, Wye Khay Fong, Sonia Troeira Henriques and Binjong Liang. I really hope to see all of them again in the near future.

It was a very intensive, extremely well organised and loaded with so many excellent talks kind of meeting, and I hope there will the possibility to attend similar meetings in the future, not near because my brain needs some time to recover a bit now…🙂

Peer Review: Writing Rebuttals

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les-satinLes Satin, is a professor of pharmacology at the University of Michigan Medical School, and is currently doing a sabbatical at the Department of Medical Cell Biology of Uppsala University in Sweden, where he is studying signal transduction mechanisms in pancreatic beta cells.

I have a guilty pleasure to report: I like to write point-by-point responses to the critiques of my papers. Ok, before you question my sanity, let me point out that I have not lost my mind—yet. Writing these responses is essential to our work, but more to the point, I find them fun to do!

You know what I am talking about. You have critiques that were written by usually three reviewers, “experts in the field” who have read your manuscript and have criticisms, suggestions, requests for new data or clarifications, or perhaps they just want to rain on your parade, destroy your ego, etc.  But they have to be dealt with if you want your paper to be published.

Now, when most of us read these things we feel like cursing or throwing objects across the room–at least at first. No one likes to be told how to do something, let alone a professional scientist. But you have to respond or no paper! So what do you say? And how do you say it in a polite way?

This is the part that is fun for me, the challenge! Can I convince them? Do I have good enough arguments? Can I strike just the right tone in my response? Yes, of course I can!

The first part of a successful rebuttal is getting yourself into the right mood. This is essential. You have to be willing to swallow your pride and tell the reviewers straight off (and with a straight face) that you appreciate their careful consideration of your paper and their ”constructive criticisms” (even if you do not really appreciate them in the slightest). After all, you want your paper to be accepted don’t you? So you have to play the game.

Once I am in the right frame of mind, I make a list of the critical points of each of the reviewers, quoting directly (but carefully) from the review itself and extracting the most salient points that were made. I then leave a space under each point and proceed to address the criticism in a polite, sometimes contrite, and always careful and objective manner. This is the part I find to be so much fun; gosh, I am getting excited already just writing this!

“We thank Reviewer #1 (2,3…) for his/her (don’t assume gender) insightful suggestion that we revise our statistics strategy, include an additional control, or consider mechanism Y instead of our preferred mechanism X, etc.” And I personally stress the major points as it is important to be very concise and clear and not get bogged down by extraneous or more minor points of the critiques.

Of course, the more substantive points of a critique do require careful thinking and often, new data as well. You should carefully point out any findings that clarify the scientific matter in question, and address the points that were made: No reviewer wants their concerns to be dismissed, or to put it more casually, blown off. That, you most assuredly, must not do.

At this point, you might be saying, “Well, what if I don’t agree with the points made by the reviewer, what do I do then”? You can and should “respectfully disagree” and then make a very clear and convincing argument as to why you don’t agree. It is critical you do this using the right tone and in the proper spirit. You have very good reasons for thinking what you think and they would too if they were privy to the information you have access to.

Another issue that often comes up is that one reviewer will echo the point made by another, even though in almost every case this is not because they communicated with one another beforehand, but likely because they are right (!). Or since they have the same bias (you decide!). So, in this case you need to simply state: “See my response to Reviewer #1 that addresses this point.” And then add “Thank you.”

Reviewers and authors have much in common. Often a good review can be very helpful to the ultimate paper, especially if the reviewers accurately identify the weaknesses of the paper and help identify errors. In fact, the vitality of our peer review system depends on objective, critical, and constructive criticism.

Just as reviewers need to review papers critically and fairly, authors need to communicate our rebuttals to their critiques clearly, calmly, and with consideration for the reviewers’ time and sincere efforts. Everyone benefits from robust, fair, and rigorous peer review.

Look at it this way. If you develop a liking for writing rebuttals of your manuscript’s critiques, then you will have even more reason to write a lot of papers. This will be good for your career, and you will also learn to better cope with rejection and temporary defeats. You will also become a better reviewer yourself.

It’s all part of the learning process!

Good luck, and please send me your comments at lsatin@umich.edu.

Domain Organization in the 54kDa Chloroplast Signal Recognition Particle

BPJ_111_6.c1.inddPlanes, trains, ships, and automobiles — all machines that transport goods and materials from where they are found or made to where they are needed and used. Much the way these modern transport machines are essential to complex trade around the world, the biological world relies on transport machines to move materials and goods at the cellular level. Nanoscale transport machinery has evolved the ability to pick up and carry biological cargo, such as newly synthesized proteins, from places in the cell where proteins are made to cellular sites where the proteins must function.  The image on the cover of this issue of the Biophysical Journal depicts a cellular transport machine in chloroplasts, a chloroplast signal recognition particle (cpSRP).  Its job is to bind newly made components of the light harvesting complexes and direct them to the thylakoid membrane where they are assembled with chlorophyll to efficiently capture light energy for photosynthesis.

Understanding how these nanoscale machines operate may make it possible to design bioinspired machines that can be used to build or repair artificial solar energy conversion devices.  But ”seeing” a nanoscale machine operate presents a tremendous challenge.  We have used a wide array of techniques including bioinformatics, molecular dynamics, Small Angle X-ray Scattering (SAXS), and single-molecule Fluorescence Resonance Energy Transfer (smFRET)  to produce ”movies” of how one of the components of this molecular machine – the protein cpSRP54, a 54 kDa subunit of cpSRP – moves during its operation. Bioinformatics and molecular dynamics use structural data from similar proteins and physical theories to predict the multiple structures that the protein can adopt and how they interconvert between each other. These structural predictions are then tested using SAXS and smFRET experiments. The idea of smFRET — also depicted on the cover —employs the use of two fluorescent dyes placed at distinct sites on cpSRP54, shown in red and green. By exciting only the green dye of a single molecule that is within the confocal volume of a microscope (which is a tightly focused beam of laser light in an hourglass shape, as seen in the cover image), it is possible to transfer some of this energy to the red dye molecule on that same molecule if the two dyes are in close proximity. In fact, we can quantify exactly how much energy is transferred by measuring the brightness of the green versus red colors emitted. If there is more green light emitted, the dyes are far apart and if there is more red light emitted, the dyes are close together. This allows us to accurately measure the distance between the dye attachment sites on the single protein molecule, which is then compared to the structural predictions that we obtained from the other techniques. These data were combined and used to produce the model of cpSRP54 shown in the center of the confocal volume of the cover image.  Furthermore, since smFRET is measured at the single-molecule level, it is possible to directly show that each protein can adopt a range of different structures, which all depend on what else the protein is interacting with during the transport process. The findings show that cpSRP54 goes through multiple structural states that can interconvert between each other – a finding that is supported by the SAXS data. Importantly, the model is predictive of structural states required to load cpSRP with LHC cargo and deliver it to the chloroplast thylakoid membrane.  A small site-specific mutation predicted from the model to adversely affect the transport activity of cpSRP54 was verified in functional assays, providing a high degree of confidence in our structural models.

—Rory Henderson, Feng Gao, Srinivas Jayanthi, Alicia Kight, Priyanka Sharma, Robyn Goforth, Colin Heyes, Ralph Henry, Thallapuranam Suresh Kumar

The Human Side of Liposomes, Exosomes, and Virosomes

Our thematic meeting was insightful, inspiring, and full of opportunities to talk. Most people I talked to like the fact that we were allowed a lot of free time.  For example, lunch happened over a 2 hour period and we were scheduled a free hour before dinner. Monte Verita is also a great place to encourage interactions as it has a lot of open spaces where people can talk, open their computers/electronic devices or grab a napkin (or a paper place mat) and start scribbling stuff.

We sat on round tables with 8 people for all of our meals (breakfast was available on the terrace during the sunny days). That also allowed for a lot of very nice conversations. I recall having a great breakfast with Ana Bouchet a couple of mornings.

I didn’t know most people at the meeting as I am a relative newbie in the exosome field. Tony Hyman and Suzanne Eaton worked at EMBL/Heidelberg when I was a predoc there, but I didn’t know them personally. The first interactions happened at the Locarno train stations, where I met Sarah Veatch. I ended up in the wrong hotel and saw Oksanna Sergeeva (from Lausanne) there. I met my fellow blogger Andrea Catte (Norwich) and his roommate the first evening over the reception. Andrea saw a friend of his, Luca Monticelli from Lyon so we ended up sitting together for dinner. We then met Nikhil Gandasi and M. Omar Hmeadi from Uppsala.

The line to get coffee was another place to meet people. I met Rasmus Herlo from Copenhagen there. During the poster session I met Joel Chopineau from Montpellier and Roy Ziblat from Harvard.

Of course, the system of having roommates that you don’t know could be terrifying or highly rewarding. I happened to have a great roommate, Giulia Rossi from Genova. We shared a lot of the same common interests and schedules.

I tend to sit around the same place during a conference. In this case, the conference room at Monte Verita has double desks and 4 columns of double desks. I always sit on front because I don’t hear very well from the back of the room. During the first day I met Jean-Marie Ruysschaert from Brussels. He was kind enough to share with me a lot of his experience and insights when a question lingered about a particular topic. Philip Bastiens also sat around my desk and always had really insightful and out of the box thoughts to share. Raya Sorkin also sat around the front. She gave an excellent talk and she came to talk to me during the poster session. Andrea’s roommate always asked very good questions and we usually followed up the conversation on our way out of the conference room to get coffee or lunch. Sarah Keller and Luca Monticelli allowed me to overhear their discussion about phase diagrams, aided by scribbles on place mats.

I cannot forget to mention Albert, who remained quiet for the most time, although expressed his dissagreement at times in a quite vocal way.

The meeting organizers allowed free time during Wednesday afternoon. We decided to go hiking around Monte Verita. Helen Saibil joined Giulia, Luca, Joel, and I for a lovely afternoon.

Any Biophysical Society meeting cannot be complete without the ‘dance’. We improvised to have a good time on the poster session room (and everyone taking down their posters helped clear the room for dancing) and Roy Ziblat put together a great playlist.

We danced and laughed until midnight. I was sorry to leave such a great place and fantastic group of people…until the next time when Biophysical Society brings us back together.

 

-Marina Ramirez-Alvarado

2017 BPS Bridging Funds Travel Grant

In an effort to assist members in the current difficult funding situation, the Membership Committee is accepting applications for the Bridging Funds Travel Grant for the second year.

Biophysical_1071(2-8-15)

BPS understands that while some resources are limited, networking and staying up-to-date with current research is important to our members. This grant is designed to provide support to regular members who would normally attend the Annual Meeting, but cannot due to a temporary lack of funding. We encourage independent and principal investigators to apply for this travel grant to help alleviate some meeting costs.

Applicants must be 2017 members by the October 3, 2016 abstract deadline, presenting or senior author on an abstract submitted for the Annual Meeting, and must be actively seeking funding.

For more information about Bridging Funds and the other travel awards, visit the Travel Awards page.