LST-Day 2016 Poster Abstracts

1. STED nanoscopy in optically cleared kidney tissue

David Unnersjö-Jess¹, Hans Blom¹, Lena Scott², Hjalmar Brismar^1,2

¹Department of Applied Physics, Royal Institute of Technology, Stockholm,
²Department of Women’s and Children’s Health, Karolinska Institutet, Solna

Hans Blom, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
08-52481214; hblom@kth.se

In our study, we found that hydrogel-based optical clearing is a beneficial tool when studying the finest renal tissue morphology at the nanometer scale. When imaging samples using super-resolution STED microscopy, superb staining (low background, homogeneous signal) is crucial to be able to extract correct information from the resulting nanoscale image. We show that signal-to-noise ratio and the generated immunosignal homogeneity are both increased in optically cleared kidney tissue. These findings open up for superresolution light microscopy studies of slit diaphragms in fluorescently labeled intact kidney samples, which adds an important tool in studying glomerular filtration barrier in healthy and diseased states (1).

(1) Unnersjö-Jess et al. Kidney International (2016) 89, 243–247

2. The Mechanism of Infrared Neural Stimulation(INS) in Virto Study

Qingling Xia, Tobias Nyberg

Division of Neuronics, School of Technology and Healthy
Royal Institute of Technology (KTH)
Hälsovägen 11 C, SE - 141 57 Huddinge, Sweden
Mobile: 0046-0765942151, Email: qingling@kth.se

Recently years, Infrared neural stimulation (INS) has a widely use both in vivo and in vitro without any genetic or chemical pre-treatment. It has been proposed as an alternative method for neural stimulation due to higher space resolution and safety. Although, there are a lot of researches about INS but underlying mechanism(s) are unclear. Our research focuses to understand and quantify the possible mechanisms and effects of INS on cultures of cells from the central nervous system. Finally, we hope use this potential method in clinic application.

3. ProQ4: a single structure model quality assessment program

David Menéndez Hurtado, Arne Elofsson

Department of Biochemistry and Biophysics, Stockholm University and Scilifelab.

Introduction Protein structure prediction is one of the first steps to many processes in structural bioinformatics. Unfortunately, not every combination of method and target is successful, so we need tools that can predict the reliability of the predictions.

We are interested in two scores: global scores (the quality of the whole model) and local scores (the quality of each specific residue).

In this project we are developing an automatic assessor that requires as sole inputs a single structure and a multiple sequence alignment, and outputs a prediction for the local and global scores.

Methods We combine structural input features, such as secondary structure, relative surface area accessibility, and dihedral angles; with PSSMs and sequence, into a deep convolutional-recurrent neural network.

Our target function is LDDT, the training data all the models submitted to CASP 9 and 10, and our test set is CASP 11.

Results (work in progress) At the time of writing, we have included only secondary structure and sequence information, and the results are comparable to these of ProQ2 (see table 1). It must be noted that the most relevant features or ProQ2, atom contacts, were not included, as it is shown ins the ProQ2-trimmed column.

Table 1: Correlations comparing the different predictors. Per target is the average of the correlations for each target protein.

4. An engineered affibody molecule with pH-dependent binding to FcRn mediates extended circulatory half-life of a fusion protein

Shengze Yu, Torbjörn Gräslund

School of Biotechnology, Molecular Biotechnology Department  

One of the central questions in biopharmaceutical development is how to extend circulation residence times of protein-based drugs to improve efficacy and patient comfort. Human serum albumin (HSA) and IgG are two proteins with naturally long serum half-lives due to FcRn-mediated rescue from degradation in cells in contact with blood. Here, we describe development and characterization of affibody molecules that can hitchhike on the FcRn rescue system. We found that fusion of the generated FcRn-binding affibody molecules to a model protein, already engineered for increased half-life by inclusion of an albumin binding domain, leads to a close to 200% further increase in circulation residence time in mice. Such affibody molecules may have general usage as fusion partners to biopharmaceuticals for extension of their circulation residence times.

In addition, the affibody molecules were found to compete with IgG for binding to FcRn and injection of a large amount of one of the affibody molecules into mice lead to a significant decrease in the total level of IgG, possibly by saturating the FcRn rescue system. 

Affibody molecules are small (58 amino acids, 6-7 kDa), non-immunoglobulin based scaffold proteins with a triple-helical fold. Affibody molecules have been generated to a large number of target proteins with exquisite specificity and high affinity (low nanomolar to picomolar)

5. Power System Stability Enhancement through Operating Point Adjustment in a VSC-MTDC Network

Omar Kotb, Mehrdad Ghandhari​

Department of Electric Power and Energy Systems
KTH Royal Institute of Technology
Osquldas väg 6, S-100 44, Stockholm, Sweden
omar.kotb@ee.kth.se, Tel.: +46 728-408-726

This paper investigates eigenvalue sensitivity to the operating point of an AC/DC power system with a VSC-MTDC network. As VSC-MTDC networks are expected to become an integral part of future power systems, there is a growing need to utilize the converter controls for stability enhancement. The paper presents a sensitivity analysis of the eigenvalues obtained through small signal stability analysis of the combined AC/DC power system. The range of controller gains for small signal stable operation is established and their impact on the stability margin of the system is discussed. Based on the conducted sensitivity analysis, a supplementary control strategy is proposed to handle heavy power flow scenarios on weak AC tie lines. The results of linear analysis are corroborated by time-domain simulations in DIgSILENT. The results indicate the ability of the proposed strategy to enhance stability in the AC/DC power system.

6. Missing genes and supplementary tissue profiles in the Human Protein Atlas

Evelina Sjöstedt, Åsa Sivertsson, Feria Noraddin Hikmet, Borbala Katona, Ingmarie Olsson, Fredrik Pontén, Mathias Uhlén, Cecilia Lindskog

Department of Proteomics
School of Biotechnology
Royal Institute of Technology (KTH)
Science for Life Laboratory
+46 (0)739567077, Evelina.sjostedt@scilifelab.se

Within the Human Protein Atlas Project (HPA) there is an ongoing quest to explore the basic building blocks constituting the human body. This is done by systematically exploring all proteins with immunohistochemistry approaches analyzing the majority of human tissue types and comparing with transcriptomic data. Internal RNA-seq data was generated for 37 different tissue types and used for gene classification, more than 1000 genes were not detected on RNA level in these 37 tissues. Uniprot was used to better understand the list of not detected genes, we found potential pseudo genes, uncharacterized genes, olfactory receptors, keratins, interferons but also secreted proteins, proteins related to seeing, hearing, brain functions and skin. Three tissue types, new to the HPA, were analyzed for relevant target proteins; eye, mammary glands and pituitary gland. We have also started to investigate brain, skin and adrenal gland for supplementary details.By expanding the tissues types used for analysis and adding supplementary samples we hope to better understand genes related to the eye, mammary glands, pituitary glands, brain, adrenal gland, skin and hair. 

7. Characterization of a spin Hall nano-oscillator to be used as a building block
of magnetic biosensors
Seyed Amir Hossein Banuazizi¹* , Ahmad Awad², Philipp Dürrenfeld², Hamid Mazraati^1,3, and Johan Åkerman^1,2,3
1Department of Material and Nano Physics, School of Information and Communication Technology,
KTH-Royal Institute of Technology, Electrum 229, 164 40 Kista, Sweden.
²Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden.
³NanOsc AB, Electrum 205, 164 40 Kista, Sweden.
* ahba@kth.se

Spin-wave excitations driven by spin transfer torque (STT) [1] have become an important area of research since the past decade, in term of studying the properties of the excitation, as well as their capabilities for applications in spintronic devices and magnetic biosensors. Recent investigations have shown that the spin Hall effect (SHE) can induce pure spin currents that could be used to exert STT to adjacent ferromagnetic thin films (using nonmagnetic metals with strong spin–orbit interaction, such as Pt as the spin hall metal for example). These kinds of oscillators are called spin Hall nano-oscillators (SHNOs) [2-3] and have a high potential for applications as they are easy to fabricate and have reasonably good emission characteristics.

The oscillation frequencies and the excited modes in the nano-oscillators depend on the applied external magnetic field and the DC current. The current induces an Oe field which modifies the effective field landscape in the SHNOs affecting some of the main properties of high frequency emission in these devices such as their oscillation frequencies and modes localization.

In this study, we investigate Oe field (H_Oe) induced by current in the SHNO via analysis of the anisotropic magnetoresistance (AMR) measurements. The SHNO consists of a Py(5nm)/Pt(6nm) bilayer patterned in a disc shape with radius of 2 µm, gold electrodes (150nm thick) are deposited on top of the bilayer and are 100nm separated from each other, see Fig. (a) and (b).

To estimate the H_Oe the changes of AMR curves is analyzed in a wide range of applied magnetic field, angles and currents, The effect of H_Oe is in the Py layer induced by the current in the Pt layer, as in active region-the gap, current mainly flows through the Pt (>80% from our calculation, see also Ref. [4]), see Fig. (c). The H_Oe direction is taken into account thus estimations of the H_Oe for different currents, which is illustrated in Fig. (i), could be made. These results in addition of giving a good estimation of H_Oe, they help to have an understanding of the excited modes of the SHNO and their field confinement which is crucial in our aim to use a series of SHNOs as a platform for a new type of magnetic biosensors.

References:

[1] M. Tsoi et al., Phys. Rev. Lett. 80, 4281 (1998).
[2] V. E. Demidov et al., Nature Mater. 11, 1028 (2012).
[3] V. E. Demidov et al., Nat. Commun. 5, 3179 (2014).
[4] H. Ulrichs et al., Appl. Phys. Lett. 104, 042407 (2014).

8. Hydrodynamics regulation in mammalian cell perfusion culture

Caijuan Zhan, Veronique Chotteau

Cell Technology Group (CETEG), Division of Industrial Biotechnology
,
School of Biotechnology, KTH
cajuan@kth.se, +46 8 790 77 43

Perfusion culture is receiving interest due to its advantage of high cell density and high productivity in small-scale bioreactor. In comparison with fed-batch, this operation mode has the advantage to use smaller bioreactor, compatible with disposable equipment, and involving lower capital expenditure. Continuous medium is fed and a good separation device is used to retain cells in the bioreactor. In our study, we employed tangential flow filtration used hollow fiber membrane to separate the cells, this is due to its advantages of reduced clogging and fouling from constant passing flow compared to spin filter or depth filter and high filter surface area to volume ratio. Many mailman cells are shear or mechanical force sensitive, therefore the operating conditions for feed flow rate and the mixing in the bioreactors should be chosen in the safe range of cells. For this purpose, we investigate the mechanisms behind the shear damage in both hollow fiber and bioreactor, which are the two main source of shear force. The shear limitations are studied theoretically and validation experiments are performed to examine the cell behavior under these certain mechanical forces. We found the high shear will depress the cell growth and then further introduce cell apoptosis. The shear safe ranges for HEK cells are documented and can be used for guiding perfusion process.

9. Class V alcohol dehydrogenase – the odd sibling

Linus J Östberg¹, Bengt Persson², Jan-Olov Höög¹

¹Department of Medical Biochemistry and Biophysics, Karolinska Institutet,Scheeles väg 2, 171 65 Solna
²Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University,Husargatan 3, 751 23 Uppsala
+46 738055152; linus.ostberg@ki.se

All known attempts to isolate and characterize mammalian class V alcohol dehydrogenase (ADH5), a member of the large ADH protein family, at the protein level have failed. This indicates that the ADH5 protein is not stable in a non-cellular environment, which is in contrast to all other human ADH enzymes. Using a combination of structural calculations and sequence analyses, we were able to identify local structural differences between human ADH5 and other human ADHs, including an elongated β-strands and a labile α-helix at the subunit interface region of each chain that probably disturb it. Several amino acid residues are strictly conserved in class I-IV, but altered in ADH5. There is an evolutionary pressure among the mammalian ADH5s, which for most proteins indicate that they fulfill a physiological function. We thus propose that ADH5 is expressed, but unable to form active dimers in a non-cellular environment, and is an atypical mammalian ADH.