<i>P. berghei</i> telomerase subunit TERT is essential for parasite survival

Telomeres define the ends of chromosomes protecting eukaryotic cells from chromosome instability and eventual cell death. The complex regulation of telomeres involves various proteins including telomerase, which is a specialized ribonucleoprotein responsible for telomere maintenance. Telomeres of chromosomes of malaria parasites are kept at a constant length during blood stage proliferation. The 7-bp telomere repeat sequence is universal across different Plasmodium species (GGGTTT/CA), though the average telomere length varies. The catalytic subunit of telomerase, telomerase reverse transcriptase (TERT), is present in all sequenced Plasmodium species and is approximately three times larger than other eukaryotic TERTs. The Plasmodium RNA component of TERT has recently been identified in silico. A strategy to delete the gene encoding TERT via double cross-over (DXO) homologous recombination was undertaken to study the telomerase function in P. berghei. Expression of both TERT and the RNA component (TR) in P. berghei blood stages was analysed by Western blotting and Northern analysis. Average telomere length was measured in several Plasmodium species using Telomere Restriction Fragment (TRF) analysis. TERT and TR were detected in blood stages and an average telomere length of ~950 bp established. Deletion of the tert gene was performed using standard transfection methodologies and we show the presence of tert− mutants in the transfected parasite populations. Cloning of tert- mutants has been attempted multiple times without success. Thorough analysis of the transfected parasite populations and the parasite obtained from extensive parasite cloning from these populations provide evidence for a so called delayed death phenotype as observed in different organisms lacking TERT. The findings indicate that TERT is essential for P. berghei cell survival. The study extends our current knowledge on telomere biology in malaria parasites and validates further investigations to identify telomerase inhibitors to induce parasite cell death

Involvement of Plasmodium falciparum protein kinase CK2 in the chromatin assembly pathway

<p>Abstract</p> <p>Background</p> <p>Protein kinase CK2 is a pleiotropic serine/threonine protein kinase with hundreds of reported substrates, and plays an important role in a number of cellular processes. The cellular functions of <it>Plasmodium falciparum </it>CK2 (PfCK2) are unknown. The parasite's genome encodes one catalytic subunit, PfCK2α, which we have previously shown to be essential for completion of the asexual erythrocytic cycle, and two putative regulatory subunits, PfCK2β1 and PfCK2β2.</p> <p>Results</p> <p>We now show that the genes encoding both regulatory PfCK2 subunits (PfCK2β1 and PfCK2β2) cannot be disrupted. Using immunofluorescence and electron microscopy, we examined the intra-erythrocytic stages of transgenic parasite lines expressing hemagglutinin (HA)-tagged catalytic and regulatory subunits (HA-CK2α, HA-PfCK2β1 or HA-PfCK2β2), and localized all three subunits to both cytoplasmic and nuclear compartments of the parasite. The same transgenic parasite lines were used to purify PfCK2β1- and PfCK2β2-containing complexes, which were analyzed by mass spectrometry. The recovered proteins were unevenly distributed between various pathways, with a large proportion of components of the chromatin assembly pathway being present in both PfCK2β1 and PfCK2β2 precipitates, implicating PfCK2 in chromatin dynamics. We also found that chromatin-related substrates such as nucleosome assembly proteins (Naps), histones, and two members of the Alba family are phosphorylated by PfCK2α <it>in vitro</it>.</p> <p>Conclusions</p> <p>Our reverse-genetics data show that each of the two regulatory PfCK2 subunits is required for completion of the asexual erythrocytic cycle. Our interactome study points to an implication of PfCK2 in many cellular pathways, with chromatin dynamics being identified as a major process regulated by PfCK2. This study paves the way for a kinome-wide interactomics-based approach to elucidate protein kinase function in malaria parasites.</p

Temperature dependent photoluminescence of organic semiconductors with varying backbone conformation

We present photoluminescence studies as a function of temperature from a series of conjugated polymers and a conjugated molecule with distinctly different backbone conformations. The organic materials investigated here are: planar methylated ladder type poly para-phenylene, semi-planar polyfluorene, and non-planar para hexaphenyl. In the longer-chain polymers the photoluminescence transition energies blue shift with increasing temperatures. The conjugated molecules, on the other hand, red shift their transition energies with increasing temperatures. Empirical models that explain the temperature dependence of the band gap energies in inorganic semiconductors can be extended to explain the temperature dependence of the transition energies in conjugated molecules.Comment: 8 pages, 9 figure

linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser

In biology, we are often confronted with information-rich, large-scale trajectory data, but exploring and communicating patterns in such data can be a cumbersome task. Ideally, the data should be wrapped with an interactive visualisation in one concise packet that makes it straightforward to create and test hypotheses collaboratively. To address these challenges, we have developed a tool, linus, which makes the process of exploring and sharing 3D trajectories as easy as browsing a website. We provide a python script that reads trajectory data, enriches them with additional features such as edge bundling or custom axes, and generates an interactive web-based visualisation that can be shared online. linus facilitates the collaborative discovery of patterns in complex trajectory data

Bakteerinanoselluloosan teollisen tuotannon haasteita ja ratkaisuja

Tiivistelmä. Työn tavoite on kartoittaa bakteerinanoselluloosan (BNC) teollisen mittakaavan tuotannon edellytyksiä, haasteita ja mahdollisia ratkaisuja. Työn alussa taustoitetaan materiaalin alkuperää ja erityisiä ominaisuuksia. Puhtaus, huokoisuus, korkea kiteisyys sekä polymeroitumisaste tekevät BNC materiaaleista muun muassa mekaanisesti kestäviä, helposti muokattavia ja bioyhteensopivia. Monipuoliset ominaisuudet takaavat laajan skaalan erilaisia sovelluksia ja käyttökohteita, joista on kerätty BNC:n ominaisuuksia esiin tuova taulukko. Optimoitu kasvatusliuos on edellytys tehokkaalle BNC-synteesille, jota on pystytty tehostamaan muutamalla melko edullisellakin lisäkomponentilla. Sopivien olosuhteiden ylläpitoon on kehitetty monenlaisia fermentoreita, joista sekoituksella varustetut jatkuvatoimiset bioreaktorit soveltunevat parhaiten suurivolyymiseen tuotantoon. Työ sisältää hahmotelman edellä mainitun kaltaisesta bioreaktorin kokoonpanosta mahdollisine prosessi-instrumentteineen sekä pohdintaa ajomallista. Tieteellisten avoimen tutkimuksen lisäksi tunnustellaan kaupallisten toimijoiden nykyistä tilannetta sekä selvennetään, kuinka merkittävästi sivuvirtojen hyödyntäminen ja kiihtyvä geenitekniikan kehitys voivat lähitulevaisuudessa parantaa saantoa ja osaltaan mahdollistaa suuremman volyymin tuotannon. Työ on toteutettu kirjallisuuskatsauksena

Pan-embryo cell dynamics of germlayer formation in zebrafish

Cell movements are coordinated across spatio-temporal scales to achieve precise positioning of organs during vertebrate gastrulation. In zebrafish, mechanisms governing such morphogenetic movements have so far only been studied within a local region or a single germlayer. Here, we present pan-embryo analyses of fate specification and dynamics of all three germlayers simultaneously within a gastrulating embryo, showing that cell movement characteristics are predominantly determined by its position within the embryo, independent of its germlayer identity. The spatially confined fate specification establishes a distinct distribution of cells in each germlayer during early gastrulation. The differences in the initial distribution are subsequently amplified by a unique global movement, which organizes the organ precursors along the embryonic body axis, giving rise to the blueprint of organ formation

Spectral and Photophysical Studies of Poly[2,6-(1,5-dioctylnaphthalene)]thiophenes

A complete spectroscopic and photophysical study of three alternating naphthalene-α-thiophene copolymers was undertaken in solution (room and low temperature) and in the solid state (thin films in a Zeonex matrix). The study comprises absorption, emission, and triplet−triplet spectra together with quantitative measurements of quantum yield (fluorescence, intersystem-crossing, internal conversion, and singlet oxygen formation) lifetimes and singlet and triplet energies. The overall data allow the determination of the rate constants for all the decay processes. Comparison between the behavior of analogous 1-naphthyl(oligo)thiophenes and the 2,6-naphthalene(oligo)thiophene copolymers allows several important observations. First, the polymers display higher fluorescence quantum yields and lower S1→T1 intersystem-crossing yields than the oligomers. This can be attributed to the presence of the 1,5-dioctyloxynaphthalene groups in the copolymers leading to a more rigid polymer backbone, which decreases radiationless deactivation and increases the radiative efficiency. Second, the singlet and triplet energies are significantly lower in the polymers than with the corresponding oligomers. This implies a lower HOMO−LUMO energy difference in the polymers due to an extended π-delocalization. Third, the singlet-to-triplet (S1−T1) energy splitting is higher in the oligomers than with the polymers, even though the former display higher intersystem-crossing yields. It is suggested that this may result from intersystem-crossing in the oligomers involving significant charge-transfer (CT) character (spin-orbit coupling is mediated by CT mixing involving the singlet and triplet states in matrix elements of the type 1ΨCT |H‘|3Ψ1) of the relevant excited states but that is less important with the polymers. We believe that this may be relevant to understanding the nature of CT states in conjugated copolymers

The basophil activation test differentiates between patients with wheat-dependent exercise-induced anaphylaxis and control subjects using gluten and isolated gluten protein types

Background: Oral food challenge using gluten and cofactors is the gold standard to diagnose wheat-dependent exercise-induced anaphylaxis (WDEIA), but this procedure puts patients at risk of an anaphylactic reaction. Specific IgE to ω5-gliadins as major allergens and skin prick tests to wheat may yield negative results. Thus, we designed a proof-of-principle study to investigate the utility of the basophil activation test (BAT) for WDEIA diagnosis. Methods: Different gluten protein types (GPT; α-, γ-, ω1,2- and ω5-gliadins, high-molecular-weight glutenin subunits [HMW-GS] and low-molecular-weight glutenin subunits [LMW-GS]) and gluten were used in different concentrations to measure basophil activation in 12 challenge-confirmed WDEIA patients and 10 control subjects. The results were compared to routine allergy diagnostics. Parameters analyzed include the percentage of CD63+ basophils, the ratio of %CD63+ basophils induced by GPT/gluten to %CD63+ basophils induced by anti-FcεRI antibody, area under the dose-response curve and test sensitivity and specificity. Results: GPT and gluten induced strong basophil activation for %CD63+ basophils and for %CD63+/anti-FcɛRI ratio in a dose-dependent manner in patients, but not in controls (p < 0.001, respectively). BAT performance differed from acceptable (0.73 for LMW-GS) to excellent (0.91 for ω5-gliadins) depending on the specific GPT as evaluated by the area under the receiver operating characteristic curve. Patients showed individual sensitization profiles. After determination of the best cut-off points, ω5-gliadins and HMW-GS showed the best discrimination between patients and controls with a sensitivity/specificity of 100/70 and 75/100, respectively. Conclusion: This study shows the alternative role of BAT in better defining WDEIA and the causative wheat allergens. The best BAT parameters to distinguish WDEIA patients from controls were %CD63+ basophil values for ω5-gliadins and HMW-GS

Quality control for more reliable integration of deep learning-based image segmentation into medical workflows

Machine learning algorithms underpin modern diagnostic-aiding software, whichhas proved valuable in clinical practice, particularly in radiology. However,inaccuracies, mainly due to the limited availability of clinical samples fortraining these algorithms, hamper their wider applicability, acceptance, andrecognition amongst clinicians. We present an analysis of state-of-the-artautomatic quality control (QC) approaches that can be implemented within thesealgorithms to estimate the certainty of their outputs. We validated the mostpromising approaches on a brain image segmentation task identifying whitematter hyperintensities (WMH) in magnetic resonance imaging data. WMH are acorrelate of small vessel disease common in mid-to-late adulthood and areparticularly challenging to segment due to their varied size, anddistributional patterns. Our results show that the aggregation of uncertaintyand Dice prediction were most effective in failure detection for this task.Both methods independently improved mean Dice from 0.82 to 0.84. Our workreveals how QC methods can help to detect failed segmentation cases andtherefore make automatic segmentation more reliable and suitable for clinicalpractice.<br

[Ge₂]⁴⁻Dumbbells with Very Short Ge−Ge Distances in the Zintl Phase Li₃NaGe₂: A Solid-State Equivalent to Molecular O₂

The novel ternary Zintl phase Li3NaGe2 comprises alkali-metal cations and [Ge2]4− dumbbells. The diatomic [Ge2]4− unit is characterized by the shortest Ge−Ge distance (2.390(1) Å) ever observed in a Zintl phase and thus represents the first Ge=Ge double bond under such conditions, as also suggested by the (8−N) rule. Raman measurements support these findings. The multiple-bond character is confirmed by electronic-structure calculations, and an upfield 6Li NMR shift of −10.0 ppm, which was assigned to the Li cations surrounded by the π systems of three Ge dumbbells, further underlines this interpretation. For the unperturbed, ligand-free dumbbell in Li3NaGe2, the π- bonding py and pz orbitals are degenerate as in molecular oxygen, which has singly occupied orbitals. The partially filled π-type bands of the neat solid Li3NaGe2 cross the Fermi level, resulting in metallic properties. Li3NaGe2 was synthesized from the elements as well as from binary reactants and subsequently characterized crystallographically.O.P. acknowledges support from a Marie Skłodowska-Curie Individual Fellowship. L.M.S. is further grateful to the Fonds der Chemischen Industrie and the Studienstiftung des deutschen Volkes for her fellowships. A.J.K. gratefully acknowledges funding from the Alfred Kordelin Foundation and computational resources from CSC – the Finnish IT Center for Science.This is the accepted manuscript. The final version is available at http://onlinelibrary.wiley.com/wol1/doi/10.1002/ange.201508044/abstract