Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome

Monogenic neurodevelopmental disorders provide key insights into the pathogenesis of disease and help us understand how specific genes control the development of the human brain. Timothy syndrome is caused by a missense mutation in the L-type calcium channel Ca(v)1.2 that is associated with developmental delay and autism. We generated cortical neuronal precursor cells and neurons from induced pluripotent stem cells derived from individuals with Timothy syndrome. Cells from these individuals have defects in calcium (Ca(2+)) signaling and activity-dependent gene expression. They also show abnormalities in differentiation, including decreased expression of genes that are expressed in lower cortical layers and in callosal projection neurons. In addition, neurons derived from individuals with Timothy syndrome show abnormal expression of tyrosine hydroxylase and increased production of norepinephrine and dopamine. This phenotype can be reversed by treatment with roscovitine, a cyclin-dependent kinase inhibitor and atypical L-type-channel blocker. These findings provide strong evidence that Ca(v)1.2 regulates the differentiation of cortical neurons in humans and offer new insights into the causes of autism in individuals with Timothy syndrome.     

Properties of zeaxanthin and its radical cation bound to the minor light-harvesting complexes CP24, CP26 and CP29

Nonphotochemical quenching (NPQ) is a fundamental mechanism in photosynthesis by which plants protect themselves against excess excitation energy and which is thus of crucial importance for plant survival and fitness. Recently, carotenoid radical cation (Car^•+) formation has been discovered to be a key step in the feedback deexcitation quenching component (qE) of NPQ, whose molecular mechanism and location remains elusive. A recent model for qE suggests that the replacement of violaxanthin (Vio) by zeaxanthin (Zea) in photosynthetic pigment binding pockets can in principle result in qE via the so-called “gear-shift” or electron transfer quenching mechanisms. We performed pump-probe measurements on individual antenna complexes of photosystem II (CP24, CP26 and CP29) upon excitation of the chlorophylls (Chl) into their first excited Q_y state at 660 nm when either Vio or Zea was bound to those complexes. The Chl lifetime was then probed by measuring the decay kinetics of the Chl excited state absorption (ESA) at 900 nm. The charge-transfer quenching mechanism, which is characterized by a spectral signature of the transiently formed Zea radical cation (Zea^•+) in the near-IR, has also been addressed, both in solution and in light-harvesting complexes of photosystem II (LHC-II). Applying resonant two-photon two-color ionization (R2P2CI) spectroscopy we show here the formation of β-Car^•+ in solution, which occurs on a femtosecond time-scale by direct electron transfer to the solvent. The β-Car^•+ maxima strongly depend on the solvent polarity. Moreover, our two-color two-photon spectroscopy on CP29 reveals the spectral position of Zea^•+ in the near-IR region at 980 nm.     

Evaluation of the LIVE/DEAD BacLight kit for detection of extremophilic archaea and visualization of microorganisms in environmental hypersaline samples

Extremophilic archaea were stained with the LIVE/DEAD BacLight kit under conditions of high ionic strength and over a pH range of 2.0 to 9.3. The reliability of the kit was tested with haloarchaea following permeabilization of the cells. Microorganisms in hypersaline environmental samples were detectable with the kit, which suggests its potential application to future extraterrestrial halites.     

Importance of flood zones for nitrogen and phosphorus dynamics in the Danube Delta

The change of concentration of total reactive phosphorus (TRP) and dissolved inorganic nitrogen (DIN) was studied in the lower Danube river and in selected lakes situated in the wetland area of the Danube Delta. The differences Danube Delta in nutrient concentration in the river waters entering the delta and the delta in different sites (especially lakes) of the wetland area are considered to reflect retention in the system. The highest retention was found in periods of moderate and low water level when the surface-to-volume ratio of the lakes was high. In these periods the in-lake concentration of TRP and DIN could be as low as 11 and 23% of the values found in the inflowing river.     

Triuret as a potential hypokalemic agent: Structure characterization of triuret and triuret-alkali metal adducts by mass spectrometric techniques

Triuret (also known as carbonyldiurea, dicarbamylurea, or 2,4-diimidotricarbonic diamide) is a byproduct of purine degradation in living organisms. An abundant triuret precursor is uric acid, whose level is altered in multiple metabolic pathologies. Triuret can be generated via urate oxidation by peroxynitrite, the latter being produced by the reaction of nitric oxide radical with superoxide radical anion. From this standpoint, an excess production of superoxide radical anions could indirectly favor triuret formation; however very little is known about the potential in vivo roles of this metabolite. Triuret’s structure is suggestive of its ability to adopt various conformations and act as a flexible ligand for metal ions. In the current study, HPLC-MS/MS, energy-resolved mass spectrometry, selected ion monitoring, collision-induced dissociation, IRMPD spectroscopy, Fourier transform-ion cyclotron resonance mass spectrometry and computational methods were employed to characterize the structure of triuret and its metal complexes, to determine the triuret-alkali metal binding motif, and to evaluate triuret affinity toward alkali metal ions, as well as its affinity for Na⁺ and K⁺ relative to other organic ligands. The most favored binding motif was determined to be a bidentate chelation of triuret with the alkali metal cation involving two carbonyl oxygens. Using the complexation selectivity method, it was observed that in solution triuret has an increased affinity for potassium ions, compared to sodium and other alkali metal ions. We propose that triuret may act as a potential hypokalemic agent under pathophysiological conditions conducive to its excessive formation and thus contribute to electrolyte disorders. The collision- or photo-induced fragmentation channels of deprotonated and protonated triuret, as well as its alkali metal adducts, are likely to mimic the triuret degradation pathways in vivo.     

Paraoxonase 1 activities and polymorphisms in autism spectrum disorders

Autism spectrum disorders (ASD) comprise a complex and heterogeneous group of conditions of unknown aetiology, characterized by significant disturbances in social, communicative and behavioural functioning. Recent studies suggested a possible implication of the high-density lipoprotein associated esterase/lactonase paraoxonase 1 (PON1) in ASD. In the present study, we aimed at investigating the PON1 status in a group of 50 children with ASD as compared to healthy age and sex matched control participants. We evaluated PON1 bioavailability (i.e. arylesterase activity) and catalytic activity (i.e. paraoxonase activity) in plasma using spectrophotometric methods and the two common polymorphisms in the PON1 coding region (Q192R, L55M) by employing Light Cycler real-time PCR. We found that both PON1 arylesterase and PON1 paraoxonase activities were decreased in autistic patients (respectively, P < 0.001, P < 0.05), but no association with less active variants of the PON1 gene was found. The PON1 phenotype, inferred from the two-dimensional enzyme analysis, had a similar distribution in the ASD group and the control group. In conclusion, both the bioavailability and the catalytic activity of PON1 are impaired in ASD, despite no association with the Q192R and L55M polymorphisms in the PON1 gene and a normal distribution of the PON1 phenotype.     

Evolution of robust and efficient system topologies

Mutation/selection algorithms were applied to increase the efficiency and the robustness of sparse random networks. Selection for better efficiency leads to the well-known star topology, while selection for robustness only results in a relatively dense core and a small periphery. Concomitant selection for both efficiency and robustness leads to networks with intermittent center/periphery values. Networks evolving under multiple attack regimes develop distinct topologies with larger cores, and are characterized by parameter distributions different from those developing under single-attack regimes.     

Secure top most significant genome variants search: iDASH 2017 competition

Background

One of the 3 tracks of iDASH Privacy & Security Workshop 2017 competition was to execute a whole genome variants search on private genomic data. Particularly, the search application was to find the top most significant SNPs (Single-Nucleotide Polymorphisms) in a database of genome records labeled with control or case. In this paper we discuss the solution submitted by our team to this competition.

Methods

Privacy and confidentiality of genome data had to be ensured using Intel SGX enclaves. The typical use-case of this application is the multi-party computation (each party possessing one or several genome records) of the SNPs which statistically differentiate control and case genome datasets.

Results

Our solution consists of two applications: (i) compress and encrypt genome files and (ii) perform genome processing (top most important SNPs search). We have opted for a horizontal treatment of genome records and heavily used parallel processing. Rust programming language was employed to develop both applications.

Conclusions

Execution performance of the processing applications scales well and very good performance metrics are obtained. Contest organizers selected it as the best submission amongst other received competition entries and our team was awarded the first prize on this track.

     

Roles of CD147 on T lymphocytes activation and MMP-9 secretion in systemic lupus erythematosus

The cellular and molecular mechanisms involved in many abnormalities described in Systemic Lupus Erythematosus (SLE) are still unclear. Some of these abnormalities referred to the hyperactivation of T lymphocytes and the enhanced secretion of MMP-9 by peripheral blood mononuclear cells (PBMCs). Therefore, in this paper we investigated the potential role of CD147 molecule in these abnormalities. Our results demonstrated that CD147 molecule is overexpressed on CD3+T lymphocytes from SLE patients when compared with CD3+T lymphocytes from healthy donors. Monoclonal anti-CD147 antibodies, MEM-M6/1 clone, were able to inhibit protein tyrosine phosphorylation only in CD3 x CD28 costimulated T lymphocytes from SLE patients. However, this monoclonal antibody was unable to inhibit the enhanced activity of MMP-9 secreted by SLE PBMCs.