Probing contacts of inhibitor locked in transition states in the catalytic triad of DENV2 type serine protease and its mutants by 1H, 19F and 15 N NMR spectroscopy

Background: Detailed structural knowledge of enzyme-inhibitor complexes trapped in intermediate state is the key for a fundamental understanding of reaction mechanisms taking place in enzymes and is indispensable as a structure-guided drug design tool. Solution state NMR uniquely allows the study of active sites of enzymes in equilibrium between different tautomeric forms. In this study 1H, 19F and 15 N NMR spectroscopy has been used to probe the interaction contacts of inhibitors locked in transition states of the catalytic triad of a serine protease. It was demonstrated on the serotype II Dengue virus NS2B:NS3pro serine protease and its mutants, H51N and S135A, in complex with high-affinity ligands containing trifluoromethyl ketone (tfk) and boronic groups in the C-terminal of tetra-peptides. Results: Monitoring 19F resonances, shows that only one of the two isomers of the tfk tetra-peptide binds with NS2B:NS3pro and that access to the bulk of the active site is limited. Moreover, there were no bound water found in proximity of the active site for any of the ligands manifesting in a favorable condition for formation of low barrier hydrogen bonds (LBHB) in the catalytic triad. Based on this data we were able to identify a locked conformation of the protein active site. The data also indicates that the different parts of the binding site most likely act independently of each other. Conclusions: Our reported findings increases the knowledge of the detailed function of the catalytic triad in serine proteases and could facilitate the development of rational structure based inhibitors that can selectively target the NS3 protease of Dengue type II (DENV2) virus. In addition the results shows the usefulness of probing active sites using F-19 NMR spectroscopy

Photoassociation of cold metastable helium atoms

During the last decades the study of cold atoms has grown in a great measure. Research in this field has been made possible due to the development of laser cooling and trapping techniques. We use laser cooling to cool helium atoms down to a temperature of 1 mK and we are able to trap 106 atoms in our magneto-optical trap. The helium atoms are in a metastable state, the He 23S1 state, which has a lifetime of more than 2 hours. With cold atoms phenomena can be studied that are not accessible using thermal atoms, such as high resolution spectroscopy. Furthermore cold atoms are the first step towards Bose-Einstein condensation. Cold alkali-metal atoms have been extensively studied, using photoassociation spectroscopy. In this thesis the first photoassociation results for rare gas atoms, namely metastable helium atoms will be discussed. Various experiments are described and an analysis of the results is given

Constipation in pediatric Cystic Fibrosis patients: An underestimated medical condition

AbstractBackgroundThe aims of this study were to determine prevalence, risk factors and treatment of constipation in patients with Cystic Fibrosis (CF), as well as the diagnostic value of abdominal radiography.MethodsA cohort of 214 pediatric CF patients was investigated. Furthermore, 106 abdominal radiographs of CF patients with or without constipation were independently assessed by three observers on two separate occasions using the Barr and Leech scores.ResultsThe prevalence of constipation was 47%. Low total fat absorption and meconium ileus were independent risk factors for constipation in CF, while fiber and fluid intake were not associated. In CF patients the inter and intraobserver variabilities of the Barr and Leech scores were poor to moderate.ConclusionConstipation is a significant medical issue in CF and was associated with low total fat absorption and a history of meconium ileus. Finally, abdominal radiography seems of little value in the regular follow-up of CF patients

Multi Domain Design: Integration and Reuse

Design of mechatronic systems is becoming increasingly complex. Companies must continuously reduce time-to-market while increasing the quality, diversity, and functionality of their products. As a result, more and more specialists from various domains are needed to develop such products. To reduce time-to-market, many companies look to reducing the time it takes to design a product. Many focus on the reuse of design objects, leading to libraries of templates and standard components to speed up their design process. However, these reusable design objects are developed and maintained in the specialists’ domains, resulting in communication and integration issues between these domains. This paper discusses these issues and proposes a combined approach for model reuse, design integration, and communication between the designers, design tools, and models involved. A case study at a multi-national company successfully demonstrated that the approach leads to a faster and more consistent design process

Integrated transcriptomic and proteomic analyses ofP. falciparumgametocytes: molecular insight into sex-specific processes and translational repression

Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these 'repressed transcripts' have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies

Frequency shifts of photoassociative spectra of ultracold metastable Helium atoms : a new measurement of the s-wave scattering length

We observe light-induced frequency shifts in one-color photoassociative spectra of magnetically trapped $^4$He$^*$ atoms in the metastable $2^3S_1$ state. A pair of ultracold spin-polarized $2^3S_1$ helium atoms is excited into a molecular bound state in the purely long range $0_u^+$ potential connected to the $2^3S_1 - 2^3P_0$ asymptote. The shift arises from the optical coupling of the molecular excited bound state with the scattering states and the bound states of two colliding $2^3S_1$ atoms. We measure the frequency-shifts for several ro-vibrational levels in the $0^+_u$ potential and find a linear dependence on the photoassociation laser intensity. Comparison with a theoretical analysis provides a good indication for the s-wave scattering length $a$ of the quintet ($^5\Sigma_g^+$) potential, $a=7.2\pm 0.6$ nm, which is significantly lower than most previous results obtained by non-spectroscopic methods.Comment: 7 pages, 4 figure

Spectral analysis and resolving spatial ambiguities in human sound localization

This dissertation provides an overview of my research over the last five years into the spectral analysis involved in human sound localization. The work involved conducting psychophysical tests of human auditory localization performance and then applying analytical techniques to analyze and explain the data. It is a fundamental thesis of this work that human auditory localization response directions are primarily driven by the auditory localization cues associated with the acoustic filtering properties of the external auditory periphery, i.e., the head, torso, shoulder, neck, and external ears. This work can be considered as composed of three parts. In the first part of this work, I compared the auditory localization performance of a human subject and a time-delay neural network model under three sound conditions: broadband, high-pass, and low-pass. A “black-box” modeling paradigm was applied. The modeling results indicated that training the network to localize sounds of varying center-frequency and bandwidth could degrade localization performance results in a manner demonstrating some similarity to human auditory localization performance. As the data collected during the network modeling showed that humans demonstrate striking localization errors when tested using bandlimited sound stimuli, the second part of this work focused on human sound localization of bandpass filtered noise stimuli. Localization data was collected from 5 subjects and for 7 sound conditions: 300 Hz to 5 kHz, 300 Hz to 7 kHz, 300 Hz to 10 kHz, 300 Hz to 14 kHz, 3 to 8 kHz, 4 to 9 kHz, and 7 to 14 kHz. The localization results were analyzed using the method of cue similarity indices developed by Middlebrooks (1992). The data indicated that the energy level in relatively wide frequency bands could be driving the localization response directions, just as in Butler’s covert peak area model (see Butler and Musicant, 1993). The question was then raised as to whether the energy levels in the various frequency bands, as described above, are most likely analyzed by the human auditory localization system on a monaural or an interaural basis. In the third part of this work, an experiment was conducted using virtual auditory space sound stimuli in which the monaural spectral cues for auditory localization were disrupted, but the interaural spectral difference cue was preserved. The results from this work showed that the human auditory localization system relies primarily on a monaural analysis of spectral shape information for its discrimination of directions on the cone of confusion. The work described in the three parts lead to the suggestion that a spectral contrast model based on overlapping frequency bands of varying bandwidth and perhaps multiple frequency scales can provide a reasonable algorithm for explaining much of the current psychophysical and neurophysiological data related to human auditory localization

A Molecular Assay to Quantify Male and Female Plasmodium falciparum Gametocytes: Results From 2 Randomized Controlled Trials Using Primaquine for Gametocyte Clearance.

Background: Single low-dose primaquine (PQ) reduces Plasmodium falciparum infectivity before it impacts gametocyte density. Here, we examined the effect of PQ on gametocyte sex ratio as a possible explanation for this early sterilizing effect. Methods: Quantitative reverse-transcription polymerase chain reaction assays were developed to quantify female gametocytes (targeting Pfs25 messenger RNA [mRNA]) and male gametocytes (targeting Pf3D7_1469900 mRNA) in 2 randomized trials in Kenya and Mali, comparing dihydroartemisinin-piperaquine (DP) alone to DP with PQ. Gametocyte sex ratio was examined in relation to time since treatment and infectivity to mosquitoes. Results: In Kenya, the median proportion of male gametocytes was 0.33 at baseline. Seven days after treatment, gametocyte density was significantly reduced in the DP-PQ arm relative to the DP arm (females: 0.05% [interquartile range {IQR}, 0.0-0.7%] of baseline; males: 3.4% [IQR, 0.4%-32.9%] of baseline; P 0.125 mg/kg) 48 hours after treatment, and gametocyte sex ratio was not associated with mosquito infection rates. Conclusions: The early sterilizing effects of PQ may not be explained by the preferential clearance of male gametocytes and may be due to an effect on gametocyte fitness

Photoassociation spectroscopy of cold He(2(3)S) atoms

We observe vibrational states by photoassociation spectroscopy of cold He(2 3S) atoms. Photoassociation resonances are detected as peaks in the Penning ionization rate over a frequency range of 20 GHz below the atomic 2 3S1-2 3P2 transition frequency. We have observed three vibrational series, of which two can be identified. A possible mechanism to explain the observed increase of the Penning ionization rate is discussed

Identification of soluble protein fragments by gene fragmentation and genetic selection

We describe a new method, which identifies protein fragments for soluble expression in Escherichia coli from a randomly fragmented gene library. Inhibition of E. coli dihydrofolate reductase (DHFR) by trimethoprim (TMP) prevents growth, but this can be relieved by murine DHFR (mDHFR). Bacterial strains expressing mDHFR fusions with the soluble proteins green fluroscent protein (GFP) or EphB2 (SAM domain) displayed markedly increased growth rates with TMP compared to strains expressing insoluble EphB2 (TK domain) or ketosteroid isomerase (KSI). Therefore, mDHFR is affected by the solubility of fusion partners and can act as a reporter of soluble protein expression. Random fragment libraries of the transcription factor Fli1 were generated by deoxyuridine incorporation and endonuclease V cleavage. The fragments were cloned upstream of mDHFR and TMP resistant clones expressing soluble protein were identified. These were found to cluster around the DNA binding ETS domain. A selected Fli1 fragment was expressed independently of mDHFR and was judged to be correctly folded by various biophysical methods including NMR. Soluble fragments of the cell-surface receptor Pecam1 were also identified. This genetic selection method was shown to generate expression clones useful for both structural studies and antibody generation and does not require a priori knowledge of domain architecture