From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology.

Classical physiological studies using electrophysiological, biophysical, biochemical, and molecular techniques have created a detailed picture of molecular transport, bioenergetics, contractility and movement, and growth, as well as the regulation of these processes by external stimuli in cells and organisms. Newer systems biology approaches are beginning to provide deeper and broader understanding of these complex biological processes and their dynamic responses to a variety of environmental cues. In the past decade, advances in mass spectrometry-based proteomic technologies have provided invaluable tools to further elucidate these complex cellular processes, thereby confirming, complementing, and advancing common views of physiology. As one notable example, the application of proteomics to study the regulation of kidney function has yielded novel insights into the chemical and physical processes that tightly control body fluids, electrolytes, and metabolites to provide optimal microenvironments for various cellular and organ functions. Here, we systematically review, summarize, and discuss the most significant key findings from functional proteomic studies in renal epithelial physiology. We also identify further improvements in technological and bioinformatics methods that will be essential to advance precision medicine in nephrology.

Quantitative structure determination of adsorbed formate and surface hydroxyls on Fe3O4(001).

Using the chemically specific techniques of normal incidence X-ray standing waves and photoelectron diffraction, we have investigated the dissociative adsorption of formic acid on the Fe3O4(001) surface, specifically probing the local structures of both the adsorbed formate and resulting surface hydroxyl. Using model independent direct methods, we reinforce the observations of a previous surface X-ray diffraction study that the formate molecule adsorbs with both oxygens atop octahedrally coordinated surface Fe cations and that ∼60% of the formate is adsorbed in the so called tet site. We additionally determine, for the first time, that the surface hydroxyl species are found at the so called int site. This confirms previous DFT predictions and reinforces the pivotal role the surface hydroxyl plays in lifting the subsurface cation vacancy termination of the Fe3O4(001) surface.

Probing structural changes upon carbon monoxide coordination to single metal adatoms.

In this work, the adsorption height of Ag adatoms on the Fe3O4(001) surface after exposure to CO was determined using normal incidence x-ray standing waves. The Ag adatoms bound to CO (Ag1 CO) are found to be pulled out of the surface to an adsorption height of 1.15 Å ± 0.08 Å, compared to the previously measured height of 0.96 Å ± 0.03 Å for bare Ag adatoms and clusters. Utilizing DFT+vdW+U calculations with the substrate unit cell dimension fixed to the experimental value, the predicted adsorption height for Ag1 CO was 1.16 Å, in remarkably good agreement with the experimental results.

AbDesigner3D: a structure-guided tool for peptide-based antibody production.

Summary: We present AbDesigner3D, a new tool for identification of optimal immunizing peptides for antibody production using a peptide-based strategy. AbDesigner3D integrates 3D structural data from the Protein Data Bank (PDB) with UniProt data, which includes basic sequence data, post-translational modification sites, SNP occurrences and more. Other features, such as uniqueness and conservation scores, are calculated based on sequences from UniProt. The 3D visualization capabilities allow an intuitive interface, while an abundance of quantitative output simplifies the process of comparing immunogen peptides. Important quantitative features added in this tool include calculation and display of accessible surface area (ASA) and protein-protein interacting residues (PPIR). The specialized data visualization features of AbDesigner3D will greatly assist users to optimize their choice of immunizing peptides. Availability and implementation: AbDesigner3D is freely available at http://sysbio.chula.ac.th/AbDesigner3D or https://hpcwebapps.cit.nih.gov/AbDesigner3D/. Supplementary information: Supplementary data are available at Bioinformatics online.

Direct measurement of Ni incorporation into Fe3O4(001).

The normal incidence X-ray standing wave (NIXSW) technique has been used to follow the evolution of the adsorption geometry of Ni adatoms on the Fe3O4(001)-(√2 × âˆš2)R45° surface as a function of temperature. Two primary surface region sites are identified: a bulk-continuation tetrahedral site and a sub-surface octahedral site, the latter site being preferred at higher annealing temperatures. The ease of incorporation is linked to the presence of subsurface cation vacancies in the (√2 × âˆš2)R45° reconstruction and is consistent with the preference for octahedral coordination observed in the spinel compound NiFe2O4.

Hypercalcemia induces targeted autophagic degradation of aquaporin-2 at the onset of nephrogenic diabetes insipidus.

Hypercalcemia can cause renal dysfunction such as nephrogenic diabetes insipidus (NDI), but the mechanisms underlying hypercalcemia-induced NDI are not well understood. To elucidate the early molecular changes responsible for this disorder, we employed mass spectrometry-based proteomic analysis of inner medullary collecting ducts (IMCD) isolated from parathyroid hormone-treated rats at onset of hypercalcemia-induced NDI. Forty-one proteins, including the water channel aquaporin-2, exhibited significant changes in abundance, most of which were decreased. Bioinformatic analysis revealed that many of the downregulated proteins were associated with cytoskeletal protein binding, regulation of actin filament polymerization, and cell-cell junctions. Targeted LC-MS/MS and immunoblot studies confirmed the downregulation of 16 proteins identified in the initial proteomic analysis and in additional experiments using a vitamin D treatment model of hypercalcemia-induced NDI. Evaluation of transcript levels and estimated half-life of the downregulated proteins suggested enhanced protein degradation as the possible regulatory mechanism. Electron microscopy showed defective intercellular junctions and autophagy in the IMCD cells from both vitamin D- and parathyroid hormone-treated rats. A significant increase in the number of autophagosomes was confirmed by immunofluorescence labeling of LC3. Colocalization of LC3 and Lamp1 with aquaporin-2 and other downregulated proteins was found in both models. Immunogold electron microscopy revealed aquaporin-2 in autophagosomes in IMCD cells from both hypercalcemia models. Finally, parathyroid hormone withdrawal reversed the NDI phenotype, accompanied by termination of aquaporin-2 autophagic degradation and normalization of both nonphoshorylated and S256-phosphorylated aquaporin-2 levels. Thus, enhanced autophagic degradation of proteins plays an important role in the initial mechanism of hypercalcemic-induced NDI.

A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.

BACKGROUND: One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins. The ability to predict whether sites of protein modifications are inside or outside of PPIRs would be useful in further elucidating the regulatory mechanisms by which modifications of specific proteins regulate their cellular functions. RESULTS: Using two of the comprehensive databases for protein-protein interaction and protein modification site data (PDB and PhosphoSitePlus, respectively), we created new databases that map PTMs to their locations inside or outside of PPIRs. The mapped PTMs represented only 5 % of all known PTMs. Thus, in order to predict localization within or outside of PPIRs for the vast majority of PTMs, a machine learning strategy was used to generate predictive models from these mapped databases. For the three mapped PTM databases which had sufficient numbers of modification sites for generating models (acetylation, phosphorylation, and ubiquitylation), the resulting models yielded high overall predictive performance as judged by a combined performance score (CPS). Among the multiple properties of amino acids that were used in the classification tasks, hydrophobicity was found to contribute substantially to the performance of the final predictive models. Compared to the other classifiers we also evaluated, the SVM provided the best performance overall. CONCLUSIONS: These models are the first to predict whether PTMs are located inside or outside of PPIRs, as demonstrated by their high predictive performance. The models and data presented here should be useful in prioritizing both known and newly identified PTMs for further studies to determine the functional relationship between specific PTMs and protein-protein interactions. The implemented R package is available online ( http://sysbio.chula.ac.th/PtmPPIR ).

Communication networks beyond the capacity crunch.

This issue of Philosophical Transactions of the Royal Society, Part A represents a summary of the recent discussion meeting 'Communication networks beyond the capacity crunch'. The purpose of the meeting was to establish the nature of the capacity crunch, estimate the time scales associated with it and to begin to find solutions to enable continued growth in a post-crunch era. The meeting confirmed that, in addition to a capacity shortage within a single optical fibre, many other 'crunches' are foreseen in the field of communications, both societal and technical. Technical crunches identified included the nonlinear Shannon limit, wireless spectrum, distribution of 5G signals (front haul and back haul), while societal influences included net neutrality, creative content generation and distribution and latency, and finally energy and cost. The meeting concluded with the observation that these many crunches are genuine and may influence our future use of technology, but encouragingly noted that research and business practice are already moving to alleviate many of the negative consequences.

Broadband wavelength and angle-resolved scattering characterization for nanophotonics investigations.

The characterization of scattered light is complex and relatively nonstandardized despite being of great importance to many optical technologies. While total scatter can be efficiently measured using integrating-sphere-based techniques, a detailed determination of the full bidirectional scattering distribution function is far more challenging, often requiring complicated and expensive equipment as well as substantial measurement time. Due to this, many research groups rely on simpler, angle-resolved scattering (ARS) measurements, yet these are typically carried out using a single wavelength source, therefore providing limited information. Here, we demonstrate a custom-built broadband angle-resolved optical spectrometer, which utilizes a supercontinuum white light laser source combined with a custom automated goniometer and a Si CCD array spectrometer in order to carry out broad spectral measurements of ARS. The use of a collimated supercontinuum allows for small area measurements that are often crucial for investigation of nanophotonic samples created using expensive fabrication techniques. The system has been tested and calibrated, and accuracy and reproducibility have been verified by integrating wavelength and ARS data over the angular range and comparing to calibrated integrating sphere measurements.

Understanding the electronic structure of IrO2 using hard-X-ray photoelectron spectroscopy and density-functional theory.

The electronic structure of IrO2 has been investigated using hard x-ray photoelectron spectroscopy and density-functional theory. Excellent agreement is observed between theory and experiment. We show that the electronic structure of IrO2 involves crystal field splitting of the iridium 5d orbitals in a distorted octahedral field. The behavior of IrO2 closely follows the theoretical predictions of Goodenough for conductive rutile-structured oxides [J. B. Goodenough, J. Solid State Chem. 3, 490 (1971).

Streptococcus pneumoniae serogroup 6 clones over two decades.

The major evolutionary stresses on Streptococcus pneumoniae are thought to be the widespread use of antibiotics and the deployment of effective vaccines against the capsular polysaccharides. Our current knowledge of genetic lineages among pneumococcal isolates comes largely from investigations just before and after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) introduced in 2000. We examined 66 serogroup 6 isolates from the 1970s, long before the introduction of PCV7 and before widespread penicillin resistance was common in Birmingham, Alabama, to look for ancestors of the clones that came into play around the introduction of the PCV7 vaccine. The hypothesis was that some clonal complexes, if not individual clones, would be stable enough to persist over this period of time. We compared the 1970s isolates with 122 isolates from the 1990s in US and worldwide collections. Genotyping with pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) revealed that while some clones were probably localized to our area, others have persisted within groups that have expanded or diminished over the years.

Regulation of growth factor receptor degradation by ADP-ribosylation factor domain protein (ARD) 1.

ADP-ribosylation factor domain protein 1 (ARD1) is a 64-kDa protein containing a functional ADP-ribosylation factor (GTP hydrolase, GTPase), GTPase-activating protein, and E3 ubiquitin ligase domains. ARD1 activation by the guanine nucleotide-exchange factor cytohesin-1 was known. GTPase and E3 ligase activities of ARD1 suggest roles in protein transport and turnover. To explore this hypothesis, we used mouse embryo fibroblasts (MEFs) from ARD1-/- mice stably transfected with plasmids for inducible expression of wild-type ARD1 protein (KO-WT), or ARD1 protein with inactivating mutations in E3 ligase domain (KO-E3), or containing persistently active GTP-bound (KO-GTP), or inactive GDP-bound (KO-GDP) GTPase domains. Inhibition of proteasomal proteases in mifepristone-induced KO-WT, KO-GDP, or KO-GTP MEFs resulted in accumulation of these ARD1 proteins, whereas KO-E3 accumulated without inhibitors. All data were consistent with the conclusion that ARD1 regulates its own steady-state levels in cells by autoubiquitination. Based on reported growth factor receptor-cytohesin interactions, EGF receptor (EGFR) was investigated in induced MEFs. Amounts of cell-surface and total EGFR were higher in KO-GDP and lower in KO-GTP than in KO-WT MEFs, with levels in both mutants greater (p = 0.001) after proteasomal inhibition. Significant differences among MEF lines in content of TGF-ß receptor III were similar to those in EGFR, albeit not as large. Differences in amounts of insulin receptor mirrored those in EGFR, but did not reach statistical significance. Overall, the capacity of ARD1 GTPase to cycle between active and inactive forms and its autoubiquitination both appear to be necessary for the appropriate turnover of EGFR and perhaps additional growth factor receptors.

Characteristics of TPT initiation and completion among people living with HIV.

BACKGROUND: TB preventive treatment (TPT) reduces morbidity and mortality among people living with HIV (PLHIV). Despite the successful scale-up of TPT in Malawi, monitoring and evaluation have been suboptimal. We utilized the Malawi Population-Based HIV Impact Assessment (MPHIA) 2020-2021 survey data to estimate TPT uptake and completion among self-reported HIV-positive persons. METHODS: We estimated the proportion of HIV-positive respondents who had ever undergone TPT, and determined the percentage of those currently on TPT who had completed more than 6 months of treatment. Bivariate and multivariable logistic regression were performed to calculate the odds ratios for factors associated with ever-taking TPT. All variables were self-reported, and the analysis was weighted and accounted for in the survey design. RESULTS: Of the HIV+ respondents, 38.8% (95% CI 36.4-41.3) had ever taken TPT. The adjusted odds of ever taking TPT were 8.0 and 5.2 times as high in the Central and Southern regions, respectively, compared to the Northern region; 1.9 times higher among those in the highest wealth quintile, and 2.1 times higher for those on antiretroviral therapy >10 years. Of those currently taking TPT, 56.2% completed >6 months of TPT. CONCLUSION: These results suggest low TPT uptake and >6 months' completion rates among self-reported HIV+ persons. Initiatives to create demand and strengthen adherence would improve TPT uptake.

CONTEXTE: Le traitement préventif de la TB (TPT) réduit la morbidité et la mortalité chez les personnes vivant avec le VIH (PVVIH). Malgré l'extension réussie du TPT au Malawi, le suivi et l'évaluation n'ont pas été optimaux. Nous avons utilisé les données de l'enquête MPHIA (Malawi Population-Based HIV Impact Assessment) 2020­2021 pour estimer l'adoption et l'achèvement du TPT parmi les personnes se déclarant séropositives. MÉTHODES: Nous avons estimé la proportion de répondants séropositifs qui avaient déjà subi un TPT et déterminé le pourcentage de ceux qui sont actuellement sous TPT et qui ont terminé plus de 6 mois de traitement. Une régression logistique bivariée et multivariable a été effectuée pour calculer les rapports de cotes des facteurs associés au fait d'avoir déjà pris un TPT. Toutes les variables étaient autodéclarées et l'analyse a été pondérée et prise en compte dans la conception de l'enquête. RÉSULTATS: Parmi les répondants séropositifs, 38,8% (IC 95% 36,4­41,3) avaient déjà pris du TPT. Les probabilités ajustées de prise de TPT étaient 8,0 et 5,2 fois plus élevées dans les régions du centre et du sud, respectivement, que dans la région du nord ; 1,9 fois plus élevées chez les personnes appartenant au quintile de richesse le plus élevé, et 2,1 fois plus élevées chez les personnes suivant une thérapie antirétrovirale depuis plus de 10 ans. Parmi ceux qui prennent actuellement un TPT, 56,2% ont terminé >6 mois de TPT. CONCLUSION: Ces résultats suggèrent un faible taux d'utilisation du TPT et des taux d'achèvement de >6 mois parmi les personnes déclarées séropositives. Des initiatives visant à créer une demande et à renforcer l'adhésion permettraient d'améliorer l'utilisation du TPT.

Advanced Methods for Analyzing in-Situ Observations of Magnetic Reconnection.

There is ample evidence for magnetic reconnection in the solar system, but it is a nontrivial task to visualize, to determine the proper approaches and frames to study, and in turn to elucidate the physical processes at work in reconnection regions from in-situ measurements of plasma particles and electromagnetic fields. Here an overview is given of a variety of single- and multi-spacecraft data analysis techniques that are key to revealing the context of in-situ observations of magnetic reconnection in space and for detecting and analyzing the diffusion regions where ions and/or electrons are demagnetized. We focus on recent advances in the era of the Magnetospheric Multiscale mission, which has made electron-scale, multi-point measurements of magnetic reconnection in and around Earth's magnetosphere.

Erbium-doped multi-element fiber amplifiers for space-division multiplexing operations.

Erbium-doped multi-element fiber (MEF) amplifiers have been fabricated to simultaneously amplify multiple transmission channels. MEF devices comprise of multiple single-core fibers (elements) combined in a common coating, with each element working as a single fiber in isolation. MEFs containing 3-elements and 7-elements have been fabricated and characterized. Each element of the fabricated MEFs provides nearly 32 dB of gain with a noise figure of <5 dB for an input signal level of -23 dBm at 1530 nm. Different permutations of element pairs within the MEFs were checked for crosstalk and none was detected, confirming the simultaneous multi-channel amplification capabilities of MEFs.

Towards new business models for R&D for novel antibiotics.

In the face of a growing global burden of resistance to existing antibiotics, a combination of scientific and economic challenges has posed significant barriers to the development of novel antibacterials over the past few decades. Yet the bottlenecks at each stage of the pharmaceutical value chain-from discovery to post-marketing-present opportunities to reengineer an innovation pipeline that has fallen short. The upstream hurdles to lead identification and optimization may be eased with greater multi-sectoral collaboration, a growing array of alternatives to high-throughput screening, and the application of open source approaches. Product development partnerships and South-South innovation platforms have shown promise in bolstering the R&D efforts to tackle neglected diseases. Strategies that delink product sales from the firms' return on investment can help ensure that the twin goals of innovation and access are met. To effect these changes, both public and private sector stakeholders must show greater commitment to an R&D agenda that will address this problem, not only for industrialized countries but also globally.

Consideration-of-concept of EvolvRehab-Body for upper limb virtual rehabilitation at home for people late after stroke.

OBJECTIVE: EvolvRehab-Body is a non-immersive virtual rehabilitation system that could provide high-dose, exercise-based upper limb therapy after stroke. This consideration-of-concept study investigated: adherence rate to prescribed repetitions; viability of repeated measures in preparation for a dose-articulation study; and preliminary signal of potential benefit. METHODS: Pre-post and repeated measures with people at least six months after stroke. Twelve-week intervention: exercise-based therapy via EvolvRehab-Body. Pre-post-intervention measures: Wolf Motor Function Test (WMFT); hand grip force. Repeated-during-intervention measures: Motricity Index (MI) and Action Research Arm Test (ARAT). ANALYSIS: adherence rate (%) to set repetitions; percentage of total possible measures collected; pre-to-post-intervention change estimated in relation to published minimally detectable changes of WMFT and hand grip force; and slope of plotted data for MI and ARAT (linear regression). RESULTS: Eight of twelve participants completed the 12-week intervention phase. Adherence: 88% (1710-9377 repetitions performed). Viability repeated measures: 88 of 96 (92%) ARAT and MI scores collected. Preliminary signal of potential benefit was observed in five participants but not always for the same measures. Three participants improved WMFT-time (-7.9 to -27.2 s/item), four improved WMFT-function (0.2-1.1 points/item), and nobody changed grip force. Slope of plotted data over the 12-week intervention ranged from: - 1.42 (p = 0.26) to 1.36 (p = 0.24) points-per-week for MI and - 0.30 (p = 0.40) to 1.71 (p < 0.001) points-per-week for ARAT. CONCLUSION: Findings of good adherence rate in home settings and preliminary signal of benefit for some participants gives support to proceed to a dose-articulation study. These findings cannot inform clinical practice. CONTRIBUTION OF THE PAPER.

Clinical outcomes of adult patients with primary intracranial germinomas treated with low-dose craniospinal radiotherapy and local boost.

The authors document the long term follow up of adult patients with histologically proven primary intracranial germinoma treated with radiotherapy alone using a craniospinal with local boost technique. A retrospective review was conducted on adults diagnosed with intracranial germinoma who received radiotherapy at the Princess Margaret Hospital, Toronto from 1990 to 2007. The study group consisted of 10 males with a median age of 24.1 years. All patients received radiotherapy alone using craniospinal radiotherapy and local boost. There were 10 patients (all male) with a median follow up of 10.9 years (range 2.2-18.9 years). At date of last follow up all patients were still alive, none with relapsed disease. Seven of ten patients (70%) had panhypopituitarianism prior to commencing radiotherapy and hormonal function was not affected in those with an intact pituitary axis. There was no reported cognitive decline in the treated cohort. For adult intracranial germinomas, with long term follow up, low-dose craniospinal radiotherapy with in field boost is highly effective with minimal morbidity.

Validation of the inverted adsorption structure for free-base tetraphenyl porphyrin on Cu(111).

Utilising normal incidence X-ray standing waves we rigourously scrutinise the "inverted model" as the adsorption structure of free-base tetraphenyl porphyrin on Cu(111). We demonstrate that the iminic N atoms are anchored at near-bridge adsorption sites on the surface displaced laterally by 1.1 ± 0.2 Å in excellent agreement with previously published calculations.

Corticosteroid responsiveness and clinical characteristics in childhood difficult asthma.

This study describes the clinical characteristics and corticosteroid responsiveness of children with difficult asthma (DA). We hypothesised that complete corticosteroid responsiveness (defined as improved symptoms, normal spirometry, normal exhaled nitric oxide fraction (F(eNO)) and no bronchodilator responsiveness (BDR <12%)) is uncommon in paediatric DA. We report on 102 children, mean+/-sd age 11.6+/-2.8 yrs, with DA in a cross-sectional study. 89 children underwent spirometry, BDR and F(eNO) before and after 2 weeks of systemic corticosteroids (corticosteroid response study). Bronchoscopy was performed after the corticosteroid trial. Of the 102 patients in the cross-sectional study, 88 (86%) were atopic, 60 (59%) were male and 52 (51%) had additional or alternative diagnoses. Out of the 81 patients in the corticosteroid response study, nine (11%) were complete responders. Of the 75 patients with symptom data available, 37 (49%) responded symptomatically, which was less likely if there were smokers in the home (OR 0.31, 95% CI 0.02-0.82). Of the 75 patients with available spirometry data, 35 (46%) had normal spirometry, with associations being BAL eosinophilia (OR 5.43, 95% CI 1.13-26.07) and high baseline forced expiratory volume in 1 s (FEV(1)) (OR 1.08, 95% CI 1.02-1.12). Of these 75 patients, BDR data were available in 64, of whom 36 (56%) had <12% BDR. F(eNO) data was available in 70 patients, of whom 53 (75%) had normal F(eNO). Airflow limitation data was available in 75 patients, of whom 17 (26%) had persistent airflow limitation, which was associated with low baseline FEV(1) (OR 0.93, 95% CI 0.90-0.97). Only 11% of DA children exhibited complete corticosteroid responsiveness. The rarity of complete corticosteroid responsiveness suggests alternative therapies are needed for children with DA.