An Endogenous Inhibitor of Ca++-ATPase from Human Placenta

Intracellular free calcium is regulated by Ca⁺⁺-ATPase, one form present on the plasma membrane (PM Ca⁺⁺-ATPase) and the other on sarcoplasmic (endoplasmic) reticulum (SR/ER Ca⁺⁺-ATPase). An endogenous inhibitor of SR Ca⁺⁺-ATPase from human placenta was shown to be present in normal placenta and the activity was not detectable in placenta from preeclamptic patients. The inhibitor was distributed in cytosol and microsomes. The inhibition of Ca⁺⁺-ATPase by this inhibitor was concentration-and time-dependent. The inhibitor neither bound to DEAE-nor CM-sepharose resins at pH 7.5 and 8.5. Furthermore, it was heat stable for 15min up to 55°C and completely destroyed at 80°C in a few minutes. It was also observed to be stable at room temperature for at least 3 months. The purification and characterization of this inhibitor would be valuable in achieving an understanding of the normal regulation of Ca⁺⁺-ATPase in the placenta during pregnancy.     

Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics

Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community.The majority of proteins function as part of multiprotein complexes and not as isolated polypeptides. These protein complexes range from simple homodimers to large structures composed of many different polypeptides. Protein complexes vary in their size and shape from small globular dimers, such as 14-3-3 proteins, to large elongated filaments of variable length, such as microtubules. The wide variety of possible protein–protein interactions within multiprotein complexes contributes to the diversity of functions that are involved in cellular processes and regulatory mechanisms.Another important source of functional diversity and regulation is the large number of protein isoforms that may be generated from each gene. Functionally and structurally distinct isoforms can arise via multiple mechanisms, including alternative splicing, post-translational modification (PTM),¹ and proteolytic cleavage. Distinct isoforms can exhibit radically different properties. For example, including or excluding individual exons can either create or remove protein–protein interaction interfaces for binding specific interaction partners. Similarly, phosphorylation, and other PTMs, can either create or remove binding sites for interacting proteins, substrates, or ligands. PTMs can also promote structural changes in proteins and affect catalytic activity.The association of protein isoforms and post-translationally modified factors in multiprotein complexes can influence their subcellular location, activity, and substrate specificity. This can be dynamically regulated to modulate protein complex composition, and hence localization and function, to allow cells to respond to spatial and temporal stimuli. It is therefore important to characterize protein complexes at the level of the protein isoforms and post-translationally modified forms they contain in order to fully decipher the network of signaling and regulatory pathways within cells.Although many types of protein complexes have been studied in detail, in-depth analysis of the composition, dynamics, and isoform association of protein complexes formed in either human cells or model organisms is still not well documented at a system-wide level. The CORUM database, compiled using a variety of information from the literature describing protein interactions and assemblies, currently provides the largest public dataset of protein complexes (1). CORUM contains information relating to ∼1,970 protein complexes identified in human cells. However, these complexes are formed from proteins encoded by only ∼16% of the known human protein-coding genes, indicating that many forms of protein complexes still remain to be identified and characterized (1). Furthermore, the CORUM database does not describe how the protein compositions of the complexes may vary, either dynamically or in different subcellular locations, or how this relates to protein isoforms and PTMs. This illustrates that there is still a major deficit in our knowledge of the structure and functions of cellular protein complexes and how they contribute to biological regulatory mechanisms.The technique that is now most widely used to identify the components of protein complexes is affinity purification of an individual “bait” protein and subsequent analysis of the co-isolated proteins, usually via mass spectrometry (2). Affinity purification can use antibodies specific for an endogenous target protein (3, 4), if available, or, alternatively, can utilize a genetically constructed, epitope-tagged bait protein. The latter procedure is now widely used and is advantageous in that many different complexes can be compared using an identical antibody, or other affinity-purification method, targeted to the tag on the bait (for examples, see Refs. 5–7; for reviews, see Refs. 8 and 9). In contrast, it is harder to directly compare the results from immunoprecipitation of different endogenous protein complexes because each specific antibody that is used has different affinities and properties. Nonetheless, although epitope-tag “pull-down” techniques are now commonly used, they also have limitations. Not least, the addition of epitope tags to the bait can affect protein function and interactions (10, 11).To help determine whether co-purifying proteins detected using pull-down strategies represent specific partner proteins in bona fide complexes or are nonspecific contaminants, we and others have developed quantitative approaches, for example, based on variations of the stable isotope labeling of amino acids in cell culture (12–16). Additional data analysis procedures, including the use of a “super experiment” database that predicts the likelihood of nonspecific protein interactions based on the frequency with which any given protein is co-purified across many separate experiments, can also help to define the composition of protein complexes (17). Nonetheless, affinity purification strategies have a limited ability to distinguish multiple related complexes that may differ with respect to isoforms and PTMs. They are also costly and difficult to implement for large-scale studies to survey cellular complexes, and thus not well suited to study variations in complexes under different cellular growth conditions and responses.For system-wide studies of the composition and dynamics of protein complexes, alternative methods, in addition to immune-affinity purification, are required for convenient separation, characterization, and comparison of cellular protein complexes. To address this, a number of studies have utilized various forms of either column chromatography or native gel electrophoresis in combination with mass-spectrometry-based proteomics. For example, protein complexes have been separated using techniques including blue native polyacrylamide gel electrophoresis (18, 19), ion-exchange chromatography (20), and size-exclusion chromatography (21, 22) prior to MS analysis of proteins in the fractionated complexes. Size-exclusion chromatography (SEC) is a well-established technique used to separate proteins and protein complexes in solution on the basis of their shape/size (rotational cross-section) (23). SEC has been extensively used as an intermediate step in conventional multistep biochemical protein purification strategies. In contrast, SEC has been less commonly combined with mass-spectrometry-based proteomics for the high-throughput characterization of protein complexes. However, this has been demonstrated in previous studies that analyzed native protein complexes in plant chloroplasts (22) or large cytosolic complexes in mammalian cells (21).In this study, we combined native SEC with high-throughput mass-spectrometry-based proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma cells. Herein we demonstrate the utility and reproducibility of this approach for the system-wide characterization of endogenous, untagged protein complexes and show how it can be used to identify specific protein isoforms and PTMs associated with distinct protein complexes. The resulting data are available to the community in a convenient format in the Encyclopedia of Proteome Dynamics (EPD) (www.peptracker.com/encyclopediaInformation/), a user-friendly, searchable online database.     

A Next-Generation Cleaved,Soluble HIV-1 Env Trimer,BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies

A desirable but as yet unachieved property of a human immunodeficiency virus type 1 (HIV-1) vaccine candidate is the ability to induce broadly neutralizing antibodies (bNAbs). One approach to the problem is to create trimeric mimics of the native envelope glycoprotein (Env) spike that expose as many bNAb epitopes as possible, while occluding those for non-neutralizing antibodies (non-NAbs). Here, we describe the design and properties of soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A transmitted/founder strain, BG505. These trimers are highly stable, more so even than the corresponding gp120 monomer, as judged by differential scanning calorimetry. They are also homogenous and closely resemble native virus spikes when visualized by negative stain electron microscopy (EM). We used several techniques, including ELISA and surface plasmon resonance (SPR), to determine the relationship between the ability of monoclonal antibodies (MAbs) to bind the soluble trimers and neutralize the corresponding virus. In general, the concordance was excellent, in that virtually all bNAbs against multiple neutralizing epitopes on HIV-1 Env were highly reactive with the BG505 SOSIP.664 gp140 trimers, including quaternary epitopes (CH01, PG9, PG16 and PGT145). Conversely, non-NAbs to the CD4-binding site, CD4-induced epitopes or gp41_ECTO did not react with the trimers, even when their epitopes were present on simpler forms of Env (e.g. gp120 monomers or dissociated gp41 subunits). Three non-neutralizing MAbs to V3 epitopes did, however, react strongly with the trimers but only by ELISA, and not at all by SPR and to only a limited extent by EM. These new soluble trimers are useful for structural studies and are being assessed for their performance as immunogens.     

Ethnic Variation in Inflammatory Profile in Tuberculosis

Distinct phylogenetic lineages of Mycobacterium tuberculosis (MTB) cause disease in patients of particular genetic ancestry, and elicit different patterns of cytokine and chemokine secretion when cultured with human macrophages in vitro. Circulating and antigen-stimulated concentrations of these inflammatory mediators might therefore be expected to vary significantly between tuberculosis patients of different ethnic origin. Studies to characterise such variation, and to determine whether it relates to host or bacillary factors, have not been conducted. We therefore compared circulating and antigen-stimulated concentrations of 43 inflammatory mediators and 14 haematological parameters (inflammatory profile) in 45 pulmonary tuberculosis patients of African ancestry vs. 83 patients of Eurasian ancestry in London, UK, and investigated the influence of bacillary and host genotype on these profiles. Despite having similar demographic and clinical characteristics, patients of differing ancestry exhibited distinct inflammatory profiles at presentation: those of African ancestry had lower neutrophil counts, lower serum concentrations of CCL2, CCL11 and vitamin D binding protein (DBP) but higher serum CCL5 concentrations and higher antigen-stimulated IL-1 receptor antagonist and IL-12 secretion. These differences associated with ethnic variation in host DBP genotype, but not with ethnic variation in MTB strain. Ethnic differences in inflammatory profile became more marked following initiation of antimicrobial therapy, and immunological correlates of speed of elimination of MTB from the sputum differed between patients of African vs. Eurasian ancestry. Our study demonstrates a hitherto unappreciated degree of ethnic heterogeneity in inflammatory profile in tuberculosis patients that associates primarily with ethnic variation in host, rather than bacillary, genotype. Candidate immunodiagnostics and immunological biomarkers of response to antimicrobial therapy should be derived and validated in tuberculosis patients of different ethnic origin.     

The Effect of Riboflavin/UVA Collagen Cross-linking Therapy on the Structure and Hydrodynamic Behaviour of the Ungulate and Rabbit Corneal Stroma

Purpose

To examine the effect of riboflavin/UVA corneal crosslinking on stromal ultrastructure and hydrodynamic behaviour.

Methods

One hundred and seventeen enucleated ungulate eyes (112 pig and 5 sheep) and 3 pairs of rabbit eyes, with corneal epithelium removed, were divided into four treatment groups: Group 1 (28 pig, 2 sheep and 3 rabbits) were untreated; Group 2 (24 pig) were exposed to UVA light (3.04 mW/cm²) for 30 minutes and Group 3 (29 pig) and Group 4 (31 pig, 3 sheep and 3 rabbits) had riboflavin eye drops applied to the corneal surface every 5 minutes for 35 minutes. Five minutes after the initial riboflavin instillation, the corneas in Group 4 experienced a 30 minute exposure to UVA light (3.04 mW/cm²). X-ray scattering was used to obtain measurements of collagen interfibrillar spacing, spatial order, fibril diameter, D-periodicity and intermolecular spacing throughout the whole tissue thickness and as a function of tissue depth in the treated and untreated corneas. The effect of each treatment on the hydrodynamic behaviour of the cornea (its ability to swell in saline solution) and its resistance to enzymatic digestion were assessed using in vitro laboratory techniques.

Results

Corneal thickness decreased significantly following riboflavin application (p<0.01) and also to a lesser extent after UVA exposure (p<0.05). With the exception of the spatial order factor, which was higher in Group 4 than Group 1 (p<0.01), all other measured collagen parameters were unaltered by cross-linking, even within the most anterior 300 microns of the cornea. The cross-linking treatment had no effect on the hydrodynamic behaviour of the cornea but did cause a significant increase in its resistance to enzymatic digestion.

Conclusions

It seems likely that cross-links formed during riboflavin/UVA therapy occur predominantly at the collagen fibril surface and in the protein network surrounding the collagen.     

Development of VHH Antibodies against Dengue Virus Type 2 NS1 and Comparison with Monoclonal Antibodies for Use in Immunological Diagnosis

The possibility of using variable domain heavy-chain antibodies (VHH antibodies) as diagnostic tools for dengue virus (DENV) type 2 NS1 protein was investigated and compared with the use of conventional monoclonal antibodies. After successful expression of DENV type 2 NS1 protein, the genes of VHH antibodies against NS1 protein were biopanned from a non-immune llama library by phage display. VHH antibodies were then expressed and purified from Escherichia coli. Simultaneously, monoclonal antibodies were obtained by the conventional route. Sequence analysis of the VHH antibodies revealed novel and long complementarity determining regions 3 (CDR3). Epitope mapping was performed via a phage display peptide library using purified VHH and monoclonal antibodies as targets. Interestingly, the same region of NS1, which comprises amino acids ²²⁴HWPKPHTLW²³², was conserved for both kinds of antibodies displaying the consensus motif histidine-tryptophan-tryptophan or tryptophan-proline-tryptophan. The two types of antibodies were used to prepare rapid diagnostic kits based on immunochromatographic assay. The VHH antibody immobilized rapid diagnostic kit showed better sensitivity and specificity than the monoclonal antibody immobilized rapid diagnostic kit, which might be due to the long CDR3 regions of the VHH antibodies and their ability to bind to the pocket and cleft of the targeted antigen. This demonstrates that VHH antibodies are likely to be an option for developing point-of-care tests against DENV infection.     

Rabies healthcare-seeking behaviors of urban and peri-urban residents: Results from a rabies knowledge,attitudes, and practices survey,Bangladesh, 2018

Rabies is one of the most lethal infectious diseases, with those living in Asia and Africa having the highest risk of dying from rabies. We conducted a knowledge, attitudes and practices survey in urban and peri-urban areas of Bangladesh to describe canine bite rates, rabies knowledge, and healthcare seeking behaviors and barriers to human and dog vaccination. A bite risk assessment score (BRAS) and healthcare-seeking behavior score (HSBS) was calculated for each bite victim. Respondents were given two hypothetical situations to assess potential behaviors after a bite and willingness to pay for rabies vaccine and immunoglobulin. In total, 2,447 households participated in the survey and 85 bite victims were identified. The BRAS identified that 31% of bites posed no risk of rabies transmission. Multivariate analyses showed that living in Chittagong (β = 1.4; 95% CI: 0.1, 2.7) was associated with a higher HSBS. Findings presented here provide useful information regarding bite occurrences, healthcare-seeking behaviors, and a need for strategies to increase rabies awareness.     

Microbial-enhanced Selenium and Iron Biofortification of Wheat (Triticum aestivum L.) - Applications in Phytoremediation and Biofortification

Selenium (Se) is an essential trace element for humans and other mammals. Most dietary Se is derived from crops. To develop a Se biofortification strategy for wheat, the effect of selenate fertilization and bacterial inoculation on Se uptake and plant growth was investigated. YAM2, a bacterium with 99% similarity to Bacillus pichinotyi, showed many plant growth promoting characteristics. Inoculation with YAM2 enhanced wheat growth, both in the presence and absence of selenate: YAM2-inoculated plants showed significantly higher dry weight, shoot length and spike length compared to un-inoculated plants. Selenate also stimulated wheat growth; Un-inoculated Se-treated plants showed a significantly higher dry weight and shoot length compared to control plants without Se. Bacterial inoculation significantly enhanced Se concentration in wheat kernels (167%) and stems (252%), as well as iron (Fe) levels in kernels (70%) and stems (147%), compared to un-inoculated plants. Inoculated Se-treated plants showed a significant increase in acid phosphatase activity, which may have contributed to the enhanced growth. In conclusion; Inoculation with Bacillus sp. YAM2 is a promising Se biofortification strategy for wheat and potentially other crops.