Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

Novel proteomics platforms, such as the aptamer‐based SOMAscan platform, can quantify large numbers of proteins efficiently and cost‐effectively and are rapidly growing in popularity. However, comparisons to conventional immunoassays remain underexplored, leaving investigators unsure when cross‐assay comparisons are appropriate. The correlation of results from immunoassays with relative protein quantification is explored by SOMAscan. For 63 proteins assessed in two chronic obstructive pulmonary disease (COPD) cohorts, subpopulations and intermediate outcome measures in COPD Study (SPIROMICS), and COPDGene, using myriad rules based medicine multiplex immunoassays and SOMAscan, Spearman correlation coefficients range from ?0.13 to 0.97, with a median correlation coefficient of ≈0.5 and consistent results across cohorts. A similar range is observed for immunoassays in the population‐based Multi‐Ethnic Study of Atherosclerosis and for other assays in COPDGene and SPIROMICS. Comparisons of relative quantification from the antibody‐based Olink platform and SOMAscan in a small cohort of myocardial infarction patients also show a wide correlation range. Finally, cis pQTL data, mass spectrometry aptamer confirmation, and other publicly available data are integrated to assess relationships with observed correlations. Correlation between proteomics assays shows a wide range and should be carefully considered when comparing and meta‐analyzing proteomics data across assays and studies.     

CERCIDIUM FLORIDUM SEED COAT,LIGHT AND ELECTRON MICROSCOPIC STUDY

Scott , Flora Murray , B. G. Bystrom , and E. Bowler . (U. California, Los Angeles.) Cercidium floridum seed coat, light and electron microscopic study. Amer. Jour. Bot. 49(8): 821–833. Illus. 1962.—The structure of the seed coat of the desert tree Cercidium is typical of the family Leguminosae, but the inner integument is mucilaginous. The characteristic palisade cells of the epidermis and the many-armed cells of the mucilaginous zone are discussed in detail. The minute wax rodlets on the surface of the young seed fuse later into a film of wax. The epidermal palisade cells are polygonal in transection and the walls are strengthened by cellulose flanges. The palisade cells are enclosed in a thin suberin-like sheath which connects with the film which lines all air-filled intercellular spaces in the outer integument. Plasmodesmata extend from the protoplast through the subcuticular zone to the cuticle and also interconnect with adjacent cells through numerous pits in the interflange areas of the main wall. The cells of the inner integument are many-armed. Intercellular spaces at all stages of growth observed are occluded with mucilage; nevertheless, they are lined with a suberin-like film similar in reaction to that of the air-filled intercellular spaces of the outer integument. The distribution of wall materials and ergastic substances was determined by microchemical tests. For electron microscopic study, the epidermis and the mucilaginous zone were fragmented ultrasonically, after chemical treatment when necessary. Cuticular fragments, frequently polygonal in outline, are dense to the electron beam at photographic illumination. When exposed to the electron beam, full-strength, volatile components are driven off and condense on other wall fragments or on substrate. Unique structures occur in the subcuticular zone, termed here, collar, cone and paddle structure. The basic material of the cell wall as a whole is cellulose impregnated with matrix materials, mainly non-cellulosic polysaccharides. In addition, lipid-like substances are conspicuous particularly in the flanges of the palisade cells. Under the electron beam, full-strength, these substances volatilize and leave the flanges with a blistered outline except in the region of the light line. The volatile substances may be absent from this zone or the microfibrillar structure may prevent distortion. The microfibrillar pattern throughout the length of the flanges is dominantly parallel, but a change to reticulate arrangement occurs in the light-line region. Numerous pits mark the paths of the plasmodesmata in the subcuticular zone and also through flange and interflange areas of the wall. The dominant microfibrillar pattern in the mucilage cells is reticulate in young and old cells, except for helical orientation in extending arms. Pits occur on arm ends but are infrequent elsewhere. The loose microfibrillar structure presumably allows continuous secretion of mucilage.     

Residual structure in unfolded proteins

The denatured state ensemble (DSE) of unfolded proteins, once considered to be well-modeled by an energetically featureless random coil, is now well-known to contain flickering elements of residual structure. The position and nature of DSE residual structure may provide clues toward deciphering the protein folding code. This review focuses on recent advances in our understanding of the nature of DSE collapse under folding conditions, the quantification of the stability of residual structure in the DSE, the determination of the location and types of residues involved in thermodynamically significant residual structure and advances in detection of long-range interactions in the DSE.     

An investigation into the effects of inhibitors of fluid production by Locusta Malpighian tubule Type I cells on their secretion and elemental composition

The intracellular elemental concentrations of K, Na, Cl, P, Mg and Ca within Type I cells of the Malpighian tubules of Locusta migratoria have been measured using electron probe X-ray microanalysis. The distribution of Na, K and Cl was not homogeneous within the cells and concentration gradients exist from basal to apical surfaces. The rate of secretion and the cationic composition of the secreted tubule fluid have also been determined. Furosemide (1 mM) inhibited fluid secretion by about 60%, raised the [Na(+)] but did not significantly alter the [K(+)] of the secreted tubule fluid. When Rb(+) replaced K(+) in the saline fluid secretion was also inhibited by about 60%, but no additional inhibition occurred by the simultaneous inclusion of furosemide. Thus, Rb(+) and furosemide probably act at the same transport site, and Rb(+) cannot substitute for K(+) at the basal membrane cotransporter. Bafilomycin (1 μM) dramatically inhibited fluid production by 85%, the [K(+)] of the secreted fluid was reduced by about 30% but the [Na(+)] was almost doubled. Furosemide, in common with other inhibitors of fluid secretion acting at the basal surface (ouabain and Rb(+)), caused a fall in intracellular [K] and a rise in [Na]. Bafilomycin, in common with N-ethyl maleimide, which acts at the apical surface, increased the intracellular [K] but did not affect the [Na].     

Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14

Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome.     

Interspecies recombination, and phylogenetic distortions, within the glutamine synthetase and shikimate dehydrogenase genes of Neisseria meningitidis and commensal Neisseria species

Visual inspection showed clear evidence of a history of intraspecies recombinational exchanges within the neighbouring meningococcal shikimate dehydrogenase ( aroE  ) and glutamine synthetase ( glnA) genes, which was supported by the non-congruence of the trees constructed from the sequences of these genes from different meningococcal strains, and by statistical tests for mosaic structure. Many examples were also found of highly localized interspecies recombinational exchanges between the meningococcal aroE and glnA genes and those of commensal Neisseria species. These exchanges appear to have inflated the sequence variation at these loci, and have resulted in major distortions of the phylogenetic trees constructed from the sequences of the aroE and glnA genes of human pathogenic and commensal Neisseria species. Statistical tests for sequence mosaicism, and for anomalies within the Neisseria species trees, strongly supported the view that frequent interspecies recombination has occurred within aroE and glnA . The high levels of sequence variation, and intra- and interspecies recombination, within aroE and glnA did not appear to be due to a 'hitch-hiking' effect caused by positive selection for variation at a neighbouring gene. Our results suggest that interspecies recombinational exchanges with commensal Neisseria occur frequently in some meningococcal 'housekeeping' genes as they can be observed readily even when there appears to be no obvious selection for the recombinant phenotypes.     

Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c′

Changing the helical propensity of a polypeptide sequence might be expected to affect the conformational properties of the denatured state of a protein. To test this hypothesis, alanines at positions 83 and 87 near the center of helix 3 of cytochrome c′ from Rhodopseudomonas palustris were mutated to serine to decrease the stability of this helix. A set of 13 single histidine variants in the A83S/A87S background were prepared to permit assessment of the conformational properties of the denatured state using histidine-loop formation in 3 M guanidine hydrochloride. The data are compared with previous histidine-heme loop formation data for wild-type cytochrome c′. As expected, destabilization of helix 3 decreases the global stabilities of the histidine variants in the A83S/A87S background relative to the wild-type background. Loop stability versus loop size data yields a scaling exponent of 2.1 ± 0.2, similar to the value of 2.3 ± 0.2 obtained for wild-type cytochrome c′. However, the stabilities of all histidine-heme loops, which contain the helix 3 sequence segment, are increased in the A83S/A87S background compared to the wild-type background. Rate constants for histidine-heme loop breakage are similar for the wild-type and A83S/A87S variants. However, for histidine-heme loops that contain the helix 3 sequence segment, the rate constants for loop formation increase in the A83S/A87S background compared to the wild-type background. Thus, residual helical structure appears to stiffen the polypeptide chain slowing loop formation in the denatured state. The implications of these results for protein folding mechanisms are discussed.     

Interaction of human 3-phosphoglycerate kinase with its two substrates: is substrate antagonism a kinetic advantage?

Substrate antagonism has been described for a variety of enzymes with more than one substrate and is characterized by a lowering of the affinity of one substrate in the presence of the other(s). 3-Phosphoglycerate kinase (PGK) catalyzes phosphotransfer from 1,3-bisphosphoglycerate (bPG) to ADP to give 3-phosphoglycerate (PG) and ATP, and is subject to substrate antagonism. Because of the instability of bPG, antagonism has only been described between PG and ATP or ADP. Here, we show that antagonism also occurs between bPG and ADP. Using the stopped-flow method, we show that the dissociation constant for one substrate increases in the presence of the other, and that this decrease in affinity is mainly due to an increase in the dissociation rate constant. As a consequence, there is an increase in the overall interaction kinetics. Interestingly, in the presence of the mirror image of natural d-ADP, l-ADP (a good substrate for PGK), antagonism is absent. Using rapid-quench-flow, we studied the kinetics of ATP formation. The time courses present the following: (1) a lag with l-ADP, but not with d-ADP, the kinetics of which were similar to the interaction kinetics measured by stopped-flow; (2) a burst that is directed by the phosphotransfer; and (3) a steady-state that is rate limited by the release of product kinetics. Structural explanations for these results are proposed by analyzing the crystallographic structure of the fully closed conformation of PGK in complex with l-ADP, PG, and the transition-state analogue AlF₄⁻ compared to previously determined structures.