Comparative transcriptomic and phenotypic analysis of induced pluripotent stem cell hepatocyte-like cells and primary human hepatocytes

Primary human hepatocytes (PHHs) are used extensively for in vitro liver cultures to study hepatic functions. However, limited availability and invasive retrieval prevent their widespread use. Induced pluripotent stem cells exhibit significant potential since they can be obtained non-invasively and differentiated into hepatic lineages, such as hepatocyte-like cells (iHLCs). However, there are concerns about their fetal phenotypic characteristics and their hepatic functions compared to PHHs in culture. Therefore, we performed an RNA-sequencing (RNA-seq) analysis to understand pathways that are either up- or downregulated in each cell type. Analysis of the RNA-seq data showed an upregulation in the bile secretion pathway where genes such as AQP9 and UGT1A1 were higher expressed in PHHs compared to iHLCs by 455- and 15-fold, respectively. Upon immunostaining, bile canaliculi were shown to be present in PHHs. The TCA cycle in PHHs was upregulated compared to iHLCs. Cellular analysis showed a 2-2.5-fold increase in normalized urea production in PHHs compared to iHLCs. In addition, drug metabolism pathways, including cytochrome P450 (CYP450) and UDP-glucuronosyltransferase enzymes, were upregulated in PHHs compared to iHLCs. Of note, CYP2E1 gene expression was significantly higher (21,810-fold) in PHHs. Acetaminophen and ethanol were administered to PHH and iHLC cultures to investigate differences in biotransformation. CYP450 activity of baseline and toxicant-treated samples was significantly higher in PHHs compared to iHLCs. Our analysis revealed that iHLCs have substantial differences from PHHs in critical hepatic functions. These results have highlighted the differences in gene expression and hepatic functions between PHHs and iHLCs to motivate future investigation.

Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2

BACKGROUND

Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction.

RESULTS

We design a network propagation framework with 2 novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents.

CONCLUSIONS

We examine how our provenance-tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly emerging viruses.

AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata

BACKGROUND

Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance.

RESULTS

Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis.

CONCLUSION

AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .

Curved flight paths and sideways vision in peregrine falcons (Falco peregrinus)

When diving at prey straight ahead from great distances at high speeds, a peregrine has a conflict between vision and aerodynamics: it must turn its head approximately 40 degrees to one side to see the prey with maximum visual acuity at the deep fovea of one eye, but the head in this position increases aerodynamic drag and slows the falcon down. The falcon could resolve this conflict by holding its head straight and flying along a logarithmic spiral path that keeps the line of sight of the deep fovea pointed sideways at the prey. Wild peregrines, observed with binoculars, telescopes and a tracking device, did approach prey the size of American robins (Turdus migratorius) and smaller birds from distances of up to 1500 m by holding their heads straight and flying along curved paths that resembled the logarithmic spiral.

Sensitive assays for urinary retinol-binding protein and beta-2-glycoprotein-1 based on commercially available standards

Measurements of urinary retinol-binding protein (RBP) and beta-2-glycoprotein-1 (beta 2G1) provide sensitive indicators of proximal renal tubular malfunction. beta 2G1 is very stable in urine but RBP, which is much less stable, has been more extensively studied. We have designed two similar immunoassays allowing measurement of both proteins from one urine dilution. The assays both use widely available commercial standards and permit accurate measurement throughout most of the reference range. We measured both proteins in the urine of 70 healthy adults and 80 healthy children aged between three and 16 years, expressing the results as a ratio to creatinine concentration. Using the 98th centile as the upper reference limit, adults excreted up to 17 micrograms/mmol RBP (median 8) and up to 30 micrograms/mmol beta 2G1 (median 15) with no difference between the sexes. Children had different ranges to adults with excretion of up to 22 micrograms/mmol RBP (median 10) and up to 80 micrograms/mmol beta 2G1 (median 24).

Activation of gelatinase A (72-kDa type IV collagenase) induced by monensin in normal human fibroblasts

In monolayer culture, fibroblasts secrete all matrix metalloproteinases, including gelatinase A (72-kDa type IV collagenase), as inactive zymogens. Whereas limited proteolysis by plasmin or other matrix metalloproteinases (MMPs) can accomplish the extracellular activation of other proenzymes in this family, gelatinase A proenzyme is uniquely refractory to cleavage by such proteinases. Previously it has been shown that fibroblasts cultured in the presumably more physiologic culture milieu of a type I collagen lattice can be induced to secrete active gelatinase A. In monolayer culture, however, the plant lectin concanavalin A will induce gelatinase A activation. Here we show that in monolayer culture activation of gelatinase A by normal fibroblasts is also induced by the sodium ionophore monensin. The monensin response is dose-dependent, time-dependent, requires protein synthesis, and is specific to gelatinase A among the secreted matrix metalloproteinases. The activator appears to be associated with cell membranes and may be membrane-type matrix metalloproteinase 1(MT-MMP1). Both mRNA and immunodetectable protein of MT-MMP1 are increased with monensin treatment while message for the protein inhibitor of gelatinase A, TIMP-2, is unchanged. The monensin-induced signal transduction pathway leading to gelatinase activation in monolayer culture appears to be different from the integrin-mediated pathway operative in the collagen lattice system. The tyrosine kinase inhibitor genistein blocks monensin activation of gelatinase A in monolayer culture. In contrast, genistein has no effect on proenzyme activation in the collagen lattice. Likewise, the cyclooxygenase inhibitor indomethacin abrogates the monensin effect in monolayer culture and can be reversed by addition of exogenous prostaglandin E2 (PGE2). Neither indomethacin nor PGE2 affects activation of gelatinase A in the collagen lattice.

Comparison of cleavage site specificity of gelatinases A and B using collagenous peptides

The gelatinases (type IV collagenases) are members of the matrix metalloproteinase family that not only have a high degree of structural homology but are known to be nearly identical in their digestion profile against macromolecular substrates. We have shown previously that the preferred cleavage sites in the hydrolysis of type I gelatin, catalyzed by gelatinase A (72 kDa type IV collagenase), are bracketed by hydroxyproline in the P5 and P5' positions. In this report, a kinetic investigation using a series of collagenous dodecylpeptides in which the P5 and P5' hydroxyprolines were systematically varied and used as substrates for recombinant human gelatinase A, we show that replacement with either proline or alanine always resulted in increased Km. In contrast, substitution of the hydroxylated amino acids tyrosine and serine at P5 and P5' reduced the Km significantly, indicating that the hydroxyl moiety of the hydroxyproline is the functional group responsible for favorable enzyme-substrate affinity. This was shown by the kcat/Km ratio, which was doubled by the substitution of serine in that site. Cleavage of the same series of dodecylpeptides by recombinant human gelatinase B (92 kDa type IV collagenase) showed a very different kinetic profile for which no patterns were discernible. In subsequent comparisons of the two enzymes, it was found that gelatinase B cleaved the thiopeptolide substrate AcProLeuGly-S-LeuGly-OC2H5 at double the velocity of gelatinase A. In contrast, gelatinase A digested type I gelatin about 2.5-times faster than gelatinase B. SDS-PAGE analysis of gelatin cleavage products showed different patterns of product peptides for each enzyme. Further comparisons of the proteinases using synthetic peptide substrates with variations in size and in substituents at the P2' site again showed marked kinetic differences. Although these two matrix metalloproteinases seem similar in that they are both gelatinolytic and can degrade a nearly identical battery of macromolecular matrix components including type IV collagen, it is clear from these results that they are very different enzymatically. Since the regulatory portions of gelatinases A and B differ markedly, it has been assumed that the enzymes serve the same function, but respond to different stimuli. The differences in substrate specificity described herein suggest that their proposed physiological roles may require reevaluation.

Order-Disorder Transition in Polycrystalline C 60 Films

High-resolution Raman spectroscopy of polycrystalline films of C(60) deposited under ultrahigh-vacuum conditions show that the spectrum below 244 +/- 3 kelvin consists of a superposition of two components whose relative contributions are temperature-dependent. The spectrum of the more intense of the two components is similar to that obtained for air- or oxygen-exposed samples of C(60) at room temperature, whereas the spectrum above 244 +/- 3 kelvin corresponds to one previously reported for oxygen-free samples of C(60). The results may indicate an order-disorder phase transition involving the percolation of a cluster of C(60) molecules engaged in coherent Raman scattering.

Effect of BiTek agar on lysostaphin susceptibility of staphylococci

Staphylococci which were considered to be lysostaphin susceptible on P agar containing Bacto-Agar showed different degrees of resistance to lysostaphin when tested on P agar made with BiTek agar. As a result, lysostaphin-susceptible strains were misidentified as lysostaphin-resistant strains.

Comparison of methods for determining DNase and phosphatase activities of staphylococci

A greater percentage of DNase-positive strains was detected with DNase test agar than with DNase test agar containing 0.005% methyl green or 0.005% toluidine blue (P less than 0.01). No significant differences were obtained in the percentage of phosphatase-positive strains with the four methods compared. On the basis of ease of use, P agar containing para-nitrophenylphosphate disodium (0.495 mg/ml) would be the preferred method for determining phosphatase activity of staphylococci.

Use of Lysostaphin and Bacitracin Susceptibility for Routine Presumptive Identification of Staphylococci of Bovine Origin 1

A simple agar plate system based on susceptibility to lysostaphin and bacitracin to differentiate between staphylococci and micrococci is described. The system also uses susceptibility to novobiocin to aid in identification to species level of staphylococci. Growth from the agar plate can be used to prepare inocula for inoculation of rapid identification systems.

Identification of Staphylococcus species of bovine origin with the DMS Staph-Trac system

The DMS Staph-Trac system was evaluated as a means for identifying the species of bovine strains of staphylococci routinely isolated from quarter-milk samples. The species identity of 83 of 91 (91.2%) isolates of staphylococci was correctly determined by this method. One isolate could not be identified by this system. The Staph-Trac system was able to distinguish between Staphylococcus hyicus and Staphylococcus epidermidis. We obtained a higher percentage of correct identifications with the DMS Staph-Trac system (91.2%) than we did in a previous study with the API Staph-Ident system (45.1%), using the same isolates (Langlois et al., J. Clin. Microbiol. 18:1212-1219, 1983).

Identification of Staphylococcus species of bovine origin with the API Staph-Ident system

The API Staph-Ident system was evaluated as a means for identifying the species of bovine strains of staphylococci routinely isolated from quarter-milk samples. The species identity of 314 of 581 (54%) isolates of staphylococci was correctly determined by this method. The API Staph-Ident system was more accurate in correctly identifying Staphylococcus aureus (93.9%) than in correctly identifying non-S. aureus species (41.8%). False identifications of Staphylococcus epidermidis and Staphylococcus hominis were the main reasons for the incorrect identifications of the non-S. aureus species.