Laminin switches terminal differentiation fate of human trophoblast stem cells under chemically defined culture conditions.

Human trophoblast stem cells (hTSCs) have emerged as a powerful tool to model early placental development in vitro. Analogous to the epithelial cytotrophoblast in the placenta, hTSCs can differentiate into cells of the extravillous trophoblast (EVT) lineage or the multinucleate syncytiotrophoblast (STB). Here we present a chemically defined culture system for STB and EVT differentiation of hTSCs. Notably, in contrast to current approaches, we neither utilize forskolin for STB formation nor transforming growth factor-beta (TGFß) inhibitors or a passage step for EVT differentiation. Strikingly, the presence of a single additional extracellular cue-laminin-111-switched the terminal differentiation of hTSCs from STB to the EVT lineage under these conditions. In the absence of laminin-111, STB formation occurred, with cell fusion comparable to that obtained with differentiation mediated by forskolin; however, in the presence of laminin-111, hTSCs differentiated to the EVT lineage. Protein expression of nuclear hypoxia-inducible factors (HIF1α and HIF2α) was upregulated during EVT differentiation mediated by laminin-111 exposure. A heterogeneous mixture of Notch1+ EVTs in colonies and HLA-G+ single-cell EVTs were obtained without a passage step, reminiscent of heterogeneity in vivo. Further analysis showed that inhibition of TGFß signaling affected both STB and EVT differentiation mediated by laminin-111 exposure. TGFß inhibition during EVT differentiation resulted in decreased HLA-G expression and increased Notch1 expression. On the other hand, TGFß inhibition prevented STB formation. The chemically defined culture system for hTSC differentiation established herein facilitates quantitative analysis of heterogeneity that arises during hTSC differentiation and will enable mechanistic studies in vitro.

Two distinct trophectoderm lineage stem cells from human pluripotent stem cells.

The trophectoderm layer of the blastocyst-stage embryo is the precursor for all trophoblast cells in the placenta. Human trophoblast stem (TS) cells have emerged as an attractive tool for studies on early trophoblast development. However, the use of TS cell models is constrained by the limited genetic diversity of existing TS cell lines and restrictions on using human fetal tissue or embryos needed to generate additional lines. Here we report the derivation of two distinct stem cell types of the trophectoderm lineage from human pluripotent stem cells. Analogous to villous cytotrophoblasts in vivo, the first is a CDX2- stem cell comparable with placenta-derived TS cells-they both exhibit identical expression of key markers, are maintained in culture and differentiate under similar conditions, and share high transcriptome similarity. The second is a CDX2+ stem cell with distinct cell culture requirements, and differences in gene expression and differentiation, relative to CDX2- stem cells. Derivation of TS cells from pluripotent stem cells will significantly enable construction of in vitro models for normal and pathological placental development.

Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity.

Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.

Screening of Yeast Display Libraries of Enzymatically Treated Peptides to Discover Macrocyclic Peptide Ligands.

We present the construction and screening of yeast display libraries of post-translationally modified peptides wherein site-selective enzymatic treatment of linear peptides is achieved using bacterial transglutaminase. To this end, we developed two alternative routes, namely (i) yeast display of linear peptides followed by treatment with recombinant transglutaminase in solution; or (ii) intracellular co-expression of linear peptides and transglutaminase to achieve peptide modification in the endoplasmic reticulum prior to yeast surface display. The efficiency of peptide modification was evaluated via orthogonal detection of epitope tags integrated in the yeast-displayed peptides by flow cytometry, and via comparative cleavage of putative cyclic vs. linear peptides by tobacco etch virus (TEV) protease. Subsequently, yeast display libraries of transglutaminase-treated peptides were screened to isolate binders to the N-terminal region of the Yes-Associated Protein (YAP) and its WW domains using magnetic selection and fluorescence activated cell sorting (FACS). The identified peptide cyclo[E-LYLAYPAH-K] featured a KD of 1.75 µM for YAP and 0.68 µM for the WW domains of YAP as well as high binding selectivity against albumin and lysozyme. These results demonstrate the usefulness of enzyme-mediated cyclization in screening combinatorial libraries to identify cyclic peptide binders.

Acetylation of Isoniazid Is a Novel Mechanism of Isoniazid Resistance in Mycobacterium tuberculosis.

Isoniazid (INH), one of the first-line drugs used for the treatment of tuberculosis, is a prodrug which is activated by the intracellular KatG enzyme of Mycobacterium tuberculosis The activated drug hinders cell wall biosynthesis by inhibiting the InhA protein. INH-resistant strains of M. tuberculosis usually have mutations in katG, inhA, ahpC, kasA, and ndh genes. However, INH-resistant strains which do not have mutations in any of these genes are reported, suggesting that these strains may adopt some other mechanism to become resistant to INH. In the present study, we characterized Rv2170, a putative acetyltransferase in M. tuberculosis, to elucidate its role in inactivating isoniazid. The purified recombinant protein was able to catalyze the transfer of the acetyl group to INH from acetyl coenzyme A (acetyl-CoA). High-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) analyses showed that following acetylation by Rv2170, INH is broken down into isonicotinic acid and acetylhydrazine. A drug susceptibility assay and confocal analysis showed that Mycobacterium smegmatis, which is susceptible to INH, is not inhibited by INH acetylated with Rv2170. Mutant proteins of Rv2170 failed to acetylate INH. Recombinant M. smegmatis and M. tuberculosis H37Ra overexpressing Rv2170 were found to be resistant to INH at MICs that inhibited wild-type strains. Besides, intracellular M. tuberculosis H37Ra overexpressing Rv2170 survived better in macrophages when treated with INH. Our results strongly indicate that Rv2170 acetylates INH, and this could be one of the strategies adopted by at least some M. tuberculosis strains to overcome INH toxicity, although this needs to be tested in INH-resistant clinical strains.

Discovery of Membrane-Permeating Cyclic Peptides via mRNA Display.

Small synthetic peptides capable of crossing biological membranes represent valuable tools in cell biology and drug delivery. While several cell-penetrating peptides (CPPs) of natural or synthetic origin have been reported, no peptide is currently known to cross both cytoplasmic and outer embryonic membranes. Here, we describe a method to engineer membrane-permeating cyclic peptides (MPPs) with broad permeation activity by screening mRNA display libraries of cyclic peptides against embryos at different developmental stages. The proposed method was demonstrated by identifying peptides capable of permeating Drosophila melanogaster (fruit fly) embryos and mammalian cells. The selected peptide cyclo[Glut-MRKRHASRRE-K*] showed a strong permeation activity of embryos exposed to minimal permeabilization pretreatment, as well as human embryonic stem cells and a murine fibroblast cell line. Notably, in both embryos and mammalian cells, the cyclic peptide outperformed its linear counterpart and the control MPPs. Confocal microscopy and single cell flow cytometry analysis were utilized to assess the degree of permeation both qualitatively and quantitatively. These MPPs have potential application in studying and nondisruptively controlling intracellular or intraembryonic processes.

Nano fibrous carbon produced from chromium bearing tannery solid waste as the bitumen modifier.

Bitumen binders play a major role in reducing the aging and oxidation property of bitumen. Carbon nanomaterials act as an effective bitumen modifier due to its stiffness and strength. Thus, nano fibrous carbon (NFC) was prepared from Chrome Tanned Buffing Dust (a solidwaste generated from leather industries) with proper care of avoiding oxidation of Cr(III) to Cr(VI) through pulse pyrolysis system. Morphology analysis using TEM confirmed the nano fibrous structure of NFC. XRD pattern of NFC depicts the graphitic phases of carbon along with the Cr2O3. Prepared NFC has been used as bitumen modifier and the blending of NFC with bitumen were done using both conventional and microwave heating methods to study the proper blending methods to enhance the bitumen properties. Thermogram of the modified bitumen showed that the decomposition temperature increases by increasing the percentage of NFC (5-25%) in both the heating methods, but comparatively the thermal stability is more in microwave mixing than in conventional mixing. The morphology analysis of the modified bitumen showed that non-uniform blending in conventional type of heating and homogeneously blended mixture in microwave type of heating. The penetration value and ductility decreases while softening point and kinematic viscosity increases by increasing the quantity of NFC from 5 to 25% in modified bitumen. Microwave heat mixing method yielded better modified bitumen with NFC than conventional heating method in terms of stability, uniform blending and physical properties. The non-leachability of the Cr(III) in the NFC modified bitumen was confirmed through total chromium analysis in the leachate. But, chromium analysis in leachate of NFC immersed in acetate buffer for one month showed leaching of Cr(III) 5.5 µg/L in the 25% NFC modified bitumen block mixed using conventional heating method.

Design and Fabrication of Wettability Gradients with Tunable Profiles through Degrafting Organosilane Layers from Silica Surfaces by Tetrabutylammonium Fluoride.

Surface-bound wettability gradients allow for a high-throughput approach to evaluate surface interactions for many biological and chemical processes. Here we describe the fabrication of surface wettability gradients on flat surfaces by a simple, two-step procedure that permits precise tuning of the gradient profile. This process involves the deposition of homogeneous silane SAMs followed by the formation of a surface coverage gradient through the selective removal of silanes from the substrate. Removal of silanes from the surface is achieved by using tetrabutylammonium fluoride which selectively cleaves the Si-O bonds at the headgroup of the silane. The kinetics of degrafting has been modeled by using a series of first order rate equations, based on the number of attachment points broken to remove a silane from the surface. Degrafting of monofunctional silanes exhibits a single exponential decay in surface coverage; however, there is a delay in degrafting of trifunctional silanes due to the presence of multiple attachment points. The effects of degrafting temperature and time are examined in detail and demonstrate the ability to reliably and precisely control the gradient profile on the surface. We observe a relatively homogeneous coverage of silane (i.e., without the presence of islands or holes) throughout the degrafting process, providing a much more uniform surface when compared to additive approaches of gradient formation. Linear gradients were formed on the substrates to demonstrate the reproducibility and tuneability of this subtractive approach.

A mathematical analysis of rebound in a target-mediated drug disposition model: II. With feedback.

We consider the possibility of free receptor (antigen/cytokine) levels rebounding to higher than the baseline level after the application of an antibody drug using a target-mediated drug disposition model. It is assumed that the receptor synthesis rate experiences homeostatic feedback from the receptor levels. It is shown for a very fast feedback response, that the occurrence of rebound is determined by the ratio of the elimination rates, in a very similar way as for no feedback. However, for a slow feedback response, there will always be rebound. This result is illustrated with an example involving the drug efalizumab for patients with psoriasis. It is shown that slow feedback can be a plausible explanation for the observed rebound in this example.

Identification of Epigenetic Factor Proteins Expressed in Human Embryonic Stem Cell-Derived Trophoblasts and in Human Placental Trophoblasts.

Human embryonic stem cells (hESCs) have been used to derive trophoblasts through differentiation in vitro. Intriguingly, mouse ESCs are prevented from differentiation to trophoblasts by certain epigenetic factor proteins such as Dnmt1, thus necessitating the study of epigenetic factor proteins during hESC differentiation to trophoblasts. We used stable isotope labeling by amino acids in cell culture and quantitative proteomics to study changes in the nuclear proteome during hESC differentiation to trophoblasts and identified changes in the expression of 30 epigenetic factor proteins. Importantly, the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B were downregulated. Additionally, we hypothesized that nuclear proteomics of hESC-derived trophoblasts may be used for screening epigenetic factor proteins expressed by primary trophoblasts in human placental tissue. Accordingly, we conducted immunohistochemistry analysis of six epigenetic factor proteins identified from hESC-derived trophoblasts-DNMT1, DNMT3B, BAF155, BAF60A, BAF57, and ING5-in 6-9 week human placentas. Indeed, expression of these proteins was largely, though not fully, consistent with that observed in 6-9 week placental trophoblasts. Our results support the use of hESC-derived trophoblasts as a model for placental trophoblasts, which will enable further investigation of epigenetic factors involved in human trophoblast development.

Activin/nodal signaling switches the terminal fate of human embryonic stem cell-derived trophoblasts.

Human embryonic stem cells (hESCs) have been routinely treated with bone morphogenetic protein and/or inhibitors of activin/nodal signaling to obtain cells that express trophoblast markers. Trophoblasts can terminally differentiate to either extravillous trophoblasts or syncytiotrophoblasts. The signaling pathways that govern the terminal fate of these trophoblasts are not understood. We show that activin/nodal signaling switches the terminal fate of these hESC-derived trophoblasts. Inhibition of activin/nodal signaling leads to formation of extravillous trophoblast, whereas loss of activin/nodal inhibition leads to the formation of syncytiotrophoblasts. Also, the ability of hESCs to form bona fide trophoblasts has been intensely debated. We have examined hESC-derived trophoblasts in the light of stringent criteria that were proposed recently, such as hypomethylation of the ELF5-2b promoter region and down-regulation of HLA class I antigens. We report that trophoblasts that possess these properties can indeed be obtained from hESCs.

The role of alpha oscillations in deriving and maintaining spatial relations in working memory.

Previous research has demonstrated distinct neural correlates for maintenance of abstract, relational versus concrete, sensory information in working memory (WM). Storage of spatial relations in WM results in suppression of posterior sensory regions, which suggests that sensory information is task-irrelevant when relational representations are maintained in WM. However, the neural mechanisms by which abstract representations are derived from sensory information remain unclear. Here, using electroencephalography, we investigated the role of alpha oscillations in deriving spatial relations from a sensory stimulus and maintaining them in WM. Participants encoded two locations into WM, then after an initial maintenance period, a cue indicated whether to convert the spatial information to another sensory representation or to a relational representation. Results revealed that alpha power increased over posterior electrodes when sensory information was converted to a relational representation, but not when the information was converted to another sensory representation. Further, alpha phase synchrony between posterior and frontal regions increased for relational compared to sensory trials during the maintenance period. These results demonstrate that maintaining spatial relations and locations in WM rely on distinct neural oscillatory patterns.

Targeted Mutagenesis and Combinatorial Library Screening Enables Control of Protein Orientation on Surfaces and Increased Activity of Adsorbed Proteins.

While nonspecific adsorption is widely used for immobilizing proteins on solid surfaces, the random nature of protein adsorption may reduce the activity of immobilized proteins due to occlusion of the active site. We hypothesized that the orientation a protein assumes on a given surface can be controlled by systematically introducing mutations into a region distant from its active site, thereby retaining activity of the immobilized protein. To test this hypothesis, we generated a combinatorial protein library by randomizing six targeted residues in a binding protein derived from highly stable, nonimmunoglobulin Sso7d scaffold; mutations were targeted in a region that is distant from the binding site. This library was screened to isolate binders that retain binding to its cognate target (chicken immunoglobulin Y, cIgY) as well as exhibit adsorption on unmodified silica at pH 7.4 and high ionic strength conditions. A single mutant, Sso7d-2B5, was selected for further characterization. Sso7d-2B5 retained binding to cIgY with an apparent dissociation constant similar to that of the parent protein; both mutant and parent proteins saturated the surface of silica with similar densities. Strikingly, however, silica beads coated with Sso7d-2B5 could achieve up to 7-fold higher capture of cIgY than beads coated with the parent protein. These results strongly suggest that mutations introduced in Sso7d-2B5 alter its orientation relative to the parent protein, when adsorbed on silica surfaces. Our approach also provides a generalizable strategy for introducing mutations in proteins so as to improve their activity upon immobilization, and has direct relevance to development of protein-based biosensors and biocatalysts.

Maintenance of relational information in working memory leads to suppression of the sensory cortex.

Working memory (WM) for sensory-based information about individual objects and their locations appears to involve interactions between lateral prefrontal and sensory cortexes. The mechanisms and representations for maintenance of more abstract, nonsensory information in WM are unknown, particularly whether such actively maintained information can become independent of the sensory information from which it was derived. Previous studies of WM for individual visual items found increased electroencephalogram (EEG) alpha (8-13 Hz) power over posterior electrode sites, which appears to correspond to the suppression of cortical areas that represent irrelevant sensory information. Here, we recorded EEG while participants performed a visual WM task that involved maintaining either concrete spatial coordinates or abstract relational information. Maintenance of relational information resulted in higher alpha power in posterior electrodes. Furthermore, lateralization of alpha power due to a covert shift of attention to one visual hemifield was marginally weaker during storage of relational information than during storage of concrete information. These results suggest that abstract relational information is maintained in WM differently from concrete, sensory representations and that during maintenance of abstract information, posterior sensory regions become task irrelevant and are thus suppressed.

Inhibition drives early feature-based attention.

Attention can modulate processing of visual input according to task-relevant features, even as early as approximately 100 ms after stimulus presentation. In the present study, event-related potential and behavioral data revealed that inhibition of distractor features, rather than activation of target features, is the primary driver of early feature-based selection in human observers. This discovery of inhibition consistent with task goals during early visual processing suggests that inhibition plays a much larger role at an earlier stage of target selection than previously recognized. It also highlights the importance of understanding the role of inhibition (in addition to activation) in attention.

Protein selection using yeast surface display.

Binding proteins are typically isolated from combinatorial libraries of scaffold proteins using one of the many library screening tools available, such as phage display, yeast surface display or mRNA display. A key principle underlying these screening technologies is the establishment of a link between each unique mutant protein and its corresponding genetic code. The mutant proteins binding a desired target species are separated and subsequently identified using the genetic code. In this review, we largely focus on the use of yeast surface display for the isolation of binding proteins from combinatorial libraries. In yeast surface display, the yeast cell links the mutant protein to its coding DNA. Each yeast cell expresses the mutant proteins as fusions to a yeast cell wall protein; the yeast cell also carries plasmid DNA that codes for the mutant protein. Over the years, the yeast surface display platform has emerged as a powerful tool for protein engineering, and has been used in a variety of applications including affinity maturation, epitope mapping and biophysical characterization of proteins. Here we present a broad overview of the yeast surface display system and its applications, and compare it with other contemporary screening platforms. Further, we present detailed protocols for the use of yeast surface display to isolate de novo binding proteins from combinatorial libraries, and subsequent biophysical characterization of binders. These protocols can also be easily modified for affinity maturation of the isolated de novo binders.

Targeted proteomics of the secretory pathway reveals the secretome of mouse embryonic fibroblasts and human embryonic stem cells.

Proteins endogenously secreted by human embryonic stem cells (hESCs) and those present in hESC culture medium are critical regulators of hESC self-renewal and differentiation. Current MS-based approaches for identifying secreted proteins rely predominantly on MS analysis of cell culture supernatants. Here we show that targeted proteomics of secretory pathway organelles is a powerful alternate approach for interrogating the cellular secretome. We have developed procedures to obtain subcellular fractions from mouse embryonic fibroblasts (MEFs) and hESCs that are enriched in secretory pathway organelles while ensuring retention of the secretory cargo. MS analysis of these fractions from hESCs cultured in MEF conditioned medium (MEF-CM) or MEFs exposed to hESC medium revealed 99 and 129 proteins putatively secreted by hESCs and MEFs, respectively. Of these, 53 and 62 proteins have been previously identified in cell culture supernatants of MEFs and hESCs, respectively, thus establishing the validity of our approach. Furthermore, 76 and 37 putatively secreted proteins identified in this study in MEFs and hESCs, respectively, have not been reported in previous MS analyses. The identification of low abundance secreted proteins via MS analysis of cell culture supernatants typically necessitates the use of altered culture conditions such as serum-free medium. However, an altered medium formulation might directly influence the cellular secretome. Indeed, we observed significant differences between the abundances of several secreted proteins in subcellular fractions isolated from hESCs cultured in MEF-CM and those exposed to unconditioned hESC medium for 24 h. In contrast, targeted proteomics of secretory pathway organelles does not require the use of customized media. We expect that our approach will be particularly valuable in two contexts highly relevant to hESC biology: obtaining a temporal snapshot of proteins secreted in response to a differentiation trigger, and identifying proteins secreted by cells that are isolated from a heterogeneous population.

A mathematical analysis of rebound in a target-mediated drug disposition model: I.without feedback.

We consider the possibility of free receptor (antigen/cytokine) levels rebounding to higher than the baseline level after one or more applications of an antibody drug using a target-mediated drug disposition model. Using geometry and dynamical systems analysis, we show that rebound will occur if and only if the elimination rate of the drug-receptor product is slower than the elimination rates of the drug and of the receptor. We also analyse the magnitude of rebound through approximations and simulations and demonstrate that it increases if the drug dose increases or if the difference between the elimination rate of the drug-receptor product and the minimum of the elimination rates of the drug and of the receptor increases.

Comment on "gemcitabine, PI3kinase-Akt pathway inhibition and radiation in human glioma cell lines" by M.S. Elnaggar et al.1.

The combination of gemcitabine, PI3K-Akt pathway inhibitors, and radiation in human glioma cell lines shows potential to enhance radiation sensitivity in aggressive brain tumors. Inhibiting the overactive PI3K-Akt pathway may increase tumor vulnerability to treatment. However, variability in responses among different glioma cell lines highlights the need for personalized approaches. Future research should focus on identifying biomarkers to tailor treatment for individual patients. Additionally, addressing safety concerns and the challenges of translating preclinical findings into clinical practice is crucial. Further studies should explore the therapy's molecular mechanisms and evaluate its clinical potential.

Diethylbenzene and ethyltoluene adsorption studies on novel beta antimonide phosphorus nanosheets-a first-principle study.

CONTEXT: In the present work, we examined the sensing behavior of monolayer beta antimonide phosphorus (ß-SbP) sheets towards toxic volatile organic compounds (VOCs) namely, 1,2-diethylbenzene and 2-ethyltoluene using density functional theory (DFT) method. At first, using cohesive energy structural stability of the monolayer ß-SbP is confirmed. The calculated energy band gap value of monolayer ß-SbP is 2.168 eV, which is a semiconductor. Furthermore, the adsorption properties of 1,2-diethylbenzene and 2-ethyltoluene on ß-SbP are studied through key factors, such as adsorption energy, Mulliken charge transfer, and relative band gap variation. The adsorption energy clearly shows (- 0.335 to - 0.903 eV) that both 1,2-diethylbenzene and 2-ethyltoluene are physisorbed on ß-SbP monolayer. Besides, Mulliken charge transfer falls in the range of - 0.465 to 0.933 e; this information clearly shows that the ß-SbP monolayer is a potential candidate for sensing 1,2-diethylbenzene and 2-ethyltoluene molecules. METHODS: The structural firmness including electronic and adsorption properties of 1,2-diethylbenzene and 2-ethyltoluene on ß-SbP monolayer are investigated with the support of the DFT method. Particularly, the hybrid generalized gradient approximation (hybrid GGA) along with Beck's three-parameter + Lee-Yang-Parr (B3LYP) exchange-correlation functional is utilized for relaxing the ß-SbP monolayer. In the present work, all calculations are performed using the Quantum Atomistic Tool Kit (ATK) simulation package. In the present work, we utilized ß-SbP monolayer as a chief sensing element to detect 1,2-diethylbenzene and 2-ethyltoluene to safeguard humans from toxic environments.