Site-directed mutagenesis reveals functional contribution of Thr218, Lys220 and Asp304 in chymosin

The functional contributions of amino acid residues Thr218 and Asp304 of chymosin, both of which are highly conserved in the aspartic proteinases, are analysed by means of site-directed mutagenesis. The optimum pH values, milk-clotting (C) and proteolytic (P) activities and kinetic parameters for synthetic oligopeptides as substrates were examined for the mutant enzymes. The mutation Thr218Ser caused a marked increase in the C/P ratio, which seemed to be due to a change in substrate recognition. Although the negative charge of Asp304 had been expected to play a role in lowering the optimum pH values in the aspartic proteinases, this turned out not to be the case in chymosin because both the mutations Asp304Ala and Asp304Glu caused a similar shift of the optimum pH towards the acidic side. In addition, the mutation Lys220Leu, which we generated previously, was found to cause a decrease in the C/P ratio, mainly due to the increase in the proteolytic activity.     

Measuring the contribution of community members to functional diversity

Although the contribution of community members to functional diversity is a key question of conservation ecology, its measurement and interpretation are rather problematic. In this paper, we suggest a novel method for decomposing functional diversity. To do this we consider functional units (i.e. species or a group of species with identical traits) as the functional building blocks of communities. Then we propose the use of a recently developed measure of functional diversity (called modified functional attribute diversity or MFAD) and suggest additive decomposition of MFAD into functional values contributed by the functional units. We point out that functional values are related to changes in MFAD if the functional unit is removed from the community. This property of decomposition allows the quantification of the contribution of community members to functional diversity. By studying artificial and actual communities we compare the performance of our new method with other recently developed contribution measures, which are based on dendrograms and ordinations. Both theoretical considerations and analyses of artificial and actual data sets suggest that the proposed method of calculating functional values expresses more explicitly the contribution of community members to functional diversity and hereby can be used as a simple, yet efficient method for searching for functional keystones in ecological communities or for quantifying the contribution of community members to functional diversity.     

In-depth proteomic analyses of ovarian cancer cell line exosomes reveals differential enrichment of functional categories compared to the NCI 60 proteome

Molecular communication between cancer cells and its stromal microenvironment is a key factor for cancer progression. Alongside classic secretory pathways, it has recently been proposed that small membranous vesicles are alternative mediators of intercellular communication. Exosomes carry an effector-rich proteome with the ability to modulate various functional properties of the recipient cell. In this study, exosomes isolated from four epithelial ovarian cancer cell lines (OVCAR3, OVCAR433, OVCAR5 and SKOV3) were characterized using mass spectrometry-based proteomics. Using an optimized workflow consisting of efficient exosome solubilization and the latest generation of proteomic instrumentation, we demonstrate improved detection depth. Systematic comparison of our cancer cell line exosome proteome against public data (Exocarta) and the recently published NCI 60 proteome revealed enrichment of functional categories related to signaling biology and biomarker discovery.     

An integrated platform of genomic assays reveals small-molecule bioactivities

Bioactive compounds are widely used to modulate protein function and can serve as important leads for drug development. Identifying the in vivo targets of these compounds remains a challenge. Using yeast, we integrated three genome-wide gene-dosage assays to measure the effect of small molecules in vivo. A single TAG microarray was used to resolve the fitness of strains derived from pools of (i) homozygous deletion mutants, (ii) heterozygous deletion mutants and (iii) genomic library transformants. We demonstrated, with eight diverse reference compounds, that integration of these three chemogenomic profiles improves the sensitivity and specificity of small-molecule target identification. We further dissected the mechanism of action of two protein phosphatase inhibitors and in the process developed a framework for the rational design of multidrug combinations to sensitize cells with specific genotypes more effectively. Finally, we applied this platform to 188 novel synthetic chemical compounds and identified both potential targets and structure-activity relationships.     

Single-cell imaging of inflammatory caspase dimerization reveals differential recruitment to inflammasomes

The human inflammatory caspases, including caspase-1, -4, -5 and -12, are considered as key regulators of innate immunity protecting from sepsis and numerous inflammatory diseases. Caspase-1 is activated by proximity-induced dimerization following recruitment to inflammasomes but the roles of the remaining inflammatory caspases in inflammasome assembly are unclear. Here, we use caspase bimolecular fluorescence complementation to visualize the assembly of inflammasomes and dimerization of inflammatory caspases in single cells. We observed caspase-1 dimerization induced by the coexpression of a range of inflammasome proteins and by lipospolysaccharide (LPS) treatment in primary macrophages. Caspase-4 and -5 were only dimerized by select inflammasome proteins, whereas caspase-12 dimerization was not detected by any investigated treatment. Strikingly, we determined that certain inflammasome proteins could induce heterodimerization of caspase-1 with caspase-4 or -5. Caspase-5 homodimerization and caspase-1/-5 heterodimerization was also detected in LPS-primed primary macrophages in response to cholera toxin subunit B. The subcellular localization and organization of the inflammasome complexes varied markedly depending on the upstream trigger and on which caspase or combination of caspases were recruited. Three-dimensional imaging of the ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain)/caspase-1 complexes revealed a large spherical complex of ASC with caspase-1 dimerized on the outer surface. In contrast, NALP1 (NACHT leucine-rich repeat protein 1)/caspase-1 complexes formed large filamentous structures. These results argue that caspase-1, -4 or -5 can be recruited to inflammasomes under specific circumstances, often leading to distinctly organized and localized complexes that may impact the functions of these proteases.Correct assembly and regulation of inflammasomes is critical for mediating inflammation and preventing uncontrolled inflammation under infectious and sterile conditions. These supramolecular structures converge on the activation of caspase-1. Upon activation, caspase-1 cleaves the proinflammatory cytokines interleukin1β (IL-1β) and IL-18 to their active mature forms,^{1, 2} which are then released from the cell to direct the immediate removal of pathogens.Caspase-1 is activated by proximity-induced dimerization upon recruitment to inflammasomes, which are multiprotein signaling complexes that act as activation platforms.³ Many distinct inflammasomes exist, and each inflammasome includes a sensor protein (e.g., NALP1 (NACHT leucine-rich repeat protein 1)/NLRP1 (NOD-like receptor protein 1), NALP3/NLRP3, AIM2 (absent in melanoma 2) or IPAF (ICE protease-activating factor)/NLRC4 (NLR family CARD domain-containing protein 4)), which is activated by specific proinflammatory molecules. These include pathogen-derived stimuli, known as pathogen-associated molecular patterns (PAMPs), or non-pathogenic inflammatory stimuli, known as damage-associated molecular patterns.⁴ Inflammasome assembly is governed by a series of homotypic interactions, which are mediated by specific protein:protein interaction domains, such as the pyrin domain (PYD) and the caspase recruitment domain (CARD).^{5, 6} For example, NALP1 and NALP3 both contain a PYD at their C terminus that binds to the PYD in the adaptor protein, ASC (apoptosis-associated speck-like protein containing a CARD).^{7, 8} ASC also contains a CARD,⁹ which binds to the CARD in the prodomain of caspase-1 (C1-Pro), resulting in caspase-1 dimerization and activation.¹⁰ Inflammasomes can also be ASC-independent, such as IPAF, which interacts directly with caspase-1.¹¹ Interestingly, ASC can enhance IPAF-induced caspase-1 activation,^{12, 13} which indicates that more complex interactions between these proteins may exist.Caspase-1 is one of the inflammatory caspases, including the human caspases (caspase-1, -4, -5 and -12) and murine caspase-11.¹⁴ The roles of caspase-4, -5, and -12 in caspase-1 activation and inflammasome pathways are not clear. Full-length caspase-12, which is only expressed by ~20% of people of African descent, can inhibit caspase-1 activity.¹⁵ Most of all human populations express the short form of caspase-12 (caspase-12 S or C12S), which arose from a point mutation leading to a premature stop codon just after the prodomain. This truncated form of caspase-12 is associated with increased resistance to sepsis,¹⁵ indicating that caspase-12 has an important role in inflammation. Caspase-11 mediates caspase-1 activation in response to Escherichia coli and Citrobacter rodentium in mice.¹⁶ Caspase-11 also triggers an inflammatory form of cell death, known as pyroptosis, independent of caspase-1, ASC and NALP3. This is known as the noncanonical inflammasome pathway.¹⁶ Humans do not express caspase-11 and express caspase-4 and -5 instead. Recent evidence indicates that caspase-4 and -5 act as direct intracellular sensors for lipopolysaccharide (LPS) to induce pyroptosis, independent of any additional inflammasome proteins.¹⁷ However, this does not rule out the possibility that caspase-4 and -5 can be recruited to inflammasomes under certain circumstances.The inflammatory caspases are considered to be initiator caspases, based on structural similarities between them and caspase-2, -8 and -9.¹⁸ We previously reported the use of caspase bimolecular fluorescence complementation (BiFC) to measure induced proximity of the initiator caspase, caspase-2.¹⁹ We adapted BiFC, where non-fluorescent fragments of the yellow fluorescent protein, Venus (‘split Venus''), can associate to reform the fluorescent complex when fused to interacting proteins. When caspase-2 was fused to each half of split Venus, the recruitment of caspase-2 to its activation platform and the subsequent induced proximity resulted in association of the two Venus halves. This resulted in an increase in fluorescence that represents caspase dimerization. Our caspase BiFC method facilitates specific analysis of caspase interactions at the level of the activation platform. Importantly, caspase BiFC can reveal the structural organization and localization of activation platforms in living cells.Here, we extend the caspase BiFC approach to interrogate the inflammatory caspases. We show that there are considerable differences in the organization and distribution of different inflammasomes depending on the upstream signals and on which inflammatory caspase is recruited. Our studies reveal unexpected heterodimerization interactions between caspase-1 and additional inflammatory caspases, presenting a new outcome of inflammasome assembly.     

Weight-dependent differential contribution of insulin secretion and clearance to hyperinsulinemia of obesity

Obesity is associated with insulin resistance and the resulting hyperinsulinemia has been attributed to an increase of insulin secretion and a reduction of insulin clearance. The present study was intended to further characterize the relative contribution of secretion and clearance especially in the postprandial state. In relation to WHO body weight classes 291 subjects were divided in 5 subgroups Basal insulin concentrations rose stepwise and significantly with increasing BMI. This was paralleled by C-peptide concentrations and insulin secretion, while the reduction of insulin clearance was less stringent in relation to BMI. Basal glucose was unchanged in the BMI25 group and 8% higher in the obese groups (BMI 30, 35, 40) compared to normal weight (NW). Although postprandial insulin concentrations were significantly higher in the overweight and obese groups compared to NW the correlation was not as tight as in the basal state. Furthermore, the present data demonstrate for the first time that insulin secretion only increased in the overweight group without further augmentation in the obese groups. Further hyperinsulinemia of the latter was due to weight-dependent reduction of insulin clearance. The postprandial glucose response was 38–82% higher with increasing weight compared to NW. In summary basal hyperinsulinemia is mainly due to weight related increase of insulin secretion with moderate contribution of reduced insulin clearance. Postprandially, hyperinsulinemia of overweight is predominantly due to secretion while further postprandial hyperinsulinemia of obese subjects is mainly due to reduced clearance. Thus, postprandial insulin secretion cannot respond adequately to the challenge of weight-dependent insulin resistance already in non-diabetic obese subjects.     

Superantigen stimulation reveals the contribution of Lck to negative regulation of T cell activation

The conventional paradigm of T cell activation through the TCR states that Lck plays a critical activating role in this signaling process. However, the T cell response to bacterial superantigens does not require Lck. In this study we report that not only is Lck dispensable for T cell activation by superantigens, but it actively inhibits this signaling pathway. Disruption of Lck function, either by repression of Lck gene expression or by selective pharmacologic inhibitors of Lck, led to increased IL-2 production in response to superantigen stimulation. This negative regulatory effect of Lck on superantigen-induced T cell responses required the kinase activity of Lck and correlated with early TCR signaling, but was independent of immunological synapse formation and TCR internalization. Our data demonstrate that the multistage role of Lck in T cell signaling includes the activation of a negative regulatory pathway of T cell activation.     

A simple and economical route to generate functional hepatocyte-like cells from hESCs and their application in evaluating alcohol induced liver damage

The in vitro derived hepatocytes from human embryonic stem cells (hESC) is a promising tool to acquire improved knowledge of the cellular and molecular events underlying early human liver development under physiological and pathological conditions. Here we report a simple two-step protocol employing conditioned medium (CM) from human hepatocellular carcinoma cell line, HepG2 to generate functional hepatocyte-like cells from hESC. Immunocytochemistry, flow cytometry, quantitative RT-PCR, and biochemical analyses revealed that the endodermal progenitors appeared as pockets in culture, and the cascade of genes associated with the formation of definitive endoderm (HNF-3β, SOX-17, DLX-5, CXCR4) was consistent and in concurrence with the up-regulation of the markers for hepatic progenitors [alpha-feto protein (AFP), HNF-4α, CK-19, albumin, alpha-1-antitrypsin (AAT)], followed by maturation into functional hepatocytes [tyrosine transferase (TAT), tryptophan-2, 3-dioxygenase (TDO), glucose 6-phosphate (G6P), CYP3A4, CYP7A1]. We witnessed that the gene expression profile during this differentiation process recapitulated in vivo liver development demonstrating a gradual down-regulation of extra embryonic endodermal markers (SOX-7, HNF-1β, SNAIL-1, LAMININ-1, CDX2), and the generated hepatic cells performed multiple liver functions. Since prenatal alcohol exposure is known to provoke irreversible abnormalities in the fetal cells and developing tissues, we exposed in vitro generated hepatocytes to ethanol (EtOH) and found that EtOH treatment not only impairs the survival and proliferation, but also induces apoptosis and perturbs differentiation of progenitor cells into hepatocytes. This disruption was accompanied by alterations in the expression of genes and proteins involved in hepatogenesis. Our results provide new insights into the wider range of destruction caused by alcohol on the dynamic process of liver organogenesis.     

Where eagles soar: Fine‐resolution tracking reveals the spatiotemporal use of differential soaring modes in a large raptor

Unlike smaller raptors, which can readily use flapping flight, large raptors are mainly restricted to soaring flight due to energetic constraints. Soaring comprises of two main strategies: thermal and orographic soaring. These soaring strategies are driven by discrete uplift sources determined by the underlying topography and meteorological conditions in an area. High‐resolution GPS tracking of raptor flight allows the identification of these flight strategies and interpretation of the spatiotemporal occurrence of thermal and orographic soaring. In this study, we develop methods to identify soaring flight behaviors from high‐resolution GPS tracking data of Verreaux’s eagle Aquila verreauxii and analyze these data to understand the conditions that promote the use of thermal and orographic soaring. We use these findings to predict the use of soaring flight both spatially (across the landscape) and temporally (throughout the year) in two topographically contrasting regions in South Africa. We found that topography is important in determining the occurrence of soaring flight and that thermal soaring occurs in relatively flat areas which are likely to have good thermal uplift availability. The predicted use of orographic soaring was predominately determined by terrain slope. Contrary to our expectations, the topography and meteorology of eagle territories in the Sandveld promoted the use of soaring flight to a greater extent than in territories in the more mountainous Cederberg region. Spatiotemporal mapping of predicted flight behaviors can broaden our understanding of how large raptors like the Verreaux’s eagle use their habitat and how that links to energetics (as the preferential use of areas that maximize net energy gain is expected), reproductive success, and ultimately population dynamics. Understanding the fine‐scale landscape use and environmental drivers of raptor flight can also help to predict and mitigate potential detrimental effects of anthropogenic developments, such as mortality via collision with wind turbines.     

Rapid functional assays of recombinant IP3 receptors

Functional assays of inositol 1,4,5-trisphosphate receptors (IP3R) currently use 45Ca2+ release methods, fluorescent Ca2+ indicators within either the ER or cytosol, or electrophysiological analyses of IP3R in the nuclear envelope or artificial bilayers. None of the methods is presently amenable to the rapid, high-throughput quantitative analyses of IP3R function needed to address the structural determinants of IP3R behavior. We use a low-affinity Ca2+ indicator (Mag-fluo-4) to measure free [Ca2+] within the ER of permeabilized DT40 cells expressing only rat type 1 IP(3)R, and establish that the indicator is capable of reliably reporting the Ca(2+) release evoked by IP3. A 96-well fluorescence plate reader equipped for automated fluid additions (FlexStation, Molecular Devices) is used to monitor IP3-evoked Ca2+ release. The method allows quick and economical functional assays of recombinant IP3R in small volumes (< or = 100 microl).     

Proteomics of breast cancer: From differential to functional analysis

From differential analysis to identify biomarkers, to functional analysis for finding new therapeutic targets, proteomics bring new comprehensive information for a better understanding of the molecular basis of oncology and new perspectives for the clinic. However the major limitation of proteomic investigations, more generally of post-genomic approaches, remains the molecular and cellular complexity of the mammary gland that is still a major challenge.     

Assessing the relative contribution of functional divergence and guild aggregation to overall functional structure of species assemblages

The study of functional structure in species assemblages emphasizes the detection of significant guild aggregation patterns. Thus, protocols based on intensive resampling of empirical data have been proposed to assess guild structure. Such protocols obtain the frequency distribution of a given functional similarity metric, and identify a threshold value (often the 95th percentile) beyond which clusters in a functional dendrogram are considered as significant guilds (using one-tailed tests). An alternative approach sequentially searches for significant differences between clusters at decreasing levels of similarity in a dendrogram until one is detected, then assumes that all subsequent nodes should also be significant. Nevertheless, these protocols do not test both the significance and sign of deviations from random at all levels of functional similarity within a dendrogram. Here, we propose a new bootstrapping approach that: (1) overcomes such pitfalls by performing two-tailed tests for each node in a dendrogram of functional similarity after separately determining their respective sample distributions, and (2) enables the quantification of the relative contribution of guild aggregation and functional divergence to the overall functional structure of the entire assemblage. We exemplify this approach by using long-term data on guild dynamics in a vertebrate predator assemblage of central Chile. Finally, we illustrate how the interpretation of functional structure is improved by applying this new approach to the data set available.