Distinct Chains Research Articles

Quantitative Proteomic Approach Targeted to Fibrinogen β Chain in Tissue Gastric Carcinoma.

Elevated plasma fibrinogen levels and tumor progression in patients with gastric cancer (GC) have been largely reported. However, distinct fibrinogen chains and domains have different effects on coagulation, inflammation, and angiogenesis. The aim of this study was to characterize fibrinogen β chain (FGB) in GC tissues. Retrospectively we analyzed the data of matched pairs of normal (N) and malignant tissues (T) of 28 consecutive patients with GC at diagnosis by combining one- and two-dimensional electrophoresis (1DE and 2DE) with immunoblotting and mass spectrometry together with two-dimensional difference in gel electrophoresis (2D-DIGE). 1DE showed bands of the intact FGB at 50 kDa and the cleaved forms containing the fragment D at ~37–40 kDa, which corresponded to 19 spots in 2DE. In particular, spot 402 at ~50 kDa and spots 526 and 548 at ~37 kDa were of interest by showing an increased expression in tumor tissues. A higher content of spot 402 was associated with stomach antrum, while spots 526 and 548 amounts correlated with corpus and high platelet count (>208 × 109/L). The quantification of FGB and cleaved products may help to further characterize the interconnections between GC and platelet/coagulation pathways.

Structural characterization of polysaccharides from Saposhnikovia divaricata and their antagonistic effects against the immunosuppression by the culture supernatants of melanoma cells on RAW264.7 macrophages

Two purified native polysaccharides, namely, SDNP-1 and SDNP-2 with apparent molecular weight of 67.9×103 and 5.2×103, separately, were isolated from the water extract of Saposhnikovia divaricata by combined ion-exchange and gel permeation chromatography. The structures of these polysaccharides were characterized by high-performance gel permeation chromatography, chemical derivative analysis, GC–MS, FT-IR spectroscopy, and NMR spectroscopy. Results showed that SDNP-1 and SDNP-2 were composed of arabinose and galactose with molar ratio of approximately 1:1. The polysaccharides were deduced to be AGII-type arabinogalactans with distinct molecular weights and backbone chains. The backbone chain of SDNP-2 mainly consisted of (1→3)-linked and (1→6)-linked Galp residues with an approximate molar ratio of 1:3. Approximately half of the (1→6)-linked Galp residues were substituted at O-3, and small amounts of (1→6)-linked Galp were substituted at O-3 and O-4 by branches that mainly consisted of terminal and (1→5)-linked Araf residues. Bioactivity tests showed that SDNP-2 exhibited significant antagonistic effect against immunosuppression as shown by the cell viability of the culture supernatants of melanoma cells on RAW264.7 macrophages. However, SDNP-1 showed no effect. Thus, molecular weight and backbone chain may be the key factors for the antagonistic effects against immunosuppression.

A study on the effects of supply chain relationship quality on firm performance-under the aspect of shared vision

Shared vision among organizations could reinforce the constructive cooperation of the entire supply chain. From social capital theory and the viewpoints of network embeddedness, this study intends to explore the effect of supply chain relationship quality of enterprises in a supply chain on the firm performance with distinct supply chain embeddedness under the aspect of shared vision. With questionnaire survey, 160 precise mold enterprises in Taiwan are collected, and Hierarchical Linear Regression Analysis is used for test the effects of shared vision and social capital on the promotion of firm performance of enterprises with supply chain relationship quality and supply chain embeddedness. The empirical results reveal the positive and significant effect of supply chain structure embeddedness on firm performance, showing the high structure embeddedness of the supply chain of precise mold enterprises. Meanwhile, it also finds out the positive and remarkable moderation effects of shared vision and social capital, presenting that enterprises in a supply chain could reinforce the effect of embeddedness on firm performance through shared vision and social capital.

Polarity-Induced Surface Recognition and Self-Assembly of Noncanonical DNA Nucleobases on h-BN Monolayer

A systematic understanding of the self-assembly of DNA nucleobases is essential for biomolecular recognition on surfaces of novel 2D materials. Using atomistic molecular dynamics (MD) simulations, we investigate the self-assembly of guanine and cytosine nucleobases on the hexagonal boron nitride (h-BN) monolayer. We find that the self-assembly is driven by the inherent polarity of the bases determining the nature of molecular ordering and growth patterns: guanine into 2D aggregates and cytosine into 1D linear arrays and interconnected molecular chains. The base–base H-bond interactions guide the self-assembly, and the base-surface interactions facilitate surface recognition and monolayer adsorption. Simulations at elevated temperatures find reconstruction at the surface with cytosine forming distinct 1D chains and guanine forming an extended network. We propose that the distinctive patterns in assembly, unique to the DNA nucleobases, would serve as fingerprints for biomolecular recognition at the solid/li...

Three lysophosphatidic acids with a distinct long chain moiety differently affect cell differentiation of human colon epithelial cells to goblet cells

AimThe intestinal mucus layer helps maintain intestinal homeostasis. In this study, we investigated the effects of lysophosphatidic acids (LPA) on differentiation of human colon carcinoma cell line, HT-29, to goblet cells with and without sodium butyrate, a known differentiation factor for intestinal cells. Main methodsNumber and average size of cells with goblet-like morphology in five photographs per dish were measured for assessment of differentiation of HT-29 cells to goblet cells as well as their relative portion of surface of to whole surface area of the photograph. Key findingsOur results revealed that 18:1 LPA enhanced butyrate-induced differentiation of HT-29 cells. Because increased mRNA expression of LPA5 and decreased mRNA expression of LPA6 were observed in HT-29 cells after treatment with butyrate, we explored the effects of alkyl LPA and 20:4 LPA, which show preferentially higher affinities to LPA5 and LPA6, respectively. As a result, the cell differentiation to goblet cell was increased by alkyl LPA but decreased by 20:4 LPA. Further, alkyl LPA and 18:1 LPA, but not 20:4 LPA, were found to reduce the numbers of cells surviving after incubation in a standard culture medium containing 10% fetal calf serum. SignificanceWe suggest that the three LPAs positively and negatively affect the differentiation of HT-29 cells to goblet cells, which may be associated with their reduced survival through the activation of distinct LPA receptor(s).

Ub-ProT reveals global length and composition of protein ubiquitylation in cells

Protein ubiquitylation regulates diverse cellular processes via distinct ubiquitin chains that differ by linkage type and length. However, a comprehensive method for measuring these properties has not been developed. Here we describe a method for assessing the length of substrate-attached polyubiquitin chains, “ubiquitin chain protection from trypsinization (Ub-ProT).” Using Ub-ProT, we found that most ubiquitylated substrates in yeast-soluble lysate are attached to chains of up to seven ubiquitin molecules. Inactivation of the ubiquitin-selective chaperone Cdc48 caused a dramatic increase in chain lengths on substrate proteins, suggesting that Cdc48 complex terminates chain elongation by substrate extraction. In mammalian cells, we found that ligand-activated epidermal growth factor receptor (EGFR) is rapidly modified with K63-linked tetra- to hexa-ubiquitin chains following EGF treatment in human cells. Thus, the Ub-ProT method can contribute to our understanding of mechanisms regulating physiological ubiquitin chain lengths and composition.

Classifying Heterotaxy Syndrome

Heterotaxy syndrome is a complex set of abnormalities related to abnormal left–right axis patterning. Although rare (occurring in just over 1 in 10 000 live births1), congenital heart defects associated with heterotaxy syndrome carry a disproportionate burden of morbidity and mortality.2,3 Despite numerous investigations on the genetic underpinning, epidemiology, anatomic pathology, diagnostic imaging, and management, agreement regarding the best method to classify patients with heterotaxy continues to elude our field.4 Specifically, a growing body of experience has noted that the 2 most common methods of classifying patients with heterotaxy—based on the status of the spleen or on the morphology of the atrial appendages—is frequently incongruent with the expected pattern of cardiac and noncardiac anomalies,5 is difficult to ascertain clinically, and may not be helpful in guiding clinical management.2–4 See Article by Yim et al In this issue of Circulation: Cardiovascular Imaging , Yim et al6 provide further evidence that the prevailing classification schemes used in heterotaxy syndrome are flawed. In a retrospective analysis of noninvasive imaging data from 114 patients with heterotaxy, they noted that the classic pattern of isomerism was breached in 1 of every 5 patients. Furthermore, they documented the limited clinical utility of relying on atrial appendage morphology or the status of the spleen and …

Cutoffs for product chains

We consider products of ergodic Markov chains and discuss their cutoffs in total variation. Our framework is general in that rates to pick up coordinates are not necessary equal, and different coordinates may correspond to distinct chains. We give necessary and sufficient conditions for cutoffs of product chains in terms of those of coordinate chains under certain conditions. A comparison of mixing times between the product chain and its coordinate chains is made in detail as well. Examples are given to show that neither cutoffs for product chains nor for coordinate chains imply others in general.

Information Sharing along the Global Textile Supply Chain for Maximizing their Added Values

Information flows within global textile supply chains and between supply chains stakeholders should be suppressed as much as possible so as to maximize the added value of textile products when they move along the supply chain process. However, information flows between supply chain stakeholders with their corresponding distinct supply chains should not be suppressed in order to make sure that the supply meets the demand effectively and efficiently. Because stakeholders reduce the bullwhip effect by ordering the commercial textiles’ consignments based on the demand order sizes which they get from their downstream firms by means of information sharing technology. Out of many reengineering efforts taken by many textile supply chain giants to improve their supply chain operating efficiencies, information sharing between partners is one key initiative and sharing sales information is a significant strategy to counter bullwhip effect. Hence, it is high time; textile scientist as well as the merchandisers gave thought in this segment of global textile supply chain and maximized the revenue by means of information sharing from backward linkage industries to forward linkage industries.

Dynamic Characteristic of High Strength Ring Chain under Different Launch Parameters

The aim of this study is to investigate the mechanical characteristics of the high strength ring chain under various launch parameters and the energy consumption law caused by this. Particularly, the contact dynamics simulation is implemented in Abaqus. In this study, the stress and strain contours of the high strength ring chain under the chain speeds of 1.85 m/min, 5.6 m/min, and 7.8 m/min and under the transportation loads of 2t, 3t, and 3.5t are obtained, plus their stress histories. Simulation results show that the corresponding steady stresses under distinct chain speeds are 748.2 MPa, 754.5 MPa, and 755.6 MPa, determining the optimal chain speed of 5.6m min-1. After reaching the steady state, the maximum stresses under the loads of 2t, 3t, and 3.5t are 774.8 MPa, 758.1 MPa, and 747 MPa, respectively. Furthermore, the experimental results illustrate that the energy consumption caused by the friction among high strength ring chains under no-load operation occupies 23.8% of the resistance consumption. With the rise in loads, the total resistance consumption grows linearly. As a consequence, the research on the dynamic characteristics of the high strength ring chain is valuable for improving the working efficiency of the electromotor.

Individual Impact of Distinct Polysialic Acid Chain Lengths on the Cytotoxicity of Histone H1, H2A, H2B, H3 and H4.

Neutrophils are able to neutralize pathogens by phagocytosis, by the release of antimicrobial components, as well as by the formation of neutrophil extracellular traps (NETs). The latter possibility is a DNA-meshwork mainly consisting of highly concentrated extracellular histones, which are not only toxic for pathogens, but also for endogenous cells triggering several diseases. To reduce the negative outcomes initiated by extracellular histones, different approaches like antibodies against histones, proteases, and the polysaccharide polysialic acid (polySia) were discussed. We examined whether each of the individual histones is a binding partner of polySia, and analyzed their respective cytotoxicity in the presence of this linear homopolymer. Interestingly, all of the histones (H1, H2A, H2B, H3, and H4) seem to interact with α2,8-linked sialic acids. However, we observed strong differences regarding the required chain length of polySia to bind histone H1, H2A, H2B, H3, and H4. Moreover, distinct degrees of polymerization were necessary to act as a cytoprotective agent in the presence of the individual histones. In sum, the outlined results described polySia-based strategies to bind and/or to reduce the cytotoxicity of individual histones using distinct polySia chain length settings.

Preparation of PEGylated liposomes incorporating lipophilic lomeguatrib derivatives for the sensitization of chemo-resistant gliomas

Liposomal delivery is a well-established approach to increase the therapeutic index of drugs, mainly in the field of cancer chemotherapy. Here, we report the preparation and characterization of a new liposomal formulation of a derivative of lomeguatrib, a potent O6-methylguanine-DNA methyltransferase (MGMT) inactivator. The drug had been tested in clinical trials to revert chemoresistance, but was associated with a low therapeutic index. A series of lomeguatrib conjugates with distinct alkyl chain lengths – i.e. C12, C14, C16, and C18 – was synthesized, and the MGMT depleting activity as well as cytotoxicity were determined on relevant mouse and human glioma cell lines. Drug-containing liposomes were prepared and characterized in terms of loading and in vitro release kinetics. The lipophilic lomeguatrib conjugates did not exert cytotoxic effects at 5 μM in the mouse glioma cell line and exhibited a similar MGMT depleting activity pattern as lomeguatrib. Overall, drug loading could be improved by up to 50-fold with the lipophilic conjugates, and the slowest leakage was achieved with the C18 derivative. The present data show the applicability of lipophilic lomeguatrib derivatization for incorporation into liposomes, and identify the C18 derivative as the lead compound for in vivo studies.

Regulation of the Tumor-Suppressor BECLIN 1 by Distinct Ubiquitination Cascades.

Autophagy contributes to cellular homeostasis through the degradation of various intracellular targets such as proteins, organelles and microbes. This relates autophagy to various diseases such as infections, neurodegenerative diseases and cancer. A central component of the autophagy machinery is the class III phosphatidylinositol 3-kinase (PI3K-III) complex, which generates the signaling lipid phosphatidylinositol 3-phosphate (PtdIns3P). The catalytic subunit of this complex is the lipid-kinase VPS34, which associates with the membrane-targeting factor VPS15 as well as the multivalent adaptor protein BECLIN 1. A growing list of regulatory proteins binds to BECLIN 1 and modulates the activity of the PI3K-III complex. Here we discuss the regulation of BECLIN 1 by several different types of ubiquitination, resulting in distinct polyubiquitin chain linkages catalyzed by a set of E3 ligases. This contribution is part of the Special Issue “Ubiquitin System”.

Conformational Clusters of Phosphorylated Tyrosine.

Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.

Cross-reactivity in β-Lactam Allergy

β-Lactam drugs (penicillins, amoxicillin, and cephalosporins) account for 42.6% of all severe drug-induced anaphylaxis. In this review, we focus on clinically significant immunologic cross-reactivity in patients with confirmed penicillin allergy to cephalosporins, and the structural involvement of the R1 and R2 chemical side chains of the cephalosporins causing IgE-mediated cross-reactivity with penicillin and other cephalosporins. Skin tests predict IgE-mediated reactions and showed cross-reactivity between penicillins and early generation cephalosporins that shared side chains, but confirmatory challenge data are lacking. Later-generation cephalosporins, which have distinct side chains, do not have any skin test cross-reactivity with penicillin/amoxicillin. There is debate as to the involvement of R2 side chains as the antigenic determinants that cause IgE-mediated hypersensitivity with various cephalosporins. Avoidance of cephalosporins, when they are the drug of choice in a penicillin-allergic individual, results in significant morbidity that outweighs the low risk of anaphylaxis. We conclude that there is ample evidence to allow the safe use of cephalosporins in patients with isolated confirmed penicillin or amoxicillin allergy.

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab.

Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å2, which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface.

An Innovative Approach to Detect Isomorphism in Planar and Geared Kinematic Chains Using Graph Theory

Detection of isomorphism in planar and geared kinematic chains (GKCs) is an interesting area since many years. Enumeration of planar and geared kinematic chains becomes easy only when isomorphism problem is resolved effectively. Many researchers proposed algorithms based on topological characteristics or some coding which need lot of computations and comparisons. In this paper, a novel and simple algorithm is proposed based on graph theory by which elimination of isomorphic chains can be done very easily without any tedious calculations or comparisons. A new concept “Net distance” is proposed based on the graph theory to be a quantitative measure to assess isomorphism in planar kinematic chains (PKCs) as well as GKCs. The proposed algorithm is applied on nine-link two-degrees-of-freedom (DOF) distinct kinematic chains completely and the results are presented. Algorithm is tested on examples from eight-link 1-DOF, ten-link 1-DOF, 12-link 1-DOF, and 15link 4-DOF PKCs. The algorithm is also tested on four-, six-link 1-DOF GKCs to detect isomorphism. All the results are in agreement with the existing literature.

Optimal dual-channel supply chain configuration for product categories with different customer preference of online channel

This study addresses the supply chain configuration problem of manufacturer faced with multiple channel choices. We investigate the optimal combination of traditional and online sales channels for different product categories with differing customer preference of the online channel. We have considered three distinct dual-channel supply chain configurations comprising of a manufacturer, a traditional channel and an online channel viz. retailer–e-tailer; company store–e-tailer; and retailer–e-marketplace. As the manufacturer will face a quantity allocation decision between traditional and online channels, the competition is modeled using Cournot model with the manufacturer as the Stackelberg leader. Values of optimal order quantity and price for the different entities have been established. Influence of variation in customer preference of online channel on the optimal policies is also examined. We find that the manufacturer prefers retailer–e-marketplace configuration for products with high customer preference of online channel and company store–e-tailer configuration for products with low customer preference of online channel. In addition, we find that the retailer–e-tailer configuration is dominated by company store–e-tailer and retailer–e-marketplace configuration irrespective of the product’s customer preference of online channel.

Novel CH1:CL interfaces that enhance correct light chain pairing in heterodimeric bispecific antibodies.

Targeting two unique antigens with a single bispecific antibody is an attractive approach with potential broad therapeutic applicability. However, the production of heterodimeric bispecific antibodies (bsAbs) presents a challenge, requiring the co-expression and accurate pairing of two distinct heavy and light chain units. Several undesirable by-products can be formed in the production process, including heavy chain homodimers and non-cognate light chain pairings. Although additional downstream purification methods exist, they are often time consuming and restrict practical large-scale production. In this study, we identify and validate novel Fab interface mutations that increase cognate light chain pairing efficiencies within heterodimeric bsAbs. Importantly, the variable domains remain unaltered as interface mutations were restricted to the CH1 and CL domains. We performed several biochemical assays to demonstrate that the novel engineered interfaces do not adversely impact bispecific antibody expression, stability, affinity and biological function. The designs reported here can easily be applied in a generic manner to use existing antibodies as building blocks for bsAbs which will help to accelerate the identification and production of next generation bispecific antibody therapeutics.

New morphological mapping and interpretation of ejecta deposits from Orientale Basin on the Moon

Orientale Basin is one of the youngest and best-preserved multi-ring impact basins in the Solar System. The structure is ∼950 km across and is located on the western edge of the nearside of the Moon. The interior of the basin, which possesses three distinct rings and a post-impact mare fill, has been studied extensively using modern high-resolution datasets. Exterior to these rings, Orientale has an extensive ejecta blanket that extends out radially for at least 800 km from the basin rim in all directions and covers portions of both the nearside and farside of the Moon. These deposits, known as the Hevelius Formation, were first mapped using photographic data from the Lunar Orbiter IV probe. In this study, we map in detail the morphology of each distinct facies observed within the Orientale ejecta blanket using high resolution Lunar Reconnaissance Orbiter (LRO) Wide Angle Camera (WAC) and Narrow Angle Camera (NAC) images and Lunar Orbiter Laser Altimeter (LOLA) elevation data. We identified 5 unique facies within the ejecta blanket. Facies A is identified as a region of hummocky plains located in a low-lying topographic region between the Outer Rook and Cordillera rings. This facies is interpreted to be a mix of crater-derived impact melt and km-scale blocks of ballistic ejecta and host rock broken up during the modification stage and formation of the Cordillera ring. Facies B is an inner facies marked by radial grooves extending outward from the direction of the basin center. This facies is interpreted as the continuous ballistic ejecta blanket. Facies C consists of inner and outer groupings of flat smooth-surfaced deposits isolated in local topographic lows. Facies D displays characteristic sinuous ridges and lobate extensions. Facies C and D are interpreted to be impact melt-rich materials, which manifest as flows and ponds. Our observations suggest that these facies were emplaced subsequent to the ballistic ejecta blanket – most likely during the modification stage of crater formation – and flowed and ponded in topographically low-lying regions. Facies E consists of distinct crater chains emanating radially from the basin center and extending from ∼700 to ∼1000 km from the center of Orientale. This facies is considered to be chains of secondary craters formed from large blocks of ballistic ejecta. Our mapping effort shows that the individual ejecta facies were influenced and controlled to varying degrees by pre-existing slopes and topography. At the basin scale, the overall downslope direction toward the lunar lowlands to the east and southeast of the basin center resulted in large impact melt flows 100's of kilometers in length, while the regional upslope trends in the west and northwest inhibited the development of extensive impact melt flows. On a smaller scale it can be observed that ground-hugging ejecta collected behind and flowed around high topographic obstacles while diverting into topographic low regions (e.g., around uplifted pre-existing crater rims, but down into pre-existing crater floors).The dispersion of the various ejecta facies mapped here also indicates both a direction and an angle for the impact event that formed Orientale Basin. The bilateral distribution of both ballistic and impact melt-rich ejecta deposits across a line running northeast – southwest suggests the impact occurred from the northeast toward the southwest. Careful mapping of the secondary impact crater chains (Facies E) shows the development of a “forbidden zone” lacking these impacts to the northeast as well as a concentration of the longest secondary crater chains to the northwest and southeast, perpendicular to the aforementioned line of bilateral ejecta distribution. This distribution of secondary impact craters contrasts with the circularity of the basin and suggests that Orientale Basin was formed by ∼ 25–45° impact from the northeast.