Modeling the three-dimensional structure of the monocyte chemo-attractant and activating protein MCAF/MCP-1 on the basis of the solution structure of interleukin-8

A model of the three-dimensional structure of the monocyte chemo-attractantand activating protein MCAF/MCP-1 is presented. The model ispredicted based on the previously determined solution structureof interleukin-8 (IL-8/NAP-1) [Clore, G.M., Appella, E., Yamada,M., Matsushima, K. and Gronenborn, A.M. (1990) Biochemistry29, 1689–1696]. Both proteins belong to a superfamilyof cytokine proteins involved in cell-specific chemotaxis, hostdefense and the inflammatory response. The amino acid sequenceidentity between the two proteins is 24%. It is shown that theregular secondary structure elements of the parent structurecan be retained in the modeled structure, such that the backbonehydrogen bonding pattern is very similar in the two structures.The polypeptide backbone is superimposable with an atomic r.m.s.difference of 0.9 Å and all side chains can be modeledby transferring the parent side chain conformation to the newstructure. Thus, the deduced structure, like the parent one,is a dimer and consists of a six-stranded antiparallel /3-sheet,formed by two three-stranded Greek keys, one from each monomer,upon which lie two symmetry-related antiparallel a-helices,24 Å long and separated by 14 Å. All amino acidsequence changes can be accommodated within the parent polypeptideframework without major rearrangements. This is borne out bythe fact that the IL-8/NAP-1 and modeled MCAF/MCP-1 structureshave similar non-bonding energies. These results strongly suggestthat both proteins and all other members of the superfamilymost likely have the same tertiary structure. Analysis of thedistribution of the solvent-exposed residues can be interpretedin the context of the different receptors involved in mediatingthe specific responses to both proteins and suggests that thedifferent activities of the two proteins, namely neutrophil(IL-8) versus monocyte (MCAF/MCP-1) activation and chemotaxis,reside in the specific arrangements of amino acid side chainspointing outwards from and lying in the cleft between the twoexposed long a-helices.     

A two-stage heuristic for multi-activity and task assignment to work shifts

The multi-activity assignment problem consists of assigning interruptible activities to given work shifts so as to match as much as possible for each activity a demand curve in function of time. In this paper we consider an extension to this problem, called the multi-activity and task assignment problem, that additionally considers the assignment of uninterruptible pieces of work, called tasks. These possess properties such as worker qualifications, time windows for completion, fixed lengths and precedence relationships. We propose a mixed-integer programming formulation and a two-stage method to solve this problem. The first stage consists of an approximation mixed-integer programming model to assign tasks approximately taking into account the activities and the second involves a column generation heuristic for assigning activities and reassigning tasks at the same time. We suggest four different strategies for reassigning tasks. We conducted extensive computational tests on randomly generated instances in order to validate our method and to compare the various strategies. One strategy proved universally best when compared to the other three policies.     

Study on highly thermostable low-k polymer films based on fluorene-containing polyetherimides

Highly thermostable low-k polymer films with potential applications as dielectric materials in microelectronic industry were synthesized starting from 9,9-bis[4-(3,4-dicarboxyphenoxy)phenyl]fluorene dianhydride and various diamines. A polyetherimide/silica nanocomposite film was obtained using methyltriethoxysilane as precursor of inorganic phase. The chemical structure was confirmed by FTIR and ¹H NMR spectroscopy. Water vapor's sorption capacity, thermal stability, glass transition temperature, thermal diffusivity, specific heat, thermal conductivity, and dielectric characteristics of the films were determined. All the films exhibited excellent thermal stability, with an initial decomposition temperature in the range of 500–530°C. They showed low dielectric constant of 1.98–2.86 and low dielectric loss of 0.0037–0.011, at a frequency of 1 Hz and room temperature. The subglass γ- and β-relaxations, primary α-relaxation, and conductivity relaxation processes were discussed according to the chemical structure of the samples. Quantitative structure–property relationship (QSPR) study was conducted, and linear regression models were formulated to describe the causal relationships between different parameters and polyetherimide properties.     

Fuzzy semantics for direction relations between composite regions

This paper proposes a model that combines qualitative spatial reasoning with fuzzy semantic typing to derive direction relations between two composite regions in a spatial configuration. It extends Goyal and Egenhofer’s direction relation model, initially proposed for simple regions, towards composite regions. A fuzzy semantics typing qualifies the overall direction relations of two composite regions. We introduce flexible fuzzy measures that allow for both a qualitative and metric study of direction relation similarities.     

New Investigations with Lupane Type A-Ring Azepane Triterpenoids for Antimycobacterial Drug Candidate Design

Twenty lupane type A-ring azepano-triterpenoids were synthesized from betulin and its related derivatives and their antitubercular activity against Mycobacterium tuberculosis, mono-resistant MTB strains, and nontuberculous strains Mycobacterium abscessus and Mycobacterium avium were investigated in the framework of AToMIc (Anti-mycobacterial Target or Mechanism Identification Contract) realized by the Division of Microbiology and Infectious Diseases, NIAID, National Institute of Health. Of all the tested triterpenoids, 17 compounds showed antitubercular activity and 6 compounds were highly active on the H37Rv wild strain (with MIC 0.5 µM for compound 7), out of which 4 derivatives also emerged as highly active compounds on the three mono-resistant MTB strains. Molecular docking corroborated with a machine learning drug-drug similarity algorithm revealed that azepano-triterpenoids have a rifampicin-like antitubercular activity, with compound 7 scoring the highest as a potential M. tuberculosis RNAP potential inhibitor. FIC testing demonstrated an additive effect of compound 7 when combined with rifampin, isoniazid and ethambutol. Most compounds were highly active against M. avium with compound 14 recording the same MIC value as the control rifampicin (0.0625 µM). The antitubercular ex vivo effectiveness of the tested compounds on THP-1 infected macrophages is correlated with their increased cell permeability. The tested triterpenoids also exhibit low cytotoxicity and do not induce antibacterial resistance in MTB strains.     

Time-Dependent Molecular Motifs of Pulmonary Fibrogenesis in COVID-19

(1) Background: In COVID-19 survivors there is an increased prevalence of pulmonary fibrosis of which the underlying molecular mechanisms are poorly understood; (2) Methods: In this multicentric study, n = 12 patients who succumbed to COVID-19 due to progressive respiratory failure were assigned to an early and late group (death within ≤7 and >7 days of hospitalization, respectively) and compared to n = 11 healthy controls; mRNA and protein expression as well as biological pathway analysis were performed to gain insights into the evolution of pulmonary fibrogenesis in COVID-19; (3) Results: Median duration of hospitalization until death was 3 (IQR25-75, 3–3.75) and 14 (12.5–14) days in the early and late group, respectively. Fifty-eight out of 770 analyzed genes showed a significantly altered expression signature in COVID-19 compared to controls in a time-dependent manner. The entire study group showed an increased expression of BST2 and IL1R1, independent of hospitalization time. In the early group there was increased activity of inflammation-related genes and pathways, while fibrosis-related genes (particularly PDGFRB) and pathways dominated in the late group; (4) Conclusions: After the first week of hospitalization, there is a shift from pro-inflammatory to fibrogenic activity in severe COVID-19. IL1R1 and PDGFRB may serve as potential therapeutic targets in future studies.     

IPACT a dynamic protocol for an Ethernet PON (EPON)

We investigate design issues for access networks based on passive optical network technology. A PON based on polling, with data encapsulated in Ethernet frames, possesses many desirable qualities, such as dynamic bandwidth distribution, use of a single downstream and a single upstream wavelength, ability to provision a fractional wavelength capacity to each user, and ease of adding a new user. To support dynamic bandwidth distribution, we propose an interleaved polling algorithm called IPACT. We also suggest a scheme for in-band signaling that allows using a single wavelength for both downstream data and control message transmission. To obtain realistic simulation results, we generated synthetic traffic that exhibits the properties of self-similarity and long-range dependence. We then analyzed the network performance under varying offered loads     

Slow filament dynamics and viscoelasticity in entangled and active actin networks

This paper deals with correlations between the viscoelastic impedance of entangled actin networks and the slow conformational dynamics and diffusive motions of single filaments. The single filament dynamics is visualized and analysed by analysing the Brownian motion of attached colloidal beads, which enables independent measurements of characteristic viscoelastic response times such as the entanglement and reptation times. We further studied the frequency-dependent viscoelastic impedance of active actin-heavy-meromyosin II networks by magnetic-tweezers microrheometry to gain insight into the effect of such highly dynamic and force-generating crosslinkers (exhibiting bond lifetimes of less than 1 s) on the rheological properties. We show that at high frequencies (higher than 1 Hz) the viscoelastic loss modulus is slightly increased relative to the entangled network (associated with an increase in the energy dissipated during mechanical excitations), while at low frequencies the plateau of the impedance spectrum becomes more pronounced as a consequence of the cross-linking of the network and the suppression of the terminal regime. Our data provide evidence that the myosin motor protein may play a role as softener of the actin cortex, enabling the adaptive reduction of the yield stress of cells and thus facilitating cellular deformations.     

Differences in CLA isomer distribution of cow's milk lipids

The uniqueness of ruminant milk lipids is based on their high concentration of CLA. Maximal CLA concentrations in milk lipids require optimal conditions of ruminal fermentation and substrate availability, conditions like those present in pasture-fed cows. Our previous work showed that farm management (indoor feeding vs. pasture feeding) markedly influenced the CLA concentration. In this study, the objective was to evaluate the influence of the farm management system as dependent on different locations. Milk samples from different locations (Thuringia and the Alps, representing diverse altitudes) were collected during the summer months and analyzed for FA profile and CLA isomer distribution. The proportion of PUFA and total CLA in milk fat was significantly lower in milk from indoor cows compared with the pasture cows in the Alps. The trans-11 18∶1 in milk fat of Alpine cows was elevated, in contrast to lower values for trans-10 18∶1. Milk from cows grazing pasture in the Alps was higher in EPA and lower in arachidonic acid than milk from indoor-fed cows. The proportion of cis,trans/trans,cis isomers of CLA was 10 times higher from the indoor cows than from the Alpine cows. In addition to the major isomer cis-9,trans-11, this difference also occurred for the trans-11,cis-13 isomer, which represented more than a fourth of the total CLA present in milk fat. This is the first report showing a special isomer distribution in the milk fat of cows living under very natural conditions. We hypothesize that the CLA isomer trans-11,cis-13 is formed in large quantity as a result of grazing mountain pasture, which is rich in α-linolenic acid.     

Applied macroinorganics. IV. Effect of the crosslinking agent on protonation,and metal ions complexing abilities,of ion exchange resins with poly(amido–amine) structure

Two classes of resins, having a poly(amido–amine) structure, have been synthesized. The basicity constants and the complexing abilities toward copper (II) and nickel (II) ions have been investigated by potentiometric techniques. The influence of the nature of the crosslinking agent on the basicities and the complexing abilities has been studied.