Search results for: molecular biology

Authors: Stefanie Ficht, Lukas Schübel, Magdalena Kleybolte, Markus Eblenkamp, Jana Steger, Dirk Wilhelm, Petra Mela

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Although 3D printing as transformative technology has become of increasing interest in the medical field and the demand for biodegradable polymers has developed to a considerable extent, there are only a few additively manufactured, biodegradable implants on the market. Additionally, the sterilization of such implants and its side effects on degradation have still not been sufficiently studied. Within this work, thermosensitive poly p-dioxanone (PPDO) samples were printed with fused filament fabrication (FFF) and investigated. Subsequently, H₂O₂ plasma and gamma radiation were used as low-temperature sterilization techniques and compared among each other and the control group (no sterilization). In order to assess the effect of different sterilization on the degradation behavior of PPDO, the samples were immersed in phosphate-buffered solution (PBS) over 28 days, and surface morphology, thermal properties, molecular weight, inherent viscosity, and mechanical properties were examined at regular time intervals. The study demonstrates that PPDO was printed with great success and that thermal properties, molecular weight (Mw), and inherent viscosity (IV) were not significantly affected by the printing process itself. H₂O₂ plasma sterilization did not significantly harm the thermosensitive polymer, while gamma radiation lowered IV and Mw statistically significantly compared to the control group (p < 0.001). During immersion in PBS, a decrease in Mw and mechanical strength occurred for all samples. However, gamma sterilized samples were affected to a much higher extent compared to the two other sample groups both in final values and timeline. This was confirmed by scanning electron microscopy showing no changes of surface morphology of (non-sterilized) control samples, first microcracks appearing on plasma sterilized samples after two weeks while being present on gamma sterilized samples already immediately after radiation to then further deteriorate over immersion duration. To conclude, we demonstrated that FFF and H₂O₂ plasma sterilization are well suited for processing thermosensitive, biodegradable polymers used for the development of innovative short-term medical applications.

Keywords: additive manufacturing, sterilization, biodegradable, thermosensitive, medical application

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Authors: Jong Il Rhee

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The polypeptide representing the mature part of human BMP-7 was cloned and efficiently expressed in Escherichia coli and Bacillus subtilis, which had a clear band for hBMP-7, a homodimeric protein with an apparent molecular weight of 15.4 kDa. Recombinant E.coli produced 111 pg hBMP-7/mg of protein hBMP-7 through IPTG induction. Recombinant B. subtilis also produced 350 pg hBMP-7/ml of culture medium. The hBMP-7 was purified in 2 steps using an FPLC system with an ion exchange column and a gel filtration column. The hBMP-7 produced in this work also stimulated the alkaline phosphatase (ALP) activity in a dose-dependent manner, i.e. 2.5- and 8.9-fold at 100 and 300 ng hBMP-7/ml, respectively, and showed intact biological activity.

Keywords: B. subtilis, E. coli, fermentation, hBMP-7

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Authors: Anitha Kandasamy, Thirumurugan Ramaiah

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Interestingly, organic materials exhibit large optical nonlinearity with quick responses and having the flexibility of molecular tailoring using computational modelling and favourable synthetic methodologies. Pyridine based organic compounds and carboxylic acid contained aromatic compounds play a crucial role in crystal engineering of NCS complexes that displays admirable optical nonlinearity with fast response and favourable physicochemical properties such as low dielectric constant, wide optical transparency and large laser damage threshold value requires for optoelectronics device applications. Based on these facts, it was projected to form an acentric molecule of π-conjugated system interaction with appropriately replaced electron donor and acceptor groups for achieving higher SHG activity in which quinoline-2-carboyxlic acid is chosen as an electron acceptor and capable of acting as an acid as well as a base molecule, while 2-amino-4-methylpyridine is used as an electron donor and previously employed in numerous proton transfer complexes for synthesis of NLO materials for optoelectronic applications. 2-amino-4-mehtylpyridinium quinoline-2-carboxylate molecular complex (2AQ) is having π-donor-acceptor groups in which 2-amino-4-methylpyridine donates one of its electron to quinoline -2-carboxylic acid thereby forming a protonated 2-amino-4-methyl pyridinium moiety and mono ionized quinoline-2-carboxylate moiety which are connected via N-H…O intermolecular interactions with non-centrosymmetric crystal packing arrangement at microscopic scale is accountable to the enhancement of macroscopic second order NLO activity. The 2AQ crystal was successfully grown by a slow evaporation solution growth technique and its structure was determined in orthorhombic crystal system with acentric, P212121, space group. Hirshfeld surface analysis reveals that O…H intermolecular interactions primarily contributed with 31.0 % to the structural stabilization of 2AQ. The molecular structure of title compound has been confirmed by 1H and 13C NMR spectral studies. The vibrational modes of functional groups present in 2AQ have been assigned by using FTIR and FT-Raman spectroscopy. The grown 2AQ crystal exhibits high optical transparency with lower cut-off wavelength (275 nm) within the region of 275-1500 nm. The laser study confirmed that 2AQ exhibits high SHG efficiency of 12.6 times greater than that of KDP. TGA-DTA analysis revealed that 2AQ crystal had a thermal stability of 223 °C. The low dielectric constant and low dielectric loss at higher frequencies confirmed good crystalline nature with fewer defects of grown 2AQ crystal. The grown crystal exhibits soft material and positive photoconduction behaviour. Mulliken atomic distribution and FMOs analysis suggested that the strong intermolecular hydrogen bonding which lead to the enhancement of NLO activity. These properties suggest that 2AQ crystal is a suitable material for optoelectronic and laser frequency conversion applications.

Keywords: crystal growth, NLO activity, proton transfer complex, quantum chemical investigation

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Authors: Peyman Sheikholharam Mashhadi

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Difficulties in analyzing real world images in classical image processing and machine vision framework have motivated researchers towards considering the biology-based vision. It is a common belief that mammalian visual cortex has been adapted to the statistics of the real world images through the evolution process. There are two well-known successful models of mammalian visual cortical cells: Independent Component Analysis (ICA) and Independent Subspace Analysis (ISA). In this paper, we statistically analyze the dependencies which remain in the components after applying these models to the natural images. Also, we investigate the response of feature detectors to gratings with various parameters in order to find optimal parameters of the feature detectors. Finally, the selectiveness of feature detectors to phase, in both models is considered.

Keywords: statistics, independent component analysis, independent subspace analysis, phase, natural images

Procedia PDF Downloads 339

Authors: Don Anushka Sandaruwan Elvitigala, P. D. S. U. Wickramasinghe, Jehee Lee

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Cystatins are a large superfamily of proteins which act as reversible inhibitors of cysteine proteases. Papain proteases and cysteine cathepsins are predominant substrates of cystatins. Cystatin superfamily can be further clustered into three groups as Stefins, Cystatins, and Kininogens. Among them, stefines are also known as family 1 cystatins which harbors cystatin Bs and cystatin As. In this study, a homologue of family one cystatins more close to cystatin Bs was identified from Korean black rockfish (Sebastes schlegeli) using a prior constructed cDNA (complementary deoxyribonucleic acid) database and designated as RfCyt1. The full-length cDNA of RfCyt1 consisted of 573 bp, with a coding region of 294 bp. It comprised a 5´-untranslated region (UTR) of 55 bp, and 3´-UTR of 263 bp. The coding sequence encodes a polypeptide consisting of 97 amino acids with a predicted molecular weight of 11kDa and theoretical isoelectric point of 6.3. The RfCyt1 shared homology with other teleosts and vertebrate species and consisted conserved features of cystatin family signature including single cystatin-like domain, cysteine protease inhibitory signature of pentapeptide (QXVXG) consensus sequence and N-terminal two conserved neighboring glycine (⁸GG⁹) residues. As expected, phylogenetic reconstruction developed using the neighbor-joining method showed that RfCyt1 is clustered with the cystatin family 1 members, in which more closely with its teleostan orthologues. An SYBR Green qPCR (quantitative polymerase chain reaction) assay was performed to quantify the RfCytB transcripts in different tissues in healthy and immune stimulated fish. RfCyt1 was ubiquitously expressed in all tissue types of healthy animals with gill and spleen being the highest. Temporal expression of RfCyt1 displayed significant up-regulation upon infection with Aeromonas salmonicida. Recombinantly expressed RfCyt1 showed concentration-dependent papain inhibitory activity. Collectively these findings evidence for detectable protease inhibitory and immunity relevant roles of RfCyt1 in Sebastes schlegeli.

Keywords: Sebastes schlegeli, family 1 cystatin, immune stimulation, expressional modulation

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Authors: Mateen A Khan, Taj Mohammad, Md. Imtaiyaz Hassan

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Alzheimer’s disease is characterized by the accumulation of the processing products of the amyloid beta peptide cleaved by amyloid precursor protein (APP). Iron increases the synthesis of amyloid beta peptides, which is why iron is present in Alzheimer's disease patients' amyloid plaques. Iron misregulation in the brain is linked to the overexpression of APP protein, which is directly related to amyloid-β aggregation in Alzheimer’s disease. The APP 5'-UTR region encodes a functional iron-responsive element (IRE) stem-loop that represents a potential target for modulating amyloid production. Targeted regulation of APP gene expression through the modulation of 5’-UTR sequence function represents a novel approach for the potential treatment of AD because altering APP translation can be used to improve both the protective brain iron balance and provide anti-amyloid efficacy. The molecular docking analysis of APP IRE RNA with eukaryotic translation initiation factors yields several models exhibiting substantial binding affinity. The finding revealed that the interaction involved a set of functionally active residues within the binding sites of eIF4F. Notably, APP IRE RNA and eIF4F interaction were stabilized by multiple hydrogen bonds with residues of APP IRE RNA and eIF4F. It was evident that APP IRE RNA exhibited a structural complementarity that tightly fit within binding pockets of eIF4F. The simulation studies further revealed the stability of the complexes formed between RNA and eIF4F, which is crucial for assessing the strength of these interactions and subsequent roles in the pathophysiology of Alzheimer’s disease. In addition, MD simulations would capture conformational changes in the IRE RNA and protein molecules during their interactions, illustrating the mechanism of interaction, conformational change, and unbinding events and how it may affect aggregation propensity and subsequent therapeutic implications. Our binding studies correlated well with the translation efficiency of APP mRNA. Overall, the outcome of this study suggests that the genomic modification and/or inhibiting the expression of amyloid protein by targeting APP IRE RNA can be a viable strategy to identify potential therapeutic targets for AD and subsequently be exploited for developing novel therapeutic approaches.

Keywords: Alzheimer's disease, Protein-RNA interaction analysis, molecular docking simulations, conformational dynamics, binding stability, binding kinetics, protein synthesis.

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Authors: R. I. You, C. L. Ho, M. S. Dai, H. M. Hung, S. F. Yen, C. S. Chen, T. Y. Chao

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Neutrophils are the most abundant innate immune cells to against invading microorganisms. Numerous data shown neutrophils have plasticity in response to physiological and pathological conditions. Tumor-associated neutrophils (TAN) exist in distinct types of tumor and play an important role in cancer biology. Different transcriptomic profiles of neutrophils in tumor and non-tumor samples have been identified. Several miRNAs have been recognized as regulators of gene expression in neutrophil, which may have key roles in neutrophil activation. However, the miRNAs expression patterns in TAN are not well known. To address this question, magnetic bead isolated neutrophils from tumor-bearing mice were used in this study. We analyzed production of reactive oxygen species (ROS) by luminol-dependent chemiluminescence assay. The expression of miRNAs targeting NADPH oxidase, ROS generation and autophagy was explored using quantitative real-time polymerase chain reaction. Our data suggest that tumor environment influence neutrophil develop to differential states of activation via miRNAs regulation.

Keywords: tumor-associated neutrophil, miRNAs, neutrophil, ROS

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Authors: Restu Misrianti

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The amino acid variation of Asn (allele A) at position 631 in Mx gene was specific to positive antiviral to avian viral desease. This research was aimed at identifying polymorphism of Mx gene in duck using molecular technique. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique was used to select the genotype of AA, AG and GG. There were thirteen duck from Indragiri Hulu regency (Riau Province) used in this experiment. DNA amplification results showed that the Mx gene in duck is found in a 73 bp fragment. Mx gene in duck did not show any polymorphism. The frequency of the resistant allele (AA) was 0%, while the frequency of the susceptible allele (GG) was 100%.

Keywords: duck, Mx gene, PCR, RFLP

Procedia PDF Downloads 324

Authors: I. Belyamani, M. K. Hassan, J. U. Otaigbe, W. R. Fielding, K. A. Mauritz, J. S. Wiggins, W. L. Jarrett

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We have investigated the flame-retardant efficiency of special new phosphate glass (P-glass) compositions having different glass transition temperatures (Tg) on the processing conditions of polyamide 6,6 (PA6,6) and the final hybrid flame retardancy (FR). We have showed that the low Tg P glass composition (i.e., ILT 1) is a promising flame retardant for PA6,6 at a concentration of up to 15 wt. % compared to intermediate (IIT 3) and high (IHT 1) Tg P glasses. Cone calorimetry data showed that the ILT 1 decreased both the peak heat release rate and the total heat amount released from the PA6,6/ILT 1 hybrids, resulting in an efficient formation of a glassy char layer. These intriguing findings prompted to address several questions concerning the mechanism of action of the different P glasses studied. The general mechanism of action of phosphorous based FR additives occurs during the combustion stage by enhancing the morphology of the char and the thermal shielding effect. However, the present work shows that P glass based FR additives act during melt processing of PA6,6/P glass hybrids. Dynamic mechanical analysis (DMA) revealed that the Tg of PA6,6/ILT 1 was significantly shifted to a lower Tg (~65 oC) and another transition appeared at high temperature (~ 166 oC), thus indicating a strong interaction between PA6,6 and ILT 1. This was supported by a drop in the melting point and crystallinity of the PA6,6/ILT 1 hybrid material as detected by differential scanning calorimetry (DSC). The dielectric spectroscopic investigation of the networks’ molecular level structural variations (i.e. hybrids chain motion, Tg and sub-Tg relaxations) agreed very well with the DMA and DSC findings; it was found that the three different P glass compositions did not show any effect on the PA6,6 sub-Tg relaxations (related to the NH2 and OH chain end groups motions). Nevertheless, contrary to IIT 3 and IHT 1 based hybrids, the PA6,6/ILT 1 hybrid material showed an evidence of splitting the PA6,6 Tg relaxations into two peaks. Finally, the CPMAS 31P-NMR data confirmed the miscibility between ILT 1 and PA6,6 at the molecular level, as a much larger enhancement in cross-polarization for the PA6,6/15%ILT 1 hybrids was observed. It can be concluded that compounding low Tg P-glass (i.e. ILT 1) with PA6,6 facilitates hydrolytic chain scission of the PA6,6 macromolecules through a potential chemical interaction between phosphate and the alpha-Carbon of the amide bonds of the PA6,6, leading to better flame retardant properties.

Keywords: broadband dielectric spectroscopy, composites, flame retardant, polyamide, phosphate glass, sustainable

Procedia PDF Downloads 236

Authors: Sayani Chatterjee, Kusum Lata Pangtey, Sarita Singh, Harvir Singh

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Biodegradation leads to a systematic alteration of the chemical and physical properties of crude oil showing sequential depletion of n-alkane, cycloalkanes, aromatic which increases its specific gravity, viscosity and the abundance of heteroatom-containing compounds. The biodegradation leads to a change in the molecular fingerprints and geochemical parameters of degraded oils, thus make source and maturity identification inconclusive or ambiguous. Asphaltene is equivalent to the most labile part of the respective kerogen and generally has high molecular weight. Its complex chemical structure with substantial microporous units makes it suitable to occlude the hydrocarbon expelled from the source. The occluded molecules are well preserved by the macromolecular structure and thus prevented from secondary alterations. They retain primary organic geochemical information over the geological time. The present study involves the extraction of this occluded hydrocarbon from the asphaltene cage through mild oxidative degradation using mild oxidative reagents like Hydrogen Peroxide (H₂O₂) and Acetic Acid (CH₃COOH) on purified asphaltene of the biodegraded oils of Mansa, Lanwa and Santhal fields in Cambay Basin. The study of these extracted occluded hydrocarbons was carried out for establishing oil to oil and oil to source correlation in the Mehsana block of Cambay Basin. The n-alkane and biomarker analysis through GC and GC-MS of these occluded hydrocarbons show similar biomarker imprint as the normal oil in the area and hence correlatable with them. The abundance of C29 steranes, presence of Oleanane, Gammacerane and 4-Methyl sterane depicts that the oils are derived from terrestrial organic matter deposited in the stratified saline water column in the marine environment with moderate maturity (VRc 0.6-0.8). The oil source correlation study suggests that the oils are derived from Jotana-Warosan Low area. The developed geochemical technique to extract the occluded hydrocarbon has effectively resolved the ambiguity that resulted from the inconclusive fingerprint of the biodegraded oil and the method can be also applied in other biodegraded oils as well.

Keywords: asphaltene, biomarkers, correlation, mild oxidation, occluded hydrocarbon

Procedia PDF Downloads 158

Authors: Fakhreldin O. Suliman, Alia H. Al-Battashi

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This work explored the interaction of three different imidazoline drugs, naphazoline nitrate (NPH), oxymetazoline hydrochloride (OXY) and xylometazoline hydrochloride (XYL) with two different synthesized cucurbit[n]urils CB[n], cucurbit[7]uril (CB[7]) and cucuribit[8]uril (CB[8]). Three binary inclusion complexes have been investigated in solution and in the solid state. The solid complexes were obtained by lyophilization, whereas the physical mixtures of guests and hosts at a stoichiometric ratio of 1:1 were obtained for each drug. 1HNMR, electrospray ionization mass spectrometry (ESI-MS), and matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry was used to study the complexes prepared in aqueous media. The lyophilized solid complexes were characterized by Fourier transform-infrared spectroscopy (FT-IR), powder X-ray diffractometry (PXRD), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). MS, FT-IR and PXRD experimental results established in this work reveal that NPH, OXY and XYL molecules form stable inclusion complexes with the two hosts. The TGA and DSC confirmed the enhancement of the thermal stability of each drug and the production of a thermally stable solid complex. The 1HNMR has shown that the protons of the guests faced shifting in ppm and broadening of their peaks upon the formation of inclusion complexes with the selected CB[n]. The aromatic protons of the guest exhibited the highest changes in the chemical shifts and shape of the NMR peaks, suggesting their inclusion into the cavity of the CB[n]. The diffusion coefficients (D), developed from the diffusion-controlled NMR Spectroscopy (DOSY) measurements, for the complexation of the selected imidazoline drugs with CB[7] and CB[8], were decreased in the presence of hosts compared to the free guests indicating the formation of the guest-host adduct. Furthermore, we conducted molecular dynamic simulations and quantum mechanics calculations on these complexes. The results of the theoretical study corroborate the experimental findings and have also shed light on the mechanism of inclusion of the guests into the two hosts. This study generates initial data for potential drug delivery or drug formulation systems for these three selected imidazoline drug compounds based on their inclusion into the CB[n] cavities.

Keywords: cucurbit[n]urils, imidazoline, inclusion complexes, molecular dynamics, DFT calculations, mass spectrometry

Procedia PDF Downloads 68

Authors: Viktor Kochkodan

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The main problem arising upon water treatment and desalination using pressure driven membrane processes such as microfiltration, ultrafiltration, nanofiltration and reverse osmosis is membrane fouling that seriously hampers the application of the membrane technologies. One of the main approaches to mitigate membrane fouling is to minimize adhesion interactions between a foulant and a membrane and the surface coating of the membranes with polyelectrolytes seems to be a simple and flexible technique to improve the membrane fouling resistance. In this study composite polyamide membranes NF-90, NF-270, and BW-30 were modified using electrostatic deposition of polyelectrolyte multilayers made from various polycationic and polyanionic polymers of different molecular weights. Different anionic polyelectrolytes such as: poly(sodium 4-styrene sulfonate), poly(vinyl sulfonic acid, sodium salt), poly(4-styrene sulfonic acid-co-maleic acid) sodium salt, poly(acrylic acid) sodium salt (PA) and cationic polyelectrolytes such as poly(diallyldimethylammonium chloride), poly(ethylenimine) and poly(hexamethylene biguanide were used for membrane modification. An effect of deposition time and a number of polyelectrolyte layers on the membrane modification has been evaluated. It was found that degree of membrane modification depends on chemical nature and molecular weight of polyelectrolytes used. The surface morphology of the prepared composite membranes was studied using atomic force microscopy. It was shown that the surface membrane roughness decreases significantly as a number of the polyelectrolyte layers on the membrane surface increases. This smoothening of the membrane surface might contribute to the reduction of membrane fouling as lower roughness most often associated with a decrease in surface fouling. Zeta potentials and water contact angles on the membrane surface before and after modification have also been evaluated to provide addition information regarding membrane fouling issues. It was shown that the surface charge of the membranes modified with polyelectrolytes could be switched between positive and negative after coating with a cationic or an anionic polyelectrolyte. On the other hand, the water contact angle was strongly affected when the outermost polyelectrolyte layer was changed. Finally, a distinct difference in the performance of the noncoated membranes and the polyelectrolyte modified membranes was found during treatment of seawater in the non-continuous regime. A possible mechanism of the higher fouling resistance of the modified membranes has been discussed.

Keywords: contact angle, membrane fouling, polyelectrolytes, surface modification

Procedia PDF Downloads 251

Authors: Cheryl Leggon

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Although women in the aggregate are earning more doctorates in science and engineering from U.S. institutions, they continue to concentrate in some fields--e.g., biology--and underrepresented in others--e.g., engineering. Traditionally, most studies of women doctorate recipients in the sciences (including the social, behavioral and economic sciences) or engineering do not report their findings by demographic subgroups. This study extends the literature on these topics by using an intersectional approach to examine decadal trends. Intersectionality suggests that race, gender, and nation are not separate mutually exclusive entities whose impacts are summative, but rather as a confluence of synergistic factors that shape complex social inequities. Drawing on critical aspects of the intersectionality approach is particularly well suited for a more fine-grained analysis of the representation of women doctorate recipients in science and engineering. The implications of the findings are discussed in terms of policies and evidence-based programmatic strategies for enhancing women’s participation in fields in which they are especially underrepresented.

Keywords: doctorates, engineering, science, women

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Authors: Alper T. Celebi, Ali Beskok

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Electroosmotic (EO) slip flows in nanochannels are investigated using non-equilibrium molecular dynamics (MD) simulations, and the results are compared with analytical solution of Poisson-Boltzmann and Stokes (PB-S) equations with slip contribution. The ultimate objective of this study is to show that well-known continuum flow model can accurately predict the EO velocity profiles in nanochannels using the slip lengths and apparent viscosities obtained from force-driven flow simulations performed at various liquid-wall interaction strengths. EO flow of aqueous NaCl solution in silicon nanochannels are simulated under realistic electrochemical conditions within the validity region of Poisson-Boltzmann theory. A physical surface charge density is determined for nanochannels based on dissociations of silanol functional groups on channel surfaces at known salt concentration, temperature and local pH. First, we present results of density profiles and ion distributions by equilibrium MD simulations, ensuring that the desired thermodynamic state and ionic conditions are satisfied. Next, force-driven nanochannel flow simulations are performed to predict the apparent viscosity of ionic solution between charged surfaces and slip lengths. Parabolic velocity profiles obtained from force-driven flow simulations are fitted to a second-order polynomial equation, where viscosity and slip lengths are quantified by comparing the coefficients of the fitted equation with continuum flow model. Presence of charged surface increases the viscosity of ionic solution while the velocity-slip at wall decreases. Afterwards, EO flow simulations are carried out under uniform electric field for different liquid-wall interaction strengths. Velocity profiles present finite slips near walls, followed with a conventional viscous flow profile in the electrical double layer that reaches a bulk flow region in the center of the channel. The EO flow enhances with increased slip at the walls, which depends on wall-liquid interaction strength and the surface charge. MD velocity profiles are compared with the predictions from analytical solutions of the slip modified PB-S equation, where the slip length and apparent viscosity values are obtained from force-driven flow simulations in charged silicon nano-channels. Our MD results show good agreements with the analytical solutions at various slip conditions, verifying the validity of PB-S equation in nanochannels as small as 3.5 nm. In addition, the continuum model normalizes slip length with the Debye length instead of the channel height, which implies that enhancement in EO flows is independent of the channel height. Further MD simulations performed at different channel heights also shows that the flow enhancement due to slip is independent of the channel height. This is important because slip enhanced EO flow is observable even in micro-channels experiments by using a hydrophobic channel with large slip and high conductivity solutions with small Debye length. The present study provides an advanced understanding of EO flows in nanochannels. Correct characterization of nanoscale EO slip flow is crucial to discover the extent of well-known continuum models, which is required for various applications spanning from ion separation to drug delivery and bio-fluidic analysis.

Keywords: electroosmotic flow, molecular dynamics, slip length, velocity-slip

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Authors: Duc Dong Do, Ngoc Ha Tran, Thanh Hai Dang, Cao Cuong Dang, Xuan Huan Hoang

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Global aligning two protein-protein interaction networks is an essentially important task in bioinformatics/computational biology field of study. It is a challenging and widely studied research topic in recent years. Accurately aligned networks allow us to identify functional modules of proteins and/ororthologous proteins from which unknown functions of a protein can be inferred. We here introduce a novel efficient heuristic global network alignment algorithm called FASTAn, including two phases: the first to construct an initial alignment and the second to improve such alignment by exerting a local optimization repeated procedure. The experimental results demonstrated that FASTAn outperformed the state-of-the-art global network alignment algorithm namely SPINAL in terms of both commonly used objective scores and the run-time.

Keywords: FASTAn, Heuristic algorithm, biological network alignment, protein-protein interaction networks

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Authors: M. Khlifa, A. Youssef. M. Almakki

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The addition of silica nanoparticles to poly(methyl methacrylate) (PMMA) can influence its mechanical and aging properties. Dispersed PMMA in colloidal and aggregated silica revealed considerable increase in modulus above the glass transition temperature when aggregated silica nanoparticles were used, whereas colloidally dispersed silica nanoparticles showed only a marginal improvement. In addition, Dispersed PMMA in both aggregated and colloidally silica nanoparticles accelerated physical ageing.

Keywords: nanoparticles, physical aging, PMMA, chemical and molecular engineering

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Authors: Ramin Mehdiabadi

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Background: Breast cancer remains the most prevalent cancer diagnosis and the leading cause of cancer death among women globally, representing 11.7% of new cases and 6.9% of deaths. While the incidence and mortality of major cancers are declining in developed regions like the United States and Western Europe, underdeveloped and developing countries exhibit an increasing trend, attributed to lifestyle factors such as smoking, physical inactivity, and high-calorie diets. Objective: This study explores the intricate relationship between the mammalian transcription factor forkhead box (FoxM1) and the microRNA miR-216b-5p in various subtypes of breast cancer, aiming to deepen the understanding of their roles in tumorigenesis, metastasis, and drug resistance. Methods: Breast cancer subtypes were categorized based on key biomarkers: estrogen receptors, progesterone receptors, and human epidermal growth factor receptor 2. These include luminal A, luminal B, HER2 enriched, triple-negative, and normal-like subtypes. We focused on analyzing the expression levels of FoxM1 and miR-216b-5p, given the known role of FoxM1 in cell proliferation and its implications in cancer pathologies such as lung, gastric, and breast cancers. Concurrently, miR-216b-5p's function as a tumor suppressor was evaluated to ascertain its regulatory effects on FoxM1. Results: Preliminary data indicate a nuanced interplay between FoxM1 and miR-216b-5p, suggesting a potential inverse relationship that varies across breast cancer subtypes. This relationship underscores the dual role of these biomarkers in modulating cancer progression and response to treatments. Conclusion: The findings advocate for the potential of miR-216b-5p to serve as a prognostic biomarker and a therapeutic target, particularly in subtypes where FoxM1 is prominently expressed. Understanding these molecular interactions provides crucial insights into the personalized treatment strategies and could lead to more effective therapeutic interventions in breast cancer management. Implications: The study highlights the importance of molecular profiling in breast cancer treatment and emphasizes the need for targeted therapeutic approaches in managing diverse cancer subtypes, particularly in varying global contexts where lifestyle factors significantly impact cancer dynamics.

Keywords: breast cancer, gene expression, FoxM1, microRNA

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Authors: F. Pires, V. Geraldo, O. N. Oliveira Jr., M. Raposo

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Catechins are powerful antioxidants which have attractive properties useful for tumor therapy. Considering their antioxidant activity, these molecules can act as a scavenger of the reactive oxygen species (ROS), alleviating the damage of cell membrane induced by oxidative stress. The complexity and dynamic nature of the cell membrane compromise the analysis of the biophysical interactions between drug and cell membrane and restricts the transport or uptake of the drug by intracellular targets. To avoid the cell membrane complexity, we used biomimetic systems as liposomes and Langmuir monolayers to study the interaction between catechin and membranes at the molecular level. Liposomes were formed after the dispersion of anionic 1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)(sodium salt) (DPPG) phospholipids in an aqueous solution, which mimic the arrangement of lipids in natural cell membranes and allows the entrapment of catechins. Langmuir monolayers were formed after dropping amphiphilic molecules, DPPG phospholipids, dissolved in an organic solvent onto the water surface. In this work, we mixed epigallocatechin-3-gallate (EGCG) with DPPG liposomes and exposed them to ultra-violet radiation in order to evaluate the antioxidant potential of these molecules against oxidative stress induced by radiation. The presence of EGCG in the mixture decreased the rate of lipid peroxidation, proving that EGCG protects membranes through the quenching of the reactive oxygen species. Considering the high amount of hydroxyl groups (OH groups) on structure of EGCG, a possible mechanism to these molecules interact with membrane is through hydrogen bonding. We also investigated the effect of EGCG at various concentrations on DPPG Langmuir monolayers. The surface pressure isotherms and infrared reflection-absorption spectroscopy (PM-IRRAS) results corroborate with absorbance results preformed on liposome-model, showing that EGCG interacts with polar heads of the monolayers. This study elucidates the physiological action of EGCG which can be incorporated in lipid membrane. These results are also relevant for the improvement of the current protocols used to incorporate catechins in drug delivery systems.

Keywords: catechins, lipid membrane, anticancer agent, molecular interactions

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Authors: Abdelkader Nouri, M’hamed Bouslama, Faouzi Saidi, Hassan Maaref, Michel Gendry

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Self-organized InAs quantum dots (QDs) have been grown on 3,1% InP (110) lattice mismatched substrate by Solid Source Molecular Beam Epitaxy (SSMBE). Stranski-Krastanov mode growth has been used to create self-assembled 3D islands on InAs wetting layer (WL). The optical quality depending on the temperature and power is evaluated. In addition, Atomic Force Microscopy (AFM) images shows inhomogeneous island dots size distribution due to temperature coalescence. The quantum size effect was clearly observed through the spectra photoluminescence (PL) shape.

Keywords: AFM, InAs QDs, PL, SSMBE

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Authors: Aktar-Uz-Zaman, M. Tuhina-Khatun, Mohamed Hanafi Musa

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Three rust diseases: leaf (brown) rust caused by Puccinia triticina Eriks, stripe (yellow) rust caused by Puccinia striiformis West, and stem (black) rust caused by Puccinia graminis f. sp. tritici are economically important diseases of wheat in world wide. Yield loss due to leaf rust is 40% in susceptible cultivars. Yield losses caused by the stem rust pathogens in the mid of 20 century reached 20-30% in Eastern and Central Europe and the most virulent stem rust race Ug99 emerged first in Uganda and after that in Kenya, Ethiopia, Yemen, in the Middle East and South Asia. Yield losses were estimated up to 100%, whereas, up to 80% have been reported in Kenya during 1999. In case of stripe rust, severity level has been recorded 60% - 70% as compared to 100% severity of susceptible check in disease screening nurseries in Kenya. Improvement of resistant varieties or cultivars is the sustainable, economical and environmentally friendly approaches for increasing the global wheat production to suppress the rust diseases. More than 68 leaf rust, 49 stripe rust and 53 stem rust resistance genes have been identified in the global wheat cultivars or varieties using different molecular breeding approaches. Among these, Lr1, Lr9, Lr10, Lr19, Lr21, Lr24, Lr25, Lr28, Lr29, Lr34, Lr35, Lr37, Lr39, Lr47, Lr51, Lr3bg, Lr18, Lr40, Lr46, and Lr50 leaf rust resistance genes have been identified by using molecular, enzymatic and microsatellite markers from African, Asian, European cultivars of hexaploid wheat (Triticum aestivum), durum wheat and diploid wheat species. These genes are located on 20, of the 21 chromosomes of hexaploid wheat. Similarly, Sr1, Sr2, Sr24, and Sr3, Sr31 stem rust resistance genes have been recognized from wheat cultivars of Pakistan, India, Kenya, and Uganda etc. A race of P. striiformis (stripe rust) Yr9, Yr18, and Yr29 was first observed in East Africa, Italy, Pakistan and India wheat cultivars. These stripe rust resistance genes are located on chromosomes 1BL, 4BL, 6AL, 3BS and 6BL in bread wheat cultivars. All these identified resistant genes could be used for notable improvement of susceptible wheat cultivars in the future.

Keywords: hexaploid wheat, resistance genes, rust disease, triticum aestivum

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Authors: Kiran Nawaz, Ahmad Ali Shahid, Sehrish Iftikhar, Waheed Anwar, Muhammad Nasir Subhani

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Chili (Solanum annum L.) attacks by many fungal pathogens, including members of Oomycetes which are responsible for root rot in different chili growing areas of the world. Oomycetes pathogens cause economic losses in different regions of the Pakistan. Most of the plant tissues, including roots, crowns, fruit, and leaves, are vulnerable to Phytophthora capsici. It is very difficult to manage the Phytophthora root rot of chili as many commercial varieties are tremendously vulnerable to P. capsici. The causal agent of the disease was isolated on corn meal agar (CMA) and identified on a morphological basis by using available taxonomic keys. The pathogen was also confirmed on the molecular basis through internal transcribed spacer region and with other molecular markers.The Blastn results showed 100% homology with already reported sequences of P. capsici in NCBI database. Most of the farmers have conventionally relied on foliar fungicide applications to control Phytophthora root rot in spite of their incomplete effectiveness. In this study, in vitro plate assay, seed soaking and foliar applications of 6 fungicides were evaluated against root rot of chili. In vitro assay revealed that significant inhibition of linear growth was obtained with Triflumizole at 7.0%, followed by Thiophanate methyl (8.9%), Etridiazole (6.0%), Propamocarb (5.9%) and 7.5% with Mefenoxam and Iprodione for P. capsici. The promising treatments of in vitro plate bioassay were evaluated in pot experiments under controlled conditions in the greenhouse. All fungicides were applied after at 6-day intervals. Results of pot experiment showed that all treatments considerably inhibited the percentage of P. capsici root rot incidence. In addition, application of seed soaking with all six fungicides combined with the foliar spray of the same components showed the significant reduction in root rot incidence. The combine treatments of all fungicides as in vitro bioassay, seed soaking followed by foliar spray is considered non-harmful control methods which have advantages and limitation. Hence, these applications proved effective and harmless for the management of soil-borne plant pathogens.

Keywords: blastn, bioassay, corn meal agar(CMA), oomycetes

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Authors: Giselle Tran, Ralitza Parina, Phuong T. Nguyen

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Background/Aims: Pancreatic cysts (PC) have recently become an increasingly common entity, often diagnosed as incidental findings on cross-sectional imaging. Clinically, management of the lesions is difficult because of uncertainties in their potential for malignant degeneration. Prior series have reported that carcinoembryonic antigen (CEA), a biomarker collected from cyst fluid aspiration, has a high diagnostic accuracy for discriminating between mucinous and non-mucinous lesions, at the patient’s initial presentation. To the author’s best knowledge, no prior studies have reported PC CEA levels obtained from endoscopic ultrasound fine-needle aspiration (EUS-FNA) over years of serial EUS surveillance imaging. Methods: We report a consecutive retrospective series of 624 patients who underwent EUS evaluation for a PC between 11/20/2009 and 11/13/2018. Of these patients, 401 patients had CEA values obtained at the point of entry. Of these, 157 patients had two or more CEA values obtained over the course of their EUS surveillance. Of the 157 patients (96 F, 61 M; mean age 68 [range, 62-76]), the mean interval of EUS follow-up was 29.7 months [3.5-128]. The mean number of EUS procedures was 3 [2-7]. To assess CEA value fluctuations, we defined an appreciable increase in CEA as "spikes" – two-times increase in CEA on a subsequent EUS-FNA of the same cyst, with the second CEA value being greater than 1000 ng/mL. Using this definition, cysts with a spike in CEA were compared to those without a spike in a bivariate analysis to determine if a CEA spike is associated with poorer outcomes and the presence of high-risk features. Results: Of the 157 patients analyzed, 29 had a spike in CEA. Of these 29 patients, 5 had a cyst with size increase >0.5cm (p=0.93); 2 had a large cyst, >3cm (p=0.77); 1 had a cyst that developed a new solid component (p=0.03); 7 had a cyst with a solid component at any time during surveillance (p=0.08); 21 had a complex cyst (p=0.34); 4 had a cyst categorized as "Statistically Higher Risk" based on molecular analysis (p=0.11); and 0 underwent surgical resection (p=0.28). Conclusion: With serial EUS imaging in the surveillance of PC, an increase in CEA level defined as a spike did not predict poorer outcomes. Most notably, a spike in CEA did not correlate with the number of patients sent to surgery or patients with an appreciable increase in cyst size. A spike in CEA did not correlate with the development of a solid nodule within the PC nor progression on molecular analysis. Future studies should focus on the selected use of CEA analysis when patients undergo EUS surveillance evaluation for PCs.

Keywords: carcinoembryonic antigen (CEA), endoscopic ultrasound (EUS), fine-needle aspiration (FNA), pancreatic cyst, spike

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Authors: Shen Jian, Hu Jie, Qi Jin, Liu Wei Jie, Chen Ji Yi, Peng Ying Hong

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In order to settle the problem of acquiring case in biological related to design problems, a biometrics instance acquisition method based on text mining is presented. Through the construction of corpus text vector space and knowledge mining, the feature selection, similarity measure and case retrieval method of text in the field of biology are studied. First, we establish a vector space model of the corpus in the biological field and complete the preprocessing steps. Then, the corpus is retrieved by using the vector space model combined with the functional keywords to obtain the biological domain examples related to the design problems. Finally, we verify the validity of this method by taking the example of text.

Keywords: text mining, vector space model, feature selection, biologically inspired design

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Authors: Chengcao Sun, Shujun Li, Dejia Li

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Sulforaphane (SFN) possesses powerful chemo-preventive effects and plays a crucial role on oxidative stress and inflammatory. In our recent study, SFN treatment could relieve muscular dystrophy in mdx mice by activating Nrf2 (NF-E2 related factor 2). Moreover, our findings indicated that SFN-activated Nrf2 alleviated muscle inflammation in dystrophin-deficient mdx mice through suppressing NF-κB signaling pathway. Collectively, SFN-induced Nrf2 molecular pathway might be a promising approach for treatment of the patients with Duchenne muscular dystrophy.

Keywords: sulforaphane, Duchenne muscular dystrophy, Nrf2, inflammation, fibrosis, oxidative stress

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Authors: Akimitsu Kugimiya, Kouhei Iwato, Toru Saito, Jiro Kohda, Yasuhisa Nakano, Yu Takano

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The measurement of amino acid content is reported to be useful for the diagnosis of several types of diseases, including lung cancer, gastric cancer, colorectal cancer, breast cancer, prostate cancer, and diabetes. The conventional detection methods for amino acid are high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS), but they have several drawbacks as the equipment is cumbersome and the techniques are costly in terms of time and costs. In contrast, biosensors and biosensing methods provide more rapid and facile detection strategies that use simple equipment. The authors have reported a novel approach for the detection of each amino acid that involved the use of aminoacyl-tRNA synthetase (aaRS) as a molecular recognition element because aaRS is expected to a selective binding ability for corresponding amino acid. The consecutive enzymatic reactions used in this study are as follows: aaRS binds to its cognate amino acid and releases inorganic pyrophosphate. Hydrogen peroxide (H₂O₂) was produced by the enzyme reactions of inorganic pyrophosphatase and pyruvate oxidase. The Trinder’s reagent was added into the reaction mixture, and the absorbance change at 556 nm was measured using a microplate reader. In this study, an amino acid-sensing method using histidyl-tRNA synthetase (HisRS; histidine-specific aaRS) as molecular recognition element in combination with the Trinder’s reagent spectrophotometric method was developed. The quantitative performance and selectivity of the method were evaluated, and the optimal enzyme reaction and detection conditions were determined. The authors developed a simple and rapid method for detecting histidine with a combination of enzymatic reaction and spectrophotometric detection. In this study, HisRS was used to detect histidine, and the reaction and detection conditions were optimized for quantitation of these amino acids in the ranges of 1–100 µM histidine. The detection limits are sufficient to analyze these amino acids in biological fluids. This work was partly supported by Hiroshima City University Grant for Special Academic Research (General Studies).

Keywords: amino acid, aminoacyl-tRNA synthetase, biosensing, enzyme reaction

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Authors: Silvia Moreno, Banu Iyisan, Hannes Gumz, Brigitte Voit, Dietmar Appelhans

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Polymersomes are materials which are considered as artificial counterparts of natural vesicles. The nanotechnology of such smart nanovesicles is very useful to enhance the efficiency of many therapeutic and diagnostic drugs. Those compounds show a higher stability, flexibility, and mechanical strength to the membrane compared to natural liposomes. In addition, they can be designed in detail, the permeability of the membrane can be controlled by different stimuli, and the surface can be functionalized with different biological molecules to facilitate monitoring and target. For this purpose, this study demonstrates the formation of multifunctional and pH sensitive polymersomes and their functionalization with different reactive groups or biomolecules inside and outside of polymersomes´ membrane providing by crossing the membrane and docking/undocking processes for biomedical applications. Overall, they are highly versatile and thus present new opportunities for the design of targeted and selective recognition systems, for example, in mimicking cell functions and in synthetic biology.

Keywords: multifunctionalized, pH stimulus, controllable release, cellular uptake

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Authors: Debanjan Dey, Tamal Banerjee, Kaustubha Mohanty

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Global scalar properties are calculated based on higher occupied molecular orbital (HOMO) and lower unoccupied molecular orbital (LUMO) energy to study the interaction between ionic liquids with Bituminous and Anthracite coal using density function theory (DFT) method. B3LYP/6-31G* calculation predicts HOMO-LUMO energy gap, electronegativity, global hardness, global softness, chemical potential and global softness for individual compounds with their clusters. HOMO-LUMO interaction, electron delocalization, electron donating and accepting is the main source of attraction between individual compounds with their complexes. Cation used in this study: 1-butyl-1-methylpyrrolidinium [BMPYR], 1-methyl -3-propylimmidazolium [MPIM], Tributylmethylammonium [TMA] and Tributylmethylphosphonium [MTBP] with the combination of anion: bis(trifluromethylsulfonyl)imide [Tf2N], methyl carbonate [CH3CO3], dicyanamide [N(CN)2] and methylsulfate [MESO4]. Basically three-tier approach comprising HOMO/LUMO energy, Scalar quantity and infinite dilution activity coefficient (IDAC) by sigma profile generation with COSMO-RS (Conductor like screening model for real solvent) model was chosen for simultaneous interaction. [BMPYR]CH3CO3] (1-butyl-1-methylpyrrolidinium methyl carbonate) and [MPIM][CH3CO3] (1-methyl -3-propylimmidazolium methyl carbonate ) are the best effective ILs on the basis of HOMO-LUMO band gap for Anthracite and Bituminous coal respectively and the corresponding band gap is 0.10137 hartree for Anthracite coal and 0.12485 hartree for Bituminous coal. Further ionic liquids are screened quantitatively with all the scalar parameters and got the same result based on CH-π interaction which is found for HOMO-LUMO gap. To check our findings IDAC were predicted using quantum chemical based COSMO-RS methodology which gave the same trend as observed our scalar quantity calculation. Thereafter a qualitative measurement is doing by sigma profile analysis which gives complementary behavior between IL and coal that means highly miscible with each other.

Keywords: coal-ionic liquids cluster, COSMO-RS, DFT method, HOMO-LUMO interaction

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Authors: Olubukayo-Opeyemi Oyetayo, Oscar Mendez-Lucio, Andreas Bender, Hans Kiefer

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The thermal melting curve of a protein provides information on its conformational stability and could provide cues on its aggregation behavior. Naturally-occurring osmolytes have been shown to improve the thermal stability of most proteins in a concentration-dependent manner. They are therefore commonly employed as additives in therapeutic protein purification and formulation. A number of intertwined and seemingly conflicting mechanisms have been put forward to explain the observed stabilizing effects, the most prominent being the preferential exclusion mechanism. We attempted to probe and summarize molecular mechanisms for thermal stabilization of a monoclonal antibody (mAb) by developing quantitative structure-activity relationships using a rationally-selected library of 120 osmolyte-like compounds in the polyhydric alcohols, amino acids and methylamines classes. Thermal stabilization potencies were experimentally determined by thermal shift assays based on differential scanning fluorimetry. The cross-validated QSAR model was developed by partial least squares regression using descriptors generated from Molecular Operating Environment software. Careful evaluation of the results with the use of variable importance in projection parameter (VIP) and regression coefficients guided the selection of the most relevant descriptors influencing mAb thermal stability. For the mAb studied and at pH 7, the thermal stabilization effects of tested compounds correlated positively with their fractional polar surface area and inversely with their fractional hydrophobic surface area. We cannot claim that the observed trends are universal for osmolyte-protein interactions because of protein-specific effects, however this approach should guide the quick selection of (de)stabilizing compounds for a protein from a chemical library. Further work with a large variety of proteins and at different pH values would help the derivation of a solid explanation as to the nature of favorable osmolyte-protein interactions for improved thermal stability. This approach may be beneficial in the design of novel protein stabilizers with optimal property values, especially when the influence of solution conditions like the pH and buffer species and the protein properties are factored in.

Keywords: thermal stability, monoclonal antibodies, quantitative structure-activity relationships, osmolytes

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Authors: Yuhei Kunihiro, Sorin V. Sabau, Kazuhiro Shibuya

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We study the molecular evolution of insulin from the metric geometry point of view. In mathematics, and particularly in geometry, distances and metrics between objects are of fundamental importance. Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological sequences (DNA, mRNA, or proteins) space. We analyze from the geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.

Keywords: metric geometry, evolution, insulin, C. elegans

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Authors: V. Radulescu, S. Dumitru

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Introduction: Determination of the temperature field inside a fluid in motion has many practical issues, especially in the case of turbulent flow. The phenomenon is greater when the solid walls have a different temperature than the fluid. The turbulent heat and mass transfer have an essential role in case of the thermal pollution, as it was the recorded during the damage of the Thermoelectric Power-plant Oradea (closed even today). Basic Methods: Solving the theoretical turbulent thermal pollution represents a particularly difficult problem. By using the semi-empirical theories or by simplifying the made assumptions, based on the experimental measurements may be assured the elaboration of the mathematical model for further numerical simulations. The three zones of flow are analyzed separately: the vicinity of the solid wall, the turbulent transition zone, and the turbulent core. For each area are determined the distribution law of temperature. It is determined the dependence of between the Stanton and Prandtl numbers with correction factors, based on measurements experimental. Major Findings/Results: The limitation of the laminar thermal substrate was determined based on the theory of Landau and Levice, using the assumption that the longitudinal component of the velocity pulsation and the pulsation’s frequency varies proportionally with the distance to the wall. For the calculation of the average temperature, the formula is used a similar solution as for the velocity, by an analogous mediation. On these assumptions, the numerical modeling was performed with a gradient of temperature for the turbulent flow in pipes (intact or damaged, with cracks) having 4 different diameters, between 200-500 mm, as there were in the Thermoelectric Power-plant Oradea. Conclusions: It was made a superposition between the molecular viscosity and the turbulent one, followed by addition between the molecular and the turbulent transfer coefficients, necessary to elaborate the theoretical and the numerical modeling. The concept of laminar boundary layer has a different thickness when it is compared the flow with heat transfer and that one without a temperature gradient. The obtained results are within the margin of error of 5%, between the semi-empirical classical theories and the developed model, based on the experimental data. Finally, it is obtained a general correlation between the Stanton number and the Prandtl number, for a specific flow (with associated Reynolds number).

Keywords: experimental measurements, numerical correlations, thermal pollution through pipelines, turbulent thermal flow

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