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Kevin P Bishop, Pierre-Nicholas Roy
Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details...
March 14, 2018: Journal of Chemical Physics
Eva Vargas, Eloy Povedano, Víctor Ruiz-Valdepeñas Montiel, Rebeca M Torrente-Rodríguez, Mohamed Zouari, Juan José Montoya, Noureddine Raouafi, Susana Campuzano, José M Pingarrón
This work reports an amperometric biosensor for the determination of miRNA-21, a relevant oncogene. The methodology involves a competitive DNA-target miRNA hybridization assay performed on the surface of magnetic microbeads (MBs) and amperometric transduction at screen-printed carbon electrodes (SPCEs). The target miRNA competes with a synthetic fluorescein isothiocyanate (FITC)-modified miRNA with an identical sequence for hybridization with a biotinylated and complementary DNA probe (b-Cp) immobilized on the surface of streptavidin-modified MBs (b-Cp-MBs)...
March 15, 2018: Sensors
A S Vikulina, N A Feoktistova, N G Balabushevich, A G Skirtach, D Volodkin
Porous vaterite CaCO3 crystals are nowadays extensively used as high-capacity bio-friendly sacrificial templates for the fabrication of such protein-containing nano- and micro-particles as capsules and beads. The first step in the protein encapsulation is performed through loading of the protein molecules into the crystals. Co-synthesis is one of the most useful and simple methods proven to effectively load crystals with proteins; however, the loading mechanism is still unknown. To understand the mechanism, in this study, we focus on the loading of a model protein catalase into the crystals by means of adsorption into pre-formed crystals (ADS) and co-synthesis (COS)...
March 15, 2018: Physical Chemistry Chemical Physics: PCCP
Amine Charfi, Eunyoung Park, Muhammad Aslam, Jeonghwan Kim
The study presents a mathematical model developed to better understand and control membrane fouling in a single-staged, anaerobic fluidized bed membrane bioreactor (AFMBR) using polyethylene terephthalate (PET) beads as scouring media. The model was based on combining the anaerobic biological model AM2b and a fouling model applied in membrane filtration. The presented model was validated using experimental data obtained by a laboratory scaled AFMBR reactor run during 250 d under various operational conditions...
March 10, 2018: Bioresource Technology
Rabia Iqbal, Tahir Zahoor, Nuzhat Huma, Amer Jamil, Gülhan Ünlü
Longevity of probiotic is the main concern for getting maximum benefits when added in food product. Bifidobacterium, a probiotic, tends to lose its viability during gastrointestinal track (GIT) transit and storage of food. Their viability can be enhanced through microencapsulation technology. In this study, Bifidobacterium bifidum (B. bifidum) ATCC 35914 was encapsulated by using two experimental plans. In the first plan, chitosan (CH) at 0.6, 0.8, and 1.0% and sodium alginate (SA) at 4, 5, and 6% were used...
March 12, 2018: Probiotics and Antimicrobial Proteins
K Michael Salerno, Noam Bernstein
Coarse-grained (CG) polymer simulations can access longer times and larger lengths than all-atom (AA) molecular dynamics simulations, however not all CG models correctly reproduce polymer properties on all length scales. Here we coarse grain atomistic position data from polyethylene (PE) and polytetrafluoroethylene (PTFE) melt simulations by combining λ backbone carbon atoms in a single CG bead. Resulting CG variables have correlations along the chain backbone that depend on the coarse-graining scale λ, and are generally not reproduced by independent bond-length, bond-angle and torsion-angle distributions...
March 12, 2018: Journal of Chemical Theory and Computation
Farzana Jasmine, Justin Shinkle, Mekala Sabarinathan, Habibul Ahsan, Brandon L Pierce, Muhammad G Kibriya
OBJECTIVES: Relative telomere length (RTL) is a potential biomarker of aging and risk for chronic disease. Previously, we developed a probe-based RTL assay on Luminex platform, where probes for Telomere (T) and reference gene (R) for a given DNA sample were tested in a single well. Here, we describe a method of pooling multiple samples in one well to increase the throughput and cost-effectiveness. METHODS: We used four different microbeads for the same T-probe and four different microbeads for the same R-probe...
March 12, 2018: American Journal of Human Biology: the Official Journal of the Human Biology Council
Jian Zhang, Jie Su, Shuxiang Hu, Jindun Zhang, Rui Ding, Jitong Guo, Guifang Cao, Rongfeng Li, Qing-Yuan Sun, Xihe Li
Ubiquitination is an important cellular process in spermatogenesis and involves the regulation of spermatid differentiation and spermiogenesis. In the current study, the correlation between bull sperm ubiquitination and sperm defects was analyzed, and the feasibility using anti-ubiquitin specific antibody immobilized magnetic beads to remove the spermatozoa with defects was assessed. A total of nine bulls were examined, and the amount of sperm ubiquitination ranged from 55 to 151. Correspondingly, the percentage of sperm deformity ranged from 9...
February 12, 2018: Animal Reproduction Science
Anna K Trull, Jelle van der Horst, Lucas J van Vliet, Jeroen Kalkman
We present a comparison of image reconstruction techniques for optical projection tomography. We compare conventional filtered back projection, sinogram filtering using the frequency-distance relationship (FDR), image deconvolution, and 2D point-spread-function-based iterative reconstruction. The latter three methods aim to remove the spatial blurring in the reconstructed image originating from the limited depth of field caused by the point spread function of the imaging system. The methods are compared based on simulated data, experimental optical projection tomography data of single fluorescent beads, and high-resolution optical projection tomography imaging of an entire zebrafish larva...
March 10, 2018: Applied Optics
Olivier R Costa, Katrijn Verhaeghen, Sarah Roels, Geert Stangé, Zhidong Ling, Daniel Pipeleers, Frans K Gorus, Geert A Martens
A disproportional increase of circulating GAD65 within hours from an intraportal islet allotransplantation has been validated as biomarker of beta cell loss and poor functional outcome. More sensitive assays are, however, needed to allow detection of episodes of subtle beta cell loss during late-stage graft rejection or in the peri-onset period of type 1 diabetes. We applied the same sandwich monoclonal antibody couple reactive towards the C- and N-terminus of GAD65 on three advanced immunoassay platforms-the Cytometric Bead Array (CBA, Becton, Dickinson and Company), ElectroChemiLuminescence ImmunoAssay (ECLIA, Meso Scale Discovery) and digital ELISA technology (Single Molecule Array-SIMOA, Quanterix...
2018: PloS One
Vanessa Santos Viterbo, Bryan Irvine Mamuad Lopez, Hyun Sung Kang, Hoonseop Kim, Choul Won Song, Kang Seok Seo
Objective: Genome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork. Methods: A total of 480 purebreed Duroc pigs were genotyped using IlluminaPorcine60k bead chips while the association test was implemented following Genome-wide Rapid Association using Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. Results: A total of 25, 29, and 16 single nucleotide polymorphisms (SNPs) were significantly associated with stearic (18:0), oleic (18:1) and saturated fatty acids (SFA), respectively...
March 2, 2018: Asian-Australasian Journal of Animal Sciences
Jenia Gutin, Ronen Sadeh, Nitzan Bodenheimer, Daphna Joseph-Strauss, Avital Klein-Brill, Adi Alajem, Oren Ram, Nir Friedman
Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures...
March 6, 2018: Cell Reports
R A Bray, H M Gebel, R Townsend, M E Roberts, M Polinsky, L Yang, H-U Meier-Kriesche, C P Larsen
Donor-specific antibodies (DSAs) are associated with an increased risk of antibody-mediated rejection and graft failure. In BENEFIT and BENEFIT-EXT, kidney transplant recipients were randomized to receive belatacept more intense (MI)-based, belatacept less intense (LI)-based, or cyclosporine-based immunosuppression for up to 7 years (84 months). The presence/absence of HLA-specific antibodies was determined at baseline, at months 6, 12, 24, 36, 48, 60, and 84, and at the time of clinically suspected episodes of acute rejection, using solid-phase flow cytometry screening...
March 6, 2018: American Journal of Transplantation
Jin-Ju Byeon, Min-Ho Park, Seok-Ho Shin, Byeong Ill Lee, Yuri Park, Jangmi Choi, Nahye Kim, Yeonjae Kang, Young G Shin
A single hybrid affinity-captured-LC-TOF-MS/MS method was developed and applied for the quantification of total antibody, antibody conjugated drug and free payload of antibody drug conjugate (ADC). Adcetris®, one of the valine-citrulline MMAE (vc-MMAE) conjugated ADC, was used as a model ADC compound. A quadratic regression (weighted 1/concentration) was used to fit calibration curves over the concentration range of 30.65-613.00 ng/mL with an equation y=ax2 +bx+c for the acDrug of Adcetris®. The qualification run met the acceptance criteria of ± 25% accuracy and precision values for quality control samples...
March 5, 2018: Biomedical Chromatography: BMC
Kristen L Huber, Banyuhay P Serrano, Jeanne A Hardy
Caspase-9 is a critical factor in the initiation of apoptosis, and as a result is tightly regulated by a number of mechanisms. Caspase-9 contains a Caspase Activation and Recruitment Domain (CARD), which enables caspase-9 to form a tight interaction with the apoptosome, a heptameric activating platform. The caspase-9 CARD has been thought to be principally involved in recruitment to the apoptosome, but its roles outside this interaction have yet to be uncovered. In this work we show that the CARD is involved in physical interactions with the catalytic core of caspase-9 in the absence of the apoptosome; this interaction requires a properly formed caspase-9 active site...
March 2, 2018: Biochemical Journal
Christian A Tryon, Jason E Lewis, Kathryn L Ranhorn, Amandus Kwekason, Bridget Alex, Myra F Laird, Curtis W Marean, Elizabeth Niespolo, Joelle Nivens, Audax Z P Mabulla
The archaeology of East Africa during the last ~65,000 years plays a central role in debates about the origins and dispersal of modern humans, Homo sapiens. Despite the historical importance of the region to these discussions, reliable chronologies for the nature, tempo, and timing of human behavioral changes seen among Middle Stone Age (MSA) and Later Stone Age (LSA) archaeological assemblages are sparse. The Kisese II rockshelter in the Kondoa region of Tanzania, originally excavated in 1956, preserves a ≥ 6-m-thick archaeological succession that spans the MSA/LSA transition, with lithic artifacts such as Levallois and bladelet cores and backed microliths, the recurrent use of red ochre, and >5,000 ostrich eggshell beads and bead fragments...
2018: PloS One
Gerald S Manning
The physical principles underlying expansion of a single-chain polyelectrolyte coil caused by Coulomb repulsions among its ionized groups, and the expansion of a cross-linked polyelectrolyte gel, are probably the same. In this paper, we analyze a "one-dimensional" version of a gel, namely, a linear chain of charged beads connected by Hooke's law springs. In the Debye-Hückel range of relatively weak Coulomb strength, where counterion condensation does not occur, the springs are realistically stretched on a nanolength scale by the repulsive interactions among the beads, if we use a spring constant normalized by the inverse square of the solvent Bjerrum length...
February 28, 2018: Soft Matter
Frederique Ruf-Zamojski, Miguel Fribourg, Yongchao Ge, Venugopalan Nair, Hanna Pincas, Elena Zaslavsky, German Nudelman, Stephanie J Tuminello, Hideo Watanabe, Judith L Turgeon, Stuart C Sealfon
The LβT2 mouse pituitary cell line has many characteristics of a mature gonadotrope and is a widely used model system for studying the developmental processes and the response to gonadotropin-releasing hormone (GnRH). The global epigenetic landscape, which contributes to cell-specific gene regulatory mechanisms, and the single-cell transcriptome response variation of LβT2 cells have not been previously investigated. Here, we integrate the transcriptome and genome-wide chromatin accessibility state of LβT2 cells during GnRH stimulation...
2018: Frontiers in Endocrinology
Aleksandra Elzbieta Dawid, Dominik Gront, Andrzej Kolinski
We recently developed a new coarse-grained model of protein structure and dynamics (SURPASS Low-Resolution Coarse-Grained Protein Modeling, JCTC. 2017, 13 (11), 5766-5779). The model assumed a single bead representation of amino acid residues, where positions of such united residues were defined by centers of mass of four amino acid fragments. Replica exchange Monte Carlo sampling of the model chains provided good pictures of modeled structures and their dynamics. In its generic form the statistical knowledge-based force field of the model has been dedicated for single-domain globular proteins...
February 27, 2018: Journal of Chemical Theory and Computation
Wen-Ling Kuo, Shir-Hwa Ueng, Chun-Hsing Wu, Li-Yu Lee, Yun-Shien Lee, Ming-Chin Yu, Shin-Cheh Chen, Chi-Chang Yu, Chi-Neu Tsai
The research of carcinogenetic mechanisms of breast cancer in different ethnic backgrounds is an interesting field, as clinical features of breast cancers vary among races. High premenopausal incidence is distinctive in East-Asian breast cancer. However, human cell lines derived from Asian primary breast tumor are rare. To provide alternative cell line models with a relevant genetic background, we aimed to establish breast cancer cell lines from Taiwanese patients of Han-Chinese ethnicity. Fresh tissue from mammary tumors were digested into organoids, plated and grown in basal serum-free medium of human mammary epithelial cells (HuMEC) with supplements...
February 26, 2018: Human Cell
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