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BMC Biotechnology

Christian A Schaer, Catherine Owczarek, Jeremy W Deuel, Stefan Schauer, Jin Hyen Baek, Ayla Yalamanoglu, Matthew P Hardy, Pierre D Scotney, Peter M Schmidt, Matthias Pelzing, Peter Soupourmas, Paul W Buehler, Dominik J Schaer
BACKGROUND: Preclinical studies have evaluated haptoglobin (Hp) polymers from pooled human plasma as a therapeutic protein to attenuate toxic effects of cell-free hemoglobin (Hb). Proof of concept studies have demonstrated efficacy of Hp in hemolysis associated with transfusion and sickle cell anemia. However, phenotype-specific Hp products might be desirable to exploit phenotype specific activities of Hp 1-1 versus Hp 2-2, offering opportunities for recombinant therapeutics. Prohaptoglobin (proHp) is the primary translation product of the Hp mRNA...
March 15, 2018: BMC Biotechnology
Sopita Wongin, Saranatra Waikakul, Pojchong Chotiyarnwong, Wanwipa Siriwatwechakul, Masahiro Kino-Oka, Mee-Hae Kim, Kwanchanok Viravaidya-Pasuwat
BACKGROUND: Dedifferentiation of chondrocytes during cell expansion is one of the barriers in tissue construction for cartilage repair. To understand chondrocyte behavior and improve cell expansion in monolayer culture, this study investigated the effects of morphological changes and cellular aggregation on the maintenance of chondrogenic capacity by observing the expression patterns of chondrogenic (collagen type II and aggrecan) and dedifferentiation (collagen type I) markers. Primary human chondrocytes were cultured on either a polystyrene surface (PS) or a polyamidoamine dendrimer surface with a fifth-generation (G5) dendron structure to create a one-step process of cell expansion and the maintenance of chondrogenic activities prior to the construction of cell sheets...
March 14, 2018: BMC Biotechnology
Boris Zacchetti, Agathoklis Andrianos, Dino van Dissel, Evelien de Ruiter, Gilles P van Wezel, Dennis Claessen
BACKGROUND: Filamentous bacteria of the genus Streptomyces produce a large arsenal of industrially relevant antibiotics and enzymes. The industrial production of these molecules occurs in large fermenters, where many streptomycetes form dense mycelial networks called pellets. Pellets are characterized by slow growth and inefficient nutrient transfer and therefore regarded as undesirable from the perspective of productivity. Although non-pelleting strains have increased growth rates, their morphology also leads to a dramatic increase in the viscosity of the culture broth, which negatively impacts the process dynamics...
March 12, 2018: BMC Biotechnology
Shasha Yang, Sili Wei, Yun Mao, Hanxue Zheng, Juantao Feng, Jihong Cui, Xin Xie, Fulin Chen, Honmgmin Li
BACKGROUND: Safe and effective hemostatic materials are important for reducing mortality resulting from excessive hemorrhage. In this work, new biomaterials with hemostatic effects were created by fusing the gene coding for RADA-16, a self-assembling peptide with the sequence RADARADARADARADA, to the 3'-end of the open reading frame (ORF) encoding elastin-like polypeptides through gene recombination. RESULTS: The fusion proteins, termed 36R, 60R and 96R, were solubly over-expressed in Escherichia coli BL21 (DE3) based on genetic manipulation of the high-efficiency prokaryotic expression vector pET28a (+) and bacterial transformation...
March 7, 2018: BMC Biotechnology
Paola Mini, Olivia Costantina Demurtas, Silvia Valentini, Patrizia Pallara, Giuseppe Aprea, Paola Ferrante, Giovanni Giuliano
BACKGROUND: Chlamydomonas reinhardtii is an unicellular green alga used for functional genomics studies and heterologous protein expression. A major hindrance in these studies is the low level and instability of expression of nuclear transgenes, due to their rearrangement and/or silencing over time. RESULTS: We constructed dedicated vectors for Agrobacterium-mediated transformation carrying, within the T-DNA borders, the Paromomycin (Paro) selectable marker and an expression cassette containing the Luciferase (Luc) reporter gene...
February 17, 2018: BMC Biotechnology
Anil S Prajapati, Vishakha A Pawar, Ketankumar J Panchal, Ankit P Sudhir, Bhaumik R Dave, Darshan H Patel, R B Subramanian
BACKGROUND: The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from Bacillus amyloliquefaciens were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates. RESULTS: Wild type and mutated genes were cloned and overexpressed in BL21...
February 13, 2018: BMC Biotechnology
D A Doronin, N V Barykina, O M Subach, V P Sotskov, V V Plusnin, O A Ivleva, E A Isaakova, A M Varizhuk, G E Pozmogova, A Y Malyshev, I V Smirnov, K D Piatkevich, K V Anokhin, G N Enikolopov, F V Subach
BACKGROUND: The recently developed genetically encoded calcium indicator (GECI), called NTnC, has a novel design with reduced size due to utilization of the troponin C (TnC) as a Ca 2+ -binding moiety inserted into the mNeonGreen fluorescent protein. NTnC binds two times less Ca 2+ ions while maintaining a higher fluorescence brightness at the basal level of Ca 2+ in neurons as compared with the calmodulin-based GECIs, such as GCaMPs. In spite of NTnC's high brightness, pH-stability, and high sensitivity to single action potentials, it has a limited fluorescence contrast (F -Ca2+ /F +Ca2+ ) and slow Ca 2+ dissociation kinetics...
February 13, 2018: BMC Biotechnology
Christoph Geisler
BACKGROUND: Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although extremely sensitive for known viruses, this approach can easily miss viruses that are too dissimilar to viruses in the database...
February 7, 2018: BMC Biotechnology
Zhen Jia, Yueyi Shi, Lei Zhang, Yipeng Ren, Tong Wang, Lejun Xing, Baorong Zhang, Guolan Gao, Rongfa Bu
BACKGROUND: Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-wide at single-base resolution with small amount of sequencing data and could not avoid detecting the methylation of repetitive elements which are considered as "junk DNA". METHODS: In this study, we have developed a novel DNA methylome profiling technology named MB-seq with its ability to identify genome-wide 5mC and quantify DNA methylation levels by introduced an assistant adapter AluI-linker This linker can be ligated to sonicated DNA and then be digested after the bisulfite treatment and amplification, which has no effect of MeDIP enrichment...
February 6, 2018: BMC Biotechnology
Russell D Wolfinger, Sudheer Beedanagari, Eric Boitier, Tao Chen, Philippe Couttet, Heidrun Ellinger-Ziegelbauer, Gregory Guillemain, Claire Mariet, Peter Mouritzen, Raegan O'Lone, P Scott Pine, Tatiana Sharapova, Jian Yan, Peter S Yuen, Karol L Thompson
BACKGROUND: Circulating microRNAs are undergoing exploratory use as safety biomarkers in drug development. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is one common approach used to quantitate levels of microRNAs in samples that includes the use of a standard curve of calibrators fit to a regression model. Guidelines are needed for setting assay quantitation thresholds that are appropriate for this method and to biomarker pre-validation. RESULTS: In this report, we develop two workflows for determining a lower limit of quantitation (LLOQ) for RT-qPCR assays of microRNAs in exploratory studies...
February 2, 2018: BMC Biotechnology
Yongfei Liu, Yiran Xu, Dongqin Ding, Jianping Wen, Beiwei Zhu, Dawei Zhang
BACKGROUND: L-phenylalanine (L-Phe) is an essential amino acid for mammals and applications expand into human health and nutritional products. In this study, a system level engineering was conducted to enhance L-Phe biosynthesis in Escherichia coli. RESULTS: We inactivated the PTS system and recruited glucose uptake via combinatorial modulation of galP and glk to increase PEP supply in the Xllp01 strain. In addition, the HTH domain of the transcription factor TyrR was engineered to decrease the repression on the transcriptional levels of L-Phe pathway enzymes...
January 30, 2018: BMC Biotechnology
Zhang Zhang, Shunfang Qiu, Xiaopeng Zhang, Wei Chen
BACKGROUND: Effective gene-delivery systems for primary human T cell engineering are useful tools for both basic research and clinical immunotherapy applications. Pseudovirus-based systems and electro-transfection are the most popular strategies for genetic material transduction. Compared with viral-particle-mediated approaches, electro-transfection is theoretically safer, because it does not promote transgene integration into the host genome. Additionally, the simplicity and speed of the procedure increases the attractiveness of electroporation...
January 30, 2018: BMC Biotechnology
Po-Hao Wang, Greg Schulenberg, Shannon Whitlock, Andrew Worden, Ning Zhou, Stephen Novak, Wei Chen
BACKGROUND: RNA interference (RNAi) technology has been widely used to knockdown target genes via post-transcriptional silencing. In plants, RNAi is used as an effective tool with diverse applications being developed such as resistance against insects, fungi, viruses, and metabolism manipulation. To develop genetically modified (GM) RNAi traits for insect control, a transgene is created and composed of an inversely-repeated sequence of the target gene with a spacer region inserted between the repeats...
January 17, 2018: BMC Biotechnology
Agnieszka J Turlo, Yalda Ashraf Kharaz, Peter D Clegg, James Anderson, Mandy J Peffers
BACKGROUND: The concept of tissue engineering is to deliver to the injury site biological scaffolds carrying functional cells that will enhance healing response. The preferred cell source is autologous in order to reduce immune response in the treated individual. However, in elderly patients age-related changes in synthetic activity of the implanted cells and subsequent alterations in tissue protein content may affect therapeutic outcomes. In this study we investigated the effect of donor age on proteome composition of tenocyte-derived tendon tissue-engineered constructs...
January 16, 2018: BMC Biotechnology
Gerlinde Doenz, Sebastian Dorn, Narges Aghaallaei, Baubak Bajoghli, Elisabeth Riegel, Michaela Aigner, Holger Bock, Birgit Werner, Thomas Lindhorst, Thomas Czerny
BACKGROUND: The application of antisense molecules, such as morpholino oligonucleotides, is an efficient method of gene inactivation in vivo. We recently introduced phosphonic ester modified peptide nucleic acids (PNA) for in vivo loss-of-function experiments in medaka embryos. Here we tested novel modifications of the PNA backbone to knockdown the medaka tcf3 gene. RESULTS: A single tcf3 gene exists in the medaka genome and its inactivation strongly affected eye development of the embryos, leading to size reduction and anophthalmia in severe cases...
January 9, 2018: BMC Biotechnology
Jacob J Messner, Honor L Glenn, Deirdre R Meldrum
Precise spatial positioning and isolation of mammalian cells is a critical component of many single cell experimental methods and biological engineering applications. Although a variety of cell patterning methods have been demonstrated, many of these methods subject cells to high stress environments, discriminate against certain phenotypes, or are a challenge to implement. Here, we demonstrate a rapid, simple, indiscriminate, and minimally perturbing cell patterning method using a laser fabricated polymer stencil...
December 19, 2017: BMC Biotechnology
Tracy Dudding-Byth, Anne Baxter, Elizabeth G Holliday, Anna Hackett, Sheridan O'Donnell, Susan M White, John Attia, Han Brunner, Bert de Vries, David Koolen, Tjitske Kleefstra, Seshika Ratwatte, Carlos Riveros, Steve Brain, Brian C Lovell
BACKGROUND: Massively parallel genetic sequencing allows rapid testing of known intellectual disability (ID) genes. However, the discovery of novel syndromic ID genes requires molecular confirmation in at least a second or a cluster of individuals with an overlapping phenotype or similar facial gestalt. Using computer face-matching technology we report an automated approach to matching the faces of non-identical individuals with the same genetic syndrome within a database of 3681 images [1600 images of one of 10 genetic syndrome subgroups together with 2081 control images]...
December 19, 2017: BMC Biotechnology
Erick Abreu Silveira, Sonia Moreno-Perez, Alessandra Basso, Simona Serban, Rita Pestana Mamede, Paulo W Tardioli, Cristiane Sanchez Farinas, Javier Rocha-Martin, Gloria Fernandez-Lorente, Jose M Guisan
BACKGROUND: Enzymatic ethanolysis of oils (for example, high oleic sunflower oil containing 90% of oleic acid) may yield two different reaction products depending on the regioselectivity of the immobilized lipase biocatalyst. Some lipase biocatalysts exhibit a 1,3-regioselectivity and they produced 2 mols of fatty acid ethyl ester plus 1 mol of sn2-monoacylglycerol (2-MAG) per mol of triglyceride without the release of glycerol. Other lipase biocatalysts are completely non-regioselective releasing 3 mols of fatty acid ethyl ester and 1 mol of glycerol per mol of triglyceride...
December 16, 2017: BMC Biotechnology
Yilei Wei, Yu Zhan, Pengfei Chen, Zhi Liu, Haohao Zhang, Dandan Liu, Jie Zhang, Min Yu, Wei Mo, Jun Zhang, Xiaoren Zhang
BACKGROUND: Receptor activator of NF-κB ligand (RANKL)/RANK signaling essentially functions within the skeletal system, particularly participating in osteoclastogenesis and bone resorption. In addition, this signaling pathway has also been shown to influence tumor progression as well as the development and function of the immune system. Therefore, blocking the interaction between RANKL and RANK is a new therapeutic approach to prevent bone-related diseases and cancer. RESULTS: The coding sequence encoding the extracellular domain of human RANK (RANK-N) was codon optimized for Pichia pastoris and cloned into the pPIC9K vector, and the recombinant plasmid was then transformed into P...
December 4, 2017: BMC Biotechnology
Xing-Feng Huang, Farhad Nazarian, Jean-Paul Vincken, Richard G F Visser, Luisa M Trindade
BACKGROUND: Starch-binding domains from carbohydrate binding module family 20 have been used as a tool for starch engineering. Previous studies showed that expression of starch binding domain fusion proteins in planta resulted in modified starch granule structures and physicochemical properties. However, although 13 carbohydrate binding module families have been reported to contain starch-binding domains, only starch-binding domains from carbohydrate binding module family 20 have been well studied and introduced into plants successfully...
December 4, 2017: BMC Biotechnology
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