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Protein design

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https://www.readbyqxmd.com/read/28723948/integrative-functional-analyses-using-rainbow-trout-selected-for-tolerance-to-plant-diets-reveal-nutrigenomic-signatures-for-soy-utilization-without-the-concurrence-of-enteritis
#1
Jason Abernathy, Andreas Brezas, Kevin R Snekvik, Ronald W Hardy, Ken Overturf
Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation...
2017: PloS One
https://www.readbyqxmd.com/read/28723942/comparative-analysis-of-vaginal-microbiota-sampling-using-16s-rrna-gene-analysis
#2
Seppo Virtanen, Ilkka Kalliala, Pekka Nieminen, Anne Salonen
BACKGROUND: Molecular methods such as next-generation sequencing are actively being employed to characterize the vaginal microbiota in health and disease. Previous studies have focused on characterizing the biological variation in the microbiota, and less is known about how factors related to sampling contribute to the results. Our aim was to investigate the impact of a sampling device and anatomical sampling site on the quantitative and qualitative outcomes relevant for vaginal microbiota research...
2017: PloS One
https://www.readbyqxmd.com/read/28723647/set-contributes-to-the-epithelial-mesenchymal-transition-of-pancreatic-cancer
#3
Hardik R Mody, Sau Wai Hung, Kineta Naidu, Haesung Lee, Caitlin A Gilbert, Toan Thanh Hoang, Rakesh K Pathak, Radhika Manoharan, Shanmugam Muruganandan, Rajgopal Govindarajan
Pancreatic cancer has a devastating prognosis due to 80-90% of diagnostic cases occurring when metastasis has already presented. Activation of the epithelial-mesenchymal transition (EMT) is a prerequisite for metastasis because it allows for the dissemination of tumor cells to blood stream and secondary organs. Here, we sought to determine the role of SET oncoprotein, an endogenous inhibitor of PP2A, in EMT and pancreatic tumor progression. Among the two major isoforms of SET (isoform 1 and isoform 2), higher protein levels of SET isoform 2 were identified in aggressive pancreatic cancer cell lines...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28723577/enabling-tools-for-high-throughput-detection-of-metabolites-metabolic-engineering-and-directed-evolution-applications
#4
REVIEW
Jyun-Liang Lin, James M Wagner, Hal S Alper
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection...
July 16, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28723493/proteinuria-in-patients-undergoing-renal-cancer-surgery-impact-on-overall-survival-and-stability-of-renal-function
#5
Zhiling Zhang, Juping Zhao, Joseph Zabell, Erick Remer, Jianbo Li, Jack Campbell, Wen Dong, Diego Aguilar Palacios, Tulsi Patel, Sevag Demirjian, Steven C Campbell
BACKGROUND: Proteinuria is included in the Kidney Disease: Improving Global Outcomes (KDIGO) risk stratification for chronic kidney disease (CKD) in the general population. However, the importance of proteinuria in patients with renal cancer has not been adequately studied. OBJECTIVE: To evaluate the prognostic impact of preoperative proteinuria on overall survival (OS) and renal function stability (RFS) for patients managed with renal cancer surgery. DESIGN, SETTING, AND PARTICIPANTS: From 1999 to 2008, 977 patients who underwent renal cancer surgery had preoperative data recorded for the glomerular filtration rate (GFR) estimated using the CKD Epidemiology Collaboration equation (G1 ≥90, G2 60-89, G3a 45-59, G3b 30-44, G4 15-29, and G5 <15ml/min/1...
December 15, 2016: European Urology Focus
https://www.readbyqxmd.com/read/28723234/flexible-small-molecular-anti-estrogens-with-n-n-dialkylated-2-5-diethoxy-4-morpholinoaniline-scaffold-targets-multiple-estrogen-receptor-conformations
#6
Bethany K Asare, Emmanuel Yawson, Rajendram V Rajnarayanan
Estrogen mediates various cellular processes including cell proliferation, differentiation, growth and mammary gland function. Estrogen Receptors (ERs) are expressed in 70% of breast cancers. Consequently, estrogen mediated ER signaling plays a critical role in breast cancer diagnosis, prognosis, and treatment. Estrogen Receptors are ligand-triggered transcription factors. However, in the absence of a cognate estrogenic ligand, ERs can be activated by a variety of other extracellular signals. Tamoxifen, an anti-estrogen that selectively targets ER, induces substantial regression of breast tumors and an increase in disease-free survival...
July 19, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28723212/engineering-recombinant-protein-sensors-for-quantifying-histone-acetylation
#7
Oscar F Sanchez, Agnes Mendonca, Ana D Carneiro, Chongli Yuan
H3K14ac (acetylation of lysine 14 of histone H3) is one of the most important epigentic modifications. Aberrant changes in H3K14ac have been associated with various diseases, including cancers and neurological disorders. Tools that enable detection and quantification of H3K14ac levels in cell extracts and in situ are thus of critical importance to reveal its role in various biological processes. Current detection techniques of specific histone modifications, however, are constrained by tedious sample pretreatments, lack of quantitative accuracy, and reliance on high quality antibodies...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723211/improving-fore-a-new-inlet-design-for-filtering-samples-through-individual-microarray-spots
#8
Victoria de Lange, Marco Habegger, Marco Schmidt, János Vörös
In this publication we present an improvement to our previously introduced vertical flow microarray, the FoRe array, which capitalizes on the fusion of immunofiltration and densely packed micron test sites. Filtering samples through individual microarray spots allows us to rapidly analyze dilute samples with high-throughput and high signal-to-noise. Unlike other flowthrough microarrays, in the FoRe design samples are injected into micron channels and sequentially exposed to different targets. This arrangement makes it possible to increase the sensitivity of the microarray by simply increasing the sample volume or to rapidly reconcentrate samples after preprocessing steps dilute the analyte...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723202/structure-guided-design-of-protein-biosensors-for-phenolic-pollutants
#9
Shamayeeta Ray, Santosh Panjikar, Ruchi Anand
Phenolic aromatic compounds are a major source of environmental pollution. Currently there are no in situ methods for specifically and selectively detecting these pollutants. Here, we exploit the nature's biosensory machinery by employing Acinetobacter calcoaceticus NCIB8250 protein, MopR, as a model system to develop biosensors for selective detection of a spectrum of these pollutants. The X-ray structure of the sensor domain of MopR was used as a scaffold for logic-based tunable biosensor design. By employing a combination of in silico structure guided approaches, mutagenesis and isothermal calorimetric studies, we were able to generate biosensor templates, that can selectively and specifically sense harmful compounds like chlorophenols, cresols, catechol, and xylenols...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723181/mixed-self-assembled-aptamer-and-newly-designed-zwitterionic-peptide-as-antifouling-biosensing-interface-for-electrochemical-detection-of-alpha-fetoprotein
#10
Min Cui, Yu Wang, Mingxia Jiao, Silambarasan Jayachandran, Yumin Wu, Xiaojian Fan, Xiliang Luo
A sensitive and low-fouling aptasensor for alpha-fetoprotein (AFP) was developed based on mixed self-assembled aptamers and newly designed zwitterionic peptides, where densely immobilized peptides formed an antifouling layer to resist nonspecific protein adsorption, and sparsely attached aptamers acted as the recognizing layer to achieve target binding. The obtained biosensing interface responded to the target AFP with a strikingly selective and sensitive manner, exhibited excellent protein-resistant performance even in complex human serum solution, and showed promising feasibility for the quantitative analysis of AFP in real human serum samples...
April 28, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723107/chemical-approaches-to-investigate-labile-peptide-and-protein-phosphorylation
#11
Anett Hauser, Martin Penkert, Christian P R Hackenberger
Protein phosphorylation is by far the most abundant and most studied post-translational modification (PTM). For a long time, phosphate monoesters of serine (pSer), threonine (pThr), and tyrosine (pTyr) have been considered as the only relevant forms of phosphorylation in organisms. Recently, several research groups have dedicated their efforts to the investigation of other, less characterized phosphoamino acids as naturally occurring PTMs. Such apparent peculiar phosphorylations include the phosphoramidates of histidine (pHis), arginine (pArg), and lysine (pLys), the phosphorothioate of cysteine (pCys), and the anhydrides of pyrophosphorylated serine (ppSer) and threonine (ppThr)...
July 19, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28722797/highly-selective-enrichment-of-phosphopeptides-by-on-chip-indium-oxide-functionalized-magnetic-nanoparticles-coupled-with-maldi-tof-ms
#12
Dandan Jiang, Naizhong Song, Xiqian Li, Jiutong Ma, Qiong Jia
Selective and efficient preconcentration is indispensable for low concentration of phosphopeptides in phosphorylated protein-related samples prior to MS-based analysis. Herein, an on-chip system coupled magnetic SPE with MALDI-TOF MS was designed. A metal oxide affinity chromatography (MOAC) material, indium oxide, was coated on the surface of Fe3 O4 magnetic nanoparticles (MNPs) to prepare the adsorbent, spatially confined with an applied magnetic field. The adsorbent exhibited high selectivity for phosphopeptides in tryptic digests of the mixture of β-casein and BSA (1:1000) and the mixture of β-casein, BSA, and ovalbumin (1:100:100)...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28722437/surface-plasmon-resonance-clinical-biosensors-for-medical-diagnostics
#13
Jean-Francois Masson
The design and application of sensors for monitoring biomolecules in clinical samples is a common goal of the sensing research community. Surface plasmon resonance (SPR) and other plasmonic techniques such as localized surface plasmon resonance (LSPR) and imaging SPR are reaching a maturity level sufficient for their application in monitoring biomolecules in clinical samples. In recent years, the first examples for monitoring antibodies, proteins, enzymes, drugs, small molecules, peptides, and nucleic acids in biofluids collected from patients afflicted with a series of medical conditions (Alzheimer's, hepatitis, diabetes, leukemia, and cancers such as prostate and breast cancers, among others) demonstrate the progress of SPR sensing in clinical chemistry...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722358/chemoenzymatic-synthesis-of-polypeptides-for-use-as-functional-and-structural-materials
#14
REVIEW
Kousuke Tsuchiya, Keiji Numata
Polypeptides inspired by the natural functional and structural proteins present in living systems are promising materials for various fields in terms of their versatile functionality and physical properties. Designing and synthesizing mimetic sequences of specific peptide motifs in proteins are important for exploring the functionality of natural proteins. Chemoenzymatic polymerization, which utilizes aminolysis (i.e., the reverse reaction of hydrolysis catalyzed by proteases), is a useful technique for synthesizing artificial polypeptide materials and has several advantages, including facile synthesis protocols, environmental friendliness, scalability, and atom economy...
July 19, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/28722303/differential-electrochemical-conductance-imaging-at-the-nanoscale
#15
Montserrat López-Martínez, Juan Manuel Artés, Veronica Sarasso, Marco Carminati, Ismael Díez-Pérez, Fausto Sanz, Pau Gorostiza
Electron transfer in proteins is essential in crucial biological processes. Although the fundamental aspects of biological electron transfer are well characterized, currently there are no experimental tools to determine the atomic-scale electronic pathways in redox proteins, and thus to fully understand their outstanding efficiency and environmental adaptability. This knowledge is also required to design and optimize biomolecular electronic devices. In order to measure the local conductance of an electrode surface immersed in an electrolyte, this study builds upon the current-potential spectroscopic capacity of electrochemical scanning tunneling microscopy, by adding an alternating current modulation technique...
July 19, 2017: Small
https://www.readbyqxmd.com/read/28722055/the-amyloid-architecture-provides-a-scaffold-for-enzyme-like-catalysts
#16
Z S Al-Garawi, B A McIntosh, D Neill-Hall, A A Hatimy, S M Sweet, M C Bagley, L C Serpell
Natural biological enzymes possess catalytic sites that are generally surrounded by a large three-dimensional scaffold. However, the proportion of the protein molecule that participates in the catalytic reaction is relatively small. The generation of artificial or miniature enzymes has long been a focus of research because enzyme mimetics can be produced with high activity at low cost. These enzymes aim to mimic the active sites without the additional architecture contributed by the protein chain. Previous work has shown that amyloidogenic peptides are able to self-assemble to create an active site that is capable of binding zinc and catalysing an esterase reaction...
July 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28721831/transient-production-of-recombinant-pharmaceutical-proteins-in-plants-evolution-and-perspectives
#17
Lilya Kopertekh, Joachim Schiemann
During the last two decades the production of pharmaceutical proteins in plants evolved from proof of concept to established technology adopted by several biotechnological companies. This progress is particularly based on intensive research starting stable genetic transformation and moving to transient expression. Due to its advantages in yield and speed of protein production transient expression platforms became leading plant-based manufacturing technology. Current transient expression methods rely on Agrobacterium-mediated delivery of expression vectors into plant cells...
July 18, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28721210/current-progress-and-future-perspectives-in-the-development-of-anti-polo-like-kinase-1-therapeutic-agents
#18
REVIEW
Jung-Eun Park, David Hymel, Terrence R Burke, Kyung S Lee
Although significant levels of side effects are often associated with their use, microtubule-directed agents that primarily target fast-growing mitotic cells have been considered to be some of the most effective anti-cancer therapeutics. With the hope of developing new-generation anti-mitotic agents with reduced side effects and enhanced tumor specificity, researchers have targeted various proteins whose functions are critically required for mitotic progression. As one of the highly attractive mitotic targets, polo-like kinase 1 (Plk1) has been the subject of an extensive effort for anti-cancer drug discovery...
2017: F1000Research
https://www.readbyqxmd.com/read/28720665/targeted-exome-sequencing-of-krebs-cycle-genes-reveals-candidate-cancer-predisposing-mutations-in-pheochromocytomas-and-paragangliomas
#19
Laura Remacha, Iñaki Comino-Méndez, Susan Richter, Laura Contreras, Maria Currás-Freixes, Guillermo Pita, Rocío Letón, Antonio Galarreta, Rafael Torres-Pérez, Emiliano Honrado, Scherezade Jiménez, Lorena Maestre, Sebastian Moran, Manel Esteller, Jorgina Satrústegui, Graeme Eisenhofer, Mercedes Robledo, Alberto Cascon
Purpose: Mutations in Krebs cycle genes are frequently found in patients with pheochromocytomas/paragangliomas. Disruption of SDH, FH or MDH2 enzymatic activities lead to accumulation of specific metabolites, which give rise to epigenetic changes in the genome that cause a characteristic hypermethylated phenotype. Tumors showing this phenotype, but no alterations in the known predisposing genes, could harbor mutations in other Krebs cycle genes. <p>Experimental Design: We used downregulation and methylation of RBP1, as a marker of a hypermethylation phenotype, to select eleven pheochromocytomas and paragangliomas for targeted exome sequencing of a panel of Krebs cycle-related genes...
July 18, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28720542/one-step-reverse-transcription-loop-mediated-isothermal-amplification-assay-for-detection-of-apple-chlorotic-leaf-spot-virus
#20
Dandan Peng, Jipeng Xie, Wei Qiang, Kai-Shu Ling, Liyun Guo, Zaifeng Fan, Tao Zhou
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV). In this method, a set of four primers was designed based on the conserved regions in the coat protein gene of ACLSV, and the primers were synthesized for the RT-LAMP assay using total RNA extracted from ACLSV-infected leaf tissues. The optimal reaction temperature and assay time were determined to be 64°C and 75min, respectively. The sensitivity of RT-LAMP reactions was reliable up to a maximum dilution of 1:3125, which was more sensitive than the RT-PCR assay...
July 15, 2017: Journal of Virological Methods
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