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Protein footprinting

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https://www.readbyqxmd.com/read/29237569/identification-of-an-industrial-microalgal-strain-for-starch-production-in-biorefinery-context-the-effect-of-nitrogen-and-carbon-concentration-on-starch-accumulation
#1
Imma Gifuni, Giuseppe Olivieri, Antonino Pollio, Antonio Marzocchella
The recent trends in microalgal cultures are focused on the biorefinery of the biomass components. Some of them are not completely valorised, for example starch. Since there is a wide market for starch products in food and non-food industries, the exploitation of microalgal starch fractions could improve the economic sustainability of microalgae production. In this perspective, the optimization of nitrogen and carbon source uptake for starch accumulation is a critical point for reducing the nitrogen requirement footprint and to increase CO2 capture...
December 10, 2017: New Biotechnology
https://www.readbyqxmd.com/read/29235477/nucleotide-and-mal3-dependent-changes-in-fission-yeast-microtubules-suggest-a-structural-plasticity-view-of-dynamics
#2
Ottilie von Loeffelholz, Neil A Venables, Douglas Robert Drummond, Miho Katsuki, Robert Cross, Carolyn A Moores
Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29225199/structure-of-bacterial-chromosome-an-analysis-of-dna-protein-interactions-in-vivo
#3
Joanna Hołówka, Małgorzata Płachetka
According to recent reports, bacterial chromosomes exhibit a hierarchical organization. The number of proteins that bind DNA are responsible for local and global organization of the DNA ensuring proper chromosome compaction. Advanced molecular biology techniques combined with high-throughput DNA sequencing methods allow a precise analysis of bacterial chromosome structures on a local and global scale. Methods such as in vivo footprinting and ChIP-seq allow to map binding sites of analyzed proteins in certain chromosomal regions or along the whole chromosome while analysis of the spatial interactions on global scale could be performed by 3C techniques...
December 8, 2017: Postȩpy Higieny i Medycyny Doświadczalnej
https://www.readbyqxmd.com/read/29218563/a-practical-guide-to-ispot-modeling-an-integrative-structural-biology-platform
#4
An Hsieh, Lanyuan Lu, Mark R Chance, Sichun Yang
Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or computational perspectives, and complementary structural information from these different techniques are integrated for accurate characterization of the structures of large protein-protein complexes...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29211035/high-resolution-structure-analysis-of-antibody-v5-and-u4-conformational-epitopes-on-human-papillomavirus-16
#5
Jian Guan, Stephanie M Bywaters, Sarah A Brendle, Robert E Ashley, Alexander M Makhov, James F Conway, Neil D Christensen, Susan Hafenstein
Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Identifying the conformational epitopes on the virus capsid supports the development of improved recombinant vaccines to maximize long-term protection against multiple types of HPV. Fragments of antibody (Fab) digested from the neutralizing monoclonal antibodies H16.V5 (V5) and H16...
December 6, 2017: Viruses
https://www.readbyqxmd.com/read/29192498/membrane-protein-structure-in-live-cells-methodology-for-studying-drug-interaction-by-mass-spectrometry-based-footprinting
#6
Guo-Min Shen, Shuang Li, Weidong Cui, Shixuan Liu, Yihu Yang, Michael L Gross, Weikai Li
Mass spectrometry (MS) based footprinting is an emerging approach to study protein structure. Because integral membrane proteins are difficult targets for conventional structural biology, we recently developed a MS footprinting method to probe membrane protein/drug interactions in live cells. This method can detect structural difference between apo and drug-bound states of membrane proteins, with the changes inferred from MS quantification of the cysteine modification pattern, generated by residue-specific chemical labeling...
December 1, 2017: Biochemistry
https://www.readbyqxmd.com/read/29184566/selection-signatures-in-the-first-exon-of-paralogous-receptor-kinase-genes-from-the-sym2-region-of-the-pisum-sativum-l-genome
#7
Anton S Sulima, Vladimir A Zhukov, Alexey A Afonin, Aleksandr I Zhernakov, Igor A Tikhonovich, Ludmila A Lutova
During the initial step of the symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria (rhizobia), the bacterial signal molecule known as the Nod factor (nodulation factor) is recognized by plant LysM motif-containing receptor-like kinases (LysM-RLKs). The fifth chromosome of barrel medic (Medicago truncatula Gaertn.) contains a cluster of paralogous LysM-RLK genes, one of which is known to participate in symbiosis. In the syntenic region of the pea (Pisum sativum L.) genome, three genes have been identified: PsK1 and PsSym37, two symbiosis-related LysM-RLK genes with known sequences, and the unsequenced PsSym2 gene which presumably encodes a LysM-RLK and is associated with increased selectivity to certain Nod factors...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29184003/il-10-promoter-transactivation-by-the-viral-k-rta-protein-involves-the-host-cell-transcription-factors-specificity-protein-1-and-3
#8
Masanori Miyazawa, Kohji Noguchi, Mana Kujirai, Kazuhiro Katayama, Satoshi Yamagoe, Yoshikazu Sugimoto
Kaposi's sarcoma-associated herpesvirus (KSHV)/human herpesvirus-8 (HHV-8) causes a persistent infection, presenting latent and lytic replication phases during its life cycle. KSHV-related diseases are associated with deregulated expression of inflammatory cytokines, including IL-6 and IL-10, but the mechanisms underlying this dysregulation are unclear. Herein, we report a molecular mechanism for KSHV-induced IL-10 gene expression. KSHV replication and transcription activator (K-RTA) is a molecular switch for the initiation of expression of viral lytic genes, and we describe, for the first time, that K-RTA significantly activates the promoter of the human IL-10 gene...
November 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29183994/translation-efficiency-is-maintained-at-elevated-temperature-in-e-coli
#9
Gareth J Morgan, David H Burkhardt, Jeffery W Kelly, Evan T Powers
Cellular protein levels are dictated by the balance between gene transcription, mRNA translation and protein degradation, among other factors. Translation requires the interplay of several RNA hybridization processes, which are expected to be temperature sensitive. We used ribosome profiling to monitor translation in E. coli at 30 °C and investigate how this changes after 10-20 minutes of heat shock at 42 °C. Translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat shock response transcriptional program at 30 °C by overexpressing the heat shock sigma factor encoded by the rpoH gene...
November 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29175620/introducing-the-green-protein-footprint-method-as-an-understandable-measure-of-the-environmental-cost-of-anchovy-consumption
#10
Jara Laso, María Margallo, María Serrano, Ian Vázquez-Rowe, Angel Avadí, Pere Fullana, Alba Bala, Cristina Gazulla, Ángel Irabien, Rubén Aldaco
In a global framework of growing concern for food security and environmental protection, the selection of food products with higher protein content and lower environmental impact is a challenge. To assess the reliability of different strategies along the food supply chain, a measure of food cost through the environmental impact-protein content binomial is necessary. This study proposes a standardized method to calculate the Green Protein Footprint (GPF) index, a method that assesses both the environmental impact of a food product and its protein content provided to consumers...
November 22, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29165690/the-regulatory-g4-motif-of-the-kirsten-ras-kras-gene-is-sensitive-to-guanine-oxidation-implications-on-transcription
#11
Susanna Cogoi, Annalisa Ferino, Giulia Miglietta, Erik B Pedersen, Luigi E Xodo
KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleotides mimicking the KRAS G4-motif and found that 8-oxoG impacts folding and stability of the G-quadruplex. Dimethylsulphate-footprinting showed that the G-run carrying 8-oxoG is excluded from the G-tetrads and replaced by a redundant G-run in the KRAS G4-motif...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155789/efficient-generation-and-editing-of-feeder-free-ipscs-from-human-pancreatic-cells-using-the-crispr-cas9-system
#12
Anjali Nandal, Barbara Mallon, Bhanu P Telugu
Embryonic and induced pluripotent stem cells can self-renew and differentiate into multiple cell types of the body. The pluripotent cells are thus coveted for research in regenerative medicine and are currently in clinical trials for eye diseases, diabetes, heart diseases, and other disorders. The potential to differentiate into specialized cell types coupled with the recent advances in genome editing technologies including the CRISPR/Cas system have provided additional opportunities for tailoring the genome of iPSC for varied applications including disease modeling, gene therapy, and biasing pathways of differentiation, to name a few...
November 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29146908/lrpprc-mediated-folding-of-the-mitochondrial-transcriptome
#13
Stefan J Siira, Henrik Spåhr, Anne-Marie J Shearwood, Benedetta Ruzzenente, Nils-Göran Larsson, Oliver Rackham, Aleksandra Filipovska
The expression of the compact mammalian mitochondrial genome requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, and here we use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA-protein interactions in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145050/can-farmers-mitigate-environmental-impacts-through-combined-production-of-food-fuel-and-feed-a-consequential-life-cycle-assessment-of-integrated-mixed-crop-livestock-system-with-a-green-biorefinery
#14
Ranjan Parajuli, Tommy Dalgaard, Morten Birkved
This study evaluates environmental impacts of an integrated mixed crop-livestock system with a green biorefinery (GBR). System integration included production of feed crops and green biomasses (Sys-I) to meet the demand of a livestock system (Sys-III) and to process green biomasses in a GBR system (Sys-II). Processing of grass-clover to produce feed protein was considered in Sys-II, particularly to substitute the imported soybean meal. Waste generated from the livestock and GBR systems were considered for the conversion to biomethane (Sys-IV)...
November 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29134801/adsorbed-polyzwitterion-copolymer-layers-designed-for-protein-repellency-and-interfacial-retention
#15
S Kalasin, R A Letteri, T Emrick, M M Santore
Poly(2-methacryloyloxyethyl phosphorylcholine) (pMPC), when end-tethered to surfaces by the adsorption of copolymeric cationic segments, forms adsorbed layers that substantially reduce protein adsorption. This study examined variations in the molecular architecture of copolymers containing cationic poly(trimethylammonium ethyl methacrylate (pTMAEMA) anchor blocks that adsorbed strongly to negative surfaces. With appropriate copolymer design, the pTMAEMA blocks were shielded, by pMPC tethers, from solution-phase proteins...
November 14, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29108072/rapid-communication-large-exploitable-genetic-variability-exists-to-shorten-age-at-slaughter-in-cattle
#16
D P Berry, A R Cromie, M M Judge
Apprehension among consumers is mounting on the efficiency by which cattle convert feedstuffs into human edible protein and energy as well as the consequential effects on the environment. Most (genetic) studies that attempt to address these issues have generally focused on efficiency metrics defined over a certain time period of an animal's life cycle, predominantly the period representing the linear phase of growth. The age at which an animal reaches the carcass specifications for slaughter, however, is also known to vary between breeds; less is known on the extent of the within-breed variability in age at slaughter...
October 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/29107364/environmental-and-water-sustainability-of-milk-production-in-northeast-spain
#17
I Noya, S González-García, J Berzosa, F Baucells, G Feijoo, M T Moreira
This study focuses on the assessment of the environmental profile of a milk farm, representative of the dairy sector in Northeast Spain, from a cradle-to-gate perspective. The Life Cycle Assessment (LCA) principles established by ISO standards together with the carbon footprint guidelines proposed by International Dairy Federation (IDF) were followed. The environmental results showed two critical contributing factors: the production of the livestock feed (e.g., alfalfa) and the on-farm emissions from farming activities, with contributions higher than 50% in most impact categories...
October 26, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29106428/modified-acellular-nerve-delivering-pmscs-improve-functional-recovery-in-rats-after-complete-spinal-cord-transection
#18
Ting Tian, Zhenhai Yu, Naili Zhang, Yingwei Chang, Yuqiang Zhang, Luping Zhang, Shuai Zhou, Chunlei Zhang, Guoying Feng, Fei Huang
Due to the poor regeneration capacity of neurons and the inhibitory microenvironment, spontaneous regeneration in spinal cord injury (SCI) remains challenging. Tissue engineering is considered a promising approach for enhancing the regeneration of SCI by reconstructing the inherent structure and improving the microenvironment. In this study, the possibility of engineering a nerve complex, which is constructed by acellular nerve delivering placenta mesenchymal stem cells (PMSCs), was assessed for the recovery of a transected spinal cord...
November 6, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/29101025/cyanobacteria-biorefinery-production-of-poly-3-hydroxybutyrate-with-synechocystis-salina-and-utilisation-of-residual-biomass
#19
K Meixner, A Kovalcik, E Sykacek, M Gruber-Brunhumer, W Zeilinger, K Markl, C Haas, I Fritz, N Mundigler, F Stelzer, M Neureiter, W Fuchs, B Drosg
This study evaluates a biorefinery concept for producing poly(3-hydroxybutyrate) (PHB) with the cyanobacterial strain Synechocystis salina. Due to this reason, pigment extraction and cell disruption were investigated as pre-treatment steps for the harvested cyanobacterial biomass. The results demonstrated that at least pigment removal was necessary to obtain PHB with processable quality (weight average molecular weight: 569-988kgmol(-1), melting temperature: 177-182°C), which was comparable to heterotrophically produced PHB...
October 31, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29100679/changes-in-carbon-footprint-when-integrating-production-of-filamentous-fungi-in-1st-generation-ethanol-plants
#20
Pedro Brancoli, Jorge A Ferreira, Kim Bolton, Mohammad J Taherzadeh
Integrating the cultivation of edible filamentous fungi in the thin stillage from ethanol production is presently being considered. This integration can increase the ethanol yield while simultaneously producing a new value-added protein-rich biomass that can be used for animal feed. This study uses life cycle assessment to determine the change in greenhouse gas (GHG) emissions when integrating the cultivation of filamentous fungi in ethanol production. The result shows that the integration performs better than the current scenario when the fungal biomass is used as cattle feed for system expansion and when energy allocation is used...
October 31, 2017: Bioresource Technology
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