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https://www.readbyqxmd.com/read/29161615/more-than-a-tad-spatiotemporal-control-of-caulobacter-pili
#1
REVIEW
Johann Mignolet, Gaël Panis, Patrick H Viollier
The Type IV pilus (T4P) is a powerful and sophisticated bacterial nanomachine involved in numerous cellular processes, including adhesion, DNA uptake and motility. Aside from the well-described subtype T4aP of the Gram-negative genera, including Myxococcus, Pseudomonas and Neisseria, the Tad (tight adherence) pilus secretion system re-shuffles homologous parts from other secretion systems along with uncharacterized components into a new type of protein translocation apparatus. A representative of the Tad apparatus, the Caulobacter crescentus pilus assembly (Cpa) machine is built exclusively at the newborn cell pole once per cell cycle...
November 18, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29158545/a-potent-cas9-derived-gene-activator-for-plant-and-mammalian-cells
#2
Zhenxiang Li, Dandan Zhang, Xiangyu Xiong, Bingyu Yan, Wei Xie, Jen Sheen, Jian-Feng Li
Overexpression of complementary DNA represents the most commonly used gain-of-function approach for interrogating gene functions and for manipulating biological traits. However, this approach is challenging and inefficient for multigene expression due to increased labour for cloning, limited vector capacity, requirement of multiple promoters and terminators, and variable transgene expression levels. Synthetic transcriptional activators provide a promising alternative strategy for gene activation by tethering an autonomous transcription activation domain (TAD) to an intended gene promoter at the endogenous genomic locus through a programmable DNA-binding module...
November 20, 2017: Nature Plants
https://www.readbyqxmd.com/read/29156561/adsorptive-stripping-voltammetric-determination-of-amaranth-and-tartrazine-in-drinks-and-gelatins-using-a-screen-printed-carbon-electrode
#3
Yeny Perdomo, Verónica Arancibia, Olimpo García-Beltrán, Edgar Nagles
A fast, sensitive, and selective method for the simultaneous determination of one pair of synthetic colorants commonly found mixed in food products, Amaranth (AM) and Tartrazine (TZ), based on their adsorption and oxidation on a screen-printed electrode (SPE) is presented. The variation of peak current with pH, supporting electrolyte, adsorption time, and adsorption potential were optimized using square wave adsorptive voltammetry. The optimal conditions were found to be: pH 3.2 (PBS), Eads 0.00 V, and tads 30 s...
November 18, 2017: Sensors
https://www.readbyqxmd.com/read/29149264/sim3c-simulation-of-hi-c-and-meta3c-proximity-ligation-sequencing-technologies
#4
Matthew Z DeMaere, Aaron E Darling
Background: Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings: We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences...
November 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29145969/late-postoperative-analysis-of-the-tip-apex-distance-tad-in-pertrochanteric-fractures-is-there-an-accommodation-of-the-implant-within-the-bone
#5
Leandro Jun Aihara, Rafael Augusto Nanni, Marina Sousa Carvalho, Caio Zamboni, Jorge R Durigan, José S Hungria Neto, Marcelo T Mercadante, Ralph W Christian, José O S Hungria
INTRODUCTION: This study measured the tip-apex distance (TAD) values in the immediate postoperative period and following weight-bearing and fracture impaction in patients undergoing osteosynthesis with dynamic hip screw and cephalomedullary nail. OBJECTIVE: To correlate the Baumgaertner index in the immediate postoperative period with values obtained after impaction of the fracture with the accommodation of the cephalic implant in the femoral head. PATIENTS AND METHODS: Radiographic TAD measurements were taken with AGFA-VIEW(®) of 82 patients with a mean age of 72 years with pertrochanteric fractures who were operated on and the fracture fixed with DHS- Synthes(®), TFN-Synthes(®), or Gamma Nail III-Stryker(®) in the immediate postoperative period, and following weight-bearing and fracture impaction (mean 3-8 weeks after surgery)...
October 2017: Injury
https://www.readbyqxmd.com/read/29145649/single-molecule-compaction-of-megabase-long-chromatin-molecules-by-multivalent-cations
#6
Anatoly Zinchenko, Nikolay V Berezhnoy, Sai Wang, William M Rosencrans, Nikolay Korolev, Johan R C van der Maarel, Lars Nordenskiöld
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29141193/evolution-of-the-clock-and-bmal1-genes-in-a-subterranean-rodent-species-lasiopodomys-mandarinus
#7
Hong Sun, Yifeng Zhang, Yuhua Shi, Yangwei Li, Wei Li, Zhenlong Wang
Lasiopodomys mandarinus, a subterranean rodent, spends its entire life underground. To test whether the CLOCK and BMAL1 genes of L. mandarinus have undergone adaptive evolution to underground darkness, we cloned and analyzed their complete cDNA sequences, using Lasiopodomys brandtii as a control. The phylogenetic trees of the CLOCK and BMAL1 genes were similar to the trees of the conserved Cyt b gene,further, L. mandarinus clustered with L. brandtii and Microtus ochrogaster in the phylogenetic tree. The Q-rich region of the CLOCK gene in L...
November 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29140466/transcription-induced-supercoiling-as-the-driving-force-of-chromatin-loop-extrusion-during-formation-of-tads-in-interphase-chromosomes
#8
Dusan Racko, Fabrizio Benedetti, Julien Dorier, Andrzej Stasiak
Using molecular dynamics simulations, we show here that growing plectonemes resulting from transcription-induced supercoiling have the ability to actively push cohesin rings along chromatin fibres. The pushing direction is such that within each topologically associating domain (TAD) cohesin rings forming handcuffs move from the source of supercoiling, constituted by RNA polymerase with associated DNA topoisomerase TOP1, towards borders of TADs, where supercoiling is released by topoisomerase TOPIIB. Cohesin handcuffs are pushed by continuous flux of supercoiling that is generated by transcription and is then progressively released by action of TOPIIB located at TADs borders...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#9
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137225/circular-rna-expression-profile-and-potential-function-of-hsa_circrna_101238-in-human-thoracic-aortic-dissection
#10
Meisheng Zou, Chixiong Huang, Xinzhong Li, Xiang He, Yanmei Chen, Wangjun Liao, Yulin Liao, Jie Sun, Ze Liu, Lintao Zhong, Jianping Bin
Objective: To assess the circular RNAs (circRNAs) expression profile and explore the potential functions in human thoracic aortic dissection (TAD). Methods: The differentially expressed circRNAs profiles of the aortic segments between human type A TAD patients (n=3) and age-matched normal donors (NA; n=3) were analyzed using the Arraystar human circRNAs microarray. Quantitative real-time PCR was used to validate the expression pattern of circRNAs, parental genes, and hsa-miR-320a; Western blotting confirmed MMP9 expression with additional samples...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29125994/enhanced-human-somatic-cell-reprogramming-efficiency-by-fusion-of-the-myc-transactivation-domain-and-oct4
#11
Ling Wang, Delun Huang, Chang Huang, Yexuan Yin, Kaneha Vali, Ming Zhang, Young Tang
The development of human induced pluripotent stem cells (iPSCs) holds great promise for regenerative medicine. However the iPSC induction efficiency is still very low and with lengthy reprogramming process. We utilized the highly potent transactivation domain (TAD) of MYC protein to engineer the human OCT4 fusion proteins. Applying the MYC-TAD-OCT4 fusion proteins in mouse iPSC generation leads to shorter reprogramming dynamics, with earlier activation of pluripotent markers in reprogrammed cells than wild type OCT4 (wt-OCT4)...
October 26, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29104039/increased-levels-of-interleukin-22-in-thoracic-aorta-and-plasma-from-patients-with-acute-thoracic-aortic-dissection
#12
Jing Ye, Menglong Wang, Huimin Jiang, Qingwei Ji, Ying Huang, Jianfang Liu, Tao Zeng, Yao Xu, Zhen Wang, Yingzhong Lin, Jun Wan
BACKGROUND: Interleukin (IL)-22 plays important roles in the development of arterial disease, including atherosclerosis and hypertension. However, the relationship between IL-22 and acute thoracic aortic dissection (TAD) remains unknown. METHODS: Blood samples were collected from patients with chest pain who underwent computed tomography angiography of the thoracic aorta but had no known preoperative diagnosis of coronary artery disease, peripheral artery disease, arthritis, and/or membranous nephropathy...
November 3, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29099722/formation-and-magnetic-properties-of-infep-ag-nano-rods-fabricated-with-noble-metal-ag-using-ion-milling-method
#13
Jae Min Sohn, Hyungsang Kim, Hyunsik Im, Hyungbae Kim, Juwon Lee, Yoon Shon, Ganapathi Subramaniam, Tae Won Kang, Deuk Young Kim, Hyun Cheol Koo, Joo-Hyeon Lee, Jin Dong Song, Chang-Soo Park, Eun Kyu Kim
The formation including density, and height of InFeP:Ag nano-rods doped with noble metal Ag using ion milling method was preponderantly determined from TEM and XRD analyses. We investigate especially the enhanced ferromagnetism of the well aligned InFeP:Ag nano-rods. AES and XPS measurements were carried out in order to investigate the incorporation of Ag and to verify the local chemical bonding of InFeP:Ag nano-rods. The variation of FWHM for DCRC and TAD peaks demonstrates that noble metal Ag is incorporated into InFeP:Ag nano-rods...
November 3, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29098119/process-review-for-development-of-quantitative-risk-analyses-for-transboundary-animal-disease-to-pathogen-free-territories
#14
REVIEW
Jonathan Miller, Ken Burton, Joe Fund, Adrian Self
Outbreaks of transboundary animal diseases (TADs) have the potential to cause significant detriment to animal, human, and environmental health; severe economic implications; and national security. Challenges concerning data sharing, model development, decision support, and disease emergence science have recently been promoted. These challenges and recommendations have been recognized and advocated in the disciplines intersecting with outbreak prediction and forecast modeling regarding infectious diseases. To advance the effective application of computation and risk communication, analytical products ought to follow a collaboratively agreed common plan for implementation...
2017: BioResearch Open Access
https://www.readbyqxmd.com/read/29096935/long-term-outcome-of-251-patients-with-takayasu-arteritis-on-combination-immunosuppressant-therapy-single-centre-experience-from-a-large-tertiary-care-teaching-hospital-in-southern-india
#15
Ruchika Goel, Debashish Danda, George Joseph, Raheesh Ravindran, Sathish Kumar, Visali Jayaseelan, Lakshmanan Jayaseelan, Paul Bacon
INTRODUCTION: Long-term outcome studies in Takayasu arteritis (TA) are few and limited by small sample size. In this study, we analysed the outcome of treatment in a large series of TA patients with a minimum follow-up period of ≥12 months by objective instruments. MATERIALS AND METHODS: Patients with TA satisfying the 1990 ACR, Ishikawa's, Sharma's or EULAR/PRESS criteria were recruited from our clinics between 1998 and 2016. Only patients with a minimum follow up of 12 months were studied...
September 30, 2017: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/29094699/two-independent-modes-of-chromatin-organization-revealed-by-cohesin-removal
#16
Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian H Haering, Leonid Mirny, Francois Spitz
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes...
November 2, 2017: Nature
https://www.readbyqxmd.com/read/29091848/fate-of-antibiotic-resistance-genes-and-metal-resistance-genes-during-thermophilic-aerobic-digestion-of-sewage-sludge
#17
Hyun Min Jang, Jangwoo Lee, Young Beom Kim, Jong Hun Jeon, Jingyeong Shin, Mee-Rye Park, Young Mo Kim
This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed...
October 20, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29080533/pt-nanoparticles-supported-on-nitrogen-doped-porous-graphene-for-sensitive-detection-of-tadalafil
#18
Abdulwahab Salah, Mehboob Hassan, Jian Liu, Minghui Li, Xiangjie Bo, Jean Chrysostome Ndamanisha, Liping Guo
Graphene (GR) is one of the most promising candidates for utilization in the electroanalytical field because of its superior electrocatalytic activity, excellent electronic conductivity, and high chemical stability. However, the GR sheets usually tend to stack together with π-π interaction. The spontaneous stacking leads to the aggregation of the GR sheets and imposes a negative feedback in the surface area of the GR, which obviously limits its electrochemical application. In this study, nitrogen-doped porous GR (NPGR) with different pore sizes is prepared by using silica (SiO2) as a template...
October 7, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/29079864/anaerobic-digestion-of-spent-mushroom-substrate-under-thermophilic-conditions-performance-and-microbial-community-analysis
#19
Zheng Xiao, Manhong Lin, Jinlin Fan, Yixuan Chen, Chao Zhao, Bin Liu
Spent mushroom substrate (SMS) is the residue of edible mushroom production occurring in huge amounts. The SMS residue can be digested for biogas production in the mesophilic anaerobic digestion. In the present study, performance of batch thermophilic anaerobic digestion (TAD) of SMS was investigated as well as the interconnected microbial population structure changes. The analyzed batch TAD process lasted for 12 days with the cumulative methane yields of 177.69 mL/g volatile solid (VS). Hydrolytic activities of soluble sugar, crude protein, and crude fat in SMS were conducted mainly in the initial phase, accompanied by the excessive accumulation of volatile fatty acids and low methane yield...
October 28, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29078370/algorithm-for-cellular-reprogramming
#20
Scott Ronquist, Geoff Patterson, Lindsey A Muir, Stephen Lindsly, Haiming Chen, Markus Brown, Max S Wicha, Anthony Bloch, Roger Brockett, Indika Rajapakse
The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
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