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https://www.readbyqxmd.com/read/29677467/vibrational-and-nonadiabatic-coherence-in-2d-electronic-spectroscopy-the-jahn-teller-effect-and-energy-transfer
#1
David M Jonas
Femtosecond two-dimensional (2D) Fourier transform spectroscopy generates and probes several types of coherence that characterize the couplings between vibrational and electronic motions. These couplings have been studied in molecules with Jahn-Teller conical intersections, pseudo-Jahn-Teller funnels, dimers, molecular aggregates, photosynthetic light harvesting complexes, and photosynthetic reaction centers. All have closely related Hamiltonians and at least two types of vibrations, including one that is decoupled from the electronic dynamics and one that is nonadiabatically coupled...
April 20, 2018: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/29677213/ifn-%C3%AE-and-micrornas-are-important-modulators-of-the-pulmonary-innate-immune-response-against-influenza-a-h1n2-infection-in-pigs
#2
Louise Brogaard, Lars E Larsen, Peter M H Heegaard, Christian Anthon, Jan Gorodkin, Ralf Dürrwald, Kerstin Skovgaard
The innate immune system is paramount in the response to and clearance of influenza A virus (IAV) infection in non-immune individuals. Known factors include type I and III interferons and antiviral pathogen recognition receptors, and the cascades of antiviral and pro- and anti-inflammatory gene expression they induce. MicroRNAs (miRNAs) are increasingly recognized to participate in post-transcriptional modulation of these responses, but the temporal dynamics of how these players of the antiviral innate immune response collaborate to combat infection remain poorly characterized...
2018: PloS One
https://www.readbyqxmd.com/read/29676649/asbestos-induces-epigenetic-repression-of-ras-association-domain-containing-protein-1-p16-kinase-4a-inhibitor-and-p14-alternative-reading-frame-in-normal-human-mesothelial-cells
#3
Sichuan Xi, Eden C Payabyab, David M Straughan, Emily S Reardon, Mary Zhang, Julie A Hong, R Taylor Ripley, Chuong D Hoang, David S Schrump
RATIONALE: Whereas asbestos burden has been linked to cytogenetic alterations in malignant pleural mesotheliomas, epigenetic aberrations induced by these fibers have not been fully delineated. OBJECTIVES: The objective of this study was to establish an in vitro model to characterize early epigenetic events potentially contributing to malignant pleural mesothelioma. METHODS: Normal human mesothelial cells (LP9 and LP3) were cultured with or without crocidolite asbestos fibers (1 or 2 μg/cm2 ) for up to 10 days...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676091/-identification-of-dioscorea-nipponica-and-its-sects-based-on-psba-trnh-barcode
#4
Rong Zhao, Fei Shao, Hai-Bo Yin, Ting-Guo Kang
A rapid and accurate method was established by psbA-trnH sequence to distinguish Dioscorea nipponica from other species belonging to the same genus.In this study, we collected 144 samples of D. nipponica from 17 different producing areas in China, the psbA-trnH sequenced of 23 nucleotide sequences were downloaded from GenBank, the sequences from Dioscorea genus. DNAMAN 8.0 software was used to show splicing, MEGA 6.0 software was applied for sequence analysis and comparison. The results showed that the genetic relationship between D...
March 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29675009/genomic-structural-variations-affecting-virulence-during-clonal-expansion-of-pseudomonas-syringae-pv-actinidiae-biovar-3-in-europe
#5
Giuseppe Firrao, Emanuela Torelli, Cesare Polano, Patrizia Ferrante, Francesca Ferrini, Marta Martini, Simone Marcelletti, Marco Scortichini, Paolo Ermacora
Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29675006/the-rapid-emergence-of-tigecycline-resistance-in-bla-kpc-2-harboring-klebsiella-pneumoniae-as-mediated-in-vivo-by-mutation-in-teta-during-tigecycline-treatment
#6
Xiaoxing Du, Fang He, Qiucheng Shi, Feng Zhao, Juan Xu, Ying Fu, Yunsong Yu
Tigecycline is one of the last resort treatments for carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. Tigecycline resistance often occurs during the clinical treatment of CRKP, yet its mechanism has still not been clearly elucidated. This study presents an analysis of a tigecycline resistance mechanism that developed in clinical isolates from a 56-year-old female patient infected with CRKP during tigecycline treatment. Consecutive clonal consistent K. pneumoniae isolates were obtained during tigecycline treatment...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29674548/draft-genome-sequence-of-mycobacterium-porcinum-csurp1564
#7
A Bouam, A Levasseur, M Drancourt
Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for opportunistic infections. The 7,025,616-bp draft genome of M. porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex.
April 19, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29674053/chimeric-dna-lna-based-biosensor-for-the-rapid-detection-of-african-swine-fever-virus
#8
Massimo Biagetti, Massimiliano Cuccioloni, Laura Bonfili, Valentina Cecarini, Carla Sebastiani, Ludovica Curcio, Monica Giammarioli, Gian Mario De Mia, Anna Maria Eleuteri, Mauro Angeletti
African swine fever (ASF) virus is a DNA virus responsible for a severe haemorrhagic fever in pigs, which (still in the absence of vaccination strategies) results in high mortality rates. Herein, we present a biosensor-based method for the detection of ASF viral DNA in the blood of pigs. The biosensor exploits a single-strand DNA probe with locked nucleic acid nucleotides (LNA) substitutions as the complementary recognition element for the conserved region of vp72 gene of ASF virus. The biosensor was calibrated using qPCR-quantified ASF viral DNA extracted from the blood of pigs experimentally infected with the virulent Italian isolate 49/08, genotype I...
July 1, 2018: Talanta
https://www.readbyqxmd.com/read/29673906/interest-of-next-generation-sequencing-in-bcg-treated-high-risk-bladder-cancer
#9
C Jungels, N Martinez Chanza, S Albisinni, M Mercier, N d'Haene, S Rorive, T Roumeguère
OBJECTIVES: There are only few predictive factors for response of non-musculo-invasive bladder cancer (NMIBC) to Bacillus Calmette-Guérin (BCG) therapy. Our study analyzed the results of the sequencing of new generation (NGS) targeted on 50 genes of oncological interest obtained on bladder resection parts in high-risk NMIBC patients treated with BCG, to describe this population from a molecular point of view and try to correlate these results in patients who present or not recurrence after BCG...
April 16, 2018: Progrès en Urologie
https://www.readbyqxmd.com/read/29673868/corrigendum-to-acute-and-repeated-exposure-to-social-stress-reduces-gut-microbiota-diversity-in-syrian-hamsters-behav-brain-res-345-2018-39-48
#10
Katherine A Partrick, Benoit Chassaing, Linda Q Beach, Katharine E McCann, Andrew T Gewirtz, Kim L Huhman
Social stress can promote a variety of neuropsychiatric illnesses, many of which have a high co-morbidity with gastrointestinal disorders. Recent data indicate that gastrointestinal microbiota can affect their host's brain and behavior. Syrian hamsters are ideal subjects for social stress research because they are territorial, aggressive, and rapidly form dominant/subordinate relationships. The purpose of this study was to determine if exposure to social stress in hamsters alters gut microbiota in dominants and subordinates after an agonistic encounter and if pre-stress gut microbiota composition is correlated with the outcome of such a conflict...
April 16, 2018: Behavioural Brain Research
https://www.readbyqxmd.com/read/29673443/taqman-real-time-rt-pcr-assay-for-detecting-and-differentiating-japanese-encephalitis-virus
#11
Nan Shao, Fan Li, Kai Nie, Shi Hong Fu, Wei Jia Zhang, Ying He, Wen Wen Lei, Qian Ying Wang, Guo Dong Liang, Yu Xi Cao, Huan Yu Wang
OBJECTIVE: To detect Japanese encephalitis virus (JEV) rapidly and distinguish its genotypes, a TaqMan-based reverse transcriptase quantitative polymerase chain reaction (RT-PCR) detection system was developed. METHODS: By aligning the full-length sequences of JEV (G1-G5), six sets of highly specific TaqMan real-time RT-PCR primers and probes were designed based on the highly conserved NS1, NS2, and M genes of JEV, which included one set for non-specific JEV detection and five sets for the detection of specific JEV genotypes...
March 2018: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/29673435/decompression-sickness-in-the-f-a-18c-after-atypical-cabin-pressure-fluctuations
#12
Katherine J Lee, Aliye Z Sanou
BACKGROUND: The spectrum of altitude decompression sickness (DCS) is evolving as more cases of atypical pressure fluctuations occur. This ongoing change makes it a difficult condition to diagnose and even more difficult to identify. Both Flight Surgeons and Undersea Medical Officers (UMOs) must keep DCS on the differential. These two cases describe altitude DCS after unique pressure patterns, with one at a markedly lower than expected altitude for DCS. CASE REPORT: Both cases occurred in the F/A-18C and resulted in DCS requiring hyperbaric chamber treatment...
May 1, 2018: Aerospace Medicine and Human Performance
https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#13
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29673256/a-novel-easy-and-rapid-method-for-constructing-yeast-two-hybrid-vectors-using-in-fusion-technology
#14
Deshui Yu, Libing Liao, Ju Zhang, Yi Zhang, Kedong Xu, Kun Liu, Xiaoli Li, Guangxuan Tan, Ran Chen, Yulu Wang, Xia Liu, Xuan Zhang, Xiaomeng Han, Zhangkun Wei, Chengwei Li
Yeast two-hybrid systems are powerful tools for analyzing interactions between proteins. Vector construction is an essential step in yeast two-hybrid experiments, which require bait and prey plasmids. In this study, we modified the multiple cloning site sequence of the yeast plasmid pGADT7 by site-directed mutagenesis PCR to generate the pGADT7-In vector, which result in an easy and rapid method for constructing yeast two-hybrid vectors using the In-Fusion cloning technique. This method has three key advantages: only one pair of primers and one round of PCR are needed to generate bait and prey plasmids for each gene; it is restriction endonuclease- and ligase-independent and it is fast and easily performed...
April 19, 2018: BioTechniques
https://www.readbyqxmd.com/read/29672803/magnetic-resonance-imaging-of-rheumatoid-arthritis-peripheral-joints-and-spine
#15
Monique Reijnierse, Annette van der Helm-Mil, Iris Eshed, Claudia Schueller-Weidekamm
Both the fields of rheumatology and radiology are changing rapidly. Effective medication has become available for rheumatoid arthritis (RA) and transformed it from a progressive disabling disease into a chronic disease. Indications for magnetic resonance imaging (MRI) have changed accordingly, shifting toward early detection. There is also an overall increased clinical demand for high-end imaging. Together with improvement of MRI units and sequences, MRI protocols are adapted based on clinical indications. This article addresses (1) the clinical background and present role of MRI in early disease detection, (2) RA involvement of peripheral joints, (3) RA involvement of the spine, and (4) state-of-the-art RA MRI protocols...
April 2018: Seminars in Musculoskeletal Radiology
https://www.readbyqxmd.com/read/29672183/identification-of-key-pathways-and-genes-in-l4-dorsal-root-ganglion-drg-after-sciatic-nerve-injury-via-microarray-analysis
#16
He Zhao, Li-Jun Duan, Qing-Ling Sun, Yu-Shan Gao, Yong-Dong Yang, Xiang-Sheng Tang, Ding-Yan Zhao, Yang Xiong, Zhen-Guo Hu, Chuan-Hong Li, Si-Xue Chen, Tao Liu, Xing Yu
BACKGROUND: Peripheral nerve injury (PNI) has devastating consequences. Dorsal root ganglion as a pivotal locus participates in the process of neuropathic pain and nerve regeneration. In recent years, gene sequencing technology has seen rapid rise in the biomedicine field. So, we attempt to gain insight into in the mechanism of neuropathic pain and nerve regeneration in the transcriptional level and to explore novel genes through bioinformatics analysis. METHODS: The gene expression profiles of GSE96051 were downloaded from GEO database...
April 19, 2018: Journal of Investigative Surgery: the Official Journal of the Academy of Surgical Research
https://www.readbyqxmd.com/read/29671759/full-mitogenomes-in-the-critically-endangered-k%C3%A4-k%C3%A4-p%C3%A5-reveal-major-post-glacial-and-anthropogenic-effects-on-neutral-genetic-diversity
#17
Nicolas Dussex, Johanna von Seth, Bruce C Robertson, Love Dalén
Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō ( Strigops habroptilus )...
April 19, 2018: Genes
https://www.readbyqxmd.com/read/29671176/rapid-and-reliable-diagnostic-method-to-detect-zika-virus-by-real-time-fluorescence-reverse-transcription-loop-mediated-isothermal-amplification
#18
Xu-Guang Guo, Yong-Zhuo Zhou, Qin Li, Wei Wang, Jin-Zhou Wen, Lei Zheng, Qian Wang
To detect Zika virus more rapidly and accurately, we developed a novel method that utilized a real-time fluorescence reverse transcription loop-mediated isothermal amplification (LAMP) technique. The NS5 gene was amplified by a set of six specific primers that recognized six distinct sequences. The amplification process, including 60 min of thermostatic reaction with Bst DNA polymerase following real-time fluorescence reverse transcriptase using genomic Zika virus standard strain (MR766), was conducted through fluorescent signaling...
April 18, 2018: AMB Express
https://www.readbyqxmd.com/read/29671115/utility-of-dna-rna-protein-and-functional-approaches-to-solve-cryptic-immunodeficiencies
#19
Margot A Cousin, Matthew J Smith, Ashley N Sigafoos, Jay J Jin, Marine I Murphree, Nicole J Boczek, Patrick R Blackburn, Gavin R Oliver, Ross A Aleff, Karl J Clark, Eric D Wieben, Avni Y Joshi, Pavel N Pichurin, Roshini S Abraham, Eric W Klee
PURPOSE: We report a female infant identified by newborn screening for severe combined immunodeficiencies (NBS SCID) with T cell lymphopenia (TCL). The patient had persistently elevated alpha-fetoprotein (AFP) with IgA deficiency, and elevated IgM. Gene sequencing for a SCID panel was uninformative. We sought to determine the cause of the immunodeficiency in this infant. METHODS: We performed whole-exome sequencing (WES) on the patient and parents to identify a genetic diagnosis...
April 18, 2018: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/29670836/construction-and-development-of-a-cardiac-tissue-specific-and-hypoxia-inducible-expression-vector
#20
Shahrooz Ghaderi, Neda Alidadiani, Jafar Soleimani Rad, Hamid Reza Heidari, Nafi Dilaver, Behzad Mansoori, Reza Rhabarghazi, Rezayat Parvizi, Vahid Khaze Shahgoli, Behzad Baradaran
Purpose: Cardiovascular gene therapy is a sophisticated approach, thanks to the safety of vectors, stable transgene expression, delivery method, and different layers of the heart. To date, numerous expression vectors have been introduced in biotechnology and biopharmacy industries in relation to genetic manipulation. Despite the rapid growth of these modalities, they must be intelligently designed, addressing the cardiac-specific transgene expression and less side effects. Herein, we conducted a pilot project aiming to design a cardiac-specific hypoxia-inducible expression cassette...
March 2018: Advanced Pharmaceutical Bulletin
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