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https://www.readbyqxmd.com/read/28921845/detection-and-delineation-of-squamous-neoplasia-with-hyperspectral-imaging-in-a-mouse-model-of-tongue-carcinogenesis
#1
Guolan Lu, Dongsheng Wang, Xulei Qin, Susan Muller, Xu Wang, Amy Y Chen, Zhuo Georgia Chen, Baowei Fei
yperspectral imaging (HSI) holds the potential for the noninvasive detection of cancers. Oral cancers are often diagnosed at a late stage when treatment is less effective and the mortality and morbidity rates are high. Early detection of oral cancer is, therefore, crucial in order to improve the clinical outcomes. To investigate the potential of HSI as a non-invasive diagnostic tool, an animal study was designed to acquire hyperspectral images of in vivo and ex vivo mouse tongues from a chemically induced tongue carcinogenesis model...
September 17, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28918057/one-step-piggybac-transposon-based-crispr-cas9-activation-of-multiple-genes
#2
Shenglan Li, Anqi Zhang, Haipeng Xue, Dali Li, Ying Liu
Neural cell fate is determined by a tightly controlled transcription regulatory network during development. The ability to manipulate the expression of multiple transcription factors simultaneously is required to delineate the complex picture of neural cell development. Because of the limited carrying capacity of the commonly used viral vectors, such as lentiviral or retroviral vectors, it is often challenging to perform perturbation experiments on multiple transcription factors. Here we have developed a piggyBac (PB) transposon-based CRISPR activation (CRISPRa) all-in-one system, which allows for simultaneous and stable endogenous transactivation of multiple transcription factors and long non-coding RNAs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917839/m2b-macrophage-polarization-accompanied-with-reduction-of-long-noncoding-rna-gas5
#3
Ichiaki Ito, Akira Asai, Sumihiro Suzuki, Makiko Kobayashi, Fujio Suzuki
Macrophages (Mϕ) are highly plastic and change their functional phenotypes depending on microenvironmental signals. Recent studies have shown that microRNAs are involved in the polarization of Mϕ. In this study, we demonstrated that the phenotype of M2bMϕ [CCL1(+) IL-10(+) LIGHT(+)] switches to other phenotypes with interchangeability attained through the increased expression of growth arrest-specific 5 RNA (GAS5 RNA), a long non-coding RNA. GAS5 RNA has been described as a silencer of the CCL1 gene. Various phenotypes of Mϕ were prepared from bone marrow-derived Mϕ (BMDMϕ) after stimulation with IFNγ [M(IFNγ)]/M1Mϕ, IL-4 [M(IL-4)]/M2aMϕ, LPS and immobilized IgG [M(LPS + IC)]/M2bMϕ, and IL-10 [M(IL-10)/M2cMϕ]...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28916155/ancestral-resurrection-of-anthropoid-estrogen-receptor-%C3%AE-demonstrates-functional-consequences-of-positive-selection
#4
Amy Weckle, Michael R McGowen, Jun Xing, Caoyi Chen, Kirstin N Sterner, Zhuo-Cheng Hou, Roberto Romero, Derek E Wildman
Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40 mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator...
September 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28914467/cloning-expression-pattern-analysis-and-subcellular-localization-of-capra-hircus-scd1-gene-with-production-of-transgenic-mice
#5
Qisheng Zuo, Kai Jin, Jiuzhou Song, Yani Zhang, Bichun Li
This study aimed to clone the Stearoyl-CoA desaturase 1 (SCD1) gene derived from Xuhuai goat (Capra hircus), and analyze the sub-cellular localization in cells and tissues. The cDNA was cloned by reverse transcription polymerase chain reaction (RT-PCR). pEGFP-SCD1 vector was constructed to detect sub-cellular localization and tissue distribution. pEGFP-SCD1 was transfected into NIH-3T3 cells using polyethylene imine (PEI) and observed under fluorescence inversion microscope system 48 h after transfection. The expression level of SCD1 was detected by RT-PCR...
September 15, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28906473/engineered-disease-resistance-in-cotton-using-rna-interference-to-knock-down-cotton-leaf-curl-kokhran-virus-burewala-and-cotton-leaf-curl-multan-betasatellite-expression
#6
Aftab Ahmad, Muhammad Zia-Ur-Rehman, Usman Hameed, Abdul Qayyum Rao, Ammara Ahad, Aneela Yasmeen, Faheem Akram, Kamran Shahzad Bajwa, Jodi Scheffler, Idrees Ahmad Nasir, Ahmad Ali Shahid, Muhammad Javed Iqbal, Tayyab Husnain, Muhammad Saleem Haider, Judith K Brown
Cotton leaf curl virus disease (CLCuD) is caused by a suite of whitefly-transmitted begomovirus species and strains, resulting in extensive losses annually in India and Pakistan. RNA-interference (RNAi) is a proven technology used for knockdown of gene expression in higher organisms and viruses. In this study, a small interfering RNA (siRNA) construct was designed to target the AC1 gene of Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu) and the βC1 gene and satellite conserved region of the Cotton leaf curl Multan betasatellite (CLCuMB)...
September 14, 2017: Viruses
https://www.readbyqxmd.com/read/28903359/expression-of-sialyl-tn-sugar-antigen-in-bladder-cancer-cells-affects-response-to-bacillus-calmette-gu%C3%A3-rin-bcg-and-to-oxidative-damage
#7
Paulo F Severino, Mariana Silva, Mylene Carrascal, Nadia Malagolini, Mariella Chiricolo, Giulia Venturi, Annalisa Astolfi, Mariangela Catera, Paula A Videira, Fabio Dall'Olio
The sialyl-Tn (sTn) antigen is an O-linked carbohydrate chain aberrantly expressed in bladder cancer (BC), whose biosynthesis is mainly controlled by the sialyltransferase ST6GALNAC1. Treatment with Bacillus Calmette-Guérin (BCG) is the most effective adjuvant immunotherapy for superficial BC but one third of the patients fail to respond. A poorly understood correlation between the expression of sTn and BC patient's response to BCG was previously observed. By analyzing tumor tissues, we showed that patients with high ST6GALNAC1 and IL-6 mRNA expression were BCG responders...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28898276/liver-myofibroblasts-of-murine-origins-express-mesothelin-identification-of-novel-rat-mesothelin-splice-variants
#8
Michel Fausther, Elise G Lavoie, Jonathan A Dranoff
Liver myofibroblasts are specialized effector cells that drive hepatic fibrosis, a hallmark process of chronic liver diseases, leading to progressive scar formation and organ failure. Liver myofibroblasts are increasingly recognized as heterogeneous with regards to their origin, phenotype, and functions. For instance, liver myofibroblasts express cell markers that are universally represented such as, ItgαV and Pdgfrβ, or restricted to a given subpopulation such as, Lrat exclusively expressed in hepatic stellate cells, and Gpm6a in mesothelial cells...
2017: PloS One
https://www.readbyqxmd.com/read/28895361/-cloning-and-characterization-of-two-glutathione-s-transferases-cdnas-in-foc4-and-expression-under-exogenous-oxidative-stress
#9
Xingzhu Qi, Jun Wang, Lei Liu
In order to identify two putative glutathione S-transferase (GSTs) genes in Fusarium oxysporum f. sp. cubense race 4 (Foc4), cDNA sequences of the entire coding regions of the two genes were cloned from Foc4 using RT-PCR method. Subsequently, the two genes were named Fogst1 and Fogst2 respectively. The length of open reading frame of Fogst1 was 609 bp and encoded a protein including 202 amino acid residues, Fogst2 possessed an open reading frame with 693 bp which encoded a 230-amino acid protein. Phylogenetic analysis showed that Fogst1 belonged to sigma (σ) subtype members of the GSTs superfamily, and Fogst2 was a new member of an unknown subfamily in the GSTs superfamily...
June 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28893928/content-specific-codes-of-parametric-vibrotactile-working-memory-in-humans
#10
Timo Torsten Schmidt, Yuan-Hao Wu, Felix Blankenburg
To understand how the brain flexibly handles mentally represented information in the absence of sensory stimulation, working memory (WM) studies have been essential. A seminal finding in monkey research is that neurons in the prefrontal cortex (PFC) retain stimulus-specific information when vibrotactile frequencies were memorized. A direct mapping between monkey studies and human fMRI research is still controversial. While oscillatory signatures, in terms of frequency dependent parametric beta-band modulation, have recently been observed in human EEG studies, the content-specificity of these representations in terms of multivariate pattern analysis has not yet been shown...
September 11, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28893606/expression-of-stable-and-active-human-dna-topoisomerase-i-in-pichia-pastoris
#11
Mooi Kwai Chan, Shern Kwok Lim, Noorizan Miswan, Ai Lan Chew, Rahmah Noordin, Boon Yin Khoo
This study described the isolation of the coding region of human topoisomerase I (TopoI) from MDA-MB-231 and the expression of multiple copy recombinant genes in four Pichia pastoris strains. First, polymerase chain reaction (PCR)-amplification of the enzyme coding region was performed. The PCR fragment was cloned into pPICZ-α-A vector and sequenced. It was then transformed into X33, GS115, SMD1168H and KM71H strains of Pichia. PCR-screening for positive clones was performed, and estimation of multiple copy integrants in each yeast strain was carried out using agar plates containing increasing concentrations of Zeocin(®)...
September 8, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28891513/electrode-channel-selection-based-on-backtracking-search-optimization-in-motor-imagery-brain-computer-interfaces
#12
Shengfa Dai, Qingguo Wei
Common spatial pattern algorithm is widely used to estimate spatial filters in motor imagery based brain-computer interfaces. However, use of a large number of channels will make common spatial pattern tend to over-fitting and the classification of electroencephalographic signals time-consuming. To overcome these problems, it is necessary to choose an optimal subset of the whole channels to save computational time and improve the classification accuracy. In this paper, a novel method named backtracking search optimization algorithm is proposed to automatically select the optimal channel set for common spatial pattern...
2017: Journal of Integrative Neuroscience
https://www.readbyqxmd.com/read/28888183/periodic-population-codes-from-a-single-circular-variable-to-higher-dimensions-multiple-nested-scales-and-conceptual-spaces
#13
REVIEW
Andreas Vm Herz, Alexander Mathis, Martin Stemmler
Across the nervous system, neurons often encode circular stimuli using tuning curves that are not sine or cosine functions, but that belong to the richer class of von Mises functions, which are periodic variants of Gaussians. For a population of neurons encoding a single circular variable with such canonical tuning curves, computing a simple population vector is the optimal read-out of the most likely stimulus. We argue that the advantages of population vector read-outs are so compelling that even the neural representation of the outside world's flat Euclidean geometry is curled up into a torus (a circle times a circle), creating the hexagonal activity patterns of mammalian grid cells...
September 6, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28884158/a-geo-coded-inventory-of-anophelines-in-the-afrotropical-region-south-of-the-sahara-1898-2016
#14
David Kyalo, Punam Amratia, Clara W Mundia, Charles M Mbogo, Maureen Coetzee, Robert W Snow
Background: Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods: We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28881979/identification-of-associations-between-genotypes-and-longitudinal-phenotypes-via-temporally-constrained-group-sparse-canonical-correlation-analysis
#15
Xiaoke Hao, Chanxiu Li, Jingwen Yan, Xiaohui Yao, Shannon L Risacher, Andrew J Saykin, Li Shen, Daoqiang Zhang
Motivation: Neuroimaging genetics identifies the relationships between genetic variants (i.e., the single nucleotide polymorphisms) and brain imaging data to reveal the associations from genotypes to phenotypes. So far, most existing machine-learning approaches are widely used to detect the effective associations between genetic variants and brain imaging data at one time-point. However, those associations are based on static phenotypes and ignore the temporal dynamics of the phenotypical changes...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881973/biosses-a-semantic-sentence-similarity-estimation-system-for-the-biomedical-domain
#16
Gizem Sogancioglu, Hakime Öztürk, Arzucan Özgür
Motivation: The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881969/chromatin-accessibility-prediction-via-convolutional-long-short-term-memory-networks-with-k-mer-embedding
#17
Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang
Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881961/rectified-factor-networks-for-biclustering-of-omics-data
#18
Djork-Arné Clevert, Thomas Unterthiner, Gundula Povysil, Sepp Hochreiter
Motivation: Biclustering has become a major tool for analyzing large datasets given as matrix of samples times features and has been successfully applied in life sciences and e-commerce for drug design and recommender systems, respectively. actor nalysis for cluster cquisition (FABIA), one of the most successful biclustering methods, is a generative model that represents each bicluster by two sparse membership vectors: one for the samples and one for the features. However, FABIA is restricted to about 20 code units because of the high computational complexity of computing the posterior...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881755/identification-of-long-non-coding-rnas-biomarkers-associated-with-progression-of-endometrial-carcinoma-and-patient-outcomes
#19
Yanan Sun, Xiaoyan Zou, Jun He, Yuqin Mao
Endometrial carcinoma is a complex disease characterized by both genetic, epigenetic and environmental factors. Increasing evidence has suggested that long non-coding RNAs (lncRNAs) play important roles in the development and progression of cancers. In this study, we performed a comparison analysis for lncRNA expression between patients with early-stage (stage I/II) and those with advanced-stage (stage III/IV) derived from The Cancer Genome Atlas (TCGA) project and identified 17 differentially expressed lncRNAs using student t-test...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28876040/-secreted-expression-of-japanese-encephalitis-virus-prme-in-pichia-pastoris-and-immunogenicity-evaluation-of-the-virus-like-particles-in-mice
#20
Peng Zhao, Ya Jiang, Jingman Wang, Haojie Fan, Ruibing Cao
The study was to express prME protein of Japanese encephalitis virus (JEV) in Pichia pastoris and then to evaluate the immunological properties of the recombinant protein in mice, so as to explore a new way for subunit vaccine development of JEV. The JEV prME gene was amplified by RT-PCR with genome RNA of JEV vaccine strain SA14-14-2 and subcloned into pPICZa-A vector, designated as pPICZα-prME. pPICZα-SprME was constructed same as pPICZα-prME besides with the additional 19 Aa signal peptides coding gene of the JEV cap protein C terminal...
May 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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